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simongravellesimongravelle
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worked on inputs
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‎files/tutorial6/solution/cracking-mod.data‎

Lines changed: 1482 additions & 0 deletions
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‎files/tutorial6/solution/cracking.data‎

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‎files/tutorial6/solution/cracking.log‎

Lines changed: 49 additions & 40 deletions
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,7 @@
11
using 8 OpenMP thread(s) per MPI task
22
using multi-threaded neighbor list subroutines
33
Reading data file ...
4-
orthogonal box = (0.91061361 1.6226589 -1.2373349) to (24.821359 18.962919 21.822913)
4+
orthogonal box = (2.3535666 -1.6556717 0.86165627) to (23.378406 22.241249 19.723921)
55
1 by 1 by 1 MPI processor grid
66
reading atom labelmap ...
77
reading atoms ...
@@ -16,15 +16,24 @@ Finding 1-2 1-3 1-4 neighbors ...
1616
0 = max # of 1-4 neighbors
1717
1 = max # of special neighbors
1818
special bonds CPU = 0.000 seconds
19-
read_data CPU = 0.020 seconds
19+
read_data CPU = 0.021 seconds
2020
Reading vashishta potential file SiO.1990.vashishta with DATE: 2015-10-14
21+
22+
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
23+
24+
Your simulation uses code contributions which should be cited:
25+
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
26+
The log file lists these citations in BibTeX format.
27+
28+
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
29+
2130
Last active /omp style is pair_style vashishta/omp
2231
Neighbor list info ...
2332
update: every = 1 steps, delay = 1 steps, check = yes
2433
max neighbors/atom: 2000, page size: 100000
2534
master list distance cutoff = 11
2635
ghost atom cutoff = 11
27-
binsize = 5.5, bins = 5 4 5
36+
binsize = 5.5, bins = 4 5 4
2837
1 neighbor lists, perpetual/occasional/extra = 1 0 0
2938
(1) pair vashishta/omp, perpetual
3039
attributes: full, newton on, omp
@@ -35,58 +44,58 @@ Setting up Verlet run ...
3544
Unit style : metal
3645
Current step : 0
3746
Time step : 0.001
38-
Per MPI rank memory allocation (min/avg/max) = 12.52 | 12.52 | 12.52 Mbytes
47+
Per MPI rank memory allocation (min/avg/max) = 12.55 | 12.55 | 12.55 Mbytes
3948
Step Temp TotEng Volume Lx Ly Lz
40-
0 301.17448 -6427.659 9561.206 23.910745 17.34026 23.060247
41-
1000 279.44119 -6428.5784 9704.624 24.269406 17.34026 23.060247
42-
2000 295.50824 -6425.4113 9848.0421 24.628067 17.34026 23.060247
43-
3000 298.6945 -6419.5557 9991.4602 24.986728 17.34026 23.060247
44-
4000 282.51392 -6416.8589 10134.878 25.34539 17.34026 23.060247
45-
5000 304.60827 -6405.7082 10278.296 25.704051 17.34026 23.060247
46-
6000 298.10251 -6398.6524 10421.714 26.062712 17.34026 23.060247
47-
7000 295.81949 -6388.8453 10565.133 26.421373 17.34026 23.060247
48-
8000 319.62403 -6375.837 10708.551 26.780034 17.34026 23.060247
49-
9000 314.49787 -6368.534 10851.969 27.138695 17.34026 23.060247
50-
10000 296.82693 -6360.4751 10995.387 27.497357 17.34026 23.060247
51-
11000 287.74596 -6348.8833 11138.805 27.856018 17.34026 23.060247
52-
12000 289.74339 -6342.7617 11282.223 28.214679 17.34026 23.060247
53-
13000 301.77567 -6334.3267 11425.641 28.57334 17.34026 23.060247
54-
14000 294.91747 -6340.0743 11569.059 28.932001 17.34026 23.060247
55-
15000 294.22476 -6329.1306 11712.477 29.290663 17.34026 23.060247
56-
16000 311.42893 -6327.6932 11855.895 29.649324 17.34026 23.060247
57-
17000 303.34378 -6324.195 11999.313 30.007985 17.34026 23.060247
58-
18000 302.47749 -6319.3108 12142.732 30.366646 17.34026 23.060247
59-
19000 312.49613 -6310.5494 12286.15 30.725307 17.34026 23.060247
60-
20000 332.7128 -6323.9637 12429.568 31.083968 17.34026 23.060247
61-
Loop time of 38.4353 on 8 procs for 20000 steps with 720 atoms
49+
0 315.30616 -6422.9954 9476.9475 21.024839 23.896921 18.862265
50+
1000 314.40986 -6418.3281 9619.1017 21.340212 23.896921 18.862265
51+
2000 305.19895 -6417.0503 9761.2559 21.655584 23.896921 18.862265
52+
3000 290.22122 -6410.5095 9903.4101 21.970957 23.896921 18.862265
53+
4000 290.45222 -6404.7785 10045.564 22.286329 23.896921 18.862265
54+
5000 320.89323 -6392.0183 10187.719 22.601702 23.896921 18.862265
55+
6000 310.20616 -6387.1654 10329.873 22.917074 23.896921 18.862265
56+
7000 296.86661 -6378.8858 10472.027 23.232447 23.896921 18.862265
57+
8000 297.92464 -6367.6875 10614.181 23.54782 23.896921 18.862265
58+
9000 281.59301 -6361.4666 10756.335 23.863192 23.896921 18.862265
59+
10000 327.19137 -6345.2258 10898.49 24.178565 23.896921 18.862265
60+
11000 299.00911 -6338.1612 11040.644 24.493937 23.896921 18.862265
61+
12000 308.18876 -6326.3002 11182.798 24.80931 23.896921 18.862265
62+
13000 292.34221 -6322.4983 11324.952 25.124683 23.896921 18.862265
63+
14000 282.21484 -6322.5689 11467.106 25.440055 23.896921 18.862265
64+
15000 300.08569 -6325.4864 11609.261 25.755428 23.896921 18.862265
65+
16000 297.40828 -6319.7046 11751.415 26.0708 23.896921 18.862265
66+
17000 288.41005 -6316.6014 11893.569 26.386173 23.896921 18.862265
67+
18000 315.47013 -6308.467 12035.723 26.701545 23.896921 18.862265
68+
19000 302.91553 -6306.4915 12177.877 27.016918 23.896921 18.862265
69+
20000 321.47552 -6305.0489 12320.032 27.332291 23.896921 18.862265
70+
Loop time of 35.638 on 8 procs for 20000 steps with 720 atoms
6271

63-
Performance: 44.959 ns/day, 0.534 hours/ns, 520.356 timesteps/s, 374.656 katom-step/s
64-
773.7% CPU use with 1 MPI tasks x 8 OpenMP threads
72+
Performance: 48.488 ns/day, 0.495 hours/ns, 561.199 timesteps/s, 404.063 katom-step/s
73+
768.5% CPU use with 1 MPI tasks x 8 OpenMP threads
6574

6675
MPI task timing breakdown:
6776
Section | min time | avg time | max time |%varavg| %total
6877
---------------------------------------------------------------
69-
Pair | 33.078 | 33.078 | 33.078 | 0.0 | 86.06
70-
Bond | 0.0013156 | 0.0013156 | 0.0013156 | 0.0 | 0.00
71-
Neigh | 0.50724 | 0.50724 | 0.50724 | 0.0 | 1.32
72-
Comm | 0.75904 | 0.75904 | 0.75904 | 0.0 | 1.97
73-
Output | 2.7063 | 2.7063 | 2.7063 | 0.0 | 7.04
74-
Modify | 1.3162 | 1.3162 | 1.3162 | 0.0 | 3.42
75-
Other | | 0.06739 | | | 0.18
78+
Pair | 30.349 | 30.349 | 30.349 | 0.0 | 85.16
79+
Bond | 0.0013098 | 0.0013098 | 0.0013098 | 0.0 | 0.00
80+
Neigh | 0.52153 | 0.52153 | 0.52153 | 0.0 | 1.46
81+
Comm | 0.61264 | 0.61264 | 0.61264 | 0.0 | 1.72
82+
Output | 2.8732 | 2.8732 | 2.8732 | 0.0 | 8.06
83+
Modify | 1.2231 | 1.2231 | 1.2231 | 0.0 | 3.43
84+
Other | | 0.0571 | | | 0.16
7685

7786
Nlocal: 720 ave 720 max 720 min
7887
Histogram: 1 0 0 0 0 0 0 0 0 0
79-
Nghost: 5018 ave 5018 max 5018 min
88+
Nghost: 4660 ave 4660 max 4660 min
8089
Histogram: 1 0 0 0 0 0 0 0 0 0
8190
Neighs: 0 ave 0 max 0 min
8291
Histogram: 1 0 0 0 0 0 0 0 0 0
83-
FullNghs: 241106 ave 241106 max 241106 min
92+
FullNghs: 239664 ave 239664 max 239664 min
8493
Histogram: 1 0 0 0 0 0 0 0 0 0
8594

86-
Total # of neighbors = 241106
87-
Ave neighs/atom = 334.86944
95+
Total # of neighbors = 239664
96+
Ave neighs/atom = 332.86667
8897
Ave special neighs/atom = 0
89-
Neighbor list builds = 385
98+
Neighbor list builds = 402
9099
Dangerous builds = 0
91100
System init for write_data ...
92101
Last active /omp style is pair_style vashishta/omp

‎files/tutorial6/solution/gcmc.lmp‎

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Original file line numberDiff line numberDiff line change
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1+
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units metal
3+
boundary p p p
4+
atom_style full
5+
6+
pair_style hybrid/overlay vashishta lj/cut/tip4p/long OW HW OW-HW HW-OW-HW 0.1546 10
7+
kspace_style pppm/tip4p 1.0e−4
8+
bond_style harmonic
9+
angle_style harmonic
10+
11+
neighbor 1.0 bin
12+
neigh_modify delay 1
13+
14+
read_data cracking-mod.data
15+
molecule h2omol H2O.mol
16+
lattice sc 6
17+
create_atoms 0 box mol h2omol 45585
18+
lattice none 1
19+
20+
group SiO type Si O
21+
group H2O type OW HW
22+
23+
pair_coeff * * vashishta SiO.1990.vashishta Si O NULL NULL
24+
pair_coeff * * lj/cut/tip4p/long 0 0
25+
pair_coeff Si OW lj/cut/tip4p/long 0.0057 4.42
26+
pair_coeff O OW lj/cut/tip4p/long 0.0043 3.12
27+
pair_coeff OW OW lj/cut/tip4p/long 0.008 3.1589
28+
pair_coeff HW HW lj/cut/tip4p/long 0.0 0.0
29+
bond_coeff OW-HW 0 0.9572
30+
angle_coeff HW-OW-HW 0 104.52
31+
32+
variable oxygen atom type==label2type(atom,OW)
33+
group oxygen dynamic all var oxygen
34+
variable nO equal count(oxygen)
35+
thermo_style custom step temp etotal v_nO
36+
thermo 1000
37+
38+
fix shak H2O shake 1.0e−4 200 0 b OW-HW a HW-OW-HW mol h2omol
39+
40+
delete_atoms overlap 2 H2O SiO mol yes
41+
42+
dump mydmp all image 200 myimage-*.ppm type type &
43+
shiny 0.1 box no 0.01 view 180 90 zoom 1.2 size 1000 650
44+
dump_modify mydmp backcolor white &
45+
acolor Si yellow adiam Si 2.5 &
46+
acolor O red adiam O 2 &
47+
acolor OW cyan adiam OW 2 &
48+
acolor HW white adiam HW 1
49+
50+
thermo 1000
51+
thermo_style custom step temp etotal v_nO
52+
53+
compute ctH2O H2O temp
54+
#compute ctSiO SiO temp
55+
compute_modify thermo_temp dynamic yes
56+
compute_modify ctH2O dynamic yes
57+
fix mynvt1 H2O nvt temp 300 300 0.1
58+
fix_modify mynvt1 temp ctH2O
59+
fix mynvt2 SiO nvt temp 300 300 0.1
60+
#fix_modify mynvt2 temp ctSiO
61+
62+
timestep 0.001
63+
64+
variable tfac equal 5.0/3.0
65+
fix fgcmc H2O gcmc 100 100 0 0 65899 300 -0.5 0.1 &
66+
mol h2omol tfac_insert ${tfac} shake shak full_energy pressure 100
67+
68+
run 25000

‎files/tutorial6/solution/gcmc.log‎

Lines changed: 191 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,191 @@
1+
using 8 OpenMP thread(s) per MPI task
2+
using multi-threaded neighbor list subroutines
3+
Reading data file ...
4+
orthogonal box = (-0.80015924 -1.6556717 0.86165627) to (26.532131 22.241249 19.723921)
5+
1 by 1 by 1 MPI processor grid
6+
reading atom labelmap ...
7+
reading bond labelmap ...
8+
reading angle labelmap ...
9+
reading atoms ...
10+
720 atoms
11+
reading velocities ...
12+
720 velocities
13+
Finding 1-2 1-3 1-4 neighbors ...
14+
special bond factors lj: 0 0 0
15+
special bond factors coul: 0 0 0
16+
0 = max # of 1-2 neighbors
17+
0 = max # of 1-3 neighbors
18+
0 = max # of 1-4 neighbors
19+
3 = max # of special neighbors
20+
special bonds CPU = 0.000 seconds
21+
read_data CPU = 0.016 seconds
22+
Read molecule template h2omol:
23+
# Water molecule.
24+
1 molecules
25+
0 fragments
26+
3 atoms with max type 4
27+
2 bonds with max type 1
28+
1 angles with max type 1
29+
0 dihedrals with max type 0
30+
0 impropers with max type 0
31+
Lattice spacing in x,y,z = 6 6 6
32+
Created 180 atoms
33+
using lattice units in orthogonal box = (-0.80015924 -1.6556717 0.86165627) to (26.532131 22.241249 19.723921)
34+
create_atoms CPU = 0.001 seconds
35+
720 atoms in group SiO
36+
180 atoms in group H2O
37+
Reading vashishta potential file SiO.1990.vashishta with DATE: 2015-10-14
38+
dynamic group oxygen defined
39+
Finding SHAKE clusters ...
40+
0 = # of size 2 clusters
41+
0 = # of size 3 clusters
42+
0 = # of size 4 clusters
43+
60 = # of frozen angles
44+
find clusters CPU = 0.000 seconds
45+
System init for delete_atoms ...
46+
PPPM initialization ...
47+
extracting TIP4P info from pair style
48+
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
49+
G vector (1/distance) = 0.27547142
50+
grid = 15 15 12
51+
stencil order = 5
52+
estimated absolute RMS force accuracy = 0.0010683502
53+
estimated relative force accuracy = 7.4192812e-05
54+
using double precision KISS FFT
55+
3d grid and FFT values/proc = 6800 2700
56+
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (src/pair.cpp:243)
57+
WARNING: Communication cutoff 0 is shorter than a bond length based estimate of 2.4358. This may lead to errors. (src/comm.cpp:731)
58+
WARNING: Increasing communication cutoff to 12.1118 for TIP4P pair style (src/KSPACE/pair_lj_cut_tip4p_long.cpp:497)
59+
Hybrid pair style last /omp style lj/cut/tip4p/long
60+
Last active /omp style is kspace_style pppm/tip4p/omp
61+
Neighbor list info ...
62+
update: every = 1 steps, delay = 1 steps, check = yes
63+
max neighbors/atom: 2000, page size: 100000
64+
master list distance cutoff = 11.3092
65+
ghost atom cutoff = 12.1118
66+
binsize = 5.6546, bins = 5 5 4
67+
4 neighbor lists, perpetual/occasional/extra = 3 1 0
68+
(1) command delete_atoms, occasional
69+
attributes: full, newton on, omp
70+
pair build: full/bin/omp
71+
stencil: full/bin/3d
72+
bin: standard
73+
(2) pair vashishta, perpetual, skip from (4)
74+
attributes: full, newton on, omp, cut 11
75+
pair build: skip/omp
76+
stencil: none
77+
bin: none
78+
(3) pair lj/cut/tip4p/long, perpetual
79+
attributes: half, newton on, omp
80+
pair build: half/bin/newton/omp
81+
stencil: half/bin/3d
82+
bin: standard
83+
(4) neighbor class addition, perpetual
84+
attributes: full, newton on, omp, cut 11
85+
pair build: full/bin/omp
86+
stencil: full/bin/3d
87+
bin: standard
88+
WARNING: Ignoring 'compress yes' for molecular system (src/delete_atoms.cpp:141)
89+
Deleted 168 atoms, new total = 732
90+
Deleted 112 bonds, new total = 8
91+
Deleted 56 angles, new total = 4
92+
WARNING: Temperature for fix modify is not for group all (src/fix_nh.cpp:1399)
93+
PPPM initialization ...
94+
extracting TIP4P info from pair style
95+
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
96+
G vector (1/distance) = 0.27541196
97+
grid = 15 15 12
98+
stencil order = 5
99+
estimated absolute RMS force accuracy = 0.00096021482
100+
estimated relative force accuracy = 6.6683229e-05
101+
using double precision KISS FFT
102+
3d grid and FFT values/proc = 6800 2700
103+
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (src/pair.cpp:243)
104+
Hybrid pair style last /omp style lj/cut/tip4p/long
105+
Last active /omp style is kspace_style pppm/tip4p/omp
106+
0 atoms in group FixGCMC:gcmc_exclusion_group:fgcmc
107+
0 atoms in group FixGCMC:rotation_gas_atoms:fgcmc
108+
WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (src/neighbor.cpp:658)
109+
Neighbor list info ...
110+
update: every = 1 steps, delay = 1 steps, check = yes
111+
max neighbors/atom: 2000, page size: 100000
112+
master list distance cutoff = 11.3092
113+
ghost atom cutoff = 12.1118
114+
binsize = 5.6546, bins = 5 5 4
115+
3 neighbor lists, perpetual/occasional/extra = 3 0 0
116+
(1) pair vashishta, perpetual, skip from (3)
117+
attributes: full, newton on, omp, cut 11
118+
pair build: skip/omp
119+
stencil: none
120+
bin: none
121+
(2) pair lj/cut/tip4p/long, perpetual
122+
attributes: half, newton on, omp
123+
pair build: half/bin/newton/omp
124+
stencil: half/bin/3d
125+
bin: standard
126+
(3) neighbor class addition, perpetual
127+
attributes: full, newton on, omp, cut 11
128+
pair build: full/bin/omp
129+
stencil: full/bin/3d
130+
bin: standard
131+
Setting up Verlet run ...
132+
Unit style : metal
133+
Current step : 0
134+
Time step : 0.001
135+
Per MPI rank memory allocation (min/avg/max) = 22.71 | 22.71 | 22.71 Mbytes
136+
Step Temp TotEng v_nO
137+
0 317.93796 -9098.11 4
138+
1000 310.64509 -9173.6688 9
139+
2000 299.62874 -9181.6692 18
140+
3000 309.80847 -9188.4328 26
141+
4000 312.14415 -9191.7325 30
142+
5000 302.35851 -9196.118 31
143+
6000 307.10153 -9198.3025 32
144+
7000 300.24203 -9198.3843 33
145+
8000 309.77088 -9197.3516 33
146+
9000 305.07691 -9198.7366 35
147+
10000 287.13495 -9200.9842 35
148+
11000 301.44728 -9200.4619 38
149+
12000 293.85092 -9201.9628 39
150+
13000 316.58003 -9201.3133 39
151+
14000 306.50234 -9199.5372 40
152+
15000 288.52362 -9203.0413 41
153+
16000 295.13102 -9204.2141 41
154+
17000 296.8422 -9204.8686 44
155+
18000 291.67361 -9205.026 44
156+
19000 306.62569 -9203.2865 44
157+
20000 297.58464 -9204.3223 44
158+
21000 293.04607 -9203.5425 44
159+
22000 317.01586 -9202.4492 44
160+
23000 302.5997 -9205.2128 46
161+
24000 296.84114 -9205.3287 46
162+
25000 308.30355 -9205.4674 46
163+
Loop time of 741.158 on 8 procs for 25000 steps with 858 atoms
164+
165+
Performance: 2.914 ns/day, 8.235 hours/ns, 33.731 timesteps/s, 28.941 katom-step/s
166+
724.5% CPU use with 1 MPI tasks x 8 OpenMP threads
167+
168+
MPI task timing breakdown:
169+
Section | min time | avg time | max time |%varavg| %total
170+
---------------------------------------------------------------
171+
Pair | 92.6 | 92.6 | 92.6 | 0.0 | 12.49
172+
Bond | 5.6754 | 5.6754 | 5.6754 | 0.0 | 0.77
173+
Kspace | 39.188 | 39.188 | 39.188 | 0.0 | 5.29
174+
Neigh | 22.973 | 22.973 | 22.973 | 0.0 | 3.10
175+
Comm | 1.5188 | 1.5188 | 1.5188 | 0.0 | 0.20
176+
Output | 4.7673 | 4.7673 | 4.7673 | 0.0 | 0.64
177+
Modify | 574.09 | 574.09 | 574.09 | 0.0 | 77.46
178+
Other | | 0.3495 | | | 0.05
179+
180+
Nlocal: 858 ave 858 max 858 min
181+
Histogram: 1 0 0 0 0 0 0 0 0 0
182+
Nghost: 6581 ave 6581 max 6581 min
183+
Histogram: 1 0 0 0 0 0 0 0 0 0
184+
Neighs: 181115 ave 181115 max 181115 min
185+
Histogram: 1 0 0 0 0 0 0 0 0 0
186+
187+
Total # of neighbors = 181115
188+
Ave neighs/atom = 211.08974
189+
Ave special neighs/atom = 0.32167832
190+
Neighbor list builds = 27195
191+
Dangerous builds = 0

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