Merge branch 'master' into chem_snap
This commit is contained in:
1
examples/USER/mesont/C_10_10.mesocnt
Symbolic link
1
examples/USER/mesont/C_10_10.mesocnt
Symbolic link
@ -0,0 +1 @@
|
||||
../../../potentials/C_10_10.mesocnt
|
||||
19
examples/USER/mesont/README
Normal file
19
examples/USER/mesont/README
Normal file
@ -0,0 +1,19 @@
|
||||
=== USER-MESONT examples ===
|
||||
===============================
|
||||
|
||||
The files in this folder provide examples of using the CNT
|
||||
mesoscopic force field (USER-MESONT).
|
||||
|
||||
Contributing author: Maxim Shugaev (UVA), mvs9t@virginia.edu
|
||||
|
||||
"bundle" is an example with a single bundle composed of 7 nanotubes
|
||||
using the mesont/tpm pair style
|
||||
|
||||
"film" is an example with a film composed of 396 200-nm-long
|
||||
nanotubes (79596 nodes) using the mesont/tpm pair style
|
||||
|
||||
|
||||
Contributing author: Philipp Kloza (U Cambridge), pak37@cam.ac.uk
|
||||
|
||||
"cnt" is an example showing CNT aerogel formation
|
||||
using the mesocnt pair style
|
||||
1
examples/USER/mesont/TABTP_10_10.mesont
Symbolic link
1
examples/USER/mesont/TABTP_10_10.mesont
Symbolic link
@ -0,0 +1 @@
|
||||
../../../potentials/TABTP_10_10.mesont
|
||||
93
examples/USER/mesont/data.bundle
Normal file
93
examples/USER/mesont/data.bundle
Normal file
@ -0,0 +1,93 @@
|
||||
|
||||
|
||||
77 atoms
|
||||
|
||||
1 atom types
|
||||
|
||||
-143.89 143.89 xlo xhi
|
||||
-143.89 143.89 ylo yhi
|
||||
0 220 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 1.0
|
||||
|
||||
Atoms
|
||||
|
||||
1 1 1 11 2 5860.43 6.785 20 0 0 0 0 0 0 0
|
||||
2 1 1 1 3 5860.43 6.785 20 0 0 0 20 0 0 0
|
||||
3 1 1 2 4 5860.43 6.785 20 0 0 0 40 0 0 0
|
||||
4 1 1 3 5 5860.43 6.785 20 0 0 0 60 0 0 0
|
||||
5 1 1 4 6 5860.43 6.785 20 0 0 0 80 0 0 0
|
||||
6 1 1 5 7 5860.43 6.785 20 0 0 0 100 0 0 0
|
||||
7 1 1 6 8 5860.43 6.785 20 0 0 0 120 0 0 0
|
||||
8 1 1 7 9 5860.43 6.785 20 0 0 0 140 0 0 0
|
||||
9 1 1 8 10 5860.43 6.785 20 0 0 0 160 0 0 0
|
||||
10 1 1 9 11 5860.43 6.785 20 0 0 0 180 0 0 0
|
||||
11 1 1 10 1 5860.43 6.785 20 0 0 0 200 0 0 0
|
||||
12 2 1 22 13 5860.43 6.785 20 0 16.6992 0 0 0 0 0
|
||||
13 2 1 12 14 5860.43 6.785 20 0 16.6992 0 20 0 0 0
|
||||
14 2 1 13 15 5860.43 6.785 20 0 16.6992 0 40 0 0 0
|
||||
15 2 1 14 16 5860.43 6.785 20 0 16.6992 0 60 0 0 0
|
||||
16 2 1 15 17 5860.43 6.785 20 0 16.6992 0 80 0 0 0
|
||||
17 2 1 16 18 5860.43 6.785 20 0 16.6992 0 100 0 0 0
|
||||
18 2 1 17 19 5860.43 6.785 20 0 16.6992 0 120 0 0 0
|
||||
19 2 1 18 20 5860.43 6.785 20 0 16.6992 0 140 0 0 0
|
||||
20 2 1 19 21 5860.43 6.785 20 0 16.6992 0 160 0 0 0
|
||||
21 2 1 20 22 5860.43 6.785 20 0 16.6992 0 180 0 0 0
|
||||
22 2 1 21 12 5860.43 6.785 20 0 16.6992 0 200 0 0 0
|
||||
23 3 1 33 24 5860.43 6.785 20 0 8.3496 14.4619 0 0 0 0
|
||||
24 3 1 23 25 5860.43 6.785 20 0 8.3496 14.4619 20 0 0 0
|
||||
25 3 1 24 26 5860.43 6.785 20 0 8.3496 14.4619 40 0 0 0
|
||||
26 3 1 25 27 5860.43 6.785 20 0 8.3496 14.4619 60 0 0 0
|
||||
27 3 1 26 28 5860.43 6.785 20 0 8.3496 14.4619 80 0 0 0
|
||||
28 3 1 27 29 5860.43 6.785 20 0 8.3496 14.4619 100 0 0 0
|
||||
29 3 1 28 30 5860.43 6.785 20 0 8.3496 14.4619 120 0 0 0
|
||||
30 3 1 29 31 5860.43 6.785 20 0 8.3496 14.4619 140 0 0 0
|
||||
31 3 1 30 32 5860.43 6.785 20 0 8.3496 14.4619 160 0 0 0
|
||||
32 3 1 31 33 5860.43 6.785 20 0 8.3496 14.4619 180 0 0 0
|
||||
33 3 1 32 23 5860.43 6.785 20 0 8.3496 14.4619 200 0 0 0
|
||||
34 4 1 44 35 5860.43 6.785 20 0 -8.3496 14.4619 0 0 0 0
|
||||
35 4 1 34 36 5860.43 6.785 20 0 -8.3496 14.4619 20 0 0 0
|
||||
36 4 1 35 37 5860.43 6.785 20 0 -8.3496 14.4619 40 0 0 0
|
||||
37 4 1 36 38 5860.43 6.785 20 0 -8.3496 14.4619 60 0 0 0
|
||||
38 4 1 37 39 5860.43 6.785 20 0 -8.3496 14.4619 80 0 0 0
|
||||
39 4 1 38 40 5860.43 6.785 20 0 -8.3496 14.4619 100 0 0 0
|
||||
40 4 1 39 41 5860.43 6.785 20 0 -8.3496 14.4619 120 0 0 0
|
||||
41 4 1 40 42 5860.43 6.785 20 0 -8.3496 14.4619 140 0 0 0
|
||||
42 4 1 41 43 5860.43 6.785 20 0 -8.3496 14.4619 160 0 0 0
|
||||
43 4 1 42 44 5860.43 6.785 20 0 -8.3496 14.4619 180 0 0 0
|
||||
44 4 1 43 34 5860.43 6.785 20 0 -8.3496 14.4619 200 0 0 0
|
||||
45 5 1 55 46 5860.43 6.785 20 0 -16.6992 0 0 0 0 0
|
||||
46 5 1 45 47 5860.43 6.785 20 0 -16.6992 0 20 0 0 0
|
||||
47 5 1 46 48 5860.43 6.785 20 0 -16.6992 0 40 0 0 0
|
||||
48 5 1 47 49 5860.43 6.785 20 0 -16.6992 0 60 0 0 0
|
||||
49 5 1 48 50 5860.43 6.785 20 0 -16.6992 0 80 0 0 0
|
||||
50 5 1 49 51 5860.43 6.785 20 0 -16.6992 0 100 0 0 0
|
||||
51 5 1 50 52 5860.43 6.785 20 0 -16.6992 0 120 0 0 0
|
||||
52 5 1 51 53 5860.43 6.785 20 0 -16.6992 0 140 0 0 0
|
||||
53 5 1 52 54 5860.43 6.785 20 0 -16.6992 0 160 0 0 0
|
||||
54 5 1 53 55 5860.43 6.785 20 0 -16.6992 0 180 0 0 0
|
||||
55 5 1 54 45 5860.43 6.785 20 0 -16.6992 0 200 0 0 0
|
||||
56 6 1 66 57 5860.43 6.785 20 0 -8.3496 -14.4619 0 0 0 0
|
||||
57 6 1 56 58 5860.43 6.785 20 0 -8.3496 -14.4619 20 0 0 0
|
||||
58 6 1 57 59 5860.43 6.785 20 0 -8.3496 -14.4619 40 0 0 0
|
||||
59 6 1 58 60 5860.43 6.785 20 0 -8.3496 -14.4619 60 0 0 0
|
||||
60 6 1 59 61 5860.43 6.785 20 0 -8.3496 -14.4619 80 0 0 0
|
||||
61 6 1 60 62 5860.43 6.785 20 0 -8.3496 -14.4619 100 0 0 0
|
||||
62 6 1 61 63 5860.43 6.785 20 0 -8.3496 -14.4619 120 0 0 0
|
||||
63 6 1 62 64 5860.43 6.785 20 0 -8.3496 -14.4619 140 0 0 0
|
||||
64 6 1 63 65 5860.43 6.785 20 0 -8.3496 -14.4619 160 0 0 0
|
||||
65 6 1 64 66 5860.43 6.785 20 0 -8.3496 -14.4619 180 0 0 0
|
||||
66 6 1 65 56 5860.43 6.785 20 0 -8.3496 -14.4619 200 0 0 0
|
||||
67 7 1 77 68 5860.43 6.785 20 0 8.3496 -14.4619 0 0 0 0
|
||||
68 7 1 67 69 5860.43 6.785 20 0 8.3496 -14.4619 20 0 0 0
|
||||
69 7 1 68 70 5860.43 6.785 20 0 8.3496 -14.4619 40 0 0 0
|
||||
70 7 1 69 71 5860.43 6.785 20 0 8.3496 -14.4619 60 0 0 0
|
||||
71 7 1 70 72 5860.43 6.785 20 0 8.3496 -14.4619 80 0 0 0
|
||||
72 7 1 71 73 5860.43 6.785 20 0 8.3496 -14.4619 100 0 0 0
|
||||
73 7 1 72 74 5860.43 6.785 20 0 8.3496 -14.4619 120 0 0 0
|
||||
74 7 1 73 75 5860.43 6.785 20 0 8.3496 -14.4619 140 0 0 0
|
||||
75 7 1 74 76 5860.43 6.785 20 0 8.3496 -14.4619 160 0 0 0
|
||||
76 7 1 75 77 5860.43 6.785 20 0 8.3496 -14.4619 180 0 0 0
|
||||
77 7 1 76 67 5860.43 6.785 20 0 8.3496 -14.4619 200 0 0 0
|
||||
79612
examples/USER/mesont/data.film
Normal file
79612
examples/USER/mesont/data.film
Normal file
File diff suppressed because it is too large
Load Diff
29
examples/USER/mesont/in.bundle
Normal file
29
examples/USER/mesont/in.bundle
Normal file
@ -0,0 +1,29 @@
|
||||
processors 1 1 *
|
||||
newton on
|
||||
units metal
|
||||
lattice sc 1.0
|
||||
boundary fs fs p
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 5 delay 0 check yes
|
||||
|
||||
atom_style mesont
|
||||
# cut, path, BendingMode, TPMType
|
||||
pair_style mesont/tpm 45.0 MESONT-TABTP_10_10.xrs 0 0
|
||||
read_data data.bundle
|
||||
pair_coeff * *
|
||||
|
||||
velocity all create 6000.0 2019
|
||||
timestep 0.005
|
||||
fix 1 all nve
|
||||
thermo 10
|
||||
reset_timestep 0
|
||||
|
||||
compute Es all mesont estretch
|
||||
compute Eb all mesont ebend
|
||||
compute Et all mesont etube
|
||||
compute B all property/atom buckling
|
||||
|
||||
thermo_style custom step time temp etotal ke pe c_Es c_Eb c_Et
|
||||
#dump out_dump all custom 50 dump.bundle id type x y z c_Es c_Eb c_Et c_B ix iy iz
|
||||
|
||||
run 100
|
||||
28
examples/USER/mesont/in.film
Normal file
28
examples/USER/mesont/in.film
Normal file
@ -0,0 +1,28 @@
|
||||
newton on
|
||||
units metal
|
||||
lattice sc 1.0
|
||||
boundary p p fs
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 5 delay 0 check yes
|
||||
|
||||
atom_style mesont
|
||||
# cut, path, BendingMode, TPMType
|
||||
pair_style mesont/tpm 30.0 MESONT-TABTP_10_10.xrs 1 0
|
||||
read_data data.film
|
||||
pair_coeff * *
|
||||
|
||||
velocity all create 600.0 2019
|
||||
timestep 0.01
|
||||
fix 1 all nve
|
||||
thermo 10
|
||||
reset_timestep 0
|
||||
|
||||
compute Es all mesont estretch
|
||||
compute Eb all mesont ebend
|
||||
compute Et all mesont etube
|
||||
compute B all property/atom buckling
|
||||
|
||||
thermo_style custom step time temp etotal ke pe c_Es c_Eb c_Et
|
||||
#dump out_dump all custom 10 dump.film id type x y z c_Es c_Eb c_Et c_B ix iy iz
|
||||
|
||||
run 20
|
||||
90
examples/USER/mesont/log.2Jun2020.bundle.g++.1
Normal file
90
examples/USER/mesont/log.2Jun2020.bundle.g++.1
Normal file
@ -0,0 +1,90 @@
|
||||
LAMMPS (5 May 2020)
|
||||
processors 1 1 *
|
||||
newton on
|
||||
units metal
|
||||
lattice sc 1.0
|
||||
Lattice spacing in x,y,z = 1 1 1
|
||||
boundary fs fs p
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 5 delay 0 check yes
|
||||
|
||||
atom_style mesont
|
||||
# cut, path, BendingMode, TPMType
|
||||
pair_style mesont/tpm 45.0 MESONT-TABTP_10_10.xrs 0 0
|
||||
read_data data.bundle
|
||||
orthogonal box = (-143.89 -143.89 0) to (143.89 143.89 220)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
77 atoms
|
||||
read_data CPU = 0.000613213 secs
|
||||
pair_coeff * *
|
||||
|
||||
velocity all create 6000.0 2019
|
||||
timestep 0.005
|
||||
fix 1 all nve
|
||||
thermo 10
|
||||
reset_timestep 0
|
||||
|
||||
compute Es all mesont estretch
|
||||
compute Eb all mesont ebend
|
||||
compute Et all mesont etube
|
||||
compute B all property/atom buckling
|
||||
|
||||
thermo_style custom step time temp etotal ke pe c_Es c_Eb c_Et
|
||||
#dump out_dump all custom 50 dump.bundle id type x y z c_Es c_Eb c_Et c_B ix iy iz
|
||||
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 5 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 46
|
||||
ghost atom cutoff = 46
|
||||
binsize = 23, bins = 7 7 10
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair mesont/tpm, perpetual
|
||||
attributes: full, newton on, ghost
|
||||
pair build: full/bin/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.675 | 4.675 | 4.675 Mbytes
|
||||
Step Time Temp TotEng KinEng PotEng c_Es c_Eb c_Et
|
||||
0 0 6000 -201.86935 58.942626 -260.81198 0 0 -260.81198
|
||||
10 0.05 5114.1875 -201.86234 50.240607 -252.10295 4.8334861 2.3998206 -259.33626
|
||||
20 0.1 3437.2958 -201.8522 33.767207 -235.61941 11.42384 8.3426957 -255.38594
|
||||
30 0.15 2430.6571 -201.85242 23.878219 -225.73064 10.346152 14.72688 -250.80367
|
||||
40 0.2 2154.4755 -201.85683 21.165074 -223.0219 6.8146112 18.325709 -248.16222
|
||||
50 0.25 2021.7899 -201.85503 19.861601 -221.71663 9.2972022 17.644143 -248.65798
|
||||
60 0.3 2234.553 -201.85193 21.951737 -223.80367 13.541921 13.673721 -251.01931
|
||||
70 0.35 3099.6503 -201.85721 30.450255 -232.30747 11.833679 9.0583807 -253.19953
|
||||
80 0.4 3849.9855 -201.8635 37.821376 -239.68487 7.9899173 6.4332848 -254.10807
|
||||
90 0.45 3618.1311 -201.85967 35.543692 -237.40336 9.2616931 7.0452637 -253.71032
|
||||
100 0.5 2866.2722 -201.85273 28.157602 -230.01033 12.204916 10.284525 -252.49977
|
||||
Loop time of 0.419735 on 1 procs for 100 steps with 77 atoms
|
||||
|
||||
Performance: 102.922 ns/day, 0.233 hours/ns, 238.245 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.41922 | 0.41922 | 0.41922 | 0.0 | 99.88
|
||||
Neigh | 5.8174e-05 | 5.8174e-05 | 5.8174e-05 | 0.0 | 0.01
|
||||
Comm | 7.0333e-05 | 7.0333e-05 | 7.0333e-05 | 0.0 | 0.02
|
||||
Output | 0.00017667 | 0.00017667 | 0.00017667 | 0.0 | 0.04
|
||||
Modify | 0.00011945 | 0.00011945 | 0.00011945 | 0.0 | 0.03
|
||||
Other | | 8.702e-05 | | | 0.02
|
||||
|
||||
Nlocal: 77 ave 77 max 77 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 35 ave 35 max 35 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
|
||||
FullNghs: 2222 ave 2222 max 2222 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 2222
|
||||
Ave neighs/atom = 28.8571
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:01
|
||||
90
examples/USER/mesont/log.2Jun2020.bundle.g++.4
Normal file
90
examples/USER/mesont/log.2Jun2020.bundle.g++.4
Normal file
@ -0,0 +1,90 @@
|
||||
LAMMPS (5 May 2020)
|
||||
processors 1 1 *
|
||||
newton on
|
||||
units metal
|
||||
lattice sc 1.0
|
||||
Lattice spacing in x,y,z = 1 1 1
|
||||
boundary fs fs p
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 5 delay 0 check yes
|
||||
|
||||
atom_style mesont
|
||||
# cut, path, BendingMode, TPMType
|
||||
pair_style mesont/tpm 45.0 MESONT-TABTP_10_10.xrs 0 0
|
||||
read_data data.bundle
|
||||
orthogonal box = (-143.89 -143.89 0) to (143.89 143.89 220)
|
||||
1 by 1 by 4 MPI processor grid
|
||||
reading atoms ...
|
||||
77 atoms
|
||||
read_data CPU = 0.000590563 secs
|
||||
pair_coeff * *
|
||||
|
||||
velocity all create 6000.0 2019
|
||||
timestep 0.005
|
||||
fix 1 all nve
|
||||
thermo 10
|
||||
reset_timestep 0
|
||||
|
||||
compute Es all mesont estretch
|
||||
compute Eb all mesont ebend
|
||||
compute Et all mesont etube
|
||||
compute B all property/atom buckling
|
||||
|
||||
thermo_style custom step time temp etotal ke pe c_Es c_Eb c_Et
|
||||
#dump out_dump all custom 50 dump.bundle id type x y z c_Es c_Eb c_Et c_B ix iy iz
|
||||
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 5 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 46
|
||||
ghost atom cutoff = 46
|
||||
binsize = 23, bins = 7 7 10
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair mesont/tpm, perpetual
|
||||
attributes: full, newton on, ghost
|
||||
pair build: full/bin/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.671 | 4.671 | 4.671 Mbytes
|
||||
Step Time Temp TotEng KinEng PotEng c_Es c_Eb c_Et
|
||||
0 0 6000 -201.86935 58.942626 -260.81198 0 0 -260.81198
|
||||
10 0.05 5114.1875 -201.86234 50.240607 -252.10295 4.8334861 2.3998206 -259.33626
|
||||
20 0.1 3437.2958 -201.8522 33.767207 -235.61941 11.42384 8.3426957 -255.38594
|
||||
30 0.15 2430.6571 -201.85242 23.878219 -225.73064 10.346152 14.72688 -250.80367
|
||||
40 0.2 2154.4755 -201.85683 21.165074 -223.0219 6.8146112 18.325709 -248.16222
|
||||
50 0.25 2021.7899 -201.85503 19.861601 -221.71663 9.2972022 17.644143 -248.65798
|
||||
60 0.3 2234.553 -201.85193 21.951737 -223.80367 13.541921 13.673721 -251.01931
|
||||
70 0.35 3099.6503 -201.85721 30.450255 -232.30747 11.833679 9.0583807 -253.19953
|
||||
80 0.4 3849.9855 -201.8635 37.821376 -239.68487 7.9899173 6.4332848 -254.10807
|
||||
90 0.45 3618.1311 -201.85967 35.543692 -237.40336 9.2616931 7.0452637 -253.71032
|
||||
100 0.5 2866.2722 -201.85273 28.157602 -230.01033 12.204916 10.284525 -252.49977
|
||||
Loop time of 0.145545 on 4 procs for 100 steps with 77 atoms
|
||||
|
||||
Performance: 296.815 ns/day, 0.081 hours/ns, 687.071 timesteps/s
|
||||
95.9% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.046723 | 0.097529 | 0.14388 | 11.0 | 67.01
|
||||
Neigh | 2.5511e-05 | 2.8729e-05 | 3.171e-05 | 0.0 | 0.02
|
||||
Comm | 0.00058556 | 0.045174 | 0.098462 | 16.5 | 31.04
|
||||
Output | 0.0001483 | 0.0010182 | 0.002851 | 3.5 | 0.70
|
||||
Modify | 3.8147e-05 | 4.065e-05 | 4.4107e-05 | 0.0 | 0.03
|
||||
Other | | 0.001755 | | | 1.21
|
||||
|
||||
Nlocal: 19.25 ave 21 max 16 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
||||
Nghost: 33.25 ave 40 max 28 min
|
||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 555.5 ave 606 max 460 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
||||
|
||||
Total # of neighbors = 2222
|
||||
Ave neighs/atom = 28.8571
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:01
|
||||
81
examples/USER/mesont/log.2Jun2020.film.g++.1
Normal file
81
examples/USER/mesont/log.2Jun2020.film.g++.1
Normal file
@ -0,0 +1,81 @@
|
||||
LAMMPS (5 May 2020)
|
||||
newton on
|
||||
units metal
|
||||
lattice sc 1.0
|
||||
Lattice spacing in x,y,z = 1 1 1
|
||||
boundary p p fs
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 5 delay 0 check yes
|
||||
|
||||
atom_style mesont
|
||||
# cut, path, BendingMode, TPMType
|
||||
pair_style mesont/tpm 30.0 MESONT-TABTP_10_10.xrs 1 0
|
||||
read_data data.film
|
||||
orthogonal box = (-2500 -2500 -300) to (2500 2500 402.42)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
79596 atoms
|
||||
read_data CPU = 0.0860629 secs
|
||||
pair_coeff * *
|
||||
|
||||
velocity all create 600.0 2019
|
||||
timestep 0.01
|
||||
fix 1 all nve
|
||||
thermo 10
|
||||
reset_timestep 0
|
||||
|
||||
compute Es all mesont estretch
|
||||
compute Eb all mesont ebend
|
||||
compute Et all mesont etube
|
||||
compute B all property/atom buckling
|
||||
|
||||
thermo_style custom step time temp etotal ke pe c_Es c_Eb c_Et
|
||||
#dump out_dump all custom 10 dump.film id type x y z c_Es c_Eb c_Et c_B ix iy iz
|
||||
|
||||
run 20
|
||||
Neighbor list info ...
|
||||
update every 5 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 31
|
||||
ghost atom cutoff = 31
|
||||
binsize = 15.5, bins = 323 323 26
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair mesont/tpm, perpetual
|
||||
attributes: full, newton on, ghost
|
||||
pair build: full/bin/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 37.43 | 37.43 | 37.43 Mbytes
|
||||
Step Time Temp TotEng KinEng PotEng c_Es c_Eb c_Et
|
||||
0 0 600 1347.2158 6173.0767 -4825.8609 28.669574 21.29406 -4875.8245
|
||||
10 0.1 389.40755 1373.7864 4006.4045 -2632.6181 848.00267 1404.4323 -4885.053
|
||||
20 0.2 313.65714 1399.9427 3227.0494 -1827.1067 1201.1732 1882.1342 -4910.4141
|
||||
Loop time of 10.2438 on 1 procs for 20 steps with 79596 atoms
|
||||
|
||||
Performance: 1.687 ns/day, 14.228 hours/ns, 1.952 timesteps/s
|
||||
99.0% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 10.226 | 10.226 | 10.226 | 0.0 | 99.82
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00081086 | 0.00081086 | 0.00081086 | 0.0 | 0.01
|
||||
Output | 0.00046563 | 0.00046563 | 0.00046563 | 0.0 | 0.00
|
||||
Modify | 0.015165 | 0.015165 | 0.015165 | 0.0 | 0.15
|
||||
Other | | 0.001869 | | | 0.02
|
||||
|
||||
Nlocal: 79596 ave 79596 max 79596 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1879 ave 1879 max 1879 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
|
||||
FullNghs: 642270 ave 642270 max 642270 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 642270
|
||||
Ave neighs/atom = 8.06912
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:11
|
||||
81
examples/USER/mesont/log.2Jun2020.film.g++.4
Normal file
81
examples/USER/mesont/log.2Jun2020.film.g++.4
Normal file
@ -0,0 +1,81 @@
|
||||
LAMMPS (5 May 2020)
|
||||
newton on
|
||||
units metal
|
||||
lattice sc 1.0
|
||||
Lattice spacing in x,y,z = 1 1 1
|
||||
boundary p p fs
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 5 delay 0 check yes
|
||||
|
||||
atom_style mesont
|
||||
# cut, path, BendingMode, TPMType
|
||||
pair_style mesont/tpm 30.0 MESONT-TABTP_10_10.xrs 1 0
|
||||
read_data data.film
|
||||
orthogonal box = (-2500 -2500 -300) to (2500 2500 402.42)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
79596 atoms
|
||||
read_data CPU = 0.0704217 secs
|
||||
pair_coeff * *
|
||||
|
||||
velocity all create 600.0 2019
|
||||
timestep 0.01
|
||||
fix 1 all nve
|
||||
thermo 10
|
||||
reset_timestep 0
|
||||
|
||||
compute Es all mesont estretch
|
||||
compute Eb all mesont ebend
|
||||
compute Et all mesont etube
|
||||
compute B all property/atom buckling
|
||||
|
||||
thermo_style custom step time temp etotal ke pe c_Es c_Eb c_Et
|
||||
#dump out_dump all custom 10 dump.film id type x y z c_Es c_Eb c_Et c_B ix iy iz
|
||||
|
||||
run 20
|
||||
Neighbor list info ...
|
||||
update every 5 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 31
|
||||
ghost atom cutoff = 31
|
||||
binsize = 15.5, bins = 323 323 26
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair mesont/tpm, perpetual
|
||||
attributes: full, newton on, ghost
|
||||
pair build: full/bin/ghost
|
||||
stencil: full/ghost/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 12.81 | 12.81 | 12.83 Mbytes
|
||||
Step Time Temp TotEng KinEng PotEng c_Es c_Eb c_Et
|
||||
0 0 600 1347.2158 6173.0767 -4825.8609 28.669574 21.29406 -4875.8245
|
||||
10 0.1 389.40755 1373.7864 4006.4045 -2632.6181 848.00267 1404.4323 -4885.053
|
||||
20 0.2 313.65714 1399.9427 3227.0494 -1827.1067 1201.1732 1882.1342 -4910.4141
|
||||
Loop time of 3.67186 on 4 procs for 20 steps with 79596 atoms
|
||||
|
||||
Performance: 4.706 ns/day, 5.100 hours/ns, 5.447 timesteps/s
|
||||
95.8% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.7317 | 3.1286 | 3.6556 | 18.8 | 85.20
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0036943 | 0.53094 | 0.92822 | 45.8 | 14.46
|
||||
Output | 0.00026512 | 0.00035298 | 0.00055647 | 0.0 | 0.01
|
||||
Modify | 0.010463 | 0.010884 | 0.011153 | 0.3 | 0.30
|
||||
Other | | 0.001109 | | | 0.03
|
||||
|
||||
Nlocal: 19899 ave 21951 max 18667 min
|
||||
Histogram: 1 1 0 1 0 0 0 0 0 1
|
||||
Nghost: 970.75 ave 1031 max 920 min
|
||||
Histogram: 1 0 0 1 1 0 0 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 160568 ave 181723 max 147382 min
|
||||
Histogram: 1 0 2 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 642270
|
||||
Ave neighs/atom = 8.06912
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:04
|
||||
@ -1,5 +1,4 @@
|
||||
LAMMPS (09 Jan 2020)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93)
|
||||
LAMMPS (2 Jun 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
units metal
|
||||
atom_style atomic
|
||||
@ -14,11 +13,11 @@ lattice fcc 4.05
|
||||
Lattice spacing in x,y,z = 4.05 4.05 4.05
|
||||
region simbox prism 0 5 0 5 0 5 0 0 0 units lattice
|
||||
create_box 2 simbox
|
||||
Created triclinic box = (0 0 0) to (20.25 20.25 20.25) with tilt (0 0 0)
|
||||
Created triclinic box = (0.0 0.0 0.0) to (20.25 20.25 20.25) with tilt (0.0 0.0 0.0)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 2 box
|
||||
Created 500 atoms
|
||||
create_atoms CPU = 0.000987053 secs
|
||||
create_atoms CPU = 0.000 seconds
|
||||
|
||||
# Atomic mass:
|
||||
mass 1 58.69
|
||||
@ -93,21 +92,21 @@ Step Temp Pxx Pyy Pzz Pxy Pxz Pyz
|
||||
700 466.86592 5224.2421 4121.434 4368.4226 230.85768 -65.765274 -1271.8354
|
||||
800 491.38828 -233.79818 2799.6028 5023.998 919.08469 -411.66796 422.33219
|
||||
900 473.16465 6486.5426 4028.6955 2503.9771 451.96928 1309.8322 -557.83472
|
||||
1000 472.85932 4303.6923 4674.969 5268.2263 94.551286 1425.2222 -1352.0883
|
||||
Loop time of 1.24705 on 1 procs for 1000 steps with 500 atoms
|
||||
1000 472.85932 4303.6923 4674.969 5268.2263 94.551283 1425.2222 -1352.0883
|
||||
Loop time of 0.667831 on 1 procs for 1000 steps with 500 atoms
|
||||
|
||||
Performance: 138.567 ns/day, 0.173 hours/ns, 801.892 timesteps/s
|
||||
94.0% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
Performance: 258.748 ns/day, 0.093 hours/ns, 1497.385 timesteps/s
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.112 | 1.112 | 1.112 | 0.0 | 89.17
|
||||
Neigh | 0.063329 | 0.063329 | 0.063329 | 0.0 | 5.08
|
||||
Comm | 0.01994 | 0.01994 | 0.01994 | 0.0 | 1.60
|
||||
Output | 0.0014246 | 0.0014246 | 0.0014246 | 0.0 | 0.11
|
||||
Modify | 0.045429 | 0.045429 | 0.045429 | 0.0 | 3.64
|
||||
Other | | 0.004881 | | | 0.39
|
||||
Pair | 0.60535 | 0.60535 | 0.60535 | 0.0 | 90.64
|
||||
Neigh | 0.031207 | 0.031207 | 0.031207 | 0.0 | 4.67
|
||||
Comm | 0.0072828 | 0.0072828 | 0.0072828 | 0.0 | 1.09
|
||||
Output | 0.00013593 | 0.00013593 | 0.00013593 | 0.0 | 0.02
|
||||
Modify | 0.021677 | 0.021677 | 0.021677 | 0.0 | 3.25
|
||||
Other | | 0.002176 | | | 0.33
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
@ -130,43 +129,43 @@ Using fix npt/cauchy with alpha=0.001000
|
||||
run 1000
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.056 | 4.056 | 4.056 Mbytes
|
||||
Step Temp Pxx Pyy Pzz Pxy Pxz Pyz
|
||||
1000 472.85932 4303.6923 4674.969 5268.2263 94.551286 1425.2222 -1352.0883
|
||||
1100 471.04772 5593.1614 5874.9867 3608.9922 -1861.938 459.86813 -813.36882
|
||||
1200 473.34727 2337.4765 2050.4694 4330.2198 -3590.2198 -1285.2197 748.05137
|
||||
1300 465.46145 4909.5722 2880.9183 4995.0091 -2860.6934 -895.40937 -382.07531
|
||||
1400 508.53262 92.57534 3722.1136 557.50974 -3121.7615 349.6147 194.5089
|
||||
1500 498.34579 -5755.2352 -3798.1466 -1445.2047 -3218.0887 1733.9103 -555.96371
|
||||
1600 546.45882 -257.80132 407.73403 -39.803803 -3578.1137 1438.3526 -1710.3139
|
||||
1700 570.72785 -2951.9658 -622.89945 1138.4113 -4573.7982 -984.65235 2906.3144
|
||||
1800 650.75622 6086.1524 1111.2919 1726.5115 -3504.716 1140.9767 414.81284
|
||||
1900 690.32264 2763.2044 -609.41535 289.85307 -3788.8761 -1306.8569 760.00116
|
||||
2000 724.01451 -675.72484 522.04263 -468.58167 -6603.3906 -1712.7317 47.61212
|
||||
Loop time of 1.27211 on 1 procs for 1000 steps with 500 atoms
|
||||
1000 472.85932 4303.6923 4674.969 5268.2263 94.551283 1425.2222 -1352.0883
|
||||
1100 471.04772 5593.1614 5874.9866 3608.9922 -1861.938 459.86813 -813.36883
|
||||
1200 473.34727 2337.4765 2050.4694 4330.2198 -3590.2197 -1285.2197 748.05138
|
||||
1300 465.46146 4909.5722 2880.9183 4995.0092 -2860.6934 -895.40937 -382.07529
|
||||
1400 508.53262 92.575576 3722.114 557.50955 -3121.7616 349.61453 194.50883
|
||||
1500 498.3458 -5755.2341 -3798.1481 -1445.2041 -3218.0889 1733.9101 -555.96313
|
||||
1600 546.45888 -257.8015 407.74313 -39.808565 -3578.1152 1438.3545 -1710.3112
|
||||
1700 570.72803 -2951.9777 -622.89115 1138.4111 -4573.8049 -984.65144 2906.3201
|
||||
1800 650.7567 6086.093 1111.3418 1726.5919 -3504.6481 1140.9639 414.77939
|
||||
1900 690.31291 2762.9298 -609.22637 289.53512 -3788.5686 -1307.3139 759.83909
|
||||
2000 724.0376 -676.49959 522.5367 -468.29812 -6602.9226 -1712.1389 46.769914
|
||||
Loop time of 0.665662 on 1 procs for 1000 steps with 500 atoms
|
||||
|
||||
Performance: 135.837 ns/day, 0.177 hours/ns, 786.093 timesteps/s
|
||||
93.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
Performance: 259.591 ns/day, 0.092 hours/ns, 1502.265 timesteps/s
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.0529 | 1.0529 | 1.0529 | 0.0 | 82.77
|
||||
Neigh | 0.13671 | 0.13671 | 0.13671 | 0.0 | 10.75
|
||||
Comm | 0.018747 | 0.018747 | 0.018747 | 0.0 | 1.47
|
||||
Output | 0.00075722 | 0.00075722 | 0.00075722 | 0.0 | 0.06
|
||||
Modify | 0.057984 | 0.057984 | 0.057984 | 0.0 | 4.56
|
||||
Other | | 0.00499 | | | 0.39
|
||||
Pair | 0.56182 | 0.56182 | 0.56182 | 0.0 | 84.40
|
||||
Neigh | 0.069662 | 0.069662 | 0.069662 | 0.0 | 10.47
|
||||
Comm | 0.0090612 | 0.0090612 | 0.0090612 | 0.0 | 1.36
|
||||
Output | 0.00015483 | 0.00015483 | 0.00015483 | 0.0 | 0.02
|
||||
Modify | 0.02264 | 0.02264 | 0.02264 | 0.0 | 3.40
|
||||
Other | | 0.00232 | | | 0.35
|
||||
|
||||
Nlocal: 500 ave 500 max 500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 2040 ave 2040 max 2040 min
|
||||
Nghost: 2044 ave 2044 max 2044 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 23757 ave 23757 max 23757 min
|
||||
Neighs: 23800 ave 23800 max 23800 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 23757
|
||||
Ave neighs/atom = 47.514
|
||||
Neighbor list builds = 78
|
||||
Total # of neighbors = 23800
|
||||
Ave neighs/atom = 47.6
|
||||
Neighbor list builds = 77
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:02
|
||||
Total wall time: 0:00:01
|
||||
@ -1 +0,0 @@
|
||||
../../../../potentials/C_10_10.mesocnt
|
||||
File diff suppressed because it is too large
Load Diff
1
examples/snap/He_He_JW2013.table
Symbolic link
1
examples/snap/He_He_JW2013.table
Symbolic link
@ -0,0 +1 @@
|
||||
../../potentials/He_He_JW2013.table
|
||||
@ -1,333 +0,0 @@
|
||||
# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Juslin, N. and Wirth, B. D. Journal of Nuclear Materials, 423, (2013) p61-63
|
||||
#
|
||||
#-> LAMMPS Potential File in tabular format. <-#
|
||||
# N. Juslin and B.D. Wirth, J. Nucl. Mater. 432: 61-66 (2013). #
|
||||
# Implemented by K.D. Hammond (2013) karlh@utk.edu
|
||||
WHe
|
||||
N 325
|
||||
|
||||
1 0.000001 193967.941432641 21165142.7035409
|
||||
2 0.02 88781.7058271842 5199760.86773195
|
||||
3 0.03 54461.7226844158 2255783.27652381
|
||||
4 0.04 37754.4525147374 1233285.07338825
|
||||
5 0.05 28027.0551422937 765154.791685769
|
||||
6 0.06 21746.7711436002 514318.047209743
|
||||
7 0.07 17407.2122555268 365457.111099578
|
||||
8 0.08 14260.380890756 270524.172812057
|
||||
9 0.09 11894.315375388 206649.630589727
|
||||
10 0.1 10064.3593879466 161847.200920021
|
||||
11 0.11 8616.61401638085 129358.142417815
|
||||
12 0.12 7449.7679909506 105145.917230655
|
||||
13 0.13 6494.61875555217 86685.1834957916
|
||||
14 0.14 5702.42313976808 72334.2424211515
|
||||
15 0.15 5037.94580316996 60990.8171175998
|
||||
16 0.16 4475.14199778904 51894.0939422829
|
||||
17 0.17 3994.38401078788 44506.229619365
|
||||
18 0.18 3580.62666819885 38438.9489608325
|
||||
19 0.19 3222.16279673461 33406.7013437966
|
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|
||||
304 3.04 0.00691903768080766 0.128734499561665
|
||||
305 3.05 0.00570323205109961 0.114535711972949
|
||||
306 3.06 0.0046261239723178 0.100996673020243
|
||||
307 3.07 0.00368107000826405 0.088126119710232
|
||||
308 3.08 0.00286135278937321 0.0759301171045549
|
||||
309 3.09 0.00216020726148435 0.0644121533205429
|
||||
310 3.1 0.00157084595956787 0.0535732394484653
|
||||
311 3.11 0.00108648325995938 0.0434120138431347
|
||||
312 3.12 0.000700358570037423 0.0339248502550448
|
||||
313 3.13 0.000405758419588332 0.0251059692749879
|
||||
314 3.14 0.000196037423311657 0.0169475525761798
|
||||
315 3.15 6.46380890244662E-05 0.00943985944932857
|
||||
316 3.16 5.1094511057313E-06 0.00257134513861945
|
||||
317 3.17 0 0
|
||||
318 3.18 0 0
|
||||
319 3.19 0 0
|
||||
320 3.2 0 0
|
||||
321 3.21 0 0
|
||||
322 3.22 0 0
|
||||
323 3.23 0 0
|
||||
324 3.24 0 0
|
||||
325 3.25 0 0
|
||||
1
examples/snap/W_He_JW2013.table
Symbolic link
1
examples/snap/W_He_JW2013.table
Symbolic link
@ -0,0 +1 @@
|
||||
../../potentials/W_He_JW2013.table
|
||||
Reference in New Issue
Block a user