ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Bugfix electrode piston example

Browse Source
This commit is contained in:
Ludwig Ahrens-Iwers
2024-06-13 17:00:01 +02:00
committed by Shern Tee
parent 1909233c69
commit 80e96d8c9b
4 changed files with 2147 additions and 2129 deletions
Download Patch File Download Diff File Expand all files Collapse all files

4064
examples/PACKAGES/electrode/piston/data.piston.final
View File

File diff suppressed because it is too large Load Diff

6
examples/PACKAGES/electrode/piston/in.piston
View File

@ -42,7 +42,11 @@ fix fxforce_au gold setforce 0.0 0.0 0.0
# equilibrate z-coordinate of upper electrode while keeping the electrode rigid
fix fxforce_wa wall setforce 0.0 0.0 NULL
fix fxpressure wall aveforce 0 0 -0.005246 # atomspheric pressure: area/force->nktv2p
variable atm equal 1/68568.415 # 1/force->nktv2p
variable area equal (xhi-xlo)*(yhi-ylo)
variable wall_force equal -v_atm*v_area/count(wall)
print "Wall force per atom: ${wall_force}"
fix fxpressure wall aveforce 0 0 ${wall_force} # atomspheric pressure: area/force->nktv2p
fix fxdrag wall viscous 100
fix fxrigid wall rigid/nve single

97
examples/PACKAGES/electrode/piston/log.1Dec2022.piston.g++.1 → examples/PACKAGES/electrode/piston/log.22May2024.piston.g++.1
View File

@ -1,4 +1,5 @@
LAMMPS (3 Nov 2022)
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-217-g1909233c69-modified)
using 1 OpenMP thread(s) per MPI task
# The intention is to find the average position of one wall at atmospheric
# pressure. The output is the wall position over time which can be used to
# find the average position for a run with fixed wall position.
@ -40,8 +41,8 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.011 seconds
special bonds CPU = 0.000 seconds
read_data CPU = 0.012 seconds
# ----------------- Settings Section -----------------
@ -77,7 +78,13 @@ fix fxforce_au gold setforce 0.0 0.0 0.0
# equilibrate z-coordinate of upper electrode while keeping the electrode rigid
fix fxforce_wa wall setforce 0.0 0.0 NULL
fix fxpressure wall aveforce 0 0 -0.005246 # atomspheric pressure: area/force->nktv2p
variable atm equal 1/68568.415 # 1/force->nktv2p
variable area equal (xhi-xlo)*(yhi-ylo)
variable wall_force equal -v_atm*v_area/count(wall)
print "Wall force per atom: ${wall_force}"
Wall force per atom: -0.000109285996244287
fix fxpressure wall aveforce 0 0 ${wall_force} # atomspheric pressure: area/force->nktv2p
fix fxpressure wall aveforce 0 0 -0.000109285996244287
fix fxdrag wall viscous 100
fix fxrigid wall rigid/nve single
1 rigid bodies with 48 atoms
@ -134,7 +141,7 @@ PPPM/electrode initialization ...
stencil order = 5
estimated absolute RMS force accuracy = 0.02930901
estimated relative force accuracy = 8.8263214e-05
using double precision MKL FFT
using double precision FFTW3
3d grid and FFT values/proc = 15884 6480
Generated 6 of 6 mixed pair_coeff terms from arithmetic mixing rule
Neighbor list info ...
@ -157,54 +164,54 @@ Neighbor list info ...
Per MPI rank memory allocation (min/avg/max) = 11.7 | 11.7 | 11.7 Mbytes
Step c_temp_mobile c_qwa c_qau v_top_wall
0 303.38967 -0.042963484 0.042963484 21.4018
5000 285.08828 -0.26105255 0.26105255 25.155629
10000 323.19176 -0.26264003 0.26264003 24.541676
15000 310.479 -0.27318148 0.27318148 23.141522
20000 295.18544 -0.11313444 0.11313444 23.828735
25000 295.38607 -0.25433086 0.25433086 23.673314
30000 288.0613 -0.30099901 0.30099901 23.438086
35000 278.5591 -0.15823576 0.15823576 24.311915
40000 303.95751 -0.19941381 0.19941381 23.69594
45000 279.026 -0.1659962 0.1659962 23.588604
50000 298.79278 -0.28866703 0.28866703 23.372508
55000 301.03353 -0.078370381 0.078370381 23.192985
60000 306.77965 -0.12807205 0.12807205 23.968574
65000 309.86008 -0.27162663 0.27162663 23.616704
70000 287.31116 -0.029751882 0.029751882 23.667495
75000 312.48654 -0.10759866 0.10759866 23.504105
80000 309.94267 -0.2558548 0.2558548 23.810576
85000 328.04389 -0.1575471 0.1575471 24.013437
90000 302.9806 -0.032002164 0.032002164 24.264432
95000 294.20804 -0.27797238 0.27797238 23.291758
100000 307.63019 -0.19047448 0.19047448 23.632147
Loop time of 530.844 on 1 procs for 100000 steps with 726 atoms
5000 311.85363 0.03543775 -0.03543775 24.79665
10000 285.91321 -0.16873703 0.16873703 23.103088
15000 295.39476 -0.44424612 0.44424612 23.767107
20000 296.12969 -0.14120993 0.14120993 23.96361
25000 306.59629 -0.29333182 0.29333182 23.884488
30000 297.98559 -0.10749684 0.10749684 23.73316
35000 297.98503 -0.11809975 0.11809975 23.984669
40000 300.26292 -0.32784184 0.32784184 23.462748
45000 295.68441 -0.25940165 0.25940165 23.516403
50000 315.12883 -0.36037614 0.36037614 23.627879
55000 290.55151 -0.0032838106 0.0032838106 23.684931
60000 316.4625 -0.17245368 0.17245368 24.126883
65000 296.79343 -0.054061851 0.054061851 23.695094
70000 305.99923 -0.11363801 0.11363801 23.55476
75000 297.40131 -0.27054153 0.27054153 23.928994
80000 306.54811 -0.25409719 0.25409719 23.869448
85000 303.95231 -0.17895561 0.17895561 23.658833
90000 313.43739 -0.059036514 0.059036514 23.36056
95000 290.3077 -0.31394478 0.31394478 23.885538
100000 297.5156 -0.30730083 0.30730083 23.511674
Loop time of 1586.06 on 1 procs for 100000 steps with 726 atoms
Performance: 32.552 ns/day, 0.737 hours/ns, 188.379 timesteps/s, 136.763 katom-step/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 10.895 ns/day, 2.203 hours/ns, 63.049 timesteps/s, 45.774 katom-step/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 190.47 | 190.47 | 190.47 | 0.0 | 35.88
Bond | 0.10754 | 0.10754 | 0.10754 | 0.0 | 0.02
Kspace | 73.179 | 73.179 | 73.179 | 0.0 | 13.79
Neigh | 24.209 | 24.209 | 24.209 | 0.0 | 4.56
Comm | 1.6857 | 1.6857 | 1.6857 | 0.0 | 0.32
Output | 0.0016861 | 0.0016861 | 0.0016861 | 0.0 | 0.00
Modify | 240.23 | 240.23 | 240.23 | 0.0 | 45.26
Other | | 0.9595 | | | 0.18
Pair | 460.91 | 460.91 | 460.91 | 0.0 | 29.06
Bond | 0.047873 | 0.047873 | 0.047873 | 0.0 | 0.00
Kspace | 341.4 | 341.4 | 341.4 | 0.0 | 21.53
Neigh | 52.868 | 52.868 | 52.868 | 0.0 | 3.33
Comm | 5.2321 | 5.2321 | 5.2321 | 0.0 | 0.33
Output | 0.00099102 | 0.00099102 | 0.00099102 | 0.0 | 0.00
Modify | 724.63 | 724.63 | 724.63 | 0.0 | 45.69
Other | | 0.9741 | | | 0.06
Nlocal: 726 ave 726 max 726 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2335 ave 2335 max 2335 min
Nghost: 2336 ave 2336 max 2336 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 120271 ave 120271 max 120271 min
Neighs: 120321 ave 120321 max 120321 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 120271
Ave neighs/atom = 165.66253
Total # of neighbors = 120321
Ave neighs/atom = 165.7314
Ave special neighs/atom = 1.7355372
Neighbor list builds = 7722
Neighbor list builds = 7670
Dangerous builds = 0
write_data "data.piston.final"
System init for write_data ...
@ -213,11 +220,11 @@ PPPM/electrode initialization ...
G vector (1/distance) = 0.32814871
grid = 12 15 36
stencil order = 5
estimated absolute RMS force accuracy = 0.029311365
estimated relative force accuracy = 8.8270304e-05
using double precision MKL FFT
estimated absolute RMS force accuracy = 0.029311329
estimated relative force accuracy = 8.8270197e-05
using double precision FFTW3
3d grid and FFT values/proc = 15884 6480
Generated 6 of 6 mixed pair_coeff terms from arithmetic mixing rule
Average conjugate gradient steps: 1.981
Total wall time: 0:08:50
Total wall time: 0:26:26

109
examples/PACKAGES/electrode/piston/log.1Dec2022.piston.g++.4 → examples/PACKAGES/electrode/piston/log.22May2024.piston.g++.4
View File

@ -1,4 +1,5 @@
LAMMPS (3 Nov 2022)
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-217-g1909233c69-modified)
using 1 OpenMP thread(s) per MPI task
# The intention is to find the average position of one wall at atmospheric
# pressure. The output is the wall position over time which can be used to
# find the average position for a run with fixed wall position.
@ -41,8 +42,8 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.017 seconds
special bonds CPU = 0.000 seconds
read_data CPU = 0.012 seconds
# ----------------- Settings Section -----------------
@ -66,7 +67,7 @@ Finding SHAKE clusters ...
0 = # of size 3 clusters
0 = # of size 4 clusters
210 = # of frozen angles
find clusters CPU = 0.002 seconds
find clusters CPU = 0.000 seconds
pair_modify mix arithmetic
# ----------------- Run Section -----------------
@ -78,7 +79,13 @@ fix fxforce_au gold setforce 0.0 0.0 0.0
# equilibrate z-coordinate of upper electrode while keeping the electrode rigid
fix fxforce_wa wall setforce 0.0 0.0 NULL
fix fxpressure wall aveforce 0 0 -0.005246 # atomspheric pressure: area/force->nktv2p
variable atm equal 1/68568.415 # 1/force->nktv2p
variable area equal (xhi-xlo)*(yhi-ylo)
variable wall_force equal -v_atm*v_area/count(wall)
print "Wall force per atom: ${wall_force}"
Wall force per atom: -0.000109285996244287
fix fxpressure wall aveforce 0 0 ${wall_force} # atomspheric pressure: area/force->nktv2p
fix fxpressure wall aveforce 0 0 -0.000109285996244287
fix fxdrag wall viscous 100
fix fxrigid wall rigid/nve single
1 rigid bodies with 48 atoms
@ -135,7 +142,7 @@ PPPM/electrode initialization ...
stencil order = 5
estimated absolute RMS force accuracy = 0.02930901
estimated relative force accuracy = 8.8263214e-05
using double precision MKL FFT
using double precision FFTW3
3d grid and FFT values/proc = 8512 2880
Generated 6 of 6 mixed pair_coeff terms from arithmetic mixing rule
Neighbor list info ...
@ -158,54 +165,54 @@ Neighbor list info ...
Per MPI rank memory allocation (min/avg/max) = 10.06 | 10.22 | 10.41 Mbytes
Step c_temp_mobile c_qwa c_qau v_top_wall
0 303.38967 -0.042963484 0.042963484 21.4018
5000 292.03027 -0.19040435 0.19040435 24.581338
10000 309.52764 -0.48308301 0.48308301 23.776985
15000 295.00243 -0.16591109 0.16591109 23.672038
20000 293.5536 -0.086669084 0.086669084 23.426455
25000 303.0079 -0.16488112 0.16488112 23.862966
30000 306.31463 -0.23192653 0.23192653 23.819882
35000 303.66268 -0.2317907 0.2317907 23.495344
40000 301.39435 -0.34661329 0.34661329 23.657835
45000 291.61205 -0.30539427 0.30539427 23.437303
50000 298.65319 -0.096107034 0.096107034 23.57809
55000 282.65069 -0.14943539 0.14943539 23.823728
60000 310.64182 -0.17418813 0.17418813 23.286959
65000 308.47141 -0.02075662 0.02075662 23.91313
70000 292.5186 -0.080163162 0.080163162 23.96283
75000 270.13928 -0.029528648 0.029528648 23.488972
80000 322.10914 0.030761045 -0.030761045 23.47592
85000 310.60347 -0.24069996 0.24069996 23.987091
90000 294.35695 -0.070458235 0.070458235 23.397929
95000 308.69043 -0.2652581 0.2652581 23.473813
100000 318.71883 0.024035956 -0.024035956 23.449863
Loop time of 590.232 on 4 procs for 100000 steps with 726 atoms
5000 291.6303 -0.1820085 0.1820085 24.641399
10000 299.42886 -0.19823095 0.19823095 23.820522
15000 288.23071 -0.065261869 0.065261869 23.360845
20000 299.4644 -0.042993777 0.042993777 23.987554
25000 304.26497 -0.15665293 0.15665293 23.729006
30000 292.29674 -0.25142779 0.25142779 23.960725
35000 295.57492 -0.01269228 0.01269228 23.445383
40000 303.38438 -0.13941727 0.13941727 23.517483
45000 302.211 -0.19589892 0.19589892 23.704043
50000 281.64939 -0.18057298 0.18057298 23.542137
55000 274.90565 -0.15453379 0.15453379 23.734347
60000 290.70459 -0.27977436 0.27977436 23.835365
65000 293.42241 -0.2454241 0.2454241 23.59269
70000 295.20229 -0.041314995 0.041314995 23.73856
75000 297.79519 -0.11231755 0.11231755 23.57262
80000 285.17858 -0.070796508 0.070796508 23.817135
85000 311.71609 -0.068920177 0.068920177 23.861127
90000 287.80446 -0.19183387 0.19183387 23.369393
95000 309.43345 -0.15238671 0.15238671 23.597792
100000 294.12422 -0.14284353 0.14284353 23.526286
Loop time of 876.546 on 4 procs for 100000 steps with 726 atoms
Performance: 29.277 ns/day, 0.820 hours/ns, 169.425 timesteps/s, 123.003 katom-step/s
72.5% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 19.714 ns/day, 1.217 hours/ns, 114.084 timesteps/s, 82.825 katom-step/s
98.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 57.391 | 75.867 | 96.292 | 212.1 | 12.85
Bond | 0.10177 | 0.11042 | 0.12415 | 2.7 | 0.02
Kspace | 102.79 | 123.16 | 141.5 | 165.7 | 20.87
Neigh | 12.808 | 12.895 | 12.982 | 2.3 | 2.18
Comm | 18.885 | 19.973 | 21.064 | 24.0 | 3.38
Output | 0.0022573 | 0.0022749 | 0.0023225 | 0.1 | 0.00
Modify | 355.89 | 356.74 | 357.61 | 4.2 | 60.44
Other | | 1.478 | | | 0.25
Pair | 123.63 | 171.23 | 215.73 | 336.6 | 19.53
Bond | 0.068261 | 0.075883 | 0.081822 | 1.9 | 0.01
Kspace | 187.59 | 231.71 | 279.01 | 287.1 | 26.43
Neigh | 29.28 | 29.462 | 29.637 | 2.5 | 3.36
Comm | 12.544 | 13.731 | 14.929 | 29.1 | 1.57
Output | 0.0010182 | 0.0014585 | 0.0016071 | 0.7 | 0.00
Modify | 428.74 | 429.25 | 429.74 | 2.3 | 48.97
Other | | 1.092 | | | 0.12
Nlocal: 181.5 ave 207 max 169 min
Histogram: 2 0 1 0 0 0 0 0 0 1
Nghost: 1961.5 ave 1984 max 1926 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Neighs: 30051 ave 41646 max 20775 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Nlocal: 181.5 ave 195 max 166 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Nghost: 1955.5 ave 1978 max 1931 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Neighs: 30343 ave 39847 max 20428 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 120204
Ave neighs/atom = 165.57025
Total # of neighbors = 121372
Ave neighs/atom = 167.17906
Ave special neighs/atom = 1.7355372
Neighbor list builds = 7663
Neighbor list builds = 7698
Dangerous builds = 0
write_data "data.piston.final"
System init for write_data ...
@ -214,11 +221,11 @@ PPPM/electrode initialization ...
G vector (1/distance) = 0.32814871
grid = 12 15 36
stencil order = 5
estimated absolute RMS force accuracy = 0.029311028
estimated relative force accuracy = 8.8269289e-05
using double precision MKL FFT
estimated absolute RMS force accuracy = 0.029310954
estimated relative force accuracy = 8.8269069e-05
using double precision FFTW3
3d grid and FFT values/proc = 8512 2880
Generated 6 of 6 mixed pair_coeff terms from arithmetic mixing rule
Average conjugate gradient steps: 1.982
Total wall time: 0:09:50
Average conjugate gradient steps: 1.981
Total wall time: 0:14:36