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This commit is contained in:
iafoss
2020-03-25 20:18:07 -04:00
parent c793db66d2
commit fa4ef70829
56 changed files with 1275 additions and 2252 deletions
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3
examples/USER/mesont/README
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@ -9,7 +9,6 @@ Contributing author: Maxim Shugaev (UVA), mvs9t@virginia.edu
"bundle" is an example with a single bundle composed of 7 nanotubes.
"system" is an example with a film composed of 396 200-nm-long
"film" is an example with a film composed of 396 200-nm-long
nanotubes (79596 nodes).

45
examples/USER/mesont/bundle.in
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@ -1,45 +0,0 @@
newton on
log cnt.log
echo both
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 ../../../potentials/CNT_10_10 0 0
read_data bundle.init
pair_coeff * *
velocity all create 6000.0 2019
timestep 0.005
fix 1 all nve
#fix 1 all nvt temp 3000.0 3000.0 1.0
thermo_modify flush yes
thermo 10
reset_timestep 0
compute Es all mesont/Es
compute Eb all mesont/Eb
compute Et all mesont/Et
compute Ek all ke/atom
compute Es_tot all mesont/Es_tot
compute Eb_tot all mesont/Eb_tot
compute Et_tot all mesont/Et_tot
compute Ep_tot all pe
compute Ek_tot all ke
variable time_ equal time
variable Ep_ equal c_Ep_tot
variable Ek_ equal c_Ek_tot
variable Etot_ equal v_Ek_+v_Ep_
variable Es_ equal c_Es_tot
variable Eb_ equal c_Eb_tot
variable Et_ equal c_Et_tot
dump out_dump all custom 50 config.dump id type x y z c_Es c_Eb c_Et c_Ek ix iy iz
fix out_info all print 10 "${time_} ${Etot_} ${Ek_} ${Ep_} ${Es_} ${Eb_} ${Et_}" file "E.txt" screen no
run 10000
write_data system.data

46
examples/USER/mesont/bundle_h.in
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@ -1,46 +0,0 @@
newton on
log cnt.log
echo both
units metal
lattice sc 1.0
boundary p p p
neighbor 1.0 bin
neigh_modify every 5 delay 0 check yes
atom_style mesont
# cut, path, BendingMode, TPMType
pair_style hybrid mesont/tpm 45.0 ../../../potentials/CNT_10_10 0 0 lj/cut 7.5
read_data bundle_h.init
pair_coeff 1*2 2 lj/cut 0.1 3.0
pair_coeff 1 1 mesont/tpm
#velocity all create 6000.0 2019
timestep 0.005
fix 1 all nve
#fix 1 all nvt temp 3000.0 3000.0 1.0
thermo_modify flush yes
thermo 10
reset_timestep 0
compute Es all mesont/Es
compute Eb all mesont/Eb
compute Et all mesont/Et
compute Ek all ke/atom
compute Es_tot all mesont/Es_tot
compute Eb_tot all mesont/Eb_tot
compute Et_tot all mesont/Et_tot
compute Ep_tot all pe
compute Ek_tot all ke
variable time_ equal time
variable Ep_ equal c_Ep_tot
variable Ek_ equal c_Ek_tot
variable Etot_ equal v_Ek_+v_Ep_
variable Es_ equal c_Es_tot
variable Eb_ equal c_Eb_tot
variable Et_ equal c_Et_tot
dump out_dump all custom 50 config.dump id type x y z c_Es c_Eb c_Et c_Ek ix iy iz
fix out_info all print 10 "${time_} ${Etot_} ${Ek_} ${Ep_} ${Es_} ${Eb_} ${Et_}" file "E.txt" screen no
run 10000
write_data system.data

96
examples/USER/mesont/bundle_h.init
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@ -1,96 +0,0 @@
79 atoms
2 atom types
-143.89 143.89 xlo xhi
-143.89 143.89 ylo yhi
0 220 zlo zhi
Masses
1 1.0
2 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
78 8 2 -1 -1 100.0 0.0 0 0 20.0 20.0 100.0 0 0 0
79 9 2 -1 -1 100.0 0.0 0 0 20.0 20.0 103.8 0 0 0

0
examples/USER/mesont/bundle.init → examples/USER/mesont/data.bundle
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0
examples/USER/mesont/system.init → examples/USER/mesont/data.film
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32
examples/USER/mesont/in.bundle Normal file
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@ -0,0 +1,32 @@
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 ../../../potentials/CNT_10_10 0 0
read_data data.bundle
pair_coeff * *
velocity all create 6000.0 2019
timestep 0.005
fix 1 all nve
thermo_modify flush yes
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
compute Es_tot all mesont estretch_tot
compute Eb_tot all mesont ebend_tot
compute Et_tot all mesont etube_tot
thermo_style custom step time temp etotal ke pe c_Es_tot c_Eb_tot c_Et_tot
#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

32
examples/USER/mesont/in.film Normal file
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@ -0,0 +1,32 @@
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 25.0 ../../../potentials/CNT_10_10 1 0
read_data data.film
pair_coeff * *
velocity all create 600.0 2019
timestep 0.01
fix 1 all nve
thermo_modify flush yes
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
compute Es_tot all mesont estretch_tot
compute Eb_tot all mesont ebend_tot
compute Et_tot all mesont etube_tot
thermo_style custom step time temp etotal ke pe c_Es_tot c_Eb_tot c_Et_tot
#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 10

94
examples/USER/mesont/log.3Mar2020.bundle.g++.1 Normal file
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@ -0,0 +1,94 @@
LAMMPS (3 Mar 2020)
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 ../../../potentials/CNT_10_10 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 = 0.442627 secs
pair_coeff * *
velocity all create 6000.0 2019
timestep 0.005
fix 1 all nve
thermo_modify flush yes
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
compute Es_tot all mesont estretch_tot
compute Eb_tot all mesont ebend_tot
compute Et_tot all mesont etube_tot
thermo_style custom step time temp etotal ke pe c_Es_tot c_Eb_tot c_Et_tot
WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:708)
#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_tot c_Eb_tot c_Et_tot
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 0.455531 on 1 procs for 100 steps with 77 atoms
Performance: 94.834 ns/day, 0.253 hours/ns, 219.524 timesteps/s
99.7% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.4551 | 0.4551 | 0.4551 | 0.0 | 99.91
Neigh | 6.485e-05 | 6.485e-05 | 6.485e-05 | 0.0 | 0.01
Comm | 3.0994e-05 | 3.0994e-05 | 3.0994e-05 | 0.0 | 0.01
Output | 0.00020385 | 0.00020385 | 0.00020385 | 0.0 | 0.04
Modify | 8.6069e-05 | 8.6069e-05 | 8.6069e-05 | 0.0 | 0.02
Other | | 4.697e-05 | | | 0.01
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

85
examples/USER/mesont/log.3Mar2020.film.g++.1 Normal file
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@ -0,0 +1,85 @@
LAMMPS (3 Mar 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 25.0 ../../../potentials/CNT_10_10 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 = 0.0903821 secs
pair_coeff * *
velocity all create 600.0 2019
timestep 0.01
fix 1 all nve
thermo_modify flush yes
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
compute Es_tot all mesont estretch_tot
compute Eb_tot all mesont ebend_tot
compute Et_tot all mesont etube_tot
thermo_style custom step time temp etotal ke pe c_Es_tot c_Eb_tot c_Et_tot
WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:708)
#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 10
Neighbor list info ...
update every 5 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 26
ghost atom cutoff = 26
binsize = 13, bins = 385 385 31
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) = 44.83 | 44.83 | 44.83 Mbytes
Step Time Temp TotEng KinEng PotEng c_Es_tot c_Eb_tot c_Et_tot
0 0 600 1347.2177 6173.0767 -4825.859 28.669574 21.29406 -4875.8226
10 0.1 389.40755 1373.7883 4006.4045 -2632.6161 848.00269 1404.4323 -4885.0511
Loop time of 4.21003 on 1 procs for 10 steps with 79596 atoms
Performance: 2.052 ns/day, 11.695 hours/ns, 2.375 timesteps/s
97.8% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.1942 | 4.1942 | 4.1942 | 0.0 | 99.62
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00046039 | 0.00046039 | 0.00046039 | 0.0 | 0.01
Output | 0.00029182 | 0.00029182 | 0.00029182 | 0.0 | 0.01
Modify | 0.012385 | 0.012385 | 0.012385 | 0.0 | 0.29
Other | | 0.002726 | | | 0.06
Nlocal: 79596 ave 79596 max 79596 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1567 ave 1567 max 1567 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: 412798 ave 412798 max 412798 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 412798
Ave neighs/atom = 5.18617
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:05

45
examples/USER/mesont/system.in
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@ -1,45 +0,0 @@
newton on
log cnt.log
echo both
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 25.0 ../../../potentials/CNT_10_10 0 0
read_data system.init
pair_coeff * *
velocity all create 600.0 2019
timestep 0.010
fix 1 all nve
#fix 1 all nvt temp 300.0 300.0 1.0
thermo_modify flush yes
thermo 10
reset_timestep 0
compute Es all mesont/Es
compute Eb all mesont/Eb
compute Et all mesont/Et
compute Ek all ke/atom
compute Es_tot all mesont/Es_tot
compute Eb_tot all mesont/Eb_tot
compute Et_tot all mesont/Et_tot
compute Ep_tot all pe
compute Ek_tot all ke
variable time_ equal time
variable Ep_ equal c_Ep_tot
variable Ek_ equal c_Ek_tot
variable Etot_ equal v_Ek_+v_Ep_
variable Es_ equal c_Es_tot
variable Eb_ equal c_Eb_tot
variable Et_ equal c_Et_tot
dump out_dump all custom 50 config_E.dump id type x y z c_Es c_Eb c_Et c_Ek ix iy iz
fix out_info all print 10 "${time_} ${Etot_} ${Ek_} ${Ep_} ${Es_} ${Eb_} ${Et_}" file "E.txt" screen no
run 50
write_data system_E.data