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2017-08-18 17:33:42 -06:00
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This directory contains input scripts for performing
simulations with these models:
eDPD - energy-conserving dissipative particle dynamics
mDPD - many-body dissipative particle dynamics
tDPD - transport dissipative particle dynamics
1) eDPD: The input script in.mdpd is an example simulation of
measuring the thermal conductivity by heat conduction analog of
periodic Poiseuille flow. The initial eDPD system is randomly filled
by many eDPD particles, and a set command "edpd/temp" gives the
initial temperature and a set command "edpd/cv" gives the heat
capacity of eDPD particles. A non-contact heat source/sink term is
applied by a fix command "edpd/source". A compute command
"edpd/temp/atom" obtain the temperature on each eDPD particle. The
simulation will generate a file named "temp.profile" showing the
temperature profile. For details please see online LAMMPS
documentation and Fig.12 in the paper Z. Li, et al. J Comput Phys,
2014, 265: 113-127. DOI: 10.1016/j.jcp.2014.02.003
2) mDPD: The input script "in.mdpd" is an example simulation of
oscillations of a free liquid droplet. The initial configuration is a
liquid film whose particles are in a fcc lattice created by the
command "create atoms". Then the liquid film has a tendency to form a
spherical droplet under the effect of surface tension. For details
please see online LAMMPS documentation and the paper Z. Li, et
al. Phys Fluids, 2013, 25: 072103. DOI: 10.1063/1.4812366
3) tDPD: The input script in.tdpd is an example simulation of
computing the effective diffusion coefficient of a tDPD system using a
method analogous to the periodic Poiseuille flow. Command "atom_style
tdpd 2" specifies the tDPD system with two chemical species. The
initial tDPD system is randomly filled by many tDPD particles, and a
set "cc" command gives initial concentration for each chemical
species. Fix commands "tdpd/source" add source terms and compute
commands "tdpd/cc/atom" obtain the chemical concentration on each tDPD
particle. The simulation will generate a file named "cc.profile"
showing the concentration profiles of the two chemical species. For
details please see online LAMMPS documentation and Fig.1 in the paper
Z. Li, et al. J Chem Phys, 2015, 143: 014101. DOI: 10.1063/1.4923254

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########################################################################
### Heat conduction analog of periodic Poiseuille flow problem ###
### using energy-conserving DPD (eDPD) simulation ###
### ###
### Created : Zhen Li (zhen_li@brown.edu) ###
### Division of Applied Mathematics, Brown University. ###
### ###
### mDPD system setup follows Fig.12 in the publication: ###
### Z. Li, Y.-H. Tang, H. Lei, B. Caswell and G.E. Karniadakis. ###
### "Energy-conserving dissipative particle dynamics with ###
### temperature-dependent properties". J. Comput. Phys., ###
### 2014, 265: 113-127. DOI: 10.1016/j.jcp.2014.02.003 ###
########################################################################
units lj
dimension 3
boundary p p p
neighbor 0.2 bin
neigh_modify every 1 delay 0 check yes
atom_style edpd
region edpd block -10 10 -10 10 -5 5 units box
create_box 1 edpd
create_atoms 1 random 16000 276438 NULL
mass 1 1.0
set atom * edpd/temp 1.0
set atom * edpd/cv 1.0E5
pair_style edpd 1.58 9872598
#pair_coeff 1 1 18.75 4.5 0.41 1.58 1.45E-5 2.0 1.58
pair_coeff 1 1 18.75 4.5 0.41 1.58 1.41E-5 2.0 1.58 &
power 10.54 -3.66 3.44 -4.10 &
kappa -0.44 -3.21 5.04 0.00
compute mythermo all temp
thermo 100
thermo_modify temp mythermo
thermo_modify flush yes
velocity all create 1.0 432982 loop local dist gaussian
fix mvv all mvv/edpd 0.5
fix upper all edpd/source cuboid 0.0 5.0 0.0 20.0 10.0 10.0 0.01
fix lower all edpd/source cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 -0.01
timestep 0.01
run 500
reset_timestep 0
compute temp all edpd/temp/atom
compute ccT all chunk/atom bin/1d y 0.0 1.0
fix stat all ave/chunk 1 500 500 ccT c_temp density/number norm sample file temp.profile
run 500

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LAMMPS (11 Aug 2017)
########################################################################
### Heat conduction analog of periodic Poiseuille flow problem ###
### using energy-conserving DPD (eDPD) simulation ###
### ###
### Created : Zhen Li (zhen_li@brown.edu) ###
### Division of Applied Mathematics, Brown University. ###
### ###
### mDPD system setup follows Fig.12 in the publication: ###
### Z. Li, Y.-H. Tang, H. Lei, B. Caswell and G.E. Karniadakis. ###
### "Energy-conserving dissipative particle dynamics with ###
### temperature-dependent properties". J. Comput. Phys., ###
### 2014, 265: 113-127. DOI: 10.1016/j.jcp.2014.02.003 ###
########################################################################
units lj
dimension 3
boundary p p p
neighbor 0.2 bin
neigh_modify every 1 delay 0 check yes
atom_style edpd
region edpd block -10 10 -10 10 -5 5 units box
create_box 1 edpd
Created orthogonal box = (-10 -10 -5) to (10 10 5)
1 by 1 by 1 MPI processor grid
create_atoms 1 random 16000 276438 NULL
Created 16000 atoms
mass 1 1.0
set atom * edpd/temp 1.0
16000 settings made for edpd/temp
set atom * edpd/cv 1.0E5
16000 settings made for edpd/cv
pair_style edpd 1.58 9872598
#pair_coeff 1 1 18.75 4.5 0.41 1.58 1.45E-5 2.0 1.58
pair_coeff 1 1 18.75 4.5 0.41 1.58 1.41E-5 2.0 1.58 power 10.54 -3.66 3.44 -4.10 kappa -0.44 -3.21 5.04 0.00
compute mythermo all temp
thermo 100
thermo_modify temp mythermo
thermo_modify flush yes
velocity all create 1.0 432982 loop local dist gaussian
fix mvv all mvv/edpd 0.5
fix upper all edpd/source cuboid 0.0 5.0 0.0 20.0 10.0 10.0 0.01
fix lower all edpd/source cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 -0.01
timestep 0.01
run 500
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.78
ghost atom cutoff = 1.78
binsize = 0.89, bins = 23 23 12
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair edpd, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 11.64 | 11.64 | 11.64 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 48.948932 0 50.448838 201.73366
100 1.0069712 43.754293 0 45.264656 199.5369
200 0.98667561 43.716052 0 45.195973 196.72854
300 1.0036944 43.706299 0 45.211746 195.35714
400 1.0024228 43.697014 0 45.200554 197.0062
500 0.99968161 43.687445 0 45.186873 193.80596
Loop time of 80.7995 on 1 procs for 500 steps with 16000 atoms
Performance: 5346.567 tau/day, 6.188 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 75.106 | 75.106 | 75.106 | 0.0 | 92.95
Neigh | 4.9836 | 4.9836 | 4.9836 | 0.0 | 6.17
Comm | 0.31199 | 0.31199 | 0.31199 | 0.0 | 0.39
Output | 0.00048232 | 0.00048232 | 0.00048232 | 0.0 | 0.00
Modify | 0.29985 | 0.29985 | 0.29985 | 0.0 | 0.37
Other | | 0.09751 | | | 0.12
Nlocal: 16000 ave 16000 max 16000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 14091 ave 14091 max 14091 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 749111 ave 749111 max 749111 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 749111
Ave neighs/atom = 46.8194
Neighbor list builds = 181
Dangerous builds = 0
reset_timestep 0
compute temp all edpd/temp/atom
compute ccT all chunk/atom bin/1d y 0.0 1.0
fix stat all ave/chunk 1 500 500 ccT c_temp density/number norm sample file temp.profile
run 500
Per MPI rank memory allocation (min/avg/max) = 12.14 | 12.14 | 12.14 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.99968161 43.687397 0 45.186825 196.38426
100 1.0041443 43.668196 0 45.174318 195.38066
200 0.99628392 43.666173 0 45.160505 197.84675
300 1.0029116 43.66224 0 45.166513 199.67414
400 0.99922193 43.64406 0 45.142799 196.94404
500 0.99355431 43.623266 0 45.113505 195.94136
Loop time of 80.7742 on 1 procs for 500 steps with 16000 atoms
Performance: 5348.242 tau/day, 6.190 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 75.073 | 75.073 | 75.073 | 0.0 | 92.94
Neigh | 4.8786 | 4.8786 | 4.8786 | 0.0 | 6.04
Comm | 0.31086 | 0.31086 | 0.31086 | 0.0 | 0.38
Output | 0.00045919 | 0.00045919 | 0.00045919 | 0.0 | 0.00
Modify | 0.4139 | 0.4139 | 0.4139 | 0.0 | 0.51
Other | | 0.09731 | | | 0.12
Nlocal: 16000 ave 16000 max 16000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 14091 ave 14091 max 14091 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 749667 ave 749667 max 749667 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 749667
Ave neighs/atom = 46.8542
Neighbor list builds = 178
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:02:41

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LAMMPS (11 Aug 2017)
########################################################################
### Heat conduction analog of periodic Poiseuille flow problem ###
### using energy-conserving DPD (eDPD) simulation ###
### ###
### Created : Zhen Li (zhen_li@brown.edu) ###
### Division of Applied Mathematics, Brown University. ###
### ###
### mDPD system setup follows Fig.12 in the publication: ###
### Z. Li, Y.-H. Tang, H. Lei, B. Caswell and G.E. Karniadakis. ###
### "Energy-conserving dissipative particle dynamics with ###
### temperature-dependent properties". J. Comput. Phys., ###
### 2014, 265: 113-127. DOI: 10.1016/j.jcp.2014.02.003 ###
########################################################################
units lj
dimension 3
boundary p p p
neighbor 0.2 bin
neigh_modify every 1 delay 0 check yes
atom_style edpd
region edpd block -10 10 -10 10 -5 5 units box
create_box 1 edpd
Created orthogonal box = (-10 -10 -5) to (10 10 5)
2 by 2 by 1 MPI processor grid
create_atoms 1 random 16000 276438 NULL
Created 16000 atoms
mass 1 1.0
set atom * edpd/temp 1.0
16000 settings made for edpd/temp
set atom * edpd/cv 1.0E5
16000 settings made for edpd/cv
pair_style edpd 1.58 9872598
#pair_coeff 1 1 18.75 4.5 0.41 1.58 1.45E-5 2.0 1.58
pair_coeff 1 1 18.75 4.5 0.41 1.58 1.41E-5 2.0 1.58 power 10.54 -3.66 3.44 -4.10 kappa -0.44 -3.21 5.04 0.00
compute mythermo all temp
thermo 100
thermo_modify temp mythermo
thermo_modify flush yes
velocity all create 1.0 432982 loop local dist gaussian
fix mvv all mvv/edpd 0.5
fix upper all edpd/source cuboid 0.0 5.0 0.0 20.0 10.0 10.0 0.01
fix lower all edpd/source cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 -0.01
timestep 0.01
run 500
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.78
ghost atom cutoff = 1.78
binsize = 0.89, bins = 23 23 12
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair edpd, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.969 | 4.979 | 4.985 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 48.948932 0 50.448838 199.51547
100 1.0106415 43.744371 0 45.260239 196.39598
200 1.0053215 43.714413 0 45.222301 195.35298
300 0.99886399 43.713356 0 45.211559 196.74821
400 1.0035264 43.699086 0 45.204282 195.47446
500 1.0025285 43.698051 0 45.20175 197.27042
Loop time of 21.165 on 4 procs for 500 steps with 16000 atoms
Performance: 20411.046 tau/day, 23.624 timesteps/s
99.9% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 18.713 | 19.101 | 19.41 | 6.0 | 90.25
Neigh | 1.2687 | 1.2925 | 1.3177 | 1.5 | 6.11
Comm | 0.33013 | 0.66337 | 1.0747 | 34.3 | 3.13
Output | 0.00023484 | 0.00028092 | 0.00036526 | 0.0 | 0.00
Modify | 0.073931 | 0.075277 | 0.076306 | 0.3 | 0.36
Other | | 0.03227 | | | 0.15
Nlocal: 4000 ave 4067 max 3930 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Nghost: 5997.5 ave 6052 max 5943 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Neighs: 187388 ave 193157 max 181221 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Total # of neighbors = 749552
Ave neighs/atom = 46.847
Neighbor list builds = 181
Dangerous builds = 0
reset_timestep 0
compute temp all edpd/temp/atom
compute ccT all chunk/atom bin/1d y 0.0 1.0
fix stat all ave/chunk 1 500 500 ccT c_temp density/number norm sample file temp.profile
run 500
Per MPI rank memory allocation (min/avg/max) = 5.221 | 5.23 | 5.236 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.0025285 43.69801 0 45.201708 194.00452
100 0.9885969 43.679927 0 45.16273 196.28442
200 1.0028463 43.663067 0 45.167242 198.25592
300 1.0027516 43.648817 0 45.152851 198.82226
400 0.99695312 43.641469 0 45.136805 197.97499
500 0.98202292 43.627163 0 45.100105 199.16319
Loop time of 21.576 on 4 procs for 500 steps with 16000 atoms
Performance: 20022.203 tau/day, 23.174 timesteps/s
99.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 18.438 | 19.121 | 19.812 | 14.1 | 88.62
Neigh | 1.2568 | 1.2885 | 1.325 | 2.5 | 5.97
Comm | 0.29482 | 1.0219 | 1.7352 | 63.9 | 4.74
Output | 0.00027728 | 0.00029719 | 0.0003531 | 0.0 | 0.00
Modify | 0.11153 | 0.11265 | 0.1135 | 0.2 | 0.52
Other | | 0.03194 | | | 0.15
Nlocal: 4000 ave 4092 max 3899 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 5974 ave 6019 max 5915 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Neighs: 187414 ave 196149 max 178418 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 749658
Ave neighs/atom = 46.8536
Neighbor list builds = 181
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:42

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# Chunk-averaged data for fix stat and group density/number
# Timestep Number-of-chunks Total-count
# Chunk Coord1 Ncount c_temp density/number
500 20 16000
1 -9.5 801.636 0.986368 4.00818
2 -8.5 809.788 0.966281 4.04894
3 -7.5 819.754 0.952764 4.09877
4 -6.5 820.364 0.944592 4.10182
5 -5.5 826.146 0.940968 4.13073
6 -4.5 819.52 0.941415 4.0976
7 -3.5 815.182 0.945887 4.07591
8 -2.5 817.168 0.95487 4.08584
9 -1.5 817.282 0.969225 4.08641
10 -0.5 804.204 0.989552 4.02102
11 0.5 793.266 1.01015 3.96633
12 1.5 789.056 1.0308 3.94528
13 2.5 784.344 1.04568 3.92172
14 3.5 780.592 1.05508 3.90296
15 4.5 772.218 1.05968 3.86109
16 5.5 776.968 1.06003 3.88484
17 6.5 780.858 1.05612 3.90429
18 7.5 786.174 1.04752 3.93087
19 8.5 788.922 1.03347 3.94461
20 9.5 796.558 1.01278 3.98279

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# Chunk-averaged data for fix stat and group density/number
# Timestep Number-of-chunks Total-count
# Chunk Coord1 Ncount c_temp density/number
500 20 16000
1 -9.5 801.642 0.986089 4.00821
2 -8.5 819.168 0.966072 4.09584
3 -7.5 817.382 0.952718 4.08691
4 -6.5 818 0.944633 4.09
5 -5.5 817.806 0.941105 4.08903
6 -4.5 826.11 0.941499 4.13055
7 -3.5 821.946 0.945922 4.10973
8 -2.5 816.202 0.954889 4.08101
9 -1.5 813.202 0.969281 4.06601
10 -0.5 798.904 0.989463 3.99452
11 0.5 798.056 1.01005 3.99028
12 1.5 793.114 1.03073 3.96557
13 2.5 782.812 1.04569 3.91406
14 3.5 775.69 1.05498 3.87845
15 4.5 778.094 1.05965 3.89047
16 5.5 778.856 1.06002 3.89428
17 6.5 780.51 1.05621 3.90255
18 7.5 780.518 1.04782 3.90259
19 8.5 789.698 1.03348 3.94849
20 9.5 792.29 1.01261 3.96145

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########################################################################
#### 3D droplet oscilation using many-body DPD simulation ###
#### ###
#### Created : Zhen Li (zhen_li@brown.edu) ###
#### Division of Applied Mathematics, Brown University. ###
#### ###
#### mDPD parameters follow the choice of the publication: ###
#### Z. Li et al. "Three dimensional flow structures in a moving ###
#### droplet on substrate: a dissipative particle dynamics study" ###
#### Physics of Fluids, 2013, 25: 072103. DOI: 10.1063/1.4812366 ###
########################################################################
units lj
dimension 3
boundary p p p
neighbor 0.3 bin
neigh_modify every 1 delay 0 check yes
atom_style mdpd
region mdpd block -25 25 -10 10 -10 10 units box
create_box 1 mdpd
lattice fcc 6
region film block -20 20 -7.5 7.5 -2.0 2.0 units box
create_atoms 1 region film
pair_style hybrid/overlay mdpd/rhosum mdpd 1.0 1.0 9872598
pair_coeff 1 1 mdpd/rhosum 0.75
pair_coeff 1 1 mdpd -40 25 18.0 1.0 0.75
mass 1 1.0
compute mythermo all temp
thermo 100
thermo_modify temp mythermo
thermo_modify flush yes
velocity all create 1.0 38497 loop local dist gaussian
fix mvv all mvv/dpd
#dump mydump all atom 100 atom.lammpstrj
#dump jpg all image 200 image.*.jpg type type zoom 5 adiam 0.5 &
# view 90 90 box no 0 size 600 200
#dump_modify jpg pad 4
#dump avi all movie 200 movie.avi type type zoom 5 adiam 0.5 &
# view 90 90 box no 0 size 600 200
#dump_modify avi pad 4
timestep 0.01
run 4000

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LAMMPS (11 Aug 2017)
########################################################################
#### 3D droplet oscilation using many-body DPD simulation ###
#### ###
#### Created : Zhen Li (zhen_li@brown.edu) ###
#### Division of Applied Mathematics, Brown University. ###
#### ###
#### mDPD parameters follow the choice of the publication: ###
#### Z. Li et al. "Three dimensional flow structures in a moving ###
#### droplet on substrate: a dissipative particle dynamics study" ###
#### Physics of Fluids, 2013, 25: 072103. DOI: 10.1063/1.4812366 ###
########################################################################
units lj
dimension 3
boundary p p p
neighbor 0.3 bin
neigh_modify every 1 delay 0 check yes
atom_style mdpd
region mdpd block -25 25 -10 10 -10 10 units box
create_box 1 mdpd
Created orthogonal box = (-25 -10 -10) to (25 10 10)
1 by 1 by 1 MPI processor grid
lattice fcc 6
Lattice spacing in x,y,z = 0.87358 0.87358 0.87358
region film block -20 20 -7.5 7.5 -2.0 2.0 units box
create_atoms 1 region film
Created 14333 atoms
pair_style hybrid/overlay mdpd/rhosum mdpd 1.0 1.0 9872598
pair_coeff 1 1 mdpd/rhosum 0.75
pair_coeff 1 1 mdpd -40 25 18.0 1.0 0.75
mass 1 1.0
compute mythermo all temp
thermo 100
thermo_modify temp mythermo
thermo_modify flush yes
velocity all create 1.0 38497 loop local dist gaussian
fix mvv all mvv/dpd
dump mydump all atom 100 atom.lammpstrj
#dump jpg all image 200 image.*.jpg type type zoom 5 adiam 0.5 # view 90 90 box no 0 size 600 200
#dump_modify jpg pad 4
#dump avi all movie 200 movie.avi type type zoom 5 adiam 0.5 # view 90 90 box no 0 size 600 200
#dump_modify avi pad 4
timestep 0.01
run 4000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.3
ghost atom cutoff = 1.3
binsize = 0.65, bins = 77 31 31
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair mdpd/rhosum, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(2) pair mdpd, perpetual, half/full from (1)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 9.931 | 9.931 | 9.931 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 -13.346542 0 -11.846647 -6.8495478
100 1.0321029 -7.2846779 0 -5.7366316 -0.77640205
200 1.042287 -6.9534532 0 -5.3901317 -0.27750815
300 1.0583027 -6.8483105 0 -5.2609672 -0.30347708
400 1.0493719 -6.8648608 0 -5.2909127 -0.15312495
500 1.0723786 -6.8341085 0 -5.2256528 0.017227511
600 1.0545695 -6.8152957 0 -5.2335517 -0.024362439
700 1.0507193 -6.8076033 0 -5.2316344 -0.07101536
800 1.0531856 -6.9378568 0 -5.3581886 -0.053943939
900 1.0442995 -6.8501126 0 -5.2837726 -0.13347942
1000 1.0335049 -6.8883554 0 -5.3382062 -0.18420426
1100 1.0287276 -6.8298226 0 -5.2868389 -0.12081558
1200 1.0322527 -6.9462828 0 -5.3980117 -0.18047625
1300 1.0599443 -6.9449975 0 -5.355192 -0.011763589
1400 1.0560932 -6.845479 0 -5.2614498 0.032130055
1500 1.0432786 -6.9035877 0 -5.338779 -0.10268662
1600 1.064183 -6.9116836 0 -5.3155205 -0.060722129
1700 1.0586249 -6.8768278 0 -5.2890013 0.037005566
1800 1.0576064 -7.0060193 0 -5.4197204 -0.036211254
1900 1.0595141 -6.838741 0 -5.2495807 -0.12395681
2000 1.0650509 -6.897976 0 -5.3005111 0.003594807
2100 1.0768273 -6.8874245 0 -5.2722962 0.033283489
2200 1.0511606 -6.9823162 0 -5.4056854 0.015008427
2300 1.0461138 -6.8820601 0 -5.3129988 0.064646933
2400 1.0485369 -6.9437148 0 -5.3710191 -0.16534939
2500 1.0507221 -6.9394786 0 -5.3635054 -0.098289859
2600 1.0518352 -6.8947578 0 -5.3171152 -0.011666785
2700 1.0402369 -6.9273377 0 -5.3670913 0.035267073
2800 1.0426109 -6.912024 0 -5.3482168 0.049597305
2900 1.0358928 -6.9574778 0 -5.4037471 -0.063216561
3000 1.0351023 -6.9844192 0 -5.4318742 -0.10323465
3100 1.0255005 -6.9382486 0 -5.4001052 -0.073954735
3200 1.0150616 -6.9843183 0 -5.4618321 -0.095136405
3300 1.0118112 -6.9522082 0 -5.4345973 -0.12686179
3400 1.0071522 -6.970158 0 -5.4595351 -0.012487475
3500 1.0041758 -6.9773019 0 -5.4711433 -0.098027653
3600 1.0189298 -6.9393039 0 -5.4110158 0.061631719
3700 1.012442 -6.9341423 0 -5.4155852 0.10442772
3800 1.0021246 -6.9594374 0 -5.4563553 -0.081535223
3900 1.0165002 -6.9045321 0 -5.3798882 -0.0088283303
4000 1.0077099 -6.9145511 0 -5.4030918 0.048349691
Loop time of 135.409 on 1 procs for 4000 steps with 14333 atoms
Performance: 25522.736 tau/day, 29.540 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 93.074 | 93.074 | 93.074 | 0.0 | 68.74
Neigh | 40.192 | 40.192 | 40.192 | 0.0 | 29.68
Comm | 0.19625 | 0.19625 | 0.19625 | 0.0 | 0.14
Output | 0.41756 | 0.41756 | 0.41756 | 0.0 | 0.31
Modify | 1.0706 | 1.0706 | 1.0706 | 0.0 | 0.79
Other | | 0.4581 | | | 0.34
Nlocal: 14333 ave 14333 max 14333 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 11 ave 11 max 11 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 401803 ave 401803 max 401803 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 803606 ave 803606 max 803606 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 803606
Ave neighs/atom = 56.0668
Neighbor list builds = 1050
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:02:15

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LAMMPS (11 Aug 2017)
########################################################################
#### 3D droplet oscilation using many-body DPD simulation ###
#### ###
#### Created : Zhen Li (zhen_li@brown.edu) ###
#### Division of Applied Mathematics, Brown University. ###
#### ###
#### mDPD parameters follow the choice of the publication: ###
#### Z. Li et al. "Three dimensional flow structures in a moving ###
#### droplet on substrate: a dissipative particle dynamics study" ###
#### Physics of Fluids, 2013, 25: 072103. DOI: 10.1063/1.4812366 ###
########################################################################
units lj
dimension 3
boundary p p p
neighbor 0.3 bin
neigh_modify every 1 delay 0 check yes
atom_style mdpd
region mdpd block -25 25 -10 10 -10 10 units box
create_box 1 mdpd
Created orthogonal box = (-25 -10 -10) to (25 10 10)
4 by 1 by 1 MPI processor grid
lattice fcc 6
Lattice spacing in x,y,z = 0.87358 0.87358 0.87358
region film block -20 20 -7.5 7.5 -2.0 2.0 units box
create_atoms 1 region film
Created 14333 atoms
pair_style hybrid/overlay mdpd/rhosum mdpd 1.0 1.0 9872598
pair_coeff 1 1 mdpd/rhosum 0.75
pair_coeff 1 1 mdpd -40 25 18.0 1.0 0.75
mass 1 1.0
compute mythermo all temp
thermo 100
thermo_modify temp mythermo
thermo_modify flush yes
velocity all create 1.0 38497 loop local dist gaussian
fix mvv all mvv/dpd
dump mydump all atom 100 atom.lammpstrj
#dump jpg all image 200 image.*.jpg type type zoom 5 adiam 0.5 # view 90 90 box no 0 size 600 200
#dump_modify jpg pad 4
#dump avi all movie 200 movie.avi type type zoom 5 adiam 0.5 # view 90 90 box no 0 size 600 200
#dump_modify avi pad 4
timestep 0.01
run 4000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.3
ghost atom cutoff = 1.3
binsize = 0.65, bins = 77 31 31
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair mdpd/rhosum, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(2) pair mdpd, perpetual, half/full from (1)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 6.265 | 6.655 | 7.045 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 -13.346542 0 -11.846647 -6.9757225
100 1.0406108 -7.2500697 0 -5.6892624 -0.80306477
200 1.0535506 -6.9452928 0 -5.3650772 -0.39911584
300 1.0644295 -6.8599907 0 -5.2634577 -0.2997968
400 1.0780123 -6.9471342 0 -5.3302286 -0.06274869
500 1.0672153 -6.8269984 0 -5.2262872 0.021251762
600 1.0634304 -6.8366569 0 -5.2416226 -0.021863333
700 1.0544807 -6.8272074 0 -5.2455967 -0.0064688066
800 1.0556172 -6.8859788 0 -5.3026634 0.023983333
900 1.0436201 -6.9246523 0 -5.3593313 -0.12409618
1000 1.0617016 -6.8632331 0 -5.2707919 -0.1145505
1100 1.0323831 -6.951554 0 -5.4030874 -0.030031884
1200 1.0407785 -6.931048 0 -5.3699892 -0.018362136
1300 1.0380953 -6.8785296 0 -5.3214953 -0.099308737
1400 1.0418898 -6.8998 0 -5.3370743 -0.14199421
1500 1.0487254 -6.9671212 0 -5.3941429 -0.12132644
1600 1.0561042 -6.8948881 0 -5.3108424 -0.09627292
1700 1.0524479 -6.9531441 0 -5.3745823 -0.11959782
1800 1.0541197 -6.9219819 0 -5.3409126 0.032964029
1900 1.0531221 -6.8805815 0 -5.3010085 0.030124685
2000 1.0531819 -6.8612868 0 -5.2816242 -0.076876781
2100 1.0757791 -6.919875 0 -5.3063189 -0.04060439
2200 1.069423 -6.9005754 0 -5.2965527 0.015347467
2300 1.0403109 -6.9015402 0 -5.3411827 0.0034687897
2400 1.0547448 -6.9325539 0 -5.3505471 -0.021202325
2500 1.0404195 -6.8494675 0 -5.2889472 0.086947847
2600 1.0499828 -6.9861392 0 -5.4112749 -0.018079308
2700 1.0294278 -6.8525151 0 -5.3084811 0.16911472
2800 1.0220652 -6.8993978 0 -5.366407 0.064820531
2900 1.0347904 -6.9322703 0 -5.3801929 -0.11384964
3000 1.0391372 -6.9519088 0 -5.3933117 0.003050577
3100 1.0335828 -7.0090074 0 -5.4587413 -0.17366664
3200 1.0211896 -6.9421289 0 -5.4104513 0.025299853
3300 1.0019232 -6.9426488 0 -5.4398688 -0.098334724
3400 1.0203541 -6.9310981 0 -5.4006737 -0.0015544982
3500 1.0076794 -6.9519932 0 -5.4405796 -0.056956902
3600 1.0086525 -6.9620979 0 -5.4492247 0.020014884
3700 1.0046112 -7.0011625 0 -5.4943508 -0.083936527
3800 1.0096867 -6.9470382 0 -5.4326138 -0.089521759
3900 1.0074482 -6.9959414 0 -5.4848745 -0.11873698
4000 1.01222 -6.9535694 0 -5.4353454 0.042191466
Loop time of 63.0327 on 4 procs for 4000 steps with 14333 atoms
Performance: 54828.695 tau/day, 63.459 timesteps/s
98.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 16.591 | 29.795 | 42.814 | 236.6 | 47.27
Neigh | 2.0347 | 10.239 | 18.555 | 255.6 | 16.24
Comm | 0.70099 | 6.0601 | 11.386 | 207.4 | 9.61
Output | 0.20713 | 0.40902 | 0.61087 | 31.5 | 0.65
Modify | 0.058089 | 0.27033 | 0.4851 | 40.7 | 0.43
Other | | 16.26 | | | 25.79
Nlocal: 3583.25 ave 7207 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 1055.75 ave 2131 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 100549 ave 202192 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 2
FullNghs: 201098 ave 404372 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 804390
Ave neighs/atom = 56.1215
Neighbor list builds = 1049
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:01:03

24
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# Chunk-averaged data for fix stat and group c_cc2
# Timestep Number-of-chunks Total-count
# Chunk Coord1 Ncount c_cc1 c_cc2
100 20 16000
1 -9.5 797.17 0.986661 1.0077
2 -8.5 802.61 0.967974 1.02003
3 -7.5 795.46 0.957045 1.02873
4 -6.5 806.46 0.951271 1.03428
5 -5.5 802.34 0.94898 1.03692
6 -4.5 799.84 0.949378 1.03673
7 -3.5 798.4 0.952505 1.03374
8 -2.5 800.36 0.959322 1.02778
9 -1.5 797.65 0.971516 1.01867
10 -0.5 808.88 0.990644 1.00626
11 0.5 786.29 1.00924 0.993828
12 1.5 807.16 1.02831 0.981436
13 2.5 797.54 1.04071 0.972184
14 3.5 799.67 1.04749 0.966258
15 4.5 799.61 1.05063 0.963256
16 5.5 806.11 1.05105 0.963052
17 6.5 803.67 1.04877 0.965688
18 7.5 797.39 1.04305 0.971187
19 8.5 801.85 1.03208 0.97993
20 9.5 791.54 1.01351 0.992209

24
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# Chunk-averaged data for fix stat and group c_cc2
# Timestep Number-of-chunks Total-count
# Chunk Coord1 Ncount c_cc1 c_cc2
100 20 16000
1 -9.5 806.92 0.986675 1.00766
2 -8.5 798.01 0.96792 1.02003
3 -7.5 805.43 0.956909 1.02883
4 -6.5 800.54 0.951207 1.03432
5 -5.5 794.14 0.948967 1.03691
6 -4.5 799.75 0.949379 1.03672
7 -3.5 799.65 0.952492 1.03374
8 -2.5 799.94 0.959331 1.02778
9 -1.5 800.96 0.971664 1.01861
10 -0.5 803.97 0.99074 1.00622
11 0.5 800.66 1.00949 0.993673
12 1.5 779.22 1.02824 0.981461
13 2.5 809.13 1.04056 0.972274
14 3.5 805.23 1.04747 0.966272
15 4.5 795.95 1.05061 0.96327
16 5.5 796.4 1.05105 0.963035
17 6.5 806.1 1.04883 0.965621
18 7.5 806.41 1.04305 0.971224
19 8.5 792.2 1.03211 0.979955
20 9.5 799.39 1.01362 0.992156

54
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########################################################################
### Pure diffusion with a reaction source term analog of a periodic ###
### Poiseuille flow problem using transport DPD (tDPD) simulation ###
### ###
### Created : Zhen Li (zhen_li@brown.edu) ###
### Division of Applied Mathematics, Brown University. ###
### ###
### tDPD system setup follows Fig.1 in the publication: ###
### Z. Li, A. Yazdani, A. Tartakovsky and G.E. Karniadakis. ###
### "Transport dissipative particle dynamics model for mesoscopic ###
### advection-diffusion-reaction problems. J. Chem. Phys., ###
### 2015, 143: 014101. DOI: 10.1063/1.4923254 ###
########################################################################
units lj
dimension 3
boundary p p p
neighbor 0.2 bin
neigh_modify every 1 delay 0 check yes
atom_style tdpd 2
region tdpd block -10 10 -10 10 -5 5 units box
create_box 1 tdpd
create_atoms 1 random 16000 276438 NULL
mass 1 1.0
set atom * cc 1 1.0
set atom * cc 2 1.0
pair_style tdpd 1.0 1.58 9872598
pair_coeff 1 1 18.75 4.5 0.41 1.58 1.58 1.0 1.0E-5 2.0 3.0 1.0E-5 2.0
compute mythermo all temp
thermo 50
thermo_modify temp mythermo
thermo_modify flush yes
velocity all create 1.0 432982 loop local dist gaussian
fix mvv all mvv/tdpd 0.5
fix upper1 all tdpd/source 1 cuboid 0.0 5.0 0.0 20.0 10.0 10.0 0.01
fix lower1 all tdpd/source 1 cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 -0.01
fix upper2 all tdpd/source 2 cuboid 0.0 5.0 0.0 20.0 10.0 10.0 -0.01
fix lower2 all tdpd/source 2 cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 0.01
timestep 0.01
run 500
reset_timestep 0
compute cc1 all tdpd/cc/atom 1
compute cc2 all tdpd/cc/atom 2
compute bin all chunk/atom bin/1d y 0.0 1.0
fix stat all ave/chunk 1 100 100 bin c_cc1 c_cc2 norm sample file cc.profile
run 100

146
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LAMMPS (11 Aug 2017)
########################################################################
### Pure diffusion with a reaction source term analog of a periodic ###
### Poiseuille flow problem using transport DPD (tDPD) simulation ###
### ###
### Created : Zhen Li (zhen_li@brown.edu) ###
### Division of Applied Mathematics, Brown University. ###
### ###
### tDPD system setup follows Fig.1 in the publication: ###
### Z. Li, A. Yazdani, A. Tartakovsky and G.E. Karniadakis. ###
### "Transport dissipative particle dynamics model for mesoscopic ###
### advection-diffusion-reaction problems. J. Chem. Phys., ###
### 2015, 143: 014101. DOI: 10.1063/1.4923254 ###
########################################################################
units lj
dimension 3
boundary p p p
neighbor 0.2 bin
neigh_modify every 1 delay 0 check yes
atom_style tdpd 2
region tdpd block -10 10 -10 10 -5 5 units box
create_box 1 tdpd
Created orthogonal box = (-10 -10 -5) to (10 10 5)
1 by 1 by 1 MPI processor grid
create_atoms 1 random 16000 276438 NULL
Created 16000 atoms
mass 1 1.0
set atom * cc 1 1.0
16000 settings made for cc index 1
set atom * cc 2 1.0
16000 settings made for cc index 2
pair_style tdpd 1.0 1.58 9872598
pair_coeff 1 1 18.75 4.5 0.41 1.58 1.58 1.0 1.0E-5 2.0 3.0 1.0E-5 2.0
compute mythermo all temp
thermo 50
thermo_modify temp mythermo
thermo_modify flush yes
velocity all create 1.0 432982 loop local dist gaussian
fix mvv all mvv/tdpd 0.5
fix upper1 all tdpd/source 1 cuboid 0.0 5.0 0.0 20.0 10.0 10.0 0.01
fix lower1 all tdpd/source 1 cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 -0.01
fix upper2 all tdpd/source 2 cuboid 0.0 5.0 0.0 20.0 10.0 10.0 -0.01
fix lower2 all tdpd/source 2 cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 0.01
timestep 0.01
run 500
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.78
ghost atom cutoff = 1.78
binsize = 0.89, bins = 23 23 12
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tdpd, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 11.3 | 11.3 | 11.3 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 48.948932 0 50.448838 202.19166
50 0.99837766 43.949877 0 45.447349 195.80936
100 0.99846831 43.756995 0 45.254604 198.22348
150 1.0026903 43.72408 0 45.228021 196.61676
200 1.0063144 43.722388 0 45.231765 194.17954
250 1.0032304 43.721864 0 45.226615 197.85829
300 0.9932656 43.703526 0 45.193331 196.57406
350 1.0002916 43.720498 0 45.220841 193.55346
400 0.99475486 43.722965 0 45.215004 196.81546
450 1.0011803 43.712447 0 45.214124 200.46118
500 1.0009006 43.708984 0 45.210241 197.38953
Loop time of 96.0326 on 1 procs for 500 steps with 16000 atoms
Performance: 4498.474 tau/day, 5.207 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 90.083 | 90.083 | 90.083 | 0.0 | 93.80
Neigh | 5.049 | 5.049 | 5.049 | 0.0 | 5.26
Comm | 0.34141 | 0.34141 | 0.34141 | 0.0 | 0.36
Output | 0.00092816 | 0.00092816 | 0.00092816 | 0.0 | 0.00
Modify | 0.45991 | 0.45991 | 0.45991 | 0.0 | 0.48
Other | | 0.09865 | | | 0.10
Nlocal: 16000 ave 16000 max 16000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 14091 ave 14091 max 14091 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 749379 ave 749379 max 749379 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 749379
Ave neighs/atom = 46.8362
Neighbor list builds = 183
Dangerous builds = 0
reset_timestep 0
compute cc1 all tdpd/cc/atom 1
compute cc2 all tdpd/cc/atom 2
compute bin all chunk/atom bin/1d y 0.0 1.0
fix stat all ave/chunk 1 100 100 bin c_cc1 c_cc2 norm sample file cc.profile
run 100
Per MPI rank memory allocation (min/avg/max) = 11.8 | 11.8 | 11.8 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.0009006 43.708984 0 45.210241 199.3205
50 1.0007276 43.704844 0 45.205842 197.77053
100 1.0039032 43.714201 0 45.219961 197.31118
Loop time of 19.0326 on 1 procs for 100 steps with 16000 atoms
Performance: 4539.577 tau/day, 5.254 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 17.842 | 17.842 | 17.842 | 0.0 | 93.74
Neigh | 0.98674 | 0.98674 | 0.98674 | 0.0 | 5.18
Comm | 0.066013 | 0.066013 | 0.066013 | 0.0 | 0.35
Output | 0.00016284 | 0.00016284 | 0.00016284 | 0.0 | 0.00
Modify | 0.11795 | 0.11795 | 0.11795 | 0.0 | 0.62
Other | | 0.02012 | | | 0.11
Nlocal: 16000 ave 16000 max 16000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 14126 ave 14126 max 14126 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 748927 ave 748927 max 748927 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 748927
Ave neighs/atom = 46.8079
Neighbor list builds = 37
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:01:55

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LAMMPS (11 Aug 2017)
########################################################################
### Pure diffusion with a reaction source term analog of a periodic ###
### Poiseuille flow problem using transport DPD (tDPD) simulation ###
### ###
### Created : Zhen Li (zhen_li@brown.edu) ###
### Division of Applied Mathematics, Brown University. ###
### ###
### tDPD system setup follows Fig.1 in the publication: ###
### Z. Li, A. Yazdani, A. Tartakovsky and G.E. Karniadakis. ###
### "Transport dissipative particle dynamics model for mesoscopic ###
### advection-diffusion-reaction problems. J. Chem. Phys., ###
### 2015, 143: 014101. DOI: 10.1063/1.4923254 ###
########################################################################
units lj
dimension 3
boundary p p p
neighbor 0.2 bin
neigh_modify every 1 delay 0 check yes
atom_style tdpd 2
region tdpd block -10 10 -10 10 -5 5 units box
create_box 1 tdpd
Created orthogonal box = (-10 -10 -5) to (10 10 5)
2 by 2 by 1 MPI processor grid
create_atoms 1 random 16000 276438 NULL
Created 16000 atoms
mass 1 1.0
set atom * cc 1 1.0
16000 settings made for cc index 1
set atom * cc 2 1.0
16000 settings made for cc index 2
pair_style tdpd 1.0 1.58 9872598
pair_coeff 1 1 18.75 4.5 0.41 1.58 1.58 1.0 1.0E-5 2.0 3.0 1.0E-5 2.0
compute mythermo all temp
thermo 50
thermo_modify temp mythermo
thermo_modify flush yes
velocity all create 1.0 432982 loop local dist gaussian
fix mvv all mvv/tdpd 0.5
fix upper1 all tdpd/source 1 cuboid 0.0 5.0 0.0 20.0 10.0 10.0 0.01
fix lower1 all tdpd/source 1 cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 -0.01
fix upper2 all tdpd/source 2 cuboid 0.0 5.0 0.0 20.0 10.0 10.0 -0.01
fix lower2 all tdpd/source 2 cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 0.01
timestep 0.01
run 500
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.78
ghost atom cutoff = 1.78
binsize = 0.89, bins = 23 23 12
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tdpd, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.814 | 4.823 | 4.829 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 48.948932 0 50.448838 199.65978
50 1.0153476 43.948796 0 45.471722 198.3346
100 1.0064284 43.754875 0 45.264424 197.5308
150 0.99609985 43.726751 0 45.220807 197.50623
200 1.0016604 43.720283 0 45.22268 197.81129
250 1.0054979 43.718568 0 45.22672 195.79405
300 0.9997618 43.716617 0 45.216166 197.84788
350 0.99170101 43.72093 0 45.208389 196.07711
400 1.0043692 43.71648 0 45.22294 199.55247
450 1.0086263 43.709988 0 45.222833 198.20516
500 1.0029076 43.717879 0 45.222146 197.26281
Loop time of 24.5533 on 4 procs for 500 steps with 16000 atoms
Performance: 17594.412 tau/day, 20.364 timesteps/s
99.9% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 22.236 | 22.418 | 22.736 | 4.0 | 91.30
Neigh | 1.2759 | 1.2883 | 1.3077 | 1.1 | 5.25
Comm | 0.35749 | 0.69526 | 0.88462 | 24.1 | 2.83
Output | 0.00043321 | 0.00050318 | 0.00070691 | 0.0 | 0.00
Modify | 0.11555 | 0.11648 | 0.11888 | 0.4 | 0.47
Other | | 0.03473 | | | 0.14
Nlocal: 4000 ave 4012 max 3982 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Nghost: 5986.25 ave 6016 max 5956 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Neighs: 187309 ave 188264 max 186087 min
Histogram: 1 0 0 0 1 0 0 1 0 1
Total # of neighbors = 749235
Ave neighs/atom = 46.8272
Neighbor list builds = 180
Dangerous builds = 0
reset_timestep 0
compute cc1 all tdpd/cc/atom 1
compute cc2 all tdpd/cc/atom 2
compute bin all chunk/atom bin/1d y 0.0 1.0
fix stat all ave/chunk 1 100 100 bin c_cc1 c_cc2 norm sample file cc.profile
run 100
Per MPI rank memory allocation (min/avg/max) = 5.065 | 5.074 | 5.082 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.0029076 43.717879 0 45.222146 198.45789
50 1.0077982 43.713264 0 45.224867 196.56183
100 1.0036823 43.708022 0 45.213451 196.00815
Loop time of 4.79577 on 4 procs for 100 steps with 16000 atoms
Performance: 18015.870 tau/day, 20.852 timesteps/s
99.9% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.3481 | 4.39 | 4.4398 | 1.7 | 91.54
Neigh | 0.25477 | 0.25675 | 0.25963 | 0.4 | 5.35
Comm | 0.059327 | 0.11194 | 0.15608 | 11.0 | 2.33
Output | 0.00011206 | 0.00011748 | 0.00011992 | 0.0 | 0.00
Modify | 0.030417 | 0.030622 | 0.030739 | 0.1 | 0.64
Other | | 0.006301 | | | 0.13
Nlocal: 4000 ave 4010 max 3987 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Nghost: 5985.25 ave 6025 max 5959 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Neighs: 187304 ave 188092 max 186449 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Total # of neighbors = 749216
Ave neighs/atom = 46.826
Neighbor list builds = 38
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:29