mirror of https://github.com/lammps/lammps.git
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@23 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
24de4ed57b
commit
f25713e3b0
|
|
@ -0,0 +1,50 @@
|
|||
LAMMPS example problems
|
||||
|
||||
Each of these sub-directories contains a sample problem you can run
|
||||
with LAMMPS. Most are 2d models so that they run quickly, requiring a
|
||||
few seconds to a few minutes to run on a desktop machine. Each
|
||||
problem has an input script (in.*) and produces a log file (log.*) and
|
||||
dump file (dump.*) when it runs. Some use a data file (data.*) of
|
||||
initial coordinates as additional input.
|
||||
|
||||
A few sample log file outputs on different machines and different
|
||||
numbers of processors are included in the directories to compare your
|
||||
answers to. E.g. a log file like log.crack.date.foo.P means it ran on
|
||||
P processors of machine "foo" with the dated version of LAMMPS. Note
|
||||
that these problems should get statistically similar answers when run
|
||||
on different machines or different numbers of processors, but not
|
||||
identical answers to those in the log of dump files included here.
|
||||
See the Errors section of the LAMMPS documentation for more
|
||||
discussion.
|
||||
|
||||
The dump files produced by the example runs can be animated using the
|
||||
xmovie tool described in the Examples section of the LAMMPS
|
||||
documentation. MPEG versions of most of the xmovie animations are
|
||||
also viewable from the Examples section of the LAMMPS WWW Site.
|
||||
|
||||
These are the sample problems in the various sub-directories:
|
||||
|
||||
couple: illustration of how to link to LAMMPS as a library
|
||||
crack: crack propagation in a 2d solid
|
||||
flow: Couette and Poisseuille flow in a 2d channel
|
||||
friction: frictional contact of spherical asperities between 2d surfaces
|
||||
indent: spherical indenter into a 2d solid
|
||||
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
|
||||
obstacle: flow around two voids in a 2d channel
|
||||
peptide: dynamics of a small solvated peptide chain (5-mer)
|
||||
pour: pouring of granular particles into a 3d box, then chute flow
|
||||
rigid: rigid bodies modeled as independent or coupled
|
||||
shear: sideways shear applied to 2d solid, with and without a void
|
||||
|
||||
Here is how you might run and visualize one of the sample problems:
|
||||
|
||||
cd indent
|
||||
cp ../../src/lmp_linux . # copy LAMMPS executable to this dir
|
||||
lmp_linux < in.indent # run the problem
|
||||
|
||||
Running the simulation produces the files dump.indent and log.lammps.
|
||||
You can visualize the dump file as follows:
|
||||
|
||||
../../tools/xmovie/xmovie -scale dump.indent
|
||||
|
|
@ -0,0 +1,43 @@
|
|||
This directory has a code that shows how LAMMPS can be linked to a
|
||||
driver application as a library. The purpose is to illustrate how
|
||||
another code could perform computations while using LAMMPS to perform
|
||||
MD, or how an umbrella code or script could call both LAMMPS and some
|
||||
other code to perform a coupled calculation.
|
||||
|
||||
Umbrella.cpp is the simple driving code that will call LAMMPS.
|
||||
|
||||
LAMMPS must first be built as a library. See the "Making LAMMPS"
|
||||
section of Section_start.html in the documentation for info on how to
|
||||
do this. Basically, you type something like
|
||||
|
||||
make makelib
|
||||
make -f Makefile.lib g++
|
||||
|
||||
in the LAMMPS src directory to create liblmp_g++.a
|
||||
|
||||
You can then build the umbrella code with a compile line something
|
||||
like this, which includes paths to the LAMMPS library interface, MPI,
|
||||
and FFTW.
|
||||
|
||||
g++ -I/home/sjplimp/tools/mpich/include -I/home/sjplimp/lammps/src
|
||||
-L/home/sjplimp/lammps/src -L/home/sjplimp/tools/mpich/lib
|
||||
-L/home/sjplimp/tools/fftw/lib umbrella.cpp
|
||||
-llmp_g++ -lfftw -lmpich -o umbrella
|
||||
|
||||
You then run umbrella on a parallel machine on some number
|
||||
of processors Q with 2 arguments:
|
||||
|
||||
mpirun -np Q umbrella P in.lj
|
||||
|
||||
P is the number of procs you want LAMMPS to run on (must be <= Q).
|
||||
In.lj is a LAMMPS input script.
|
||||
|
||||
Umbrella will launch LAMMPS on P procs, read the input
|
||||
script a line at a time, and pass each command line to LAMMPS. The
|
||||
final line of the script is a "run" command, so LAMMPS will run
|
||||
the problem.
|
||||
|
||||
Umbrella then requests all the atom coordinates from LAMMPS, moves one
|
||||
of the atoms a small amount "epsilon", passes the coordinates back to
|
||||
LAMMPS, and runs LAMMPS again. If you look at the output, you should
|
||||
see a small energy change between runs, due to the moved atom.
|
||||
|
|
@ -0,0 +1,24 @@
|
|||
# 3d Lennard-Jones melt
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
atom_modify map array
|
||||
|
||||
lattice fcc 0.8442
|
||||
region box block 0 4 0 4 0 4
|
||||
create_box 1 box
|
||||
create_atoms 1
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 20 check no
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
run 10
|
||||
|
||||
|
|
@ -0,0 +1,115 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
www.cs.sandia.gov/~sjplimp/lammps.html
|
||||
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
// umbrella = simple example of how an umbrella program
|
||||
// can invoke LAMMPS as a library on some subset of procs
|
||||
// Syntax: umbrella P in.lammps
|
||||
// P = # of procs to run LAMMPS on
|
||||
// must be <= # of procs the umbrella code itself runs on
|
||||
// in.lammps = LAMMPS input script
|
||||
// See README for compilation instructions
|
||||
|
||||
#include "stdio.h"
|
||||
#include "stdlib.h"
|
||||
#include "string.h"
|
||||
#include "mpi.h"
|
||||
#include "library.h"
|
||||
|
||||
int main(int narg, char **arg)
|
||||
{
|
||||
// setup MPI and various communicators
|
||||
// umbrella is all procs in MPI_COMM_WORLD
|
||||
// comm_lammps only has 1st P procs (could be all or any subset)
|
||||
|
||||
MPI_Init(&narg,&arg);
|
||||
|
||||
if (narg != 3) {
|
||||
printf("Syntax: umbrella P in.lammps\n");
|
||||
exit(1);
|
||||
}
|
||||
|
||||
int me,nprocs;
|
||||
MPI_Comm_rank(MPI_COMM_WORLD,&me);
|
||||
MPI_Comm_size(MPI_COMM_WORLD,&nprocs);
|
||||
|
||||
int nprocs_lammps = atoi(arg[1]);
|
||||
if (nprocs_lammps > nprocs) {
|
||||
if (me == 0)
|
||||
printf("ERROR: LAMMPS cannot use more procs than available\n");
|
||||
MPI_Abort(MPI_COMM_WORLD,1);
|
||||
}
|
||||
|
||||
int lammps;
|
||||
if (me < nprocs_lammps) lammps = 1;
|
||||
else lammps = MPI_UNDEFINED;
|
||||
MPI_Comm comm_lammps;
|
||||
MPI_Comm_split(MPI_COMM_WORLD,lammps,0,&comm_lammps);
|
||||
|
||||
// open LAMMPS input script
|
||||
|
||||
FILE *fp;
|
||||
if (me == 0) {
|
||||
fp = fopen(arg[2],"r");
|
||||
if (fp == NULL) {
|
||||
printf("ERROR: Could not open LAMMPS input script\n");
|
||||
MPI_Abort(MPI_COMM_WORLD,1);
|
||||
}
|
||||
}
|
||||
|
||||
// run the input script thru LAMMPS one line at a time until end-of-file
|
||||
// umbrella proc 0 reads a line, Bcasts it to all procs
|
||||
// (could just send it to proc 0 of comm_lammps and let it Bcast)
|
||||
// all LAMMPS procs call lammps_command() on the line
|
||||
|
||||
if (lammps == 1) lammps_open(0,NULL,comm_lammps);
|
||||
|
||||
int n;
|
||||
char line[1024];
|
||||
while (1) {
|
||||
if (me == 0) {
|
||||
if (fgets(line,1024,fp) == NULL) n = 0;
|
||||
else n = strlen(line) + 1;
|
||||
if (n == 0) fclose(fp);
|
||||
}
|
||||
MPI_Bcast(&n,1,MPI_INT,0,MPI_COMM_WORLD);
|
||||
if (n == 0) break;
|
||||
MPI_Bcast(line,n,MPI_CHAR,0,MPI_COMM_WORLD);
|
||||
if (lammps == 1) lammps_command(line);
|
||||
}
|
||||
|
||||
// run 10 steps
|
||||
// get coords from LAMMPS
|
||||
// change coords of 1st atom
|
||||
// put coords back into LAMMPS
|
||||
// run a single step with changed coords
|
||||
|
||||
if (lammps == 1) {
|
||||
lammps_command("run 10");
|
||||
|
||||
int natoms = lammps_get_natoms();
|
||||
double *x = new double[3*natoms];
|
||||
lammps_get_coords(x);
|
||||
double epsilon = 0.1;
|
||||
x[0] += epsilon;
|
||||
lammps_put_coords(x);
|
||||
delete [] x;
|
||||
|
||||
lammps_command("run 1");
|
||||
}
|
||||
|
||||
if (lammps == 1) lammps_close();
|
||||
|
||||
// close down MPI
|
||||
|
||||
MPI_Finalize();
|
||||
}
|
||||
|
|
@ -0,0 +1,67 @@
|
|||
# 2d LJ crack simulation
|
||||
|
||||
dimension 2
|
||||
boundary s s p
|
||||
|
||||
atom_style atomic
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
# create geometry
|
||||
|
||||
lattice hex 0.93
|
||||
region box block 0 100 0 40 -0.25 0.25
|
||||
create_box 5 box
|
||||
create_atoms 1
|
||||
|
||||
mass 1 1.0
|
||||
mass 2 1.0
|
||||
mass 3 1.0
|
||||
mass 4 1.0
|
||||
mass 5 1.0
|
||||
|
||||
# LJ potentials
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff * * 1.0 1.0 2.5
|
||||
|
||||
# define groups
|
||||
|
||||
region 1 block INF INF INF 1.25 INF INF
|
||||
group lower region 1
|
||||
region 2 block INF INF 38.75 INF INF INF
|
||||
group upper region 2
|
||||
group boundary union lower upper
|
||||
group mobile subtract all boundary
|
||||
|
||||
region leftupper block INF 20 20 INF INF INF
|
||||
region leftlower block INF 20 INF 20 INF INF
|
||||
group leftupper region leftupper
|
||||
group leftlower region leftlower
|
||||
|
||||
set leftupper atom 2
|
||||
set leftlower atom 3
|
||||
set lower atom 4
|
||||
set upper atom 5
|
||||
|
||||
# initial velocities
|
||||
|
||||
temperature new mobile full
|
||||
velocity mobile create 0.01 887723 temp new
|
||||
velocity upper set 0.0 0.02 0.0
|
||||
velocity mobile ramp vy 0.0 0.02 y 1.25 38.75 sum yes
|
||||
|
||||
# fixes
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 boundary setforce NULL 0.0 0.0
|
||||
|
||||
# run
|
||||
|
||||
timestep 0.003
|
||||
thermo 1000
|
||||
thermo_modify temp new
|
||||
|
||||
neigh_modify exclude type 2 3
|
||||
dump 1 all atom 250 dump.crack
|
||||
run 50000
|
||||
|
|
@ -0,0 +1,153 @@
|
|||
LAMMPS (1 Oct 2006)
|
||||
# 2d LJ crack simulation
|
||||
|
||||
dimension 2
|
||||
boundary s s p
|
||||
|
||||
atom_style atomic
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
# create geometry
|
||||
|
||||
lattice hex 0.93
|
||||
region box block 0 100 0 40 -0.25 0.25
|
||||
create_box 5 box
|
||||
Created box = (0 0 -0.278569) to (111.428 77.1994 0.278569)
|
||||
2 by 2 by 1 processor grid
|
||||
create_atoms 1
|
||||
Created 8141 atoms
|
||||
|
||||
mass 1 1.0
|
||||
mass 2 1.0
|
||||
mass 3 1.0
|
||||
mass 4 1.0
|
||||
mass 5 1.0
|
||||
|
||||
# LJ potentials
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff * * 1.0 1.0 2.5
|
||||
|
||||
# define groups
|
||||
|
||||
region 1 block INF INF INF 1.25 INF INF
|
||||
group lower region 1
|
||||
302 atoms in group lower
|
||||
region 2 block INF INF 38.75 INF INF INF
|
||||
group upper region 2
|
||||
302 atoms in group upper
|
||||
group boundary union lower upper
|
||||
604 atoms in group boundary
|
||||
group mobile subtract all boundary
|
||||
7537 atoms in group mobile
|
||||
|
||||
region leftupper block INF 20 20 INF INF INF
|
||||
region leftlower block INF 20 INF 20 INF INF
|
||||
group leftupper region leftupper
|
||||
841 atoms in group leftupper
|
||||
group leftlower region leftlower
|
||||
841 atoms in group leftlower
|
||||
|
||||
set leftupper atom 2
|
||||
841 settings made
|
||||
set leftlower atom 3
|
||||
841 settings made
|
||||
set lower atom 4
|
||||
302 settings made
|
||||
set upper atom 5
|
||||
302 settings made
|
||||
|
||||
# initial velocities
|
||||
|
||||
temperature new mobile full
|
||||
velocity mobile create 0.01 887723 temp new
|
||||
velocity upper set 0.0 0.02 0.0
|
||||
velocity mobile ramp vy 0.0 0.02 y 1.25 38.75 sum yes
|
||||
|
||||
# fixes
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 boundary setforce NULL 0.0 0.0
|
||||
|
||||
# run
|
||||
|
||||
timestep 0.003
|
||||
thermo 1000
|
||||
thermo_modify temp new
|
||||
|
||||
neigh_modify exclude type 2 3
|
||||
dump 1 all atom 250 dump.crack
|
||||
run 50000
|
||||
Memory usage per processor = 1.59725 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 0.010256205 -3.2595015 0 -3.2500081 -0.10145136 4792.6107
|
||||
1000 0.0050437246 -3.254635 0 -3.2499665 -0.12740271 4792.6107
|
||||
2000 0.0051505282 -3.2543692 0 -3.2496018 -0.15978403 4805.4017
|
||||
3000 0.0052701189 -3.2540454 0 -3.2491672 -0.17795883 4809.4575
|
||||
4000 0.0050604962 -3.2533431 0 -3.2486589 -0.18962575 4812.2411
|
||||
5000 0.0049888551 -3.2525578 0 -3.24794 -0.23962697 4815.939
|
||||
6000 0.0049676582 -3.251678 0 -3.2470799 -0.30927631 4820.4945
|
||||
7000 0.0051188772 -3.2507304 0 -3.2459922 -0.3909741 4828.8381
|
||||
8000 0.0048922662 -3.2493836 0 -3.2448552 -0.47790517 4841.9077
|
||||
9000 0.0049338477 -3.2480837 0 -3.2435168 -0.53340641 4849.3327
|
||||
10000 0.0049211223 -3.2466777 0 -3.2421226 -0.55379297 4855.6764
|
||||
11000 0.004895836 -3.2450776 0 -3.2405459 -0.56007065 4862.5721
|
||||
12000 0.004847489 -3.2434006 0 -3.2389137 -0.57998486 4863.9277
|
||||
13000 0.0047955582 -3.2415024 0 -3.2370635 -0.62542252 4870.6003
|
||||
14000 0.0048552089 -3.2396028 0 -3.2351087 -0.697236 4879.871
|
||||
15000 0.0048752032 -3.2375516 0 -3.233039 -0.76918523 4884.5734
|
||||
16000 0.0046965458 -3.2352968 0 -3.2309496 -0.82908331 4893.1926
|
||||
17000 0.0047868592 -3.2330762 0 -3.2286454 -0.85754888 4901.71
|
||||
18000 0.0047852616 -3.2307132 0 -3.2262838 -0.86919067 4909.8698
|
||||
19000 0.0047361082 -3.2281639 0 -3.2237801 -0.85109691 4912.5836
|
||||
20000 0.0048659736 -3.2257135 0 -3.2212095 -0.83986478 4916.5374
|
||||
21000 0.0049814043 -3.2232926 0 -3.2186817 -0.86128523 4923.9807
|
||||
22000 0.0049472744 -3.2207762 0 -3.2161969 -0.90337572 4931.7271
|
||||
23000 0.0053349592 -3.218575 0 -3.2136369 -0.97893232 4945.9715
|
||||
24000 0.0057755443 -3.2162642 0 -3.2109182 -1.0095182 4956.3791
|
||||
25000 0.0062190601 -3.2140052 0 -3.2082487 -1.0088874 4960.5377
|
||||
26000 0.0068001305 -3.2117942 0 -3.2054998 -0.96727393 4962.4079
|
||||
27000 0.0068225494 -3.2091441 0 -3.2028289 -0.91504959 4962.4468
|
||||
28000 0.0069100602 -3.2064225 0 -3.2000264 -0.9131624 4963.4009
|
||||
29000 0.0077073146 -3.2044225 0 -3.1972885 -0.97931905 4976.6434
|
||||
30000 0.0085530911 -3.2023628 0 -3.1944458 -1.0335604 4991.859
|
||||
31000 0.0090489847 -3.2000739 0 -3.191698 -1.0499238 5006.1205
|
||||
32000 0.009457073 -3.197803 0 -3.1890493 -1.0415395 5007.1136
|
||||
33000 0.0097449781 -3.1954191 0 -3.1863989 -0.97523426 5008.9351
|
||||
34000 0.010638648 -3.1933196 0 -3.1834722 -0.90641914 5009.8972
|
||||
35000 0.011724943 -3.1915042 0 -3.1806513 -0.86280832 5030.2601
|
||||
36000 0.012543854 -3.1897197 0 -3.1781088 -0.84498685 5058.0726
|
||||
37000 0.01425216 -3.1884117 0 -3.1752195 -0.89131599 5072.3266
|
||||
38000 0.017711377 -3.188949 0 -3.1725549 -0.83909256 5084.0891
|
||||
39000 0.022008898 -3.19099 0 -3.1706181 -0.75142283 5087.7576
|
||||
40000 0.026220897 -3.1935289 0 -3.1692583 -0.62636117 5093.7415
|
||||
41000 0.025508399 -3.1919886 0 -3.1683775 -0.42605643 5088.3384
|
||||
42000 0.026889328 -3.192089 0 -3.1671996 -0.34017637 5066.1245
|
||||
43000 0.028720644 -3.1925244 0 -3.1659399 -0.19561049 5083.1913
|
||||
44000 0.031213331 -3.1937329 0 -3.1648411 -0.35065498 5095.7582
|
||||
45000 0.031451475 -3.1922953 0 -3.1631831 -0.53502981 5109.9177
|
||||
46000 0.030623132 -3.1903208 0 -3.1619753 -0.55300441 5125.4041
|
||||
47000 0.031375 -3.1895766 0 -3.1605352 -0.5385838 5157.0846
|
||||
48000 0.030875482 -3.1879308 0 -3.1593517 -0.48509753 5161.8136
|
||||
49000 0.031761391 -3.1879906 0 -3.1585915 -0.44146775 5160.5089
|
||||
50000 0.032235944 -3.1871767 0 -3.1573383 -0.38658394 5152.5279
|
||||
Loop time of 71.1028 on 4 procs for 50000 steps with 8141 atoms
|
||||
|
||||
Pair time (%) = 45.4344 (63.8997)
|
||||
Neigh time (%) = 0.87692 (1.23331)
|
||||
Comm time (%) = 10.6446 (14.9707)
|
||||
Outpt time (%) = 2.95593 (4.15726)
|
||||
Other time (%) = 11.1909 (15.7391)
|
||||
|
||||
Nlocal: 2035.25 ave 2081 max 1974 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 1 1
|
||||
Nghost: 203.5 ave 245 max 162 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 17703.8 ave 18117 max 17273 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 70815
|
||||
Ave neighs/atom = 8.69856
|
||||
Neighbor list builds = 467
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,153 @@
|
|||
LAMMPS (1 Oct 2006)
|
||||
# 2d LJ crack simulation
|
||||
|
||||
dimension 2
|
||||
boundary s s p
|
||||
|
||||
atom_style atomic
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
# create geometry
|
||||
|
||||
lattice hex 0.93
|
||||
region box block 0 100 0 40 -0.25 0.25
|
||||
create_box 5 box
|
||||
Created box = (0 0 -0.278569) to (111.428 77.1994 0.278569)
|
||||
1 by 1 by 1 processor grid
|
||||
create_atoms 1
|
||||
Created 8141 atoms
|
||||
|
||||
mass 1 1.0
|
||||
mass 2 1.0
|
||||
mass 3 1.0
|
||||
mass 4 1.0
|
||||
mass 5 1.0
|
||||
|
||||
# LJ potentials
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff * * 1.0 1.0 2.5
|
||||
|
||||
# define groups
|
||||
|
||||
region 1 block INF INF INF 1.25 INF INF
|
||||
group lower region 1
|
||||
302 atoms in group lower
|
||||
region 2 block INF INF 38.75 INF INF INF
|
||||
group upper region 2
|
||||
302 atoms in group upper
|
||||
group boundary union lower upper
|
||||
604 atoms in group boundary
|
||||
group mobile subtract all boundary
|
||||
7537 atoms in group mobile
|
||||
|
||||
region leftupper block INF 20 20 INF INF INF
|
||||
region leftlower block INF 20 INF 20 INF INF
|
||||
group leftupper region leftupper
|
||||
841 atoms in group leftupper
|
||||
group leftlower region leftlower
|
||||
841 atoms in group leftlower
|
||||
|
||||
set leftupper atom 2
|
||||
841 settings made
|
||||
set leftlower atom 3
|
||||
841 settings made
|
||||
set lower atom 4
|
||||
302 settings made
|
||||
set upper atom 5
|
||||
302 settings made
|
||||
|
||||
# initial velocities
|
||||
|
||||
temperature new mobile full
|
||||
velocity mobile create 0.01 887723 temp new
|
||||
velocity upper set 0.0 0.02 0.0
|
||||
velocity mobile ramp vy 0.0 0.02 y 1.25 38.75 sum yes
|
||||
|
||||
# fixes
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 boundary setforce NULL 0.0 0.0
|
||||
|
||||
# run
|
||||
|
||||
timestep 0.003
|
||||
thermo 1000
|
||||
thermo_modify temp new
|
||||
|
||||
neigh_modify exclude type 2 3
|
||||
dump 1 all atom 250 dump.crack
|
||||
run 50000
|
||||
Memory usage per processor = 2.04243 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 0.010233422 -3.2595015 0 -3.2500292 -0.10147524 4792.6107
|
||||
1000 0.0051057052 -3.2546357 0 -3.2499098 -0.13099352 4792.6107
|
||||
2000 0.0051305159 -3.2543693 0 -3.2496204 -0.16341482 4807.4758
|
||||
3000 0.005186568 -3.2539935 0 -3.2491927 -0.17782954 4808.2338
|
||||
4000 0.005087842 -3.2533474 0 -3.248638 -0.18347851 4814.6291
|
||||
5000 0.004952798 -3.2525326 0 -3.2479482 -0.23680218 4819.1809
|
||||
6000 0.004991209 -3.2516461 0 -3.2470261 -0.30814679 4826.0224
|
||||
7000 0.004944807 -3.2506197 0 -3.2460426 -0.39136722 4830.7072
|
||||
8000 0.0049376929 -3.2494443 0 -3.2448739 -0.48674075 4839.3787
|
||||
9000 0.0050078092 -3.2482053 0 -3.24357 -0.53039175 4853.1439
|
||||
10000 0.004983781 -3.2466688 0 -3.2420557 -0.55385151 4857.416
|
||||
11000 0.0049723432 -3.2451304 0 -3.2405279 -0.56009417 4862.5452
|
||||
12000 0.0049013912 -3.243408 0 -3.2388712 -0.57381742 4865.356
|
||||
13000 0.0048043804 -3.2415478 0 -3.2371007 -0.62822628 4866.3058
|
||||
14000 0.0048263329 -3.2395963 0 -3.2351289 -0.69278151 4872.0789
|
||||
15000 0.0047872575 -3.2375073 0 -3.2330761 -0.77081332 4885.8904
|
||||
16000 0.0047945553 -3.2353167 0 -3.2308787 -0.82826028 4893.1664
|
||||
17000 0.0047216486 -3.2330128 0 -3.2286423 -0.86086905 4902.0617
|
||||
18000 0.0047886085 -3.2306714 0 -3.226239 -0.86709584 4912.8232
|
||||
19000 0.0048029287 -3.2282267 0 -3.223781 -0.8478792 4914.5926
|
||||
20000 0.0049477774 -3.22582 0 -3.2212403 -0.83551748 4917.3514
|
||||
21000 0.0050097792 -3.2233599 0 -3.2187228 -0.83827951 4924.4496
|
||||
22000 0.0052037073 -3.2210367 0 -3.21622 -0.87712941 4935.4747
|
||||
23000 0.005250599 -3.2186209 0 -3.2137608 -0.95723098 4947.854
|
||||
24000 0.0056583383 -3.2164899 0 -3.2112524 -0.99733057 4959.3194
|
||||
25000 0.006177144 -3.2143646 0 -3.2086469 -0.99156085 4966.2512
|
||||
26000 0.0065570098 -3.2120894 0 -3.2060201 -0.94420666 4960.9584
|
||||
27000 0.0065182894 -3.2093666 0 -3.2033331 -0.87993179 4961.9079
|
||||
28000 0.0068038044 -3.2067846 0 -3.2004869 -0.86598793 4967.889
|
||||
29000 0.0077170662 -3.2049416 0 -3.1977985 -0.91334819 4981.938
|
||||
30000 0.0081816546 -3.2027043 0 -3.1951312 -0.9653003 4996.292
|
||||
31000 0.0089120183 -3.2008682 0 -3.192619 -0.99183521 5012.9271
|
||||
32000 0.0095675927 -3.1988646 0 -3.1900086 -0.98991289 5018.881
|
||||
33000 0.010803232 -3.1974474 0 -3.1874477 -0.94112062 5012.4944
|
||||
34000 0.011158339 -3.195224 0 -3.1848955 -0.88514756 5006.3799
|
||||
35000 0.011756548 -3.193118 0 -3.1822359 -0.83787516 5002.794
|
||||
36000 0.011908147 -3.1908085 0 -3.179786 -0.82041392 5013.2137
|
||||
37000 0.01424843 -3.1903622 0 -3.1771736 -0.86593745 5045.4358
|
||||
38000 0.015513677 -3.1889279 0 -3.1745681 -0.84618406 5058.7819
|
||||
39000 0.017516672 -3.1885197 0 -3.1723059 -0.73798007 5086.8443
|
||||
40000 0.019448731 -3.1885754 0 -3.1705732 -0.59681319 5093.1044
|
||||
41000 0.021088915 -3.1885922 0 -3.1690718 -0.5085097 5089.6132
|
||||
42000 0.023948616 -3.1898036 0 -3.1676362 -0.45605083 5082.7572
|
||||
43000 0.025588509 -3.1896794 0 -3.1659941 -0.34855967 5111.1438
|
||||
44000 0.027568866 -3.1906457 0 -3.1651273 -0.41081127 5116.295
|
||||
45000 0.028445821 -3.1899978 0 -3.1636677 -0.36970991 5130.3322
|
||||
46000 0.028961863 -3.1898316 0 -3.1630238 -0.30874643 5129.4113
|
||||
47000 0.029932222 -3.1901868 0 -3.1624809 -0.28285013 5154.4915
|
||||
48000 0.030490267 -3.1898412 0 -3.1616187 -0.29218244 5175.3972
|
||||
49000 0.031743277 -3.1900262 0 -3.1606438 -0.26145795 5180.1115
|
||||
50000 0.031723195 -3.1891208 0 -3.1597571 -0.2519514 5202.1573
|
||||
Loop time of 512.873 on 1 procs for 50000 steps with 8141 atoms
|
||||
|
||||
Pair time (%) = 421.19 (82.1237)
|
||||
Neigh time (%) = 6.63742 (1.29416)
|
||||
Comm time (%) = 0.619009 (0.120694)
|
||||
Outpt time (%) = 7.54941 (1.47198)
|
||||
Other time (%) = 76.8767 (14.9894)
|
||||
|
||||
Nlocal: 8141 ave 8141 max 8141 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 70611 ave 70611 max 70611 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 70611
|
||||
Ave neighs/atom = 8.6735
|
||||
Neighbor list builds = 495
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,69 @@
|
|||
# 2-d LJ flow simulation
|
||||
|
||||
dimension 2
|
||||
boundary p s p
|
||||
|
||||
atom_style atomic
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
# create geometry
|
||||
|
||||
lattice hex 0.7
|
||||
region box block 0 20 0 10 -0.25 0.25
|
||||
create_box 3 box
|
||||
create_atoms 1
|
||||
|
||||
mass 1 1.0
|
||||
mass 2 1.0
|
||||
mass 3 1.0
|
||||
|
||||
# LJ potentials
|
||||
|
||||
pair_style lj/cut 1.12246
|
||||
pair_coeff * * 1.0 1.0 1.12246
|
||||
|
||||
# define groups
|
||||
|
||||
region 1 block INF INF INF 1.25 INF INF
|
||||
group lower region 1
|
||||
region 2 block INF INF 8.75 INF INF INF
|
||||
group upper region 2
|
||||
group boundary union lower upper
|
||||
group flow subtract all boundary
|
||||
|
||||
set lower atom 2
|
||||
set upper atom 3
|
||||
|
||||
# initial velocities
|
||||
|
||||
temperature mobile flow full
|
||||
velocity flow create 1.0 482748 temp mobile
|
||||
fix 1 all nve
|
||||
fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
|
||||
fix_modify 2 temp mobile
|
||||
|
||||
# Couette flow
|
||||
|
||||
velocity lower set 0.0 0.0 0.0
|
||||
velocity upper set 3.0 0.0 0.0
|
||||
fix 3 boundary setforce 0.0 0.0 0.0
|
||||
fix 4 all enforce2d
|
||||
|
||||
# Poisseuille flow
|
||||
|
||||
#velocity boundary set 0.0 0.0 0.0
|
||||
#fix 3 lower setforce 0.0 0.0 0.0
|
||||
#fix 4 upper setforce 0.0 NULL 0.0
|
||||
#fix 5 upper aveforce 0.0 -1.0 0.0
|
||||
#fix 6 flow addforce 0.5 0.0 0.0
|
||||
#fix 7 all enforce2d
|
||||
|
||||
# Run
|
||||
|
||||
timestep 0.003
|
||||
thermo 500
|
||||
thermo_modify temp mobile
|
||||
|
||||
dump 1 all atom 50 dump.flow
|
||||
run 10000
|
||||
|
|
@ -0,0 +1,69 @@
|
|||
# 2-d LJ flow simulation
|
||||
|
||||
dimension 2
|
||||
boundary p s p
|
||||
|
||||
atom_style atomic
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
# create geometry
|
||||
|
||||
lattice hex 0.7
|
||||
region box block 0 20 0 10 -0.25 0.25
|
||||
create_box 3 box
|
||||
create_atoms 1
|
||||
|
||||
mass 1 1.0
|
||||
mass 2 1.0
|
||||
mass 3 1.0
|
||||
|
||||
# LJ potentials
|
||||
|
||||
pair_style lj/cut 1.12246
|
||||
pair_coeff * * 1.0 1.0 1.12246
|
||||
|
||||
# define groups
|
||||
|
||||
region 1 block INF INF INF 1.25 INF INF
|
||||
group lower region 1
|
||||
region 2 block INF INF 8.75 INF INF INF
|
||||
group upper region 2
|
||||
group boundary union lower upper
|
||||
group flow subtract all boundary
|
||||
|
||||
set lower atom 2
|
||||
set upper atom 3
|
||||
|
||||
# initial velocities
|
||||
|
||||
temperature mobile flow full
|
||||
velocity flow create 1.0 482748 temp mobile
|
||||
fix 1 all nve
|
||||
fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
|
||||
fix_modify 2 temp mobile
|
||||
|
||||
# Couette flow
|
||||
|
||||
#velocity lower set 0.0 0.0 0.0
|
||||
#velocity upper set 3.0 0.0 0.0
|
||||
#fix 3 boundary setforce 0.0 0.0 0.0
|
||||
#fix 4 all enforce2d
|
||||
|
||||
# Poisseuille flow
|
||||
|
||||
velocity boundary set 0.0 0.0 0.0
|
||||
fix 3 lower setforce 0.0 0.0 0.0
|
||||
fix 4 upper setforce 0.0 NULL 0.0
|
||||
fix 5 upper aveforce 0.0 -1.0 0.0
|
||||
fix 6 flow addforce 0.5 0.0 0.0
|
||||
fix 7 all enforce2d
|
||||
|
||||
# Run
|
||||
|
||||
timestep 0.003
|
||||
thermo 500
|
||||
thermo_modify temp mobile
|
||||
|
||||
dump 1 all atom 25 dump.flow
|
||||
run 10000
|
||||
|
|
@ -0,0 +1,121 @@
|
|||
LAMMPS (1 Oct 2006)
|
||||
# 2-d LJ flow simulation
|
||||
|
||||
dimension 2
|
||||
boundary p s p
|
||||
|
||||
atom_style atomic
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
# create geometry
|
||||
|
||||
lattice hex 0.7
|
||||
region box block 0 20 0 10 -0.25 0.25
|
||||
create_box 3 box
|
||||
Created box = (0 0 -0.321089) to (25.6871 22.2457 0.321089)
|
||||
2 by 2 by 1 processor grid
|
||||
create_atoms 1
|
||||
Created 420 atoms
|
||||
|
||||
mass 1 1.0
|
||||
mass 2 1.0
|
||||
mass 3 1.0
|
||||
|
||||
# LJ potentials
|
||||
|
||||
pair_style lj/cut 1.12246
|
||||
pair_coeff * * 1.0 1.0 1.12246
|
||||
|
||||
# define groups
|
||||
|
||||
region 1 block INF INF INF 1.25 INF INF
|
||||
group lower region 1
|
||||
60 atoms in group lower
|
||||
region 2 block INF INF 8.75 INF INF INF
|
||||
group upper region 2
|
||||
60 atoms in group upper
|
||||
group boundary union lower upper
|
||||
120 atoms in group boundary
|
||||
group flow subtract all boundary
|
||||
300 atoms in group flow
|
||||
|
||||
set lower atom 2
|
||||
60 settings made
|
||||
set upper atom 3
|
||||
60 settings made
|
||||
|
||||
# initial velocities
|
||||
|
||||
temperature mobile flow full
|
||||
velocity flow create 1.0 482748 temp mobile
|
||||
fix 1 all nve
|
||||
fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
|
||||
fix_modify 2 temp mobile
|
||||
|
||||
# Couette flow
|
||||
|
||||
velocity lower set 0.0 0.0 0.0
|
||||
velocity upper set 3.0 0.0 0.0
|
||||
fix 3 boundary setforce 0.0 0.0 0.0
|
||||
fix 4 all enforce2d
|
||||
|
||||
# Poisseuille flow
|
||||
|
||||
#velocity boundary set 0.0 0.0 0.0
|
||||
#fix 3 lower setforce 0.0 0.0 0.0
|
||||
#fix 4 upper setforce 0.0 NULL 0.0
|
||||
#fix 5 upper aveforce 0.0 -1.0 0.0
|
||||
#fix 6 flow addforce 0.5 0.0 0.0
|
||||
#fix 7 all enforce2d
|
||||
|
||||
# Run
|
||||
|
||||
timestep 0.003
|
||||
thermo 500
|
||||
thermo_modify temp mobile
|
||||
|
||||
dump 1 all atom 50 dump.flow
|
||||
run 10000
|
||||
Memory usage per processor = 1.44615 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 1 0 0 0.71071429 0.54228995 366.96236
|
||||
500 1.0967867 -0.3465085 0 0.43299345 3.3754137 366.96236
|
||||
1000 1 -0.36129869 0 0.3494156 3.254923 366.96236
|
||||
1500 1.1299217 -0.37859354 0 0.42445795 3.0386513 366.96236
|
||||
2000 1 -0.34287377 0 0.36784052 3.1412593 366.96236
|
||||
2500 1.0899881 -0.38633626 0 0.38833382 2.9555542 366.96236
|
||||
3000 1 -0.39357685 0 0.31713744 2.9220544 366.96236
|
||||
3500 1.0725076 -0.43228066 0 0.32996578 3.0634077 366.96236
|
||||
4000 0.98425607 -0.50499218 0 0.19453267 2.6894642 366.96236
|
||||
4500 1.12295 -0.43026613 0 0.36783048 2.8383488 366.96236
|
||||
5000 1 -0.38936492 0 0.32134937 2.7396424 366.96236
|
||||
5500 1.0704014 -0.42922975 0 0.33151984 2.9491395 366.96236
|
||||
6000 1 -0.44518162 0 0.26553266 2.558761 366.96236
|
||||
6500 1.027497 -0.39375667 0 0.33650011 2.6024776 366.96236
|
||||
7000 1 -0.36769731 0 0.34301697 2.5197126 366.96236
|
||||
7500 1.0817191 -0.41108702 0 0.35770623 2.5206643 366.96236
|
||||
8000 1 -0.38737307 0 0.32334122 2.9522698 366.96236
|
||||
8500 1.1947509 -0.43799992 0 0.4111266 2.5630133 366.96236
|
||||
9000 1 -0.37870561 0 0.33200868 3.0568213 366.96236
|
||||
9500 1.1262643 -0.38699772 0 0.41345443 2.631997 366.96236
|
||||
10000 1 -0.39282605 0 0.31788823 2.7840067 366.96236
|
||||
Loop time of 1.95426 on 4 procs for 10000 steps with 420 atoms
|
||||
|
||||
Pair time (%) = 0.093526 (4.78575)
|
||||
Neigh time (%) = 0.0450768 (2.30659)
|
||||
Comm time (%) = 1.28476 (65.7414)
|
||||
Outpt time (%) = 0.177726 (9.0943)
|
||||
Other time (%) = 0.353174 (18.072)
|
||||
|
||||
Nlocal: 105 ave 113 max 98 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
Nghost: 41.5 ave 44 max 39 min
|
||||
Histogram: 1 0 0 0 1 0 1 0 0 1
|
||||
Neighs: 239.25 ave 292 max 197 min
|
||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 957
|
||||
Ave neighs/atom = 2.27857
|
||||
Neighbor list builds = 997
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,121 @@
|
|||
LAMMPS (1 Oct 2006)
|
||||
# 2-d LJ flow simulation
|
||||
|
||||
dimension 2
|
||||
boundary p s p
|
||||
|
||||
atom_style atomic
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
# create geometry
|
||||
|
||||
lattice hex 0.7
|
||||
region box block 0 20 0 10 -0.25 0.25
|
||||
create_box 3 box
|
||||
Created box = (0 0 -0.321089) to (25.6871 22.2457 0.321089)
|
||||
1 by 1 by 1 processor grid
|
||||
create_atoms 1
|
||||
Created 420 atoms
|
||||
|
||||
mass 1 1.0
|
||||
mass 2 1.0
|
||||
mass 3 1.0
|
||||
|
||||
# LJ potentials
|
||||
|
||||
pair_style lj/cut 1.12246
|
||||
pair_coeff * * 1.0 1.0 1.12246
|
||||
|
||||
# define groups
|
||||
|
||||
region 1 block INF INF INF 1.25 INF INF
|
||||
group lower region 1
|
||||
60 atoms in group lower
|
||||
region 2 block INF INF 8.75 INF INF INF
|
||||
group upper region 2
|
||||
60 atoms in group upper
|
||||
group boundary union lower upper
|
||||
120 atoms in group boundary
|
||||
group flow subtract all boundary
|
||||
300 atoms in group flow
|
||||
|
||||
set lower atom 2
|
||||
60 settings made
|
||||
set upper atom 3
|
||||
60 settings made
|
||||
|
||||
# initial velocities
|
||||
|
||||
temperature mobile flow full
|
||||
velocity flow create 1.0 482748 temp mobile
|
||||
fix 1 all nve
|
||||
fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
|
||||
fix_modify 2 temp mobile
|
||||
|
||||
# Couette flow
|
||||
|
||||
velocity lower set 0.0 0.0 0.0
|
||||
velocity upper set 3.0 0.0 0.0
|
||||
fix 3 boundary setforce 0.0 0.0 0.0
|
||||
fix 4 all enforce2d
|
||||
|
||||
# Poisseuille flow
|
||||
|
||||
#velocity boundary set 0.0 0.0 0.0
|
||||
#fix 3 lower setforce 0.0 0.0 0.0
|
||||
#fix 4 upper setforce 0.0 NULL 0.0
|
||||
#fix 5 upper aveforce 0.0 -1.0 0.0
|
||||
#fix 6 flow addforce 0.5 0.0 0.0
|
||||
#fix 7 all enforce2d
|
||||
|
||||
# Run
|
||||
|
||||
timestep 0.003
|
||||
thermo 500
|
||||
thermo_modify temp mobile
|
||||
|
||||
dump 1 all atom 50 dump.flow
|
||||
run 10000
|
||||
Memory usage per processor = 1.45035 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 1 0 0 0.71071429 0.54228995 366.96236
|
||||
500 1.0604224 -0.31549525 0 0.4381621 3.1208962 366.96236
|
||||
1000 1 -0.34356865 0 0.36714563 3.0305145 366.96236
|
||||
1500 1.1738082 -0.38202601 0 0.45221625 2.9197883 366.96236
|
||||
2000 1 -0.42682396 0 0.28389033 2.8469301 366.96236
|
||||
2500 1.024752 -0.41856176 0 0.30974413 2.9396683 366.96236
|
||||
3000 1 -0.43670738 0 0.27400691 2.7241981 366.96236
|
||||
3500 1.0895615 -0.42577755 0 0.34858934 2.6026891 366.96236
|
||||
4000 1 -0.44573495 0 0.26497934 2.4799192 366.96236
|
||||
4500 1.0711285 -0.4375466 0 0.32371976 2.8408151 366.96236
|
||||
5000 1 -0.46692482 0 0.24378947 2.7249453 366.96236
|
||||
5500 1.0960047 -0.497188 0 0.28175821 2.5610363 366.96236
|
||||
6000 1 -0.4129622 0 0.29775209 2.3978555 366.96236
|
||||
6500 1.0887159 -0.39206737 0 0.3816986 2.5437398 366.96236
|
||||
7000 1 -0.36776877 0 0.34294551 2.7427873 366.96236
|
||||
7500 1.1794747 -0.45276333 0 0.38550621 2.4854834 366.96236
|
||||
8000 1 -0.42255618 0 0.2881581 2.5061969 366.96236
|
||||
8500 1.098024 -0.45909879 0 0.32128255 2.4143874 366.96236
|
||||
9000 1 -0.42247096 0 0.28824333 2.2773041 366.96236
|
||||
9500 1.1248064 -0.40810854 0 0.39130741 2.1964254 366.96236
|
||||
10000 1 -0.36640887 0 0.34430541 2.4787391 366.96236
|
||||
Loop time of 2.20605 on 1 procs for 10000 steps with 420 atoms
|
||||
|
||||
Pair time (%) = 0.754591 (34.2056)
|
||||
Neigh time (%) = 0.308539 (13.9861)
|
||||
Comm time (%) = 0.107975 (4.8945)
|
||||
Outpt time (%) = 0.41017 (18.593)
|
||||
Other time (%) = 0.624773 (28.3209)
|
||||
|
||||
Nlocal: 420 ave 420 max 420 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 50 ave 50 max 50 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 957 ave 957 max 957 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 957
|
||||
Ave neighs/atom = 2.27857
|
||||
Neighbor list builds = 1000
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,121 @@
|
|||
LAMMPS (1 Oct 2006)
|
||||
# 2-d LJ flow simulation
|
||||
|
||||
dimension 2
|
||||
boundary p s p
|
||||
|
||||
atom_style atomic
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
# create geometry
|
||||
|
||||
lattice hex 0.7
|
||||
region box block 0 20 0 10 -0.25 0.25
|
||||
create_box 3 box
|
||||
Created box = (0 0 -0.321089) to (25.6871 22.2457 0.321089)
|
||||
2 by 2 by 1 processor grid
|
||||
create_atoms 1
|
||||
Created 420 atoms
|
||||
|
||||
mass 1 1.0
|
||||
mass 2 1.0
|
||||
mass 3 1.0
|
||||
|
||||
# LJ potentials
|
||||
|
||||
pair_style lj/cut 1.12246
|
||||
pair_coeff * * 1.0 1.0 1.12246
|
||||
|
||||
# define groups
|
||||
|
||||
region 1 block INF INF INF 1.25 INF INF
|
||||
group lower region 1
|
||||
60 atoms in group lower
|
||||
region 2 block INF INF 8.75 INF INF INF
|
||||
group upper region 2
|
||||
60 atoms in group upper
|
||||
group boundary union lower upper
|
||||
120 atoms in group boundary
|
||||
group flow subtract all boundary
|
||||
300 atoms in group flow
|
||||
|
||||
set lower atom 2
|
||||
60 settings made
|
||||
set upper atom 3
|
||||
60 settings made
|
||||
|
||||
# initial velocities
|
||||
|
||||
temperature mobile flow full
|
||||
velocity flow create 1.0 482748 temp mobile
|
||||
fix 1 all nve
|
||||
fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
|
||||
fix_modify 2 temp mobile
|
||||
|
||||
# Couette flow
|
||||
|
||||
#velocity lower set 0.0 0.0 0.0
|
||||
#velocity upper set 3.0 0.0 0.0
|
||||
#fix 3 boundary setforce 0.0 0.0 0.0
|
||||
#fix 4 all enforce2d
|
||||
|
||||
# Poisseuille flow
|
||||
|
||||
velocity boundary set 0.0 0.0 0.0
|
||||
fix 3 lower setforce 0.0 0.0 0.0
|
||||
fix 4 upper setforce 0.0 NULL 0.0
|
||||
fix 5 upper aveforce 0.0 -1.0 0.0
|
||||
fix 6 flow addforce 0.5 0.0 0.0
|
||||
fix 7 all enforce2d
|
||||
|
||||
# Run
|
||||
|
||||
timestep 0.003
|
||||
thermo 500
|
||||
thermo_modify temp mobile
|
||||
|
||||
dump 1 all atom 25 dump.flow
|
||||
run 10000
|
||||
Memory usage per processor = 1.44615 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 1 0 0 0.71071429 0.54228995 366.96236
|
||||
500 1.0778761 -0.35048279 0 0.41557918 2.8792129 369.20271
|
||||
1000 1 -0.38740705 0 0.32330724 2.2684877 375.93354
|
||||
1500 1.2052679 -0.37768559 0 0.47891551 1.6193029 376.17118
|
||||
2000 1 -0.38060118 0 0.33011311 1.4972142 371.27032
|
||||
2500 1.2211446 -0.39689946 0 0.47098547 1.5612989 364.09539
|
||||
3000 1 -0.4663268 0 0.24438748 1.5629904 356.17692
|
||||
3500 1.2338563 -0.57458788 0 0.3023314 1.8175737 344.96843
|
||||
4000 1 -0.69828914 0 0.012425149 2.3062239 333.07337
|
||||
4500 1.2223948 -0.68025643 0 0.18851702 3.0030445 323.53576
|
||||
5000 1 -0.77041655 0 -0.059702267 3.1645089 320.77015
|
||||
5500 1.206787 -0.74655306 0 0.11112772 2.6751057 324.35217
|
||||
6000 1 -0.68123467 0 0.029479617 2.3163646 329.78023
|
||||
6500 1.1974539 -0.67787899 0 0.17316861 2.1501471 332.21584
|
||||
7000 1 -0.63878551 0 0.071928781 1.9059071 332.869
|
||||
7500 1.2099494 -0.6450312 0 0.21489713 2.0613881 331.14731
|
||||
8000 1 -0.662565 0 0.048149283 2.1186993 326.88679
|
||||
8500 1.2200684 -0.75842085 0 0.10869919 2.566873 324.24936
|
||||
9000 1 -0.72471449 0 -0.0140002 2.5966104 323.69555
|
||||
9500 1.1858651 -0.72008706 0 0.12272424 2.6583911 324.95806
|
||||
10000 1 -0.6877267 0 0.022987584 2.263132 327.94921
|
||||
Loop time of 2.32195 on 4 procs for 10000 steps with 420 atoms
|
||||
|
||||
Pair time (%) = 0.0970009 (4.17756)
|
||||
Neigh time (%) = 0.026122 (1.125)
|
||||
Comm time (%) = 1.20093 (51.7207)
|
||||
Outpt time (%) = 0.296236 (12.758)
|
||||
Other time (%) = 0.701664 (30.2187)
|
||||
|
||||
Nlocal: 105 ave 107 max 103 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
Nghost: 41.75 ave 42 max 41 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 3
|
||||
Neighs: 279 ave 283 max 274 min
|
||||
Histogram: 1 0 0 0 1 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 1116
|
||||
Ave neighs/atom = 2.65714
|
||||
Neighbor list builds = 560
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,121 @@
|
|||
LAMMPS (1 Oct 2006)
|
||||
# 2-d LJ flow simulation
|
||||
|
||||
dimension 2
|
||||
boundary p s p
|
||||
|
||||
atom_style atomic
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
# create geometry
|
||||
|
||||
lattice hex 0.7
|
||||
region box block 0 20 0 10 -0.25 0.25
|
||||
create_box 3 box
|
||||
Created box = (0 0 -0.321089) to (25.6871 22.2457 0.321089)
|
||||
1 by 1 by 1 processor grid
|
||||
create_atoms 1
|
||||
Created 420 atoms
|
||||
|
||||
mass 1 1.0
|
||||
mass 2 1.0
|
||||
mass 3 1.0
|
||||
|
||||
# LJ potentials
|
||||
|
||||
pair_style lj/cut 1.12246
|
||||
pair_coeff * * 1.0 1.0 1.12246
|
||||
|
||||
# define groups
|
||||
|
||||
region 1 block INF INF INF 1.25 INF INF
|
||||
group lower region 1
|
||||
60 atoms in group lower
|
||||
region 2 block INF INF 8.75 INF INF INF
|
||||
group upper region 2
|
||||
60 atoms in group upper
|
||||
group boundary union lower upper
|
||||
120 atoms in group boundary
|
||||
group flow subtract all boundary
|
||||
300 atoms in group flow
|
||||
|
||||
set lower atom 2
|
||||
60 settings made
|
||||
set upper atom 3
|
||||
60 settings made
|
||||
|
||||
# initial velocities
|
||||
|
||||
temperature mobile flow full
|
||||
velocity flow create 1.0 482748 temp mobile
|
||||
fix 1 all nve
|
||||
fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
|
||||
fix_modify 2 temp mobile
|
||||
|
||||
# Couette flow
|
||||
|
||||
#velocity lower set 0.0 0.0 0.0
|
||||
#velocity upper set 3.0 0.0 0.0
|
||||
#fix 3 boundary setforce 0.0 0.0 0.0
|
||||
#fix 4 all enforce2d
|
||||
|
||||
# Poisseuille flow
|
||||
|
||||
velocity boundary set 0.0 0.0 0.0
|
||||
fix 3 lower setforce 0.0 0.0 0.0
|
||||
fix 4 upper setforce 0.0 NULL 0.0
|
||||
fix 5 upper aveforce 0.0 -1.0 0.0
|
||||
fix 6 flow addforce 0.5 0.0 0.0
|
||||
fix 7 all enforce2d
|
||||
|
||||
# Run
|
||||
|
||||
timestep 0.003
|
||||
thermo 500
|
||||
thermo_modify temp mobile
|
||||
|
||||
dump 1 all atom 25 dump.flow
|
||||
run 10000
|
||||
Memory usage per processor = 1.45035 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 1 0 0 0.71071429 0.54228995 366.96236
|
||||
500 1.1036177 -0.37435595 0 0.4100009 2.6003586 369.52344
|
||||
1000 1 -0.40278179 0 0.30793249 2.0566706 375.56836
|
||||
1500 1.2346487 -0.41204291 0 0.46543956 1.6254791 376.55032
|
||||
2000 1 -0.40773469 0 0.3029796 1.5174808 374.73899
|
||||
2500 1.2225527 -0.43831256 0 0.43057311 1.538442 366.48806
|
||||
3000 1 -0.49535329 0 0.215361 1.5818851 355.29346
|
||||
3500 1.2493652 -0.59970719 0 0.28823452 1.7494829 344.5223
|
||||
4000 1 -0.67604277 0 0.034671516 2.0751068 332.82226
|
||||
4500 1.1963622 -0.74392294 0 0.10634877 2.9790662 322.98092
|
||||
5000 1 -0.77322139 0 -0.062507105 3.3772359 320.78002
|
||||
5500 1.2048992 -0.77634312 0 0.079995929 2.9951611 324.35044
|
||||
6000 1 -0.68526989 0 0.025444398 2.3511721 331.72304
|
||||
6500 1.2079513 -0.59742461 0 0.26108363 1.8598207 336.52669
|
||||
7000 1 -0.60208737 0 0.10862692 1.9011673 336.55357
|
||||
7500 1.2390152 -0.68215629 0 0.19842954 1.9783028 333.8701
|
||||
8000 1 -0.69342292 0 0.01729137 2.3176685 328.52309
|
||||
8500 1.23233 -0.69508948 0 0.18074504 2.4605225 324.4685
|
||||
9000 1 -0.78017888 0 -0.069464593 2.5102443 323.83769
|
||||
9500 1.2049045 -0.78839912 0 0.067943719 2.6572163 323.67252
|
||||
10000 1 -0.72912664 0 -0.018412351 2.4438564 325.74175
|
||||
Loop time of 2.71301 on 1 procs for 10000 steps with 420 atoms
|
||||
|
||||
Pair time (%) = 0.850197 (31.3377)
|
||||
Neigh time (%) = 0.171296 (6.31386)
|
||||
Comm time (%) = 0.096819 (3.56869)
|
||||
Outpt time (%) = 0.824351 (30.3851)
|
||||
Other time (%) = 0.770352 (28.3947)
|
||||
|
||||
Nlocal: 420 ave 420 max 420 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 47 ave 47 max 47 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 1117 ave 1117 max 1117 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1117
|
||||
Ave neighs/atom = 2.65952
|
||||
Neighbor list builds = 558
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,80 @@
|
|||
# 2d friction simulation
|
||||
|
||||
dimension 2
|
||||
boundary p s p
|
||||
|
||||
atom_style atomic
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
# create geometry
|
||||
|
||||
lattice hex 0.9
|
||||
region box block 0 50 0 22 -0.25 0.25
|
||||
create_box 4 box
|
||||
|
||||
mass 1 1.0
|
||||
mass 2 1.0
|
||||
mass 3 1.0
|
||||
mass 4 1.0
|
||||
|
||||
# atom regions
|
||||
|
||||
region lo-fixed block INF INF INF 1.1 INF INF
|
||||
region lo-slab block INF INF INF 7 INF INF
|
||||
region above-lo block INF INF INF 7 INF INF side out
|
||||
region hi-fixed block INF INF 20.9 INF INF INF
|
||||
region hi-slab block INF INF 15 INF INF INF
|
||||
region below-hi block INF INF 15 INF INF INF side out
|
||||
region lo-asperity sphere 32 7 0 8
|
||||
region hi-asperity sphere 18 15 0 8
|
||||
region lo-half-sphere intersect 2 lo-asperity above-lo
|
||||
region hi-half-sphere intersect 2 hi-asperity below-hi
|
||||
|
||||
# create 2 surfaces with asperities
|
||||
|
||||
create_atoms 1 lo-slab
|
||||
create_atoms 1 hi-slab
|
||||
create_atoms 2 lo-half-sphere
|
||||
create_atoms 3 hi-half-sphere
|
||||
|
||||
# LJ potentials
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff * * 1.0 1.0 2.5
|
||||
|
||||
# define groups
|
||||
|
||||
group lo region lo-slab
|
||||
group lo type 2
|
||||
group hi region hi-slab
|
||||
group hi type 3
|
||||
group lo-fixed region lo-fixed
|
||||
group hi-fixed region hi-fixed
|
||||
group boundary union lo-fixed hi-fixed
|
||||
group mobile subtract all boundary
|
||||
|
||||
set lo-fixed atom 4
|
||||
set hi-fixed atom 4
|
||||
|
||||
# initial velocities
|
||||
|
||||
temperature new mobile partial 0 1 0
|
||||
velocity mobile create 0.1 482748 temp new
|
||||
velocity hi set 1.0 0.0 0.0 sum yes
|
||||
|
||||
# fixes
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 boundary setforce 0.0 0.0 0.0
|
||||
fix 3 mobile temp/rescale 200 0.1 0.1 0.02 1.0
|
||||
fix_modify 3 temp new
|
||||
|
||||
# Run
|
||||
|
||||
timestep 0.0025
|
||||
thermo 1000
|
||||
thermo_modify temp new
|
||||
|
||||
dump 1 all atom 100 dump.friction
|
||||
run 20000
|
||||
|
|
@ -0,0 +1,139 @@
|
|||
LAMMPS (1 Oct 2006)
|
||||
# 2d friction simulation
|
||||
|
||||
dimension 2
|
||||
boundary p s p
|
||||
|
||||
atom_style atomic
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
# create geometry
|
||||
|
||||
lattice hex 0.9
|
||||
region box block 0 50 0 22 -0.25 0.25
|
||||
create_box 4 box
|
||||
Created box = (0 0 -0.283174) to (56.6348 43.1615 0.283174)
|
||||
2 by 2 by 1 processor grid
|
||||
|
||||
mass 1 1.0
|
||||
mass 2 1.0
|
||||
mass 3 1.0
|
||||
mass 4 1.0
|
||||
|
||||
# atom regions
|
||||
|
||||
region lo-fixed block INF INF INF 1.1 INF INF
|
||||
region lo-slab block INF INF INF 7 INF INF
|
||||
region above-lo block INF INF INF 7 INF INF side out
|
||||
region hi-fixed block INF INF 20.9 INF INF INF
|
||||
region hi-slab block INF INF 15 INF INF INF
|
||||
region below-hi block INF INF 15 INF INF INF side out
|
||||
region lo-asperity sphere 32 7 0 8
|
||||
region hi-asperity sphere 18 15 0 8
|
||||
region lo-half-sphere intersect 2 lo-asperity above-lo
|
||||
region hi-half-sphere intersect 2 hi-asperity below-hi
|
||||
|
||||
# create 2 surfaces with asperities
|
||||
|
||||
create_atoms 1 lo-slab
|
||||
Created 750 atoms
|
||||
create_atoms 1 hi-slab
|
||||
Created 750 atoms
|
||||
create_atoms 2 lo-half-sphere
|
||||
Created 112 atoms
|
||||
create_atoms 3 hi-half-sphere
|
||||
Created 112 atoms
|
||||
|
||||
# LJ potentials
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff * * 1.0 1.0 2.5
|
||||
|
||||
# define groups
|
||||
|
||||
group lo region lo-slab
|
||||
750 atoms in group lo
|
||||
group lo type 2
|
||||
862 atoms in group lo
|
||||
group hi region hi-slab
|
||||
750 atoms in group hi
|
||||
group hi type 3
|
||||
862 atoms in group hi
|
||||
group lo-fixed region lo-fixed
|
||||
150 atoms in group lo-fixed
|
||||
group hi-fixed region hi-fixed
|
||||
150 atoms in group hi-fixed
|
||||
group boundary union lo-fixed hi-fixed
|
||||
300 atoms in group boundary
|
||||
group mobile subtract all boundary
|
||||
1424 atoms in group mobile
|
||||
|
||||
set lo-fixed atom 4
|
||||
150 settings made
|
||||
set hi-fixed atom 4
|
||||
150 settings made
|
||||
|
||||
# initial velocities
|
||||
|
||||
temperature new mobile partial 0 1 0
|
||||
velocity mobile create 0.1 482748 temp new
|
||||
velocity hi set 1.0 0.0 0.0 sum yes
|
||||
|
||||
# fixes
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 boundary setforce 0.0 0.0 0.0
|
||||
fix 3 mobile temp/rescale 200 0.1 0.1 0.02 1.0
|
||||
fix_modify 3 temp new
|
||||
|
||||
# Run
|
||||
|
||||
timestep 0.0025
|
||||
thermo 1000
|
||||
thermo_modify temp new
|
||||
|
||||
dump 1 all atom 100 dump.friction
|
||||
run 20000
|
||||
Memory usage per processor = 1.4603 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 0.1 -3.1333672 0 -3.0921549 -1.3466755 1384.4128
|
||||
1000 0.08936608 -3.060858 0 -3.0240282 0.018536372 1384.4128
|
||||
2000 0.087353242 -3.0615115 0 -3.0255112 -0.58816858 1384.4128
|
||||
3000 0.097185838 -3.0626106 0 -3.0225581 -0.099745896 1384.4128
|
||||
4000 0.10514697 -3.0540883 0 -3.0107549 -0.40469143 1384.4128
|
||||
5000 0.10965701 -3.0502726 0 -3.0050804 0.15587748 1384.4128
|
||||
6000 0.1142368 -3.0461587 0 -2.9990791 -0.27554064 1384.4128
|
||||
7000 0.1 -3.038824 0 -2.9976117 -0.38655949 1384.4128
|
||||
8000 0.11116929 -3.0485103 0 -3.0026949 -0.50529564 1384.4128
|
||||
9000 0.11426746 -3.044549 0 -2.9974568 -0.4678125 1384.4128
|
||||
10000 0.10652378 -3.0503221 0 -3.0064212 -0.52457375 1384.4128
|
||||
11000 0.1102547 -3.0498241 0 -3.0043856 -0.45053087 1384.4128
|
||||
12000 0.11548097 -3.0510641 0 -3.0034718 -0.27052982 1384.4128
|
||||
13000 0.10919538 -3.0438158 0 -2.9988139 -0.53868739 1384.4128
|
||||
14000 0.10742456 -3.045668 0 -3.0013959 -0.25306386 1384.4128
|
||||
15000 0.10795006 -3.0436862 0 -2.9991975 -0.44644395 1384.4128
|
||||
16000 0.11271512 -3.0478462 0 -3.0013937 -0.28516203 1384.4128
|
||||
17000 0.11209577 -3.0497319 0 -3.0035347 -0.39432942 1384.4128
|
||||
18000 0.1 -3.050733 0 -3.0095207 -0.34607727 1384.4128
|
||||
19000 0.092061676 -3.048521 0 -3.0105803 -0.37268438 1384.4128
|
||||
20000 0.10666663 -3.0598394 0 -3.0158797 -0.33025583 1384.4128
|
||||
Loop time of 8.99743 on 4 procs for 20000 steps with 1724 atoms
|
||||
|
||||
Pair time (%) = 3.6897 (41.0084)
|
||||
Neigh time (%) = 0.202473 (2.25034)
|
||||
Comm time (%) = 3.18145 (35.3595)
|
||||
Outpt time (%) = 0.579402 (6.43964)
|
||||
Other time (%) = 1.3444 (14.9421)
|
||||
|
||||
Nlocal: 431 ave 484 max 381 min
|
||||
Histogram: 1 1 0 0 0 0 0 1 0 1
|
||||
Nghost: 100.5 ave 119 max 87 min
|
||||
Histogram: 1 0 0 2 0 0 0 0 0 1
|
||||
Neighs: 3597.5 ave 4163 max 3176 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 14390
|
||||
Ave neighs/atom = 8.34687
|
||||
Neighbor list builds = 720
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,139 @@
|
|||
LAMMPS (1 Oct 2006)
|
||||
# 2d friction simulation
|
||||
|
||||
dimension 2
|
||||
boundary p s p
|
||||
|
||||
atom_style atomic
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
# create geometry
|
||||
|
||||
lattice hex 0.9
|
||||
region box block 0 50 0 22 -0.25 0.25
|
||||
create_box 4 box
|
||||
Created box = (0 0 -0.283174) to (56.6348 43.1615 0.283174)
|
||||
1 by 1 by 1 processor grid
|
||||
|
||||
mass 1 1.0
|
||||
mass 2 1.0
|
||||
mass 3 1.0
|
||||
mass 4 1.0
|
||||
|
||||
# atom regions
|
||||
|
||||
region lo-fixed block INF INF INF 1.1 INF INF
|
||||
region lo-slab block INF INF INF 7 INF INF
|
||||
region above-lo block INF INF INF 7 INF INF side out
|
||||
region hi-fixed block INF INF 20.9 INF INF INF
|
||||
region hi-slab block INF INF 15 INF INF INF
|
||||
region below-hi block INF INF 15 INF INF INF side out
|
||||
region lo-asperity sphere 32 7 0 8
|
||||
region hi-asperity sphere 18 15 0 8
|
||||
region lo-half-sphere intersect 2 lo-asperity above-lo
|
||||
region hi-half-sphere intersect 2 hi-asperity below-hi
|
||||
|
||||
# create 2 surfaces with asperities
|
||||
|
||||
create_atoms 1 lo-slab
|
||||
Created 750 atoms
|
||||
create_atoms 1 hi-slab
|
||||
Created 750 atoms
|
||||
create_atoms 2 lo-half-sphere
|
||||
Created 112 atoms
|
||||
create_atoms 3 hi-half-sphere
|
||||
Created 112 atoms
|
||||
|
||||
# LJ potentials
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff * * 1.0 1.0 2.5
|
||||
|
||||
# define groups
|
||||
|
||||
group lo region lo-slab
|
||||
750 atoms in group lo
|
||||
group lo type 2
|
||||
862 atoms in group lo
|
||||
group hi region hi-slab
|
||||
750 atoms in group hi
|
||||
group hi type 3
|
||||
862 atoms in group hi
|
||||
group lo-fixed region lo-fixed
|
||||
150 atoms in group lo-fixed
|
||||
group hi-fixed region hi-fixed
|
||||
150 atoms in group hi-fixed
|
||||
group boundary union lo-fixed hi-fixed
|
||||
300 atoms in group boundary
|
||||
group mobile subtract all boundary
|
||||
1424 atoms in group mobile
|
||||
|
||||
set lo-fixed atom 4
|
||||
150 settings made
|
||||
set hi-fixed atom 4
|
||||
150 settings made
|
||||
|
||||
# initial velocities
|
||||
|
||||
temperature new mobile partial 0 1 0
|
||||
velocity mobile create 0.1 482748 temp new
|
||||
velocity hi set 1.0 0.0 0.0 sum yes
|
||||
|
||||
# fixes
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 boundary setforce 0.0 0.0 0.0
|
||||
fix 3 mobile temp/rescale 200 0.1 0.1 0.02 1.0
|
||||
fix_modify 3 temp new
|
||||
|
||||
# Run
|
||||
|
||||
timestep 0.0025
|
||||
thermo 1000
|
||||
thermo_modify temp new
|
||||
|
||||
dump 1 all atom 100 dump.friction
|
||||
run 20000
|
||||
Memory usage per processor = 1.53824 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 0.1 -3.1333672 0 -3.0921549 -1.3466755 1384.4128
|
||||
1000 0.085622556 -3.0583969 0 -3.0231098 0.040017208 1384.4128
|
||||
2000 0.085921887 -3.0572271 0 -3.0218167 -0.60479351 1384.4128
|
||||
3000 0.10739474 -3.0650606 0 -3.0208008 -0.04184404 1384.4128
|
||||
4000 0.089682132 -3.04809 0 -3.01113 -0.22441446 1384.4128
|
||||
5000 0.10934102 -3.0485926 0 -3.0035307 0.12177364 1384.4128
|
||||
6000 0.10817011 -3.0584907 0 -3.0139113 -0.36521995 1384.4128
|
||||
7000 0.10519415 -3.0511557 0 -3.0078027 -0.279893 1384.4128
|
||||
8000 0.11660453 -3.0348037 0 -2.9867483 -0.47310792 1384.4128
|
||||
9000 0.1 -3.0308672 0 -2.9896549 -0.35351908 1384.4128
|
||||
10000 0.10012993 -3.0431145 0 -3.0018486 -0.4837576 1384.4128
|
||||
11000 0.11987001 -3.0484839 0 -2.9990827 -0.45971209 1384.4128
|
||||
12000 0.11063404 -3.0457139 0 -3.000119 -0.32411476 1384.4128
|
||||
13000 0.11214672 -3.0407157 0 -2.9944974 -0.4453681 1384.4128
|
||||
14000 0.11127122 -3.0431707 0 -2.9973132 -0.35672869 1384.4128
|
||||
15000 0.11311298 -3.0456742 0 -2.9990577 -0.42235702 1384.4128
|
||||
16000 0.11003354 -3.0519914 0 -3.0066441 -0.24377861 1384.4128
|
||||
17000 0.095617549 -3.0478455 0 -3.0084393 -0.54070059 1384.4128
|
||||
18000 0.10655281 -3.0497371 0 -3.0058242 -0.2968023 1384.4128
|
||||
19000 0.096661108 -3.0630512 0 -3.0232149 -0.35284808 1384.4128
|
||||
20000 0.099961152 -3.0606412 0 -3.0194449 -0.39275101 1384.4128
|
||||
Loop time of 42.478 on 1 procs for 20000 steps with 1724 atoms
|
||||
|
||||
Pair time (%) = 34.1596 (80.4171)
|
||||
Neigh time (%) = 1.4565 (3.42883)
|
||||
Comm time (%) = 0.402718 (0.948062)
|
||||
Outpt time (%) = 1.64536 (3.87344)
|
||||
Other time (%) = 4.81384 (11.3326)
|
||||
|
||||
Nlocal: 1724 ave 1724 max 1724 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 141 ave 141 max 141 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 14389 ave 14389 max 14389 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 14389
|
||||
Ave neighs/atom = 8.34629
|
||||
Neighbor list builds = 730
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,57 @@
|
|||
# 2d indenter simulation
|
||||
|
||||
dimension 2
|
||||
boundary p s p
|
||||
|
||||
atom_style atomic
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
# create geometry
|
||||
|
||||
lattice hex 0.9
|
||||
region box block 0 20 0 10 -0.25 0.25
|
||||
create_box 2 box
|
||||
create_atoms 1
|
||||
|
||||
mass 1 1.0
|
||||
mass 2 1.0
|
||||
|
||||
# LJ potentials
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff * * 1.0 1.0 2.5
|
||||
|
||||
# define groups
|
||||
|
||||
region 1 block INF INF INF 1.25 INF INF
|
||||
group lower region 1
|
||||
group mobile subtract all lower
|
||||
set lower atom 2
|
||||
|
||||
# initial velocities
|
||||
|
||||
temperature new mobile full
|
||||
velocity mobile create 0.2 482748 temp new
|
||||
fix 1 all nve
|
||||
fix 2 lower setforce 0.0 0.0 0.0
|
||||
fix 3 all temp/rescale 100 0.1 0.1 0.01 1.0
|
||||
|
||||
# indenter
|
||||
|
||||
fix 4 all indent 1000.0 sphere 10 13 0 5.0 vel 0.0 -0.02 0.0
|
||||
fix 5 all enforce2d
|
||||
|
||||
# Run with indenter
|
||||
|
||||
timestep 0.003
|
||||
thermo 1000
|
||||
thermo_modify temp new
|
||||
|
||||
dump 1 all atom 250 dump.indent
|
||||
run 30000
|
||||
|
||||
# Run without indenter
|
||||
|
||||
unfix 4
|
||||
run 30000
|
||||
|
|
@ -0,0 +1,71 @@
|
|||
# 2d indenter simulation with minimization instead of dynamics
|
||||
|
||||
dimension 2
|
||||
boundary p s p
|
||||
|
||||
atom_style atomic
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
# create geometry
|
||||
|
||||
lattice hex 0.9
|
||||
region box block 0 20 0 10 -0.25 0.25
|
||||
create_box 2 box
|
||||
create_atoms 1
|
||||
|
||||
mass 1 1.0
|
||||
mass 2 1.0
|
||||
|
||||
# LJ potentials
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff * * 1.0 1.0 2.5
|
||||
|
||||
# define groups
|
||||
|
||||
region 1 block INF INF INF 1.25 INF INF
|
||||
group lower region 1
|
||||
group mobile subtract all lower
|
||||
set lower atom 2
|
||||
|
||||
# initial velocities
|
||||
|
||||
fix 2 lower setforce 0.0 0.0 0.0
|
||||
|
||||
# indenter
|
||||
|
||||
fix 5 all enforce2d
|
||||
|
||||
# run with indent
|
||||
|
||||
thermo 10
|
||||
|
||||
dump 1 all atom 1 tmp.dump
|
||||
dump_modify 1 scale no
|
||||
|
||||
minimize 1.0e-4 1000 1000
|
||||
|
||||
fix 4 all indent 5000.0 sphere 10 13.0 0 6.0
|
||||
fix_modify 4 energy yes thermo yes
|
||||
minimize 1.0e-4 1000 1000
|
||||
|
||||
fix 4 all indent 1000.0 sphere 10 12.5 0 6.0
|
||||
fix_modify 4 energy yes
|
||||
minimize 1.0e-4 1000 1000
|
||||
|
||||
fix 4 all indent 1000.0 sphere 10 12.0 0 6.0
|
||||
fix_modify 4 energy yes
|
||||
minimize 1.0e-4 1000 1000
|
||||
|
||||
fix 4 all indent 1000.0 sphere 10 11.4 0 6.0
|
||||
fix_modify 4 thermo yes
|
||||
minimize 1.0e-4 1000 1000
|
||||
|
||||
fix 4 all indent 1000.0 sphere 10 11.2 0 6.0
|
||||
fix_modify 4 thermo yes
|
||||
minimize 1.0e-4 1000 1000
|
||||
|
||||
fix 4 all indent 1000.0 sphere 10 11.0 0 6.0
|
||||
fix_modify 4 thermo yes
|
||||
minimize 1.0e-4 1000 1000
|
||||
|
|
@ -0,0 +1,168 @@
|
|||
LAMMPS (1 Oct 2006)
|
||||
# 2d indenter simulation
|
||||
|
||||
dimension 2
|
||||
boundary p s p
|
||||
|
||||
atom_style atomic
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
# create geometry
|
||||
|
||||
lattice hex 0.9
|
||||
region box block 0 20 0 10 -0.25 0.25
|
||||
create_box 2 box
|
||||
Created box = (0 0 -0.283174) to (22.6539 19.6189 0.283174)
|
||||
2 by 2 by 1 processor grid
|
||||
create_atoms 1
|
||||
Created 420 atoms
|
||||
|
||||
mass 1 1.0
|
||||
mass 2 1.0
|
||||
|
||||
# LJ potentials
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff * * 1.0 1.0 2.5
|
||||
|
||||
# define groups
|
||||
|
||||
region 1 block INF INF INF 1.25 INF INF
|
||||
group lower region 1
|
||||
60 atoms in group lower
|
||||
group mobile subtract all lower
|
||||
360 atoms in group mobile
|
||||
set lower atom 2
|
||||
60 settings made
|
||||
|
||||
# initial velocities
|
||||
|
||||
temperature new mobile full
|
||||
velocity mobile create 0.2 482748 temp new
|
||||
fix 1 all nve
|
||||
fix 2 lower setforce 0.0 0.0 0.0
|
||||
fix 3 all temp/rescale 100 0.1 0.1 0.01 1.0
|
||||
|
||||
# indenter
|
||||
|
||||
fix 4 all indent 1000.0 sphere 10 13 0 5.0 vel 0.0 -0.02 0.0
|
||||
fix 5 all enforce2d
|
||||
|
||||
# Run with indenter
|
||||
|
||||
timestep 0.003
|
||||
thermo 1000
|
||||
thermo_modify temp new
|
||||
|
||||
dump 1 all atom 250 dump.indent
|
||||
run 30000
|
||||
Memory usage per processor = 1.44615 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 0.2 -3.1727576 0 -3.0020433 -1.6911656 251.71282
|
||||
1000 0.11576832 -3.0966334 0 -2.9978168 -0.24095347 250.17681
|
||||
2000 0.11528823 -3.0962223 0 -2.9978155 -0.45030047 250.45856
|
||||
3000 0.11379051 -3.0840496 0 -2.9869213 -0.5022142 251.7439
|
||||
4000 0.11595816 -3.085882 0 -2.9869034 -0.047829504 249.09265
|
||||
5000 0.11272851 -3.0844605 0 -2.9882386 -0.57244294 252.48573
|
||||
6000 0.12387775 -3.0900283 0 -2.9842898 0.0072734647 249.1402
|
||||
7000 0.1113616 -3.0914902 0 -2.9964351 -0.12742916 250.29327
|
||||
8000 0.1167364 -3.0879355 0 -2.9882926 0.20678001 250.17825
|
||||
9000 0.11504768 -3.0918767 0 -2.9936753 0.35261539 249.40265
|
||||
10000 0.11864876 -3.0776022 0 -2.976327 0.45724638 249.80407
|
||||
11000 0.12749806 -3.0769801 0 -2.9681514 0.7106404 248.1776
|
||||
12000 0.11068569 -3.0664256 0 -2.9719474 0.77940328 248.88714
|
||||
13000 0.11341038 -3.0596733 0 -2.9628694 1.1566167 249.36303
|
||||
14000 0.1176102 -3.058063 0 -2.9576743 1.2083864 249.05567
|
||||
15000 0.12582681 -3.054119 0 -2.9467168 1.052489 254.01805
|
||||
16000 0.11716135 -3.0359809 0 -2.9359753 1.1111189 259.94911
|
||||
17000 0.11836201 -3.0276208 0 -2.9265904 1.0821175 257.98321
|
||||
18000 0.12271549 -3.0171543 0 -2.9124079 1.5119093 264.99586
|
||||
19000 0.11746211 -3.0102935 0 -2.9100312 1.6305879 267.60889
|
||||
20000 0.12090524 -2.9967767 0 -2.8935754 1.7995263 268.87142
|
||||
21000 0.12612028 -2.994907 0 -2.8872544 1.8540136 271.56724
|
||||
22000 0.1167364 -2.9800486 0 -2.8804058 1.5103597 276.50496
|
||||
23000 0.11371517 -3.0043157 0 -2.9072517 1.1335811 275.4202
|
||||
24000 0.12132941 -3.0096869 0 -2.9061236 1.4605526 274.49424
|
||||
25000 0.12720095 -3.0069871 0 -2.898412 1.6853695 271.79073
|
||||
26000 0.11378571 -2.9920984 0 -2.8949742 1.5810259 275.70735
|
||||
27000 0.12075739 -2.9937473 0 -2.8906722 1.1417712 284.83703
|
||||
28000 0.11405151 -2.9959463 0 -2.8985951 1.1975088 282.69832
|
||||
29000 0.11973002 -2.9904314 0 -2.8882333 0.95237047 287.29831
|
||||
30000 0.11503912 -2.9700786 0 -2.8718845 1.3547537 288.9147
|
||||
Loop time of 6.5358 on 4 procs for 30000 steps with 420 atoms
|
||||
|
||||
Pair time (%) = 1.41006 (21.5744)
|
||||
Neigh time (%) = 0.0485178 (0.742339)
|
||||
Comm time (%) = 3.8256 (58.533)
|
||||
Outpt time (%) = 0.108883 (1.66595)
|
||||
Other time (%) = 1.14274 (17.4844)
|
||||
|
||||
Nlocal: 105 ave 125 max 84 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||
Nghost: 94.5 ave 103 max 86 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||
Neighs: 921.75 ave 1178 max 667 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 3687
|
||||
Ave neighs/atom = 8.77857
|
||||
Neighbor list builds = 617
|
||||
Dangerous builds = 0
|
||||
|
||||
# Run without indenter
|
||||
|
||||
unfix 4
|
||||
run 30000
|
||||
Memory usage per processor = 1.44672 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
30000 0.11503912 -2.9700786 0 -2.8718845 1.3561767 288.61154
|
||||
31000 0.11044364 -3.0076121 0 -2.9133406 -0.52779902 292.44389
|
||||
32000 0.12019156 -2.9928375 0 -2.8902454 -0.4563394 294.0201
|
||||
33000 0.11776824 -3.0170498 0 -2.9165262 0.23283576 288.29221
|
||||
34000 0.11371582 -3.0135113 0 -2.9164467 0.0061511438 287.56456
|
||||
35000 0.11235735 -3.0121578 0 -2.9162528 -0.46926625 292.5539
|
||||
36000 0.1167364 -3.0268323 0 -2.9271895 0.060047839 287.80848
|
||||
37000 0.11117485 -3.022005 0 -2.9271093 -0.118142 289.78382
|
||||
38000 0.10552007 -3.0174083 0 -2.9273394 -0.6700554 288.73054
|
||||
39000 0.12214122 -3.0318714 0 -2.9276151 -0.020293363 284.90615
|
||||
40000 0.1167364 -3.0374431 0 -2.9378003 -0.2576625 282.39621
|
||||
41000 0.12078959 -3.0407878 0 -2.9376852 -0.32963004 283.00597
|
||||
42000 0.12532766 -3.0592415 0 -2.9522654 -0.13855832 275.59038
|
||||
43000 0.12195787 -3.0696533 0 -2.9655536 -0.59184637 276.4371
|
||||
44000 0.11819255 -3.0663983 0 -2.9655125 -0.40728614 275.67698
|
||||
45000 0.11276783 -3.0618054 0 -2.96555 -0.10571263 272.71725
|
||||
46000 0.11003631 -3.0594741 0 -2.9655503 -0.3808265 275.07036
|
||||
47000 0.11854167 -3.0792116 0 -2.9780278 -0.40824195 274.01648
|
||||
48000 0.10827298 -3.0704447 0 -2.978026 -0.22213637 271.58418
|
||||
49000 0.10975304 -3.0717077 0 -2.9780256 -0.4821176 274.12844
|
||||
50000 0.11981935 -3.0677955 0 -2.9655211 -0.26816116 274.19059
|
||||
51000 0.12079404 -3.0686263 0 -2.9655199 -0.33188148 274.5802
|
||||
52000 0.11731632 -3.076662 0 -2.9765241 -0.48748579 274.88209
|
||||
53000 0.11451375 -3.0742688 0 -2.9765231 -0.25944149 274.6574
|
||||
54000 0.11308706 -3.0730497 0 -2.9765218 -0.44356549 274.44162
|
||||
55000 0.11323885 -3.07318 0 -2.9765225 -0.34236444 275.44349
|
||||
56000 0.11199118 -3.072113 0 -2.9765205 -0.33585978 274.06495
|
||||
57000 0.11740244 -3.0767352 0 -2.9765239 -0.59185176 275.0556
|
||||
58000 0.1159403 -3.0755277 0 -2.9765644 -0.28617471 274.30591
|
||||
59000 0.12463828 -3.0829133 0 -2.9765256 -0.40473725 273.86499
|
||||
60000 0.12095326 -3.069233 0 -2.9659907 -0.39935619 276.71426
|
||||
Loop time of 6.56165 on 4 procs for 30000 steps with 420 atoms
|
||||
|
||||
Pair time (%) = 1.39105 (21.1996)
|
||||
Neigh time (%) = 0.0485317 (0.739626)
|
||||
Comm time (%) = 3.91511 (59.6666)
|
||||
Outpt time (%) = 0.117233 (1.78663)
|
||||
Other time (%) = 1.08973 (16.6075)
|
||||
|
||||
Nlocal: 105 ave 120 max 86 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 0 2
|
||||
Nghost: 87 ave 92 max 84 min
|
||||
Histogram: 1 0 2 0 0 0 0 0 0 1
|
||||
Neighs: 892.5 ave 1086 max 676 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 3570
|
||||
Ave neighs/atom = 8.5
|
||||
Neighbor list builds = 625
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,168 @@
|
|||
LAMMPS (1 Oct 2006)
|
||||
# 2d indenter simulation
|
||||
|
||||
dimension 2
|
||||
boundary p s p
|
||||
|
||||
atom_style atomic
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
# create geometry
|
||||
|
||||
lattice hex 0.9
|
||||
region box block 0 20 0 10 -0.25 0.25
|
||||
create_box 2 box
|
||||
Created box = (0 0 -0.283174) to (22.6539 19.6189 0.283174)
|
||||
1 by 1 by 1 processor grid
|
||||
create_atoms 1
|
||||
Created 420 atoms
|
||||
|
||||
mass 1 1.0
|
||||
mass 2 1.0
|
||||
|
||||
# LJ potentials
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff * * 1.0 1.0 2.5
|
||||
|
||||
# define groups
|
||||
|
||||
region 1 block INF INF INF 1.25 INF INF
|
||||
group lower region 1
|
||||
60 atoms in group lower
|
||||
group mobile subtract all lower
|
||||
360 atoms in group mobile
|
||||
set lower atom 2
|
||||
60 settings made
|
||||
|
||||
# initial velocities
|
||||
|
||||
temperature new mobile full
|
||||
velocity mobile create 0.2 482748 temp new
|
||||
fix 1 all nve
|
||||
fix 2 lower setforce 0.0 0.0 0.0
|
||||
fix 3 all temp/rescale 100 0.1 0.1 0.01 1.0
|
||||
|
||||
# indenter
|
||||
|
||||
fix 4 all indent 1000.0 sphere 10 13 0 5.0 vel 0.0 -0.02 0.0
|
||||
fix 5 all enforce2d
|
||||
|
||||
# Run with indenter
|
||||
|
||||
timestep 0.003
|
||||
thermo 1000
|
||||
thermo_modify temp new
|
||||
|
||||
dump 1 all atom 250 dump.indent
|
||||
run 30000
|
||||
Memory usage per processor = 1.45035 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 0.2 -3.1727576 0 -3.0020433 -1.6911656 251.71282
|
||||
1000 0.11979027 -3.0878285 0 -2.9855789 -0.043690155 249.58001
|
||||
2000 0.12095292 -3.0888211 0 -2.9855791 -0.46999358 251.6098
|
||||
3000 0.1167364 -3.0841547 0 -2.9845118 -0.41054969 250.8041
|
||||
4000 0.12249143 -3.1004175 0 -2.9958623 -0.060853986 248.47717
|
||||
5000 0.10957873 -3.0886367 0 -2.9951034 -0.57642649 251.31708
|
||||
6000 0.12346008 -3.0985964 0 -2.9932144 -0.072968634 250.46216
|
||||
7000 0.10994736 -3.0850721 0 -2.9912241 -0.20324168 251.37979
|
||||
8000 0.11557891 -3.086042 0 -2.9873871 0.22717975 249.49714
|
||||
9000 0.12016755 -3.084536 0 -2.9819645 0.33218396 248.89256
|
||||
10000 0.12659552 -3.0852403 0 -2.977182 0.40666454 249.67836
|
||||
11000 0.12524777 -3.0736607 0 -2.9667528 0.77561215 248.69926
|
||||
12000 0.11844672 -3.0571177 0 -2.9560149 0.77334207 249.761
|
||||
13000 0.12031569 -3.0583679 0 -2.9556699 1.2700141 247.59077
|
||||
14000 0.1167364 -3.0548463 0 -2.9552034 1.0859393 250.18904
|
||||
15000 0.1167364 -3.0549235 0 -2.9552806 1.2995978 251.78491
|
||||
16000 0.12471788 -3.052462 0 -2.9460064 1.6452635 249.66328
|
||||
17000 0.12078161 -3.0356476 0 -2.9325519 1.9172373 248.00711
|
||||
18000 0.11737985 -3.0294795 0 -2.9292874 1.9843046 254.0314
|
||||
19000 0.12273219 -3.0164914 0 -2.9117307 1.9954937 251.85839
|
||||
20000 0.12550051 -3.0011844 0 -2.8940608 1.779848 260.26132
|
||||
21000 0.12036751 -2.9934276 0 -2.8906853 1.3693509 269.07657
|
||||
22000 0.12307091 -3.0182302 0 -2.9131804 0.94154126 269.78997
|
||||
23000 0.11949164 -3.0176126 0 -2.9156179 1.19816 265.98797
|
||||
24000 0.1167364 -3.020151 0 -2.9205082 0.95639973 266.25197
|
||||
25000 0.12252115 -3.0162117 0 -2.9116312 1.5771822 264.20779
|
||||
26000 0.11367117 -3.0238072 0 -2.9267808 0.71311555 265.96581
|
||||
27000 0.12007686 -3.0147427 0 -2.9122485 1.185271 266.21643
|
||||
28000 0.11526199 -3.0019986 0 -2.9036143 1.2838023 267.44914
|
||||
29000 0.12754217 -3.0122896 0 -2.9034233 1.3382791 269.93381
|
||||
30000 0.12108464 -2.9981686 0 -2.8948142 1.0638866 269.70142
|
||||
Loop time of 16.0381 on 1 procs for 30000 steps with 420 atoms
|
||||
|
||||
Pair time (%) = 12.7017 (79.1969)
|
||||
Neigh time (%) = 0.325385 (2.02882)
|
||||
Comm time (%) = 0.319287 (1.9908)
|
||||
Outpt time (%) = 0.343728 (2.14319)
|
||||
Other time (%) = 2.34803 (14.6403)
|
||||
|
||||
Nlocal: 420 ave 420 max 420 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 111 ave 111 max 111 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 3647 ave 3647 max 3647 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 3647
|
||||
Ave neighs/atom = 8.68333
|
||||
Neighbor list builds = 621
|
||||
Dangerous builds = 0
|
||||
|
||||
# Run without indenter
|
||||
|
||||
unfix 4
|
||||
run 30000
|
||||
Memory usage per processor = 1.45035 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
30000 0.12108464 -2.9981686 0 -2.8948142 1.0650921 269.39617
|
||||
31000 0.10657868 -3.0036168 0 -2.9126443 -0.0032557036 272.44965
|
||||
32000 0.1167364 -3.0371073 0 -2.9374644 -0.35201197 275.67834
|
||||
33000 0.11914647 -3.0500345 0 -2.9483345 0.061830594 274.41844
|
||||
34000 0.11331538 -3.062714 0 -2.9659912 -0.45332011 275.96007
|
||||
35000 0.11038437 -3.0765417 0 -2.9823208 -0.36244079 275.11931
|
||||
36000 0.11892267 -3.0721585 0 -2.9706495 -0.29991556 275.37903
|
||||
37000 0.11275568 -3.0668928 0 -2.9706478 -0.48726288 275.34035
|
||||
38000 0.1208952 -3.0738053 0 -2.9706126 -0.29578963 278.34451
|
||||
39000 0.10944817 -3.0773595 0 -2.9839377 -0.37875952 274.00319
|
||||
40000 0.11332842 -3.080676 0 -2.9839421 -0.45568111 275.74499
|
||||
41000 0.12031253 -3.0762241 0 -2.9735288 -0.21242519 276.03968
|
||||
42000 0.12031396 -3.0762248 0 -2.9735282 -0.34222153 274.86604
|
||||
43000 0.11012454 -3.0675234 0 -2.9735242 -0.38191996 274.79485
|
||||
44000 0.11896309 -3.0750688 0 -2.9735254 -0.39778513 275.34531
|
||||
45000 0.11416813 -3.070974 0 -2.9735234 -0.43325648 275.80725
|
||||
46000 0.11899053 -3.0750933 0 -2.9735264 -0.35449325 275.10793
|
||||
47000 0.11629126 -3.0727892 0 -2.9735263 -0.30843482 274.0454
|
||||
48000 0.1167364 -3.0847916 0 -2.9851487 -0.50651671 275.70527
|
||||
49000 0.11521427 -3.0729187 0 -2.9745751 -0.22466242 275.84873
|
||||
50000 0.11128506 -3.0695232 0 -2.9745335 -0.24912645 275.25969
|
||||
51000 0.11019914 -3.0694308 0 -2.975368 -0.31599349 275.27739
|
||||
52000 0.11953699 -3.0773655 0 -2.9753322 -0.26602137 275.2982
|
||||
53000 0.11403111 -3.0727022 0 -2.9753685 -0.51238084 276.07268
|
||||
54000 0.11607222 -3.0744423 0 -2.9753664 -0.44949735 276.40633
|
||||
55000 0.1169534 -3.0751976 0 -2.9753695 -0.25155291 275.66943
|
||||
56000 0.11200164 -3.0709683 0 -2.9753669 -0.49059346 275.98698
|
||||
57000 0.11837073 -3.0764076 0 -2.9753698 -0.36710375 274.96496
|
||||
58000 0.11241958 -3.0713261 0 -2.9753679 -0.35883352 273.98621
|
||||
59000 0.11701473 -3.0752489 0 -2.9753684 -0.37410362 275.64889
|
||||
60000 0.11038413 -3.0695887 0 -2.975368 -0.17138902 275.08559
|
||||
Loop time of 15.4958 on 1 procs for 30000 steps with 420 atoms
|
||||
|
||||
Pair time (%) = 12.5699 (81.1182)
|
||||
Neigh time (%) = 0.328618 (2.12069)
|
||||
Comm time (%) = 0.33072 (2.13426)
|
||||
Outpt time (%) = 0.25356 (1.63632)
|
||||
Other time (%) = 2.01299 (12.9906)
|
||||
|
||||
Nlocal: 420 ave 420 max 420 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 110 ave 110 max 110 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 3560 ave 3560 max 3560 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 3560
|
||||
Ave neighs/atom = 8.47619
|
||||
Neighbor list builds = 635
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,25 @@
|
|||
# 3d Lennard-Jones melt
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
region box block 0 20 0 20 0 20
|
||||
create_box 1 box
|
||||
create_atoms 1
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 3.0 87287
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 20 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
dump id all atom 10 dump.melt
|
||||
|
||||
thermo 50
|
||||
run 250
|
||||
|
|
@ -0,0 +1,56 @@
|
|||
LAMMPS (1 Oct 2006)
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
region box block 0 20 0 20 0 20
|
||||
create_box 1 box
|
||||
Created box = (0 0 0) to (33.5919 33.5919 33.5919)
|
||||
1 by 2 by 2 processor grid
|
||||
create_atoms 1
|
||||
Created 32000 atoms
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 3.0 87287
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 20 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
dump id all atom 10 dump.melt
|
||||
|
||||
thermo 50
|
||||
run 250
|
||||
Memory usage per processor = 4.307 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 3 -6.7733681 0 -2.2735087 -3.7027964
|
||||
50 1.6751964 -4.793906 0 -2.28119 5.6449888
|
||||
100 1.6492395 -4.7543479 0 -2.2805659 5.8242183
|
||||
150 1.6468325 -4.7503201 0 -2.2801485 5.857928
|
||||
200 1.64095 -4.741475 0 -2.280127 5.8888655
|
||||
250 1.6425393 -4.7441579 0 -2.2804259 5.8751067
|
||||
Loop time of 8.12523 on 4 procs for 250 steps with 32000 atoms
|
||||
|
||||
Pair time (%) = 4.33835 (53.3935)
|
||||
Neigh time (%) = 0.377536 (4.64646)
|
||||
Comm time (%) = 1.54992 (19.0754)
|
||||
Outpt time (%) = 1.44447 (17.7775)
|
||||
Other time (%) = 0.414967 (5.10714)
|
||||
|
||||
Nlocal: 8000 ave 8011 max 7981 min
|
||||
Histogram: 1 0 0 0 0 0 0 2 0 1
|
||||
Nghost: 8616 ave 8628 max 8605 min
|
||||
Histogram: 1 1 0 0 0 0 0 1 0 1
|
||||
Neighs: 303098 ave 306712 max 300441 min
|
||||
Histogram: 1 0 1 0 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 1212392
|
||||
Ave neighs/atom = 37.8873
|
||||
Neighbor list builds = 12
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,56 @@
|
|||
LAMMPS (1 Oct 2006)
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
region box block 0 20 0 20 0 20
|
||||
create_box 1 box
|
||||
Created box = (0 0 0) to (33.5919 33.5919 33.5919)
|
||||
1 by 1 by 1 processor grid
|
||||
create_atoms 1
|
||||
Created 32000 atoms
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 3.0 87287
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 20 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
dump id all atom 10 dump.melt
|
||||
|
||||
thermo 50
|
||||
run 250
|
||||
Memory usage per processor = 14.4987 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 3 -6.7733681 0 -2.2735087 -3.7027964
|
||||
50 1.6634568 -4.7767061 0 -2.2815989 5.7060587
|
||||
100 1.6411943 -4.741815 0 -2.2801004 5.8702166
|
||||
150 1.6434235 -4.7448489 0 -2.2797906 5.868853
|
||||
200 1.6427413 -4.7436699 0 -2.279635 5.8804726
|
||||
250 1.6373146 -4.7362602 0 -2.2803651 5.8998494
|
||||
Loop time of 43.5069 on 1 procs for 250 steps with 32000 atoms
|
||||
|
||||
Pair time (%) = 34.5536 (79.421)
|
||||
Neigh time (%) = 2.68746 (6.1771)
|
||||
Comm time (%) = 0.753433 (1.73175)
|
||||
Outpt time (%) = 3.74752 (8.61363)
|
||||
Other time (%) = 1.76488 (4.05655)
|
||||
|
||||
Nlocal: 32000 ave 32000 max 32000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 18806 ave 18806 max 18806 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 1.21276e+06 ave 1.21276e+06 max 1.21276e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1212760
|
||||
Ave neighs/atom = 37.8987
|
||||
Neighbor list builds = 12
|
||||
Dangerous builds = 0
|
||||
File diff suppressed because it is too large
Load Diff
|
|
@ -0,0 +1,9 @@
|
|||
2-d micelle definition
|
||||
|
||||
0.7 rhostar
|
||||
53616456 random # seed (8 digits or less)
|
||||
30 30 initial solvent square lattice (nx by ny)
|
||||
150 # of solvent to turn into surfactants
|
||||
0.75 bond-length of surfactants (units of sigma)
|
||||
2 # of tails to add to each head (length of surfactant - 1)
|
||||
0 flag for 2nd nearest neighbor bonds (0=no, 1=yes)
|
||||
|
|
@ -0,0 +1,60 @@
|
|||
# 2d micelle simulation
|
||||
|
||||
dimension 2
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
atom_style bond
|
||||
|
||||
# Soft potential push-off
|
||||
|
||||
read_data data.micelle
|
||||
special_bonds 0 1 1
|
||||
|
||||
pair_style soft 1.12246
|
||||
pair_coeff * * 1.0 20.0 1.12246
|
||||
|
||||
bond_style harmonic
|
||||
bond_coeff 1 50.0 0.75
|
||||
|
||||
velocity all create 0.45 2349852
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
|
||||
fix 3 all enforce2d
|
||||
|
||||
thermo 50
|
||||
run 1000
|
||||
|
||||
# Main run
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
# solvent/head - full-size and long-range
|
||||
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
pair_coeff 2 2 1.0 1.0 2.5
|
||||
pair_coeff 1 2 1.0 1.0 2.5
|
||||
|
||||
# tail/tail - size-averaged and long-range
|
||||
|
||||
pair_coeff 3 3 1.0 0.75 2.5
|
||||
pair_coeff 4 4 1.0 0.50 2.5
|
||||
pair_coeff 3 4 1.0 0.67 2.5
|
||||
|
||||
# solvent/tail - full-size and repulsive
|
||||
|
||||
pair_coeff 1 3 1.0 1.0 1.12246
|
||||
pair_coeff 1 4 1.0 1.0 1.12246
|
||||
|
||||
# head/tail - size-averaged and repulsive
|
||||
|
||||
pair_coeff 2 3 1.0 0.88 1.12246
|
||||
pair_coeff 2 4 1.0 0.75 1.12246
|
||||
|
||||
thermo 1000
|
||||
dump 1 all atom 250 dump.micelle
|
||||
|
||||
reset_timestep 0
|
||||
run 60000
|
||||
|
|
@ -0,0 +1,199 @@
|
|||
LAMMPS (1 Oct 2006)
|
||||
# 2d micelle simulation
|
||||
|
||||
dimension 2
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
atom_style bond
|
||||
|
||||
# Soft potential push-off
|
||||
|
||||
read_data data.micelle
|
||||
1 = max bonds/atom
|
||||
2 by 2 by 1 processor grid
|
||||
1200 atoms
|
||||
300 bonds
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
special_bonds 0 1 1
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of special neighbors
|
||||
|
||||
pair_style soft 1.12246
|
||||
pair_coeff * * 1.0 20.0 1.12246
|
||||
|
||||
bond_style harmonic
|
||||
bond_coeff 1 50.0 0.75
|
||||
|
||||
velocity all create 0.45 2349852
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
|
||||
fix 3 all enforce2d
|
||||
|
||||
thermo 50
|
||||
run 1000
|
||||
Memory usage per processor = 1.84779 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0.45 0.40003481 2.2200223e-06 0.84947453 2.6311673
|
||||
50 0.47417944 0.67716204 0.057387153 1.2081359 4.4581428
|
||||
100 0.45 0.73037684 0.054821983 1.2346363 7.730955
|
||||
150 0.67532546 0.72388376 0.043478036 1.4418431 9.580616
|
||||
200 0.45 0.78466058 0.076912805 1.3110109 10.136457
|
||||
250 0.66488946 0.69771453 0.081047682 1.4428206 12.303975
|
||||
300 0.45 0.76794745 0.066716745 1.2841017 12.618422
|
||||
350 0.67629601 0.62549506 0.072636862 1.3735826 14.282774
|
||||
400 0.45 0.68493339 0.090717081 1.225088 14.904536
|
||||
450 0.56732174 0.64322231 0.080690687 1.2905256 15.790896
|
||||
500 0.45 0.64764573 0.078468194 1.1755514 15.970391
|
||||
550 0.56476697 0.58160926 0.080519682 1.22619 16.573931
|
||||
600 0.45 0.58331363 0.088243449 1.1209946 17.103627
|
||||
650 0.5229482 0.54530348 0.09321673 1.1608147 17.545826
|
||||
700 0.45 0.52374674 0.085166964 1.0583512 17.640835
|
||||
750 0.51528063 0.48974532 0.086434828 1.0908167 17.952674
|
||||
800 0.45 0.50467091 0.090255509 1.0443639 18.600542
|
||||
850 0.4950534 0.48512921 0.091950432 1.0715142 18.88713
|
||||
900 0.45 0.48352312 0.097223467 1.0301841 19.049897
|
||||
950 0.49451225 0.46619517 0.094098428 1.0541877 19.588988
|
||||
1000 0.45 0.46260893 0.10106179 1.0131082 19.538971
|
||||
Loop time of 0.280434 on 4 procs for 1000 steps with 1200 atoms
|
||||
|
||||
Pair time (%) = 0.0796104 (28.3883)
|
||||
Bond time (%) = 0.00600582 (2.14162)
|
||||
Neigh time (%) = 0.0159584 (5.69061)
|
||||
Comm time (%) = 0.135316 (48.2525)
|
||||
Outpt time (%) = 0.00330371 (1.17807)
|
||||
Other time (%) = 0.0402393 (14.3489)
|
||||
|
||||
Nlocal: 300 ave 302 max 294 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 3
|
||||
Nghost: 101.75 ave 105 max 100 min
|
||||
Histogram: 1 0 2 0 0 0 0 0 0 1
|
||||
Neighs: 794 ave 811 max 774 min
|
||||
Histogram: 1 0 0 0 1 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 3176
|
||||
Ave neighs/atom = 2.64667
|
||||
Ave special neighs/atom = 0.5
|
||||
Neighbor list builds = 93
|
||||
Dangerous builds = 0
|
||||
|
||||
# Main run
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
# solvent/head - full-size and long-range
|
||||
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
pair_coeff 2 2 1.0 1.0 2.5
|
||||
pair_coeff 1 2 1.0 1.0 2.5
|
||||
|
||||
# tail/tail - size-averaged and long-range
|
||||
|
||||
pair_coeff 3 3 1.0 0.75 2.5
|
||||
pair_coeff 4 4 1.0 0.50 2.5
|
||||
pair_coeff 3 4 1.0 0.67 2.5
|
||||
|
||||
# solvent/tail - full-size and repulsive
|
||||
|
||||
pair_coeff 1 3 1.0 1.0 1.12246
|
||||
pair_coeff 1 4 1.0 1.0 1.12246
|
||||
|
||||
# head/tail - size-averaged and repulsive
|
||||
|
||||
pair_coeff 2 3 1.0 0.88 1.12246
|
||||
pair_coeff 2 4 1.0 0.75 1.12246
|
||||
|
||||
thermo 1000
|
||||
dump 1 all atom 250 dump.micelle
|
||||
|
||||
reset_timestep 0
|
||||
run 60000
|
||||
Memory usage per processor = 1.85934 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0.45 -1.6864322 0.10106179 -1.1359329 12.63785
|
||||
1000 0.44914716 -1.9350719 0.071373764 -1.4151124 7.1568301
|
||||
2000 0.45 -2.017979 0.070742172 -1.4977993 4.8375385
|
||||
3000 0.46278827 -2.0089553 0.058330549 -1.488415 4.820275
|
||||
4000 0.46714531 -2.0210549 0.057888529 -1.496605 4.2962188
|
||||
5000 0.44804799 -2.0254175 0.06916971 -1.5087599 4.4157997
|
||||
6000 0.45761629 -2.0368567 0.076990577 -1.5028219 4.6540238
|
||||
7000 0.44640723 -2.0461339 0.064790763 -1.5354939 4.4179413
|
||||
8000 0.45177284 -2.0324404 0.047705359 -1.5335269 4.54304
|
||||
9000 0.43975305 -2.06401 0.069375126 -1.5554315 3.2833286
|
||||
10000 0.45308355 -2.0423211 0.056575039 -1.5332289 4.1729746
|
||||
11000 0.44229664 -2.0436958 0.065042761 -1.5369092 4.3783133
|
||||
12000 0.4688876 -2.0591494 0.058270214 -1.5325777 3.6811782
|
||||
13000 0.45151162 -2.0633938 0.053917641 -1.5585289 3.1767412
|
||||
14000 0.44571931 -2.0503046 0.0570333 -1.5481092 3.5096724
|
||||
15000 0.45 -2.0837399 0.060991769 -1.5733106 3.1370759
|
||||
16000 0.45307444 -2.0804646 0.0670541 -1.5609024 3.2516824
|
||||
17000 0.45880865 -2.072733 0.061534139 -1.5529637 3.3828133
|
||||
18000 0.45650845 -2.0811023 0.057626785 -1.5675377 2.8631577
|
||||
19000 0.45645839 -2.1137579 0.058378793 -1.5994913 2.6678277
|
||||
20000 0.44760402 -2.109567 0.06512585 -1.5973966 2.3558292
|
||||
21000 0.43651289 -2.0863769 0.057529291 -1.5928803 3.0018852
|
||||
22000 0.43440649 -2.0950161 0.063482231 -1.5976704 2.3233803
|
||||
23000 0.44572794 -2.0887627 0.061323772 -1.5822681 2.9579923
|
||||
24000 0.44306777 -2.0843912 0.050176466 -1.5917008 2.8496622
|
||||
25000 0.45 -2.1051658 0.061328265 -1.5944 2.1179388
|
||||
26000 0.45552583 -2.119375 0.058663998 -1.6057546 2.2945202
|
||||
27000 0.43912671 -2.1066914 0.051902852 -1.6162108 2.1491613
|
||||
28000 0.45168054 -2.1078102 0.067816662 -1.5888776 2.4300025
|
||||
29000 0.44173014 -2.0804191 0.05137384 -1.5878673 3.0500294
|
||||
30000 0.44407338 -2.0998759 0.053922142 -1.6024355 2.7183453
|
||||
31000 0.4431566 -2.1102821 0.061544598 -1.6061349 2.7379786
|
||||
32000 0.45 -2.1163285 0.060739023 -1.606152 2.0727532
|
||||
33000 0.46444105 -2.1050315 0.062866914 -1.5783041 1.9114822
|
||||
34000 0.44581302 -2.0954209 0.063239112 -1.5869261 2.3525995
|
||||
35000 0.45 -2.1261175 0.060452019 -1.616228 2.014967
|
||||
36000 0.43470345 -2.1034119 0.063748152 -1.6055037 2.6086075
|
||||
37000 0.44671396 -2.093898 0.057613863 -1.5901286 2.9715819
|
||||
38000 0.45751276 -2.1085734 0.058845472 -1.592787 2.5044165
|
||||
39000 0.44786323 -2.1130108 0.056041424 -1.609666 2.1432
|
||||
40000 0.43937694 -2.1125665 0.04967594 -1.6240628 2.5594741
|
||||
41000 0.45 -2.1083933 0.0547275 -1.6042283 2.4651511
|
||||
42000 0.43287348 -2.1009617 0.054318981 -1.6143103 2.1496725
|
||||
43000 0.44945469 -2.1285428 0.05863553 -1.6210144 2.2786034
|
||||
44000 0.44737235 -2.0967009 0.058373014 -1.5915148 2.7502707
|
||||
45000 0.45401167 -2.110646 0.059341015 -1.5978608 1.9203458
|
||||
46000 0.43451455 -2.1077912 0.060728016 -1.6130918 2.3294588
|
||||
47000 0.44822719 -2.1295807 0.061997031 -1.6199168 2.1463667
|
||||
48000 0.43300738 -2.1029353 0.064025843 -1.6064433 2.1373309
|
||||
49000 0.44657342 -2.1237489 0.060905756 -1.616828 2.0319341
|
||||
50000 0.4677882 -2.1242266 0.059790209 -1.597233 2.5375996
|
||||
51000 0.45536082 -2.0986081 0.052858152 -1.5909583 2.562239
|
||||
52000 0.45919514 -2.1064277 0.057955 -1.5898515 2.3499751
|
||||
53000 0.46449938 -2.1195508 0.060178993 -1.595453 2.5406265
|
||||
54000 0.43682602 -2.1035311 0.069334917 -1.5979162 2.6919587
|
||||
55000 0.45 -2.0965463 0.055320603 -1.5917882 2.5110927
|
||||
56000 0.44913495 -2.1210973 0.058848556 -1.6136752 1.8246708
|
||||
57000 0.44307699 -2.1361861 0.066761708 -1.6269012 2.4928119
|
||||
58000 0.45181349 -2.1311357 0.05656415 -1.6233228 2.1515038
|
||||
59000 0.45 -2.1345398 0.060573082 -1.6245292 1.715299
|
||||
60000 0.45068289 -2.1230762 0.055943523 -1.6170131 2.1657885
|
||||
Loop time of 22.0261 on 4 procs for 60000 steps with 1200 atoms
|
||||
|
||||
Pair time (%) = 7.22825 (32.8167)
|
||||
Bond time (%) = 0.357983 (1.62527)
|
||||
Neigh time (%) = 1.44528 (6.56168)
|
||||
Comm time (%) = 9.7253 (44.1535)
|
||||
Outpt time (%) = 0.557863 (2.53273)
|
||||
Other time (%) = 2.71144 (12.3101)
|
||||
|
||||
Nlocal: 300 ave 308 max 291 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||
Nghost: 207 ave 218 max 195 min
|
||||
Histogram: 1 0 0 0 1 0 1 0 0 1
|
||||
Neighs: 2467.25 ave 2570 max 2397 min
|
||||
Histogram: 1 0 1 1 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 9869
|
||||
Ave neighs/atom = 8.22417
|
||||
Ave special neighs/atom = 0.5
|
||||
Neighbor list builds = 4885
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,199 @@
|
|||
LAMMPS (1 Oct 2006)
|
||||
# 2d micelle simulation
|
||||
|
||||
dimension 2
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
atom_style bond
|
||||
|
||||
# Soft potential push-off
|
||||
|
||||
read_data data.micelle
|
||||
1 = max bonds/atom
|
||||
1 by 1 by 1 processor grid
|
||||
1200 atoms
|
||||
300 bonds
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
special_bonds 0 1 1
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of special neighbors
|
||||
|
||||
pair_style soft 1.12246
|
||||
pair_coeff * * 1.0 20.0 1.12246
|
||||
|
||||
bond_style harmonic
|
||||
bond_coeff 1 50.0 0.75
|
||||
|
||||
velocity all create 0.45 2349852
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
|
||||
fix 3 all enforce2d
|
||||
|
||||
thermo 50
|
||||
run 1000
|
||||
Memory usage per processor = 1.69411 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0.45 0.40003481 2.2200223e-06 0.84947453 2.6311673
|
||||
50 0.47417944 0.67716204 0.057387153 1.2081359 4.4581428
|
||||
100 0.45 0.73037684 0.054821983 1.2346363 7.730955
|
||||
150 0.67532546 0.72388376 0.043478036 1.4418431 9.580616
|
||||
200 0.45 0.78466058 0.076912805 1.3110109 10.136457
|
||||
250 0.66488946 0.69771453 0.081047682 1.4428206 12.303975
|
||||
300 0.45 0.76794745 0.066716745 1.2841017 12.618422
|
||||
350 0.67629601 0.62549506 0.072636862 1.3735826 14.282774
|
||||
400 0.45 0.68493339 0.090717081 1.225088 14.904536
|
||||
450 0.56732174 0.64322231 0.080690687 1.2905256 15.790896
|
||||
500 0.45 0.64764573 0.078468194 1.1755514 15.970391
|
||||
550 0.56476697 0.58160926 0.080519682 1.22619 16.573931
|
||||
600 0.45 0.58331363 0.088243449 1.1209946 17.103627
|
||||
650 0.5229482 0.54530348 0.09321673 1.1608147 17.545826
|
||||
700 0.45 0.52374674 0.085166964 1.0583512 17.640835
|
||||
750 0.51528063 0.48974532 0.086434828 1.0908167 17.952674
|
||||
800 0.45 0.50467091 0.090255509 1.0443639 18.600542
|
||||
850 0.4950534 0.48512921 0.091950432 1.0715142 18.88713
|
||||
900 0.45 0.48352312 0.097223467 1.0301841 19.049897
|
||||
950 0.49451225 0.46619517 0.094098428 1.0541877 19.588988
|
||||
1000 0.45 0.46260893 0.10106179 1.0131082 19.538971
|
||||
Loop time of 0.856573 on 1 procs for 1000 steps with 1200 atoms
|
||||
|
||||
Pair time (%) = 0.502955 (58.7171)
|
||||
Bond time (%) = 0.042687 (4.98346)
|
||||
Neigh time (%) = 0.117298 (13.6939)
|
||||
Comm time (%) = 0.027584 (3.22027)
|
||||
Outpt time (%) = 0.002443 (0.285206)
|
||||
Other time (%) = 0.163606 (19.1001)
|
||||
|
||||
Nlocal: 1200 ave 1200 max 1200 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 193 ave 193 max 193 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 3176 ave 3176 max 3176 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 3176
|
||||
Ave neighs/atom = 2.64667
|
||||
Ave special neighs/atom = 0.5
|
||||
Neighbor list builds = 93
|
||||
Dangerous builds = 0
|
||||
|
||||
# Main run
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
# solvent/head - full-size and long-range
|
||||
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
pair_coeff 2 2 1.0 1.0 2.5
|
||||
pair_coeff 1 2 1.0 1.0 2.5
|
||||
|
||||
# tail/tail - size-averaged and long-range
|
||||
|
||||
pair_coeff 3 3 1.0 0.75 2.5
|
||||
pair_coeff 4 4 1.0 0.50 2.5
|
||||
pair_coeff 3 4 1.0 0.67 2.5
|
||||
|
||||
# solvent/tail - full-size and repulsive
|
||||
|
||||
pair_coeff 1 3 1.0 1.0 1.12246
|
||||
pair_coeff 1 4 1.0 1.0 1.12246
|
||||
|
||||
# head/tail - size-averaged and repulsive
|
||||
|
||||
pair_coeff 2 3 1.0 0.88 1.12246
|
||||
pair_coeff 2 4 1.0 0.75 1.12246
|
||||
|
||||
thermo 1000
|
||||
dump 1 all atom 250 dump.micelle
|
||||
|
||||
reset_timestep 0
|
||||
run 60000
|
||||
Memory usage per processor = 1.85432 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0.45 -1.6864322 0.10106179 -1.1359329 12.63785
|
||||
1000 0.44914708 -1.9350711 0.071372351 -1.4151131 7.156807
|
||||
2000 0.45270543 -2.0004904 0.066419058 -1.4819318 5.5702827
|
||||
3000 0.46916283 -2.0213933 0.065872359 -1.4869445 5.0060597
|
||||
4000 0.43945376 -2.0166598 0.067641209 -1.5101142 4.6396644
|
||||
5000 0.45495437 -2.0447226 0.066285498 -1.5240515 3.9305266
|
||||
6000 0.44963328 -2.056045 0.068450242 -1.5385235 3.8603798
|
||||
7000 0.44856129 -2.0414287 0.058586674 -1.5348414 3.9952578
|
||||
8000 0.43667749 -2.0567464 0.065334814 -1.5552799 4.2727683
|
||||
9000 0.45682384 -2.0679034 0.060201786 -1.5514488 3.9267838
|
||||
10000 0.45 -2.0518982 0.055746513 -1.5467142 4.0952215
|
||||
11000 0.45708142 -2.0867219 0.069796539 -1.5604153 2.9408563
|
||||
12000 0.45241478 -2.0660119 0.05984197 -1.5543207 3.1690286
|
||||
13000 0.44107393 -2.0641661 0.05983938 -1.5638041 3.505816
|
||||
14000 0.44110861 -2.097022 0.051901352 -1.6045634 3.1530067
|
||||
15000 0.46350177 -2.0714176 0.060468155 -1.548027 3.1473645
|
||||
16000 0.44655044 -2.1091366 0.063286789 -1.5998576 3.01513
|
||||
17000 0.4669612 -2.0818303 0.06033586 -1.5551169 3.5882255
|
||||
18000 0.46094826 -2.1157008 0.066505672 -1.5888231 2.3269852
|
||||
19000 0.44560596 -2.0990576 0.065162589 -1.5888461 2.8984257
|
||||
20000 0.44208903 -2.0909757 0.059515289 -1.589924 2.8119311
|
||||
21000 0.45155589 -2.0997977 0.059798723 -1.5890075 2.8373688
|
||||
22000 0.4454493 -2.1064356 0.057219664 -1.6043234 2.5646073
|
||||
23000 0.44607005 -2.0965713 0.061416631 -1.5896422 2.4608998
|
||||
24000 0.46538564 -2.1045166 0.05774363 -1.5819691 2.3150363
|
||||
25000 0.45936625 -2.1067378 0.056323997 -1.5916218 2.048119
|
||||
26000 0.44475849 -2.1039936 0.062084383 -1.5977067 2.6218634
|
||||
27000 0.44698457 -2.0984145 0.055709014 -1.5962797 2.9317131
|
||||
28000 0.43517932 -2.0913271 0.064117709 -1.5925741 2.8086074
|
||||
29000 0.45647804 -2.1041742 0.062494065 -1.5857727 3.1137153
|
||||
30000 0.46315669 -2.0956986 0.062535694 -1.5705852 2.7393652
|
||||
31000 0.45 -2.1057734 0.06440468 -1.5919312 2.6231226
|
||||
32000 0.45070852 -2.1035845 0.058447795 -1.5949916 2.4537766
|
||||
33000 0.45666657 -2.1082739 0.062668872 -1.5895093 2.3000181
|
||||
34000 0.45 -2.1016598 0.058047346 -1.594175 2.7045891
|
||||
35000 0.45761633 -2.1166321 0.05661317 -1.6029746 2.4867114
|
||||
36000 0.4472238 -2.1032503 0.058087856 -1.5984977 2.5708579
|
||||
37000 0.45 -2.0862798 0.060216086 -1.5766262 3.0682877
|
||||
38000 0.46457862 -2.111786 0.050899355 -1.5968888 2.3837735
|
||||
39000 0.4461965 -2.0958328 0.065822692 -1.5843713 2.9356665
|
||||
40000 0.44099466 -2.1082333 0.052068542 -1.6157214 2.7461117
|
||||
41000 0.44708215 -2.1138114 0.061595428 -1.6056927 2.7512054
|
||||
42000 0.45300055 -2.1160106 0.060484049 -1.6030923 2.1170549
|
||||
43000 0.44584477 -2.1016681 0.065545873 -1.5908347 2.7168769
|
||||
44000 0.44874855 -2.0962255 0.060190909 -1.587847 2.4701379
|
||||
45000 0.43208001 -2.0985058 0.059429899 -1.607536 3.4135814
|
||||
46000 0.43328324 -2.068705 0.062466255 -1.5734971 3.1729387
|
||||
47000 0.46070055 -2.1056376 0.054706613 -1.5908063 2.4710329
|
||||
48000 0.44818286 -2.1037138 0.060858877 -1.5952323 2.2822087
|
||||
49000 0.43421688 -2.0920093 0.05524275 -1.6030924 2.9802749
|
||||
50000 0.44919305 -2.118617 0.054774617 -1.6152108 2.1728215
|
||||
51000 0.44744615 -2.1090016 0.059814306 -1.6023004 2.3189772
|
||||
52000 0.45486735 -2.1082261 0.055067991 -1.5988594 2.2933516
|
||||
53000 0.46483852 -2.1205596 0.059875293 -1.5964269 2.4109235
|
||||
54000 0.43582273 -2.0939722 0.056892621 -1.6018017 2.9757336
|
||||
55000 0.45654728 -2.1024753 0.062836674 -1.583662 2.3343503
|
||||
56000 0.45942073 -2.0961849 0.053090528 -1.584248 2.8313158
|
||||
57000 0.44650252 -2.092082 0.052991549 -1.5931461 3.0447824
|
||||
58000 0.46418464 -2.1277093 0.060472378 -1.6036325 1.7271421
|
||||
59000 0.45 -2.1304819 0.057808836 -1.6232356 1.6864115
|
||||
60000 0.45599586 -2.1338576 0.053131762 -1.6253 2.201508
|
||||
Loop time of 92.2957 on 1 procs for 60000 steps with 1200 atoms
|
||||
|
||||
Pair time (%) = 65.5829 (71.0574)
|
||||
Bond time (%) = 2.58619 (2.80207)
|
||||
Neigh time (%) = 10.2969 (11.1565)
|
||||
Comm time (%) = 2.26542 (2.45452)
|
||||
Outpt time (%) = 1.35733 (1.47063)
|
||||
Other time (%) = 10.2069 (11.0589)
|
||||
|
||||
Nlocal: 1200 ave 1200 max 1200 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 396 ave 396 max 396 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 9650 ave 9650 max 9650 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 9650
|
||||
Ave neighs/atom = 8.04167
|
||||
Ave special neighs/atom = 0.5
|
||||
Neighbor list builds = 4890
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,35 @@
|
|||
# 2d Lennard-Jones melt and subsequent energy minimization
|
||||
|
||||
units lj
|
||||
dimension 2
|
||||
atom_style atomic
|
||||
|
||||
lattice sq2 0.8442
|
||||
region box block 0 20 0 20 -0.1 0.1
|
||||
create_box 1 box
|
||||
create_atoms 1
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 5.0 87287 loop geom
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all enforce2d
|
||||
|
||||
dump 1 all atom 100 dump.min
|
||||
dump_modify 1 scale no
|
||||
|
||||
thermo 100
|
||||
|
||||
run 1000
|
||||
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
dump_modify 1 every 5
|
||||
thermo 5
|
||||
minimize 0.001 100 1000
|
||||
|
|
@ -0,0 +1,108 @@
|
|||
LAMMPS (1 Oct 2006)
|
||||
# 2d Lennard-Jones melt and subsequent energy minimization
|
||||
|
||||
units lj
|
||||
dimension 2
|
||||
atom_style atomic
|
||||
|
||||
lattice sq2 0.8442
|
||||
region box block 0 20 0 20 -0.1 0.1
|
||||
create_box 1 box
|
||||
Created box = (0 0 -0.153919) to (30.7838 30.7838 0.153919)
|
||||
2 by 2 by 1 processor grid
|
||||
create_atoms 1
|
||||
Created 800 atoms
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 5.0 87287 loop geom
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all enforce2d
|
||||
|
||||
dump 1 all atom 100 dump.min
|
||||
dump_modify 1 scale no
|
||||
|
||||
thermo 100
|
||||
|
||||
run 1000
|
||||
Memory usage per processor = 1.44958 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 5 -2.6248859 0 2.3657391 10.863748
|
||||
100 3.3056095 -0.90010417 0 2.3993073 34.161569
|
||||
200 3.3179673 -0.91237776 0 2.3993683 33.885931
|
||||
300 3.2898718 -0.88383768 0 2.3998656 34.100539
|
||||
400 3.3040789 -0.8979868 0 2.3998969 33.870872
|
||||
500 3.3858715 -0.98323293 0 2.39629 33.00502
|
||||
600 3.3016075 -0.89577331 0 2.3996436 34.094211
|
||||
700 3.3530103 -0.94642636 0 2.4002971 33.706321
|
||||
800 3.2765339 -0.87171428 0 2.3986761 34.272397
|
||||
900 3.4084164 -1.0031926 0 2.398833 32.606983
|
||||
1000 3.3077995 -0.90272314 0 2.3988743 33.989676
|
||||
Loop time of 0.366177 on 4 procs for 1000 steps with 800 atoms
|
||||
|
||||
Pair time (%) = 0.0971868 (26.5409)
|
||||
Neigh time (%) = 0.0321494 (8.77974)
|
||||
Comm time (%) = 0.162145 (44.2804)
|
||||
Outpt time (%) = 0.0241919 (6.60661)
|
||||
Other time (%) = 0.0505046 (13.7924)
|
||||
|
||||
Nlocal: 200 ave 202 max 198 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Nghost: 170.75 ave 175 max 167 min
|
||||
Histogram: 1 0 0 1 0 1 0 0 0 1
|
||||
Neighs: 1943 ave 1984 max 1900 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
|
||||
Total # of neighbors = 7772
|
||||
Ave neighs/atom = 9.715
|
||||
Neighbor list builds = 204
|
||||
Dangerous builds = 0
|
||||
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
dump_modify 1 every 5
|
||||
thermo 5
|
||||
minimize 0.001 100 1000
|
||||
Memory usage per processor = 1.90765 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
1000 3.3077995 -0.90272314 0 2.3988743 33.989676
|
||||
1005 3.3077995 -2.4464146 0 0.85518281 11.813681
|
||||
1010 3.3077995 -2.722905 0 0.5786924 7.0572259
|
||||
1015 3.3077995 -2.8240967 0 0.47750069 5.2719814
|
||||
1020 3.3077995 -2.8735068 0 0.42809061 4.4936467
|
||||
1025 3.3077995 -2.9038631 0 0.39773429 4.0902371
|
||||
1030 3.3077995 -2.9235394 0 0.37805797 3.8445956
|
||||
1035 3.3077995 -2.9410562 0 0.36054119 3.6772327
|
||||
1038 3.3077995 -2.9486794 0 0.35291801 3.5714315
|
||||
Loop time of 0.0907032 on 4 procs for 38 steps with 800 atoms
|
||||
|
||||
Minimization stats:
|
||||
E initial, next-to-last, final = -0.902723 -2.94694 -2.94868
|
||||
Gradient 2-norm init/final= 1904.03 22.323
|
||||
Gradient inf-norm init/final= 304.285 10.0504
|
||||
Iterations = 38
|
||||
Force evaluations = 185
|
||||
|
||||
Pair time (%) = 0.0224806 (24.7848)
|
||||
Neigh time (%) = 0.00274897 (3.03073)
|
||||
Comm time (%) = 0.0270339 (29.8047)
|
||||
Outpt time (%) = 0.016743 (18.4591)
|
||||
Other time (%) = 0.0216968 (23.9206)
|
||||
|
||||
Nlocal: 200 ave 201 max 198 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
||||
Nghost: 171 ave 173 max 168 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 0 2
|
||||
Neighs: 1817.75 ave 1834 max 1805 min
|
||||
Histogram: 1 1 0 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 7271
|
||||
Ave neighs/atom = 9.08875
|
||||
Neighbor list builds = 17
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,108 @@
|
|||
LAMMPS (1 Oct 2006)
|
||||
# 2d Lennard-Jones melt and subsequent energy minimization
|
||||
|
||||
units lj
|
||||
dimension 2
|
||||
atom_style atomic
|
||||
|
||||
lattice sq2 0.8442
|
||||
region box block 0 20 0 20 -0.1 0.1
|
||||
create_box 1 box
|
||||
Created box = (0 0 -0.153919) to (30.7838 30.7838 0.153919)
|
||||
1 by 1 by 1 processor grid
|
||||
create_atoms 1
|
||||
Created 800 atoms
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 5.0 87287 loop geom
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all enforce2d
|
||||
|
||||
dump 1 all atom 100 dump.min
|
||||
dump_modify 1 scale no
|
||||
|
||||
thermo 100
|
||||
|
||||
run 1000
|
||||
Memory usage per processor = 1.47247 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 5 -2.6248859 0 2.3657391 10.863748
|
||||
100 3.3056095 -0.90010417 0 2.3993073 34.161569
|
||||
200 3.3179673 -0.91237776 0 2.3993683 33.885931
|
||||
300 3.2898718 -0.88383768 0 2.3998656 34.100539
|
||||
400 3.3040789 -0.8979868 0 2.3998969 33.870872
|
||||
500 3.3858715 -0.98323293 0 2.39629 33.00502
|
||||
600 3.3016074 -0.89577327 0 2.3996436 34.094211
|
||||
700 3.3530108 -0.94642681 0 2.4002971 33.706316
|
||||
800 3.2765414 -0.87172188 0 2.398676 34.272332
|
||||
900 3.4086632 -1.003472 0 2.3988 32.603903
|
||||
1000 3.3011881 -0.89596181 0 2.3990365 34.054429
|
||||
Loop time of 1.30303 on 1 procs for 1000 steps with 800 atoms
|
||||
|
||||
Pair time (%) = 0.878404 (67.4122)
|
||||
Neigh time (%) = 0.219869 (16.8736)
|
||||
Comm time (%) = 0.035471 (2.72219)
|
||||
Outpt time (%) = 0.041925 (3.21749)
|
||||
Other time (%) = 0.127365 (9.7745)
|
||||
|
||||
Nlocal: 800 ave 800 max 800 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 314 ave 314 max 314 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 7777 ave 7777 max 7777 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 7777
|
||||
Ave neighs/atom = 9.72125
|
||||
Neighbor list builds = 204
|
||||
Dangerous builds = 0
|
||||
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
dump_modify 1 every 5
|
||||
thermo 5
|
||||
minimize 0.001 100 1000
|
||||
Memory usage per processor = 1.96838 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
1000 3.3011881 -0.89596181 0 2.3990365 34.054429
|
||||
1005 3.3011881 -2.4630946 0 0.83190371 11.52248
|
||||
1010 3.3011881 -2.7249285 0 0.57006988 7.0081459
|
||||
1015 3.3011881 -2.8249196 0 0.47007872 5.2407114
|
||||
1020 3.3011881 -2.8748561 0 0.42014222 4.4638989
|
||||
1025 3.3011881 -2.9048388 0 0.39015958 4.0705858
|
||||
1030 3.3011881 -2.9246339 0 0.37036444 3.8097613
|
||||
1035 3.3011881 -2.941932 0 0.35306633 3.6545452
|
||||
1036 3.3011881 -2.9434242 0 0.3515742 3.6268584
|
||||
Loop time of 0.255988 on 1 procs for 36 steps with 800 atoms
|
||||
|
||||
Minimization stats:
|
||||
E initial, next-to-last, final = -0.895962 -2.94193 -2.94342
|
||||
Gradient 2-norm init/final= 1920.78 20.9992
|
||||
Gradient inf-norm init/final= 304.283 9.61216
|
||||
Iterations = 36
|
||||
Force evaluations = 177
|
||||
|
||||
Pair time (%) = 0.182294 (71.2119)
|
||||
Neigh time (%) = 0.017308 (6.76125)
|
||||
Comm time (%) = 0.004652 (1.81727)
|
||||
Outpt time (%) = 0.028575 (11.1626)
|
||||
Other time (%) = 0.023159 (9.04691)
|
||||
|
||||
Nlocal: 800 ave 800 max 800 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 314 ave 314 max 314 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 7295 ave 7295 max 7295 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 7295
|
||||
Ave neighs/atom = 9.11875
|
||||
Neighbor list builds = 16
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,74 @@
|
|||
# 2d LJ obstacle flow
|
||||
|
||||
dimension 2
|
||||
boundary p s p
|
||||
|
||||
atom_style atomic
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
# create geometry
|
||||
|
||||
lattice hex 0.7
|
||||
region box block 0 40 0 10 -0.25 0.25
|
||||
create_box 3 box
|
||||
create_atoms 1
|
||||
|
||||
mass 1 1.0
|
||||
mass 2 1.0
|
||||
mass 3 1.0
|
||||
|
||||
# LJ potentials
|
||||
|
||||
pair_style lj/cut 1.12246
|
||||
pair_coeff * * 1.0 1.0 1.12246
|
||||
|
||||
# define groups
|
||||
|
||||
region 1 block INF INF INF 1.25 INF INF
|
||||
group lower region 1
|
||||
region 2 block INF INF 8.75 INF INF INF
|
||||
group upper region 2
|
||||
group boundary union lower upper
|
||||
group flow subtract all boundary
|
||||
|
||||
set lower atom 2
|
||||
set upper atom 3
|
||||
|
||||
# initial velocities
|
||||
|
||||
temperature mobile flow full
|
||||
velocity flow create 1.0 482748 temp mobile
|
||||
fix 1 all nve
|
||||
fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
|
||||
fix_modify 2 temp mobile
|
||||
|
||||
# Poiselle flow
|
||||
|
||||
velocity boundary set 0.0 0.0 0.0
|
||||
fix 3 lower setforce 0.0 0.0 0.0
|
||||
fix 4 upper setforce 0.0 NULL 0.0
|
||||
fix 5 upper aveforce 0.0 -0.5 0.0
|
||||
fix 6 flow addforce 1.0 0.0 0.0
|
||||
|
||||
# 2 obstacles
|
||||
|
||||
region void1 sphere 10 4 0 3
|
||||
delete_atoms region void1
|
||||
region void2 sphere 20 7 0 3
|
||||
delete_atoms region void2
|
||||
|
||||
fix 7 flow indent 100 sphere 10 4 0 4
|
||||
fix 8 flow indent 100 sphere 20 7 0 4
|
||||
fix 9 all enforce2d
|
||||
|
||||
# Run
|
||||
|
||||
timestep 0.003
|
||||
thermo 1000
|
||||
thermo_modify temp mobile
|
||||
|
||||
dump 1 all atom 100 dump.obstacle
|
||||
#dump 1 all custom 100 dump.custom tag type x y z vx vy
|
||||
|
||||
run 25000
|
||||
|
|
@ -0,0 +1,133 @@
|
|||
LAMMPS (1 Oct 2006)
|
||||
# 2d LJ obstacle flow
|
||||
|
||||
dimension 2
|
||||
boundary p s p
|
||||
|
||||
atom_style atomic
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
# create geometry
|
||||
|
||||
lattice hex 0.7
|
||||
region box block 0 40 0 10 -0.25 0.25
|
||||
create_box 3 box
|
||||
Created box = (0 0 -0.321089) to (51.3743 22.2457 0.321089)
|
||||
4 by 1 by 1 processor grid
|
||||
create_atoms 1
|
||||
Created 840 atoms
|
||||
|
||||
mass 1 1.0
|
||||
mass 2 1.0
|
||||
mass 3 1.0
|
||||
|
||||
# LJ potentials
|
||||
|
||||
pair_style lj/cut 1.12246
|
||||
pair_coeff * * 1.0 1.0 1.12246
|
||||
|
||||
# define groups
|
||||
|
||||
region 1 block INF INF INF 1.25 INF INF
|
||||
group lower region 1
|
||||
120 atoms in group lower
|
||||
region 2 block INF INF 8.75 INF INF INF
|
||||
group upper region 2
|
||||
120 atoms in group upper
|
||||
group boundary union lower upper
|
||||
240 atoms in group boundary
|
||||
group flow subtract all boundary
|
||||
600 atoms in group flow
|
||||
|
||||
set lower atom 2
|
||||
120 settings made
|
||||
set upper atom 3
|
||||
120 settings made
|
||||
|
||||
# initial velocities
|
||||
|
||||
temperature mobile flow full
|
||||
velocity flow create 1.0 482748 temp mobile
|
||||
fix 1 all nve
|
||||
fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
|
||||
fix_modify 2 temp mobile
|
||||
|
||||
# Poiselle flow
|
||||
|
||||
velocity boundary set 0.0 0.0 0.0
|
||||
fix 3 lower setforce 0.0 0.0 0.0
|
||||
fix 4 upper setforce 0.0 NULL 0.0
|
||||
fix 5 upper aveforce 0.0 -0.5 0.0
|
||||
fix 6 flow addforce 1.0 0.0 0.0
|
||||
|
||||
# 2 obstacles
|
||||
|
||||
region void1 sphere 10 4 0 3
|
||||
delete_atoms region void1
|
||||
Deleted 36 atoms, new total = 804
|
||||
region void2 sphere 20 7 0 3
|
||||
delete_atoms region void2
|
||||
Deleted 37 atoms, new total = 767
|
||||
|
||||
fix 7 flow indent 100 sphere 10 4 0 4
|
||||
fix 8 flow indent 100 sphere 20 7 0 4
|
||||
fix 9 all enforce2d
|
||||
|
||||
# Run
|
||||
|
||||
timestep 0.003
|
||||
thermo 1000
|
||||
thermo_modify temp mobile
|
||||
|
||||
dump 1 all atom 100 dump.obstacle
|
||||
#dump 1 all custom 100 dump.custom tag type x y z vx vy
|
||||
|
||||
run 25000
|
||||
Memory usage per processor = 1.44234 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 1.0026027 0 0 0.68692013 0.47858472 733.92473
|
||||
1000 1 -0.37738477 0 0.30775213 1.5583691 784.71717
|
||||
2000 1 -0.41654339 0 0.26859351 1.4383017 811.91076
|
||||
3000 1 -0.457908 0 0.22722889 1.4560268 840.96593
|
||||
4000 1 -0.49703654 0 0.18810036 1.6667159 875.09273
|
||||
5000 1 -0.5036762 0 0.18146069 1.5201858 896.06529
|
||||
6000 1 -0.46146759 0 0.22366931 1.2626363 910.96886
|
||||
7000 1 -0.45319553 0 0.23194137 1.2400164 919.79024
|
||||
8000 1 -0.43703324 0 0.24810365 1.1687124 917.54854
|
||||
9000 1 -0.41944398 0 0.26569292 1.1506946 919.08596
|
||||
10000 1 -0.38212395 0 0.30301294 1.2159701 922.73564
|
||||
11000 1 -0.40131109 0 0.2838258 1.0143617 928.59439
|
||||
12000 1 -0.40729865 0 0.27783825 1.1463534 927.92228
|
||||
13000 1 -0.40247949 0 0.28265741 1.0362177 932.66931
|
||||
14000 1 -0.40708584 0 0.27805106 1.05021 931.20813
|
||||
15000 1 -0.38885172 0 0.29628518 0.97302912 932.47567
|
||||
16000 1 -0.36720972 0 0.31792717 1.0900379 929.29673
|
||||
17000 1 -0.38146707 0 0.30366982 1.0608592 931.83222
|
||||
18000 1 -0.38710515 0 0.29803175 0.91156243 940.47326
|
||||
19000 1 -0.38215507 0 0.30298183 1.049551 937.81127
|
||||
20000 1 -0.33197729 0 0.35315961 0.97020648 938.40346
|
||||
21000 1 -0.33775592 0 0.34738098 1.0035901 932.85086
|
||||
22000 1 -0.38733229 0 0.29780461 1.0175281 926.40207
|
||||
23000 1 -0.35819884 0 0.32693805 1.0468418 927.63479
|
||||
24000 1 -0.36327235 0 0.32186455 1.0859266 930.98575
|
||||
25000 1 -0.41296958 0 0.27216731 1.0157726 929.59365
|
||||
Loop time of 4.53299 on 4 procs for 25000 steps with 767 atoms
|
||||
|
||||
Pair time (%) = 0.355299 (7.83807)
|
||||
Neigh time (%) = 0.1305 (2.87891)
|
||||
Comm time (%) = 1.82422 (40.2431)
|
||||
Outpt time (%) = 0.366969 (8.09551)
|
||||
Other time (%) = 1.856 (40.9444)
|
||||
|
||||
Nlocal: 191.75 ave 243 max 152 min
|
||||
Histogram: 1 1 0 0 0 1 0 0 0 1
|
||||
Nghost: 41.75 ave 45 max 40 min
|
||||
Histogram: 1 0 2 0 0 0 0 0 0 1
|
||||
Neighs: 405.5 ave 588 max 272 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 1622
|
||||
Ave neighs/atom = 2.11473
|
||||
Neighbor list builds = 1613
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,133 @@
|
|||
LAMMPS (1 Oct 2006)
|
||||
# 2d LJ obstacle flow
|
||||
|
||||
dimension 2
|
||||
boundary p s p
|
||||
|
||||
atom_style atomic
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
# create geometry
|
||||
|
||||
lattice hex 0.7
|
||||
region box block 0 40 0 10 -0.25 0.25
|
||||
create_box 3 box
|
||||
Created box = (0 0 -0.321089) to (51.3743 22.2457 0.321089)
|
||||
1 by 1 by 1 processor grid
|
||||
create_atoms 1
|
||||
Created 840 atoms
|
||||
|
||||
mass 1 1.0
|
||||
mass 2 1.0
|
||||
mass 3 1.0
|
||||
|
||||
# LJ potentials
|
||||
|
||||
pair_style lj/cut 1.12246
|
||||
pair_coeff * * 1.0 1.0 1.12246
|
||||
|
||||
# define groups
|
||||
|
||||
region 1 block INF INF INF 1.25 INF INF
|
||||
group lower region 1
|
||||
120 atoms in group lower
|
||||
region 2 block INF INF 8.75 INF INF INF
|
||||
group upper region 2
|
||||
120 atoms in group upper
|
||||
group boundary union lower upper
|
||||
240 atoms in group boundary
|
||||
group flow subtract all boundary
|
||||
600 atoms in group flow
|
||||
|
||||
set lower atom 2
|
||||
120 settings made
|
||||
set upper atom 3
|
||||
120 settings made
|
||||
|
||||
# initial velocities
|
||||
|
||||
temperature mobile flow full
|
||||
velocity flow create 1.0 482748 temp mobile
|
||||
fix 1 all nve
|
||||
fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
|
||||
fix_modify 2 temp mobile
|
||||
|
||||
# Poiselle flow
|
||||
|
||||
velocity boundary set 0.0 0.0 0.0
|
||||
fix 3 lower setforce 0.0 0.0 0.0
|
||||
fix 4 upper setforce 0.0 NULL 0.0
|
||||
fix 5 upper aveforce 0.0 -0.5 0.0
|
||||
fix 6 flow addforce 1.0 0.0 0.0
|
||||
|
||||
# 2 obstacles
|
||||
|
||||
region void1 sphere 10 4 0 3
|
||||
delete_atoms region void1
|
||||
Deleted 36 atoms, new total = 804
|
||||
region void2 sphere 20 7 0 3
|
||||
delete_atoms region void2
|
||||
Deleted 37 atoms, new total = 767
|
||||
|
||||
fix 7 flow indent 100 sphere 10 4 0 4
|
||||
fix 8 flow indent 100 sphere 20 7 0 4
|
||||
fix 9 all enforce2d
|
||||
|
||||
# Run
|
||||
|
||||
timestep 0.003
|
||||
thermo 1000
|
||||
thermo_modify temp mobile
|
||||
|
||||
dump 1 all atom 100 dump.obstacle
|
||||
#dump 1 all custom 100 dump.custom tag type x y z vx vy
|
||||
|
||||
run 25000
|
||||
Memory usage per processor = 1.46358 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 1.0019297 0 0 0.68645902 0.47826346 733.92473
|
||||
1000 1 -0.35063938 0 0.33449751 1.6522953 783.62722
|
||||
2000 1 -0.4338009 0 0.25133599 1.3442754 814.00845
|
||||
3000 1 -0.48560531 0 0.19953159 1.3851427 842.4322
|
||||
4000 1 -0.52446917 0 0.16066773 1.534073 880.36205
|
||||
5000 1 -0.46416349 0 0.22097341 1.288376 915.89876
|
||||
6000 1 -0.46692642 0 0.21821047 1.2806072 927.05522
|
||||
7000 1 -0.44824027 0 0.23689663 1.1691239 935.06903
|
||||
8000 1 -0.44835316 0 0.23678374 1.0958272 931.19324
|
||||
9000 1 -0.3927248 0 0.2924121 1.1093553 927.69772
|
||||
10000 1 -0.38347162 0 0.30166528 1.0818633 923.32891
|
||||
11000 1 -0.4036644 0 0.28147249 1.1190364 925.22091
|
||||
12000 1 -0.37573271 0 0.30940418 1.0661954 932.99191
|
||||
13000 1 -0.38127169 0 0.30386521 1.0347388 934.82878
|
||||
14000 1 -0.3917136 0 0.2934233 1.0359581 934.76479
|
||||
15000 1 -0.38159291 0 0.30354398 1.1029874 934.15381
|
||||
16000 1 -0.36036528 0 0.32477162 0.98739828 932.69222
|
||||
17000 1 -0.36939144 0 0.31574546 1.1260055 934.51009
|
||||
18000 1 -0.37198742 0 0.31314948 0.95796075 935.53765
|
||||
19000 1 -0.35008405 0 0.33505284 1.0525993 932.71924
|
||||
20000 1 -0.3946193 0 0.2905176 1.0181298 932.72262
|
||||
21000 1 -0.36508116 0 0.32005573 1.0466637 937.18711
|
||||
22000 1 -0.37402575 0 0.31111115 1.0836104 933.86271
|
||||
23000 1 -0.37087569 0 0.3142612 1.0454446 933.85941
|
||||
24000 1 -0.37779474 0 0.30734216 1.1488903 934.78585
|
||||
25000 1 -0.3530395 0 0.3320974 0.9608987 937.57522
|
||||
Loop time of 11.2929 on 1 procs for 25000 steps with 767 atoms
|
||||
|
||||
Pair time (%) = 3.08741 (27.3394)
|
||||
Neigh time (%) = 0.90573 (8.02035)
|
||||
Comm time (%) = 0.344634 (3.05178)
|
||||
Outpt time (%) = 0.923682 (8.17932)
|
||||
Other time (%) = 6.03144 (53.4092)
|
||||
|
||||
Nlocal: 767 ave 767 max 767 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 46 ave 46 max 46 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 1643 ave 1643 max 1643 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1643
|
||||
Ave neighs/atom = 2.14211
|
||||
Neighbor list builds = 1601
|
||||
Dangerous builds = 0
|
||||
File diff suppressed because it is too large
Load Diff
|
|
@ -0,0 +1,31 @@
|
|||
# Solvated 5-mer peptide
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
kspace_style pppm 0.0001
|
||||
|
||||
read_data data.peptide
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
thermo_style multi
|
||||
thermo 50
|
||||
|
||||
fix 1 all nvt 275.0 275.0 100.0
|
||||
fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||
|
||||
group peptide type <= 12
|
||||
dump 1 peptide atom 10 dump.peptide
|
||||
dump 2 peptide bond 300 dump.bond
|
||||
|
||||
run 300
|
||||
|
||||
|
|
@ -0,0 +1,154 @@
|
|||
LAMMPS (1 Oct 2006)
|
||||
# Solvated 5-mer peptide
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
kspace_style pppm 0.0001
|
||||
|
||||
read_data data.peptide
|
||||
3 = max bonds/atom
|
||||
6 = max angles/atom
|
||||
14 = max dihedrals/atom
|
||||
1 = max impropers/atom
|
||||
1 by 2 by 2 processor grid
|
||||
2004 atoms
|
||||
2004 velocities
|
||||
1365 bonds
|
||||
786 angles
|
||||
207 dihedrals
|
||||
12 impropers
|
||||
4 = max # of 1-2 neighbors
|
||||
7 = max # of 1-3 neighbors
|
||||
14 = max # of 1-4 neighbors
|
||||
18 = max # of special neighbors
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
thermo_style multi
|
||||
thermo 50
|
||||
|
||||
fix 1 all nvt 275.0 275.0 100.0
|
||||
fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||
19 = # of size 2 clusters
|
||||
6 = # of size 3 clusters
|
||||
3 = # of size 4 clusters
|
||||
640 = # of frozen angles
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
dump 1 peptide atom 10 dump.peptide
|
||||
dump 2 peptide bond 300 dump.bond
|
||||
|
||||
run 300
|
||||
PPPM initialization ...
|
||||
G vector = 0.268725
|
||||
grid = 15 15 15
|
||||
RMS precision = 4.85953e-05
|
||||
brick FFT buffer size/proc = 4312 960 3696
|
||||
SHAKE stats (type/ave/delta) on step 0
|
||||
4 1.111 1.44264e-05
|
||||
6 0.996998 7.26967e-06
|
||||
8 1.08 1.32536e-05
|
||||
10 1.111 1.22749e-05
|
||||
12 1.08 1.11767e-05
|
||||
14 0.96 0
|
||||
18 0.957206 4.37979e-05
|
||||
31 104.519 0.00396029
|
||||
Memory usage per processor = 8.89765 Mbytes
|
||||
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
|
||||
TotEng = -5237.4557 KinEng = 1134.9184 Temp = 282.1027
|
||||
PotEng = -6372.3741 E_bond = 16.5572 E_angle = 36.3726
|
||||
E_dihed = 15.5190 E_impro = 1.9426 E_vdwl = 692.8945
|
||||
E_coul = 26772.2705 E_long = -33907.9305 Press = -845.7315
|
||||
---------------- Step 50 ----- CPU = 1.4801 (sec) ----------------
|
||||
TotEng = -5247.5537 KinEng = 1132.3981 Temp = 281.4762
|
||||
PotEng = -6379.9518 E_bond = 12.2118 E_angle = 31.7364
|
||||
E_dihed = 18.8145 E_impro = 2.3612 E_vdwl = 658.1762
|
||||
E_coul = 26804.4518 E_long = -33907.7036 Press = -1332.2322
|
||||
SHAKE stats (type/ave/delta) on step 100
|
||||
4 1.111 7.81219e-07
|
||||
6 0.997 1.06269e-06
|
||||
8 1.08 6.20924e-07
|
||||
10 1.111 6.23819e-07
|
||||
12 1.08 2.68216e-07
|
||||
14 0.96 0
|
||||
18 0.957201 5.38162e-06
|
||||
31 104.52 0.000502412
|
||||
---------------- Step 100 ----- CPU = 2.9482 (sec) ----------------
|
||||
TotEng = -5258.0208 KinEng = 1078.0404 Temp = 267.9647
|
||||
PotEng = -6336.0612 E_bond = 14.4827 E_angle = 43.4425
|
||||
E_dihed = 15.2568 E_impro = 2.3160 E_vdwl = 708.3258
|
||||
E_coul = 26786.6805 E_long = -33906.5655 Press = -648.9282
|
||||
---------------- Step 150 ----- CPU = 4.4355 (sec) ----------------
|
||||
TotEng = -5287.3158 KinEng = 1098.5907 Temp = 273.0729
|
||||
PotEng = -6385.9065 E_bond = 17.4922 E_angle = 32.8590
|
||||
E_dihed = 15.1622 E_impro = 1.6521 E_vdwl = 736.9709
|
||||
E_coul = 26717.2418 E_long = -33907.2848 Press = -333.3566
|
||||
SHAKE stats (type/ave/delta) on step 200
|
||||
4 1.111 2.18765e-07
|
||||
6 0.997 1.50571e-07
|
||||
8 1.08 6.57567e-08
|
||||
10 1.111 5.57115e-07
|
||||
12 1.08 1.98908e-07
|
||||
14 0.96 0
|
||||
18 0.957201 3.59647e-06
|
||||
31 104.52 0.000388049
|
||||
---------------- Step 200 ----- CPU = 5.8989 (sec) ----------------
|
||||
TotEng = -5308.4800 KinEng = 1100.4956 Temp = 273.5463
|
||||
PotEng = -6408.9756 E_bond = 18.2711 E_angle = 33.3032
|
||||
E_dihed = 16.8153 E_impro = 2.6053 E_vdwl = 686.3176
|
||||
E_coul = 26736.1059 E_long = -33902.3940 Press = -1470.9775
|
||||
---------------- Step 250 ----- CPU = 7.3982 (sec) ----------------
|
||||
TotEng = -5294.1836 KinEng = 1071.1372 Temp = 266.2488
|
||||
PotEng = -6365.3209 E_bond = 14.2026 E_angle = 39.1962
|
||||
E_dihed = 19.4540 E_impro = 3.1384 E_vdwl = 753.6645
|
||||
E_coul = 26713.7437 E_long = -33908.7203 Press = -187.3211
|
||||
SHAKE stats (type/ave/delta) on step 300
|
||||
4 1.111 3.78222e-06
|
||||
6 0.997001 3.50327e-06
|
||||
8 1.08 2.09306e-06
|
||||
10 1.111 5.643e-06
|
||||
12 1.08 2.10265e-06
|
||||
14 0.96 0
|
||||
18 0.957202 7.61122e-06
|
||||
31 104.52 0.000804522
|
||||
---------------- Step 300 ----- CPU = 8.8909 (sec) ----------------
|
||||
TotEng = -5251.4247 KinEng = 1123.3204 Temp = 279.2198
|
||||
PotEng = -6374.7450 E_bond = 14.2228 E_angle = 38.4702
|
||||
E_dihed = 18.1329 E_impro = 2.3701 E_vdwl = 715.7685
|
||||
E_coul = 26745.4242 E_long = -33909.1337 Press = -464.7492
|
||||
Loop time of 8.89127 on 4 procs for 300 steps with 2004 atoms
|
||||
|
||||
Pair time (%) = 5.43468 (61.1237)
|
||||
Bond time (%) = 0.0192376 (0.216365)
|
||||
Kspce time (%) = 1.92633 (21.6654)
|
||||
Neigh time (%) = 0.360919 (4.05924)
|
||||
Comm time (%) = 0.683199 (7.68393)
|
||||
Outpt time (%) = 0.0141159 (0.158762)
|
||||
Other time (%) = 0.452794 (5.09256)
|
||||
|
||||
FFT time (% of Kspce) = 0.221518 (11.4995)
|
||||
FFT Gflps 3d 1d-only = 0.742666 3.96667
|
||||
|
||||
Nlocal: 501 ave 508 max 490 min
|
||||
Histogram: 1 0 0 0 0 0 1 1 0 1
|
||||
Nghost: 6586.25 ave 6628 max 6548 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
Neighs: 177010 ave 180567 max 170204 min
|
||||
Histogram: 1 0 0 0 0 0 0 1 1 1
|
||||
|
||||
Total # of neighbors = 708038
|
||||
Ave neighs/atom = 353.312
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 26
|
||||
Dangerous builds = 0
|
||||
|
||||
|
|
@ -0,0 +1,154 @@
|
|||
LAMMPS (1 Oct 2006)
|
||||
# Solvated 5-mer peptide
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
kspace_style pppm 0.0001
|
||||
|
||||
read_data data.peptide
|
||||
3 = max bonds/atom
|
||||
6 = max angles/atom
|
||||
14 = max dihedrals/atom
|
||||
1 = max impropers/atom
|
||||
1 by 1 by 1 processor grid
|
||||
2004 atoms
|
||||
2004 velocities
|
||||
1365 bonds
|
||||
786 angles
|
||||
207 dihedrals
|
||||
12 impropers
|
||||
4 = max # of 1-2 neighbors
|
||||
7 = max # of 1-3 neighbors
|
||||
14 = max # of 1-4 neighbors
|
||||
18 = max # of special neighbors
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
thermo_style multi
|
||||
thermo 50
|
||||
|
||||
fix 1 all nvt 275.0 275.0 100.0
|
||||
fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||
19 = # of size 2 clusters
|
||||
6 = # of size 3 clusters
|
||||
3 = # of size 4 clusters
|
||||
640 = # of frozen angles
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
dump 1 peptide atom 10 dump.peptide
|
||||
dump 2 peptide bond 300 dump.bond
|
||||
|
||||
run 300
|
||||
PPPM initialization ...
|
||||
G vector = 0.268725
|
||||
grid = 15 15 15
|
||||
RMS precision = 4.85953e-05
|
||||
brick FFT buffer size/proc = 10648 3375 5808
|
||||
SHAKE stats (type/ave/delta) on step 0
|
||||
4 1.111 1.44264e-05
|
||||
6 0.996998 7.26967e-06
|
||||
8 1.08 1.32536e-05
|
||||
10 1.111 1.22749e-05
|
||||
12 1.08 1.11767e-05
|
||||
14 0.96 0
|
||||
18 0.957206 4.37979e-05
|
||||
31 104.519 0.00396029
|
||||
Memory usage per processor = 19.9477 Mbytes
|
||||
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
|
||||
TotEng = -5237.4557 KinEng = 1134.9184 Temp = 282.1027
|
||||
PotEng = -6372.3741 E_bond = 16.5572 E_angle = 36.3726
|
||||
E_dihed = 15.5190 E_impro = 1.9426 E_vdwl = 692.8945
|
||||
E_coul = 26772.2705 E_long = -33907.9305 Press = -845.7315
|
||||
---------------- Step 50 ----- CPU = 7.8391 (sec) ----------------
|
||||
TotEng = -5247.5537 KinEng = 1132.3981 Temp = 281.4762
|
||||
PotEng = -6379.9518 E_bond = 12.2118 E_angle = 31.7364
|
||||
E_dihed = 18.8145 E_impro = 2.3612 E_vdwl = 658.1762
|
||||
E_coul = 26804.4518 E_long = -33907.7036 Press = -1332.2322
|
||||
SHAKE stats (type/ave/delta) on step 100
|
||||
4 1.111 7.81219e-07
|
||||
6 0.997 1.06269e-06
|
||||
8 1.08 6.20924e-07
|
||||
10 1.111 6.23819e-07
|
||||
12 1.08 2.68216e-07
|
||||
14 0.96 0
|
||||
18 0.957201 5.38162e-06
|
||||
31 104.52 0.000502412
|
||||
---------------- Step 100 ----- CPU = 15.6343 (sec) ----------------
|
||||
TotEng = -5258.0208 KinEng = 1078.0404 Temp = 267.9647
|
||||
PotEng = -6336.0612 E_bond = 14.4827 E_angle = 43.4425
|
||||
E_dihed = 15.2568 E_impro = 2.3160 E_vdwl = 708.3258
|
||||
E_coul = 26786.6805 E_long = -33906.5655 Press = -648.9282
|
||||
---------------- Step 150 ----- CPU = 23.5108 (sec) ----------------
|
||||
TotEng = -5287.3158 KinEng = 1098.5907 Temp = 273.0729
|
||||
PotEng = -6385.9065 E_bond = 17.4922 E_angle = 32.8590
|
||||
E_dihed = 15.1622 E_impro = 1.6521 E_vdwl = 736.9709
|
||||
E_coul = 26717.2418 E_long = -33907.2848 Press = -333.3566
|
||||
SHAKE stats (type/ave/delta) on step 200
|
||||
4 1.111 2.18765e-07
|
||||
6 0.997 1.50571e-07
|
||||
8 1.08 6.57567e-08
|
||||
10 1.111 5.57115e-07
|
||||
12 1.08 1.98908e-07
|
||||
14 0.96 0
|
||||
18 0.957201 3.59647e-06
|
||||
31 104.52 0.000388049
|
||||
---------------- Step 200 ----- CPU = 31.1103 (sec) ----------------
|
||||
TotEng = -5308.4800 KinEng = 1100.4956 Temp = 273.5463
|
||||
PotEng = -6408.9756 E_bond = 18.2711 E_angle = 33.3032
|
||||
E_dihed = 16.8153 E_impro = 2.6053 E_vdwl = 686.3176
|
||||
E_coul = 26736.1059 E_long = -33902.3940 Press = -1470.9775
|
||||
---------------- Step 250 ----- CPU = 39.2012 (sec) ----------------
|
||||
TotEng = -5294.1836 KinEng = 1071.1372 Temp = 266.2488
|
||||
PotEng = -6365.3209 E_bond = 14.2026 E_angle = 39.1962
|
||||
E_dihed = 19.4540 E_impro = 3.1384 E_vdwl = 753.6645
|
||||
E_coul = 26713.7437 E_long = -33908.7203 Press = -187.3211
|
||||
SHAKE stats (type/ave/delta) on step 300
|
||||
4 1.111 3.78222e-06
|
||||
6 0.997001 3.50327e-06
|
||||
8 1.08 2.09306e-06
|
||||
10 1.111 5.643e-06
|
||||
12 1.08 2.10265e-06
|
||||
14 0.96 0
|
||||
18 0.957202 7.61122e-06
|
||||
31 104.52 0.000804522
|
||||
---------------- Step 300 ----- CPU = 47.1755 (sec) ----------------
|
||||
TotEng = -5251.4247 KinEng = 1123.3204 Temp = 279.2198
|
||||
PotEng = -6374.7450 E_bond = 14.2228 E_angle = 38.4702
|
||||
E_dihed = 18.1329 E_impro = 2.3701 E_vdwl = 715.7685
|
||||
E_coul = 26745.4242 E_long = -33909.1337 Press = -464.7492
|
||||
Loop time of 47.1756 on 1 procs for 300 steps with 2004 atoms
|
||||
|
||||
Pair time (%) = 38.5968 (81.8151)
|
||||
Bond time (%) = 0.077238 (0.163724)
|
||||
Kspce time (%) = 3.51546 (7.45187)
|
||||
Neigh time (%) = 4.11099 (8.71422)
|
||||
Comm time (%) = 0.360056 (0.763225)
|
||||
Outpt time (%) = 0.017432 (0.0369513)
|
||||
Other time (%) = 0.497656 (1.0549)
|
||||
|
||||
FFT time (% of Kspce) = 1.1808 (33.5887)
|
||||
FFT Gflps 3d 1d-only = 0.139324 0.209866
|
||||
|
||||
Nlocal: 2004 ave 2004 max 2004 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11181 ave 11181 max 11181 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 708038 ave 708038 max 708038 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 708038
|
||||
Ave neighs/atom = 353.312
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 26
|
||||
Dangerous builds = 0
|
||||
|
||||
|
|
@ -0,0 +1,37 @@
|
|||
# Pour granular particles into chute container, then induce flow
|
||||
|
||||
atom_style granular
|
||||
boundary p p fm
|
||||
newton off
|
||||
|
||||
region reg block -10 10 -10 10 -0.5 16 units box
|
||||
create_box 1 reg
|
||||
|
||||
neighbor 0.2 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
# IMPORTANT NOTE: these values of stiffness (2000) and timestep (0.001)
|
||||
# are used in this example file to produce a quick simulation and movie.
|
||||
# More appropriate values for realistic simulations would be
|
||||
# k = 2.0e5 and dt = 0.0001, as in bench/in.chute.
|
||||
|
||||
pair_style gran/history 2000.0 50.0 0.50 0
|
||||
timestep 0.001
|
||||
|
||||
fix 1 all nve/gran
|
||||
fix 2 all gravity spherical 0.0 -180.0
|
||||
fix zlower all wall/gran zplane 0.0 2000.0 50.0 0.5
|
||||
|
||||
region slab block -9.0 9.0 -9.0 9.0 10.0 15.0 units box
|
||||
fix ins all insert 3000 1 300719 vol 0.13 50 region slab
|
||||
|
||||
thermo_style granular
|
||||
thermo 1000
|
||||
thermo_modify lost ignore
|
||||
|
||||
dump id all atom 125 dump.pour
|
||||
run 25000
|
||||
|
||||
unfix ins
|
||||
fix 2 all gravity chute 26.0
|
||||
run 25000
|
||||
|
|
@ -0,0 +1,38 @@
|
|||
# Pour 2d granular particles into container
|
||||
|
||||
dimension 2
|
||||
atom_style granular
|
||||
boundary p fm p
|
||||
newton off
|
||||
|
||||
region reg block 0 100 0 50 -0.5 0.5 units box
|
||||
create_box 1 reg
|
||||
|
||||
neighbor 0.2 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
# IMPORTANT NOTE: these values of stiffness (2000) and timestep (0.001)
|
||||
# are used in this example file to produce a quick simulation and movie.
|
||||
# More appropriate values for realistic simulations would be
|
||||
# k = 2.0e5 and dt = 0.0001, as in bench/in.chute.
|
||||
|
||||
pair_style gran/hertzian 2000.0 50.0 0.0 0
|
||||
timestep 0.001
|
||||
|
||||
fix 1 all nve/gran
|
||||
fix 2 all gravity spherical 90.0 -90.0
|
||||
fix xwalls all wall/gran xplane 0 100 50 0
|
||||
fix ywalls all wall/gran yplane 0 NULL 50 0
|
||||
|
||||
region slab block 1.0 99.0 30 34.5 -0.5 0.5 units box
|
||||
fix ins all insert 1000 1 4767548 vol 0.4 10 &
|
||||
diam 0.5 1.0 region slab
|
||||
|
||||
fix 3 all enforce2d
|
||||
|
||||
thermo_style granular
|
||||
thermo 1000
|
||||
thermo_modify lost ignore
|
||||
|
||||
dump id all atom 100 dump.pour
|
||||
run 25000
|
||||
|
|
@ -0,0 +1,135 @@
|
|||
LAMMPS (1 Oct 2006)
|
||||
# Pour granular particles into chute container, then induce flow
|
||||
|
||||
atom_style granular
|
||||
boundary p p fm
|
||||
newton off
|
||||
|
||||
region reg block -10 10 -10 10 -0.5 16 units box
|
||||
create_box 1 reg
|
||||
Created box = (-10 -10 -0.5) to (10 10 16)
|
||||
2 by 2 by 1 processor grid
|
||||
|
||||
neighbor 0.2 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
# IMPORTANT NOTE: these values of stiffness (2000) and timestep (0.001)
|
||||
# are used in this example file to produce a quick simulation and movie.
|
||||
# More appropriate values for realistic simulations would be
|
||||
# k = 2.0e5 and dt = 0.0001, as in bench/in.chute.
|
||||
|
||||
pair_style gran/history 2000.0 50.0 0.50 0
|
||||
timestep 0.001
|
||||
|
||||
fix 1 all nve/gran
|
||||
fix 2 all gravity spherical 0.0 -180.0
|
||||
fix zlower all wall/gran zplane 0.0 2000.0 50.0 0.5
|
||||
|
||||
region slab block -9.0 9.0 -9.0 9.0 10.0 15.0 units box
|
||||
fix ins all insert 3000 1 300719 vol 0.13 50 region slab
|
||||
Particle insertion: 402 every 3162 steps, 3000 by step 22135
|
||||
|
||||
thermo_style granular
|
||||
thermo 1000
|
||||
thermo_modify lost ignore
|
||||
|
||||
dump id all atom 125 dump.pour
|
||||
run 25000
|
||||
Memory usage per processor = 0.335693 Mbytes
|
||||
Step Atoms Trans-KE Rot-KE Volume
|
||||
0 0 0 0 6600
|
||||
1000 402 779.98578 0 6600
|
||||
2000 402 1424.4252 0 6600
|
||||
3000 402 1425.2447 14.149848 6600
|
||||
4000 804 1717.4634 46.771706 6600
|
||||
5000 804 1600.9045 53.21935 6600
|
||||
6000 804 1351.6492 60.760589 6600
|
||||
7000 1206 1565.6473 62.669488 6600
|
||||
8000 1206 1417.1737 62.758562 6600
|
||||
9000 1206 1258.9904 51.005212 6600
|
||||
10000 1608 1399.1287 49.839456 6600
|
||||
11000 1608 1243.873 48.930454 6600
|
||||
12000 1608 1195.4479 43.545487 6600
|
||||
13000 2010 1306.9138 54.570296 6600
|
||||
14000 2010 1157.9021 43.330935 6600
|
||||
15000 2010 983.9019 43.615315 6600
|
||||
16000 2412 1034.6442 42.147002 6600
|
||||
17000 2412 1031.4629 40.030993 6600
|
||||
18000 2412 893.29609 38.534882 6600
|
||||
19000 2814 1016.6024 38.562892 6600
|
||||
20000 2814 957.40159 41.423471 6600
|
||||
21000 2814 761.01108 38.191827 6600
|
||||
22000 2814 522.65734 42.380196 6600
|
||||
23000 3000 441.50278 37.280492 6600
|
||||
24000 3000 364.60716 19.154219 6600
|
||||
25000 3000 226.05523 23.102252 6600
|
||||
Loop time of 13.6809 on 4 procs for 25000 steps with 3000 atoms
|
||||
|
||||
Pair time (%) = 4.87714 (35.6493)
|
||||
Neigh time (%) = 0.748691 (5.47254)
|
||||
Comm time (%) = 3.72672 (27.2403)
|
||||
Outpt time (%) = 0.640552 (4.6821)
|
||||
Other time (%) = 3.68778 (26.9557)
|
||||
|
||||
Nlocal: 750 ave 765 max 733 min
|
||||
Histogram: 1 0 0 0 1 0 0 1 0 1
|
||||
Nghost: 392 ave 402 max 382 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 2
|
||||
Neighs: 3573.5 ave 3638 max 3540 min
|
||||
Histogram: 1 2 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 14294
|
||||
Ave neighs/atom = 4.76467
|
||||
Neighbor list builds = 1151
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix ins
|
||||
fix 2 all gravity chute 26.0
|
||||
run 25000
|
||||
Memory usage per processor = 6.82785 Mbytes
|
||||
Step Atoms Trans-KE Rot-KE Volume
|
||||
25000 3000 226.05523 23.102252 6600
|
||||
26000 3000 107.00196 18.375396 6600
|
||||
27000 3000 63.99827 10.996141 6600
|
||||
28000 3000 85.164329 8.8173571 6600
|
||||
29000 3000 117.92934 7.75666 6600
|
||||
30000 3000 163.87863 8.7138337 6600
|
||||
31000 3000 233.20236 10.329617 6600
|
||||
32000 3000 342.53254 13.898474 6600
|
||||
33000 3000 468.44696 15.99158 6600
|
||||
34000 3000 621.87103 19.886939 6600
|
||||
35000 3000 815.39747 20.705882 6600
|
||||
36000 3000 1057.2229 26.571307 6600
|
||||
37000 3000 1328.8595 30.123382 6600
|
||||
38000 3000 1657.3423 36.114002 6600
|
||||
39000 3000 1981.1213 41.318004 6600
|
||||
40000 3000 2391.9019 45.046643 6600
|
||||
41000 3000 2831.3144 50.549127 6600
|
||||
42000 3000 3235.6137 57.512833 6600
|
||||
43000 3000 3747.9079 62.890502 6600
|
||||
44000 3000 4178.1452 59.476683 6600
|
||||
45000 3000 4594.1909 70.420341 6600
|
||||
46000 3000 5147.6655 72.299465 6600
|
||||
47000 3000 5677.574 81.275593 6600
|
||||
48000 3000 6300.6258 81.736559 6600
|
||||
49000 3000 6911.4189 87.717341 6600
|
||||
50000 3000 7539.698 94.03491 6600
|
||||
Loop time of 25.886 on 4 procs for 25000 steps with 3000 atoms
|
||||
|
||||
Pair time (%) = 11.7344 (45.331)
|
||||
Neigh time (%) = 0.916894 (3.54205)
|
||||
Comm time (%) = 5.79871 (22.401)
|
||||
Outpt time (%) = 1.08395 (4.18742)
|
||||
Other time (%) = 6.35205 (24.5386)
|
||||
|
||||
Nlocal: 750 ave 761 max 733 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 0 2
|
||||
Nghost: 409.75 ave 418 max 405 min
|
||||
Histogram: 2 0 0 1 0 0 0 0 0 1
|
||||
Neighs: 3583 ave 3665 max 3470 min
|
||||
Histogram: 1 0 0 0 0 0 2 0 0 1
|
||||
|
||||
Total # of neighbors = 14332
|
||||
Ave neighs/atom = 4.77733
|
||||
Neighbor list builds = 653
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,135 @@
|
|||
LAMMPS (1 Oct 2006)
|
||||
# Pour granular particles into chute container, then induce flow
|
||||
|
||||
atom_style granular
|
||||
boundary p p fm
|
||||
newton off
|
||||
|
||||
region reg block -10 10 -10 10 -0.5 16 units box
|
||||
create_box 1 reg
|
||||
Created box = (-10 -10 -0.5) to (10 10 16)
|
||||
1 by 1 by 1 processor grid
|
||||
|
||||
neighbor 0.2 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
# IMPORTANT NOTE: these values of stiffness (2000) and timestep (0.001)
|
||||
# are used in this example file to produce a quick simulation and movie.
|
||||
# More appropriate values for realistic simulations would be
|
||||
# k = 2.0e5 and dt = 0.0001, as in bench/in.chute.
|
||||
|
||||
pair_style gran/history 2000.0 50.0 0.50 0
|
||||
timestep 0.001
|
||||
|
||||
fix 1 all nve/gran
|
||||
fix 2 all gravity spherical 0.0 -180.0
|
||||
fix zlower all wall/gran zplane 0.0 2000.0 50.0 0.5
|
||||
|
||||
region slab block -9.0 9.0 -9.0 9.0 10.0 15.0 units box
|
||||
fix ins all insert 3000 1 300719 vol 0.13 50 region slab
|
||||
Particle insertion: 402 every 3162 steps, 3000 by step 22135
|
||||
|
||||
thermo_style granular
|
||||
thermo 1000
|
||||
thermo_modify lost ignore
|
||||
|
||||
dump id all atom 125 dump.pour
|
||||
run 25000
|
||||
Memory usage per processor = 0.335693 Mbytes
|
||||
Step Atoms Trans-KE Rot-KE Volume
|
||||
0 0 0 0 6600
|
||||
1000 402 779.98578 0 6600
|
||||
2000 402 1424.4252 0 6600
|
||||
3000 402 1425.2447 14.149848 6600
|
||||
4000 804 1717.5445 46.833537 6600
|
||||
5000 804 1602.4038 53.613557 6600
|
||||
6000 804 1344.3882 61.238792 6600
|
||||
7000 1206 1551.5556 61.093446 6600
|
||||
8000 1206 1403.0526 59.960391 6600
|
||||
9000 1206 1235.4923 50.748092 6600
|
||||
10000 1608 1363.3275 53.312989 6600
|
||||
11000 1608 1240.0576 51.060525 6600
|
||||
12000 1608 1181.29 41.956851 6600
|
||||
13000 2010 1305.2234 48.405298 6600
|
||||
14000 2010 1184.9666 43.407539 6600
|
||||
15000 2010 982.48676 46.414299 6600
|
||||
16000 2412 1039.3552 40.73208 6600
|
||||
17000 2412 1021.9131 40.24246 6600
|
||||
18000 2412 918.39685 36.6021 6600
|
||||
19000 2814 1008.0642 40.503982 6600
|
||||
20000 2814 969.92049 46.359854 6600
|
||||
21000 2814 742.83883 45.261311 6600
|
||||
22000 2814 535.51412 35.78601 6600
|
||||
23000 3000 422.4646 36.018166 6600
|
||||
24000 3000 369.01471 20.276832 6600
|
||||
25000 3000 222.8011 25.262721 6600
|
||||
Loop time of 78.181 on 1 procs for 25000 steps with 3000 atoms
|
||||
|
||||
Pair time (%) = 43.4696 (55.6012)
|
||||
Neigh time (%) = 5.03235 (6.4368)
|
||||
Comm time (%) = 2.47885 (3.17066)
|
||||
Outpt time (%) = 1.71796 (2.19742)
|
||||
Other time (%) = 25.4822 (32.5939)
|
||||
|
||||
Nlocal: 3000 ave 3000 max 3000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 673 ave 673 max 673 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 13554 ave 13554 max 13554 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 13554
|
||||
Ave neighs/atom = 4.518
|
||||
Neighbor list builds = 1150
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix ins
|
||||
fix 2 all gravity chute 26.0
|
||||
run 25000
|
||||
Memory usage per processor = 7.23976 Mbytes
|
||||
Step Atoms Trans-KE Rot-KE Volume
|
||||
25000 3000 222.8011 25.262721 6600
|
||||
26000 3000 99.759326 19.389504 6600
|
||||
27000 3000 74.30069 10.522988 6600
|
||||
28000 3000 95.90836 8.0897997 6600
|
||||
29000 3000 136.21033 7.1058765 6600
|
||||
30000 3000 202.52399 9.2690664 6600
|
||||
31000 3000 282.02475 11.360363 6600
|
||||
32000 3000 375.70421 12.925874 6600
|
||||
33000 3000 501.43635 15.872649 6600
|
||||
34000 3000 656.34183 20.080962 6600
|
||||
35000 3000 859.69119 23.330343 6600
|
||||
36000 3000 1124.0709 27.369289 6600
|
||||
37000 3000 1402.6834 32.467711 6600
|
||||
38000 3000 1755.6508 36.236793 6600
|
||||
39000 3000 2127.602 43.307008 6600
|
||||
40000 3000 2514.5587 41.763683 6600
|
||||
41000 3000 2894.3174 50.043024 6600
|
||||
42000 3000 3375.7464 58.443129 6600
|
||||
43000 3000 3927.7147 63.466029 6600
|
||||
44000 3000 4361.4566 67.176165 6600
|
||||
45000 3000 4990.8433 72.328717 6600
|
||||
46000 3000 5538.4251 76.231574 6600
|
||||
47000 3000 6148.7886 82.989651 6600
|
||||
48000 3000 6759.9046 86.32529 6600
|
||||
49000 3000 7398.1553 93.870085 6600
|
||||
50000 3000 8060.7836 93.818377 6600
|
||||
Loop time of 163.879 on 1 procs for 25000 steps with 3000 atoms
|
||||
|
||||
Pair time (%) = 104.425 (63.7212)
|
||||
Neigh time (%) = 5.99224 (3.65651)
|
||||
Comm time (%) = 5.51156 (3.3632)
|
||||
Outpt time (%) = 2.83083 (1.72739)
|
||||
Other time (%) = 45.1186 (27.5317)
|
||||
|
||||
Nlocal: 3000 ave 3000 max 3000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 779 ave 779 max 779 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 13636 ave 13636 max 13636 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 13636
|
||||
Ave neighs/atom = 4.54533
|
||||
Neighbor list builds = 641
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,88 @@
|
|||
LAMMPS (1 Oct 2006)
|
||||
# Pour 2d granular particles into container
|
||||
|
||||
dimension 2
|
||||
atom_style granular
|
||||
boundary p fm p
|
||||
newton off
|
||||
|
||||
region reg block 0 100 0 50 -0.5 0.5 units box
|
||||
create_box 1 reg
|
||||
Created box = (0 0 -0.5) to (100 50 0.5)
|
||||
2 by 2 by 1 processor grid
|
||||
|
||||
neighbor 0.2 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
# IMPORTANT NOTE: these values of stiffness (2000) and timestep (0.001)
|
||||
# are used in this example file to produce a quick simulation and movie.
|
||||
# More appropriate values for realistic simulations would be
|
||||
# k = 2.0e5 and dt = 0.0001, as in bench/in.chute.
|
||||
|
||||
pair_style gran/hertzian 2000.0 50.0 0.0 0
|
||||
timestep 0.001
|
||||
|
||||
fix 1 all nve/gran
|
||||
fix 2 all gravity spherical 90.0 -90.0
|
||||
fix xwalls all wall/gran xplane 0 100 50 0
|
||||
fix ywalls all wall/gran yplane 0 NULL 50 0
|
||||
|
||||
region slab block 1.0 99.0 30 34.5 -0.5 0.5 units box
|
||||
fix ins all insert 1000 1 4767548 vol 0.4 10 diam 0.5 1.0 region slab
|
||||
Particle insertion: 224 every 3000 steps, 1000 by step 12001
|
||||
|
||||
fix 3 all enforce2d
|
||||
|
||||
thermo_style granular
|
||||
thermo 1000
|
||||
thermo_modify lost ignore
|
||||
|
||||
dump id all atom 100 dump.pour.2d
|
||||
run 25000
|
||||
Memory usage per processor = 0.335693 Mbytes
|
||||
Step Atoms Trans-KE Rot-KE Volume
|
||||
0 0 0 0 5000
|
||||
1000 224 348.20549 0 5000
|
||||
2000 224 650.98655 0 5000
|
||||
3000 224 1056.0039 0 5000
|
||||
4000 448 1941.6817 0 5000
|
||||
5000 448 2869.092 0 5000
|
||||
6000 448 3310.8798 0 5000
|
||||
7000 672 3505.2381 0 5000
|
||||
8000 672 3325.8942 0 5000
|
||||
9000 672 3165.2505 0 5000
|
||||
10000 896 3170.2639 0 5000
|
||||
11000 896 2947.3721 0 5000
|
||||
12000 896 2860.549 0 5000
|
||||
13000 1000 2845.3312 0 5000
|
||||
14000 1000 2632.0994 0 5000
|
||||
15000 1000 2195.3133 0 5000
|
||||
16000 1000 1551.8485 0 5000
|
||||
17000 1000 941.82431 0 5000
|
||||
18000 1000 684.95986 0 5000
|
||||
19000 1000 346.24904 0 5000
|
||||
20000 1000 100.47441 0 5000
|
||||
21000 1000 55.606283 0 5000
|
||||
22000 1000 47.410559 0 5000
|
||||
23000 1000 38.365449 0 5000
|
||||
24000 1000 27.535477 0 5000
|
||||
25000 1000 16.082932 0 5000
|
||||
Loop time of 7.35198 on 4 procs for 25000 steps with 1000 atoms
|
||||
|
||||
Pair time (%) = 1.18859 (16.167)
|
||||
Neigh time (%) = 0.289227 (3.934)
|
||||
Comm time (%) = 1.58685 (21.584)
|
||||
Outpt time (%) = 0.418018 (5.68578)
|
||||
Other time (%) = 3.8693 (52.6293)
|
||||
|
||||
Nlocal: 250 ave 502 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 12 ave 25 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 620.5 ave 1252 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 2482
|
||||
Ave neighs/atom = 2.482
|
||||
Neighbor list builds = 1725
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,88 @@
|
|||
LAMMPS (1 Oct 2006)
|
||||
# Pour 2d granular particles into container
|
||||
|
||||
dimension 2
|
||||
atom_style granular
|
||||
boundary p fm p
|
||||
newton off
|
||||
|
||||
region reg block 0 100 0 50 -0.5 0.5 units box
|
||||
create_box 1 reg
|
||||
Created box = (0 0 -0.5) to (100 50 0.5)
|
||||
1 by 1 by 1 processor grid
|
||||
|
||||
neighbor 0.2 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
# IMPORTANT NOTE: these values of stiffness (2000) and timestep (0.001)
|
||||
# are used in this example file to produce a quick simulation and movie.
|
||||
# More appropriate values for realistic simulations would be
|
||||
# k = 2.0e5 and dt = 0.0001, as in bench/in.chute.
|
||||
|
||||
pair_style gran/hertzian 2000.0 50.0 0.0 0
|
||||
timestep 0.001
|
||||
|
||||
fix 1 all nve/gran
|
||||
fix 2 all gravity spherical 90.0 -90.0
|
||||
fix xwalls all wall/gran xplane 0 100 50 0
|
||||
fix ywalls all wall/gran yplane 0 NULL 50 0
|
||||
|
||||
region slab block 1.0 99.0 30 34.5 -0.5 0.5 units box
|
||||
fix ins all insert 1000 1 4767548 vol 0.4 10 diam 0.5 1.0 region slab
|
||||
Particle insertion: 224 every 3000 steps, 1000 by step 12001
|
||||
|
||||
fix 3 all enforce2d
|
||||
|
||||
thermo_style granular
|
||||
thermo 1000
|
||||
thermo_modify lost ignore
|
||||
|
||||
dump id all atom 100 dump.pour.2d
|
||||
run 25000
|
||||
Memory usage per processor = 0.328064 Mbytes
|
||||
Step Atoms Trans-KE Rot-KE Volume
|
||||
0 0 0 0 5000
|
||||
1000 224 348.20549 0 5000
|
||||
2000 224 650.98655 0 5000
|
||||
3000 224 1056.0039 0 5000
|
||||
4000 448 1941.6817 0 5000
|
||||
5000 448 2869.092 0 5000
|
||||
6000 448 3310.8798 0 5000
|
||||
7000 672 3505.2381 0 5000
|
||||
8000 672 3325.8942 0 5000
|
||||
9000 672 3165.2505 0 5000
|
||||
10000 896 3170.2667 0 5000
|
||||
11000 896 2944.0565 0 5000
|
||||
12000 896 2862.9537 0 5000
|
||||
13000 1000 2862.2101 0 5000
|
||||
14000 1000 2638.5235 0 5000
|
||||
15000 1000 2218.2739 0 5000
|
||||
16000 1000 1583.5051 0 5000
|
||||
17000 1000 963.53755 0 5000
|
||||
18000 1000 666.8307 0 5000
|
||||
19000 1000 339.73655 0 5000
|
||||
20000 1000 100.52829 0 5000
|
||||
21000 1000 56.112393 0 5000
|
||||
22000 1000 47.013733 0 5000
|
||||
23000 1000 32.615049 0 5000
|
||||
24000 1000 25.853047 0 5000
|
||||
25000 1000 17.216223 0 5000
|
||||
Loop time of 22.8255 on 1 procs for 25000 steps with 1000 atoms
|
||||
|
||||
Pair time (%) = 9.2328 (40.4494)
|
||||
Neigh time (%) = 2.19741 (9.627)
|
||||
Comm time (%) = 0.301715 (1.32183)
|
||||
Outpt time (%) = 0.97282 (4.26198)
|
||||
Other time (%) = 10.1208 (44.3398)
|
||||
|
||||
Nlocal: 1000 ave 1000 max 1000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 27 ave 27 max 27 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 2441 ave 2441 max 2441 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 2441
|
||||
Ave neighs/atom = 2.441
|
||||
Neighbor list builds = 1758
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,100 @@
|
|||
# LAMMPS data file for rigid bodies
|
||||
|
||||
81 atoms
|
||||
1 atom types
|
||||
|
||||
-12 12 xlo xhi
|
||||
-12 12 ylo yhi
|
||||
-12 12 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 1
|
||||
|
||||
Pair Coeffs
|
||||
|
||||
1 1 1
|
||||
|
||||
Atoms
|
||||
|
||||
1 1 0 0 0
|
||||
2 1 0 1 0
|
||||
3 1 0 0.5 0
|
||||
4 1 0.5 0 0
|
||||
5 1 0.5 0.5 1
|
||||
6 1 1 0.5 0
|
||||
7 1 0.5 1 0
|
||||
8 1 1 0 0
|
||||
9 1 1 1 0
|
||||
10 1 2 1 0
|
||||
11 1 1 2 0
|
||||
12 1 1.5 2 0
|
||||
13 1 1.5 1 0
|
||||
14 1 1 1.5 0
|
||||
15 1 1.5 1.5 1
|
||||
16 1 2 1.5 0
|
||||
17 1 2 2 0
|
||||
18 1 2 3 0
|
||||
19 1 2 2.5 0
|
||||
20 1 2.5 2 0
|
||||
21 1 2.5 2.5 1
|
||||
22 1 3 2.5 0
|
||||
23 1 2.5 3 0
|
||||
24 1 3 2 0
|
||||
25 1 3 3 0
|
||||
26 1 4 3 0
|
||||
27 1 3 4 0
|
||||
28 1 3.5 4 0
|
||||
29 1 3.5 3 0
|
||||
30 1 3 3.5 0
|
||||
31 1 3.5 3.5 1
|
||||
32 1 4 3.5 0
|
||||
33 1 4 4 0
|
||||
34 1 4 5 0
|
||||
35 1 4 4.5 0
|
||||
36 1 4.5 4 0
|
||||
37 1 4.5 4.5 1
|
||||
38 1 5 4.5 0
|
||||
39 1 4.5 5 0
|
||||
40 1 5 4 0
|
||||
41 1 5 5 0
|
||||
42 1 6 5 0
|
||||
43 1 5 6 0
|
||||
44 1 5.5 6 0
|
||||
45 1 5.5 5 0
|
||||
46 1 5 5.5 0
|
||||
47 1 5.5 5.5 1
|
||||
48 1 6 5.5 0
|
||||
49 1 6 6 0
|
||||
50 1 6 7 0
|
||||
51 1 6 6.5 0
|
||||
52 1 6.5 6 0
|
||||
53 1 6.5 6.5 1
|
||||
54 1 7 6.5 0
|
||||
55 1 6.5 7 0
|
||||
56 1 7 6 0
|
||||
57 1 7 7 0
|
||||
58 1 8 7 0
|
||||
59 1 7 8 0
|
||||
60 1 7.5 8 0
|
||||
61 1 7.5 7 0
|
||||
62 1 7 7.5 0
|
||||
63 1 7.5 7.5 1
|
||||
64 1 8 7.5 0
|
||||
65 1 8 8 0
|
||||
66 1 8 9 0
|
||||
67 1 8 8.5 0
|
||||
68 1 8.5 8 0
|
||||
69 1 8.5 8.5 1
|
||||
70 1 9 8.5 0
|
||||
71 1 8.5 9 0
|
||||
72 1 9 8 0
|
||||
73 1 9 9 0
|
||||
74 1 10 9 0
|
||||
75 1 9 10 0
|
||||
76 1 9.5 10 0
|
||||
77 1 9.5 9 0
|
||||
78 1 9 9.5 0
|
||||
79 1 9.5 9.5 1
|
||||
80 1 10 9.5 0
|
||||
81 1 10 10 0
|
||||
|
|
@ -0,0 +1,72 @@
|
|||
# Simple rigid body system
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
read_data data.rigid
|
||||
|
||||
velocity all create 100.0 4928459
|
||||
|
||||
# unconnected bodies
|
||||
|
||||
group clump1 id <> 1 9
|
||||
group clump2 id <> 10 18
|
||||
group clump3 id <> 19 27
|
||||
group clump4 id <> 28 36
|
||||
group clump5 id <> 37 45
|
||||
group clump6 id <> 46 54
|
||||
group clump7 id <> 55 63
|
||||
group clump8 id <> 64 72
|
||||
group clump9 id <> 73 81
|
||||
|
||||
fix 1 all rigid group clump1 clump2 clump3 clump4 clump5 &
|
||||
clump6 clump7 clump8 clump9
|
||||
|
||||
# 1 chain of connected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 9 18
|
||||
#group clump3 id <> 18 27
|
||||
#group clump4 id <> 27 36
|
||||
#group clump5 id <> 36 45
|
||||
#group clump6 id <> 45 54
|
||||
#group clump7 id <> 54 63
|
||||
#group clump8 id <> 63 72
|
||||
#group clump9 id <> 72 81
|
||||
|
||||
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 &
|
||||
# clump6 clump7 clump8 clump9
|
||||
|
||||
# 2 chains of connected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 9 18
|
||||
#group clump3 id <> 18 27
|
||||
#group clump4 id <> 27 36
|
||||
#group clump5 id <> 37 45
|
||||
#group clump6 id <> 45 54
|
||||
#group clump7 id <> 54 63
|
||||
#group clump8 id <> 63 72
|
||||
#group clump9 id <> 72 81
|
||||
|
||||
#fix 1 all poems group clump1 clump2 clump3 clump4
|
||||
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
|
||||
|
||||
neigh_modify exclude group clump1 clump1
|
||||
neigh_modify exclude group clump2 clump2
|
||||
neigh_modify exclude group clump3 clump3
|
||||
neigh_modify exclude group clump4 clump4
|
||||
neigh_modify exclude group clump5 clump5
|
||||
neigh_modify exclude group clump6 clump6
|
||||
neigh_modify exclude group clump7 clump7
|
||||
neigh_modify exclude group clump8 clump8
|
||||
neigh_modify exclude group clump9 clump9
|
||||
|
||||
thermo 100
|
||||
dump 1 all atom 50 dump.rigid
|
||||
|
||||
timestep 0.0001
|
||||
thermo 50
|
||||
run 10000
|
||||
|
|
@ -0,0 +1,72 @@
|
|||
# Simple rigid body system
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
read_data data.rigid
|
||||
|
||||
velocity all create 100.0 4928459
|
||||
|
||||
# unconnected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 10 18
|
||||
#group clump3 id <> 19 27
|
||||
#group clump4 id <> 28 36
|
||||
#group clump5 id <> 37 45
|
||||
#group clump6 id <> 46 54
|
||||
#group clump7 id <> 55 63
|
||||
#group clump8 id <> 64 72
|
||||
#group clump9 id <> 73 81
|
||||
|
||||
#fix 1 all rigid group clump1 clump2 clump3 clump4 clump5 &
|
||||
# clump6 clump7 clump8 clump9
|
||||
|
||||
# 1 chain of connected bodies
|
||||
|
||||
group clump1 id <> 1 9
|
||||
group clump2 id <> 9 18
|
||||
group clump3 id <> 18 27
|
||||
group clump4 id <> 27 36
|
||||
group clump5 id <> 36 45
|
||||
group clump6 id <> 45 54
|
||||
group clump7 id <> 54 63
|
||||
group clump8 id <> 63 72
|
||||
group clump9 id <> 72 81
|
||||
|
||||
fix 1 all poems group clump1 clump2 clump3 clump4 clump5 &
|
||||
clump6 clump7 clump8 clump9
|
||||
|
||||
# 2 chains of connected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 9 18
|
||||
#group clump3 id <> 18 27
|
||||
#group clump4 id <> 27 36
|
||||
#group clump5 id <> 37 45
|
||||
#group clump6 id <> 45 54
|
||||
#group clump7 id <> 54 63
|
||||
#group clump8 id <> 63 72
|
||||
#group clump9 id <> 72 81
|
||||
|
||||
#fix 1 all poems group clump1 clump2 clump3 clump4
|
||||
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
|
||||
|
||||
neigh_modify exclude group clump1 clump1
|
||||
neigh_modify exclude group clump2 clump2
|
||||
neigh_modify exclude group clump3 clump3
|
||||
neigh_modify exclude group clump4 clump4
|
||||
neigh_modify exclude group clump5 clump5
|
||||
neigh_modify exclude group clump6 clump6
|
||||
neigh_modify exclude group clump7 clump7
|
||||
neigh_modify exclude group clump8 clump8
|
||||
neigh_modify exclude group clump9 clump9
|
||||
|
||||
thermo 100
|
||||
dump 1 all atom 50 dump.rigid
|
||||
|
||||
timestep 0.0001
|
||||
thermo 50
|
||||
run 10000
|
||||
|
|
@ -0,0 +1,72 @@
|
|||
# Simple rigid body system
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
read_data data.rigid
|
||||
|
||||
velocity all create 100.0 4928459
|
||||
|
||||
# unconnected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 10 18
|
||||
#group clump3 id <> 19 27
|
||||
#group clump4 id <> 28 36
|
||||
#group clump5 id <> 37 45
|
||||
#group clump6 id <> 46 54
|
||||
#group clump7 id <> 55 63
|
||||
#group clump8 id <> 64 72
|
||||
#group clump9 id <> 73 81
|
||||
|
||||
#fix 1 all rigid group clump1 clump2 clump3 clump4 clump5 &
|
||||
# clump6 clump7 clump8 clump9
|
||||
|
||||
# 1 chain of connected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 9 18
|
||||
#group clump3 id <> 18 27
|
||||
#group clump4 id <> 27 36
|
||||
#group clump5 id <> 36 45
|
||||
#group clump6 id <> 45 54
|
||||
#group clump7 id <> 54 63
|
||||
#group clump8 id <> 63 72
|
||||
#group clump9 id <> 72 81
|
||||
|
||||
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 &
|
||||
# clump6 clump7 clump8 clump9
|
||||
|
||||
# 2 chains of connected bodies
|
||||
|
||||
group clump1 id <> 1 9
|
||||
group clump2 id <> 9 18
|
||||
group clump3 id <> 18 27
|
||||
group clump4 id <> 27 36
|
||||
group clump5 id <> 37 45
|
||||
group clump6 id <> 45 54
|
||||
group clump7 id <> 54 63
|
||||
group clump8 id <> 63 72
|
||||
group clump9 id <> 72 81
|
||||
|
||||
fix 1 all poems group clump1 clump2 clump3 clump4
|
||||
fix 2 all poems group clump5 clump6 clump7 clump8 clump9
|
||||
|
||||
neigh_modify exclude group clump1 clump1
|
||||
neigh_modify exclude group clump2 clump2
|
||||
neigh_modify exclude group clump3 clump3
|
||||
neigh_modify exclude group clump4 clump4
|
||||
neigh_modify exclude group clump5 clump5
|
||||
neigh_modify exclude group clump6 clump6
|
||||
neigh_modify exclude group clump7 clump7
|
||||
neigh_modify exclude group clump8 clump8
|
||||
neigh_modify exclude group clump9 clump9
|
||||
|
||||
thermo 100
|
||||
dump 1 all atom 50 dump.rigid
|
||||
|
||||
timestep 0.0001
|
||||
thermo 50
|
||||
run 10000
|
||||
|
|
@ -0,0 +1,305 @@
|
|||
LAMMPS (1 Oct 2006)
|
||||
# Simple rigid body system
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
read_data data.rigid
|
||||
1 by 2 by 2 processor grid
|
||||
81 atoms
|
||||
|
||||
velocity all create 100.0 4928459
|
||||
|
||||
# unconnected bodies
|
||||
|
||||
group clump1 id <> 1 9
|
||||
9 atoms in group clump1
|
||||
group clump2 id <> 10 18
|
||||
9 atoms in group clump2
|
||||
group clump3 id <> 19 27
|
||||
9 atoms in group clump3
|
||||
group clump4 id <> 28 36
|
||||
9 atoms in group clump4
|
||||
group clump5 id <> 37 45
|
||||
9 atoms in group clump5
|
||||
group clump6 id <> 46 54
|
||||
9 atoms in group clump6
|
||||
group clump7 id <> 55 63
|
||||
9 atoms in group clump7
|
||||
group clump8 id <> 64 72
|
||||
9 atoms in group clump8
|
||||
group clump9 id <> 73 81
|
||||
9 atoms in group clump9
|
||||
|
||||
fix 1 all rigid group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
|
||||
9 rigid bodies with 81 atoms
|
||||
|
||||
# 1 chain of connected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 9 18
|
||||
#group clump3 id <> 18 27
|
||||
#group clump4 id <> 27 36
|
||||
#group clump5 id <> 36 45
|
||||
#group clump6 id <> 45 54
|
||||
#group clump7 id <> 54 63
|
||||
#group clump8 id <> 63 72
|
||||
#group clump9 id <> 72 81
|
||||
|
||||
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
|
||||
|
||||
# 2 chains of connected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 9 18
|
||||
#group clump3 id <> 18 27
|
||||
#group clump4 id <> 27 36
|
||||
#group clump5 id <> 37 45
|
||||
#group clump6 id <> 45 54
|
||||
#group clump7 id <> 54 63
|
||||
#group clump8 id <> 63 72
|
||||
#group clump9 id <> 72 81
|
||||
|
||||
#fix 1 all poems group clump1 clump2 clump3 clump4
|
||||
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
|
||||
|
||||
neigh_modify exclude group clump1 clump1
|
||||
neigh_modify exclude group clump2 clump2
|
||||
neigh_modify exclude group clump3 clump3
|
||||
neigh_modify exclude group clump4 clump4
|
||||
neigh_modify exclude group clump5 clump5
|
||||
neigh_modify exclude group clump6 clump6
|
||||
neigh_modify exclude group clump7 clump7
|
||||
neigh_modify exclude group clump8 clump8
|
||||
neigh_modify exclude group clump9 clump9
|
||||
|
||||
thermo 100
|
||||
dump 1 all atom 50 dump.rigid
|
||||
|
||||
timestep 0.0001
|
||||
thermo 50
|
||||
run 10000
|
||||
Memory usage per processor = 1.41814 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 115.29439 5235.9179 0 5272.2142 -2.7403788
|
||||
50 14910.685 571.71558 0 5265.82 32.006171
|
||||
100 16298.442 136.66184 0 5267.653 16.444229
|
||||
150 16682.606 17.490511 0 5269.4219 14.900344
|
||||
200 16733.929 1.372872 0 5269.4617 14.569267
|
||||
250 16738.853 -0.15252816 0 5269.4864 14.496404
|
||||
300 16738.588 -0.055171335 0 5269.5002 14.496025
|
||||
350 16738.492 -0.017444677 0 5269.5077 14.496446
|
||||
400 16738.464 -0.0060102023 0 5269.5104 14.496618
|
||||
450 16738.455 -0.0012713351 0 5269.5124 14.496701
|
||||
500 16738.455 -0.00081068621 0 5269.5128 14.496709
|
||||
550 16738.455 -0.00083203497 0 5269.5129 14.496707
|
||||
600 16738.455 -0.00058355356 0 5269.5131 14.496709
|
||||
650 16738.455 -0.00047226704 0 5269.5131 14.496708
|
||||
700 16738.455 0 0 5269.5136 14.496713
|
||||
750 16738.455 0 0 5269.5136 14.49671
|
||||
800 16738.455 0 0 5269.5137 14.496709
|
||||
850 16738.455 0 0 5269.5137 14.49671
|
||||
900 16738.456 0 0 5269.5138 14.496713
|
||||
950 16738.462 -0.0035323872 0 5269.5122 14.496671
|
||||
1000 16738.586 -0.051135144 0 5269.5036 14.496229
|
||||
1050 16737.358 0.32995057 0 5269.4981 14.525763
|
||||
1100 16737.892 0.16210246 0 5269.4984 14.531983
|
||||
1150 16738.703 -0.089235095 0 5269.5025 14.509899
|
||||
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
|
||||
1250 16738.456 0 0 5269.514 14.510704
|
||||
1300 16738.457 0 0 5269.5141 14.510701
|
||||
1350 16738.457 0 0 5269.5141 14.510699
|
||||
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
|
||||
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
|
||||
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
|
||||
1550 16738.457 0 0 5269.5143 14.51071
|
||||
1600 16738.457 0 0 5269.5144 14.510712
|
||||
1650 16738.457 0 0 5269.5144 14.510712
|
||||
1700 16738.458 0 0 5269.5144 14.51071
|
||||
1750 16738.458 0 0 5269.5145 14.510708
|
||||
1800 16738.458 0 0 5269.5145 14.510706
|
||||
1850 16738.458 0 0 5269.5146 14.510705
|
||||
1900 16738.458 0 0 5269.5146 14.510706
|
||||
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
|
||||
2000 16738.491 -0.013255268 0 5269.5117 14.510532
|
||||
2050 16738.556 -0.0365811 0 5269.5087 14.51029
|
||||
2100 16738.633 -0.063209659 0 5269.5065 14.510219
|
||||
2150 16738.607 -0.05601761 0 5269.5055 14.510231
|
||||
2200 16738.557 -0.038423032 0 5269.5072 14.510404
|
||||
2250 16738.515 -0.023709918 0 5269.5088 14.510539
|
||||
2300 16738.489 -0.013249035 0 5269.5111 14.510621
|
||||
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
|
||||
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
|
||||
2450 16738.464 -0.0023259756 0 5269.514 14.510746
|
||||
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
|
||||
2550 16738.581 -0.044940117 0 5269.5085 14.510315
|
||||
2600 16738.427 -7.9722842e-05 0 5269.5046 14.510657
|
||||
2650 16733.017 1.705148 0 5269.5067 14.596295
|
||||
2700 16738.761 -0.10614946 0 5269.5038 14.499584
|
||||
2750 16733.973 1.4038179 0 5269.5064 14.598107
|
||||
2800 16738.585 -0.046813448 0 5269.5076 14.511073
|
||||
2850 16738.487 -0.012558719 0 5269.5111 14.510111
|
||||
2900 16738.465 -0.0026252725 0 5269.514 14.510277
|
||||
2950 16738.476 -0.0082220764 0 5269.512 14.510223
|
||||
3000 16738.66 -0.071284779 0 5269.507 14.509758
|
||||
3050 16715.332 7.2419351 0 5269.476 14.870305
|
||||
3100 16653.226 26.818761 0 5269.5009 14.496764
|
||||
3150 16739.351 -0.30690375 0 5269.4886 13.643904
|
||||
3200 16733.238 1.6025328 0 5269.4737 12.016934
|
||||
3250 16734.374 1.2554429 0 5269.4841 11.963561
|
||||
3300 16732.156 1.9585967 0 5269.4893 12.234024
|
||||
3350 16738.655 -0.079693236 0 5269.497 12.092757
|
||||
3400 16738.543 -0.042215005 0 5269.4991 12.092809
|
||||
3450 16738.591 -0.059327511 0 5269.4972 12.092536
|
||||
3500 16738.759 -0.11761245 0 5269.4918 12.09203
|
||||
3550 16713.405 7.8460621 0 5269.4737 12.389816
|
||||
3600 16734.939 1.0821936 0 5269.4891 12.173591
|
||||
3650 16738.808 -0.13663194 0 5269.4882 12.027009
|
||||
3700 16738.602 -0.070934368 0 5269.4889 12.025288
|
||||
3750 16737.731 0.20706558 0 5269.4927 12.061948
|
||||
3800 16738.578 -0.05582043 0 5269.4965 12.035665
|
||||
3850 16738.471 -0.016307928 0 5269.5024 12.035302
|
||||
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
|
||||
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
|
||||
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
|
||||
4050 16738.437 0 0 5269.5078 12.035454
|
||||
4100 16738.437 0 0 5269.508 12.035435
|
||||
4150 16738.438 0 0 5269.5081 12.035426
|
||||
4200 16738.438 0 0 5269.5083 12.035432
|
||||
4250 16738.439 0 0 5269.5085 12.035447
|
||||
4300 16738.439 0 0 5269.5086 12.035463
|
||||
4350 16738.44 0 0 5269.5087 12.035474
|
||||
4400 16738.44 0 0 5269.5088 12.035478
|
||||
4450 16738.44 0 0 5269.5089 12.035474
|
||||
4500 16738.44 0 0 5269.509 12.035462
|
||||
4550 16738.441 0 0 5269.5092 12.035449
|
||||
4600 16738.441 0 0 5269.5093 12.035445
|
||||
4650 16738.442 0 0 5269.5095 12.035451
|
||||
4700 16738.442 0 0 5269.5096 12.03546
|
||||
4750 16738.443 0 0 5269.5097 12.035465
|
||||
4800 16738.443 0 0 5269.5098 12.035466
|
||||
4850 16738.443 0 0 5269.51 12.035463
|
||||
4900 16738.444 0 0 5269.5101 12.035456
|
||||
4950 16738.444 0 0 5269.5102 12.035447
|
||||
5000 16738.445 0 0 5269.5104 12.03544
|
||||
5050 16738.445 0 0 5269.5105 12.035442
|
||||
5100 16738.446 0 0 5269.5107 12.035455
|
||||
5150 16738.446 0 0 5269.5108 12.03547
|
||||
5200 16738.446 0 0 5269.5109 12.035479
|
||||
5250 16738.447 0 0 5269.511 12.035479
|
||||
5300 16738.447 0 0 5269.5111 12.03547
|
||||
5350 16738.447 0 0 5269.5112 12.035454
|
||||
5400 16738.448 0 0 5269.5113 12.035434
|
||||
5450 16738.448 0 0 5269.5115 12.03542
|
||||
5500 16738.449 0 0 5269.5117 12.035422
|
||||
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
|
||||
5600 16738.51 -0.021618357 0 5269.5092 12.035106
|
||||
5650 16738.622 -0.059214788 0 5269.507 12.035694
|
||||
5700 16395.28 108.06942 0 5269.5463 24.369038
|
||||
5750 16738.544 -0.033973429 0 5269.5077 12.011261
|
||||
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
|
||||
5850 16738.451 0 0 5269.5123 12.011709
|
||||
5900 16738.451 -0.0002211587 0 5269.5122 12.011687
|
||||
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
|
||||
6000 16738.452 0 0 5269.5128 12.011688
|
||||
6050 16738.453 0 0 5269.513 12.011702
|
||||
6100 16738.453 0 0 5269.5131 12.011716
|
||||
6150 16738.454 0 0 5269.5132 12.011725
|
||||
6200 16738.454 0 0 5269.5133 12.011728
|
||||
6250 16738.454 0 0 5269.5134 12.011723
|
||||
6300 16738.455 0 0 5269.5135 12.011712
|
||||
6350 16738.455 0 0 5269.5137 12.0117
|
||||
6400 16738.456 0 0 5269.5138 12.011697
|
||||
6450 16738.456 0 0 5269.514 12.011704
|
||||
6500 16738.456 0 0 5269.5141 12.011714
|
||||
6550 16738.457 0 0 5269.5142 12.011719
|
||||
6600 16738.457 0 0 5269.5143 12.011718
|
||||
6650 16738.458 0 0 5269.5144 12.011713
|
||||
6700 16738.458 0 0 5269.5146 12.011705
|
||||
6750 16738.459 0 0 5269.5147 12.011696
|
||||
6800 16738.459 0 0 5269.5149 12.01169
|
||||
6850 16738.46 0 0 5269.515 12.011695
|
||||
6900 16738.46 0 0 5269.5152 12.01171
|
||||
6950 16738.46 0 0 5269.5153 12.011726
|
||||
7000 16738.461 0 0 5269.5154 12.011736
|
||||
7050 16738.461 0 0 5269.5155 12.011737
|
||||
7100 16738.461 0 0 5269.5155 12.011728
|
||||
7150 16738.461 0 0 5269.5156 12.011712
|
||||
7200 16738.462 0 0 5269.5158 12.011691
|
||||
7250 16738.463 0 0 5269.516 12.011676
|
||||
7300 16738.463 0 0 5269.5162 12.011677
|
||||
7350 16738.464 0 0 5269.5164 12.011693
|
||||
7400 16738.464 0 0 5269.5165 12.011713
|
||||
7450 16738.465 0 0 5269.5166 12.011729
|
||||
7500 16738.465 0 0 5269.5167 12.011736
|
||||
7550 16738.465 0 0 5269.5168 12.011734
|
||||
7600 16738.465 0 0 5269.5168 12.011722
|
||||
7650 16738.466 0 0 5269.517 12.011704
|
||||
7700 16738.466 0 0 5269.5171 12.011687
|
||||
7750 16738.467 0 0 5269.5173 12.011681
|
||||
7800 16738.467 0 0 5269.5175 12.011687
|
||||
7850 16738.468 0 0 5269.5176 12.0117
|
||||
7900 16738.468 0 0 5269.5178 12.011712
|
||||
7950 16738.469 0 0 5269.5179 12.011721
|
||||
8000 16738.469 0 0 5269.518 12.011724
|
||||
8050 16738.469 0 0 5269.5181 12.01172
|
||||
8100 16738.47 0 0 5269.5182 12.011709
|
||||
8150 16738.47 0 0 5269.5183 12.0117
|
||||
8200 16738.47 0 0 5269.5185 12.0117
|
||||
8250 16738.471 0 0 5269.5186 12.011709
|
||||
8300 16738.471 0 0 5269.5187 12.011719
|
||||
8350 16738.472 0 0 5269.5189 12.011723
|
||||
8400 16738.472 0 0 5269.519 12.01172
|
||||
8450 16738.473 -0.00039690664 0 5269.5189 12.011706
|
||||
8500 16738.481 -0.0034646803 0 5269.5182 12.011643
|
||||
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
|
||||
8600 16738.474 -0.00076532812 0 5269.5189 12.011681
|
||||
8650 16738.474 0 0 5269.5197 12.011699
|
||||
8700 16738.475 0 0 5269.5199 12.011715
|
||||
8750 16738.475 0 0 5269.52 12.011732
|
||||
8800 16738.475 0 0 5269.52 12.011743
|
||||
8850 16738.476 0 0 5269.5201 12.011744
|
||||
8900 16738.476 0 0 5269.5202 12.011735
|
||||
8950 16738.476 0 0 5269.5203 12.011719
|
||||
9000 16738.477 0 0 5269.5205 12.011698
|
||||
9050 16738.477 0 0 5269.5206 12.011683
|
||||
9100 16738.478 0 0 5269.5208 12.011684
|
||||
9150 16738.479 0 0 5269.521 12.011701
|
||||
9200 16738.479 0 0 5269.5212 12.011722
|
||||
9250 16738.479 0 0 5269.5213 12.011738
|
||||
9300 16738.48 0 0 5269.5214 12.011746
|
||||
9350 16738.48 0 0 5269.5214 12.011744
|
||||
9400 16738.48 0 0 5269.5215 12.011732
|
||||
9450 16738.48 0 0 5269.5216 12.011715
|
||||
9500 16738.481 -0.00037652437 0 5269.5216 12.011692
|
||||
9550 16738.493 -0.0053156161 0 5269.5203 12.011611
|
||||
9600 16738.549 -0.02681437 0 5269.5163 12.011415
|
||||
9650 16738.765 -0.10191523 0 5269.5092 12.011013
|
||||
9700 16735.041 1.058989 0 5269.4979 12.062708
|
||||
9750 16738.013 0.1355011 0 5269.5101 11.407245
|
||||
9800 16738.512 -0.011620328 0 5269.5201 11.394974
|
||||
9850 16738.489 -0.00067270524 0 5269.5237 11.395098
|
||||
9900 16738.489 -0.00024984559 0 5269.5242 11.395085
|
||||
9950 16738.49 0 0 5269.5245 11.395076
|
||||
10000 16738.49 0 0 5269.5246 11.395075
|
||||
Loop time of 1.69721 on 4 procs for 10000 steps with 81 atoms
|
||||
|
||||
Pair time (%) = 0.0132074 (0.77818)
|
||||
Neigh time (%) = 0.023569 (1.38869)
|
||||
Comm time (%) = 1.089 (64.164)
|
||||
Outpt time (%) = 0.0916764 (5.40158)
|
||||
Other time (%) = 0.479761 (28.2676)
|
||||
|
||||
Nlocal: 20.25 ave 38 max 3 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
Nghost: 27.25 ave 48 max 13 min
|
||||
Histogram: 1 0 1 1 0 0 0 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 998
|
||||
Dangerous builds = 997
|
||||
|
|
@ -0,0 +1,305 @@
|
|||
LAMMPS (1 Oct 2006)
|
||||
# Simple rigid body system
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
read_data data.rigid
|
||||
1 by 1 by 1 processor grid
|
||||
81 atoms
|
||||
|
||||
velocity all create 100.0 4928459
|
||||
|
||||
# unconnected bodies
|
||||
|
||||
group clump1 id <> 1 9
|
||||
9 atoms in group clump1
|
||||
group clump2 id <> 10 18
|
||||
9 atoms in group clump2
|
||||
group clump3 id <> 19 27
|
||||
9 atoms in group clump3
|
||||
group clump4 id <> 28 36
|
||||
9 atoms in group clump4
|
||||
group clump5 id <> 37 45
|
||||
9 atoms in group clump5
|
||||
group clump6 id <> 46 54
|
||||
9 atoms in group clump6
|
||||
group clump7 id <> 55 63
|
||||
9 atoms in group clump7
|
||||
group clump8 id <> 64 72
|
||||
9 atoms in group clump8
|
||||
group clump9 id <> 73 81
|
||||
9 atoms in group clump9
|
||||
|
||||
fix 1 all rigid group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
|
||||
9 rigid bodies with 81 atoms
|
||||
|
||||
# 1 chain of connected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 9 18
|
||||
#group clump3 id <> 18 27
|
||||
#group clump4 id <> 27 36
|
||||
#group clump5 id <> 36 45
|
||||
#group clump6 id <> 45 54
|
||||
#group clump7 id <> 54 63
|
||||
#group clump8 id <> 63 72
|
||||
#group clump9 id <> 72 81
|
||||
|
||||
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
|
||||
|
||||
# 2 chains of connected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 9 18
|
||||
#group clump3 id <> 18 27
|
||||
#group clump4 id <> 27 36
|
||||
#group clump5 id <> 37 45
|
||||
#group clump6 id <> 45 54
|
||||
#group clump7 id <> 54 63
|
||||
#group clump8 id <> 63 72
|
||||
#group clump9 id <> 72 81
|
||||
|
||||
#fix 1 all poems group clump1 clump2 clump3 clump4
|
||||
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
|
||||
|
||||
neigh_modify exclude group clump1 clump1
|
||||
neigh_modify exclude group clump2 clump2
|
||||
neigh_modify exclude group clump3 clump3
|
||||
neigh_modify exclude group clump4 clump4
|
||||
neigh_modify exclude group clump5 clump5
|
||||
neigh_modify exclude group clump6 clump6
|
||||
neigh_modify exclude group clump7 clump7
|
||||
neigh_modify exclude group clump8 clump8
|
||||
neigh_modify exclude group clump9 clump9
|
||||
|
||||
thermo 100
|
||||
dump 1 all atom 50 dump.rigid
|
||||
|
||||
timestep 0.0001
|
||||
thermo 50
|
||||
run 10000
|
||||
Memory usage per processor = 1.42781 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 115.29439 5235.9179 0 5272.2142 -2.7403788
|
||||
50 14910.685 571.71558 0 5265.82 32.006171
|
||||
100 16298.442 136.66184 0 5267.653 16.444229
|
||||
150 16682.606 17.490511 0 5269.4219 14.900344
|
||||
200 16733.929 1.372872 0 5269.4617 14.569267
|
||||
250 16738.853 -0.15252816 0 5269.4864 14.496404
|
||||
300 16738.588 -0.055171335 0 5269.5002 14.496025
|
||||
350 16738.492 -0.017444677 0 5269.5077 14.496446
|
||||
400 16738.464 -0.0060102023 0 5269.5104 14.496618
|
||||
450 16738.455 -0.0012713351 0 5269.5124 14.496701
|
||||
500 16738.455 -0.00081068621 0 5269.5128 14.496709
|
||||
550 16738.455 -0.00083203497 0 5269.5129 14.496707
|
||||
600 16738.455 -0.00058355356 0 5269.5131 14.496709
|
||||
650 16738.455 -0.00047226704 0 5269.5131 14.496708
|
||||
700 16738.455 0 0 5269.5136 14.496713
|
||||
750 16738.455 0 0 5269.5136 14.49671
|
||||
800 16738.455 0 0 5269.5137 14.496709
|
||||
850 16738.455 0 0 5269.5137 14.49671
|
||||
900 16738.456 0 0 5269.5138 14.496713
|
||||
950 16738.462 -0.0035323872 0 5269.5122 14.496671
|
||||
1000 16738.586 -0.051135144 0 5269.5036 14.496229
|
||||
1050 16737.358 0.32995057 0 5269.4981 14.525763
|
||||
1100 16737.892 0.16210246 0 5269.4984 14.531983
|
||||
1150 16738.703 -0.089235095 0 5269.5025 14.509899
|
||||
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
|
||||
1250 16738.456 0 0 5269.514 14.510704
|
||||
1300 16738.457 0 0 5269.5141 14.510701
|
||||
1350 16738.457 0 0 5269.5141 14.510699
|
||||
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
|
||||
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
|
||||
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
|
||||
1550 16738.457 0 0 5269.5143 14.51071
|
||||
1600 16738.457 0 0 5269.5144 14.510712
|
||||
1650 16738.457 0 0 5269.5144 14.510712
|
||||
1700 16738.458 0 0 5269.5144 14.51071
|
||||
1750 16738.458 0 0 5269.5145 14.510708
|
||||
1800 16738.458 0 0 5269.5145 14.510706
|
||||
1850 16738.458 0 0 5269.5146 14.510705
|
||||
1900 16738.458 0 0 5269.5146 14.510706
|
||||
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
|
||||
2000 16738.491 -0.013255268 0 5269.5117 14.510532
|
||||
2050 16738.556 -0.0365811 0 5269.5087 14.51029
|
||||
2100 16738.633 -0.063209659 0 5269.5065 14.510219
|
||||
2150 16738.607 -0.05601761 0 5269.5055 14.510231
|
||||
2200 16738.557 -0.038423032 0 5269.5072 14.510404
|
||||
2250 16738.515 -0.023709918 0 5269.5088 14.510539
|
||||
2300 16738.489 -0.013249035 0 5269.5111 14.510621
|
||||
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
|
||||
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
|
||||
2450 16738.464 -0.0023259756 0 5269.514 14.510746
|
||||
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
|
||||
2550 16738.581 -0.044940117 0 5269.5085 14.510315
|
||||
2600 16738.427 -7.9722836e-05 0 5269.5046 14.510657
|
||||
2650 16733.017 1.7051479 0 5269.5067 14.596295
|
||||
2700 16738.761 -0.10614946 0 5269.5038 14.499584
|
||||
2750 16733.973 1.4038179 0 5269.5064 14.598107
|
||||
2800 16738.585 -0.046813448 0 5269.5076 14.511073
|
||||
2850 16738.487 -0.012558719 0 5269.5111 14.510111
|
||||
2900 16738.465 -0.0026252725 0 5269.514 14.510277
|
||||
2950 16738.476 -0.0082220764 0 5269.512 14.510223
|
||||
3000 16738.66 -0.071284779 0 5269.507 14.509758
|
||||
3050 16715.332 7.2419352 0 5269.476 14.870305
|
||||
3100 16653.226 26.818761 0 5269.5009 14.496764
|
||||
3150 16739.351 -0.30690375 0 5269.4886 13.643904
|
||||
3200 16733.238 1.6025328 0 5269.4737 12.016934
|
||||
3250 16734.374 1.2554429 0 5269.4841 11.963561
|
||||
3300 16732.156 1.9585967 0 5269.4893 12.234024
|
||||
3350 16738.655 -0.079693236 0 5269.497 12.092757
|
||||
3400 16738.543 -0.042215005 0 5269.4991 12.092809
|
||||
3450 16738.591 -0.059327511 0 5269.4972 12.092536
|
||||
3500 16738.759 -0.11761245 0 5269.4918 12.09203
|
||||
3550 16713.405 7.8460621 0 5269.4737 12.389816
|
||||
3600 16734.939 1.0821936 0 5269.4891 12.173591
|
||||
3650 16738.808 -0.13663194 0 5269.4882 12.027009
|
||||
3700 16738.602 -0.070934368 0 5269.4889 12.025288
|
||||
3750 16737.731 0.20706558 0 5269.4927 12.061948
|
||||
3800 16738.578 -0.05582043 0 5269.4965 12.035665
|
||||
3850 16738.471 -0.016307928 0 5269.5024 12.035302
|
||||
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
|
||||
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
|
||||
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
|
||||
4050 16738.437 0 0 5269.5078 12.035454
|
||||
4100 16738.437 0 0 5269.508 12.035435
|
||||
4150 16738.438 0 0 5269.5081 12.035426
|
||||
4200 16738.438 0 0 5269.5083 12.035432
|
||||
4250 16738.439 0 0 5269.5085 12.035447
|
||||
4300 16738.439 0 0 5269.5086 12.035463
|
||||
4350 16738.44 0 0 5269.5087 12.035474
|
||||
4400 16738.44 0 0 5269.5088 12.035478
|
||||
4450 16738.44 0 0 5269.5089 12.035474
|
||||
4500 16738.44 0 0 5269.509 12.035462
|
||||
4550 16738.441 0 0 5269.5092 12.035449
|
||||
4600 16738.441 0 0 5269.5093 12.035445
|
||||
4650 16738.442 0 0 5269.5095 12.035451
|
||||
4700 16738.442 0 0 5269.5096 12.03546
|
||||
4750 16738.443 0 0 5269.5097 12.035465
|
||||
4800 16738.443 0 0 5269.5098 12.035466
|
||||
4850 16738.443 0 0 5269.51 12.035463
|
||||
4900 16738.444 0 0 5269.5101 12.035456
|
||||
4950 16738.444 0 0 5269.5102 12.035447
|
||||
5000 16738.445 0 0 5269.5104 12.03544
|
||||
5050 16738.445 0 0 5269.5105 12.035442
|
||||
5100 16738.446 0 0 5269.5107 12.035455
|
||||
5150 16738.446 0 0 5269.5108 12.03547
|
||||
5200 16738.446 0 0 5269.5109 12.035479
|
||||
5250 16738.447 0 0 5269.511 12.035479
|
||||
5300 16738.447 0 0 5269.5111 12.03547
|
||||
5350 16738.447 0 0 5269.5112 12.035454
|
||||
5400 16738.448 0 0 5269.5113 12.035434
|
||||
5450 16738.448 0 0 5269.5115 12.03542
|
||||
5500 16738.449 0 0 5269.5117 12.035422
|
||||
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
|
||||
5600 16738.51 -0.021618357 0 5269.5092 12.035106
|
||||
5650 16738.622 -0.059214788 0 5269.507 12.035694
|
||||
5700 16395.28 108.06942 0 5269.5463 24.369038
|
||||
5750 16738.544 -0.033973429 0 5269.5077 12.011261
|
||||
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
|
||||
5850 16738.451 0 0 5269.5123 12.011709
|
||||
5900 16738.451 -0.0002211587 0 5269.5122 12.011687
|
||||
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
|
||||
6000 16738.452 0 0 5269.5128 12.011688
|
||||
6050 16738.453 0 0 5269.513 12.011702
|
||||
6100 16738.453 0 0 5269.5131 12.011716
|
||||
6150 16738.454 0 0 5269.5132 12.011725
|
||||
6200 16738.454 0 0 5269.5133 12.011728
|
||||
6250 16738.454 0 0 5269.5134 12.011723
|
||||
6300 16738.455 0 0 5269.5135 12.011712
|
||||
6350 16738.455 0 0 5269.5137 12.0117
|
||||
6400 16738.456 0 0 5269.5138 12.011697
|
||||
6450 16738.456 0 0 5269.514 12.011704
|
||||
6500 16738.456 0 0 5269.5141 12.011714
|
||||
6550 16738.457 0 0 5269.5142 12.011719
|
||||
6600 16738.457 0 0 5269.5143 12.011718
|
||||
6650 16738.458 0 0 5269.5144 12.011713
|
||||
6700 16738.458 0 0 5269.5146 12.011705
|
||||
6750 16738.459 0 0 5269.5147 12.011696
|
||||
6800 16738.459 0 0 5269.5149 12.01169
|
||||
6850 16738.46 0 0 5269.515 12.011695
|
||||
6900 16738.46 0 0 5269.5152 12.01171
|
||||
6950 16738.46 0 0 5269.5153 12.011726
|
||||
7000 16738.461 0 0 5269.5154 12.011736
|
||||
7050 16738.461 0 0 5269.5155 12.011737
|
||||
7100 16738.461 0 0 5269.5155 12.011728
|
||||
7150 16738.461 0 0 5269.5156 12.011712
|
||||
7200 16738.462 0 0 5269.5158 12.011691
|
||||
7250 16738.463 0 0 5269.516 12.011676
|
||||
7300 16738.463 0 0 5269.5162 12.011677
|
||||
7350 16738.464 0 0 5269.5164 12.011693
|
||||
7400 16738.464 0 0 5269.5165 12.011713
|
||||
7450 16738.465 0 0 5269.5166 12.011729
|
||||
7500 16738.465 0 0 5269.5167 12.011736
|
||||
7550 16738.465 0 0 5269.5168 12.011734
|
||||
7600 16738.465 0 0 5269.5168 12.011722
|
||||
7650 16738.466 0 0 5269.517 12.011704
|
||||
7700 16738.466 0 0 5269.5171 12.011687
|
||||
7750 16738.467 0 0 5269.5173 12.011681
|
||||
7800 16738.467 0 0 5269.5175 12.011687
|
||||
7850 16738.468 0 0 5269.5176 12.0117
|
||||
7900 16738.468 0 0 5269.5178 12.011712
|
||||
7950 16738.469 0 0 5269.5179 12.011721
|
||||
8000 16738.469 0 0 5269.518 12.011724
|
||||
8050 16738.469 0 0 5269.5181 12.01172
|
||||
8100 16738.47 0 0 5269.5182 12.011709
|
||||
8150 16738.47 0 0 5269.5183 12.0117
|
||||
8200 16738.47 0 0 5269.5185 12.0117
|
||||
8250 16738.471 0 0 5269.5186 12.011709
|
||||
8300 16738.471 0 0 5269.5187 12.011719
|
||||
8350 16738.472 0 0 5269.5189 12.011723
|
||||
8400 16738.472 0 0 5269.519 12.01172
|
||||
8450 16738.473 -0.00039690665 0 5269.5189 12.011706
|
||||
8500 16738.481 -0.0034646803 0 5269.5182 12.011643
|
||||
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
|
||||
8600 16738.474 -0.00076532811 0 5269.5189 12.011681
|
||||
8650 16738.474 0 0 5269.5197 12.011699
|
||||
8700 16738.475 0 0 5269.5199 12.011715
|
||||
8750 16738.475 0 0 5269.52 12.011732
|
||||
8800 16738.475 0 0 5269.52 12.011743
|
||||
8850 16738.476 0 0 5269.5201 12.011744
|
||||
8900 16738.476 0 0 5269.5202 12.011735
|
||||
8950 16738.476 0 0 5269.5203 12.011719
|
||||
9000 16738.477 0 0 5269.5205 12.011698
|
||||
9050 16738.477 0 0 5269.5206 12.011683
|
||||
9100 16738.478 0 0 5269.5208 12.011684
|
||||
9150 16738.479 0 0 5269.521 12.011701
|
||||
9200 16738.479 0 0 5269.5212 12.011722
|
||||
9250 16738.479 0 0 5269.5213 12.011738
|
||||
9300 16738.48 0 0 5269.5214 12.011746
|
||||
9350 16738.48 0 0 5269.5214 12.011744
|
||||
9400 16738.48 0 0 5269.5215 12.011732
|
||||
9450 16738.48 0 0 5269.5216 12.011715
|
||||
9500 16738.481 -0.00037652435 0 5269.5216 12.011692
|
||||
9550 16738.493 -0.0053156161 0 5269.5203 12.011611
|
||||
9600 16738.549 -0.026814369 0 5269.5163 12.011415
|
||||
9650 16738.765 -0.10191523 0 5269.5092 12.011013
|
||||
9700 16735.041 1.0589887 0 5269.4979 12.062708
|
||||
9750 16738.013 0.1355012 0 5269.5101 11.407246
|
||||
9800 16738.512 -0.011620328 0 5269.5201 11.394974
|
||||
9850 16738.489 -0.00067270518 0 5269.5237 11.395098
|
||||
9900 16738.489 -0.00024984554 0 5269.5242 11.395085
|
||||
9950 16738.49 0 0 5269.5245 11.395076
|
||||
10000 16738.49 0 0 5269.5246 11.395075
|
||||
Loop time of 0.887339 on 1 procs for 10000 steps with 81 atoms
|
||||
|
||||
Pair time (%) = 0.076566 (8.62872)
|
||||
Neigh time (%) = 0.130989 (14.762)
|
||||
Comm time (%) = 0.105157 (11.8508)
|
||||
Outpt time (%) = 0.116808 (13.1639)
|
||||
Other time (%) = 0.457819 (51.5946)
|
||||
|
||||
Nlocal: 81 ave 81 max 81 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 84 ave 84 max 84 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 998
|
||||
Dangerous builds = 997
|
||||
|
|
@ -0,0 +1,305 @@
|
|||
LAMMPS (1 Oct 2006)
|
||||
# Simple rigid body system
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
read_data data.rigid
|
||||
1 by 2 by 2 processor grid
|
||||
81 atoms
|
||||
|
||||
velocity all create 100.0 4928459
|
||||
|
||||
# unconnected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 10 18
|
||||
#group clump3 id <> 19 27
|
||||
#group clump4 id <> 28 36
|
||||
#group clump5 id <> 37 45
|
||||
#group clump6 id <> 46 54
|
||||
#group clump7 id <> 55 63
|
||||
#group clump8 id <> 64 72
|
||||
#group clump9 id <> 73 81
|
||||
|
||||
#fix 1 all rigid group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
|
||||
|
||||
# 1 chain of connected bodies
|
||||
|
||||
group clump1 id <> 1 9
|
||||
9 atoms in group clump1
|
||||
group clump2 id <> 9 18
|
||||
10 atoms in group clump2
|
||||
group clump3 id <> 18 27
|
||||
10 atoms in group clump3
|
||||
group clump4 id <> 27 36
|
||||
10 atoms in group clump4
|
||||
group clump5 id <> 36 45
|
||||
10 atoms in group clump5
|
||||
group clump6 id <> 45 54
|
||||
10 atoms in group clump6
|
||||
group clump7 id <> 54 63
|
||||
10 atoms in group clump7
|
||||
group clump8 id <> 63 72
|
||||
10 atoms in group clump8
|
||||
group clump9 id <> 72 81
|
||||
10 atoms in group clump9
|
||||
|
||||
fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
|
||||
1 clusters, 9 bodies, 8 joints, 81 atoms
|
||||
|
||||
# 2 chains of connected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 9 18
|
||||
#group clump3 id <> 18 27
|
||||
#group clump4 id <> 27 36
|
||||
#group clump5 id <> 37 45
|
||||
#group clump6 id <> 45 54
|
||||
#group clump7 id <> 54 63
|
||||
#group clump8 id <> 63 72
|
||||
#group clump9 id <> 72 81
|
||||
|
||||
#fix 1 all poems group clump1 clump2 clump3 clump4
|
||||
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
|
||||
|
||||
neigh_modify exclude group clump1 clump1
|
||||
neigh_modify exclude group clump2 clump2
|
||||
neigh_modify exclude group clump3 clump3
|
||||
neigh_modify exclude group clump4 clump4
|
||||
neigh_modify exclude group clump5 clump5
|
||||
neigh_modify exclude group clump6 clump6
|
||||
neigh_modify exclude group clump7 clump7
|
||||
neigh_modify exclude group clump8 clump8
|
||||
neigh_modify exclude group clump9 clump9
|
||||
|
||||
thermo 100
|
||||
dump 1 all atom 50 dump.rigid
|
||||
|
||||
timestep 0.0001
|
||||
thermo 50
|
||||
run 10000
|
||||
Memory usage per processor = 1.4946 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 217.7783 3430.3907 0 3466.6871 -2.7403788
|
||||
50 13679.637 1404.2468 0 3684.1863 12.446066
|
||||
100 16777.225 888.87665 0 3685.0808 -31.828677
|
||||
150 19595.365 418.45042 0 3684.3446 40.709078
|
||||
200 18524.188 596.47273 0 3683.8375 -0.8159371
|
||||
250 21015.789 180.96521 0 3683.5967 -10.042469
|
||||
300 20785.513 219.25314 0 3683.5053 2.6452719
|
||||
350 21072.46 171.2554 0 3683.3321 7.0609024
|
||||
400 19956.414 356.36381 0 3682.4328 19.320259
|
||||
450 20724.42 227.73284 0 3681.8028 8.1259249
|
||||
500 20152.578 322.71466 0 3681.4777 5.4929878
|
||||
550 20017.022 345.29701 0 3681.4673 5.4661666
|
||||
600 17897.743 698.72196 0 3681.6791 3.2854742
|
||||
650 17297.758 796.60256 0 3679.5623 15.191113
|
||||
700 18581.934 584.29715 0 3681.2861 5.1588289
|
||||
750 21774.158 52.821062 0 3681.8474 -10.775664
|
||||
800 21604.055 81.188546 0 3681.8644 -3.2045743
|
||||
850 17821.483 711.53827 0 3681.7854 7.4384276
|
||||
900 21033.292 175.98127 0 3681.5299 -16.345167
|
||||
950 20968.166 186.59847 0 3681.2929 -2.330456
|
||||
1000 20490.66 266.19375 0 3681.3037 11.787983
|
||||
1050 20222.396 310.94072 0 3681.34 -8.3459539
|
||||
1100 21321.687 127.61533 0 3681.2299 -1.2184718
|
||||
1150 20849.582 206.01695 0 3680.9472 -0.86699164
|
||||
1200 21815.003 45.317416 0 3681.1512 1.5988314
|
||||
1250 18655.437 572.41453 0 3681.654 10.064076
|
||||
1300 20780.781 217.36505 0 3680.8286 6.0538621
|
||||
1350 20558.972 254.3648 0 3680.8601 -3.6773984
|
||||
1400 21485.029 99.812952 0 3680.6511 -16.185471
|
||||
1450 21771.108 52.159597 0 3680.6775 -2.4756679
|
||||
1500 21520.948 93.503946 0 3680.3286 2.1023577
|
||||
1550 21351.418 121.68139 0 3680.2511 5.5159972
|
||||
1600 20778.805 216.92173 0 3680.0559 15.089183
|
||||
1650 21477.639 100.21821 0 3679.8247 -1.1045931
|
||||
1700 18501.343 596.4785 0 3680.0357 -15.679631
|
||||
1750 18563.643 587.3477 0 3681.2882 33.53217
|
||||
1800 19110.189 494.82277 0 3679.8543 18.024037
|
||||
1850 21364.196 119.23462 0 3679.9339 2.529149
|
||||
1900 20146.64 322.14631 0 3679.9197 5.7311673
|
||||
1950 20692.671 231.25338 0 3680.0319 4.2977687
|
||||
2000 20943.903 189.11238 0 3679.7629 -22.645639
|
||||
2050 19668.148 401.81475 0 3679.8394 3.6256063
|
||||
2100 20280.572 299.73979 0 3679.8351 7.4809366
|
||||
2150 19182.127 483.47805 0 3680.4992 22.615355
|
||||
2200 21299.767 130.77158 0 3680.7327 4.7114063
|
||||
2250 20487.762 266.50325 0 3681.1302 -8.6408345
|
||||
2300 18655.048 571.92772 0 3681.1023 -5.266975
|
||||
2350 21512.632 95.763771 0 3681.2025 -9.3526622
|
||||
2400 21467.744 103.31997 0 3681.2773 -29.599491
|
||||
2450 20097.033 332.78544 0 3682.291 35.886632
|
||||
2500 20761.514 222.1498 0 3682.4021 -12.52654
|
||||
2550 20410.179 280.57555 0 3682.272 -22.280218
|
||||
2600 21469.95 103.95758 0 3682.2826 -10.039024
|
||||
2650 20711.858 230.38535 0 3682.3616 5.3554349
|
||||
2700 18584.052 585.19766 0 3682.5397 21.807604
|
||||
2750 20511.368 263.53176 0 3682.0931 -4.7085799
|
||||
2800 20592.991 249.9677 0 3682.1328 -6.5329985
|
||||
2850 17078.939 835.43473 0 3681.9245 16.780854
|
||||
2900 19704.624 397.94471 0 3682.0488 -0.87435077
|
||||
2950 19282.968 468.43149 0 3682.2595 7.0271622
|
||||
3000 20552.037 256.84085 0 3682.1804 -2.9282943
|
||||
3050 20934.711 193.08576 0 3682.2043 3.8942358
|
||||
3100 21703.768 64.8113 0 3682.106 0.063237279
|
||||
3150 18722.82 561.7019 0 3682.172 -1.4520091
|
||||
3200 18284.044 634.53317 0 3681.8739 6.3415584
|
||||
3250 21255.255 139.48628 0 3682.0288 2.6455564
|
||||
3300 20558.956 255.77083 0 3682.2636 -3.9152408
|
||||
3350 20373.309 286.62048 0 3682.1719 4.5400971
|
||||
3400 20618.175 245.81811 0 3682.1806 5.7100283
|
||||
3450 19473.455 436.70128 0 3682.2771 11.870427
|
||||
3500 18903.565 531.91776 0 3682.5119 -9.3476901
|
||||
3550 21030.252 177.18619 0 3682.2282 -14.260278
|
||||
3600 19942.611 357.98433 0 3681.7528 11.183792
|
||||
3650 20388.541 283.86156 0 3681.9518 -8.2736257
|
||||
3700 20724.985 226.58383 0 3680.748 -13.429981
|
||||
3750 21586.121 84.456333 0 3682.1432 -2.7515188
|
||||
3800 21478.159 102.70951 0 3682.4027 -2.5874121
|
||||
3850 18107.437 665.11995 0 3683.0262 11.062091
|
||||
3900 19602.682 415.48105 0 3682.5947 17.867347
|
||||
3950 19208.319 480.73213 0 3682.1186 0.55405471
|
||||
4000 20700.944 232.01332 0 3682.1706 4.2790356
|
||||
4050 18241.028 641.65227 0 3681.8236 14.819974
|
||||
4100 16330.098 961.03753 0 3682.7206 -8.1781858
|
||||
4150 20507.949 263.34806 0 3681.3396 -5.2032219
|
||||
4200 21620.592 79.051795 0 3682.4838 -11.796063
|
||||
4250 20841.315 209.02052 0 3682.573 -5.781042
|
||||
4300 21378.616 119.44038 0 3682.5431 -3.0055326
|
||||
4350 21391.4 116.89963 0 3682.133 1.2620601
|
||||
4400 20092.07 333.32793 0 3682.0062 11.429014
|
||||
4450 19315.512 461.83055 0 3681.0825 1.3462703
|
||||
4500 20839.628 208.21416 0 3681.4855 4.709479
|
||||
4550 14522.388 1263.1063 0 3683.5043 -20.816537
|
||||
4600 21284.581 134.21556 0 3681.6457 -4.8183612
|
||||
4650 20126.198 327.1439 0 3681.5103 -5.5395838
|
||||
4700 21764.236 54.44036 0 3681.813 3.4863656
|
||||
4750 21095.836 165.90339 0 3681.876 6.1541649
|
||||
4800 20619.747 245.94729 0 3682.5718 2.5595916
|
||||
4850 20763.177 222.12286 0 3682.6523 -8.6266804
|
||||
4900 20537.14 259.67462 0 3682.5313 -15.421035
|
||||
4950 21422.584 112.253 0 3682.6837 -1.4727022
|
||||
5000 16257.411 972.68578 0 3682.2542 2.3147962
|
||||
5050 19857.171 373.56369 0 3683.0922 -15.300375
|
||||
5100 15635.264 1076.6903 0 3682.5676 36.8946
|
||||
5150 21553.911 90.645813 0 3682.9642 1.5400926
|
||||
5200 21559.956 89.704166 0 3683.0302 2.0981184
|
||||
5250 19117.968 496.85067 0 3683.1787 29.282193
|
||||
5300 21330.342 127.91971 0 3682.9767 2.4699055
|
||||
5350 21829.625 44.595903 0 3682.8667 -11.606558
|
||||
5400 21789.041 51.183465 0 3682.6902 -3.8674971
|
||||
5450 19143.18 491.7975 0 3682.3275 -0.6880826
|
||||
5500 19773.011 386.55132 0 3682.0532 -0.39276859
|
||||
5550 21170.746 153.72971 0 3682.1873 -0.039885143
|
||||
5600 20634.546 243.05851 0 3682.1496 -10.510731
|
||||
5650 18940.14 525.80138 0 3682.4913 -8.4026702
|
||||
5700 18137.059 658.45807 0 3681.3012 1.8086854
|
||||
5750 18402.492 614.81681 0 3681.8988 18.121726
|
||||
5800 15725.316 1060.3153 0 3681.2013 32.3919
|
||||
5850 21350.969 122.71085 0 3681.2057 1.6244497
|
||||
5900 20596.373 248.09794 0 3680.8268 -10.287271
|
||||
5950 19586.195 416.65918 0 3681.0251 7.1327258
|
||||
6000 20566.394 252.63425 0 3680.3666 9.3309712
|
||||
6050 18063.299 667.31886 0 3677.8687 -10.246241
|
||||
6100 17305.121 797.2545 0 3681.4414 14.554146
|
||||
6150 19696.433 395.50284 0 3678.2416 4.1990406
|
||||
6200 20908.19 195.69314 0 3680.3915 -9.0297611
|
||||
6250 20767.885 219.35847 0 3680.6727 -5.4239147
|
||||
6300 20271.076 302.48547 0 3680.9981 7.5881011
|
||||
6350 21510.748 96.348849 0 3681.4736 -0.28663642
|
||||
6400 21731.982 60.504382 0 3682.5014 -3.5673143
|
||||
6450 19495.709 434.28569 0 3683.5706 4.7979099
|
||||
6500 18668.623 571.92754 0 3683.3647 1.5185672
|
||||
6550 16004.711 1016.2903 0 3683.7422 8.1972253
|
||||
6600 20629.015 244.44595 0 3682.615 3.8351386
|
||||
6650 21647.055 75.493996 0 3683.3365 -0.10989704
|
||||
6700 19793.226 384.41402 0 3683.2851 7.7597696
|
||||
6750 20441.55 275.94512 0 3682.8702 3.6110747
|
||||
6800 21623.66 79.350309 0 3683.2936 -6.3458991
|
||||
6850 21644.786 75.922535 0 3683.3869 -22.166786
|
||||
6900 18150.965 657.76117 0 3682.9219 -14.903565
|
||||
6950 21192.162 150.83369 0 3682.8607 -7.6579085
|
||||
7000 20481.657 268.91866 0 3682.5281 -10.728925
|
||||
7050 19265.165 471.58584 0 3682.4467 -3.1547895
|
||||
7100 20241.165 308.92052 0 3682.4479 10.770847
|
||||
7150 20883.514 201.92495 0 3682.5106 12.276271
|
||||
7200 20675.066 236.51208 0 3682.3564 4.0653811
|
||||
7250 21464.099 105.01329 0 3682.3631 -4.2891409
|
||||
7300 19279.539 469.63353 0 3682.89 19.415276
|
||||
7350 20266.489 304.68631 0 3682.4344 -0.15439874
|
||||
7400 18978.717 519.39579 0 3682.5153 19.185958
|
||||
7450 20816.852 213.20924 0 3682.6845 18.435432
|
||||
7500 20655.662 240.16805 0 3682.7785 -4.4996568
|
||||
7550 19061.292 506.0418 0 3682.9238 -1.7545473
|
||||
7600 20564.235 255.25251 0 3682.625 -5.3903401
|
||||
7650 21273.693 137.41485 0 3683.0303 -6.9034645
|
||||
7700 20999.106 183.2458 0 3683.0968 -5.9941062
|
||||
7750 18886.194 534.2212 0 3681.9202 5.9891004
|
||||
7800 20327.925 294.85306 0 3682.8405 -2.5902629
|
||||
7850 19533.408 427.77688 0 3683.3448 -4.9977086
|
||||
7900 20973.609 187.37509 0 3682.9765 0.11759117
|
||||
7950 18164.635 654.02996 0 3681.4691 16.402128
|
||||
8000 20938.276 193.48738 0 3683.2 -5.9311301
|
||||
8050 20819.498 213.21616 0 3683.1324 1.3392987
|
||||
8100 19553.561 424.27379 0 3683.2006 -2.5040641
|
||||
8150 17524.659 759.26187 0 3680.0384 -37.279253
|
||||
8200 21104.916 165.88837 0 3683.3744 -3.8952964
|
||||
8250 19614.453 414.27984 0 3683.3553 -2.9352541
|
||||
8300 13365.081 1457.0212 0 3684.5347 100.4608
|
||||
8350 20920.925 197.0494 0 3683.8702 -11.661629
|
||||
8400 19724.857 396.41163 0 3683.8878 0.74045509
|
||||
8450 21751.144 58.967512 0 3684.1583 -4.095218
|
||||
8500 21283.998 136.40954 0 3683.7425 -5.4781843
|
||||
8550 19255.08 474.01022 0 3683.1903 0.61248835
|
||||
8600 20786.099 219.06078 0 3683.4107 9.7864578
|
||||
8650 20801.493 216.74923 0 3683.6647 7.1280503
|
||||
8700 19893.433 368.11056 0 3683.6827 -9.5312543
|
||||
8750 21072.739 171.47966 0 3683.6028 -17.222136
|
||||
8800 18791.068 551.89466 0 3683.7394 -13.425301
|
||||
8850 20323.723 296.58355 0 3683.8708 1.2544121
|
||||
8900 19160.522 487.13728 0 3680.5575 7.5449432
|
||||
8950 20247.9 309.46468 0 3684.1146 -11.397923
|
||||
9000 20721.089 230.36979 0 3683.8846 11.354348
|
||||
9050 21798.873 51.104409 0 3684.25 -9.645863
|
||||
9100 21093.423 168.78605 0 3684.3565 -1.2127948
|
||||
9150 20954.177 191.65626 0 3684.0191 0.61911701
|
||||
9200 17054.376 842.546 0 3684.942 41.714389
|
||||
9250 19253.515 475.58375 0 3684.5029 13.186069
|
||||
9300 21681.124 71.036838 0 3684.5575 -4.139581
|
||||
9350 21796.739 51.725799 0 3684.5157 -8.5902286
|
||||
9400 21631.679 79.362722 0 3684.6425 -8.7541514
|
||||
9450 18537.758 595.38459 0 3685.011 -6.2719267
|
||||
9500 17152.352 824.77642 0 3683.5018 46.593524
|
||||
9550 20928.938 196.82808 0 3684.9843 -1.5521829
|
||||
9600 15991.62 1020.98 0 3686.25 -3.8314742
|
||||
9650 19629.68 414.15513 0 3685.7685 32.867017
|
||||
9700 20900.569 201.75492 0 3685.183 6.1694301
|
||||
9750 17072.588 841.426 0 3686.8573 -4.0468499
|
||||
9800 21939.049 29.032402 0 3685.5406 -9.1896877
|
||||
9850 21261.674 141.7745 0 3685.3869 -13.02325
|
||||
9900 19393.195 452.88226 0 3685.0814 1.4304574
|
||||
9950 17226.824 814.05288 0 3685.1902 19.353254
|
||||
10000 20630.15 245.97222 0 3684.3306 0.61583151
|
||||
Loop time of 16.5532 on 4 procs for 10000 steps with 81 atoms
|
||||
|
||||
Pair time (%) = 0.12595 (0.760878)
|
||||
Neigh time (%) = 0.0543506 (0.328338)
|
||||
Comm time (%) = 1.67897 (10.1428)
|
||||
Outpt time (%) = 0.0939289 (0.567436)
|
||||
Other time (%) = 14.6 (88.2005)
|
||||
|
||||
Nlocal: 20.25 ave 74 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 42 ave 90 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
Neighs: 211.25 ave 769 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 845
|
||||
Ave neighs/atom = 10.4321
|
||||
Neighbor list builds = 991
|
||||
Dangerous builds = 929
|
||||
|
|
@ -0,0 +1,305 @@
|
|||
LAMMPS (1 Oct 2006)
|
||||
# Simple rigid body system
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
read_data data.rigid
|
||||
1 by 1 by 1 processor grid
|
||||
81 atoms
|
||||
|
||||
velocity all create 100.0 4928459
|
||||
|
||||
# unconnected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 10 18
|
||||
#group clump3 id <> 19 27
|
||||
#group clump4 id <> 28 36
|
||||
#group clump5 id <> 37 45
|
||||
#group clump6 id <> 46 54
|
||||
#group clump7 id <> 55 63
|
||||
#group clump8 id <> 64 72
|
||||
#group clump9 id <> 73 81
|
||||
|
||||
#fix 1 all rigid group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
|
||||
|
||||
# 1 chain of connected bodies
|
||||
|
||||
group clump1 id <> 1 9
|
||||
9 atoms in group clump1
|
||||
group clump2 id <> 9 18
|
||||
10 atoms in group clump2
|
||||
group clump3 id <> 18 27
|
||||
10 atoms in group clump3
|
||||
group clump4 id <> 27 36
|
||||
10 atoms in group clump4
|
||||
group clump5 id <> 36 45
|
||||
10 atoms in group clump5
|
||||
group clump6 id <> 45 54
|
||||
10 atoms in group clump6
|
||||
group clump7 id <> 54 63
|
||||
10 atoms in group clump7
|
||||
group clump8 id <> 63 72
|
||||
10 atoms in group clump8
|
||||
group clump9 id <> 72 81
|
||||
10 atoms in group clump9
|
||||
|
||||
fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
|
||||
1 clusters, 9 bodies, 8 joints, 81 atoms
|
||||
|
||||
# 2 chains of connected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 9 18
|
||||
#group clump3 id <> 18 27
|
||||
#group clump4 id <> 27 36
|
||||
#group clump5 id <> 37 45
|
||||
#group clump6 id <> 45 54
|
||||
#group clump7 id <> 54 63
|
||||
#group clump8 id <> 63 72
|
||||
#group clump9 id <> 72 81
|
||||
|
||||
#fix 1 all poems group clump1 clump2 clump3 clump4
|
||||
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
|
||||
|
||||
neigh_modify exclude group clump1 clump1
|
||||
neigh_modify exclude group clump2 clump2
|
||||
neigh_modify exclude group clump3 clump3
|
||||
neigh_modify exclude group clump4 clump4
|
||||
neigh_modify exclude group clump5 clump5
|
||||
neigh_modify exclude group clump6 clump6
|
||||
neigh_modify exclude group clump7 clump7
|
||||
neigh_modify exclude group clump8 clump8
|
||||
neigh_modify exclude group clump9 clump9
|
||||
|
||||
thermo 100
|
||||
dump 1 all atom 50 dump.rigid
|
||||
|
||||
timestep 0.0001
|
||||
thermo 50
|
||||
run 10000
|
||||
Memory usage per processor = 1.50473 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 217.7783 3430.3907 0 3466.6871 -2.7403788
|
||||
50 13679.637 1404.2468 0 3684.1863 12.446066
|
||||
100 16777.225 888.87665 0 3685.0808 -31.828677
|
||||
150 19595.365 418.45042 0 3684.3446 40.709078
|
||||
200 18524.188 596.47273 0 3683.8375 -0.8159371
|
||||
250 21015.789 180.96521 0 3683.5967 -10.042469
|
||||
300 20785.513 219.25314 0 3683.5053 2.6452719
|
||||
350 21072.46 171.2554 0 3683.3321 7.0609024
|
||||
400 19956.414 356.36381 0 3682.4328 19.320259
|
||||
450 20724.42 227.73284 0 3681.8028 8.1259249
|
||||
500 20152.578 322.71466 0 3681.4777 5.4929878
|
||||
550 20017.022 345.29701 0 3681.4673 5.4661666
|
||||
600 17897.743 698.72196 0 3681.6791 3.2854742
|
||||
650 17297.758 796.60256 0 3679.5623 15.191113
|
||||
700 18581.934 584.29715 0 3681.2861 5.1588289
|
||||
750 21774.158 52.821062 0 3681.8474 -10.775664
|
||||
800 21604.055 81.188546 0 3681.8644 -3.2045743
|
||||
850 17821.483 711.53827 0 3681.7854 7.4384278
|
||||
900 21033.292 175.98127 0 3681.5299 -16.345167
|
||||
950 20968.166 186.59847 0 3681.2929 -2.330456
|
||||
1000 20490.66 266.19375 0 3681.3037 11.787983
|
||||
1050 20222.396 310.94072 0 3681.34 -8.3459539
|
||||
1100 21321.687 127.61533 0 3681.2299 -1.2184717
|
||||
1150 20849.582 206.01695 0 3680.9472 -0.86699147
|
||||
1200 21815.003 45.317414 0 3681.1512 1.5988314
|
||||
1250 18655.437 572.41453 0 3681.654 10.064078
|
||||
1300 20780.781 217.36507 0 3680.8286 6.0538618
|
||||
1350 20558.971 254.36483 0 3680.8601 -3.6773945
|
||||
1400 21485.029 99.812915 0 3680.6511 -16.185473
|
||||
1450 21771.107 52.159616 0 3680.6775 -2.4756671
|
||||
1500 21520.948 93.503919 0 3680.3286 2.1023577
|
||||
1550 21351.418 121.68136 0 3680.2511 5.5159939
|
||||
1600 20778.805 216.92179 0 3680.0559 15.08919
|
||||
1650 21477.638 100.21841 0 3679.8247 -1.1045676
|
||||
1700 18501.338 596.47934 0 3680.0357 -15.679693
|
||||
1750 18563.641 587.34802 0 3681.2882 33.532224
|
||||
1800 19110.184 494.82361 0 3679.8543 18.024052
|
||||
1850 21364.189 119.23567 0 3679.9339 2.5290982
|
||||
1900 20146.623 322.14928 0 3679.9197 5.7313631
|
||||
1950 20692.672 231.25329 0 3680.0319 4.2977763
|
||||
2000 20943.904 189.11224 0 3679.7629 -22.644967
|
||||
2050 19668.032 401.83413 0 3679.8394 3.6250579
|
||||
2100 20280.405 299.76781 0 3679.8353 7.4807458
|
||||
2150 19181.776 483.53587 0 3680.4986 22.622025
|
||||
2200 21300.275 130.68616 0 3680.732 4.7099237
|
||||
2250 20486.714 266.67751 0 3681.1298 -8.6469998
|
||||
2300 18652.596 572.33559 0 3681.1016 -5.2628292
|
||||
2350 21513.777 95.572407 0 3681.202 -9.3648592
|
||||
2400 21465.849 103.63471 0 3681.2763 -29.550454
|
||||
2450 20100.961 332.12793 0 3682.2881 35.70449
|
||||
2500 20765.206 221.53187 0 3682.3996 -12.452833
|
||||
2550 20442.965 275.09622 0 3682.2571 -22.450229
|
||||
2600 21465.612 104.67793 0 3682.2799 -10.089769
|
||||
2650 20840.301 208.97723 0 3682.3607 5.0962323
|
||||
2700 18566.291 588.29119 0 3682.6731 22.314898
|
||||
2750 20859.619 205.61533 0 3682.2184 -8.4111045
|
||||
2800 21152.619 156.74913 0 3682.1856 -7.0841069
|
||||
2850 17034.124 843.41557 0 3682.4362 31.940811
|
||||
2900 19433.377 443.20884 0 3682.105 8.154109
|
||||
2950 20759.601 222.07863 0 3682.0121 0.94860156
|
||||
3000 20639.898 242.09747 0 3682.0805 -5.0441986
|
||||
3050 18165.856 654.36056 0 3682.0032 2.0390617
|
||||
3100 20352.11 290.03669 0 3682.055 -6.4787936
|
||||
3150 20081.761 335.00558 0 3681.9657 12.403377
|
||||
3200 20312.335 296.00002 0 3681.3892 6.6521722
|
||||
3250 20715.141 228.97633 0 3681.4998 0.29254419
|
||||
3300 21033.583 176.05884 0 3681.656 -0.82749027
|
||||
3350 20555.686 255.51202 0 3681.4596 -2.6224778
|
||||
3400 20517.425 261.8331 0 3681.404 5.7965799
|
||||
3450 21550.686 89.629485 0 3681.4104 1.7369192
|
||||
3500 18213.776 648.60728 0 3684.2366 25.179084
|
||||
3550 20181.817 317.95514 0 3681.5914 12.030205
|
||||
3600 20064.929 336.99155 0 3681.1464 0.46703252
|
||||
3650 20548.763 256.74258 0 3681.5364 5.6316258
|
||||
3700 21695.436 65.821167 0 3681.7272 -4.046094
|
||||
3750 20339.586 291.86983 0 3681.8009 -6.9843488
|
||||
3800 20556.293 255.92096 0 3681.9698 -2.4803781
|
||||
3850 20446.56 274.11342 0 3681.8735 -4.7609085
|
||||
3900 19011.276 513.44779 0 3681.9938 17.583808
|
||||
3950 20584.829 250.52631 0 3681.3311 2.2444895
|
||||
4000 20971.029 185.41558 0 3680.5871 -20.990511
|
||||
4050 18377.385 617.09077 0 3679.9882 7.178804
|
||||
4100 16844.266 873.0443 0 3680.4219 8.8851101
|
||||
4150 21182.287 149.12309 0 3679.5043 -5.7838368
|
||||
4200 20081.816 332.50466 0 3679.4741 11.141881
|
||||
4250 16039.426 1006.3467 0 3679.5845 19.421993
|
||||
4300 21194.532 147.15003 0 3679.572 6.1066469
|
||||
4350 18629.518 575.11052 0 3680.0302 -2.7680889
|
||||
4400 20141.896 323.11764 0 3680.1004 -12.100591
|
||||
4450 19515.022 427.59265 0 3680.0963 -11.941524
|
||||
4500 20713.779 227.58503 0 3679.8816 -2.0762411
|
||||
4550 20534.825 257.13203 0 3679.6029 3.9506072
|
||||
4600 16110.778 995.49492 0 3680.6245 39.113403
|
||||
4650 20050.377 337.60184 0 3679.3313 4.0339243
|
||||
4700 20714.3 226.37364 0 3678.757 1.6928839
|
||||
4750 20397.838 278.68649 0 3678.3261 0.72631759
|
||||
4800 21090.67 163.3683 0 3678.4799 -7.4766616
|
||||
4850 20410.173 276.47646 0 3678.1719 -0.48404227
|
||||
4900 17341.87 787.80944 0 3678.1212 4.7714063
|
||||
4950 20335.7 289.09005 0 3678.3734 -10.795568
|
||||
5000 20001.497 344.2494 0 3677.8322 14.312823
|
||||
5050 17359.581 784.91275 0 3678.1762 -15.0609
|
||||
5100 17595.237 745.73589 0 3678.2753 -8.3672887
|
||||
5150 17097.012 827.91859 0 3677.4206 15.446196
|
||||
5200 18757.137 552.19192 0 3678.3814 -6.9635082
|
||||
5250 20388.016 279.39834 0 3677.401 20.142181
|
||||
5300 19965.35 350.31245 0 3677.8707 -17.821737
|
||||
5350 18436.118 605.83431 0 3678.5207 0.84914232
|
||||
5400 20415.986 276.61546 0 3679.2799 -0.0037894847
|
||||
5450 20973.245 184.18908 0 3679.73 1.5256563
|
||||
5500 21320.183 126.74576 0 3680.1096 2.2287329
|
||||
5550 20328.455 292.4549 0 3680.5307 4.674135
|
||||
5600 19512.862 428.45854 0 3680.6021 2.2858232
|
||||
5650 15118.355 1162.6262 0 3682.352 66.775105
|
||||
5700 21062.257 171.98221 0 3682.3583 -0.20268203
|
||||
5750 21441.233 109.32963 0 3682.8684 -12.340852
|
||||
5800 21012.806 181.33239 0 3683.4666 -7.1699728
|
||||
5850 21023.089 179.80114 0 3683.6494 3.8101095
|
||||
5900 21015.077 181.14388 0 3683.6567 -1.176308
|
||||
5950 18343.926 626.46055 0 3683.7815 15.79278
|
||||
6000 20984.465 186.52409 0 3683.935 -6.1829013
|
||||
6050 20941.64 193.97543 0 3684.2488 1.2909073
|
||||
6100 19546.675 426.86545 0 3684.6447 -0.41477554
|
||||
6150 21264.032 140.55982 0 3684.5651 -4.953571
|
||||
6200 20343.321 293.92487 0 3684.4784 -4.8781976
|
||||
6250 20109.575 333.08805 0 3684.6839 -0.23986631
|
||||
6300 19589.511 419.53578 0 3684.4543 18.387721
|
||||
6350 20331.681 295.43346 0 3684.0469 -2.6072047
|
||||
6400 21210.3 148.28185 0 3683.3319 -13.224448
|
||||
6450 19636.964 407.42287 0 3680.2503 26.945373
|
||||
6500 21158.461 156.82542 0 3683.2355 -5.558554
|
||||
6550 21937.478 26.931715 0 3683.1781 -5.8148489
|
||||
6600 20716.445 229.76043 0 3682.5013 -5.4893734
|
||||
6650 20349.273 291.61535 0 3683.1609 -4.7078762
|
||||
6700 20397.246 281.10262 0 3680.6437 6.1633541
|
||||
6750 17336.761 793.781 0 3683.2412 16.830799
|
||||
6800 21708.663 65.02598 0 3683.1366 -13.06689
|
||||
6850 20710.866 231.36429 0 3683.1752 1.1238222
|
||||
6900 20882.087 202.43759 0 3682.7855 -11.177831
|
||||
6950 21045.002 175.62221 0 3683.1225 -3.9647121
|
||||
7000 21170.606 154.92601 0 3683.3603 -3.0075479
|
||||
7050 17340.245 793.0154 0 3683.0563 18.709167
|
||||
7100 20454.586 274.19282 0 3683.2905 4.359508
|
||||
7150 19292.634 470.28091 0 3685.72 23.379394
|
||||
7200 20398.407 283.80225 0 3683.5367 -8.1595888
|
||||
7250 19860.856 374.83326 0 3684.9759 4.3995323
|
||||
7300 21399.991 116.79899 0 3683.4642 -14.69253
|
||||
7350 18469.477 605.76977 0 3684.016 9.072211
|
||||
7400 21246.811 142.508 0 3683.6431 -2.6286469
|
||||
7450 21606.727 82.490537 0 3683.6116 -2.193408
|
||||
7500 20758.001 223.13996 0 3682.8068 3.9337703
|
||||
7550 21529.182 95.699054 0 3683.896 -2.7652731
|
||||
7600 20810.859 215.29662 0 3683.7731 -3.4678516
|
||||
7650 21441.965 109.96162 0 3683.6224 2.8688092
|
||||
7700 21393.02 117.71951 0 3683.2229 -2.0199004
|
||||
7750 21261.451 139.46728 0 3683.0424 -2.351181
|
||||
7800 20994.936 184.15383 0 3683.3099 -1.9007711
|
||||
7850 20956.664 190.40367 0 3683.1811 -4.9029478
|
||||
7900 21318.654 129.90109 0 3683.0101 -7.7655435
|
||||
7950 19343.389 458.65739 0 3682.5556 5.0414528
|
||||
8000 21252.522 140.54793 0 3682.6349 1.7604951
|
||||
8050 21323.878 128.7032 0 3682.6829 -0.66125431
|
||||
8100 20832.414 210.30335 0 3682.3724 -2.6680938
|
||||
8150 17550.263 757.30848 0 3682.3522 1.416445
|
||||
8200 20762.307 222.30426 0 3682.6887 7.061507
|
||||
8250 21016.153 180.1793 0 3682.8714 2.1107236
|
||||
8300 20995.135 183.00069 0 3682.1899 -10.79355
|
||||
8350 19663.825 405.47578 0 3682.7799 10.9075
|
||||
8400 20234.71 310.31036 0 3682.7621 -1.612016
|
||||
8450 21745.345 58.858829 0 3683.083 -3.880159
|
||||
8500 20836.685 210.48891 0 3683.2698 2.5161282
|
||||
8550 18481.486 602.92686 0 3683.1746 4.7767422
|
||||
8600 20149.663 325.20466 0 3683.4819 1.7540149
|
||||
8650 20416.882 280.56681 0 3683.3806 -5.3074807
|
||||
8700 17276.182 803.72341 0 3683.087 3.9552683
|
||||
8750 21629.427 78.173566 0 3683.0781 -1.1208261
|
||||
8800 16461.211 941.11509 0 3684.6503 58.708816
|
||||
8850 20826.403 212.13566 0 3683.2028 -3.6779809
|
||||
8900 21043.766 176.04074 0 3683.335 3.2840745
|
||||
8950 18551.011 591.38957 0 3683.2248 -15.766551
|
||||
9000 17588.62 751.70197 0 3683.1387 -0.79416225
|
||||
9050 18598.429 582.45011 0 3682.1882 -7.8121328
|
||||
9100 17574.963 755.1499 0 3684.3105 23.521269
|
||||
9150 16789.177 884.58607 0 3682.7823 28.62529
|
||||
9200 21059.662 173.26532 0 3683.209 -6.2449386
|
||||
9250 21358.259 123.53455 0 3683.2445 -25.726367
|
||||
9300 20926.413 195.70771 0 3683.4433 -10.230702
|
||||
9350 20863.621 205.86722 0 3683.1373 -1.4396828
|
||||
9400 20440.979 275.97483 0 3682.8047 -10.029174
|
||||
9450 21412.619 114.29156 0 3683.0614 1.8521419
|
||||
9500 18120.95 662.26385 0 3682.4221 23.552524
|
||||
9550 19931.385 360.93428 0 3682.8317 1.8081452
|
||||
9600 19663.03 406.00051 0 3683.1722 11.177455
|
||||
9650 19534.402 427.35484 0 3683.0885 5.3754448
|
||||
9700 20291.266 300.91321 0 3682.7908 -14.76683
|
||||
9750 17786.971 718.21275 0 3682.708 -16.653312
|
||||
9800 21065.368 171.3061 0 3682.2008 -6.6147323
|
||||
9850 19611.141 413.59775 0 3682.1213 2.9925904
|
||||
9900 20735.244 226.23444 0 3682.1084 0.29229058
|
||||
9950 18050.1 673.94746 0 3682.2975 6.6859551
|
||||
10000 19913.432 363.4788 0 3682.3842 -5.8860431
|
||||
Loop time of 33.1043 on 1 procs for 10000 steps with 81 atoms
|
||||
|
||||
Pair time (%) = 1.07997 (3.26231)
|
||||
Neigh time (%) = 0.32972 (0.996002)
|
||||
Comm time (%) = 0.104371 (0.315279)
|
||||
Outpt time (%) = 0.145776 (0.440353)
|
||||
Other time (%) = 31.4445 (94.9861)
|
||||
|
||||
Nlocal: 81 ave 81 max 81 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 80 ave 80 max 80 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 857 ave 857 max 857 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 857
|
||||
Ave neighs/atom = 10.5802
|
||||
Neighbor list builds = 992
|
||||
Dangerous builds = 944
|
||||
|
|
@ -0,0 +1,306 @@
|
|||
LAMMPS (1 Oct 2006)
|
||||
# Simple rigid body system
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
read_data data.rigid
|
||||
1 by 2 by 2 processor grid
|
||||
81 atoms
|
||||
|
||||
velocity all create 100.0 4928459
|
||||
|
||||
# unconnected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 10 18
|
||||
#group clump3 id <> 19 27
|
||||
#group clump4 id <> 28 36
|
||||
#group clump5 id <> 37 45
|
||||
#group clump6 id <> 46 54
|
||||
#group clump7 id <> 55 63
|
||||
#group clump8 id <> 64 72
|
||||
#group clump9 id <> 73 81
|
||||
|
||||
#fix 1 all rigid group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
|
||||
|
||||
# 1 chain of connected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 9 18
|
||||
#group clump3 id <> 18 27
|
||||
#group clump4 id <> 27 36
|
||||
#group clump5 id <> 36 45
|
||||
#group clump6 id <> 45 54
|
||||
#group clump7 id <> 54 63
|
||||
#group clump8 id <> 63 72
|
||||
#group clump9 id <> 72 81
|
||||
|
||||
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
|
||||
|
||||
# 2 chains of connected bodies
|
||||
|
||||
group clump1 id <> 1 9
|
||||
9 atoms in group clump1
|
||||
group clump2 id <> 9 18
|
||||
10 atoms in group clump2
|
||||
group clump3 id <> 18 27
|
||||
10 atoms in group clump3
|
||||
group clump4 id <> 27 36
|
||||
10 atoms in group clump4
|
||||
group clump5 id <> 37 45
|
||||
9 atoms in group clump5
|
||||
group clump6 id <> 45 54
|
||||
10 atoms in group clump6
|
||||
group clump7 id <> 54 63
|
||||
10 atoms in group clump7
|
||||
group clump8 id <> 63 72
|
||||
10 atoms in group clump8
|
||||
group clump9 id <> 72 81
|
||||
10 atoms in group clump9
|
||||
|
||||
fix 1 all poems group clump1 clump2 clump3 clump4
|
||||
1 clusters, 4 bodies, 3 joints, 36 atoms
|
||||
fix 2 all poems group clump5 clump6 clump7 clump8 clump9
|
||||
1 clusters, 5 bodies, 4 joints, 45 atoms
|
||||
|
||||
neigh_modify exclude group clump1 clump1
|
||||
neigh_modify exclude group clump2 clump2
|
||||
neigh_modify exclude group clump3 clump3
|
||||
neigh_modify exclude group clump4 clump4
|
||||
neigh_modify exclude group clump5 clump5
|
||||
neigh_modify exclude group clump6 clump6
|
||||
neigh_modify exclude group clump7 clump7
|
||||
neigh_modify exclude group clump8 clump8
|
||||
neigh_modify exclude group clump9 clump9
|
||||
|
||||
thermo 100
|
||||
dump 1 all atom 50 dump.rigid
|
||||
|
||||
timestep 0.0001
|
||||
thermo 50
|
||||
run 10000
|
||||
Memory usage per processor = 1.83868 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 196.00047 3632.2347 0 3668.5311 -49.218825
|
||||
50 12167.633 1505.5478 0 3758.8133 33.574274
|
||||
100 17556.978 512.66277 0 3763.9549 7.6047451
|
||||
150 19579.586 138.04942 0 3763.8987 -16.463506
|
||||
200 19757.51 105.30542 0 3764.1036 7.5942941
|
||||
250 18218.374 390.10747 0 3763.8804 19.672945
|
||||
300 19383.039 174.40688 0 3763.8586 10.032093
|
||||
350 20125.986 36.972611 0 3764.0071 6.0125969
|
||||
400 18888.816 266.10975 0 3764.0386 8.3046039
|
||||
450 19307.656 188.2511 0 3763.743 7.8887976
|
||||
500 16331.197 738.56392 0 3762.8597 13.456852
|
||||
550 19318.722 186.16172 0 3763.7027 8.2282227
|
||||
600 19455.268 161.20621 0 3764.0336 7.7732896
|
||||
650 18487.011 340.03216 0 3763.5528 3.9255991
|
||||
700 17321.201 556.32471 0 3763.9545 -6.4011523
|
||||
750 18979.187 249.04389 0 3763.7082 2.1939314
|
||||
800 19342.456 181.85552 0 3763.7918 12.876517
|
||||
850 19070.641 232.19342 0 3763.7936 8.2159078
|
||||
900 19478.873 156.65987 0 3763.8586 7.4568244
|
||||
950 19912.415 76.437437 0 3763.9216 5.8486682
|
||||
1000 16003.749 802.39753 0 3766.0548 55.191187
|
||||
1050 19859.583 86.64176 0 3764.3424 8.7977394
|
||||
1100 19229.575 203.61488 0 3764.6473 -4.0979799
|
||||
1150 18821.6 279.15861 0 3764.64 1.5304912
|
||||
1200 19392.695 173.59744 0 3764.8373 10.841959
|
||||
1250 16459.624 717.32104 0 3765.3995 40.93
|
||||
1300 19343.863 182.59043 0 3764.7874 9.4801222
|
||||
1350 20019.643 57.503573 0 3764.8448 8.041765
|
||||
1400 18549.582 329.31436 0 3764.4221 13.151345
|
||||
1450 15163.926 957.47583 0 3765.6103 -7.3048398
|
||||
1500 19223.688 204.15164 0 3764.0939 6.5539049
|
||||
1550 18147.996 404.12675 0 3764.8668 13.092195
|
||||
1600 18615.043 317.42462 0 3764.6548 5.9101585
|
||||
1650 20120.654 38.887963 0 3764.935 0.38926372
|
||||
1700 19450.904 162.98318 0 3765.0025 7.9275461
|
||||
1750 19374.634 177.37922 0 3765.2744 8.7907106
|
||||
1800 19424.403 167.93984 0 3765.0514 5.6664259
|
||||
1850 17936.476 442.80024 0 3764.3699 14.101091
|
||||
1900 19982.598 64.405734 0 3764.8868 3.8454902
|
||||
1950 16216.207 761.84618 0 3764.8475 19.873084
|
||||
2000 18584.309 322.14125 0 3763.6799 12.138411
|
||||
2050 20107.968 41.025323 0 3764.723 5.3931463
|
||||
2100 20002.381 60.584283 0 3764.7288 0.25773654
|
||||
2150 16949.202 626.70007 0 3765.4412 12.954412
|
||||
2200 20010.949 58.809053 0 3764.5403 -1.2239084
|
||||
2250 18982.71 247.01257 0 3762.3292 8.977934
|
||||
2300 18401.513 354.84007 0 3762.5277 7.0021344
|
||||
2350 19390.418 172.96117 0 3763.7793 1.8207539
|
||||
2400 16084.09 785.7786 0 3764.3137 -12.437816
|
||||
2450 18871.606 268.52952 0 3763.2713 14.613895
|
||||
2500 19686.081 117.99211 0 3763.5626 8.3329722
|
||||
2550 18875.819 267.86112 0 3763.3831 -0.48856518
|
||||
2600 17010.705 613.30983 0 3763.4405 11.630319
|
||||
2650 18797.741 282.8114 0 3763.8745 8.1020989
|
||||
2700 19726.505 110.11368 0 3763.1701 6.5575356
|
||||
2750 19436.803 164.0424 0 3763.4504 6.8766681
|
||||
2800 18357.485 362.53565 0 3762.0699 29.446982
|
||||
2850 19004.145 243.73317 0 3763.0192 8.1423479
|
||||
2900 20108.185 39.496053 0 3763.234 4.5848354
|
||||
2950 15919.562 814.90854 0 3762.9756 23.062229
|
||||
3000 17654.881 493.61172 0 3763.0342 5.545646
|
||||
3050 18711.769 298.14871 0 3763.2911 7.243461
|
||||
3100 16038.72 793.07314 0 3763.2064 14.346203
|
||||
3150 19925.087 73.363563 0 3763.1945 6.1598038
|
||||
3200 19305.94 187.89701 0 3763.0711 13.363938
|
||||
3250 19779.251 100.11507 0 3762.9394 -4.2931123
|
||||
3300 17922.539 444.12789 0 3763.1166 11.814226
|
||||
3350 18967.646 250.37413 0 3762.9011 10.599374
|
||||
3400 16940.148 625.60864 0 3762.673 27.487664
|
||||
3450 19284.152 191.53891 0 3762.6781 7.1971328
|
||||
3500 19321.512 184.58448 0 3762.6423 7.1507645
|
||||
3550 19631.049 126.97845 0 3762.358 6.6703895
|
||||
3600 18494.976 337.74154 0 3762.7371 5.2298746
|
||||
3650 19117.634 222.45812 0 3762.7607 5.5119957
|
||||
3700 19400.367 170.05551 0 3762.716 5.1505902
|
||||
3750 19912.752 75.322358 0 3762.869 4.9003403
|
||||
3800 18564.109 325.06781 0 3762.8658 14.09429
|
||||
3850 19846.304 87.655562 0 3762.8971 9.0642301
|
||||
3900 19476.444 156.1165 0 3762.8653 -2.9763615
|
||||
3950 19647.738 124.43854 0 3762.9085 6.1008067
|
||||
4000 18123.616 406.3511 0 3762.5762 12.300492
|
||||
4050 16574.617 693.99841 0 3763.372 8.1837692
|
||||
4100 18946.287 254.50552 0 3763.0773 10.419471
|
||||
4150 18466.555 343.35133 0 3763.0837 1.7173061
|
||||
4200 19477.739 156.04727 0 3763.0359 9.9334234
|
||||
4250 19680.9 118.38024 0 3762.9913 6.7698432
|
||||
4300 18320.329 369.90558 0 3762.5591 2.8725905
|
||||
4350 18767.214 286.789 0 3762.199 10.607372
|
||||
4400 16894.629 634.49312 0 3763.1281 11.825821
|
||||
4450 17915.848 444.62515 0 3762.3748 5.59808
|
||||
4500 19487.927 154.02671 0 3762.9021 4.5536547
|
||||
4550 19880.496 81.301302 0 3762.8746 9.5930235
|
||||
4600 19872.228 82.669863 0 3762.7122 6.7573135
|
||||
4650 15769.89 843.11924 0 3763.4693 15.845442
|
||||
4700 19720.045 110.85283 0 3762.7129 6.1293004
|
||||
4750 19764.607 102.5192 0 3762.6317 8.94455
|
||||
4800 17562.467 510.78691 0 3763.0956 13.972896
|
||||
4850 19463.538 158.32481 0 3762.6836 1.0093239
|
||||
4900 17932.952 441.75053 0 3762.6675 12.701684
|
||||
4950 19084.979 228.62301 0 3762.8785 11.759924
|
||||
5000 19472.38 156.9411 0 3762.9375 11.220659
|
||||
5050 19453.908 160.3778 0 3762.9533 12.301143
|
||||
5100 19521.287 147.96055 0 3763.0137 12.392696
|
||||
5150 18128.471 405.81521 0 3762.9394 11.945434
|
||||
5200 17049.524 605.73212 0 3763.0514 -0.12699639
|
||||
5250 19645.014 125.0255 0 3762.991 -0.52279382
|
||||
5300 18281.054 377.45844 0 3762.8388 20.11439
|
||||
5350 19457.083 159.77948 0 3762.9429 6.3853596
|
||||
5400 18431.165 349.7041 0 3762.8827 4.871088
|
||||
5450 19431.127 164.51144 0 3762.8682 -3.2111996
|
||||
5500 19538.523 144.42775 0 3762.6727 4.5926045
|
||||
5550 16105.678 780.35525 0 3762.8882 54.598614
|
||||
5600 20038.616 51.570638 0 3762.4254 4.5474063
|
||||
5650 19774.413 100.34213 0 3762.2704 0.78153427
|
||||
5700 19210.59 204.66324 0 3762.18 5.4298437
|
||||
5750 19146.331 216.47595 0 3762.0928 7.0574791
|
||||
5800 19058.521 232.88706 0 3762.2428 5.1938614
|
||||
5850 19195.04 207.81355 0 3762.4506 -3.7719233
|
||||
5900 18304.113 372.73776 0 3762.3882 -0.65463254
|
||||
5950 19936.776 70.443763 0 3762.4393 9.3331421
|
||||
6000 19413.016 167.50961 0 3762.5125 9.6998807
|
||||
6050 19169.847 212.36264 0 3762.3343 13.97952
|
||||
6100 19873.513 82.452317 0 3762.7325 7.797884
|
||||
6150 18911.794 260.42784 0 3762.6119 3.8761488
|
||||
6200 19153.7 215.69884 0 3762.6802 2.9164092
|
||||
6250 18802.916 280.37164 0 3762.3932 9.5188585
|
||||
6300 19385.046 172.8566 0 3762.6799 9.6703687
|
||||
6350 20042.403 51.159768 0 3762.7159 7.6850802
|
||||
6400 17671.74 490.05042 0 3762.5948 14.096008
|
||||
6450 18092.22 412.77197 0 3763.1832 0.82294201
|
||||
6500 19953.711 67.838094 0 3762.9698 8.1400023
|
||||
6550 19818.338 92.883562 0 3762.9461 8.055057
|
||||
6600 19323.833 183.93088 0 3762.4184 5.2727635
|
||||
6650 18642.816 310.35894 0 3762.7323 19.352453
|
||||
6700 16246.778 753.95834 0 3762.6209 24.682771
|
||||
6750 19362.672 176.94037 0 3762.6204 4.5345155
|
||||
6800 18813.849 278.64468 0 3762.6908 9.7383715
|
||||
6850 19386.278 172.79274 0 3762.8443 -2.8239186
|
||||
6900 19206.609 206.02588 0 3762.8054 8.1264361
|
||||
6950 18068.847 416.85422 0 3762.9369 2.3525156
|
||||
7000 18369.805 360.43314 0 3762.249 13.728295
|
||||
7050 18426.189 350.61688 0 3762.8741 14.517035
|
||||
7100 17656.982 492.79834 0 3762.6098 11.126444
|
||||
7150 18141.722 402.98387 0 3762.562 14.510638
|
||||
7200 18621.905 313.92925 0 3762.4301 1.4234708
|
||||
7250 18374.083 360.03493 0 3762.6429 -3.8128826
|
||||
7300 18040.277 421.82567 0 3762.6177 2.7635663
|
||||
7350 19146.198 217.01003 0 3762.6023 11.264741
|
||||
7400 18826.989 276.1892 0 3762.6686 12.390664
|
||||
7450 16067.243 787.1796 0 3762.5949 14.180712
|
||||
7500 18419.546 351.11771 0 3762.1448 12.922148
|
||||
7550 18446.346 346.8971 0 3762.8871 15.016254
|
||||
7600 18944.672 254.13521 0 3762.4077 10.235074
|
||||
7650 18736.984 292.8881 0 3762.7 -8.4530721
|
||||
7700 18741.654 291.39068 0 3762.0673 3.2144304
|
||||
7750 18220.361 388.04072 0 3762.1816 15.132777
|
||||
7800 19348.223 178.96147 0 3761.9658 4.4894323
|
||||
7850 19401.949 169.04328 0 3761.9968 4.9313127
|
||||
7900 18577.957 321.63399 0 3761.9965 10.7403
|
||||
7950 17739.892 476.69976 0 3761.865 15.786414
|
||||
8000 17512.557 519.37266 0 3762.4387 8.4816398
|
||||
8050 19168.123 212.38445 0 3762.0369 1.9313036
|
||||
8100 17916.044 443.46573 0 3761.2517 1.5416538
|
||||
8150 18601.23 316.95165 0 3761.6238 10.656943
|
||||
8200 17791.805 467.15931 0 3761.9381 2.2002016
|
||||
8250 18321.607 369.09405 0 3761.9843 5.815164
|
||||
8300 17334.957 552.06316 0 3762.2404 9.7175531
|
||||
8350 17207.467 575.31923 0 3761.8872 5.6916957
|
||||
8400 18225.217 387.22593 0 3762.2662 13.185636
|
||||
8450 19004.047 243.03694 0 3762.3048 13.419491
|
||||
8500 18952.876 252.61597 0 3762.4078 2.0529233
|
||||
8550 19127.437 220.08856 0 3762.2066 -3.9009433
|
||||
8600 19542.154 143.35104 0 3762.2684 9.2825505
|
||||
8650 19294.525 189.17898 0 3762.2392 15.659987
|
||||
8700 18832.532 274.05387 0 3761.5598 6.8307945
|
||||
8750 18591.931 318.93488 0 3761.885 13.12084
|
||||
8800 18576.38 322.04174 0 3762.1121 1.3006059
|
||||
8850 19922.086 72.972833 0 3762.248 7.446691
|
||||
8900 18892.839 263.55803 0 3762.2319 12.740409
|
||||
8950 16486.736 708.70288 0 3761.8022 33.657286
|
||||
9000 18628.335 312.81773 0 3762.5094 11.180187
|
||||
9050 19286.823 190.4938 0 3762.1278 3.690949
|
||||
9100 18973.378 247.96414 0 3761.5526 12.70188
|
||||
9150 17256.927 566.17648 0 3761.9038 13.94458
|
||||
9200 18507.288 334.66416 0 3761.9398 8.7036327
|
||||
9250 18961.534 250.42427 0 3761.8194 2.441337
|
||||
9300 19206.115 205.203 0 3761.8911 7.4983103
|
||||
9350 19401.191 168.92055 0 3761.7336 4.4522417
|
||||
9400 18069.392 415.54646 0 3761.7301 9.7253906
|
||||
9450 18828.428 274.89551 0 3761.6415 12.99464
|
||||
9500 18295.323 373.66825 0 3761.691 4.0189559
|
||||
9550 17709.338 482.22946 0 3761.7365 -0.16619916
|
||||
9600 19512.39 148.31281 0 3761.7184 6.188777
|
||||
9650 19742.351 105.74048 0 3761.7315 8.5310602
|
||||
9700 19892.658 77.898869 0 3761.7245 9.4480252
|
||||
9750 19035.044 236.65131 0 3761.6595 8.943227
|
||||
9800 17443.415 531.71826 0 3761.9802 20.612812
|
||||
9850 19545.912 141.99994 0 3761.6133 5.9979112
|
||||
9900 19542.173 142.22929 0 3761.1503 7.6623836
|
||||
9950 19794.356 96.034607 0 3761.6561 2.4218049
|
||||
10000 19058.563 232.34496 0 3761.7085 -1.2298428
|
||||
Loop time of 16.9577 on 4 procs for 10000 steps with 81 atoms
|
||||
|
||||
Pair time (%) = 0.0940045 (0.554347)
|
||||
Neigh time (%) = 0.04158 (0.245198)
|
||||
Comm time (%) = 1.38353 (8.15873)
|
||||
Outpt time (%) = 0.0951915 (0.561347)
|
||||
Other time (%) = 15.3434 (90.4804)
|
||||
|
||||
Nlocal: 20.25 ave 42 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
Nghost: 20.5 ave 37 max 9 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
Neighs: 164.25 ave 401 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 657
|
||||
Ave neighs/atom = 8.11111
|
||||
Neighbor list builds = 991
|
||||
Dangerous builds = 930
|
||||
|
|
@ -0,0 +1,306 @@
|
|||
LAMMPS (1 Oct 2006)
|
||||
# Simple rigid body system
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
read_data data.rigid
|
||||
1 by 1 by 1 processor grid
|
||||
81 atoms
|
||||
|
||||
velocity all create 100.0 4928459
|
||||
|
||||
# unconnected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 10 18
|
||||
#group clump3 id <> 19 27
|
||||
#group clump4 id <> 28 36
|
||||
#group clump5 id <> 37 45
|
||||
#group clump6 id <> 46 54
|
||||
#group clump7 id <> 55 63
|
||||
#group clump8 id <> 64 72
|
||||
#group clump9 id <> 73 81
|
||||
|
||||
#fix 1 all rigid group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
|
||||
|
||||
# 1 chain of connected bodies
|
||||
|
||||
#group clump1 id <> 1 9
|
||||
#group clump2 id <> 9 18
|
||||
#group clump3 id <> 18 27
|
||||
#group clump4 id <> 27 36
|
||||
#group clump5 id <> 36 45
|
||||
#group clump6 id <> 45 54
|
||||
#group clump7 id <> 54 63
|
||||
#group clump8 id <> 63 72
|
||||
#group clump9 id <> 72 81
|
||||
|
||||
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
|
||||
|
||||
# 2 chains of connected bodies
|
||||
|
||||
group clump1 id <> 1 9
|
||||
9 atoms in group clump1
|
||||
group clump2 id <> 9 18
|
||||
10 atoms in group clump2
|
||||
group clump3 id <> 18 27
|
||||
10 atoms in group clump3
|
||||
group clump4 id <> 27 36
|
||||
10 atoms in group clump4
|
||||
group clump5 id <> 37 45
|
||||
9 atoms in group clump5
|
||||
group clump6 id <> 45 54
|
||||
10 atoms in group clump6
|
||||
group clump7 id <> 54 63
|
||||
10 atoms in group clump7
|
||||
group clump8 id <> 63 72
|
||||
10 atoms in group clump8
|
||||
group clump9 id <> 72 81
|
||||
10 atoms in group clump9
|
||||
|
||||
fix 1 all poems group clump1 clump2 clump3 clump4
|
||||
1 clusters, 4 bodies, 3 joints, 36 atoms
|
||||
fix 2 all poems group clump5 clump6 clump7 clump8 clump9
|
||||
1 clusters, 5 bodies, 4 joints, 45 atoms
|
||||
|
||||
neigh_modify exclude group clump1 clump1
|
||||
neigh_modify exclude group clump2 clump2
|
||||
neigh_modify exclude group clump3 clump3
|
||||
neigh_modify exclude group clump4 clump4
|
||||
neigh_modify exclude group clump5 clump5
|
||||
neigh_modify exclude group clump6 clump6
|
||||
neigh_modify exclude group clump7 clump7
|
||||
neigh_modify exclude group clump8 clump8
|
||||
neigh_modify exclude group clump9 clump9
|
||||
|
||||
thermo 100
|
||||
dump 1 all atom 50 dump.rigid
|
||||
|
||||
timestep 0.0001
|
||||
thermo 50
|
||||
run 10000
|
||||
Memory usage per processor = 1.85083 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 196.00047 3632.2347 0 3668.5311 -49.218825
|
||||
50 12167.633 1505.5478 0 3758.8133 33.574274
|
||||
100 17556.978 512.66277 0 3763.9549 7.6047451
|
||||
150 19579.586 138.04942 0 3763.8987 -16.463506
|
||||
200 19757.51 105.30542 0 3764.1036 7.5942941
|
||||
250 18218.374 390.10747 0 3763.8804 19.672945
|
||||
300 19383.039 174.40688 0 3763.8586 10.032093
|
||||
350 20125.986 36.972611 0 3764.0071 6.0125969
|
||||
400 18888.816 266.10975 0 3764.0386 8.3046039
|
||||
450 19307.656 188.2511 0 3763.743 7.8887976
|
||||
500 16331.197 738.56392 0 3762.8597 13.456852
|
||||
550 19318.722 186.16172 0 3763.7027 8.2282227
|
||||
600 19455.268 161.20621 0 3764.0336 7.7732896
|
||||
650 18487.011 340.03216 0 3763.5528 3.9255991
|
||||
700 17321.201 556.32471 0 3763.9545 -6.4011523
|
||||
750 18979.187 249.04389 0 3763.7082 2.1939314
|
||||
800 19342.456 181.85552 0 3763.7918 12.876517
|
||||
850 19070.641 232.19342 0 3763.7936 8.2159078
|
||||
900 19478.873 156.65987 0 3763.8586 7.4568244
|
||||
950 19912.415 76.437437 0 3763.9216 5.8486682
|
||||
1000 16003.749 802.39753 0 3766.0548 55.191187
|
||||
1050 19859.583 86.64176 0 3764.3424 8.7977394
|
||||
1100 19229.575 203.61488 0 3764.6473 -4.0979799
|
||||
1150 18821.6 279.15861 0 3764.64 1.5304912
|
||||
1200 19392.695 173.59744 0 3764.8373 10.841959
|
||||
1250 16459.624 717.32104 0 3765.3995 40.93
|
||||
1300 19343.863 182.59043 0 3764.7874 9.4801222
|
||||
1350 20019.643 57.503573 0 3764.8448 8.041765
|
||||
1400 18549.582 329.31436 0 3764.4221 13.151345
|
||||
1450 15163.926 957.47582 0 3765.6103 -7.3048397
|
||||
1500 19223.689 204.1516 0 3764.0939 6.5539043
|
||||
1550 18147.996 404.12674 0 3764.8668 13.092195
|
||||
1600 18615.043 317.4246 0 3764.6548 5.9101558
|
||||
1650 20120.654 38.887979 0 3764.935 0.38926746
|
||||
1700 19450.904 162.98332 0 3765.0025 7.9275434
|
||||
1750 19374.635 177.37908 0 3765.2744 8.790711
|
||||
1800 19424.402 167.93989 0 3765.0514 5.6664303
|
||||
1850 17936.547 442.78706 0 3764.3699 14.100896
|
||||
1900 19982.599 64.405586 0 3764.8868 3.8454569
|
||||
1950 16216.319 761.8251 0 3764.8472 19.872541
|
||||
2000 18584.273 322.14785 0 3763.6798 12.138511
|
||||
2050 20107.968 41.025185 0 3764.723 5.3931166
|
||||
2100 20002.395 60.581572 0 3764.7288 0.2577697
|
||||
2150 16949.033 626.73148 0 3765.4413 12.955
|
||||
2200 20010.947 58.809301 0 3764.5403 -1.2240041
|
||||
2250 18982.708 247.01284 0 3762.3292 8.9780528
|
||||
2300 18401.571 354.8294 0 3762.5278 7.0019831
|
||||
2350 19390.394 172.9656 0 3763.7793 1.8206136
|
||||
2400 16085.032 785.60385 0 3764.3135 -12.434917
|
||||
2450 18871.953 268.46552 0 3763.2716 14.607919
|
||||
2500 19685.428 118.11323 0 3763.5629 8.3387285
|
||||
2550 18877.269 267.59235 0 3763.3828 -0.48341735
|
||||
2600 17008.289 613.75762 0 3763.4407 11.639259
|
||||
2650 18812.576 280.05888 0 3763.8693 8.0841903
|
||||
2700 19721.109 111.09615 0 3763.1533 6.5832394
|
||||
2750 19385.826 173.49011 0 3763.4578 6.9477448
|
||||
2800 18261.265 380.36977 0 3762.0854 31.328975
|
||||
2850 19262.504 195.91155 0 3763.042 7.1306245
|
||||
2900 20108.917 39.360683 0 3763.2342 4.2051073
|
||||
2950 16520.273 703.73173 0 3763.0416 20.666642
|
||||
3000 17721.082 480.84673 0 3762.5286 10.889353
|
||||
3050 18281.378 377.38446 0 3762.8248 12.727107
|
||||
3100 17813.119 464.33179 0 3763.0575 -5.9033506
|
||||
3150 17848.794 456.92067 0 3762.253 24.280682
|
||||
3200 16283.244 747.77931 0 3763.1949 -34.084455
|
||||
3250 17775.99 470.52364 0 3762.3736 31.744378
|
||||
3300 18920.688 258.84248 0 3762.6735 9.8437551
|
||||
3350 18374.481 358.89272 0 3761.5744 3.5475689
|
||||
3400 18147.71 402.29354 0 3762.9806 11.829727
|
||||
3450 19446.951 161.38162 0 3762.6688 -0.25609588
|
||||
3500 18586.947 320.84226 0 3762.8695 4.4386085
|
||||
3550 19739.703 107.24051 0 3762.7411 6.7843088
|
||||
3600 18020.123 425.86788 0 3762.9277 32.692211
|
||||
3650 17703.685 484.51122 0 3762.9715 18.888689
|
||||
3700 18571.567 323.53862 0 3762.7177 -2.5479026
|
||||
3750 19747.937 105.29513 0 3762.3204 6.9264561
|
||||
3800 19055.305 233.61597 0 3762.3762 10.269813
|
||||
3850 19390.879 171.45465 0 3762.3582 8.5051872
|
||||
3900 17669.249 489.45512 0 3761.5382 28.590013
|
||||
3950 18309.837 371.37486 0 3762.0854 17.457093
|
||||
4000 17913.77 444.38412 0 3761.7489 11.054563
|
||||
4050 19357.4 177.36212 0 3762.0659 -2.7100501
|
||||
4100 19601.584 132.10663 0 3762.0297 7.7432662
|
||||
4150 19468.348 156.55912 0 3761.8087 7.9494045
|
||||
4200 18791.279 282.08385 0 3761.9502 8.0141814
|
||||
4250 17932.214 440.54317 0 3761.3236 8.6775437
|
||||
4300 19854.413 85.385328 0 3762.1285 2.6399285
|
||||
4350 18753.885 289.43762 0 3762.3792 -3.348463
|
||||
4400 19497.1 151.47714 0 3762.0512 8.2129692
|
||||
4450 18881.054 265.79896 0 3762.2904 15.717461
|
||||
4500 19483 154.31774 0 3762.2806 4.5428504
|
||||
4550 18372.304 359.93631 0 3762.2148 2.1598549
|
||||
4600 18538.653 329.1277 0 3762.2117 9.8161015
|
||||
4650 19561.941 139.74654 0 3762.3281 10.249049
|
||||
4700 18772.917 286.03706 0 3762.5032 21.326885
|
||||
4750 19574.986 137.31432 0 3762.3117 7.4877085
|
||||
4800 18707.43 297.96418 0 3762.303 3.5977275
|
||||
4850 19084.263 228.13574 0 3762.2584 4.8620306
|
||||
4900 19256.565 196.41485 0 3762.4453 7.1493737
|
||||
4950 19692.391 115.536 0 3762.2751 9.4402989
|
||||
5000 19540.996 143.5732 0 3762.2761 8.2081649
|
||||
5050 18653.131 308.51184 0 3762.7953 12.668618
|
||||
5100 19633.591 126.5541 0 3762.4043 5.7938001
|
||||
5150 18621.364 313.78864 0 3762.1894 24.57491
|
||||
5200 19688.937 116.08545 0 3762.185 12.477508
|
||||
5250 18410.54 353.19966 0 3762.559 12.976514
|
||||
5300 19950.659 67.914691 0 3762.4811 5.8022194
|
||||
5350 20096.327 40.899907 0 3762.4419 6.0410733
|
||||
5400 19919.818 73.467027 0 3762.3221 2.2220049
|
||||
5450 19300.983 185.34644 0 3759.6026 8.1383036
|
||||
5500 19800.648 95.498164 0 3762.2848 2.3885829
|
||||
5550 20056.731 48.009231 0 3762.2186 4.3782978
|
||||
5600 19844.923 87.14203 0 3762.1277 7.7533964
|
||||
5650 17129.848 590.16296 0 3762.3571 17.511751
|
||||
5700 19711.052 111.82109 0 3762.0159 11.77834
|
||||
5750 19617.414 129.29781 0 3762.1523 7.8333492
|
||||
5800 20036.44 51.792528 0 3762.2443 1.2142201
|
||||
5850 19666.587 120.39539 0 3762.356 2.9059895
|
||||
5900 19270.785 193.72474 0 3762.3887 8.5521132
|
||||
5950 18570.273 323.50997 0 3762.4494 7.917873
|
||||
6000 19639.926 125.31297 0 3762.3363 7.8943644
|
||||
6050 19170.13 212.17653 0 3762.2006 11.073748
|
||||
6100 19477.33 155.36998 0 3762.2829 9.7741577
|
||||
6150 19489.538 153.13138 0 3762.3051 10.490838
|
||||
6200 15767.031 842.38404 0 3762.2046 17.502671
|
||||
6250 18412.418 352.52257 0 3762.2297 6.5373659
|
||||
6300 17972.252 434.26055 0 3762.4554 13.704085
|
||||
6350 18918.499 258.81778 0 3762.2436 1.9382232
|
||||
6400 18849.088 271.35964 0 3761.9315 6.6707881
|
||||
6450 18253.5 381.84702 0 3762.1248 11.492891
|
||||
6500 19249.208 197.34439 0 3762.0126 8.5573923
|
||||
6550 17155.467 584.92475 0 3761.863 10.220904
|
||||
6600 19820.303 91.781334 0 3762.2078 3.1199949
|
||||
6650 16832.666 643.9692 0 3761.1296 3.1224873
|
||||
6700 19043.731 235.36302 0 3761.9799 9.0582649
|
||||
6750 18893.629 263.25929 0 3762.0794 7.2472883
|
||||
6800 17109.53 593.22372 0 3761.6553 4.3802066
|
||||
6850 16744.117 662.34545 0 3763.1078 12.922567
|
||||
6900 19458.193 158.37115 0 3761.7402 11.006662
|
||||
6950 18725.976 294.25915 0 3762.0326 3.2140093
|
||||
7000 16598.724 687.82474 0 3761.6624 -3.6835942
|
||||
7050 18730.073 293.30419 0 3761.8363 10.884579
|
||||
7100 20018.967 54.77727 0 3761.9935 6.0028598
|
||||
7150 17113.843 592.9644 0 3762.1945 6.7236396
|
||||
7200 17196.345 575.20975 0 3759.7181 22.617984
|
||||
7250 19441.447 161.79318 0 3762.0612 8.6790347
|
||||
7300 18425.176 348.35362 0 3760.4232 1.2239447
|
||||
7350 15831.334 830.07877 0 3761.8073 12.989722
|
||||
7400 15760.367 843.93147 0 3762.5179 20.330489
|
||||
7450 19887.01 78.958802 0 3761.7384 3.9771783
|
||||
7500 17074.502 600.07806 0 3762.0229 0.40604401
|
||||
7550 19498.422 151.10349 0 3761.9224 4.5520709
|
||||
7600 19185.257 208.81514 0 3761.6406 4.2379441
|
||||
7650 18265.566 379.07997 0 3761.5921 6.3803024
|
||||
7700 18874.852 266.08897 0 3761.432 12.40484
|
||||
7750 18129.668 404.32772 0 3761.6736 10.569077
|
||||
7800 18203.274 390.12247 0 3761.0991 9.6842762
|
||||
7850 18194.832 391.87893 0 3761.2922 5.4796988
|
||||
7900 16807.558 648.88314 0 3761.3938 0.29076345
|
||||
7950 18084.122 412.78207 0 3761.6935 6.8841109
|
||||
8000 17981.757 431.92518 0 3761.8801 6.6592835
|
||||
8050 19355.253 177.54899 0 3761.855 5.5142333
|
||||
8100 20025.877 53.385491 0 3761.8812 6.9839182
|
||||
8150 18845.855 271.98132 0 3761.9544 12.093316
|
||||
8200 16272.215 748.48475 0 3761.8579 3.2379236
|
||||
8250 19924.961 72.016182 0 3761.8237 7.4249536
|
||||
8300 17765.452 471.72154 0 3761.6201 7.703297
|
||||
8350 18716.949 295.72885 0 3761.8305 3.9378764
|
||||
8400 18669.341 304.5313 0 3761.8167 6.5183661
|
||||
8450 17588.96 504.87172 0 3762.0864 10.603189
|
||||
8500 19416.561 166.00525 0 3761.6647 4.9012003
|
||||
8550 17856.962 455.50215 0 3762.347 32.77813
|
||||
8600 19538.533 143.63236 0 3761.8792 7.9996791
|
||||
8650 19155.813 213.86669 0 3761.2394 10.276167
|
||||
8700 19069.24 230.4574 0 3761.7982 3.9102709
|
||||
8750 19365.473 175.51172 0 3761.7105 11.362372
|
||||
8800 19133.09 218.25828 0 3761.4231 9.9797495
|
||||
8850 18259.293 380.39561 0 3761.7461 7.7607448
|
||||
8900 18775.775 284.73679 0 3761.7321 -1.8279748
|
||||
8950 15941.533 809.54243 0 3761.6782 20.457951
|
||||
9000 19525.004 145.86783 0 3761.6092 6.7957307
|
||||
9050 17956.771 435.7506 0 3761.0786 7.3335578
|
||||
9100 19258.953 195.12617 0 3761.5989 9.5389589
|
||||
9150 18891.927 262.8519 0 3761.357 9.7974291
|
||||
9200 17804.066 464.97231 0 3762.0215 14.446215
|
||||
9250 18975.048 247.6467 0 3761.5445 10.681583
|
||||
9300 19242.636 198.11698 0 3761.5681 1.1630841
|
||||
9350 19037.441 236.19188 0 3761.644 8.4873411
|
||||
9400 17398.22 539.36333 0 3761.2559 23.119633
|
||||
9450 18636.737 310.27156 0 3761.5192 4.5578491
|
||||
9500 19979.365 61.813877 0 3761.6963 6.4995321
|
||||
9550 18886.37 264.32082 0 3761.7967 4.2159993
|
||||
9600 18374.874 359.07673 0 3761.8312 -0.87552165
|
||||
9650 19927.34 71.462667 0 3761.7108 6.3897422
|
||||
9700 16594.729 688.47459 0 3761.5725 21.040463
|
||||
9750 19520.395 146.32272 0 3761.2106 9.4824852
|
||||
9800 17066.423 600.32957 0 3760.7782 10.240849
|
||||
9850 18262.057 379.95673 0 3761.8191 45.222639
|
||||
9900 19261.074 194.37227 0 3761.2378 -1.6957956
|
||||
9950 19695.741 113.67141 0 3761.0308 8.0826867
|
||||
10000 19798.388 94.785163 0 3761.1534 9.0475616
|
||||
Loop time of 33.9032 on 1 procs for 10000 steps with 81 atoms
|
||||
|
||||
Pair time (%) = 0.816388 (2.40799)
|
||||
Neigh time (%) = 0.259492 (0.76539)
|
||||
Comm time (%) = 0.132266 (0.390128)
|
||||
Outpt time (%) = 0.142545 (0.420446)
|
||||
Other time (%) = 32.5526 (96.016)
|
||||
|
||||
Nlocal: 81 ave 81 max 81 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 60 ave 60 max 60 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 626 ave 626 max 626 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 626
|
||||
Ave neighs/atom = 7.7284
|
||||
Neighbor list builds = 994
|
||||
Dangerous builds = 954
|
||||
|
|
@ -0,0 +1,72 @@
|
|||
# 3d metal shear simulation
|
||||
|
||||
units metal
|
||||
boundary s s p
|
||||
|
||||
atom_style atomic
|
||||
lattice fcc 3.52
|
||||
region box block 0 16.0 0 10.0 0 2.828427
|
||||
create_box 3 box
|
||||
|
||||
orient x 1 0 0
|
||||
orient y 0 1 1
|
||||
orient z 0 -1 1
|
||||
origin 0.5 0 0
|
||||
create_atoms 1
|
||||
|
||||
pair_style eam
|
||||
pair_coeff * * niu3.eam
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
region lower block INF INF INF 1.4 INF INF
|
||||
region upper block INF INF 8.6 INF INF INF
|
||||
group lower region lower
|
||||
group upper region upper
|
||||
group boundary union lower upper
|
||||
group mobile subtract all boundary
|
||||
|
||||
set lower atom 2
|
||||
set upper atom 3
|
||||
|
||||
# void
|
||||
|
||||
#region void cylinder z 8 5 2.5 INF INF
|
||||
#delete_atoms region void
|
||||
|
||||
# temp controllers
|
||||
|
||||
temperature new3d mobile full
|
||||
temperature new2d mobile partial 0 1 1
|
||||
|
||||
# equilibrate
|
||||
|
||||
velocity mobile create 300.0 5812775 temp new3d
|
||||
fix 1 all nve
|
||||
fix 2 boundary setforce 0.0 0.0 0.0
|
||||
|
||||
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
|
||||
fix_modify 3 temp new3d
|
||||
|
||||
thermo 25
|
||||
thermo_modify temp new3d
|
||||
|
||||
timestep 0.001
|
||||
run 100
|
||||
|
||||
# shear
|
||||
|
||||
velocity upper set 1.0 0 0
|
||||
velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes
|
||||
|
||||
unfix 3
|
||||
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
|
||||
fix_modify 3 temp new2d
|
||||
|
||||
dump 1 all atom 10 dump.shear
|
||||
thermo 100
|
||||
thermo_modify temp new2d
|
||||
|
||||
reset_timestep 0
|
||||
run 3000
|
||||
|
|
@ -0,0 +1,72 @@
|
|||
# 3d metal shear simulation
|
||||
|
||||
units metal
|
||||
boundary s s p
|
||||
|
||||
atom_style atomic
|
||||
lattice fcc 3.52
|
||||
region box block 0 16.0 0 10.0 0 2.828427
|
||||
create_box 3 box
|
||||
|
||||
orient x 1 0 0
|
||||
orient y 0 1 1
|
||||
orient z 0 -1 1
|
||||
origin 0.5 0 0
|
||||
create_atoms 1
|
||||
|
||||
pair_style eam
|
||||
pair_coeff * * niu3.eam
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
region lower block INF INF INF 1.4 INF INF
|
||||
region upper block INF INF 8.6 INF INF INF
|
||||
group lower region lower
|
||||
group upper region upper
|
||||
group boundary union lower upper
|
||||
group mobile subtract all boundary
|
||||
|
||||
set lower atom 2
|
||||
set upper atom 3
|
||||
|
||||
# void
|
||||
|
||||
region void cylinder z 8 5 2.5 INF INF
|
||||
delete_atoms region void
|
||||
|
||||
# temp controllers
|
||||
|
||||
temperature new3d mobile full
|
||||
temperature new2d mobile partial 0 1 1
|
||||
|
||||
# equilibrate
|
||||
|
||||
velocity mobile create 300.0 5812775 temp new3d
|
||||
fix 1 all nve
|
||||
fix 2 boundary setforce 0.0 0.0 0.0
|
||||
|
||||
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
|
||||
fix_modify 3 temp new3d
|
||||
|
||||
thermo 25
|
||||
thermo_modify temp new3d
|
||||
|
||||
timestep 0.001
|
||||
run 100
|
||||
|
||||
# shear
|
||||
|
||||
velocity upper set 1.0 0 0
|
||||
velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes
|
||||
|
||||
unfix 3
|
||||
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
|
||||
fix_modify 3 temp new2d
|
||||
|
||||
dump 1 all atom 10 dump.shear
|
||||
thermo 100
|
||||
thermo_modify temp new2d
|
||||
|
||||
reset_timestep 0
|
||||
run 3000
|
||||
|
|
@ -0,0 +1,160 @@
|
|||
LAMMPS (1 Oct 2006)
|
||||
# 3d metal shear simulation
|
||||
|
||||
units metal
|
||||
boundary s s p
|
||||
|
||||
atom_style atomic
|
||||
lattice fcc 3.52
|
||||
region box block 0 16.0 0 10.0 0 2.828427
|
||||
create_box 3 box
|
||||
Created box = (0 0 0) to (56.32 35.2 9.95606)
|
||||
2 by 2 by 1 processor grid
|
||||
|
||||
orient x 1 0 0
|
||||
orient y 0 1 1
|
||||
orient z 0 -1 1
|
||||
origin 0.5 0 0
|
||||
create_atoms 1
|
||||
Created 1912 atoms
|
||||
|
||||
pair_style eam
|
||||
pair_coeff * * niu3.eam
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
region lower block INF INF INF 1.4 INF INF
|
||||
region upper block INF INF 8.6 INF INF INF
|
||||
group lower region lower
|
||||
264 atoms in group lower
|
||||
group upper region upper
|
||||
264 atoms in group upper
|
||||
group boundary union lower upper
|
||||
528 atoms in group boundary
|
||||
group mobile subtract all boundary
|
||||
1384 atoms in group mobile
|
||||
|
||||
set lower atom 2
|
||||
264 settings made
|
||||
set upper atom 3
|
||||
264 settings made
|
||||
|
||||
# void
|
||||
|
||||
#region void cylinder z 8 5 2.5 INF INF
|
||||
#delete_atoms region void
|
||||
|
||||
# temp controllers
|
||||
|
||||
temperature new3d mobile full
|
||||
temperature new2d mobile partial 0 1 1
|
||||
|
||||
# equilibrate
|
||||
|
||||
velocity mobile create 300.0 5812775 temp new3d
|
||||
fix 1 all nve
|
||||
fix 2 boundary setforce 0.0 0.0 0.0
|
||||
|
||||
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
|
||||
fix_modify 3 temp new3d
|
||||
|
||||
thermo 25
|
||||
thermo_modify temp new3d
|
||||
|
||||
timestep 0.001
|
||||
run 100
|
||||
Memory usage per processor = 1.68686 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 300 -8317.4367 0 -8263.8088 -7102.8898 19539.346
|
||||
25 220.9212 -8272.7102 0 -8233.2184 5169.2532 19539.346
|
||||
50 300 -8239.0788 0 -8185.4509 13402.59 19669.861
|
||||
75 295.11304 -8231.409 0 -8178.6547 13739.709 19743.536
|
||||
100 300 -8250.5854 0 -8196.9575 6735.3894 19818.51
|
||||
Loop time of 0.20501 on 4 procs for 100 steps with 1912 atoms
|
||||
|
||||
Pair time (%) = 0.170366 (83.1014)
|
||||
Neigh time (%) = 0.00511163 (2.49336)
|
||||
Comm time (%) = 0.0205901 (10.0434)
|
||||
Outpt time (%) = 0.000730455 (0.356302)
|
||||
Other time (%) = 0.00821161 (4.00547)
|
||||
|
||||
Nlocal: 478 ave 490 max 468 min
|
||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||
Nghost: 1033.75 ave 1043 max 1021 min
|
||||
Histogram: 1 0 0 0 0 1 0 1 0 1
|
||||
Neighs: 11509 ave 12218 max 10874 min
|
||||
Histogram: 1 0 0 0 2 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 46036
|
||||
Ave neighs/atom = 24.0774
|
||||
Neighbor list builds = 4
|
||||
Dangerous builds = 0
|
||||
|
||||
# shear
|
||||
|
||||
velocity upper set 1.0 0 0
|
||||
velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes
|
||||
|
||||
unfix 3
|
||||
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
|
||||
fix_modify 3 temp new2d
|
||||
|
||||
dump 1 all atom 10 dump.shear
|
||||
thermo 100
|
||||
thermo_modify temp new2d
|
||||
|
||||
reset_timestep 0
|
||||
run 3000
|
||||
Memory usage per processor = 1.70559 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 292.46935 -8250.5854 0 -8215.7435 5714.5932 19847.768
|
||||
100 297.59499 -8256.7106 0 -8221.2581 1294.1819 19860.892
|
||||
200 292.19816 -8260.283 0 -8225.4734 299.28813 19869.393
|
||||
300 302.96848 -8254.8033 0 -8218.7107 -1931.9374 19978.005
|
||||
400 306.09958 -8249.231 0 -8212.7654 435.17823 20093.509
|
||||
500 296.82499 -8244.0101 0 -8208.6494 646.75953 20198.763
|
||||
600 300 -8230.1411 0 -8194.4021 3590.0541 20277.909
|
||||
700 299.5264 -8222.6973 0 -8187.0147 6328.7718 20385.21
|
||||
800 295.07726 -8207.5484 0 -8172.3958 10476.661 20524.637
|
||||
900 305.7088 -8197.6454 0 -8161.2263 12349.102 20621.333
|
||||
1000 297.84421 -8183.9807 0 -8148.4985 16146.327 20741.011
|
||||
1100 307.99301 -8170.1977 0 -8133.5065 19739.24 20871.68
|
||||
1200 300 -8162.0163 0 -8126.2773 21326.406 20996.243
|
||||
1300 300 -8151.4476 0 -8115.7086 21185.942 21118.364
|
||||
1400 304.51892 -8143.3645 0 -8107.0871 21474.828 21234.378
|
||||
1500 307.86659 -8134.7063 0 -8098.0302 21789.168 21361.383
|
||||
1600 300 -8126.473 0 -8090.734 20673.353 21484.725
|
||||
1700 300 -8129.42 0 -8093.681 17751.243 21606.846
|
||||
1800 300 -8146.0891 0 -8110.3501 12858.826 21737.514
|
||||
1900 301.48058 -8160.3481 0 -8124.4327 10026.088 21854.75
|
||||
2000 303.13886 -8159.9363 0 -8123.8233 10035.576 21979.313
|
||||
2100 302.43445 -8158.993 0 -8122.964 8142.9832 22089.221
|
||||
2200 305.6122 -8159.3597 0 -8122.9521 5981.3934 22216.227
|
||||
2300 307.57806 -8154.583 0 -8117.9413 7603.355 22333.462
|
||||
2400 303.24127 -8162.4278 0 -8126.3027 6097.2511 22469.016
|
||||
2500 305.61941 -8164.9775 0 -8128.5691 3543.4308 22585.031
|
||||
2600 309.10168 -8168.3336 0 -8131.5103 -691.16472 22701.045
|
||||
2700 307.75507 -8168.189 0 -8131.5261 -5684.463 22836.599
|
||||
2800 301.01957 -8164.8783 0 -8129.0178 -9335.7848 22947.728
|
||||
2900 305.43054 -8164.2448 0 -8127.8589 -11554.582 23075.955
|
||||
3000 303.62558 -8162.2789 0 -8126.1079 -12622.002 23199.297
|
||||
Loop time of 7.89757 on 4 procs for 3000 steps with 1912 atoms
|
||||
|
||||
Pair time (%) = 5.18402 (65.6407)
|
||||
Neigh time (%) = 0.282387 (3.57562)
|
||||
Comm time (%) = 0.885845 (11.2167)
|
||||
Outpt time (%) = 0.95221 (12.057)
|
||||
Other time (%) = 0.593105 (7.50997)
|
||||
|
||||
Nlocal: 478 ave 518 max 439 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
Nghost: 1008 ave 1048 max 973 min
|
||||
Histogram: 1 1 0 0 0 0 0 1 0 1
|
||||
Neighs: 11229 ave 12551 max 10264 min
|
||||
Histogram: 1 1 0 0 0 1 0 0 0 1
|
||||
|
||||
Total # of neighbors = 44916
|
||||
Ave neighs/atom = 23.4916
|
||||
Neighbor list builds = 217
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,160 @@
|
|||
LAMMPS (1 Oct 2006)
|
||||
# 3d metal shear simulation
|
||||
|
||||
units metal
|
||||
boundary s s p
|
||||
|
||||
atom_style atomic
|
||||
lattice fcc 3.52
|
||||
region box block 0 16.0 0 10.0 0 2.828427
|
||||
create_box 3 box
|
||||
Created box = (0 0 0) to (56.32 35.2 9.95606)
|
||||
1 by 1 by 1 processor grid
|
||||
|
||||
orient x 1 0 0
|
||||
orient y 0 1 1
|
||||
orient z 0 -1 1
|
||||
origin 0.5 0 0
|
||||
create_atoms 1
|
||||
Created 1912 atoms
|
||||
|
||||
pair_style eam
|
||||
pair_coeff * * niu3.eam
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
region lower block INF INF INF 1.4 INF INF
|
||||
region upper block INF INF 8.6 INF INF INF
|
||||
group lower region lower
|
||||
264 atoms in group lower
|
||||
group upper region upper
|
||||
264 atoms in group upper
|
||||
group boundary union lower upper
|
||||
528 atoms in group boundary
|
||||
group mobile subtract all boundary
|
||||
1384 atoms in group mobile
|
||||
|
||||
set lower atom 2
|
||||
264 settings made
|
||||
set upper atom 3
|
||||
264 settings made
|
||||
|
||||
# void
|
||||
|
||||
#region void cylinder z 8 5 2.5 INF INF
|
||||
#delete_atoms region void
|
||||
|
||||
# temp controllers
|
||||
|
||||
temperature new3d mobile full
|
||||
temperature new2d mobile partial 0 1 1
|
||||
|
||||
# equilibrate
|
||||
|
||||
velocity mobile create 300.0 5812775 temp new3d
|
||||
fix 1 all nve
|
||||
fix 2 boundary setforce 0.0 0.0 0.0
|
||||
|
||||
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
|
||||
fix_modify 3 temp new3d
|
||||
|
||||
thermo 25
|
||||
thermo_modify temp new3d
|
||||
|
||||
timestep 0.001
|
||||
run 100
|
||||
Memory usage per processor = 1.92854 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 300 -8317.4367 0 -8263.8088 -7102.8898 19539.346
|
||||
25 220.34739 -8272.574 0 -8233.1848 5168.9424 19539.346
|
||||
50 300 -8237.7904 0 -8184.1625 13744.474 19678.783
|
||||
75 292.66971 -8229.8128 0 -8177.4952 14322.493 19737.223
|
||||
100 300 -8245.8192 0 -8192.1914 9037.5551 19770.863
|
||||
Loop time of 1.32784 on 1 procs for 100 steps with 1912 atoms
|
||||
|
||||
Pair time (%) = 1.24155 (93.5014)
|
||||
Neigh time (%) = 0.037302 (2.80923)
|
||||
Comm time (%) = 0.013245 (0.997488)
|
||||
Outpt time (%) = 0.000552 (0.0415714)
|
||||
Other time (%) = 0.035192 (2.65033)
|
||||
|
||||
Nlocal: 1912 ave 1912 max 1912 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 2122 ave 2122 max 2122 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 45974 ave 45974 max 45974 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 45974
|
||||
Ave neighs/atom = 24.045
|
||||
Neighbor list builds = 4
|
||||
Dangerous builds = 0
|
||||
|
||||
# shear
|
||||
|
||||
velocity upper set 1.0 0 0
|
||||
velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes
|
||||
|
||||
unfix 3
|
||||
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
|
||||
fix_modify 3 temp new2d
|
||||
|
||||
dump 1 all atom 10 dump.shear
|
||||
thermo 100
|
||||
thermo_modify temp new2d
|
||||
|
||||
reset_timestep 0
|
||||
run 3000
|
||||
Memory usage per processor = 2.00339 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 298.53461 -8245.8192 0 -8210.2548 8058.7181 19778.392
|
||||
100 300 -8264.0486 0 -8228.3096 2691.7558 19826.894
|
||||
200 294.32149 -8259.4812 0 -8224.4187 1849.8688 19915.639
|
||||
300 293.23673 -8253.0529 0 -8218.1196 -568.76065 20023.531
|
||||
400 300.89492 -8248.1925 0 -8212.3469 -317.08468 20091.777
|
||||
500 293.55594 -8243.3219 0 -8208.3506 406.7293 20171.198
|
||||
600 301.16216 -8232.0523 0 -8196.1748 4289.0467 20256.193
|
||||
700 300 -8222.1995 0 -8186.4604 7361.3269 20388.083
|
||||
800 297.68439 -8211.4622 0 -8175.999 8573.6353 20512.646
|
||||
900 300.09026 -8197.39 0 -8161.6402 10797.992 20638.43
|
||||
1000 293.3388 -8182.0987 0 -8147.1532 13912.802 20747.117
|
||||
1100 305.0194 -8169.078 0 -8132.741 16871.039 20882.671
|
||||
1200 295.62571 -8154.0757 0 -8118.8578 20598.322 20993.801
|
||||
1300 300 -8143.9231 0 -8108.1841 21781.691 21117.142
|
||||
1400 300 -8130.6475 0 -8094.9085 24186.109 21245.369
|
||||
1500 309.0526 -8127.5064 0 -8090.6889 21858.969 21367.489
|
||||
1600 300 -8128.5701 0 -8092.8311 18560.503 21474.955
|
||||
1700 300 -8147.5253 0 -8111.7862 12751.805 21606.846
|
||||
1800 305.83763 -8164.2172 0 -8127.7828 8040.3799 21732.63
|
||||
1900 301.4629 -8160.2306 0 -8124.3173 8616.0354 21858.414
|
||||
2000 304.26807 -8152.1587 0 -8115.9112 10071.784 21973.207
|
||||
2100 305.08538 -8154.2603 0 -8117.9154 7911.69 22090.443
|
||||
2200 300 -8151.5205 0 -8115.7815 7821.2573 22215.006
|
||||
2300 300 -8154.9943 0 -8119.2553 6744.5955 22338.347
|
||||
2400 300 -8154.8809 0 -8119.1419 6094.8065 22460.468
|
||||
2500 306.30502 -8153.0721 0 -8116.582 6168.5479 22585.031
|
||||
2600 300 -8155.5915 0 -8119.8525 3322.6468 22713.257
|
||||
2700 299.94465 -8155.1357 0 -8119.4033 3475.705 22835.378
|
||||
2800 304.48054 -8154.675 0 -8118.4023 -230.17514 22946.507
|
||||
2900 299.98768 -8154.2556 0 -8118.518 -2933.046 23077.176
|
||||
3000 301.75583 -8148.8621 0 -8112.914 -2858.4431 23195.633
|
||||
Loop time of 42.2848 on 1 procs for 3000 steps with 1912 atoms
|
||||
|
||||
Pair time (%) = 36.2138 (85.6426)
|
||||
Neigh time (%) = 1.93158 (4.56802)
|
||||
Comm time (%) = 0.410137 (0.96994)
|
||||
Outpt time (%) = 2.71704 (6.42558)
|
||||
Other time (%) = 1.01224 (2.39386)
|
||||
|
||||
Nlocal: 1912 ave 1912 max 1912 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 2083 ave 2083 max 2083 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 45144 ave 45144 max 45144 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 45144
|
||||
Ave neighs/atom = 23.6109
|
||||
Neighbor list builds = 214
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,161 @@
|
|||
LAMMPS (1 Oct 2006)
|
||||
# 3d metal shear simulation
|
||||
|
||||
units metal
|
||||
boundary s s p
|
||||
|
||||
atom_style atomic
|
||||
lattice fcc 3.52
|
||||
region box block 0 16.0 0 10.0 0 2.828427
|
||||
create_box 3 box
|
||||
Created box = (0 0 0) to (56.32 35.2 9.95606)
|
||||
2 by 2 by 1 processor grid
|
||||
|
||||
orient x 1 0 0
|
||||
orient y 0 1 1
|
||||
orient z 0 -1 1
|
||||
origin 0.5 0 0
|
||||
create_atoms 1
|
||||
Created 1912 atoms
|
||||
|
||||
pair_style eam
|
||||
pair_coeff * * niu3.eam
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
region lower block INF INF INF 1.4 INF INF
|
||||
region upper block INF INF 8.6 INF INF INF
|
||||
group lower region lower
|
||||
264 atoms in group lower
|
||||
group upper region upper
|
||||
264 atoms in group upper
|
||||
group boundary union lower upper
|
||||
528 atoms in group boundary
|
||||
group mobile subtract all boundary
|
||||
1384 atoms in group mobile
|
||||
|
||||
set lower atom 2
|
||||
264 settings made
|
||||
set upper atom 3
|
||||
264 settings made
|
||||
|
||||
# void
|
||||
|
||||
region void cylinder z 8 5 2.5 INF INF
|
||||
delete_atoms region void
|
||||
Deleted 204 atoms, new total = 1708
|
||||
|
||||
# temp controllers
|
||||
|
||||
temperature new3d mobile full
|
||||
temperature new2d mobile partial 0 1 1
|
||||
|
||||
# equilibrate
|
||||
|
||||
velocity mobile create 300.0 5812775 temp new3d
|
||||
fix 1 all nve
|
||||
fix 2 boundary setforce 0.0 0.0 0.0
|
||||
|
||||
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
|
||||
fix_modify 3 temp new3d
|
||||
|
||||
thermo 25
|
||||
thermo_modify temp new3d
|
||||
|
||||
timestep 0.001
|
||||
run 100
|
||||
Memory usage per processor = 1.67464 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 300 -7358.6159 0 -7312.8984 -9603.6477 19539.346
|
||||
25 221.74248 -7320.8414 0 -7287.0497 1128.9116 19599.578
|
||||
50 300 -7293.1781 0 -7247.4606 8050.8209 19662.054
|
||||
75 293.25457 -7287.1715 0 -7242.482 7427.7697 19732.766
|
||||
100 300 -7300.054 0 -7254.3365 1198.8155 19807.388
|
||||
Loop time of 0.178373 on 4 procs for 100 steps with 1708 atoms
|
||||
|
||||
Pair time (%) = 0.147011 (82.4179)
|
||||
Neigh time (%) = 0.00538623 (3.01965)
|
||||
Comm time (%) = 0.0185187 (10.382)
|
||||
Outpt time (%) = 0.000659287 (0.369611)
|
||||
Other time (%) = 0.00679743 (3.8108)
|
||||
|
||||
Nlocal: 427 ave 435 max 419 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
Nghost: 780.25 ave 792 max 769 min
|
||||
Histogram: 1 0 0 1 0 1 0 0 0 1
|
||||
Neighs: 9878.75 ave 10203 max 9534 min
|
||||
Histogram: 1 0 0 0 1 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 39515
|
||||
Ave neighs/atom = 23.1352
|
||||
Neighbor list builds = 5
|
||||
Dangerous builds = 0
|
||||
|
||||
# shear
|
||||
|
||||
velocity upper set 1.0 0 0
|
||||
velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes
|
||||
|
||||
unfix 3
|
||||
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
|
||||
fix_modify 3 temp new2d
|
||||
|
||||
dump 1 all atom 10 dump.shear
|
||||
thermo 100
|
||||
thermo_modify temp new2d
|
||||
|
||||
reset_timestep 0
|
||||
run 3000
|
||||
Memory usage per processor = 1.69123 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 303.6848 -7300.054 0 -7269.2144 396.60777 19807.514
|
||||
100 306.67967 -7308.1308 0 -7276.9871 -5243.0172 19880.2
|
||||
200 300 -7311.1514 0 -7280.686 -9605.7539 19886.803
|
||||
300 294.96872 -7306.3327 0 -7276.3782 -10520.452 20001.558
|
||||
400 299.02699 -7301.2595 0 -7270.8929 -7900.8177 20054.29
|
||||
500 303.7645 -7300.5234 0 -7269.6757 -6471.8824 20147.506
|
||||
600 307.21531 -7295.4331 0 -7264.235 -4590.3963 20259.857
|
||||
700 306.22567 -7286.1068 0 -7255.0091 -1875.6399 20394.189
|
||||
800 308.41851 -7280.8206 0 -7249.5003 -648.51488 20511.425
|
||||
900 308.81304 -7274.5973 0 -7243.2369 -422.10864 20631.103
|
||||
1000 293.20428 -7267.7783 0 -7238.003 -3459.2985 20745.896
|
||||
1100 307.19333 -7261.032 0 -7229.8362 -4059.2658 20882.671
|
||||
1200 300 -7255.0675 0 -7224.6021 -4495.7756 20998.686
|
||||
1300 300 -7259.4244 0 -7228.959 -5500.7167 21109.815
|
||||
1400 300 -7266.3342 0 -7235.8688 -6996.9268 21249.033
|
||||
1500 309.14664 -7276.5521 0 -7245.1579 -9854.0088 21365.047
|
||||
1600 306.72473 -7276.827 0 -7245.6787 -11618.775 21489.61
|
||||
1700 304.2066 -7275.7234 0 -7244.8308 -13977.049 21603.182
|
||||
1800 300 -7275.8145 0 -7245.3491 -16910.13 21731.408
|
||||
1900 292.59665 -7280.2143 0 -7250.5007 -20332.035 21858.414
|
||||
2000 300.50593 -7275.6944 0 -7245.1776 -21045.085 21969.543
|
||||
2100 293.80834 -7272.8027 0 -7242.966 -20752.104 22101.433
|
||||
2200 300 -7272.9169 0 -7242.4515 -18905.895 22222.333
|
||||
2300 292.33116 -7272.1269 0 -7242.4403 -18279.22 22339.568
|
||||
2400 308.8105 -7269.1775 0 -7237.8174 -13554.606 22458.025
|
||||
2500 307.8757 -7270.3785 0 -7239.1133 -13783.192 22581.367
|
||||
2600 300 -7273.1821 0 -7242.7167 -13842.925 22708.372
|
||||
2700 295.48445 -7269.0293 0 -7239.0225 -14868.543 22834.156
|
||||
2800 302.07467 -7264.7268 0 -7234.0507 -13561.346 22948.95
|
||||
2900 304.03422 -7260.7326 0 -7229.8575 -11126.104 23068.628
|
||||
3000 300 -7264.6327 0 -7234.1673 -12265.417 23193.191
|
||||
Loop time of 6.74849 on 4 procs for 3000 steps with 1708 atoms
|
||||
|
||||
Pair time (%) = 4.44794 (65.9102)
|
||||
Neigh time (%) = 0.228236 (3.38204)
|
||||
Comm time (%) = 0.691189 (10.2421)
|
||||
Outpt time (%) = 0.861094 (12.7598)
|
||||
Other time (%) = 0.520027 (7.70582)
|
||||
|
||||
Nlocal: 427 ave 440 max 419 min
|
||||
Histogram: 1 0 2 0 0 0 0 0 0 1
|
||||
Nghost: 782.25 ave 832 max 731 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 9691.75 ave 10205 max 9345 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 38767
|
||||
Ave neighs/atom = 22.6973
|
||||
Neighbor list builds = 210
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,161 @@
|
|||
LAMMPS (1 Oct 2006)
|
||||
# 3d metal shear simulation
|
||||
|
||||
units metal
|
||||
boundary s s p
|
||||
|
||||
atom_style atomic
|
||||
lattice fcc 3.52
|
||||
region box block 0 16.0 0 10.0 0 2.828427
|
||||
create_box 3 box
|
||||
Created box = (0 0 0) to (56.32 35.2 9.95606)
|
||||
1 by 1 by 1 processor grid
|
||||
|
||||
orient x 1 0 0
|
||||
orient y 0 1 1
|
||||
orient z 0 -1 1
|
||||
origin 0.5 0 0
|
||||
create_atoms 1
|
||||
Created 1912 atoms
|
||||
|
||||
pair_style eam
|
||||
pair_coeff * * niu3.eam
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
region lower block INF INF INF 1.4 INF INF
|
||||
region upper block INF INF 8.6 INF INF INF
|
||||
group lower region lower
|
||||
264 atoms in group lower
|
||||
group upper region upper
|
||||
264 atoms in group upper
|
||||
group boundary union lower upper
|
||||
528 atoms in group boundary
|
||||
group mobile subtract all boundary
|
||||
1384 atoms in group mobile
|
||||
|
||||
set lower atom 2
|
||||
264 settings made
|
||||
set upper atom 3
|
||||
264 settings made
|
||||
|
||||
# void
|
||||
|
||||
region void cylinder z 8 5 2.5 INF INF
|
||||
delete_atoms region void
|
||||
Deleted 204 atoms, new total = 1708
|
||||
|
||||
# temp controllers
|
||||
|
||||
temperature new3d mobile full
|
||||
temperature new2d mobile partial 0 1 1
|
||||
|
||||
# equilibrate
|
||||
|
||||
velocity mobile create 300.0 5812775 temp new3d
|
||||
fix 1 all nve
|
||||
fix 2 boundary setforce 0.0 0.0 0.0
|
||||
|
||||
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
|
||||
fix_modify 3 temp new3d
|
||||
|
||||
thermo 25
|
||||
thermo_modify temp new3d
|
||||
|
||||
timestep 0.001
|
||||
run 100
|
||||
Memory usage per processor = 1.91124 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 300 -7358.6159 0 -7312.8984 -9603.6477 19539.346
|
||||
25 222.66472 -7321.4436 0 -7287.5114 561.45929 19539.346
|
||||
50 300 -7292.2296 0 -7246.5121 7557.1546 19680.831
|
||||
75 292.67374 -7286.2045 0 -7241.6035 6826.7501 19738.494
|
||||
100 300 -7297.4178 0 -7251.7003 1628.0506 19767.92
|
||||
Loop time of 1.14216 on 1 procs for 100 steps with 1708 atoms
|
||||
|
||||
Pair time (%) = 1.06278 (93.0502)
|
||||
Neigh time (%) = 0.032721 (2.86484)
|
||||
Comm time (%) = 0.012319 (1.07857)
|
||||
Outpt time (%) = 0.000515 (0.04509)
|
||||
Other time (%) = 0.033823 (2.96132)
|
||||
|
||||
Nlocal: 1708 ave 1708 max 1708 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1898 ave 1898 max 1898 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 39444 ave 39444 max 39444 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 39444
|
||||
Ave neighs/atom = 23.0937
|
||||
Neighbor list builds = 4
|
||||
Dangerous builds = 0
|
||||
|
||||
# shear
|
||||
|
||||
velocity upper set 1.0 0 0
|
||||
velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes
|
||||
|
||||
unfix 3
|
||||
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
|
||||
fix_modify 3 temp new2d
|
||||
|
||||
dump 1 all atom 10 dump.shear
|
||||
thermo 100
|
||||
thermo_modify temp new2d
|
||||
|
||||
reset_timestep 0
|
||||
run 3000
|
||||
Memory usage per processor = 1.97639 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 296.81571 -7297.4178 0 -7267.2757 786.4061 19771.698
|
||||
100 300 -7312.4709 0 -7282.0055 -6070.7176 19830.015
|
||||
200 298.24057 -7308.4037 0 -7278.117 -7075.3624 19911.227
|
||||
300 298.67627 -7306.0737 0 -7275.7427 -10959.707 20012.463
|
||||
400 295.45281 -7300.8028 0 -7270.7991 -8138.7479 20049.688
|
||||
500 293.51166 -7302.0379 0 -7272.2314 -6169.1551 20160.975
|
||||
600 306.56214 -7292.914 0 -7261.7822 -1497.9662 20264.741
|
||||
700 300 -7288.1794 0 -7257.714 -1694.6598 20394.189
|
||||
800 292.30303 -7280.2273 0 -7250.5436 -2492.6249 20510.204
|
||||
900 294.01762 -7273.2472 0 -7243.3893 -1408.0826 20623.776
|
||||
1000 306.33035 -7266.6178 0 -7235.5095 -1332.1587 20745.896
|
||||
1100 305.42715 -7259.4415 0 -7228.425 -1532.7103 20880.229
|
||||
1200 298.81462 -7252.7391 0 -7222.3941 -84.819805 20992.58
|
||||
1300 305.34821 -7256.2234 0 -7225.2149 -2051.4783 21117.142
|
||||
1400 300 -7261.6324 0 -7231.167 -5225.385 21249.033
|
||||
1500 304.1211 -7270.8198 0 -7239.9359 -6745.2264 21361.383
|
||||
1600 304.0601 -7268.8039 0 -7237.9262 -8095.0839 21479.84
|
||||
1700 300 -7275.418 0 -7244.9526 -12662.853 21614.173
|
||||
1800 300 -7276.2011 0 -7245.7357 -12987.776 21730.187
|
||||
1900 300 -7281.3333 0 -7250.8679 -16149.771 21851.087
|
||||
2000 300 -7272.4857 0 -7242.0203 -19420.269 21978.092
|
||||
2100 300.83156 -7266.7776 0 -7236.2278 -21604.366 22091.664
|
||||
2200 307.68394 -7267.2822 0 -7236.0365 -22271.78 22217.448
|
||||
2300 300 -7267.5846 0 -7237.1192 -18486.541 22344.453
|
||||
2400 306.73936 -7264.0905 0 -7232.9407 -15349.104 22465.353
|
||||
2500 295.97063 -7261.0612 0 -7231.005 -16523.792 22577.703
|
||||
2600 302.58731 -7260.6552 0 -7229.927 -21518.407 22713.257
|
||||
2700 300.8664 -7260.95 0 -7230.3966 -24032.38 22836.599
|
||||
2800 297.95224 -7251.7372 0 -7221.4798 -22569.009 22945.286
|
||||
2900 304.36782 -7254.3093 0 -7223.4003 -23462.932 23071.07
|
||||
3000 293.99223 -7249.0183 0 -7219.163 -23263.342 23199.297
|
||||
Loop time of 37.342 on 1 procs for 3000 steps with 1708 atoms
|
||||
|
||||
Pair time (%) = 31.7703 (85.0792)
|
||||
Neigh time (%) = 1.71104 (4.58208)
|
||||
Comm time (%) = 0.391151 (1.04748)
|
||||
Outpt time (%) = 2.45624 (6.57769)
|
||||
Other time (%) = 1.01328 (2.71351)
|
||||
|
||||
Nlocal: 1708 ave 1708 max 1708 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1877 ave 1877 max 1877 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 38584 ave 38584 max 38584 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 38584
|
||||
Ave neighs/atom = 22.5902
|
||||
Neighbor list builds = 211
|
||||
Dangerous builds = 0
|
||||
Loading…
Reference in New Issue