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

modify example input and output files

Browse Source
This commit is contained in:
Steve Plimpton
2022-05-24 16:59:27 -06:00
parent 97eb6c195f
commit 75c0287024
56 changed files with 327 additions and 72547 deletions
Download Patch File Download Diff File Expand all files Collapse all files

19492
examples/amoeba/dump.ubi.1.test
View File

File diff suppressed because it is too large Load Diff

19492
examples/amoeba/dump.ubi.32.test
View File

File diff suppressed because it is too large Load Diff

7227
examples/amoeba/dump.water_box.amoeba.1.test
View File

File diff suppressed because it is too large Load Diff

7227
examples/amoeba/dump.water_box.amoeba.32.test
View File

File diff suppressed because it is too large Load Diff

7227
examples/amoeba/dump.water_box.hippo.1.test
View File

File diff suppressed because it is too large Load Diff

7227
examples/amoeba/dump.water_box.hippo.32.test
View File

File diff suppressed because it is too large Load Diff

165
examples/amoeba/dump.water_dimer.amoeba.1.test
View File

@ -1,165 +0,0 @@
ITEM: TIMESTEP
0
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS ss ss ss
-1.4632357229999999e+00 9.3247372299999998e-01
-7.5570026690000003e-01 7.5527126690000002e-01
-8.9995638999999985e-03 2.9352285639000000e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -0.024616 -0.001154 -0.003748 7.94661 0.0143882 11.5654
2 2 -0.244211 -0.000666 0.933978 -7.05777 -0.00770443 -3.06431
3 2 0.932234 -0.000406 -0.008705 -0.956334 -0.00629552 -7.87238
4 1 -0.892721 0.00012 2.77367 -12.7377 -0.00815373 2.78728
5 2 -1.463 0.75512 2.93387 6.39935 4.06267 -1.71086
6 2 -1.46181 -0.755549 2.93493 6.40581 -4.05491 -1.70517
ITEM: TIMESTEP
10
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS ss ss ss
-1.4632357229999999e+00 9.3247372299999998e-01
-7.5570026690000003e-01 7.5527126690000002e-01
-8.9995638999999985e-03 2.9352285639000000e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -0.0210901 -0.00114727 0.00187855 -6.1441 -0.00926688 -6.30688
2 2 -0.299755 -0.000716119 0.924842 7.69349 0.00623407 0.274054
3 2 0.933941 -0.000453269 -0.0777281 -1.08824 0.00357639 6.29137
4 1 -0.89902 0.000115499 2.77431 8.40057 0.0041921 -3.3195
5 2 -1.41411 0.797948 2.92323 -4.42685 -5.12343 1.53409
6 2 -1.41285 -0.798315 2.92435 -4.43485 5.1187 1.52687
ITEM: TIMESTEP
20
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS ss ss ss
-1.4632357229999999e+00 9.3247372299999998e-01
-7.5570026690000003e-01 7.5527126690000002e-01
-8.9995638999999985e-03 2.9352285639000000e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -0.0253162 -0.0011519 9.30621e-06 6.65721 0.0114207 8.7962
2 2 -0.214112 -0.000636438 0.94263 -7.71284 -0.00678668 -1.03908
3 2 0.928921 -0.000430955 -0.0404651 0.717191 -0.00462784 -7.37266
4 1 -0.894334 0.00011596 2.76974 -10.0965 -0.00568803 3.16137
5 2 -1.45804 0.75449 2.94684 5.21348 5.11475 -1.77652
6 2 -1.45685 -0.754893 2.9479 5.22149 -5.10907 -1.76931
ITEM: TIMESTEP
30
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS ss ss ss
-1.4632357229999999e+00 9.3247372299999998e-01
-7.5570026690000003e-01 7.5527126690000002e-01
-8.9995638999999985e-03 2.9352285639000000e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -0.0221554 -0.0011439 0.00783939 -8.36895 -0.0130834 -9.24354
2 2 -0.25261 -0.000667783 0.941075 6.36112 0.00692164 2.73081
3 2 0.92432 -0.000494304 -0.125343 2.07038 0.00615069 6.42537
4 1 -0.900866 0.00010992 2.76846 11.0986 0.00640696 -3.42785
5 2 -1.40977 0.795072 2.93807 -5.57817 -3.04583 1.75974
6 2 -1.40852 -0.795411 2.93919 -5.58301 3.03943 1.75548
ITEM: TIMESTEP
40
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS ss ss ss
-1.4632357229999999e+00 9.3247372299999998e-01
-7.5570026690000003e-01 7.5527126690000002e-01
-8.9995638999999985e-03 2.9352285639000000e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -0.0269208 -0.00114842 0.00674288 5.42877 0.00730481 4.31748
2 2 -0.171607 -0.000594964 0.954009 -8.40692 -0.00484075 2.50346
3 2 0.92209 -0.000466908 -0.0840066 2.3456 -0.00296432 -6.82561
4 1 -0.895716 0.000110956 2.76419 -6.18264 -0.00259137 3.07323
5 2 -1.45218 0.754436 2.95353 3.40261 6.39649 -1.53879
6 2 -1.45099 -0.75482 2.9546 3.41259 -6.3934 -1.52976
ITEM: TIMESTEP
50
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS ss ss ss
-1.4632357229999999e+00 9.3247372299999998e-01
-7.5570026690000003e-01 7.5527126690000002e-01
-8.9995638999999985e-03 2.9352285639000000e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -0.0239329 -0.00114175 0.0128926 -8.15007 -0.014184 -11.0504
2 2 -0.230937 -0.000644481 0.949766 5.72493 0.00756591 4.36142
3 2 0.91871 -0.000511822 -0.144074 2.40885 0.00639366 6.3907
4 1 -0.899724 0.000108594 2.76531 11.5106 0.00694105 -3.03119
5 2 -1.41275 0.792848 2.92798 -5.74551 -2.08247 1.6662
6 2 -1.41151 -0.793206 2.9291 -5.7488 2.07576 1.66327
ITEM: TIMESTEP
60
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS ss ss ss
-1.4632357229999999e+00 9.3247372299999998e-01
-7.5570026690000003e-01 7.5527126690000002e-01
-8.9995638999999985e-03 2.9352285639000000e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -0.0287434 -0.0011479 0.00953424 6.82379 0.00862743 4.63675
2 2 -0.180318 -0.000600308 0.956082 -8.03241 -0.00482631 2.10983
3 2 0.922397 -0.000459471 -0.0739414 0.782565 -0.00412295 -6.72684
4 1 -0.892694 0.000113827 2.76489 -6.55004 -0.00361317 2.26756
5 2 -1.45749 0.757284 2.91975 3.48398 5.14308 -1.14726
6 2 -1.4563 -0.757724 2.92081 3.49211 -5.13915 -1.14003
ITEM: TIMESTEP
70
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS ss ss ss
-1.4632357229999999e+00 9.3247372299999998e-01
-7.5570026690000003e-01 7.5527126690000002e-01
-8.9995638999999985e-03 2.9352285639000000e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -0.025848 -0.00114271 0.0136758 -6.10179 -0.0106002 -8.24377
2 2 -0.259382 -0.000669072 0.94681 6.59121 0.0065405 1.93161
3 2 0.923692 -0.000484045 -0.110366 -0.0484081 0.00428029 6.1322
4 1 -0.894893 0.000114175 2.76783 7.43985 0.00424265 -2.1131
5 2 -1.42416 0.79251 2.88639 -3.9377 -3.53776 1.14903
6 2 -1.42292 -0.792944 2.88751 -3.94318 3.53329 1.14403
ITEM: TIMESTEP
80
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS ss ss ss
-1.4632357229999999e+00 9.3247372299999998e-01
-7.5570026690000003e-01 7.5527126690000002e-01
-8.9995638999999985e-03 2.9352285639000000e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -0.030135 -0.00114891 0.00965506 7.41429 0.0123912 9.3266
2 2 -0.213346 -0.000627628 0.954378 -6.76672 -0.00675668 -2.04974
3 2 0.924938 -0.000432456 -0.0385785 -0.591495 -0.00546702 -7.10385
4 1 -0.888796 0.000119275 2.76827 -9.03539 -0.00642914 1.05959
5 2 -1.46214 0.762697 2.87512 4.48797 2.10983 -0.617778
6 2 -1.46094 -0.763208 2.87619 4.49133 -2.10357 -0.61482
ITEM: TIMESTEP
90
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS ss ss ss
-1.4632357229999999e+00 9.3247372299999998e-01
-7.5570026690000003e-01 7.5527126690000002e-01
-8.9995638999999985e-03 2.9352285639000000e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -0.0270206 -0.00114299 0.0145983 -6.11813 -0.00811207 -4.69194
2 2 -0.274281 -0.000680382 0.947366 7.50569 0.00503125 -1.23144
3 2 0.92514 -0.000469353 -0.0912836 -0.650877 0.00352314 5.72916
4 1 -0.891964 0.000116952 2.76852 3.17186 0.0014363 -1.52231
5 2 -1.43137 0.791127 2.86377 -1.95059 -4.67792 0.861555
6 2 -1.43013 -0.791605 2.86488 -1.95795 4.67604 0.85497
ITEM: TIMESTEP
100
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS ss ss ss
-1.4632357229999999e+00 9.3247372299999998e-01
-7.5570026690000003e-01 7.5527126690000002e-01
-8.9995638999999985e-03 2.9352285639000000e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -0.030669 -0.00114759 0.0121427 6.42493 0.0120997 10.0073
2 2 -0.203569 -0.000615753 0.960107 -6.40597 -0.00736639 -3.30674
3 2 0.923036 -0.000442107 -0.0503324 -0.0528607 -0.00477186 -6.71539
4 1 -0.889443 0.000116814 2.76553 -7.7691 -0.0050422 1.37075
5 2 -1.45671 0.76736 2.88018 3.9012 0.426437 -0.678284
6 2 -1.4555 -0.767854 2.88126 3.9018 -0.421357 -0.677675

165
examples/amoeba/dump.water_dimer.amoeba.4.test
View File

@ -1,165 +0,0 @@
ITEM: TIMESTEP
0
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS ss ss ss
-1.4632357229999999e+00 9.3247372299999998e-01
-7.5570026690000003e-01 7.5527126690000002e-01
-8.9995638999999985e-03 2.9352285639000000e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -0.024616 -0.001154 -0.003748 7.94661 0.0143882 11.5654
2 2 -0.244211 -0.000666 0.933978 -7.05777 -0.00770443 -3.06431
3 2 0.932234 -0.000406 -0.008705 -0.956334 -0.00629552 -7.87238
4 1 -0.892721 0.00012 2.77367 -12.7377 -0.00815373 2.78728
5 2 -1.463 0.75512 2.93387 6.39935 4.06267 -1.71086
6 2 -1.46181 -0.755549 2.93493 6.40581 -4.05491 -1.70517
ITEM: TIMESTEP
10
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS ss ss ss
-1.4632357229999999e+00 9.3247372299999998e-01
-7.5570026690000003e-01 7.5527126690000002e-01
-8.9995638999999985e-03 2.9352285639000000e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -0.0210901 -0.00114727 0.00187855 -6.1441 -0.00926688 -6.30688
2 2 -0.299755 -0.000716119 0.924842 7.69349 0.00623407 0.274054
3 2 0.933941 -0.000453269 -0.0777281 -1.08824 0.00357639 6.29137
4 1 -0.89902 0.000115499 2.77431 8.40057 0.0041921 -3.3195
5 2 -1.41411 0.797948 2.92323 -4.42685 -5.12343 1.53409
6 2 -1.41285 -0.798315 2.92435 -4.43485 5.1187 1.52687
ITEM: TIMESTEP
20
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS ss ss ss
-1.4632357229999999e+00 9.3247372299999998e-01
-7.5570026690000003e-01 7.5527126690000002e-01
-8.9995638999999985e-03 2.9352285639000000e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -0.0253162 -0.0011519 9.30621e-06 6.65721 0.0114207 8.7962
2 2 -0.214112 -0.000636438 0.94263 -7.71284 -0.00678668 -1.03908
3 2 0.928921 -0.000430955 -0.0404651 0.717191 -0.00462784 -7.37266
4 1 -0.894334 0.00011596 2.76974 -10.0965 -0.00568803 3.16137
5 2 -1.45804 0.75449 2.94684 5.21348 5.11475 -1.77652
6 2 -1.45685 -0.754893 2.9479 5.22149 -5.10907 -1.76931
ITEM: TIMESTEP
30
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS ss ss ss
-1.4632357229999999e+00 9.3247372299999998e-01
-7.5570026690000003e-01 7.5527126690000002e-01
-8.9995638999999985e-03 2.9352285639000000e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -0.0221554 -0.0011439 0.00783939 -8.36895 -0.0130834 -9.24354
2 2 -0.25261 -0.000667783 0.941075 6.36112 0.00692164 2.73081
3 2 0.92432 -0.000494304 -0.125343 2.07038 0.00615069 6.42537
4 1 -0.900866 0.00010992 2.76846 11.0986 0.00640696 -3.42785
5 2 -1.40977 0.795072 2.93807 -5.57817 -3.04583 1.75974
6 2 -1.40852 -0.795411 2.93919 -5.58301 3.03943 1.75548
ITEM: TIMESTEP
40
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS ss ss ss
-1.4632357229999999e+00 9.3247372299999998e-01
-7.5570026690000003e-01 7.5527126690000002e-01
-8.9995638999999985e-03 2.9352285639000000e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -0.0269208 -0.00114842 0.00674288 5.42877 0.00730481 4.31748
2 2 -0.171607 -0.000594964 0.954009 -8.40692 -0.00484075 2.50346
3 2 0.92209 -0.000466908 -0.0840066 2.3456 -0.00296432 -6.82561
4 1 -0.895716 0.000110956 2.76419 -6.18264 -0.00259137 3.07323
5 2 -1.45218 0.754436 2.95353 3.40261 6.39649 -1.53879
6 2 -1.45099 -0.75482 2.9546 3.41259 -6.3934 -1.52976
ITEM: TIMESTEP
50
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS ss ss ss
-1.4632357229999999e+00 9.3247372299999998e-01
-7.5570026690000003e-01 7.5527126690000002e-01
-8.9995638999999985e-03 2.9352285639000000e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -0.0239329 -0.00114175 0.0128926 -8.15007 -0.014184 -11.0504
2 2 -0.230937 -0.000644481 0.949766 5.72493 0.00756591 4.36142
3 2 0.91871 -0.000511822 -0.144074 2.40885 0.00639366 6.3907
4 1 -0.899724 0.000108594 2.76531 11.5106 0.00694105 -3.03119
5 2 -1.41275 0.792848 2.92798 -5.74551 -2.08247 1.6662
6 2 -1.41151 -0.793206 2.9291 -5.7488 2.07576 1.66327
ITEM: TIMESTEP
60
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS ss ss ss
-1.4632357229999999e+00 9.3247372299999998e-01
-7.5570026690000003e-01 7.5527126690000002e-01
-8.9995638999999985e-03 2.9352285639000000e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -0.0287434 -0.0011479 0.00953424 6.82379 0.00862743 4.63675
2 2 -0.180318 -0.000600308 0.956082 -8.03241 -0.00482631 2.10983
3 2 0.922397 -0.000459471 -0.0739414 0.782565 -0.00412295 -6.72684
4 1 -0.892694 0.000113827 2.76489 -6.55004 -0.00361317 2.26756
5 2 -1.45749 0.757284 2.91975 3.48398 5.14308 -1.14726
6 2 -1.4563 -0.757724 2.92081 3.49211 -5.13915 -1.14003
ITEM: TIMESTEP
70
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS ss ss ss
-1.4632357229999999e+00 9.3247372299999998e-01
-7.5570026690000003e-01 7.5527126690000002e-01
-8.9995638999999985e-03 2.9352285639000000e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -0.025848 -0.00114271 0.0136758 -6.10179 -0.0106002 -8.24377
2 2 -0.259382 -0.000669072 0.94681 6.59121 0.0065405 1.93161
3 2 0.923692 -0.000484045 -0.110366 -0.0484081 0.00428029 6.1322
4 1 -0.894893 0.000114175 2.76783 7.43985 0.00424265 -2.1131
5 2 -1.42416 0.79251 2.88639 -3.9377 -3.53776 1.14903
6 2 -1.42292 -0.792944 2.88751 -3.94318 3.53329 1.14403
ITEM: TIMESTEP
80
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS ss ss ss
-1.4632357229999999e+00 9.3247372299999998e-01
-7.5570026690000003e-01 7.5527126690000002e-01
-8.9995638999999985e-03 2.9352285639000000e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -0.030135 -0.00114891 0.00965506 7.41429 0.0123912 9.3266
2 2 -0.213346 -0.000627628 0.954378 -6.76672 -0.00675668 -2.04974
3 2 0.924938 -0.000432456 -0.0385785 -0.591495 -0.00546702 -7.10385
4 1 -0.888796 0.000119275 2.76827 -9.03539 -0.00642914 1.05959
5 2 -1.46214 0.762697 2.87512 4.48797 2.10983 -0.617778
6 2 -1.46094 -0.763208 2.87619 4.49133 -2.10357 -0.61482
ITEM: TIMESTEP
90
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS ss ss ss
-1.4632357229999999e+00 9.3247372299999998e-01
-7.5570026690000003e-01 7.5527126690000002e-01
-8.9995638999999985e-03 2.9352285639000000e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -0.0270206 -0.00114299 0.0145983 -6.11813 -0.00811207 -4.69194
2 2 -0.274281 -0.000680382 0.947366 7.50569 0.00503125 -1.23144
3 2 0.92514 -0.000469353 -0.0912836 -0.650877 0.00352314 5.72916
4 1 -0.891964 0.000116952 2.76852 3.17186 0.0014363 -1.52231
5 2 -1.43137 0.791127 2.86377 -1.95059 -4.67792 0.861555
6 2 -1.43013 -0.791605 2.86488 -1.95795 4.67604 0.85497
ITEM: TIMESTEP
100
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS ss ss ss
-1.4632357229999999e+00 9.3247372299999998e-01
-7.5570026690000003e-01 7.5527126690000002e-01
-8.9995638999999985e-03 2.9352285639000000e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -0.030669 -0.00114759 0.0121427 6.42493 0.0120997 10.0073
2 2 -0.203569 -0.000615753 0.960107 -6.40597 -0.00736639 -3.30674
3 2 0.923036 -0.000442107 -0.0503324 -0.0528607 -0.00477186 -6.71539
4 1 -0.889443 0.000116814 2.76553 -7.7691 -0.0050422 1.37075
5 2 -1.45671 0.76736 2.88018 3.9012 0.426437 -0.678284
6 2 -1.4555 -0.767854 2.88126 3.9018 -0.421357 -0.677675

165
examples/amoeba/dump.water_dimer.hippo.1.test
View File

@ -1,165 +0,0 @@
ITEM: TIMESTEP
0
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS ss ss ss
-1.4632357229999999e+00 9.3247372299999998e-01
-7.5570026690000003e-01 7.5527126690000002e-01
-8.9995638999999985e-03 2.9352285639000000e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -0.024616 -0.001154 -0.003748 6.77815 0.012441 10.1043
2 2 -0.244211 -0.000666 0.933978 -6.4757 -0.0067894 -2.41462
3 2 0.932234 -0.000406 -0.008705 -0.41382 -0.00540908 -7.21892
4 1 -0.892721 0.00012 2.77367 -11.9286 -0.00716387 3.29032
5 2 -1.463 0.75512 2.93387 6.01759 3.00398 -1.88265
6 2 -1.46181 -0.755549 2.93493 6.02238 -2.99706 -1.87845
ITEM: TIMESTEP
10
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS ss ss ss
-1.4632357229999999e+00 9.3247372299999998e-01
-7.5570026690000003e-01 7.5527126690000002e-01
-8.9995638999999985e-03 2.9352285639000000e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -0.0215682 -0.00114805 0.0012979 -6.21268 -0.00924301 -6.19628
2 2 -0.293095 -0.000710409 0.925512 6.99875 0.0060121 0.73377
3 2 0.933101 -0.000449223 -0.0710512 -0.501529 0.00371221 5.82975
4 1 -0.897884 0.000116793 2.77488 7.53966 0.00410482 -2.48587
5 2 -1.42223 0.790989 2.91963 -3.9083 -4.87571 1.06275
6 2 -1.42099 -0.791374 2.92075 -3.91591 4.87112 1.05588
ITEM: TIMESTEP
20
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS ss ss ss
-1.4632357229999999e+00 9.3247372299999998e-01
-7.5570026690000003e-01 7.5527126690000002e-01
-8.9995638999999985e-03 2.9352285639000000e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -0.0258564 -0.00115245 -0.000173159 6.03126 0.0103631 7.9915
2 2 -0.214264 -0.000636469 0.942735 -7.00136 -0.00592601 -0.60904
3 2 0.929001 -0.000430037 -0.0392653 0.701856 -0.0043552 -6.96821
4 1 -0.893054 0.000118973 2.77259 -8.83712 -0.00512625 2.54445
5 2 -1.46387 0.753541 2.92502 4.54888 4.85296 -1.48277
6 2 -1.46268 -0.753984 2.92608 4.55648 -4.84791 -1.47593
ITEM: TIMESTEP
30
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS ss ss ss
-1.4632357229999999e+00 9.3247372299999998e-01
-7.5570026690000003e-01 7.5527126690000002e-01
-8.9995638999999985e-03 2.9352285639000000e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -0.0237238 -0.00114526 0.00766999 -7.81865 -0.0119879 -8.3015
2 2 -0.241061 -0.000656856 0.943727 6.09288 0.0066852 2.69388
3 2 0.923032 -0.000493736 -0.123121 1.75879 0.00552582 5.88556
4 1 -0.897978 0.000115451 2.77309 11.6501 0.00727223 -2.82116
5 2 -1.42536 0.788259 2.90023 -5.83991 -2.07218 1.27305
6 2 -1.42412 -0.788676 2.90134 -5.84324 2.06468 1.27016
ITEM: TIMESTEP
40
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS ss ss ss
-1.4632357229999999e+00 9.3247372299999998e-01
-7.5570026690000003e-01 7.5527126690000002e-01
-8.9995638999999985e-03 2.9352285639000000e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -0.0292005 -0.00114894 0.00855106 5.6712 0.00787804 4.86214
2 2 -0.153199 -0.000576377 0.959922 -7.58451 -0.00449199 2.07976
3 2 0.919336 -0.000480028 -0.0995905 1.37912 -0.00359093 -6.63778
4 1 -0.89217 0.000118771 2.77132 -5.68638 -0.00321013 1.64962
5 2 -1.47004 0.751887 2.88738 3.10503 6.73714 -0.981624
6 2 -1.46886 -0.752392 2.88844 3.11554 -6.73373 -0.972121
ITEM: TIMESTEP
50
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS ss ss ss
-1.4632357229999999e+00 9.3247372299999998e-01
-7.5570026690000003e-01 7.5527126690000002e-01
-8.9995638999999985e-03 2.9352285639000000e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -0.0276682 -0.00114169 0.0171537 -7.90829 -0.012452 -8.85967
2 2 -0.185755 -0.000598779 0.964286 5.83022 0.00671605 3.0354
3 2 0.908646 -0.000541992 -0.175729 1.96931 0.00577867 6.00768
4 1 -0.895573 0.00011689 2.77245 11.8261 0.00822001 -1.54401
5 2 -1.4336 0.787999 2.84603 -5.85703 -2.08185 0.681764
6 2 -1.43237 -0.788505 2.84714 -5.86031 2.07358 0.678838
ITEM: TIMESTEP
60
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS ss ss ss
-1.4632357229999999e+00 9.3247372299999998e-01
-7.5570026690000003e-01 7.5527126690000002e-01
-8.9995638999999985e-03 2.9352285639000000e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -0.0340777 -0.00114581 0.0184647 7.2272 0.00951667 5.4479
2 2 -0.113434 -0.000533921 0.975674 -7.44659 -0.00496006 1.26816
3 2 0.909471 -0.000512535 -0.134923 -0.287426 -0.00476073 -6.43846
4 1 -0.888126 0.000122907 2.77269 -9.08281 -0.00670232 0.725333
5 2 -1.47838 0.753365 2.8077 4.79099 4.82306 -0.504859
6 2 -1.47719 -0.753996 2.80876 4.79863 -4.81616 -0.498076
ITEM: TIMESTEP
70
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS ss ss ss
-1.4632357229999999e+00 9.3247372299999998e-01
-7.5570026690000003e-01 7.5527126690000002e-01
-8.9995638999999985e-03 2.9352285639000000e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -0.0329631 -0.00113896 0.0269437 -6.82209 -0.00981599 -6.32682
2 2 -0.16378 -0.000570078 0.980622 6.44654 0.00529861 0.332147
3 2 0.899135 -0.000560623 -0.191768 0.56204 0.00474764 6.11404
4 1 -0.890774 0.0001215 2.77364 7.6207 0.00561833 -0.364449
5 2 -1.4359 0.790393 2.75878 -3.89983 -4.84574 0.12595
6 2 -1.43466 -0.791026 2.7599 -3.90736 4.83989 0.11913
ITEM: TIMESTEP
80
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS ss ss ss
-1.4632357229999999e+00 9.3247372299999998e-01
-7.5570026690000003e-01 7.5527126690000002e-01
-8.9995638999999985e-03 2.9352285639000000e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -0.0396799 -0.00114299 0.0287108 8.10782 0.0121934 8.26954
2 2 -0.101327 -0.000514632 0.989821 -6.98655 -0.00644087 -1.35375
3 2 0.902079 -0.000521504 -0.139604 -1.23495 -0.0056704 -6.67396
4 1 -0.883488 0.000127321 2.77377 -12.2256 -0.0109573 -1.83848
5 2 -1.47309 0.755263 2.71301 6.16734 2.89071 0.796293
6 2 -1.4719 -0.756019 2.71407 6.17192 -2.87983 0.800362
ITEM: TIMESTEP
90
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS ss ss ss
-1.4632357229999999e+00 9.3247372299999998e-01
-7.5570026690000003e-01 7.5527126690000002e-01
-8.9995638999999985e-03 2.9352285639000000e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -0.0383179 -0.00113532 0.0380883 -7.16334 -0.00889532 -4.6369
2 2 -0.149498 -0.00054848 0.995531 6.83221 0.00448143 -1.26419
3 2 0.889431 -0.00057205 -0.197356 0.916 0.00477871 5.76452
4 1 -0.886952 0.000122589 2.77093 7.29365 0.00587785 0.155791
5 2 -1.42602 0.790491 2.68716 -3.93543 -4.86013 -0.00619146
6 2 -1.42478 -0.791209 2.68827 -3.94309 4.85389 -0.0130349
ITEM: TIMESTEP
100
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS ss ss ss
-1.4632357229999999e+00 9.3247372299999998e-01
-7.5570026690000003e-01 7.5527126690000002e-01
-8.9995638999999985e-03 2.9352285639000000e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -0.0443853 -0.00113803 0.0410221 7.36858 0.0108291 7.15279
2 2 -0.076648 -0.000485983 1.00287 -6.96363 -0.00585609 -0.543819
3 2 0.890615 -0.000542732 -0.157107 -0.3904 -0.00504823 -6.73186
4 1 -0.880834 0.000124898 2.7674 -9.13947 -0.00841726 -1.90715
5 2 -1.46341 0.754149 2.66816 4.55895 4.52404 1.01184
6 2 -1.46222 -0.754952 2.66922 4.56597 -4.51554 1.01819

165
examples/amoeba/dump.water_dimer.hippo.4.test
View File

@ -1,165 +0,0 @@
ITEM: TIMESTEP
0
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS ss ss ss
-1.4632357229999999e+00 9.3247372299999998e-01
-7.5570026690000003e-01 7.5527126690000002e-01
-8.9995638999999985e-03 2.9352285639000000e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -0.024616 -0.001154 -0.003748 6.77815 0.012441 10.1043
2 2 -0.244211 -0.000666 0.933978 -6.4757 -0.0067894 -2.41462
3 2 0.932234 -0.000406 -0.008705 -0.41382 -0.00540908 -7.21892
4 1 -0.892721 0.00012 2.77367 -11.9286 -0.00716387 3.29032
5 2 -1.463 0.75512 2.93387 6.01759 3.00398 -1.88265
6 2 -1.46181 -0.755549 2.93493 6.02238 -2.99706 -1.87845
ITEM: TIMESTEP
10
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS ss ss ss
-1.4632357229999999e+00 9.3247372299999998e-01
-7.5570026690000003e-01 7.5527126690000002e-01
-8.9995638999999985e-03 2.9352285639000000e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -0.0215682 -0.00114805 0.0012979 -6.21268 -0.00924301 -6.19628
2 2 -0.293095 -0.000710409 0.925512 6.99875 0.0060121 0.73377
3 2 0.933101 -0.000449223 -0.0710512 -0.501529 0.00371221 5.82975
4 1 -0.897884 0.000116793 2.77488 7.53966 0.00410482 -2.48587
5 2 -1.42223 0.790989 2.91963 -3.9083 -4.87571 1.06275
6 2 -1.42099 -0.791374 2.92075 -3.91591 4.87112 1.05588
ITEM: TIMESTEP
20
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS ss ss ss
-1.4632357229999999e+00 9.3247372299999998e-01
-7.5570026690000003e-01 7.5527126690000002e-01
-8.9995638999999985e-03 2.9352285639000000e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -0.0258564 -0.00115245 -0.000173159 6.03126 0.0103631 7.9915
2 2 -0.214264 -0.000636469 0.942735 -7.00136 -0.00592601 -0.60904
3 2 0.929001 -0.000430037 -0.0392653 0.701856 -0.0043552 -6.96821
4 1 -0.893054 0.000118973 2.77259 -8.83712 -0.00512625 2.54445
5 2 -1.46387 0.753541 2.92502 4.54888 4.85296 -1.48277
6 2 -1.46268 -0.753984 2.92608 4.55648 -4.84791 -1.47593
ITEM: TIMESTEP
30
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS ss ss ss
-1.4632357229999999e+00 9.3247372299999998e-01
-7.5570026690000003e-01 7.5527126690000002e-01
-8.9995638999999985e-03 2.9352285639000000e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -0.0237238 -0.00114526 0.00766999 -7.81865 -0.0119879 -8.3015
2 2 -0.241061 -0.000656856 0.943727 6.09288 0.0066852 2.69388
3 2 0.923032 -0.000493736 -0.123121 1.75879 0.00552582 5.88556
4 1 -0.897978 0.000115451 2.77309 11.6501 0.00727223 -2.82116
5 2 -1.42536 0.788259 2.90023 -5.83991 -2.07218 1.27305
6 2 -1.42412 -0.788676 2.90134 -5.84324 2.06468 1.27016
ITEM: TIMESTEP
40
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS ss ss ss
-1.4632357229999999e+00 9.3247372299999998e-01
-7.5570026690000003e-01 7.5527126690000002e-01
-8.9995638999999985e-03 2.9352285639000000e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -0.0292005 -0.00114894 0.00855106 5.6712 0.00787804 4.86214
2 2 -0.153199 -0.000576377 0.959922 -7.58451 -0.00449199 2.07976
3 2 0.919336 -0.000480028 -0.0995905 1.37912 -0.00359093 -6.63778
4 1 -0.89217 0.000118771 2.77132 -5.68638 -0.00321013 1.64962
5 2 -1.47004 0.751887 2.88738 3.10503 6.73714 -0.981624
6 2 -1.46886 -0.752392 2.88844 3.11554 -6.73373 -0.972121
ITEM: TIMESTEP
50
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS ss ss ss
-1.4632357229999999e+00 9.3247372299999998e-01
-7.5570026690000003e-01 7.5527126690000002e-01
-8.9995638999999985e-03 2.9352285639000000e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -0.0276682 -0.00114169 0.0171537 -7.90829 -0.012452 -8.85967
2 2 -0.185755 -0.000598779 0.964286 5.83022 0.00671605 3.0354
3 2 0.908646 -0.000541992 -0.175729 1.96931 0.00577867 6.00768
4 1 -0.895573 0.00011689 2.77245 11.8261 0.00822001 -1.54401
5 2 -1.4336 0.787999 2.84603 -5.85703 -2.08185 0.681764
6 2 -1.43237 -0.788505 2.84714 -5.86031 2.07358 0.678838
ITEM: TIMESTEP
60
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS ss ss ss
-1.4632357229999999e+00 9.3247372299999998e-01
-7.5570026690000003e-01 7.5527126690000002e-01
-8.9995638999999985e-03 2.9352285639000000e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -0.0340777 -0.00114581 0.0184647 7.2272 0.00951667 5.4479
2 2 -0.113434 -0.000533921 0.975674 -7.44659 -0.00496006 1.26816
3 2 0.909471 -0.000512535 -0.134923 -0.287426 -0.00476073 -6.43846
4 1 -0.888126 0.000122907 2.77269 -9.08281 -0.00670232 0.725333
5 2 -1.47838 0.753365 2.8077 4.79099 4.82306 -0.504859
6 2 -1.47719 -0.753996 2.80876 4.79863 -4.81616 -0.498076
ITEM: TIMESTEP
70
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS ss ss ss
-1.4632357229999999e+00 9.3247372299999998e-01
-7.5570026690000003e-01 7.5527126690000002e-01
-8.9995638999999985e-03 2.9352285639000000e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -0.0329631 -0.00113896 0.0269437 -6.82209 -0.00981599 -6.32682
2 2 -0.16378 -0.000570078 0.980622 6.44654 0.00529861 0.332147
3 2 0.899135 -0.000560623 -0.191768 0.56204 0.00474764 6.11404
4 1 -0.890774 0.0001215 2.77364 7.6207 0.00561833 -0.364449
5 2 -1.4359 0.790393 2.75878 -3.89983 -4.84574 0.12595
6 2 -1.43466 -0.791026 2.7599 -3.90736 4.83989 0.11913
ITEM: TIMESTEP
80
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS ss ss ss
-1.4632357229999999e+00 9.3247372299999998e-01
-7.5570026690000003e-01 7.5527126690000002e-01
-8.9995638999999985e-03 2.9352285639000000e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -0.0396799 -0.00114299 0.0287108 8.10782 0.0121934 8.26954
2 2 -0.101327 -0.000514632 0.989821 -6.98655 -0.00644087 -1.35375
3 2 0.902079 -0.000521504 -0.139604 -1.23495 -0.0056704 -6.67396
4 1 -0.883488 0.000127321 2.77377 -12.2256 -0.0109573 -1.83848
5 2 -1.47309 0.755263 2.71301 6.16734 2.89071 0.796293
6 2 -1.4719 -0.756019 2.71407 6.17192 -2.87983 0.800362
ITEM: TIMESTEP
90
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS ss ss ss
-1.4632357229999999e+00 9.3247372299999998e-01
-7.5570026690000003e-01 7.5527126690000002e-01
-8.9995638999999985e-03 2.9352285639000000e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -0.0383179 -0.00113532 0.0380883 -7.16334 -0.00889532 -4.6369
2 2 -0.149498 -0.00054848 0.995531 6.83221 0.00448143 -1.26419
3 2 0.889431 -0.00057205 -0.197356 0.916 0.00477871 5.76452
4 1 -0.886952 0.000122589 2.77093 7.29365 0.00587785 0.155791
5 2 -1.42602 0.790491 2.68716 -3.93543 -4.86013 -0.00619146
6 2 -1.42478 -0.791209 2.68827 -3.94309 4.85389 -0.0130349
ITEM: TIMESTEP
100
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS ss ss ss
-1.4632357229999999e+00 9.3247372299999998e-01
-7.5570026690000003e-01 7.5527126690000002e-01
-8.9995638999999985e-03 2.9352285639000000e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -0.0443853 -0.00113803 0.0410221 7.36858 0.0108291 7.15279
2 2 -0.076648 -0.000485983 1.00287 -6.96363 -0.00585609 -0.543819
3 2 0.890615 -0.000542732 -0.157107 -0.3904 -0.00504823 -6.73186
4 1 -0.880834 0.000124898 2.7674 -9.13947 -0.00841726 -1.90715
5 2 -1.46341 0.754149 2.66816 4.55895 4.52404 1.01184
6 2 -1.46222 -0.754952 2.66922 4.56597 -4.51554 1.01819

297
examples/amoeba/dump.water_hexamer.amoeba.1.test
View File

@ -1,297 +0,0 @@
ITEM: TIMESTEP
0
ITEM: NUMBER OF ATOMS
18
ITEM: BOX BOUNDS ss ss ss
-2.5173543550999997e+00 2.6752353550999999e+00
-1.5223951870999999e+00 2.0181841871000001e+00
-1.7341615612999999e+00 2.2202425613000001e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -1.50217 -0.191359 1.43493 15.8836 -7.45837 3.84323
2 2 -0.601054 -0.596972 1.55372 -22.9153 9.01978 -0.990133
3 2 -2.0067 -0.422327 2.21985 1.01155 0.118537 -0.791932
4 1 -1.74457 -0.382348 -1.30914 -6.66041 -3.92202 8.41554
5 2 -1.88894 -0.479653 -0.347624 4.77968 3.15053 -8.64245
6 2 -2.51683 -0.766765 -1.73377 2.90782 1.57916 -0.744558
7 1 -0.560409 2.01783 -0.121984 -13.2194 -12.8195 1.43178
8 2 -0.94772 1.53357 0.625228 6.08473 6.021 -1.58068
9 2 -0.989831 1.59274 -0.877419 5.83415 5.52991 -0.337029
10 1 0.964803 -1.16576 1.43999 12.6547 2.88136 -21.3636
11 2 0.979557 -1.52204 0.527833 -3.6968 -1.92725 12.6575
12 2 1.54222 -0.393692 1.34437 -3.37883 -2.73031 5.998
13 1 0.974705 -1.4015 -1.33597 -6.12193 14.8514 -0.790538
14 2 0.065161 -1.11895 -1.52289 4.56017 -6.05436 1.71545
15 2 1.47071 -0.570933 -1.27771 1.31912 -7.40942 1.06098
16 1 2.00228 1.05782 -0.124502 -10.3736 10.8414 -1.12005
17 2 1.14164 1.53227 -0.140121 11.8812 -8.20067 0.772116
18 2 2.67472 1.73534 -0.237995 -0.550493 -3.47117 0.466398
ITEM: TIMESTEP
10
ITEM: NUMBER OF ATOMS
18
ITEM: BOX BOUNDS ss ss ss
-2.5173543550999997e+00 2.6752353550999999e+00
-1.5223951870999999e+00 2.0181841871000001e+00
-1.7341615612999999e+00 2.2202425613000001e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -1.50661 -0.189383 1.4364 14.5938 -8.99605 8.72579
2 2 -0.616993 -0.604745 1.5716 -17.7352 9.03346 -4.01613
3 2 -2.01184 -0.421588 2.22126 -0.664878 1.39015 -2.52743
4 1 -1.74564 -0.383429 -1.31051 0.451442 -0.432875 3.71075
5 2 -1.85676 -0.451272 -0.342641 -1.17801 0.27861 -9.12816
6 2 -2.51648 -0.764704 -1.74119 1.00433 0.523826 3.94489
7 1 -0.565581 2.01415 -0.121947 -0.431671 0.816258 1.37224
8 2 -0.923503 1.54613 0.649943 -0.836345 -0.35076 -8.91816
9 2 -0.954982 1.61593 -0.9136 -0.398984 -1.29665 6.9827
10 1 0.971315 -1.16462 1.43403 2.66632 -4.10463 -4.1745
11 2 0.960388 -1.57587 0.54557 3.80791 8.56867 8.0783
12 2 1.545 -0.38505 1.37422 -2.3984 -5.62816 -5.66197
13 1 0.972827 -1.39712 -1.33549 -1.10638 0.442925 0.267527
14 2 0.0526434 -1.14464 -1.51395 7.06933 2.8298 1.48943
15 2 1.50554 -0.590868 -1.25662 -6.54392 -2.53639 -0.258333
16 1 2.00275 1.0584 -0.124848 -7.13185 5.38221 -0.0306111
17 2 1.13969 1.52381 -0.134074 11.7308 -4.5992 -0.113372
18 2 2.68869 1.72277 -0.237084 -2.89819 -1.32119 0.257039
ITEM: TIMESTEP
20
ITEM: NUMBER OF ATOMS
18
ITEM: BOX BOUNDS ss ss ss
-2.5173543550999997e+00 2.6752353550999999e+00
-1.5223951870999999e+00 2.0181841871000001e+00
-1.7341615612999999e+00 2.2202425613000001e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -1.51649 -0.18584 1.44395 5.65501 -4.20149 4.07802
2 2 -0.637196 -0.60535 1.5789 -10.2535 4.51311 -0.350867
3 2 -2.05196 -0.408647 2.21473 3.52072 0.575858 -3.20585
4 1 -1.74216 -0.383007 -1.31779 -5.65244 -1.7459 7.46957
5 2 -1.85838 -0.422286 -0.35262 3.57624 0.698487 -5.03248
6 2 -2.53778 -0.772973 -1.68856 2.62304 1.05785 -2.46299
7 1 -0.568621 2.01502 -0.121788 -7.49291 -10.5083 -0.07078
8 2 -0.953332 1.50031 0.601729 3.90339 5.1027 1.32659
9 2 -0.948304 1.59097 -0.90055 3.2198 4.86429 -1.5712
10 1 0.981527 -1.16776 1.43139 8.19382 2.30469 -14.0571
11 2 0.999682 -1.57682 0.548153 -4.17545 -1.46604 7.90595
12 2 1.55686 -0.401102 1.29785 -3.41945 -1.35828 5.31582
13 1 0.971997 -1.39727 -1.33295 -3.50737 11.1512 0.685267
14 2 0.0679408 -1.0929 -1.49373 1.59713 -5.72522 -0.144088
15 2 1.47933 -0.582056 -1.22295 2.04209 -4.76253 -0.234646
16 1 2.00557 1.05551 -0.12468 -4.4992 7.40197 -0.448564
17 2 1.16008 1.5422 -0.129327 5.1837 -4.83397 0.46283
18 2 2.69054 1.72007 -0.238059 -0.51465 -3.06849 0.334482
ITEM: TIMESTEP
30
ITEM: NUMBER OF ATOMS
18
ITEM: BOX BOUNDS ss ss ss
-2.5173543550999997e+00 2.6752353550999999e+00
-1.5223951870999999e+00 2.0181841871000001e+00
-1.7341615612999999e+00 2.2202425613000001e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -1.52872 -0.18011 1.45173 -0.933277 -2.21949 5.98424
2 2 -0.665459 -0.602256 1.60472 0.633036 0.719099 -1.22127
3 2 -2.07366 -0.404666 2.21589 2.60377 1.4581 -4.42661
4 1 -1.74225 -0.382648 -1.3226 2.4731 1.57235 -0.799694
5 2 -1.81423 -0.398932 -0.35676 -3.06045 -1.92828 -1.63228
6 2 -2.5352 -0.77665 -1.69294 0.0233925 -0.139311 2.03217
7 1 -0.576286 2.0073 -0.122823 5.68391 5.42307 0.543301
8 2 -0.95235 1.50691 0.611905 -2.48677 -2.29116 -3.6455
9 2 -0.915502 1.63076 -0.941481 -3.12923 -3.02599 2.90572
10 1 0.998541 -1.16996 1.42191 -2.76709 -0.0175982 4.85417
11 2 0.970261 -1.63876 0.575717 2.4618 4.28015 -0.493825
12 2 1.54742 -0.386783 1.27666 -1.41861 -3.70889 -3.67396
13 1 0.969317 -1.3895 -1.32829 2.03562 -5.48364 0.295138
14 2 0.0583035 -1.11723 -1.49206 1.73159 3.49229 -0.0543931
15 2 1.50655 -0.600283 -1.19205 -3.9925 1.94925 -1.04523
16 1 2.00848 1.05446 -0.124132 1.88868 -1.58075 0.754117
17 2 1.16959 1.53865 -0.11771 0.573913 1.34283 -0.58573
18 2 2.71517 1.69464 -0.239075 -2.32089 0.157967 0.209615
ITEM: TIMESTEP
40
ITEM: NUMBER OF ATOMS
18
ITEM: BOX BOUNDS ss ss ss
-2.5173543550999997e+00 2.6752353550999999e+00
-1.5223951870999999e+00 2.0181841871000001e+00
-1.7341615612999999e+00 2.2202425613000001e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -1.53726 -0.175397 1.46121 -7.56641 2.45844 -0.518817
2 2 -0.675238 -0.584022 1.60915 7.85196 -3.99237 1.67217
3 2 -2.08862 -0.402087 2.21789 3.0617 0.39778 -2.04562
4 1 -1.73949 -0.379604 -1.32819 -2.36016 -0.787528 -0.0315325
5 2 -1.83346 -0.428429 -0.37056 1.90026 0.717301 4.17358
6 2 -2.53017 -0.786871 -1.68316 0.151557 -0.108901 -3.75615
7 1 -0.576955 2.0043 -0.124416 -0.431513 -1.54355 -1.46354
8 2 -0.992092 1.48382 0.567817 1.09284 0.418387 6.78235
9 2 -0.944746 1.62819 -0.925975 0.76441 1.37882 -5.22407
10 1 1.00941 -1.17308 1.4189 -1.85973 4.64458 1.0889
11 2 0.973659 -1.6403 0.580693 -1.69219 -4.78957 -3.29195
12 2 1.53559 -0.396477 1.19908 0.544307 1.46508 3.63166
13 1 0.969009 -1.38744 -1.3228 -0.275569 1.85307 -0.63583
14 2 0.0737932 -1.09141 -1.50366 -4.66851 -2.83882 -1.16892
15 2 1.46633 -0.576681 -1.19175 5.00795 0.70617 0.521536
16 1 2.01183 1.05054 -0.121932 4.41526 -1.70685 -0.0836272
17 2 1.19121 1.55327 -0.120038 -7.25224 2.19125 0.154184
18 2 2.71636 1.68982 -0.237383 1.31607 -0.463304 0.195666
ITEM: TIMESTEP
50
ITEM: NUMBER OF ATOMS
18
ITEM: BOX BOUNDS ss ss ss
-2.5173543550999997e+00 2.6752353550999999e+00
-1.5223951870999999e+00 2.0181841871000001e+00
-1.7341615612999999e+00 2.2202425613000001e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -1.53986 -0.172749 1.46865 -10.3641 5.96951 -4.41562
2 2 -0.678724 -0.568486 1.60775 14.9207 -7.13278 2.04782
3 2 -2.07217 -0.405364 2.23045 -0.725799 -0.490948 1.77161
4 1 -1.74113 -0.378171 -1.32957 5.99712 2.85952 -9.13842
5 2 -1.82713 -0.447378 -0.375703 -3.89226 -1.3818 7.11516
6 2 -2.4999 -0.790471 -1.74187 -3.02333 -1.60416 1.77146
7 1 -0.579496 1.99691 -0.128028 9.72738 10.7655 -0.463519
8 2 -0.97832 1.50522 0.591572 -4.4866 -5.64841 2.33138
9 2 -0.951447 1.66071 -0.944057 -3.97244 -4.92262 -1.79974
10 1 1.01358 -1.17192 1.41393 -6.48605 2.83151 13.495
11 2 0.960671 -1.668 0.598799 0.887838 -3.18341 -9.75086
12 2 1.53449 -0.394669 1.19537 2.46945 2.14925 -1.89795
13 1 0.966791 -1.38037 -1.31946 4.73561 -12.449 -1.17286
14 2 0.0653014 -1.12956 -1.52441 -4.76491 5.51904 -0.304595
15 2 1.48076 -0.580834 -1.19775 0.0522693 6.36707 0.249418
16 1 2.01309 1.04924 -0.119438 7.79557 -11.0594 0.778107
17 2 1.18753 1.53519 -0.124654 -9.57007 7.63584 -0.456674
18 2 2.72824 1.67508 -0.226016 0.699647 3.77524 -0.159727
ITEM: TIMESTEP
60
ITEM: NUMBER OF ATOMS
18
ITEM: BOX BOUNDS ss ss ss
-2.5173543550999997e+00 2.6752353550999999e+00
-1.5223951870999999e+00 2.0181841871000001e+00
-1.7341615612999999e+00 2.2202425613000001e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -1.535 -0.173529 1.47468 -12.8115 9.37187 -10.8344
2 2 -0.673508 -0.564245 1.59147 19.3914 -9.12777 2.73797
3 2 -2.04099 -0.404174 2.24807 -3.82175 -1.70255 6.71674
4 1 -1.73996 -0.376347 -1.33351 0.570165 0.280665 -6.43548
5 2 -1.87928 -0.466718 -0.390362 1.26398 0.876645 10.7815
6 2 -2.48657 -0.801116 -1.75201 -2.14828 -1.00411 -3.66812
7 1 -0.576718 1.99595 -0.131852 3.14419 3.30092 -1.47913
8 2 -0.97416 1.49195 0.577492 -1.32391 -2.58987 8.72867
9 2 -0.983297 1.63168 -0.91691 -0.334419 -0.770035 -7.07098
10 1 1.00791 -1.1681 1.41401 -6.20027 1.07549 12.575
11 2 0.972875 -1.65454 0.593802 -0.476084 -5.46772 -10.3478
12 2 1.54632 -0.404877 1.20306 3.83119 5.88484 -0.834958
13 1 0.966385 -1.38017 -1.32091 1.49436 -4.60495 -1.57148
14 2 0.0722824 -1.10128 -1.51274 -8.16812 -0.531008 -1.13308
15 2 1.45394 -0.565765 -1.20718 7.01226 4.42564 1.66198
16 1 2.01308 1.04537 -0.116618 6.94232 -7.944 0.350248
17 2 1.19126 1.53332 -0.135036 -13.3157 5.74475 0.221956
18 2 2.70715 1.69348 -0.205764 4.95008 2.7812 -0.398561
ITEM: TIMESTEP
70
ITEM: NUMBER OF ATOMS
18
ITEM: BOX BOUNDS ss ss ss
-2.5173543550999997e+00 2.6752353550999999e+00
-1.5223951870999999e+00 2.0181841871000001e+00
-1.7341615612999999e+00 2.2202425613000001e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -1.52447 -0.177745 1.47754 -14.009 12.5988 -14.9127
2 2 -0.663619 -0.56979 1.57126 20.9018 -10.2143 3.8986
3 2 -2.00537 -0.388653 2.26816 -5.41735 -2.91391 10.0958
4 1 -1.74327 -0.377755 -1.33511 7.69657 4.1782 -9.73798
5 2 -1.88018 -0.439682 -0.388162 -4.07322 -2.33918 9.17346
6 2 -2.47021 -0.801057 -1.79014 -4.11028 -2.07522 1.70143
7 1 -0.576352 1.99233 -0.135801 8.33914 8.33997 -1.40304
8 2 -0.93279 1.50467 0.607511 -5.01196 -5.05095 3.69276
9 2 -0.967697 1.61396 -0.924499 -2.96791 -3.60448 -2.11522
10 1 0.996682 -1.16249 1.41603 -5.52393 -2.7768 9.00886
11 2 0.982553 -1.62276 0.577115 -1.00274 -4.80219 -7.71302
12 2 1.55168 -0.404501 1.24312 4.97383 8.09577 -0.603791
13 1 0.964232 -1.37715 -1.32734 3.83388 -12.0598 -0.0980446
14 2 0.0575072 -1.10802 -1.48098 -4.628 4.85469 -1.01689
15 2 1.48931 -0.58697 -1.19891 1.1914 7.02562 -0.119366
16 1 2.01083 1.04528 -0.114231 6.83173 -12.9986 1.26494
17 2 1.17034 1.50303 -0.133551 -9.79274 8.34256 -0.476042
18 2 2.7022 1.69874 -0.182183 2.76884 5.3999 -0.639748
ITEM: TIMESTEP
80
ITEM: NUMBER OF ATOMS
18
ITEM: BOX BOUNDS ss ss ss
-2.5173543550999997e+00 2.6752353550999999e+00
-1.5223951870999999e+00 2.0181841871000001e+00
-1.7341615612999999e+00 2.2202425613000001e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -1.51177 -0.182537 1.47592 -13.1365 10.3139 -11.8951
2 2 -0.654143 -0.583091 1.57918 18.6975 -8.17701 1.44433
3 2 -1.97348 -0.365352 2.2852 -6.58467 -1.56222 9.05296
4 1 -1.74352 -0.377279 -1.33693 -0.505822 0.308788 -3.25308
5 2 -1.91188 -0.438855 -0.39405 1.95743 0.358158 9.20234
6 2 -2.48397 -0.807922 -1.76244 -1.16931 -0.70018 -3.86005
7 1 -0.571778 1.99034 -0.138544 1.3921 0.315501 -1.43854
8 2 -0.938419 1.50232 0.602337 -1.22478 -1.30903 4.8686
9 2 -0.959599 1.56918 -0.90914 -0.0288155 0.574454 -3.52808
10 1 0.985435 -1.15713 1.41811 -6.25848 -6.25702 9.27302
11 2 0.972167 -1.59168 0.560031 1.69554 -0.201305 -5.06875
12 2 1.54032 -0.386652 1.30283 4.96928 5.72762 -4.15176
13 1 0.963614 -1.3793 -1.33436 0.183354 -1.1048 0.823621
14 2 0.065336 -1.06423 -1.45856 -4.4409 -1.33366 -2.05511
15 2 1.49256 -0.587857 -1.21654 4.36346 2.23441 0.338535
16 1 2.00803 1.04345 -0.110717 3.61274 -3.25471 0.639326
17 2 1.16919 1.51061 -0.133404 -8.46417 2.50048 0.10369
18 2 2.67828 1.72068 -0.16597 4.94198 1.56662 -0.49597
ITEM: TIMESTEP
90
ITEM: NUMBER OF ATOMS
18
ITEM: BOX BOUNDS ss ss ss
-2.5173543550999997e+00 2.6752353550999999e+00
-1.5223951870999999e+00 2.0181841871000001e+00
-1.7341615612999999e+00 2.2202425613000001e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -1.50159 -0.186388 1.47232 -10.1666 8.56134 -9.06842
2 2 -0.637201 -0.589948 1.58141 9.00709 -5.13609 3.43504
3 2 -1.97805 -0.327506 2.28752 -1.76215 -2.05269 5.01359
4 1 -1.7485 -0.377921 -1.33249 5.81313 3.27044 -5.4853
5 2 -1.87141 -0.433051 -0.37781 -3.50795 -2.5324 4.09176
6 2 -2.48522 -0.804273 -1.77362 -2.18894 -1.0456 2.79096
7 1 -0.568425 1.98378 -0.140489 1.33268 1.60885 -0.760228
8 2 -0.945484 1.51375 0.61188 -1.03442 -1.79649 -0.570033
9 2 -0.936389 1.56212 -0.924193 -1.07342 -0.200973 1.02154
10 1 0.975854 -1.15481 1.42351 1.86741 -2.52595 -4.21318
11 2 0.98193 -1.53917 0.537259 -2.6087 -4.02599 1.03016
12 2 1.52752 -0.379325 1.30866 2.98513 5.11632 2.51897
13 1 0.962056 -1.37771 -1.33914 1.58342 -3.36145 0.893222
14 2 0.0608833 -1.06855 -1.4877 0.530861 1.7595 -0.414339
15 2 1.52774 -0.603203 -1.25083 -2.15602 1.98356 -0.537593
16 1 2.00483 1.04652 -0.10624 2.44039 -5.05754 0.604689
17 2 1.15126 1.49959 -0.126569 -0.261743 3.34267 -0.115684
18 2 2.69252 1.71134 -0.15978 -0.800158 2.09248 -0.235157
ITEM: TIMESTEP
100
ITEM: NUMBER OF ATOMS
18
ITEM: BOX BOUNDS ss ss ss
-2.5173543550999997e+00 2.6752353550999999e+00
-1.5223951870999999e+00 2.0181841871000001e+00
-1.7341615612999999e+00 2.2202425613000001e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -1.49915 -0.184572 1.46491 -1.64286 -0.923423 4.11541
2 2 -0.634606 -0.601439 1.61658 -0.503947 1.48506 -2.91046
3 2 -1.9835 -0.312527 2.28463 -1.23961 0.673264 -1.96712
4 1 -1.74898 -0.375873 -1.32741 -4.05983 -3.09974 1.92324
5 2 -1.86884 -0.471305 -0.372769 3.24632 2.33491 1.76011
6 2 -2.50916 -0.806172 -1.72327 1.14638 0.924599 -3.12385
7 1 -0.564884 1.97778 -0.142101 -4.14881 -3.0738 -0.168062
8 2 -0.958996 1.4911 0.595477 2.25574 1.20147 -1.85844
9 2 -0.937749 1.56372 -0.930264 1.31445 2.00952 1.76263
10 1 0.975211 -1.15256 1.42364 -0.947501 -4.6035 2.62584
11 2 0.950951 -1.55837 0.541757 3.10583 4.89391 1.85772
12 2 1.52342 -0.363228 1.34082 0.672959 -1.69053 -5.30235
13 1 0.962361 -1.37851 -1.34242 -1.40487 6.54708 -1.50719
14 2 0.0703818 -1.05861 -1.53269 1.44041 -3.14031 1.12109
15 2 1.51335 -0.586474 -1.29057 -0.612624 -3.69916 1.63647
16 1 2.00445 1.04687 -0.100669 -1.02523 8.04786 -0.336895
17 2 1.16075 1.52969 -0.119062 2.24423 -4.67525 0.190963
18 2 2.68635 1.72058 -0.160395 0.158945 -3.21195 0.180894

297
examples/amoeba/dump.water_hexamer.amoeba.4.test
View File

@ -1,297 +0,0 @@
ITEM: TIMESTEP
0
ITEM: NUMBER OF ATOMS
18
ITEM: BOX BOUNDS ss ss ss
-2.5173543550999997e+00 2.6752353550999999e+00
-1.5223951870999999e+00 2.0181841871000001e+00
-1.7341615612999999e+00 2.2202425613000001e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -1.50217 -0.191359 1.43493 15.8836 -7.45837 3.84323
2 2 -0.601054 -0.596972 1.55372 -22.9153 9.01978 -0.990133
3 2 -2.0067 -0.422327 2.21985 1.01155 0.118537 -0.791932
4 1 -1.74457 -0.382348 -1.30914 -6.66041 -3.92202 8.41554
5 2 -1.88894 -0.479653 -0.347624 4.77968 3.15053 -8.64245
6 2 -2.51683 -0.766765 -1.73377 2.90782 1.57916 -0.744558
7 1 -0.560409 2.01783 -0.121984 -13.2194 -12.8195 1.43178
8 2 -0.94772 1.53357 0.625228 6.08473 6.021 -1.58068
9 2 -0.989831 1.59274 -0.877419 5.83415 5.52991 -0.337029
10 1 0.964803 -1.16576 1.43999 12.6547 2.88136 -21.3636
11 2 0.979557 -1.52204 0.527833 -3.6968 -1.92725 12.6575
12 2 1.54222 -0.393692 1.34437 -3.37883 -2.73031 5.998
13 1 0.974705 -1.4015 -1.33597 -6.12193 14.8514 -0.790538
14 2 0.065161 -1.11895 -1.52289 4.56017 -6.05436 1.71545
15 2 1.47071 -0.570933 -1.27771 1.31912 -7.40942 1.06098
16 1 2.00228 1.05782 -0.124502 -10.3736 10.8414 -1.12005
17 2 1.14164 1.53227 -0.140121 11.8812 -8.20067 0.772116
18 2 2.67472 1.73534 -0.237995 -0.550493 -3.47117 0.466398
ITEM: TIMESTEP
10
ITEM: NUMBER OF ATOMS
18
ITEM: BOX BOUNDS ss ss ss
-2.5173543550999997e+00 2.6752353550999999e+00
-1.5223951870999999e+00 2.0181841871000001e+00
-1.7341615612999999e+00 2.2202425613000001e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -1.50661 -0.189383 1.4364 14.5938 -8.99605 8.72579
2 2 -0.616993 -0.604745 1.5716 -17.7352 9.03346 -4.01613
3 2 -2.01184 -0.421588 2.22126 -0.664878 1.39015 -2.52743
4 1 -1.74564 -0.383429 -1.31051 0.451442 -0.432875 3.71075
5 2 -1.85676 -0.451272 -0.342641 -1.17801 0.27861 -9.12816
6 2 -2.51648 -0.764704 -1.74119 1.00433 0.523826 3.94489
7 1 -0.565581 2.01415 -0.121947 -0.431671 0.816258 1.37224
8 2 -0.923503 1.54613 0.649943 -0.836345 -0.35076 -8.91816
9 2 -0.954982 1.61593 -0.9136 -0.398984 -1.29665 6.9827
10 1 0.971315 -1.16462 1.43403 2.66632 -4.10463 -4.1745
11 2 0.960388 -1.57587 0.54557 3.80791 8.56867 8.0783
12 2 1.545 -0.38505 1.37422 -2.3984 -5.62816 -5.66197
13 1 0.972827 -1.39712 -1.33549 -1.10638 0.442925 0.267527
14 2 0.0526434 -1.14464 -1.51395 7.06933 2.8298 1.48943
15 2 1.50554 -0.590868 -1.25662 -6.54392 -2.53639 -0.258333
16 1 2.00275 1.0584 -0.124848 -7.13185 5.38221 -0.0306111
17 2 1.13969 1.52381 -0.134074 11.7308 -4.5992 -0.113372
18 2 2.68869 1.72277 -0.237084 -2.89819 -1.32119 0.257039
ITEM: TIMESTEP
20
ITEM: NUMBER OF ATOMS
18
ITEM: BOX BOUNDS ss ss ss
-2.5173543550999997e+00 2.6752353550999999e+00
-1.5223951870999999e+00 2.0181841871000001e+00
-1.7341615612999999e+00 2.2202425613000001e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -1.51649 -0.18584 1.44395 5.65501 -4.20149 4.07802
2 2 -0.637196 -0.60535 1.5789 -10.2535 4.51311 -0.350867
3 2 -2.05196 -0.408647 2.21473 3.52072 0.575858 -3.20585
4 1 -1.74216 -0.383007 -1.31779 -5.65244 -1.7459 7.46957
5 2 -1.85838 -0.422286 -0.35262 3.57624 0.698487 -5.03248
6 2 -2.53778 -0.772973 -1.68856 2.62304 1.05785 -2.46299
7 1 -0.568621 2.01502 -0.121788 -7.49291 -10.5083 -0.07078
8 2 -0.953332 1.50031 0.601729 3.90339 5.1027 1.32659
9 2 -0.948304 1.59097 -0.90055 3.2198 4.86429 -1.5712
10 1 0.981527 -1.16776 1.43139 8.19382 2.30469 -14.0571
11 2 0.999682 -1.57682 0.548153 -4.17545 -1.46604 7.90595
12 2 1.55686 -0.401102 1.29785 -3.41945 -1.35828 5.31582
13 1 0.971997 -1.39727 -1.33295 -3.50737 11.1512 0.685267
14 2 0.0679408 -1.0929 -1.49373 1.59713 -5.72522 -0.144088
15 2 1.47933 -0.582056 -1.22295 2.04209 -4.76253 -0.234646
16 1 2.00557 1.05551 -0.12468 -4.4992 7.40197 -0.448564
17 2 1.16008 1.5422 -0.129327 5.1837 -4.83397 0.46283
18 2 2.69054 1.72007 -0.238059 -0.51465 -3.06849 0.334482
ITEM: TIMESTEP
30
ITEM: NUMBER OF ATOMS
18
ITEM: BOX BOUNDS ss ss ss
-2.5173543550999997e+00 2.6752353550999999e+00
-1.5223951870999999e+00 2.0181841871000001e+00
-1.7341615612999999e+00 2.2202425613000001e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -1.52872 -0.18011 1.45173 -0.933277 -2.21949 5.98424
2 2 -0.665459 -0.602256 1.60472 0.633036 0.719099 -1.22127
3 2 -2.07366 -0.404666 2.21589 2.60377 1.4581 -4.42661
4 1 -1.74225 -0.382648 -1.3226 2.4731 1.57235 -0.799694
5 2 -1.81423 -0.398932 -0.35676 -3.06045 -1.92828 -1.63228
6 2 -2.5352 -0.77665 -1.69294 0.0233925 -0.139311 2.03217
7 1 -0.576286 2.0073 -0.122823 5.68391 5.42307 0.543301
8 2 -0.95235 1.50691 0.611905 -2.48677 -2.29116 -3.6455
9 2 -0.915502 1.63076 -0.941481 -3.12923 -3.02599 2.90572
10 1 0.998541 -1.16996 1.42191 -2.76709 -0.0175982 4.85417
11 2 0.970261 -1.63876 0.575717 2.4618 4.28015 -0.493825
12 2 1.54742 -0.386783 1.27666 -1.41861 -3.70889 -3.67396
13 1 0.969317 -1.3895 -1.32829 2.03562 -5.48364 0.295138
14 2 0.0583035 -1.11723 -1.49206 1.73159 3.49229 -0.0543931
15 2 1.50655 -0.600283 -1.19205 -3.9925 1.94925 -1.04523
16 1 2.00848 1.05446 -0.124132 1.88868 -1.58075 0.754117
17 2 1.16959 1.53865 -0.11771 0.573913 1.34283 -0.58573
18 2 2.71517 1.69464 -0.239075 -2.32089 0.157967 0.209615
ITEM: TIMESTEP
40
ITEM: NUMBER OF ATOMS
18
ITEM: BOX BOUNDS ss ss ss
-2.5173543550999997e+00 2.6752353550999999e+00
-1.5223951870999999e+00 2.0181841871000001e+00
-1.7341615612999999e+00 2.2202425613000001e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -1.53726 -0.175397 1.46121 -7.56641 2.45844 -0.518817
2 2 -0.675238 -0.584022 1.60915 7.85196 -3.99237 1.67217
3 2 -2.08862 -0.402087 2.21789 3.0617 0.39778 -2.04562
4 1 -1.73949 -0.379604 -1.32819 -2.36016 -0.787528 -0.0315325
5 2 -1.83346 -0.428429 -0.37056 1.90026 0.717301 4.17358
6 2 -2.53017 -0.786871 -1.68316 0.151557 -0.108901 -3.75615
7 1 -0.576955 2.0043 -0.124416 -0.431513 -1.54355 -1.46354
8 2 -0.992092 1.48382 0.567817 1.09284 0.418387 6.78235
9 2 -0.944746 1.62819 -0.925975 0.76441 1.37882 -5.22407
10 1 1.00941 -1.17308 1.4189 -1.85973 4.64458 1.0889
11 2 0.973659 -1.6403 0.580693 -1.69219 -4.78957 -3.29195
12 2 1.53559 -0.396477 1.19908 0.544307 1.46508 3.63166
13 1 0.969009 -1.38744 -1.3228 -0.275569 1.85307 -0.63583
14 2 0.0737932 -1.09141 -1.50366 -4.66851 -2.83882 -1.16892
15 2 1.46633 -0.576681 -1.19175 5.00795 0.70617 0.521536
16 1 2.01183 1.05054 -0.121932 4.41526 -1.70685 -0.0836272
17 2 1.19121 1.55327 -0.120038 -7.25224 2.19125 0.154184
18 2 2.71636 1.68982 -0.237383 1.31607 -0.463304 0.195666
ITEM: TIMESTEP
50
ITEM: NUMBER OF ATOMS
18
ITEM: BOX BOUNDS ss ss ss
-2.5173543550999997e+00 2.6752353550999999e+00
-1.5223951870999999e+00 2.0181841871000001e+00
-1.7341615612999999e+00 2.2202425613000001e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -1.53986 -0.172749 1.46865 -10.3641 5.96951 -4.41562
2 2 -0.678724 -0.568486 1.60775 14.9207 -7.13278 2.04782
3 2 -2.07217 -0.405364 2.23045 -0.725799 -0.490948 1.77161
4 1 -1.74113 -0.378171 -1.32957 5.99712 2.85952 -9.13842
5 2 -1.82713 -0.447378 -0.375703 -3.89226 -1.3818 7.11516
6 2 -2.4999 -0.790471 -1.74187 -3.02333 -1.60416 1.77146
7 1 -0.579496 1.99691 -0.128028 9.72738 10.7655 -0.463519
8 2 -0.97832 1.50522 0.591572 -4.4866 -5.64841 2.33138
9 2 -0.951447 1.66071 -0.944057 -3.97244 -4.92262 -1.79974
10 1 1.01358 -1.17192 1.41393 -6.48605 2.83151 13.495
11 2 0.960671 -1.668 0.598799 0.887838 -3.18341 -9.75086
12 2 1.53449 -0.394669 1.19537 2.46945 2.14925 -1.89795
13 1 0.966791 -1.38037 -1.31946 4.73561 -12.449 -1.17286
14 2 0.0653014 -1.12956 -1.52441 -4.76491 5.51904 -0.304595
15 2 1.48076 -0.580834 -1.19775 0.0522693 6.36707 0.249418
16 1 2.01309 1.04924 -0.119438 7.79557 -11.0594 0.778107
17 2 1.18753 1.53519 -0.124654 -9.57007 7.63584 -0.456674
18 2 2.72824 1.67508 -0.226016 0.699647 3.77524 -0.159727
ITEM: TIMESTEP
60
ITEM: NUMBER OF ATOMS
18
ITEM: BOX BOUNDS ss ss ss
-2.5173543550999997e+00 2.6752353550999999e+00
-1.5223951870999999e+00 2.0181841871000001e+00
-1.7341615612999999e+00 2.2202425613000001e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -1.535 -0.173529 1.47468 -12.8115 9.37187 -10.8344
2 2 -0.673508 -0.564245 1.59147 19.3914 -9.12777 2.73797
3 2 -2.04099 -0.404174 2.24807 -3.82175 -1.70255 6.71674
4 1 -1.73996 -0.376347 -1.33351 0.570165 0.280665 -6.43548
5 2 -1.87928 -0.466718 -0.390362 1.26398 0.876645 10.7815
6 2 -2.48657 -0.801116 -1.75201 -2.14828 -1.00411 -3.66812
7 1 -0.576718 1.99595 -0.131852 3.14419 3.30092 -1.47913
8 2 -0.97416 1.49195 0.577492 -1.32391 -2.58987 8.72867
9 2 -0.983297 1.63168 -0.91691 -0.334419 -0.770035 -7.07098
10 1 1.00791 -1.1681 1.41401 -6.20027 1.07549 12.575
11 2 0.972875 -1.65454 0.593802 -0.476084 -5.46772 -10.3478
12 2 1.54632 -0.404877 1.20306 3.83119 5.88484 -0.834958
13 1 0.966385 -1.38017 -1.32091 1.49436 -4.60495 -1.57148
14 2 0.0722824 -1.10128 -1.51274 -8.16812 -0.531008 -1.13308
15 2 1.45394 -0.565765 -1.20718 7.01226 4.42564 1.66198
16 1 2.01308 1.04537 -0.116618 6.94232 -7.944 0.350248
17 2 1.19126 1.53332 -0.135036 -13.3157 5.74475 0.221956
18 2 2.70715 1.69348 -0.205764 4.95008 2.7812 -0.398561
ITEM: TIMESTEP
70
ITEM: NUMBER OF ATOMS
18
ITEM: BOX BOUNDS ss ss ss
-2.5173543550999997e+00 2.6752353550999999e+00
-1.5223951870999999e+00 2.0181841871000001e+00
-1.7341615612999999e+00 2.2202425613000001e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -1.52447 -0.177745 1.47754 -14.009 12.5988 -14.9127
2 2 -0.663619 -0.56979 1.57126 20.9018 -10.2143 3.8986
3 2 -2.00537 -0.388653 2.26816 -5.41735 -2.91391 10.0958
4 1 -1.74327 -0.377755 -1.33511 7.69657 4.1782 -9.73798
5 2 -1.88018 -0.439682 -0.388162 -4.07322 -2.33918 9.17346
6 2 -2.47021 -0.801057 -1.79014 -4.11028 -2.07522 1.70143
7 1 -0.576352 1.99233 -0.135801 8.33914 8.33997 -1.40304
8 2 -0.93279 1.50467 0.607511 -5.01196 -5.05095 3.69276
9 2 -0.967697 1.61396 -0.924499 -2.96791 -3.60448 -2.11522
10 1 0.996682 -1.16249 1.41603 -5.52393 -2.7768 9.00886
11 2 0.982553 -1.62276 0.577115 -1.00274 -4.80219 -7.71302
12 2 1.55168 -0.404501 1.24312 4.97383 8.09577 -0.603791
13 1 0.964232 -1.37715 -1.32734 3.83388 -12.0598 -0.0980446
14 2 0.0575072 -1.10802 -1.48098 -4.628 4.85469 -1.01689
15 2 1.48931 -0.58697 -1.19891 1.1914 7.02562 -0.119366
16 1 2.01083 1.04528 -0.114231 6.83173 -12.9986 1.26494
17 2 1.17034 1.50303 -0.133551 -9.79274 8.34256 -0.476042
18 2 2.7022 1.69874 -0.182183 2.76884 5.3999 -0.639748
ITEM: TIMESTEP
80
ITEM: NUMBER OF ATOMS
18
ITEM: BOX BOUNDS ss ss ss
-2.5173543550999997e+00 2.6752353550999999e+00
-1.5223951870999999e+00 2.0181841871000001e+00
-1.7341615612999999e+00 2.2202425613000001e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -1.51177 -0.182537 1.47592 -13.1365 10.3139 -11.8951
2 2 -0.654143 -0.583091 1.57918 18.6975 -8.17701 1.44433
3 2 -1.97348 -0.365352 2.2852 -6.58467 -1.56222 9.05296
4 1 -1.74352 -0.377279 -1.33693 -0.505822 0.308788 -3.25308
5 2 -1.91188 -0.438855 -0.39405 1.95743 0.358158 9.20234
6 2 -2.48397 -0.807922 -1.76244 -1.16931 -0.70018 -3.86005
7 1 -0.571778 1.99034 -0.138544 1.3921 0.315501 -1.43854
8 2 -0.938419 1.50232 0.602337 -1.22478 -1.30903 4.8686
9 2 -0.959599 1.56918 -0.90914 -0.0288155 0.574454 -3.52808
10 1 0.985435 -1.15713 1.41811 -6.25848 -6.25702 9.27302
11 2 0.972167 -1.59168 0.560031 1.69554 -0.201305 -5.06875
12 2 1.54032 -0.386652 1.30283 4.96928 5.72762 -4.15176
13 1 0.963614 -1.3793 -1.33436 0.183354 -1.1048 0.823621
14 2 0.065336 -1.06423 -1.45856 -4.4409 -1.33366 -2.05511
15 2 1.49256 -0.587857 -1.21654 4.36346 2.23441 0.338535
16 1 2.00803 1.04345 -0.110717 3.61274 -3.25471 0.639326
17 2 1.16919 1.51061 -0.133404 -8.46417 2.50048 0.10369
18 2 2.67828 1.72068 -0.16597 4.94198 1.56662 -0.49597
ITEM: TIMESTEP
90
ITEM: NUMBER OF ATOMS
18
ITEM: BOX BOUNDS ss ss ss
-2.5173543550999997e+00 2.6752353550999999e+00
-1.5223951870999999e+00 2.0181841871000001e+00
-1.7341615612999999e+00 2.2202425613000001e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -1.50159 -0.186388 1.47232 -10.1666 8.56134 -9.06842
2 2 -0.637201 -0.589948 1.58141 9.00709 -5.13609 3.43504
3 2 -1.97805 -0.327506 2.28752 -1.76215 -2.05269 5.01359
4 1 -1.7485 -0.377921 -1.33249 5.81313 3.27044 -5.4853
5 2 -1.87141 -0.433051 -0.37781 -3.50795 -2.5324 4.09176
6 2 -2.48522 -0.804273 -1.77362 -2.18894 -1.0456 2.79096
7 1 -0.568425 1.98378 -0.140489 1.33268 1.60885 -0.760228
8 2 -0.945484 1.51375 0.61188 -1.03442 -1.79649 -0.570033
9 2 -0.936389 1.56212 -0.924193 -1.07342 -0.200973 1.02154
10 1 0.975854 -1.15481 1.42351 1.86741 -2.52595 -4.21318
11 2 0.98193 -1.53917 0.537259 -2.6087 -4.02599 1.03016
12 2 1.52752 -0.379325 1.30866 2.98513 5.11632 2.51897
13 1 0.962056 -1.37771 -1.33914 1.58342 -3.36145 0.893222
14 2 0.0608833 -1.06855 -1.4877 0.530861 1.7595 -0.414339
15 2 1.52774 -0.603203 -1.25083 -2.15602 1.98356 -0.537593
16 1 2.00483 1.04652 -0.10624 2.44039 -5.05754 0.604689
17 2 1.15126 1.49959 -0.126569 -0.261743 3.34267 -0.115684
18 2 2.69252 1.71134 -0.15978 -0.800158 2.09248 -0.235157
ITEM: TIMESTEP
100
ITEM: NUMBER OF ATOMS
18
ITEM: BOX BOUNDS ss ss ss
-2.5173543550999997e+00 2.6752353550999999e+00
-1.5223951870999999e+00 2.0181841871000001e+00
-1.7341615612999999e+00 2.2202425613000001e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -1.49915 -0.184572 1.46491 -1.64286 -0.923423 4.11541
2 2 -0.634606 -0.601439 1.61658 -0.503947 1.48506 -2.91046
3 2 -1.9835 -0.312527 2.28463 -1.23961 0.673264 -1.96712
4 1 -1.74898 -0.375873 -1.32741 -4.05983 -3.09974 1.92324
5 2 -1.86884 -0.471305 -0.372769 3.24632 2.33491 1.76011
6 2 -2.50916 -0.806172 -1.72327 1.14638 0.924599 -3.12385
7 1 -0.564884 1.97778 -0.142101 -4.14881 -3.0738 -0.168062
8 2 -0.958996 1.4911 0.595477 2.25574 1.20147 -1.85844
9 2 -0.937749 1.56372 -0.930264 1.31445 2.00952 1.76263
10 1 0.975211 -1.15256 1.42364 -0.947501 -4.6035 2.62584
11 2 0.950951 -1.55837 0.541757 3.10583 4.89391 1.85772
12 2 1.52342 -0.363228 1.34082 0.672959 -1.69053 -5.30235
13 1 0.962361 -1.37851 -1.34242 -1.40487 6.54708 -1.50719
14 2 0.0703818 -1.05861 -1.53269 1.44041 -3.14031 1.12109
15 2 1.51335 -0.586474 -1.29057 -0.612624 -3.69916 1.63647
16 1 2.00445 1.04687 -0.100669 -1.02523 8.04786 -0.336895
17 2 1.16075 1.52969 -0.119062 2.24423 -4.67525 0.190963
18 2 2.68635 1.72058 -0.160395 0.158945 -3.21195 0.180894

297
examples/amoeba/dump.water_hexamer.hippo.1.test
View File

@ -1,297 +0,0 @@
ITEM: TIMESTEP
0
ITEM: NUMBER OF ATOMS
18
ITEM: BOX BOUNDS ss ss ss
-2.5173543550999997e+00 2.6752353550999999e+00
-1.5223951870999999e+00 2.0181841871000001e+00
-1.7341615612999999e+00 2.2202425613000001e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -1.50217 -0.191359 1.43493 19.9357 -10.2022 6.39617
2 2 -0.601054 -0.596972 1.55372 -26.7746 11.7551 -3.2269
3 2 -2.0067 -0.422327 2.21985 2.27453 0.843475 -3.26617
4 1 -1.74457 -0.382348 -1.30914 -7.45906 -3.26138 10.4208
5 2 -1.88894 -0.479653 -0.347624 4.39096 1.86538 -10.993
6 2 -2.51683 -0.766765 -1.73377 3.97889 2.0308 0.238005
7 1 -0.560409 2.01783 -0.121984 -15.0354 -12.151 1.41176
8 2 -0.94772 1.53357 0.625228 7.62359 5.98784 -1.89388
9 2 -0.989831 1.59274 -0.877419 6.55934 4.96076 0.527359
10 1 0.964803 -1.16576 1.43999 15.4285 1.35636 -21.3173
11 2 0.979557 -1.52204 0.527833 -6.23862 0.631634 14.3987
12 2 1.54222 -0.393692 1.34437 -5.98579 -2.68738 6.2337
13 1 0.974705 -1.4015 -1.33597 -5.70279 13.9492 -3.53962
14 2 0.065161 -1.11895 -1.52289 5.16041 -6.4649 2.71211
15 2 1.47071 -0.570933 -1.27771 0.726496 -6.9774 1.88925
16 1 2.00228 1.05782 -0.124502 -11.1831 12.6873 -1.41281
17 2 1.14164 1.53227 -0.140121 14.1175 -10.0366 0.774885
18 2 2.67472 1.73534 -0.237995 -1.81661 -4.28693 0.646829
ITEM: TIMESTEP
10
ITEM: NUMBER OF ATOMS
18
ITEM: BOX BOUNDS ss ss ss
-2.5173543550999997e+00 2.6752353550999999e+00
-1.5223951870999999e+00 2.0181841871000001e+00
-1.7341615612999999e+00 2.2202425613000001e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -1.50519 -0.189085 1.43489 16.1346 -9.03082 7.39643
2 2 -0.613325 -0.596599 1.55623 -19.7 9.16793 -3.06694
3 2 -2.00781 -0.423676 2.21968 1.11569 1.33017 -3.51515
4 1 -1.74545 -0.38218 -1.30921 -0.873137 -0.924011 5.81502
5 2 -1.86379 -0.472478 -0.34573 -0.592473 0.521176 -9.80595
6 2 -2.51308 -0.764814 -1.7423 1.95383 0.883641 3.34899
7 1 -0.566746 2.01551 -0.121884 -0.752908 0.880358 1.51675
8 2 -0.90288 1.53899 0.653422 -0.370038 -0.282546 -8.72932
9 2 -0.948386 1.59852 -0.906373 -0.161598 -1.83495 7.27882
10 1 0.972994 -1.16632 1.4367 2.1365 -3.63541 -4.30666
11 2 0.921471 -1.54563 0.536978 3.92948 8.96444 9.02535
12 2 1.51571 -0.366599 1.37318 -3.05971 -5.7155 -5.67471
13 1 0.973913 -1.39785 -1.33834 -1.44621 0.344209 -0.720777
14 2 0.0503221 -1.15099 -1.50181 7.085 2.52089 1.36272
15 2 1.49605 -0.587274 -1.24124 -6.30793 -2.23617 0.0453877
16 1 2.00301 1.05777 -0.1249 -8.37521 5.68727 -0.0787125
17 2 1.13805 1.51682 -0.135757 12.8554 -4.94557 -0.27859
18 2 2.68412 1.72611 -0.2366 -3.57128 -1.69512 0.387339
ITEM: TIMESTEP
20
ITEM: NUMBER OF ATOMS
18
ITEM: BOX BOUNDS ss ss ss
-2.5173543550999997e+00 2.6752353550999999e+00
-1.5223951870999999e+00 2.0181841871000001e+00
-1.7341615612999999e+00 2.2202425613000001e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -1.51053 -0.184679 1.43662 2.59225 -2.34383 2.4228
2 2 -0.638864 -0.59446 1.56144 -3.81751 1.45077 0.169365
3 2 -2.02892 -0.415768 2.21112 1.3915 0.960529 -2.2268
4 1 -1.7422 -0.380161 -1.31156 -2.81538 -1.6524 5.61723
5 2 -1.87085 -0.467579 -0.355121 2.06181 1.26201 -3.01668
6 2 -2.51909 -0.769609 -1.71571 1.56589 0.868196 -2.04346
7 1 -0.571857 2.01726 -0.121524 -4.42229 -10.7497 0.101549
8 2 -0.894989 1.49275 0.621756 1.9428 5.13739 2.3456
9 2 -0.928333 1.53949 -0.878364 1.74391 4.55343 -2.63937
10 1 0.983665 -1.17004 1.43811 2.15858 5.32924 -12.0192
11 2 0.916986 -1.51176 0.532863 -0.801958 -4.34579 6.00669
12 2 1.48632 -0.356933 1.30471 -0.115562 -1.35756 5.38685
13 1 0.974155 -1.39809 -1.34091 -3.6872 9.81415 2.33229
14 2 0.0608639 -1.11508 -1.47548 0.727822 -4.45373 -1.43277
15 2 1.45945 -0.57705 -1.18377 2.74992 -3.83937 -1.32423
16 1 2.0041 1.05318 -0.12468 -4.82863 5.07797 -0.287867
17 2 1.15863 1.52924 -0.140109 2.7798 -3.05413 0.358119
18 2 2.67895 1.72504 -0.234758 0.77424 -2.65718 0.249897
ITEM: TIMESTEP
30
ITEM: NUMBER OF ATOMS
18
ITEM: BOX BOUNDS ss ss ss
-2.5173543550999997e+00 2.6752353550999999e+00
-1.5223951870999999e+00 2.0181841871000001e+00
-1.7341615612999999e+00 2.2202425613000001e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -1.5148 -0.180382 1.43888 -14.0787 7.25927 -2.0787
2 2 -0.670243 -0.596746 1.58256 15.1847 -7.27642 2.26385
3 2 -2.0578 -0.394757 2.19803 0.335566 -0.184039 0.277588
4 1 -1.73953 -0.378972 -1.31065 5.17639 2.63373 -5.13987
5 2 -1.85923 -0.443728 -0.358889 -2.57415 -1.51426 3.86387
6 2 -2.50599 -0.762479 -1.73443 -2.25678 -0.997735 0.886673
7 1 -0.57869 2.00716 -0.122116 7.46708 7.5609 -0.932554
8 2 -0.891326 1.5227 0.646189 -3.77932 -4.24552 -0.379656
9 2 -0.906489 1.54888 -0.899539 -3.74504 -3.89196 0.775918
10 1 0.993915 -1.16716 1.4314 -4.03671 -0.827424 10.5116
11 2 0.932938 -1.58361 0.567361 1.80347 1.36047 -5.88474
12 2 1.49414 -0.355801 1.3027 1.34198 0.116597 -4.03649
13 1 0.970608 -1.38983 -1.33905 4.21477 -7.05635 0.421831
14 2 0.0575618 -1.13428 -1.49637 -1.45416 4.35852 0.0411765
15 2 1.48422 -0.594211 -1.16216 -2.77696 3.0816 -1.11496
16 1 2.00096 1.05017 -0.124007 4.94447 -7.97826 1.06585
17 2 1.17138 1.53183 -0.140668 -5.63771 5.40691 -0.274313
18 2 2.7082 1.68479 -0.23083 -0.128954 2.19398 -0.267092
ITEM: TIMESTEP
40
ITEM: NUMBER OF ATOMS
18
ITEM: BOX BOUNDS ss ss ss
-2.5173543550999997e+00 2.6752353550999999e+00
-1.5223951870999999e+00 2.0181841871000001e+00
-1.7341615612999999e+00 2.2202425613000001e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -1.5186 -0.17605 1.44225 -24.1552 14.2056 -8.76949
2 2 -0.687962 -0.594151 1.59127 27.1026 -13.0552 4.45143
3 2 -2.07116 -0.378379 2.19317 -1.29427 -1.5252 3.96365
4 1 -1.73305 -0.375414 -1.31137 2.16372 2.0419 -7.75161
5 2 -1.87951 -0.450834 -0.370226 0.624847 -0.775772 11.2387
6 2 -2.50254 -0.754697 -1.72909 -2.50645 -1.07375 -3.54713
7 1 -0.578876 1.99941 -0.124067 2.19183 2.88771 -2.2033
8 2 -0.936478 1.52242 0.623048 -0.431918 -2.06784 8.93732
9 2 -0.943689 1.52907 -0.872983 -0.503357 -0.655131 -7.36871
10 1 1.00066 -1.16525 1.43041 -2.12968 1.37125 11.5778
11 2 0.974279 -1.60078 0.583019 -3.02955 -6.45349 -11.2722
12 2 1.51087 -0.375422 1.25067 2.49642 6.22795 1.24643
13 1 0.96952 -1.38626 -1.33641 3.1199 -1.09706 -1.06644
14 2 0.0736705 -1.0998 -1.50988 -8.20047 -1.85824 -0.95018
15 2 1.45433 -0.57243 -1.18601 5.63783 2.37426 1.20997
16 1 1.9962 1.04317 -0.122075 10.6231 -9.89832 0.540427
17 2 1.19663 1.55837 -0.138658 -15.3708 7.22601 0.146924
18 2 2.71508 1.6609 -0.228386 3.66149 2.12531 -0.383549
ITEM: TIMESTEP
50
ITEM: NUMBER OF ATOMS
18
ITEM: BOX BOUNDS ss ss ss
-2.5173543550999997e+00 2.6752353550999999e+00
-1.5223951870999999e+00 2.0181841871000001e+00
-1.7341615612999999e+00 2.2202425613000001e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -1.52326 -0.171807 1.44556 -19.3809 13.2253 -10.6114
2 2 -0.679923 -0.574818 1.57581 25.4624 -12.0419 4.4477
3 2 -2.05017 -0.382025 2.20867 -3.53537 -2.33472 6.62258
4 1 -1.72947 -0.37135 -1.31158 7.45117 4.03521 -12.7525
5 2 -1.85272 -0.46757 -0.370426 -4.08312 -1.86842 12.0545
6 2 -2.4914 -0.737252 -1.75485 -4.03109 -2.01148 0.403261
7 1 -0.581812 1.98886 -0.127591 8.73336 12.0451 -2.23223
8 2 -0.927295 1.54015 0.641551 -4.26906 -6.45964 5.24049
9 2 -0.953055 1.5416 -0.887204 -3.28906 -5.2042 -3.24355
10 1 1.00866 -1.16393 1.43094 -5.76797 0.688141 16.3003
11 2 0.941718 -1.59751 0.586621 -0.69625 -5.79697 -13.9615
12 2 1.5005 -0.365594 1.24465 4.16474 6.46538 -1.29083
13 1 0.968591 -1.37822 -1.33754 5.88173 -13.6635 -0.995409
14 2 0.058765 -1.13465 -1.50083 -6.65826 5.43105 -0.991523
15 2 1.47128 -0.574689 -1.20309 0.663977 7.53437 1.14922
16 1 1.99172 1.03702 -0.120004 11.7209 -15.9347 1.25003
17 2 1.18616 1.54124 -0.127765 -14.4197 10.6401 -0.950727
18 2 2.7224 1.64022 -0.223578 2.05256 5.25094 -0.438473
ITEM: TIMESTEP
60
ITEM: NUMBER OF ATOMS
18
ITEM: BOX BOUNDS ss ss ss
-2.5173543550999997e+00 2.6752353550999999e+00
-1.5223951870999999e+00 2.0181841871000001e+00
-1.7341615612999999e+00 2.2202425613000001e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -1.52514 -0.169424 1.44931 -5.6044 5.71407 -7.65735
2 2 -0.654856 -0.548823 1.55951 12.8877 -6.19997 1.70589
3 2 -2.01089 -0.399975 2.23335 -4.71544 -1.47688 6.26364
4 1 -1.72371 -0.366036 -1.3145 0.154709 0.0103655 -5.79078
5 2 -1.86537 -0.486382 -0.375504 0.204748 0.738589 9.60402
6 2 -2.49691 -0.728317 -1.74343 -1.12209 -0.453095 -3.27306
7 1 -0.582396 1.98478 -0.131637 3.0799 3.10149 -1.36944
8 2 -0.917703 1.51358 0.63199 -1.67497 -1.52591 5.69623
9 2 -0.95935 1.51373 -0.876424 -0.704912 -1.0485 -4.50039
10 1 1.01141 -1.16147 1.43332 -7.40944 0.284109 12.5023
11 2 0.911102 -1.56686 0.573359 1.73368 -3.47737 -10.1102
12 2 1.49548 -0.352196 1.26684 4.34342 4.22027 -2.29553
13 1 0.969684 -1.37685 -1.34222 -0.51092 -4.11589 -0.224969
14 2 0.0587056 -1.1173 -1.48363 -6.15339 -0.904158 -2.27293
15 2 1.44029 -0.555019 -1.20354 6.44357 4.32801 1.75924
16 1 1.98854 1.02727 -0.117121 5.38674 -4.81439 0.472007
17 2 1.17286 1.52668 -0.137432 -10.3716 4.01885 -0.196355
18 2 2.69 1.66639 -0.213741 4.03261 1.60042 -0.312306
ITEM: TIMESTEP
70
ITEM: NUMBER OF ATOMS
18
ITEM: BOX BOUNDS ss ss ss
-2.5173543550999997e+00 2.6752353550999999e+00
-1.5223951870999999e+00 2.0181841871000001e+00
-1.7341615612999999e+00 2.2202425613000001e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -1.52005 -0.170765 1.45435 7.42813 -0.682132 -3.31568
2 2 -0.627795 -0.545781 1.54703 -4.484 0.351316 0.767932
3 2 -1.9938 -0.405389 2.24937 -1.65789 -0.838399 2.61041
4 1 -1.72181 -0.363627 -1.31513 2.63115 1.26887 -2.8752
5 2 -1.86247 -0.45623 -0.365408 -2.65258 -1.1368 1.02525
6 2 -2.4895 -0.712321 -1.77001 -0.898587 -0.369019 2.21573
7 1 -0.583063 1.97962 -0.135858 1.67055 0.570004 -0.383383
8 2 -0.908051 1.51128 0.64094 -1.16679 -0.0785678 -0.520586
9 2 -0.943124 1.49995 -0.888932 -0.754685 -0.199723 0.596245
10 1 1.00431 -1.15529 1.43647 -0.676345 0.911353 -2.95012
11 2 0.95109 -1.53365 0.551095 -1.85378 -3.64627 0.0738184
12 2 1.52689 -0.36229 1.29214 1.34973 2.90443 2.73267
13 1 0.96764 -1.3732 -1.34735 0.830518 -7.82237 0.0710001
14 2 0.049796 -1.13062 -1.50565 0.0671147 3.17314 0.120857
15 2 1.46341 -0.566541 -1.18509 -0.178936 4.65822 -0.507667
16 1 1.98438 1.02188 -0.114233 -0.881295 -2.57322 0.275288
17 2 1.13419 1.48172 -0.149659 1.87909 1.86036 0.463365
18 2 2.6735 1.67987 -0.202074 -0.651386 1.64881 -0.399918
ITEM: TIMESTEP
80
ITEM: NUMBER OF ATOMS
18
ITEM: BOX BOUNDS ss ss ss
-2.5173543550999997e+00 2.6752353550999999e+00
-1.5223951870999999e+00 2.0181841871000001e+00
-1.7341615612999999e+00 2.2202425613000001e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -1.50978 -0.173017 1.45833 15.0482 -9.57345 5.77126
2 2 -0.617503 -0.581602 1.56045 -17.3455 8.85736 -2.90765
3 2 -1.99215 -0.403845 2.25671 0.833211 1.42908 -3.53001
4 1 -1.71857 -0.360372 -1.31644 -7.32338 -2.11362 6.45601
5 2 -1.89982 -0.440583 -0.365391 4.39327 0.727605 -4.87947
6 2 -2.49827 -0.701359 -1.75982 2.51785 1.20426 -1.18541
7 1 -0.581108 1.97455 -0.140769 -3.87733 -3.80002 1.10694
8 2 -0.928789 1.51932 0.641149 2.19408 2.20718 -5.07369
9 2 -0.943839 1.48954 -0.89443 1.32563 2.05291 3.72773
10 1 0.995847 -1.14613 1.43537 0.755936 -5.6909 -0.46639
11 2 0.966841 -1.55186 0.550806 1.56938 7.42451 5.54707
12 2 1.55511 -0.362342 1.35836 -2.79165 -2.9995 -5.36768
13 1 0.967816 -1.37465 -1.35163 -3.29308 4.65803 -0.872226
14 2 0.0602027 -1.09254 -1.5264 2.56737 -3.64929 1.27094
15 2 1.45854 -0.559392 -1.19328 1.84002 -1.84978 0.0538636
16 1 1.98052 1.0158 -0.111184 -7.14388 11.5516 -0.816233
17 2 1.12003 1.47724 -0.140032 8.70268 -6.85942 1.26876
18 2 2.64114 1.706 -0.201685 0.0272078 -3.57662 -0.103793
ITEM: TIMESTEP
90
ITEM: NUMBER OF ATOMS
18
ITEM: BOX BOUNDS ss ss ss
-2.5173543550999997e+00 2.6752353550999999e+00
-1.5223951870999999e+00 2.0181841871000001e+00
-1.7341615612999999e+00 2.2202425613000001e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -1.50003 -0.175917 1.46165 15.3898 -11.884 8.8546
2 2 -0.608584 -0.600731 1.57129 -23.7815 11.9323 -1.75151
3 2 -2.00991 -0.394435 2.25305 5.57059 1.55514 -7.64598
4 1 -1.72137 -0.357368 -1.31563 -1.93902 -0.246344 7.85181
5 2 -1.87234 -0.43987 -0.353482 -0.118832 -0.772284 -11.4834
6 2 -2.49861 -0.682857 -1.77755 1.48512 0.513779 4.12935
7 1 -0.579472 1.97061 -0.145894 -8.85759 -8.26094 2.77276
8 2 -0.945449 1.52054 0.635243 4.66427 4.57627 -6.94972
9 2 -0.952686 1.48464 -0.897126 3.60343 4.09955 4.74753
10 1 0.988258 -1.14419 1.44127 11.1074 1.88534 -20.9154
11 2 0.971991 -1.50516 0.531218 -4.29535 0.162687 14.3489
12 2 1.5415 -0.356231 1.32305 -5.76468 -4.25266 5.91571
13 1 0.969416 -1.37359 -1.35605 -1.23717 3.53556 0.174563
14 2 0.053578 -1.1004 -1.52114 7.10928 -0.236326 1.96556
15 2 1.49219 -0.569722 -1.21186 -5.0738 -3.24139 -1.5161
16 1 1.97824 1.01566 -0.108279 -8.95647 8.69277 0.191958
17 2 1.10027 1.45664 -0.104435 15.9218 -5.21388 -1.22481
18 2 2.64464 1.70165 -0.21558 -4.82724 -2.84557 0.534172
ITEM: TIMESTEP
100
ITEM: NUMBER OF ATOMS
18
ITEM: BOX BOUNDS ss ss ss
-2.5173543550999997e+00 2.6752353550999999e+00
-1.5223951870999999e+00 2.0181841871000001e+00
-1.7341615612999999e+00 2.2202425613000001e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -1.4951 -0.17739 1.46185 11.6291 -12.0775 13.5087
2 2 -0.608426 -0.588808 1.60852 -19.0988 9.4339 -4.86631
3 2 -2.01619 -0.397996 2.24676 4.77562 3.06476 -9.1756
4 1 -1.72287 -0.352149 -1.31567 -8.10325 -4.84048 12.8242
5 2 -1.86729 -0.479262 -0.356777 4.49726 3.58866 -11.0242
6 2 -2.51926 -0.676876 -1.74282 3.42966 1.20159 -1.20299
7 1 -0.581355 1.96754 -0.149521 -5.24612 -4.66563 2.71982
8 2 -0.935394 1.51644 0.636953 2.89489 2.96603 -9.31226
9 2 -0.942573 1.488 -0.91114 1.96254 2.34604 7.29302
10 1 0.988651 -1.14425 1.44045 0.840008 -1.36718 -7.83612
11 2 0.899639 -1.53136 0.543246 5.64911 9.69241 11.7913
12 2 1.49178 -0.318235 1.33897 -3.7582 -9.86315 -4.79205
13 1 0.974233 -1.37573 -1.35945 -3.77942 11.331 0.435153
14 2 0.0583408 -1.08758 -1.49668 6.15796 -3.89994 -0.197074
15 2 1.48764 -0.558876 -1.24121 -3.14566 -8.24544 0.525665
16 1 1.97883 1.01496 -0.10404 -9.03485 15.6667 -0.929518
17 2 1.11471 1.47883 -0.106249 11.9101 -8.77208 -0.858699
18 2 2.63671 1.70526 -0.232286 -1.57994 -5.55972 1.09694

297
examples/amoeba/dump.water_hexamer.hippo.4.test
View File

@ -1,297 +0,0 @@
ITEM: TIMESTEP
0
ITEM: NUMBER OF ATOMS
18
ITEM: BOX BOUNDS ss ss ss
-2.5173543550999997e+00 2.6752353550999999e+00
-1.5223951870999999e+00 2.0181841871000001e+00
-1.7341615612999999e+00 2.2202425613000001e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -1.50217 -0.191359 1.43493 19.9357 -10.2022 6.39617
2 2 -0.601054 -0.596972 1.55372 -26.7746 11.7551 -3.2269
3 2 -2.0067 -0.422327 2.21985 2.27453 0.843475 -3.26617
4 1 -1.74457 -0.382348 -1.30914 -7.45906 -3.26138 10.4208
5 2 -1.88894 -0.479653 -0.347624 4.39096 1.86538 -10.993
6 2 -2.51683 -0.766765 -1.73377 3.97889 2.0308 0.238005
7 1 -0.560409 2.01783 -0.121984 -15.0354 -12.151 1.41176
8 2 -0.94772 1.53357 0.625228 7.62359 5.98784 -1.89388
9 2 -0.989831 1.59274 -0.877419 6.55934 4.96076 0.527359
10 1 0.964803 -1.16576 1.43999 15.4285 1.35636 -21.3173
11 2 0.979557 -1.52204 0.527833 -6.23862 0.631634 14.3987
12 2 1.54222 -0.393692 1.34437 -5.98579 -2.68738 6.2337
13 1 0.974705 -1.4015 -1.33597 -5.70279 13.9492 -3.53962
14 2 0.065161 -1.11895 -1.52289 5.16041 -6.4649 2.71211
15 2 1.47071 -0.570933 -1.27771 0.726496 -6.9774 1.88925
16 1 2.00228 1.05782 -0.124502 -11.1831 12.6873 -1.41281
17 2 1.14164 1.53227 -0.140121 14.1175 -10.0366 0.774885
18 2 2.67472 1.73534 -0.237995 -1.81661 -4.28693 0.646829
ITEM: TIMESTEP
10
ITEM: NUMBER OF ATOMS
18
ITEM: BOX BOUNDS ss ss ss
-2.5173543550999997e+00 2.6752353550999999e+00
-1.5223951870999999e+00 2.0181841871000001e+00
-1.7341615612999999e+00 2.2202425613000001e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -1.50519 -0.189085 1.43489 16.1346 -9.03082 7.39643
2 2 -0.613325 -0.596599 1.55623 -19.7 9.16793 -3.06694
3 2 -2.00781 -0.423676 2.21968 1.11569 1.33017 -3.51515
4 1 -1.74545 -0.38218 -1.30921 -0.873137 -0.924011 5.81502
5 2 -1.86379 -0.472478 -0.34573 -0.592473 0.521176 -9.80595
6 2 -2.51308 -0.764814 -1.7423 1.95383 0.883641 3.34899
7 1 -0.566746 2.01551 -0.121884 -0.752908 0.880358 1.51675
8 2 -0.90288 1.53899 0.653422 -0.370038 -0.282546 -8.72932
9 2 -0.948386 1.59852 -0.906373 -0.161598 -1.83495 7.27882
10 1 0.972994 -1.16632 1.4367 2.1365 -3.63541 -4.30666
11 2 0.921471 -1.54563 0.536978 3.92948 8.96444 9.02535
12 2 1.51571 -0.366599 1.37318 -3.05971 -5.7155 -5.67471
13 1 0.973913 -1.39785 -1.33834 -1.44621 0.344209 -0.720777
14 2 0.0503221 -1.15099 -1.50181 7.085 2.52089 1.36272
15 2 1.49605 -0.587274 -1.24124 -6.30793 -2.23617 0.0453877
16 1 2.00301 1.05777 -0.1249 -8.37521 5.68727 -0.0787125
17 2 1.13805 1.51682 -0.135757 12.8554 -4.94557 -0.27859
18 2 2.68412 1.72611 -0.2366 -3.57128 -1.69512 0.387339
ITEM: TIMESTEP
20
ITEM: NUMBER OF ATOMS
18
ITEM: BOX BOUNDS ss ss ss
-2.5173543550999997e+00 2.6752353550999999e+00
-1.5223951870999999e+00 2.0181841871000001e+00
-1.7341615612999999e+00 2.2202425613000001e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -1.51053 -0.184679 1.43662 2.59225 -2.34383 2.4228
2 2 -0.638864 -0.59446 1.56144 -3.81751 1.45077 0.169365
3 2 -2.02892 -0.415768 2.21112 1.3915 0.960529 -2.2268
4 1 -1.7422 -0.380161 -1.31156 -2.81538 -1.6524 5.61723
5 2 -1.87085 -0.467579 -0.355121 2.06181 1.26201 -3.01668
6 2 -2.51909 -0.769609 -1.71571 1.56589 0.868196 -2.04346
7 1 -0.571857 2.01726 -0.121524 -4.42229 -10.7497 0.101549
8 2 -0.894989 1.49275 0.621756 1.9428 5.13739 2.3456
9 2 -0.928333 1.53949 -0.878364 1.74391 4.55343 -2.63937
10 1 0.983665 -1.17004 1.43811 2.15858 5.32924 -12.0192
11 2 0.916986 -1.51176 0.532863 -0.801958 -4.34579 6.00669
12 2 1.48632 -0.356933 1.30471 -0.115562 -1.35756 5.38685
13 1 0.974155 -1.39809 -1.34091 -3.6872 9.81415 2.33229
14 2 0.0608639 -1.11508 -1.47548 0.727822 -4.45373 -1.43277
15 2 1.45945 -0.57705 -1.18377 2.74992 -3.83937 -1.32423
16 1 2.0041 1.05318 -0.12468 -4.82863 5.07797 -0.287867
17 2 1.15863 1.52924 -0.140109 2.7798 -3.05413 0.358119
18 2 2.67895 1.72504 -0.234758 0.77424 -2.65718 0.249897
ITEM: TIMESTEP
30
ITEM: NUMBER OF ATOMS
18
ITEM: BOX BOUNDS ss ss ss
-2.5173543550999997e+00 2.6752353550999999e+00
-1.5223951870999999e+00 2.0181841871000001e+00
-1.7341615612999999e+00 2.2202425613000001e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -1.5148 -0.180382 1.43888 -14.0787 7.25927 -2.0787
2 2 -0.670243 -0.596746 1.58256 15.1847 -7.27642 2.26385
3 2 -2.0578 -0.394757 2.19803 0.335566 -0.184039 0.277588
4 1 -1.73953 -0.378972 -1.31065 5.17639 2.63373 -5.13987
5 2 -1.85923 -0.443728 -0.358889 -2.57415 -1.51426 3.86387
6 2 -2.50599 -0.762479 -1.73443 -2.25678 -0.997735 0.886673
7 1 -0.57869 2.00716 -0.122116 7.46708 7.5609 -0.932554
8 2 -0.891326 1.5227 0.646189 -3.77932 -4.24552 -0.379656
9 2 -0.906489 1.54888 -0.899539 -3.74504 -3.89196 0.775918
10 1 0.993915 -1.16716 1.4314 -4.03671 -0.827424 10.5116
11 2 0.932938 -1.58361 0.567361 1.80347 1.36047 -5.88474
12 2 1.49414 -0.355801 1.3027 1.34198 0.116597 -4.03649
13 1 0.970608 -1.38983 -1.33905 4.21477 -7.05635 0.421831
14 2 0.0575618 -1.13428 -1.49637 -1.45416 4.35852 0.0411765
15 2 1.48422 -0.594211 -1.16216 -2.77696 3.0816 -1.11496
16 1 2.00096 1.05017 -0.124007 4.94447 -7.97826 1.06585
17 2 1.17138 1.53183 -0.140668 -5.63771 5.40691 -0.274313
18 2 2.7082 1.68479 -0.23083 -0.128954 2.19398 -0.267092
ITEM: TIMESTEP
40
ITEM: NUMBER OF ATOMS
18
ITEM: BOX BOUNDS ss ss ss
-2.5173543550999997e+00 2.6752353550999999e+00
-1.5223951870999999e+00 2.0181841871000001e+00
-1.7341615612999999e+00 2.2202425613000001e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -1.5186 -0.17605 1.44225 -24.1552 14.2056 -8.76949
2 2 -0.687962 -0.594151 1.59127 27.1026 -13.0552 4.45143
3 2 -2.07116 -0.378379 2.19317 -1.29427 -1.5252 3.96365
4 1 -1.73305 -0.375414 -1.31137 2.16372 2.0419 -7.75161
5 2 -1.87951 -0.450834 -0.370226 0.624847 -0.775772 11.2387
6 2 -2.50254 -0.754697 -1.72909 -2.50645 -1.07375 -3.54713
7 1 -0.578876 1.99941 -0.124067 2.19183 2.88771 -2.2033
8 2 -0.936478 1.52242 0.623048 -0.431918 -2.06784 8.93732
9 2 -0.943689 1.52907 -0.872983 -0.503357 -0.655131 -7.36871
10 1 1.00066 -1.16525 1.43041 -2.12968 1.37125 11.5778
11 2 0.974279 -1.60078 0.583019 -3.02955 -6.45349 -11.2722
12 2 1.51087 -0.375422 1.25067 2.49642 6.22795 1.24643
13 1 0.96952 -1.38626 -1.33641 3.1199 -1.09706 -1.06644
14 2 0.0736705 -1.0998 -1.50988 -8.20047 -1.85824 -0.95018
15 2 1.45433 -0.57243 -1.18601 5.63783 2.37426 1.20997
16 1 1.9962 1.04317 -0.122075 10.6231 -9.89832 0.540427
17 2 1.19663 1.55837 -0.138658 -15.3708 7.22601 0.146924
18 2 2.71508 1.6609 -0.228386 3.66149 2.12531 -0.383549
ITEM: TIMESTEP
50
ITEM: NUMBER OF ATOMS
18
ITEM: BOX BOUNDS ss ss ss
-2.5173543550999997e+00 2.6752353550999999e+00
-1.5223951870999999e+00 2.0181841871000001e+00
-1.7341615612999999e+00 2.2202425613000001e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -1.52326 -0.171807 1.44556 -19.3809 13.2253 -10.6114
2 2 -0.679923 -0.574818 1.57581 25.4624 -12.0419 4.4477
3 2 -2.05017 -0.382025 2.20867 -3.53537 -2.33472 6.62258
4 1 -1.72947 -0.37135 -1.31158 7.45117 4.03521 -12.7525
5 2 -1.85272 -0.46757 -0.370426 -4.08312 -1.86842 12.0545
6 2 -2.4914 -0.737252 -1.75485 -4.03109 -2.01148 0.403261
7 1 -0.581812 1.98886 -0.127591 8.73336 12.0451 -2.23223
8 2 -0.927295 1.54015 0.641551 -4.26906 -6.45964 5.24049
9 2 -0.953055 1.5416 -0.887204 -3.28906 -5.2042 -3.24355
10 1 1.00866 -1.16393 1.43094 -5.76797 0.688141 16.3003
11 2 0.941718 -1.59751 0.586621 -0.69625 -5.79697 -13.9615
12 2 1.5005 -0.365594 1.24465 4.16474 6.46538 -1.29083
13 1 0.968591 -1.37822 -1.33754 5.88173 -13.6635 -0.995409
14 2 0.058765 -1.13465 -1.50083 -6.65826 5.43105 -0.991523
15 2 1.47128 -0.574689 -1.20309 0.663977 7.53437 1.14922
16 1 1.99172 1.03702 -0.120004 11.7209 -15.9347 1.25003
17 2 1.18616 1.54124 -0.127765 -14.4197 10.6401 -0.950727
18 2 2.7224 1.64022 -0.223578 2.05256 5.25094 -0.438473
ITEM: TIMESTEP
60
ITEM: NUMBER OF ATOMS
18
ITEM: BOX BOUNDS ss ss ss
-2.5173543550999997e+00 2.6752353550999999e+00
-1.5223951870999999e+00 2.0181841871000001e+00
-1.7341615612999999e+00 2.2202425613000001e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -1.52514 -0.169424 1.44931 -5.6044 5.71407 -7.65735
2 2 -0.654856 -0.548823 1.55951 12.8877 -6.19997 1.70589
3 2 -2.01089 -0.399975 2.23335 -4.71544 -1.47688 6.26364
4 1 -1.72371 -0.366036 -1.3145 0.154709 0.0103655 -5.79078
5 2 -1.86537 -0.486382 -0.375504 0.204748 0.738589 9.60402
6 2 -2.49691 -0.728317 -1.74343 -1.12209 -0.453095 -3.27306
7 1 -0.582396 1.98478 -0.131637 3.0799 3.10149 -1.36944
8 2 -0.917703 1.51358 0.63199 -1.67497 -1.52591 5.69623
9 2 -0.95935 1.51373 -0.876424 -0.704912 -1.0485 -4.50039
10 1 1.01141 -1.16147 1.43332 -7.40944 0.284109 12.5023
11 2 0.911102 -1.56686 0.573359 1.73368 -3.47737 -10.1102
12 2 1.49548 -0.352196 1.26684 4.34342 4.22027 -2.29553
13 1 0.969684 -1.37685 -1.34222 -0.51092 -4.11589 -0.224969
14 2 0.0587056 -1.1173 -1.48363 -6.15339 -0.904158 -2.27293
15 2 1.44029 -0.555019 -1.20354 6.44357 4.32801 1.75924
16 1 1.98854 1.02727 -0.117121 5.38674 -4.81439 0.472007
17 2 1.17286 1.52668 -0.137432 -10.3716 4.01885 -0.196355
18 2 2.69 1.66639 -0.213741 4.03261 1.60042 -0.312306
ITEM: TIMESTEP
70
ITEM: NUMBER OF ATOMS
18
ITEM: BOX BOUNDS ss ss ss
-2.5173543550999997e+00 2.6752353550999999e+00
-1.5223951870999999e+00 2.0181841871000001e+00
-1.7341615612999999e+00 2.2202425613000001e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -1.52005 -0.170765 1.45435 7.42813 -0.682132 -3.31568
2 2 -0.627795 -0.545781 1.54703 -4.484 0.351316 0.767932
3 2 -1.9938 -0.405389 2.24937 -1.65789 -0.838399 2.61041
4 1 -1.72181 -0.363627 -1.31513 2.63115 1.26887 -2.8752
5 2 -1.86247 -0.45623 -0.365408 -2.65258 -1.1368 1.02525
6 2 -2.4895 -0.712321 -1.77001 -0.898587 -0.369019 2.21573
7 1 -0.583063 1.97962 -0.135858 1.67055 0.570004 -0.383383
8 2 -0.908051 1.51128 0.64094 -1.16679 -0.0785678 -0.520586
9 2 -0.943124 1.49995 -0.888932 -0.754685 -0.199723 0.596245
10 1 1.00431 -1.15529 1.43647 -0.676345 0.911353 -2.95012
11 2 0.95109 -1.53365 0.551095 -1.85378 -3.64627 0.0738184
12 2 1.52689 -0.36229 1.29214 1.34973 2.90443 2.73267
13 1 0.96764 -1.3732 -1.34735 0.830518 -7.82237 0.0710001
14 2 0.049796 -1.13062 -1.50565 0.0671147 3.17314 0.120857
15 2 1.46341 -0.566541 -1.18509 -0.178936 4.65822 -0.507667
16 1 1.98438 1.02188 -0.114233 -0.881295 -2.57322 0.275288
17 2 1.13419 1.48172 -0.149659 1.87909 1.86036 0.463365
18 2 2.6735 1.67987 -0.202074 -0.651386 1.64881 -0.399918
ITEM: TIMESTEP
80
ITEM: NUMBER OF ATOMS
18
ITEM: BOX BOUNDS ss ss ss
-2.5173543550999997e+00 2.6752353550999999e+00
-1.5223951870999999e+00 2.0181841871000001e+00
-1.7341615612999999e+00 2.2202425613000001e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -1.50978 -0.173017 1.45833 15.0482 -9.57345 5.77126
2 2 -0.617503 -0.581602 1.56045 -17.3455 8.85736 -2.90765
3 2 -1.99215 -0.403845 2.25671 0.833211 1.42908 -3.53001
4 1 -1.71857 -0.360372 -1.31644 -7.32338 -2.11362 6.45601
5 2 -1.89982 -0.440583 -0.365391 4.39327 0.727605 -4.87947
6 2 -2.49827 -0.701359 -1.75982 2.51785 1.20426 -1.18541
7 1 -0.581108 1.97455 -0.140769 -3.87733 -3.80002 1.10694
8 2 -0.928789 1.51932 0.641149 2.19408 2.20718 -5.07369
9 2 -0.943839 1.48954 -0.89443 1.32563 2.05291 3.72773
10 1 0.995847 -1.14613 1.43537 0.755936 -5.6909 -0.46639
11 2 0.966841 -1.55186 0.550806 1.56938 7.42451 5.54707
12 2 1.55511 -0.362342 1.35836 -2.79165 -2.9995 -5.36768
13 1 0.967816 -1.37465 -1.35163 -3.29308 4.65803 -0.872226
14 2 0.0602027 -1.09254 -1.5264 2.56737 -3.64929 1.27094
15 2 1.45854 -0.559392 -1.19328 1.84002 -1.84978 0.0538636
16 1 1.98052 1.0158 -0.111184 -7.14388 11.5516 -0.816233
17 2 1.12003 1.47724 -0.140032 8.70268 -6.85942 1.26876
18 2 2.64114 1.706 -0.201685 0.0272078 -3.57662 -0.103793
ITEM: TIMESTEP
90
ITEM: NUMBER OF ATOMS
18
ITEM: BOX BOUNDS ss ss ss
-2.5173543550999997e+00 2.6752353550999999e+00
-1.5223951870999999e+00 2.0181841871000001e+00
-1.7341615612999999e+00 2.2202425613000001e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -1.50003 -0.175917 1.46165 15.3898 -11.884 8.8546
2 2 -0.608584 -0.600731 1.57129 -23.7815 11.9323 -1.75151
3 2 -2.00991 -0.394435 2.25305 5.57059 1.55514 -7.64598
4 1 -1.72137 -0.357368 -1.31563 -1.93902 -0.246344 7.85181
5 2 -1.87234 -0.43987 -0.353482 -0.118832 -0.772284 -11.4834
6 2 -2.49861 -0.682857 -1.77755 1.48512 0.513779 4.12935
7 1 -0.579472 1.97061 -0.145894 -8.85759 -8.26094 2.77276
8 2 -0.945449 1.52054 0.635243 4.66427 4.57627 -6.94972
9 2 -0.952686 1.48464 -0.897126 3.60343 4.09955 4.74753
10 1 0.988258 -1.14419 1.44127 11.1074 1.88534 -20.9154
11 2 0.971991 -1.50516 0.531218 -4.29535 0.162687 14.3489
12 2 1.5415 -0.356231 1.32305 -5.76468 -4.25266 5.91571
13 1 0.969416 -1.37359 -1.35605 -1.23717 3.53556 0.174563
14 2 0.053578 -1.1004 -1.52114 7.10928 -0.236326 1.96556
15 2 1.49219 -0.569722 -1.21186 -5.0738 -3.24139 -1.5161
16 1 1.97824 1.01566 -0.108279 -8.95647 8.69277 0.191958
17 2 1.10027 1.45664 -0.104435 15.9218 -5.21388 -1.22481
18 2 2.64464 1.70165 -0.21558 -4.82724 -2.84557 0.534172
ITEM: TIMESTEP
100
ITEM: NUMBER OF ATOMS
18
ITEM: BOX BOUNDS ss ss ss
-2.5173543550999997e+00 2.6752353550999999e+00
-1.5223951870999999e+00 2.0181841871000001e+00
-1.7341615612999999e+00 2.2202425613000001e+00
ITEM: ATOMS id type x y z fx fy fz
1 1 -1.4951 -0.17739 1.46185 11.6291 -12.0775 13.5087
2 2 -0.608426 -0.588808 1.60852 -19.0988 9.4339 -4.86631
3 2 -2.01619 -0.397996 2.24676 4.77562 3.06476 -9.1756
4 1 -1.72287 -0.352149 -1.31567 -8.10325 -4.84048 12.8242
5 2 -1.86729 -0.479262 -0.356777 4.49726 3.58866 -11.0242
6 2 -2.51926 -0.676876 -1.74282 3.42966 1.20159 -1.20299
7 1 -0.581355 1.96754 -0.149521 -5.24612 -4.66563 2.71982
8 2 -0.935394 1.51644 0.636953 2.89489 2.96603 -9.31226
9 2 -0.942573 1.488 -0.91114 1.96254 2.34604 7.29302
10 1 0.988651 -1.14425 1.44045 0.840008 -1.36718 -7.83612
11 2 0.899639 -1.53136 0.543246 5.64911 9.69241 11.7913
12 2 1.49178 -0.318235 1.33897 -3.7582 -9.86315 -4.79205
13 1 0.974233 -1.37573 -1.35945 -3.77942 11.331 0.435153
14 2 0.0583408 -1.08758 -1.49668 6.15796 -3.89994 -0.197074
15 2 1.48764 -0.558876 -1.24121 -3.14566 -8.24544 0.525665
16 1 1.97883 1.01496 -0.10404 -9.03485 15.6667 -0.929518
17 2 1.11471 1.47883 -0.106249 11.9101 -8.77208 -0.858699
18 2 2.63671 1.70526 -0.232286 -1.57994 -5.55972 1.09694

8
examples/amoeba/in.ubiquitin
View File

@ -14,16 +14,16 @@ improper_style amoeba
# per-atom properties required by AMOEBA or HIPPO
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom i_amgroup d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
fix pit all amoeba/pitorsion
fix_modify pit energy yes
fix bit all amoeba/bitorsion bitorsion.ubiquitin.data
fix_modify bit energy yes
fix extra all property/atom &
i_amgroup d_redID d_xaxis d_yaxis d_zaxis d_pval ghost yes
fix extra2 all property/atom i_polaxe
# read data file
#read_data data.ubiquitin fix amtype NULL "Tinker Types"
read_data data.ubiquitin fix amtype NULL "Tinker Types" &
fix pit "pitorsion types" "PiTorsion Coeffs" &
fix pit pitorsions PiTorsions &

56
examples/amoeba/in.ubiquitin.test
View File

@ -1,56 +0,0 @@
# solvated ubiquitin molecule with AMOEBA force field
units real
boundary p p p
atom_modify sort 0 0.0
atom_style amoeba
bond_style class2
angle_style amoeba
dihedral_style fourier
improper_style amoeba
# per-atom properties required by AMOEBA or HIPPO
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom i_amgroup d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
fix pit all amoeba/pitorsion
fix_modify pit energy yes
fix bit all amoeba/bitorsion bitorsion.ubiquitin.data
fix_modify bit energy yes
# read data file
read_data data.ubiquitin fix amtype NULL "Tinker Types" &
fix pit "pitorsion types" "PiTorsion Coeffs" &
fix pit pitorsions PiTorsions &
fix bit bitorsions BiTorsions
pair_style amoeba
pair_coeff * * amoeba_ubiquitin.prm amoeba_ubiquitin.key
special_bonds lj/coul 0.5 0.5 0.5 one/five yes
# thermo output
compute virial all pressure NULL virial
thermo_style custom step temp epair ebond eangle edihed eimp &
emol etotal press c_virial[*]
dump 1 all custom 10 dump.ubi id type x y z fx fy fz
dump_modify 1 sort id
# zero step run
#run 0
# dynamics
fix 1 all nve
thermo 1
run 10

2
examples/amoeba/in.water_box.amoeba
View File

@ -12,7 +12,7 @@ dihedral_style none
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom i_amgroup d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d_xaxis d_yaxis d_zaxis
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
# read data file

47
examples/amoeba/in.water_box.amoeba.test
View File

@ -1,47 +0,0 @@
# water box with AMOEBA or HIPPO
units real
boundary p p p
atom_style amoeba
bond_style class2
angle_style amoeba
dihedral_style none
# per-atom properties required by AMOEBA or HIPPO
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom i_amgroup d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
# read data file
read_data data.water_box.amoeba fix amtype NULL "Tinker Types"
# force field
pair_style amoeba
pair_coeff * * amoeba_water.prm amoeba_water_box.key
special_bonds lj/coul 0.5 0.5 0.5 one/five yes
# thermo output
compute virial all pressure NULL virial
thermo_style custom step temp epair ebond eangle edihed eimp &
emol etotal press c_virial[*]
dump 1 all custom 10 dump.water_box id type x y z fx fy fz
dump_modify 1 sort id
# zero step run
#run 0
# dynamics
fix 1 all nve
thermo 10
run 100

2
examples/amoeba/in.water_box.hippo
View File

@ -12,7 +12,7 @@ dihedral_style none
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom i_amgroup d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d_xaxis d_yaxis d_zaxis
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
# read data file

47
examples/amoeba/in.water_box.hippo.test
View File

@ -1,47 +0,0 @@
# water box with AMOEBA or HIPPO
units real
boundary p p p
atom_style amoeba
bond_style class2
angle_style amoeba
dihedral_style none
# per-atom properties required by AMOEBA or HIPPO
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom i_amgroup d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
# read data file
read_data data.water_box.hippo fix amtype NULL "Tinker Types"
# force field
pair_style hippo
pair_coeff * * hippo_water.prm hippo_water_box.key
special_bonds lj/coul 0.5 0.5 0.5 one/five yes
# thermo output
compute virial all pressure NULL virial
thermo_style custom step temp epair ebond eangle edihed eimp &
emol etotal press c_virial[*]
dump 1 all custom 10 dump.water_box id type x y z fx fy fz
dump_modify 1 sort id
# zero step run
#run 0
# dynamics
fix 1 all nve
thermo 10
run 100

2
examples/amoeba/in.water_dimer.amoeba
View File

@ -12,7 +12,7 @@ dihedral_style none
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom i_amgroup d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d_xaxis d_yaxis d_zaxis
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
# read data file

47
examples/amoeba/in.water_dimer.amoeba.test
View File

@ -1,47 +0,0 @@
# water dimer with AMOEBA or HIPPO
units real
boundary s s s
atom_style amoeba
bond_style class2
angle_style amoeba
dihedral_style none
# per-atom properties required by AMOEBA or HIPPO
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom i_amgroup d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
# read data file
read_data data.water_dimer.amoeba fix amtype NULL "Tinker Types"
# force field
pair_style amoeba
pair_coeff * * amoeba_water.prm amoeba_water.key
special_bonds lj/coul 0.5 0.5 0.5 one/five yes
# thermo output
compute virial all pressure NULL virial
thermo_style custom step temp epair ebond eangle edihed eimp &
emol etotal press c_virial[*]
dump 1 all custom 10 dump.water_dimer id type x y z fx fy fz
dump_modify 1 sort id
# zero step run
#run 0
# dynamics
fix 1 all nve
thermo 10
run 100

2
examples/amoeba/in.water_dimer.hippo
View File

@ -12,7 +12,7 @@ dihedral_style none
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom i_amgroup d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d_xaxis d_yaxis d_zaxis
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
# read data file

47
examples/amoeba/in.water_dimer.hippo.test
View File

@ -1,47 +0,0 @@
# water dimer with AMOEBA or HIPPO
units real
boundary s s s
atom_style amoeba
bond_style class2
angle_style amoeba
dihedral_style none
# per-atom properties required by AMOEBA or HIPPO
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom i_amgroup d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
# read data file
read_data data.water_dimer.hippo fix amtype NULL "Tinker Types"
# force field
pair_style hippo
pair_coeff * * hippo_water.prm hippo_water.key
special_bonds lj/coul 0.5 0.5 0.5 one/five yes
# thermo output
compute virial all pressure NULL virial
thermo_style custom step temp epair ebond eangle edihed eimp &
emol etotal press c_virial[*]
dump 1 all custom 10 dump.water_dimer id type x y z fx fy fz
dump_modify 1 sort id
# zero step run
#run 0
# dynamics
fix 1 all nve
thermo 10
run 100

2
examples/amoeba/in.water_hexamer.amoeba
View File

@ -12,7 +12,7 @@ dihedral_style none
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom i_amgroup d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d_xaxis d_yaxis d_zaxis
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
# read data file

47
examples/amoeba/in.water_hexamer.amoeba.test
View File

@ -1,47 +0,0 @@
# water hexamer with AMOEBA or HIPPO
units real
boundary s s s
atom_style amoeba
bond_style class2
angle_style amoeba
dihedral_style none
# per-atom properties required by AMOEBA or HIPPO
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom i_amgroup d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
# read data file
read_data data.water_hexamer.amoeba fix amtype NULL "Tinker Types"
# force field
pair_style amoeba
pair_coeff * * amoeba_water.prm amoeba_water.key
special_bonds lj/coul 0.5 0.5 0.5 one/five yes
# thermo output
compute virial all pressure NULL virial
thermo_style custom step temp epair ebond eangle edihed eimp &
emol etotal press c_virial[*]
dump 1 all custom 10 dump.water_hexamer id type x y z fx fy fz
dump_modify 1 sort id
# zero step run
#run 0
# dynamics
fix 1 all nve
thermo 10
run 100

2
examples/amoeba/in.water_hexamer.hippo
View File

@ -12,7 +12,7 @@ dihedral_style none
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom i_amgroup d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d_xaxis d_yaxis d_zaxis
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
# read data file

47
examples/amoeba/in.water_hexamer.hippo.test
View File

@ -1,47 +0,0 @@
# water hexamer with AMOEBA or HIPPO
units real
boundary s s s
atom_style amoeba
bond_style class2
angle_style amoeba
dihedral_style none
# per-atom properties required by AMOEBA or HIPPO
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom i_amgroup d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
# read data file
read_data data.water_hexamer.hippo fix amtype NULL "Tinker Types"
# force field
pair_style hippo
pair_coeff * * hippo_water.prm hippo_water.key
special_bonds lj/coul 0.5 0.5 0.5 one/five yes
# thermo output
compute virial all pressure NULL virial
thermo_style custom step temp epair ebond eangle edihed eimp &
emol etotal press c_virial[*]
dump 1 all custom 10 dump.water_hexamer id type x y z fx fy fz
dump_modify 1 sort id
# zero step run
#run 0
# dynamics
fix 1 all nve
thermo 10
run 100

48
examples/amoeba/log.ubi.1
View File

@ -15,15 +15,16 @@ improper_style amoeba
# per-atom properties required by AMOEBA or HIPPO
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom i_amgroup d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
fix pit all amoeba/pitorsion
fix_modify pit energy yes
fix bit all amoeba/bitorsion bitorsion.ubiquitin.data
fix_modify bit energy yes
fix extra all property/atom i_amgroup d_redID d_xaxis d_yaxis d_zaxis d_pval ghost yes
fix extra2 all property/atom i_polaxe
# read data file
#read_data data.ubiquitin fix amtype NULL "Tinker Types"
read_data data.ubiquitin fix amtype NULL "Tinker Types" fix pit "pitorsion types" "PiTorsion Coeffs" fix pit pitorsions PiTorsions fix bit bitorsions BiTorsions
Reading data file ...
orthogonal box = (0 0 0) to (54.99 41.91 41.91)
@ -54,7 +55,7 @@ Finding 1-2 1-3 1-4 neighbors ...
19 = max # of 1-4 neighbors
21 = max # of special neighbors
special bonds CPU = 0.004 seconds
read_data CPU = 0.075 seconds
read_data CPU = 0.082 seconds
pair_style amoeba
pair_coeff * * amoeba_ubiquitin.prm amoeba_ubiquitin.key
@ -109,7 +110,7 @@ Neighbor list info ...
stencil: half/bin/3d
bin: standard
AMOEBA/HIPPO group count: 3196
Per MPI rank memory allocation (min/avg/max) = 98.55 | 98.55 | 98.55 Mbytes
Per MPI rank memory allocation (min/avg/max) = 260.4 | 260.4 | 260.4 Mbytes
Step Temp E_pair E_bond E_angle E_dihed E_impro E_mol TotEng Press c_virial[1] c_virial[2] c_virial[3] c_virial[4] c_virial[5] c_virial[6]
0 0 -35338.057 2856.5938 1955.5431 224.37609 65.00809 5101.5211 -30247.585 -6336.5196 -5795.4272 -6329.8149 -6884.3167 349.52657 77.164877 652.41925
1 29.61379 -35356.153 2037.3541 1840.7883 223.90217 64.293945 4166.3385 -30341.522 -6486.773 -6452.8463 -6841.5982 -7386.1106 311.38025 120.72605 545.35513
@ -121,31 +122,30 @@ Per MPI rank memory allocation (min/avg/max) = 98.55 | 98.55 | 98.55 Mbytes
7 137.7204 -36521.444 782.87113 1026.745 212.04289 38.686259 2060.3452 -30479.082 -5987.83 -8386.8104 -7363.188 -7888.261 357.00835 253.66346 32.827786
8 112.66452 -36897.181 1750.0569 1269.152 210.83571 33.742799 3263.7874 -30379.432 -7886.4081 -9703.2601 -9043.015 -9555.2908 490.76046 182.31259 278.727
9 88.237359 -37209.906 2695.1766 1454.55 209.91331 29.503458 4389.1434 -30276.565 -8202.16 -9492.368 -9110.7037 -9639.2288 502.55699 107.82333 443.6705
AMEOBA/HIPPO timing info:
Init time: 0.0257147 0.00113515
Hal time: 7.6011 33.5542
Mpole time: 2.25841 9.96952
Induce time: 8.18934 36.151
Polar time: 4.5786 20.2117
Total time: 22.6532
10 108.86756 -37474.988 2240.4603 1523.7936 209.10313 26.208515 3999.5656 -30333.279 -8468.4347 -9956.923 -9709.5874 -10224.682 365.98214 95.262991 425.12746
Loop time of 22.6992 on 1 procs for 10 steps with 9737 atoms
Loop time of 21.791 on 1 procs for 10 steps with 9737 atoms
Performance: 0.038 ns/day, 630.534 hours/ns, 0.441 timesteps/s
98.8% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 0.040 ns/day, 605.307 hours/ns, 0.459 timesteps/s
99.1% CPU use with 1 MPI tasks x no OpenMP threads
AMEOBA/HIPPO timing breakdown:
Init time: 0.0264311 0.00121566
Hal time: 7.15654 32.9156
Mpole time: 2.14232 9.85334
Induce time: 7.99277 36.7617
Polar time: 4.42403 20.3477
Total time: 21.7421
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 22.653 | 22.653 | 22.653 | 0.0 | 99.80
Bond | 0.014323 | 0.014323 | 0.014323 | 0.0 | 0.06
Pair | 21.742 | 21.742 | 21.742 | 0.0 | 99.78
Bond | 0.014806 | 0.014806 | 0.014806 | 0.0 | 0.07
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0035064 | 0.0035064 | 0.0035064 | 0.0 | 0.02
Output | 0.024558 | 0.024558 | 0.024558 | 0.0 | 0.11
Modify | 0.002901 | 0.002901 | 0.002901 | 0.0 | 0.01
Other | | 0.0006384 | | | 0.00
Comm | 0.0035774 | 0.0035774 | 0.0035774 | 0.0 | 0.02
Output | 0.026947 | 0.026947 | 0.026947 | 0.0 | 0.12
Modify | 0.0028419 | 0.0028419 | 0.0028419 | 0.0 | 0.01
Other | | 0.0007034 | | | 0.00
Nlocal: 9737 ave 9737 max 9737 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -159,4 +159,4 @@ Ave neighs/atom = 579.16155
Ave special neighs/atom = 3.1364897
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:25
Total wall time: 0:00:24

162
examples/amoeba/log.ubi.1.test
View File

@ -1,162 +0,0 @@
LAMMPS (24 Mar 2022)
# solvated ubiquitin molecule with AMOEBA force field
units real
boundary p p p
atom_modify sort 0 0.0
atom_style amoeba
bond_style class2
angle_style amoeba
dihedral_style fourier
improper_style amoeba
# per-atom properties required by AMOEBA or HIPPO
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom i_amgroup d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
fix pit all amoeba/pitorsion
fix_modify pit energy yes
fix bit all amoeba/bitorsion bitorsion.ubiquitin.data
fix_modify bit energy yes
# read data file
read_data data.ubiquitin fix amtype NULL "Tinker Types" fix pit "pitorsion types" "PiTorsion Coeffs" fix pit pitorsions PiTorsions fix bit bitorsions BiTorsions
Reading data file ...
orthogonal box = (0 0 0) to (54.99 41.91 41.91)
1 by 1 by 1 MPI processor grid
reading atoms ...
9737 atoms
scanning bonds ...
4 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
18 = max dihedrals/atom
scanning impropers ...
3 = max impropers/atom
reading bonds ...
6908 bonds
reading angles ...
5094 angles
reading dihedrals ...
3297 dihedrals
reading impropers ...
651 impropers
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
4 = max # of 1-2 neighbors
9 = max # of 1-3 neighbors
19 = max # of 1-4 neighbors
21 = max # of special neighbors
special bonds CPU = 0.004 seconds
read_data CPU = 0.082 seconds
pair_style amoeba
pair_coeff * * amoeba_ubiquitin.prm amoeba_ubiquitin.key
special_bonds lj/coul 0.5 0.5 0.5 one/five yes
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0.5 0.5 0.5
special bond factors coul: 0.5 0.5 0.5
4 = max # of 1-2 neighbors
9 = max # of 1-3 neighbors
19 = max # of 1-4 neighbors
58 = max # of 1-5 neighbors
21 = max # of special neighbors
special bonds CPU = 0.006 seconds
# thermo output
compute virial all pressure NULL virial
thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*]
dump 1 all custom 10 dump.ubi id type x y z fx fy fz
dump_modify 1 sort id
# zero step run
#run 0
# dynamics
fix 1 all nve
thermo 1
run 10
AMOEBA/HIPPO force field settings
hal: cut 12 taper 10.8 vscale 0 0 1 1
multipole: cut 7 aewald 0.4 bsorder 5 FFT 60 48 48 mscale 0 0 0.4 1
polar: cut 7 aewald 0.5 bsorder 5 FFT 60 48 48
pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 1 1 1 1 d/u scale 0 1
precondition: cut 4.5
generated 0 of 15 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 8 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair amoeba, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
AMOEBA/HIPPO group count: 3196
Per MPI rank memory allocation (min/avg/max) = 260.4 | 260.4 | 260.4 Mbytes
Step Temp E_pair E_bond E_angle E_dihed E_impro E_mol TotEng Press c_virial[1] c_virial[2] c_virial[3] c_virial[4] c_virial[5] c_virial[6]
0 0 -35338.057 2856.5938 1955.5431 224.37609 65.00809 5101.5211 -30247.585 -6336.5196 -5795.4272 -6329.8149 -6884.3167 349.52657 77.164877 652.41925
1 29.61379 -35356.153 2037.3541 1840.7883 223.90217 64.293945 4166.3385 -30341.522 -6486.773 -6452.8463 -6841.5982 -7386.1106 311.38025 120.72605 545.35513
2 78.518242 -35383.65 825.39919 1538.3909 222.55095 62.191009 2648.5321 -30467.814 -5502.9841 -6410.2998 -6396.1829 -6937.8137 217.3515 210.76948 294.28051
3 88.8921 -35402.11 938.99299 1162.2914 220.5271 58.832521 2380.644 -30453.516 -1929.5417 -3331.1291 -2769.7218 -3350.5733 117.32302 279.72705 31.237776
4 68.740402 -35477.589 2048.0659 858.03795 218.14277 54.460022 3178.7066 -30316.325 2041.1138 594.25938 1665.7799 1030.8539 66.230421 304.28296 -155.80224
5 76.267862 -35707.869 2206.6534 736.37385 215.75693 49.401674 3208.1859 -30299.377 2276.9276 536.21124 1893.4621 1258.492 92.097191 299.65604 -228.58369
6 118.24373 -36092.77 1166.179 815.59206 213.67399 44.022297 2239.4673 -30435.629 -1677.8051 -3988.2428 -2669.6848 -3247.7207 197.42472 285.87129 -162.35459
7 137.7204 -36521.444 782.87113 1026.745 212.04289 38.686259 2060.3452 -30479.082 -5987.83 -8386.8104 -7363.188 -7888.261 357.00835 253.66346 32.827786
8 112.66452 -36897.181 1750.0569 1269.152 210.83571 33.742799 3263.7874 -30379.432 -7886.4081 -9703.2601 -9043.015 -9555.2908 490.76046 182.31259 278.727
9 88.237359 -37209.906 2695.1766 1454.55 209.91331 29.503458 4389.1434 -30276.565 -8202.16 -9492.368 -9110.7037 -9639.2288 502.55699 107.82333 443.6705
10 108.86756 -37474.988 2240.4603 1523.7936 209.10313 26.208515 3999.5656 -30333.279 -8468.4347 -9956.923 -9709.5874 -10224.682 365.98214 95.262991 425.12746
Loop time of 21.791 on 1 procs for 10 steps with 9737 atoms
Performance: 0.040 ns/day, 605.307 hours/ns, 0.459 timesteps/s
99.1% CPU use with 1 MPI tasks x no OpenMP threads
AMEOBA/HIPPO timing breakdown:
Init time: 0.0264311 0.00121566
Hal time: 7.15654 32.9156
Mpole time: 2.14232 9.85334
Induce time: 7.99277 36.7617
Polar time: 4.42403 20.3477
Total time: 21.7421
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 21.742 | 21.742 | 21.742 | 0.0 | 99.78
Bond | 0.014806 | 0.014806 | 0.014806 | 0.0 | 0.07
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0035774 | 0.0035774 | 0.0035774 | 0.0 | 0.02
Output | 0.026947 | 0.026947 | 0.026947 | 0.0 | 0.12
Modify | 0.0028419 | 0.0028419 | 0.0028419 | 0.0 | 0.01
Other | | 0.0007034 | | | 0.00
Nlocal: 9737 ave 9737 max 9737 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 31511 ave 31511 max 31511 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 5.6393e+06 ave 5.6393e+06 max 5.6393e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 5639296
Ave neighs/atom = 579.16155
Ave special neighs/atom = 3.1364897
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:24

48
examples/amoeba/log.ubi.32
View File

@ -15,15 +15,16 @@ improper_style amoeba
# per-atom properties required by AMOEBA or HIPPO
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom i_amgroup d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
fix pit all amoeba/pitorsion
fix_modify pit energy yes
fix bit all amoeba/bitorsion bitorsion.ubiquitin.data
fix_modify bit energy yes
fix extra all property/atom i_amgroup d_redID d_xaxis d_yaxis d_zaxis d_pval ghost yes
fix extra2 all property/atom i_polaxe
# read data file
#read_data data.ubiquitin fix amtype NULL "Tinker Types"
read_data data.ubiquitin fix amtype NULL "Tinker Types" fix pit "pitorsion types" "PiTorsion Coeffs" fix pit pitorsions PiTorsions fix bit bitorsions BiTorsions
Reading data file ...
orthogonal box = (0 0 0) to (54.99 41.91 41.91)
@ -54,7 +55,7 @@ Finding 1-2 1-3 1-4 neighbors ...
19 = max # of 1-4 neighbors
21 = max # of special neighbors
special bonds CPU = 0.002 seconds
read_data CPU = 0.125 seconds
read_data CPU = 0.112 seconds
pair_style amoeba
pair_coeff * * amoeba_ubiquitin.prm amoeba_ubiquitin.key
@ -109,7 +110,7 @@ Neighbor list info ...
stencil: half/bin/3d
bin: standard
AMOEBA/HIPPO group count: 3196
Per MPI rank memory allocation (min/avg/max) = 26.19 | 26.49 | 27.59 Mbytes
Per MPI rank memory allocation (min/avg/max) = 73.46 | 73.76 | 74.86 Mbytes
Step Temp E_pair E_bond E_angle E_dihed E_impro E_mol TotEng Press c_virial[1] c_virial[2] c_virial[3] c_virial[4] c_virial[5] c_virial[6]
0 0 -35338.057 2856.5938 1955.5431 224.37609 65.00809 5101.5211 -30247.585 -6336.5196 -5795.4272 -6329.8149 -6884.3167 349.52657 77.164877 652.41925
1 29.61379 -35356.153 2037.3541 1840.7883 223.90217 64.293945 4166.3385 -30341.522 -6486.773 -6452.8463 -6841.5982 -7386.1106 311.38025 120.72605 545.35513
@ -121,31 +122,30 @@ Per MPI rank memory allocation (min/avg/max) = 26.19 | 26.49 | 27.59 Mbytes
7 137.7204 -36521.444 782.87113 1026.745 212.04289 38.686259 2060.3452 -30479.082 -5987.83 -8386.8104 -7363.188 -7888.261 357.00835 253.66346 32.827786
8 112.66452 -36897.181 1750.0569 1269.152 210.83571 33.742799 3263.7874 -30379.432 -7886.4081 -9703.2601 -9043.015 -9555.2908 490.76046 182.31259 278.727
9 88.237359 -37209.906 2695.1766 1454.55 209.91331 29.503458 4389.1434 -30276.565 -8202.16 -9492.368 -9110.7037 -9639.2288 502.55699 107.82333 443.6705
AMEOBA/HIPPO timing info:
Init time: 0.0350369 0.0194083
Hal time: 0.274414 15.2009
Mpole time: 0.209885 11.6263
Induce time: 1.00414 55.6234
Polar time: 0.281769 15.6083
Total time: 1.80525
10 108.86756 -37474.988 2240.4603 1523.7936 209.10313 26.208515 3999.5656 -30333.279 -8468.4347 -9956.923 -9709.5874 -10224.682 365.98214 95.262991 425.12746
Loop time of 1.82311 on 32 procs for 10 steps with 9737 atoms
Loop time of 1.51355 on 32 procs for 10 steps with 9737 atoms
Performance: 0.474 ns/day, 50.642 hours/ns, 5.485 timesteps/s
99.1% CPU use with 32 MPI tasks x no OpenMP threads
Performance: 0.571 ns/day, 42.043 hours/ns, 6.607 timesteps/s
99.5% CPU use with 32 MPI tasks x no OpenMP threads
AMEOBA/HIPPO timing breakdown:
Init time: 0.0221241 0.0147382
Hal time: 0.27487 18.3107
Mpole time: 0.1964 13.0833
Induce time: 0.743514 49.5298
Polar time: 0.264231 17.602
Total time: 1.50114
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.805 | 1.8057 | 1.8065 | 0.0 | 99.05
Bond | 0.00027 | 0.00076775 | 0.0023491 | 0.0 | 0.04
Pair | 1.5006 | 1.5014 | 1.5026 | 0.1 | 99.20
Bond | 0.00023121 | 0.0006371 | 0.002095 | 0.0 | 0.04
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0098412 | 0.011853 | 0.013048 | 0.8 | 0.65
Output | 0.0038478 | 0.0041268 | 0.0045236 | 0.2 | 0.23
Modify | 0.00019451 | 0.00034384 | 0.00063207 | 0.0 | 0.02
Other | | 0.0003186 | | | 0.02
Comm | 0.0060146 | 0.008046 | 0.0092638 | 1.0 | 0.53
Output | 0.0028415 | 0.0030424 | 0.003441 | 0.2 | 0.20
Modify | 0.00011709 | 0.00019911 | 0.00036104 | 0.0 | 0.01
Other | | 0.0002509 | | | 0.02
Nlocal: 304.281 ave 326 max 273 min
Histogram: 1 1 0 5 2 8 3 6 4 2
@ -159,4 +159,4 @@ Ave neighs/atom = 579.16155
Ave special neighs/atom = 3.1364897
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:02
Total wall time: 0:00:01

162
examples/amoeba/log.ubi.32.test
View File

@ -1,162 +0,0 @@
LAMMPS (24 Mar 2022)
# solvated ubiquitin molecule with AMOEBA force field
units real
boundary p p p
atom_modify sort 0 0.0
atom_style amoeba
bond_style class2
angle_style amoeba
dihedral_style fourier
improper_style amoeba
# per-atom properties required by AMOEBA or HIPPO
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom i_amgroup d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
fix pit all amoeba/pitorsion
fix_modify pit energy yes
fix bit all amoeba/bitorsion bitorsion.ubiquitin.data
fix_modify bit energy yes
# read data file
read_data data.ubiquitin fix amtype NULL "Tinker Types" fix pit "pitorsion types" "PiTorsion Coeffs" fix pit pitorsions PiTorsions fix bit bitorsions BiTorsions
Reading data file ...
orthogonal box = (0 0 0) to (54.99 41.91 41.91)
4 by 2 by 4 MPI processor grid
reading atoms ...
9737 atoms
scanning bonds ...
4 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
18 = max dihedrals/atom
scanning impropers ...
3 = max impropers/atom
reading bonds ...
6908 bonds
reading angles ...
5094 angles
reading dihedrals ...
3297 dihedrals
reading impropers ...
651 impropers
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
4 = max # of 1-2 neighbors
9 = max # of 1-3 neighbors
19 = max # of 1-4 neighbors
21 = max # of special neighbors
special bonds CPU = 0.002 seconds
read_data CPU = 0.112 seconds
pair_style amoeba
pair_coeff * * amoeba_ubiquitin.prm amoeba_ubiquitin.key
special_bonds lj/coul 0.5 0.5 0.5 one/five yes
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0.5 0.5 0.5
special bond factors coul: 0.5 0.5 0.5
4 = max # of 1-2 neighbors
9 = max # of 1-3 neighbors
19 = max # of 1-4 neighbors
58 = max # of 1-5 neighbors
21 = max # of special neighbors
special bonds CPU = 0.002 seconds
# thermo output
compute virial all pressure NULL virial
thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*]
dump 1 all custom 10 dump.ubi id type x y z fx fy fz
dump_modify 1 sort id
# zero step run
#run 0
# dynamics
fix 1 all nve
thermo 1
run 10
AMOEBA/HIPPO force field settings
hal: cut 12 taper 10.8 vscale 0 0 1 1
multipole: cut 7 aewald 0.4 bsorder 5 FFT 60 48 48 mscale 0 0 0.4 1
polar: cut 7 aewald 0.5 bsorder 5 FFT 60 48 48
pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 1 1 1 1 d/u scale 0 1
precondition: cut 4.5
generated 0 of 15 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 8 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair amoeba, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
AMOEBA/HIPPO group count: 3196
Per MPI rank memory allocation (min/avg/max) = 73.46 | 73.76 | 74.86 Mbytes
Step Temp E_pair E_bond E_angle E_dihed E_impro E_mol TotEng Press c_virial[1] c_virial[2] c_virial[3] c_virial[4] c_virial[5] c_virial[6]
0 0 -35338.057 2856.5938 1955.5431 224.37609 65.00809 5101.5211 -30247.585 -6336.5196 -5795.4272 -6329.8149 -6884.3167 349.52657 77.164877 652.41925
1 29.61379 -35356.153 2037.3541 1840.7883 223.90217 64.293945 4166.3385 -30341.522 -6486.773 -6452.8463 -6841.5982 -7386.1106 311.38025 120.72605 545.35513
2 78.518242 -35383.65 825.39919 1538.3909 222.55095 62.191009 2648.5321 -30467.814 -5502.9841 -6410.2998 -6396.1829 -6937.8137 217.3515 210.76948 294.28051
3 88.8921 -35402.11 938.99299 1162.2914 220.5271 58.832521 2380.644 -30453.516 -1929.5417 -3331.1291 -2769.7218 -3350.5733 117.32302 279.72705 31.237776
4 68.740402 -35477.589 2048.0659 858.03795 218.14277 54.460022 3178.7066 -30316.325 2041.1138 594.25938 1665.7799 1030.8539 66.230421 304.28296 -155.80224
5 76.267862 -35707.869 2206.6534 736.37385 215.75693 49.401674 3208.1859 -30299.377 2276.9276 536.21124 1893.4621 1258.492 92.097191 299.65604 -228.58369
6 118.24373 -36092.77 1166.179 815.59206 213.67399 44.022297 2239.4673 -30435.629 -1677.8051 -3988.2428 -2669.6848 -3247.7207 197.42472 285.87129 -162.35459
7 137.7204 -36521.444 782.87113 1026.745 212.04289 38.686259 2060.3452 -30479.082 -5987.83 -8386.8104 -7363.188 -7888.261 357.00835 253.66346 32.827786
8 112.66452 -36897.181 1750.0569 1269.152 210.83571 33.742799 3263.7874 -30379.432 -7886.4081 -9703.2601 -9043.015 -9555.2908 490.76046 182.31259 278.727
9 88.237359 -37209.906 2695.1766 1454.55 209.91331 29.503458 4389.1434 -30276.565 -8202.16 -9492.368 -9110.7037 -9639.2288 502.55699 107.82333 443.6705
10 108.86756 -37474.988 2240.4603 1523.7936 209.10313 26.208515 3999.5656 -30333.279 -8468.4347 -9956.923 -9709.5874 -10224.682 365.98214 95.262991 425.12746
Loop time of 1.51355 on 32 procs for 10 steps with 9737 atoms
Performance: 0.571 ns/day, 42.043 hours/ns, 6.607 timesteps/s
99.5% CPU use with 32 MPI tasks x no OpenMP threads
AMEOBA/HIPPO timing breakdown:
Init time: 0.0221241 0.0147382
Hal time: 0.27487 18.3107
Mpole time: 0.1964 13.0833
Induce time: 0.743514 49.5298
Polar time: 0.264231 17.602
Total time: 1.50114
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.5006 | 1.5014 | 1.5026 | 0.1 | 99.20
Bond | 0.00023121 | 0.0006371 | 0.002095 | 0.0 | 0.04
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0060146 | 0.008046 | 0.0092638 | 1.0 | 0.53
Output | 0.0028415 | 0.0030424 | 0.003441 | 0.2 | 0.20
Modify | 0.00011709 | 0.00019911 | 0.00036104 | 0.0 | 0.01
Other | | 0.0002509 | | | 0.02
Nlocal: 304.281 ave 326 max 273 min
Histogram: 1 1 0 5 2 8 3 6 4 2
Nghost: 7618.59 ave 7678 max 7545 min
Histogram: 1 1 4 4 5 5 2 2 4 4
Neighs: 176228 ave 204476 max 149390 min
Histogram: 3 3 3 2 6 2 5 4 2 2
Total # of neighbors = 5639296
Ave neighs/atom = 579.16155
Ave special neighs/atom = 3.1364897
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:01

45
examples/amoeba/log.water_box.amoeba.1
View File

@ -12,8 +12,8 @@ dihedral_style none
# per-atom properties required by AMOEBA or HIPPO
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom i_amgroup d_redID d_xaxis d_yaxis d_zaxis d_pval ghost yes
fix extra2 all property/atom i_polaxe
fix extra all property/atom i_amgroup d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
# read data file
@ -39,7 +39,7 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.011 seconds
read_data CPU = 0.012 seconds
# force field
@ -96,7 +96,7 @@ Neighbor list info ...
stencil: half/bin/3d
bin: standard
AMOEBA/HIPPO group count: 216
Per MPI rank memory allocation (min/avg/max) = 10.9 | 10.9 | 10.9 Mbytes
Per MPI rank memory allocation (min/avg/max) = 58.28 | 58.28 | 58.28 Mbytes
Step Temp E_pair E_bond E_angle E_dihed E_impro E_mol TotEng Press c_virial[1] c_virial[2] c_virial[3] c_virial[4] c_virial[5] c_virial[6]
0 0 -2172.0441 166.82637 83.732524 0 0 250.5589 -1921.4852 -6181.7112 -4771.8292 -6955.3278 -6817.9765 -272.19746 3173.3487 2229.6526
10 105.50439 -2373.6865 136.67908 106.86552 0 0 243.54459 -1926.6678 -8441.2174 -10450.318 -9514.124 -9665.625 -301.45304 322.2435 1916.9694
@ -108,31 +108,30 @@ Per MPI rank memory allocation (min/avg/max) = 10.9 | 10.9 | 10.9 Mbytes
70 166.70629 -2383.4827 76.492455 55.020922 0 0 131.51338 -1930.4622 4743.9587 1916.6786 2839.9241 2670.7568 -169.67855 -187.58379 -2256.4529
80 171.82933 -2388.0347 76.463333 49.138785 0 0 125.60212 -1931.0453 2210.1222 -319.99043 330.98785 -394.25628 -44.858027 252.35533 -1985.0908
90 175.7327 -2423.7974 90.784969 63.725029 0 0 154.51 -1930.3722 -917.58179 -3941.9566 -2568.4278 -3415.3121 196.38051 2366.2885 -263.52434
AMEOBA/HIPPO timing info:
Init time: 0.0251099 0.000637177
Hal time: 0.924614 2.34626
Mpole time: 2.51306 6.37702
Induce time: 29.8839 75.8319
Polar time: 6.06136 15.381
Total time: 39.408
100 173.73319 -2422.3616 99.761403 57.29505 0 0 157.05645 -1930.2461 -3586.4169 -5733.9943 -5881.4025 -6235.1905 -230.75166 959.02899 406.2349
Loop time of 39.4372 on 1 procs for 100 steps with 648 atoms
Loop time of 38.7603 on 1 procs for 100 steps with 648 atoms
Performance: 0.219 ns/day, 109.548 hours/ns, 2.536 timesteps/s
Performance: 0.223 ns/day, 107.668 hours/ns, 2.580 timesteps/s
99.6% CPU use with 1 MPI tasks x no OpenMP threads
AMEOBA/HIPPO timing breakdown:
Init time: 0.0258209 0.000666708
Hal time: 0.889324 2.29628
Mpole time: 2.44816 6.32126
Induce time: 29.4141 75.9487
Polar time: 5.95145 15.3669
Total time: 38.7289
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 39.408 | 39.408 | 39.408 | 0.0 | 99.93
Bond | 0.0033709 | 0.0033709 | 0.0033709 | 0.0 | 0.01
Neigh | 0.0054251 | 0.0054251 | 0.0054251 | 0.0 | 0.01
Comm | 0.0035919 | 0.0035919 | 0.0035919 | 0.0 | 0.01
Output | 0.014523 | 0.014523 | 0.014523 | 0.0 | 0.04
Modify | 0.00095298 | 0.00095298 | 0.00095298 | 0.0 | 0.00
Other | | 0.001005 | | | 0.00
Pair | 38.729 | 38.729 | 38.729 | 0.0 | 99.92
Bond | 0.003226 | 0.003226 | 0.003226 | 0.0 | 0.01
Neigh | 0.0054679 | 0.0054679 | 0.0054679 | 0.0 | 0.01
Comm | 0.0036497 | 0.0036497 | 0.0036497 | 0.0 | 0.01
Output | 0.01663 | 0.01663 | 0.01663 | 0.0 | 0.04
Modify | 0.00088965 | 0.00088965 | 0.00088965 | 0.0 | 0.00
Other | | 0.001155 | | | 0.00
Nlocal: 648 ave 648 max 648 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -146,4 +145,4 @@ Ave neighs/atom = 152.07253
Ave special neighs/atom = 2
Neighbor list builds = 2
Dangerous builds = 0
Total wall time: 0:00:40
Total wall time: 0:00:39

148
examples/amoeba/log.water_box.amoeba.1.test
View File

@ -1,148 +0,0 @@
LAMMPS (24 Mar 2022)
# water box with AMOEBA or HIPPO
units real
boundary p p p
atom_style amoeba
bond_style class2
angle_style amoeba
dihedral_style none
# per-atom properties required by AMOEBA or HIPPO
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom i_amgroup d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
# read data file
read_data data.water_box.amoeba fix amtype NULL "Tinker Types"
Reading data file ...
orthogonal box = (0 0 0) to (18.643 18.643 18.643)
1 by 1 by 1 MPI processor grid
reading atoms ...
648 atoms
scanning bonds ...
2 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
432 bonds
reading angles ...
216 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.012 seconds
# force field
pair_style amoeba
pair_coeff * * amoeba_water.prm amoeba_water_box.key
special_bonds lj/coul 0.5 0.5 0.5 one/five yes
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0.5 0.5 0.5
special bond factors coul: 0.5 0.5 0.5
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of 1-5 neighbors
2 = max # of special neighbors
special bonds CPU = 0.001 seconds
# thermo output
compute virial all pressure NULL virial
thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*]
dump 1 all custom 10 dump.water_box id type x y z fx fy fz
dump_modify 1 sort id
# zero step run
#run 0
# dynamics
fix 1 all nve
thermo 10
run 100
AMOEBA/HIPPO force field settings
hal: cut 7 taper 6 vscale 0 0 1 1
multipole: cut 7 aewald 0.4 bsorder 5 FFT 50 50 50 mscale 0 0 0.4 1
polar: cut 7 aewald 0.5 bsorder 5 FFT 50 50 50
pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 1 1 1 1 d/u scale 0 1
precondition: cut 4.5
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 9
ghost atom cutoff = 9
binsize = 4.5, bins = 5 5 5
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair amoeba, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
AMOEBA/HIPPO group count: 216
Per MPI rank memory allocation (min/avg/max) = 58.28 | 58.28 | 58.28 Mbytes
Step Temp E_pair E_bond E_angle E_dihed E_impro E_mol TotEng Press c_virial[1] c_virial[2] c_virial[3] c_virial[4] c_virial[5] c_virial[6]
0 0 -2172.0441 166.82637 83.732524 0 0 250.5589 -1921.4852 -6181.7112 -4771.8292 -6955.3278 -6817.9765 -272.19746 3173.3487 2229.6526
10 105.50439 -2373.6865 136.67908 106.86552 0 0 243.54459 -1926.6678 -8441.2174 -10450.318 -9514.124 -9665.625 -301.45304 322.2435 1916.9694
20 143.90097 -2358.3516 70.951764 76.777106 0 0 147.72887 -1933.0976 -7370.463 -7728.4884 -11580.562 -8676.0017 -807.21546 780.4123 2096.7667
30 157.22768 -2375.4639 50.396281 87.108719 0 0 137.505 -1934.7321 -4449.9504 -6946.5881 -7865.3435 -4955.5443 -417.85139 -1004.0926 -36.630383
40 150.92709 -2354.1768 78.484257 53.799494 0 0 132.28375 -1930.8175 353.40845 -939.7978 -4636.1858 475.75837 -1074.4762 -1584.304 -574.27211
50 153.02614 -2388.7287 100.20124 65.814409 0 0 166.01565 -1927.5893 3975.1595 1366.008 426.2343 3887.1078 -1807.1658 -2534.8393 -2118.6912
60 155.01798 -2364.31 92.948309 44.252938 0 0 137.20125 -1928.1435 5793.7978 3521.2541 1421.9416 6110.7678 -1536.937 -2559.5674 -1502.2038
70 166.70629 -2383.4827 76.492455 55.020922 0 0 131.51338 -1930.4622 4743.9587 1916.6786 2839.9241 2670.7568 -169.67855 -187.58379 -2256.4529
80 171.82933 -2388.0347 76.463333 49.138785 0 0 125.60212 -1931.0453 2210.1222 -319.99043 330.98785 -394.25628 -44.858027 252.35533 -1985.0908
90 175.7327 -2423.7974 90.784969 63.725029 0 0 154.51 -1930.3722 -917.58179 -3941.9566 -2568.4278 -3415.3121 196.38051 2366.2885 -263.52434
100 173.73319 -2422.3616 99.761403 57.29505 0 0 157.05645 -1930.2461 -3586.4169 -5733.9943 -5881.4025 -6235.1905 -230.75166 959.02899 406.2349
Loop time of 38.7603 on 1 procs for 100 steps with 648 atoms
Performance: 0.223 ns/day, 107.668 hours/ns, 2.580 timesteps/s
99.6% CPU use with 1 MPI tasks x no OpenMP threads
AMEOBA/HIPPO timing breakdown:
Init time: 0.0258209 0.000666708
Hal time: 0.889324 2.29628
Mpole time: 2.44816 6.32126
Induce time: 29.4141 75.9487
Polar time: 5.95145 15.3669
Total time: 38.7289
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 38.729 | 38.729 | 38.729 | 0.0 | 99.92
Bond | 0.003226 | 0.003226 | 0.003226 | 0.0 | 0.01
Neigh | 0.0054679 | 0.0054679 | 0.0054679 | 0.0 | 0.01
Comm | 0.0036497 | 0.0036497 | 0.0036497 | 0.0 | 0.01
Output | 0.01663 | 0.01663 | 0.01663 | 0.0 | 0.04
Modify | 0.00088965 | 0.00088965 | 0.00088965 | 0.0 | 0.00
Other | | 0.001155 | | | 0.00
Nlocal: 648 ave 648 max 648 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4290 ave 4290 max 4290 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 98543 ave 98543 max 98543 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 98543
Ave neighs/atom = 152.07253
Ave special neighs/atom = 2
Neighbor list builds = 2
Dangerous builds = 0
Total wall time: 0:00:39

47
examples/amoeba/log.water_box.amoeba.32
View File

@ -12,8 +12,8 @@ dihedral_style none
# per-atom properties required by AMOEBA or HIPPO
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom i_amgroup d_redID d_xaxis d_yaxis d_zaxis d_pval ghost yes
fix extra2 all property/atom i_polaxe
fix extra all property/atom i_amgroup d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
# read data file
@ -39,7 +39,7 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.002 seconds
read_data CPU = 0.027 seconds
read_data CPU = 0.020 seconds
# force field
@ -55,7 +55,7 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-4 neighbors
2 = max # of 1-5 neighbors
2 = max # of special neighbors
special bonds CPU = 0.002 seconds
special bonds CPU = 0.001 seconds
# thermo output
@ -96,7 +96,7 @@ Neighbor list info ...
stencil: half/bin/3d
bin: standard
AMOEBA/HIPPO group count: 216
Per MPI rank memory allocation (min/avg/max) = 10.07 | 10.08 | 10.34 Mbytes
Per MPI rank memory allocation (min/avg/max) = 57.47 | 57.48 | 57.74 Mbytes
Step Temp E_pair E_bond E_angle E_dihed E_impro E_mol TotEng Press c_virial[1] c_virial[2] c_virial[3] c_virial[4] c_virial[5] c_virial[6]
0 0 -2172.0441 166.82637 83.732524 0 0 250.5589 -1921.4852 -6181.7112 -4771.8292 -6955.3278 -6817.9765 -272.19746 3173.3487 2229.6526
10 105.50439 -2373.6865 136.67908 106.86552 0 0 243.54459 -1926.6678 -8441.2174 -10450.318 -9514.124 -9665.625 -301.45304 322.2435 1916.9694
@ -108,31 +108,30 @@ Per MPI rank memory allocation (min/avg/max) = 10.07 | 10.08 | 10.34 Mbytes
70 166.70629 -2383.4827 76.492455 55.020922 0 0 131.51338 -1930.4622 4743.9587 1916.6786 2839.9241 2670.7568 -169.67855 -187.58379 -2256.4529
80 171.82933 -2388.0347 76.463333 49.138785 0 0 125.60212 -1931.0453 2210.1222 -319.99043 330.98785 -394.25628 -44.858027 252.35533 -1985.0908
90 175.7327 -2423.7974 90.784969 63.725029 0 0 154.51 -1930.3722 -917.58179 -3941.9566 -2568.4278 -3415.3121 196.38051 2366.2885 -263.52434
AMEOBA/HIPPO timing info:
Init time: 0.0525488 0.00776173
Hal time: 0.037136 0.548518
Mpole time: 0.586998 8.67026
Induce time: 5.01628 74.093
Polar time: 1.07725 15.9116
Total time: 6.77025
100 173.73319 -2422.3616 99.761403 57.29505 0 0 157.05645 -1930.2461 -3586.4169 -5733.9943 -5881.4025 -6235.1905 -230.75166 959.02899 406.2349
Loop time of 6.80378 on 32 procs for 100 steps with 648 atoms
Loop time of 6.48935 on 32 procs for 100 steps with 648 atoms
Performance: 1.270 ns/day, 18.899 hours/ns, 14.698 timesteps/s
99.7% CPU use with 32 MPI tasks x no OpenMP threads
Performance: 1.331 ns/day, 18.026 hours/ns, 15.410 timesteps/s
99.8% CPU use with 32 MPI tasks x no OpenMP threads
AMEOBA/HIPPO timing breakdown:
Init time: 0.0357484 0.00553355
Hal time: 0.0364815 0.564704
Mpole time: 0.541384 8.38018
Induce time: 4.89091 75.7073
Polar time: 0.955739 14.794
Total time: 6.46029
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 6.7643 | 6.7717 | 6.779 | 0.2 | 99.53
Bond | 0.00031311 | 0.00044449 | 0.00060974 | 0.0 | 0.01
Neigh | 0.00039627 | 0.00047385 | 0.00058355 | 0.0 | 0.01
Comm | 0.018079 | 0.025388 | 0.03285 | 2.6 | 0.37
Output | 0.0036767 | 0.0037103 | 0.0039596 | 0.1 | 0.05
Modify | 0.00040095 | 0.00049993 | 0.00061333 | 0.0 | 0.01
Other | | 0.001545 | | | 0.02
Pair | 6.4536 | 6.4614 | 6.4698 | 0.2 | 99.57
Bond | 0.00025488 | 0.00038243 | 0.00051904 | 0.0 | 0.01
Neigh | 0.00033789 | 0.00036365 | 0.00040331 | 0.0 | 0.01
Comm | 0.013439 | 0.021894 | 0.02956 | 2.9 | 0.34
Output | 0.0038126 | 0.0038325 | 0.0040712 | 0.1 | 0.06
Modify | 0.00021256 | 0.00028049 | 0.00035212 | 0.0 | 0.00
Other | | 0.001189 | | | 0.02
Nlocal: 20.25 ave 26 max 12 min
Histogram: 1 1 3 1 2 7 3 11 1 2

148
examples/amoeba/log.water_box.amoeba.32.test
View File

@ -1,148 +0,0 @@
LAMMPS (24 Mar 2022)
# water box with AMOEBA or HIPPO
units real
boundary p p p
atom_style amoeba
bond_style class2
angle_style amoeba
dihedral_style none
# per-atom properties required by AMOEBA or HIPPO
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom i_amgroup d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
# read data file
read_data data.water_box.amoeba fix amtype NULL "Tinker Types"
Reading data file ...
orthogonal box = (0 0 0) to (18.643 18.643 18.643)
2 by 4 by 4 MPI processor grid
reading atoms ...
648 atoms
scanning bonds ...
2 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
432 bonds
reading angles ...
216 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.002 seconds
read_data CPU = 0.020 seconds
# force field
pair_style amoeba
pair_coeff * * amoeba_water.prm amoeba_water_box.key
special_bonds lj/coul 0.5 0.5 0.5 one/five yes
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0.5 0.5 0.5
special bond factors coul: 0.5 0.5 0.5
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of 1-5 neighbors
2 = max # of special neighbors
special bonds CPU = 0.001 seconds
# thermo output
compute virial all pressure NULL virial
thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*]
dump 1 all custom 10 dump.water_box id type x y z fx fy fz
dump_modify 1 sort id
# zero step run
#run 0
# dynamics
fix 1 all nve
thermo 10
run 100
AMOEBA/HIPPO force field settings
hal: cut 7 taper 6 vscale 0 0 1 1
multipole: cut 7 aewald 0.4 bsorder 5 FFT 50 50 50 mscale 0 0 0.4 1
polar: cut 7 aewald 0.5 bsorder 5 FFT 50 50 50
pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 1 1 1 1 d/u scale 0 1
precondition: cut 4.5
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 9
ghost atom cutoff = 9
binsize = 4.5, bins = 5 5 5
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair amoeba, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
AMOEBA/HIPPO group count: 216
Per MPI rank memory allocation (min/avg/max) = 57.47 | 57.48 | 57.74 Mbytes
Step Temp E_pair E_bond E_angle E_dihed E_impro E_mol TotEng Press c_virial[1] c_virial[2] c_virial[3] c_virial[4] c_virial[5] c_virial[6]
0 0 -2172.0441 166.82637 83.732524 0 0 250.5589 -1921.4852 -6181.7112 -4771.8292 -6955.3278 -6817.9765 -272.19746 3173.3487 2229.6526
10 105.50439 -2373.6865 136.67908 106.86552 0 0 243.54459 -1926.6678 -8441.2174 -10450.318 -9514.124 -9665.625 -301.45304 322.2435 1916.9694
20 143.90097 -2358.3516 70.951764 76.777106 0 0 147.72887 -1933.0976 -7370.463 -7728.4884 -11580.562 -8676.0017 -807.21546 780.4123 2096.7667
30 157.22768 -2375.4639 50.396281 87.108719 0 0 137.505 -1934.7321 -4449.9504 -6946.5881 -7865.3435 -4955.5443 -417.85139 -1004.0926 -36.630383
40 150.92709 -2354.1768 78.484257 53.799494 0 0 132.28375 -1930.8175 353.40845 -939.7978 -4636.1858 475.75837 -1074.4762 -1584.304 -574.27211
50 153.02614 -2388.7287 100.20124 65.814409 0 0 166.01565 -1927.5893 3975.1595 1366.008 426.2343 3887.1078 -1807.1658 -2534.8393 -2118.6912
60 155.01798 -2364.31 92.948309 44.252938 0 0 137.20125 -1928.1435 5793.7978 3521.2541 1421.9416 6110.7678 -1536.937 -2559.5674 -1502.2038
70 166.70629 -2383.4827 76.492455 55.020922 0 0 131.51338 -1930.4622 4743.9587 1916.6786 2839.9241 2670.7568 -169.67855 -187.58379 -2256.4529
80 171.82933 -2388.0347 76.463333 49.138785 0 0 125.60212 -1931.0453 2210.1222 -319.99043 330.98785 -394.25628 -44.858027 252.35533 -1985.0908
90 175.7327 -2423.7974 90.784969 63.725029 0 0 154.51 -1930.3722 -917.58179 -3941.9566 -2568.4278 -3415.3121 196.38051 2366.2885 -263.52434
100 173.73319 -2422.3616 99.761403 57.29505 0 0 157.05645 -1930.2461 -3586.4169 -5733.9943 -5881.4025 -6235.1905 -230.75166 959.02899 406.2349
Loop time of 6.48935 on 32 procs for 100 steps with 648 atoms
Performance: 1.331 ns/day, 18.026 hours/ns, 15.410 timesteps/s
99.8% CPU use with 32 MPI tasks x no OpenMP threads
AMEOBA/HIPPO timing breakdown:
Init time: 0.0357484 0.00553355
Hal time: 0.0364815 0.564704
Mpole time: 0.541384 8.38018
Induce time: 4.89091 75.7073
Polar time: 0.955739 14.794
Total time: 6.46029
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 6.4536 | 6.4614 | 6.4698 | 0.2 | 99.57
Bond | 0.00025488 | 0.00038243 | 0.00051904 | 0.0 | 0.01
Neigh | 0.00033789 | 0.00036365 | 0.00040331 | 0.0 | 0.01
Comm | 0.013439 | 0.021894 | 0.02956 | 2.9 | 0.34
Output | 0.0038126 | 0.0038325 | 0.0040712 | 0.1 | 0.06
Modify | 0.00021256 | 0.00028049 | 0.00035212 | 0.0 | 0.00
Other | | 0.001189 | | | 0.02
Nlocal: 20.25 ave 26 max 12 min
Histogram: 1 1 3 1 2 7 3 11 1 2
Nghost: 1381.97 ave 1413 max 1354 min
Histogram: 3 5 4 0 6 3 1 4 5 1
Neighs: 3079.47 ave 4080 max 1858 min
Histogram: 1 3 1 2 5 6 7 5 0 2
Total # of neighbors = 98543
Ave neighs/atom = 152.07253
Ave special neighs/atom = 2
Neighbor list builds = 2
Dangerous builds = 0
Total wall time: 0:00:06

51
examples/amoeba/log.water_box.hippo.1
View File

@ -12,8 +12,8 @@ dihedral_style none
# per-atom properties required by AMOEBA or HIPPO
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom i_amgroup d_redID d_xaxis d_yaxis d_zaxis d_pval ghost yes
fix extra2 all property/atom i_polaxe
fix extra all property/atom i_amgroup d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
# read data file
@ -39,7 +39,7 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.010 seconds
read_data CPU = 0.012 seconds
# force field
@ -98,7 +98,7 @@ Neighbor list info ...
stencil: half/bin/3d
bin: standard
AMOEBA/HIPPO group count: 216
Per MPI rank memory allocation (min/avg/max) = 10.89 | 10.89 | 10.89 Mbytes
Per MPI rank memory allocation (min/avg/max) = 57.8 | 57.8 | 57.8 Mbytes
Step Temp E_pair E_bond E_angle E_dihed E_impro E_mol TotEng Press c_virial[1] c_virial[2] c_virial[3] c_virial[4] c_virial[5] c_virial[6]
0 0 -2188.594 166.82637 77.478353 0 0 244.30473 -1944.2893 -10859.589 -9285.4645 -11598.049 -11695.254 -282.7072 3164.4148 2495.2578
10 100.94691 -2350.192 116.13156 88.56605 0 0 204.69761 -1950.8098 -11480.919 -13574.139 -12190.797 -12798.212 -263.77028 280.62864 1974.1486
@ -110,33 +110,32 @@ Per MPI rank memory allocation (min/avg/max) = 10.89 | 10.89 | 10.89 Mbytes
70 184.86849 -2391.6106 39.916931 35.978152 0 0 75.895083 -1959.1811 -2146.9339 -4993.4021 -4095.6729 -4897.5768 -833.09046 1542.411 -1539.5266
80 164.75795 -2406.3017 101.94229 33.067832 0 0 135.01013 -1953.542 -8779.3265 -10545.409 -10418.702 -12098.858 -1319.194 1750.3511 -275.1272
90 151.17491 -2434.6876 152.21826 41.301673 0 0 193.51993 -1949.6141 -13330.691 -15436.505 -13791.461 -16934.674 149.25497 2289.1026 976.14333
AMEOBA/HIPPO timing info:
Init time: 0.0130348 0.00133126
Repls time: 1.10221 11.257
Disp time: 0.909199 9.28573
Mpole time: 1.75286 17.9021
Induce time: 3.46637 35.4024
Polar time: 2.22081 22.6813
Qxfer time: 0.326863 3.33828
Total time: 9.79136
100 166.99163 -2452.5298 143.57768 35.341459 0 0 178.91914 -1951.5533 -14918.51 -16077.49 -17353.738 -18140.466 19.009088 1487.0469 1084.0231
Loop time of 9.81706 on 1 procs for 100 steps with 648 atoms
Loop time of 9.27469 on 1 procs for 100 steps with 648 atoms
Performance: 0.880 ns/day, 27.270 hours/ns, 10.186 timesteps/s
98.8% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 0.932 ns/day, 25.763 hours/ns, 10.782 timesteps/s
99.0% CPU use with 1 MPI tasks x no OpenMP threads
AMEOBA/HIPPO timing breakdown:
Init time: 0.012403 0.00134127
Repulse time: 1.04474 11.2979
Disp time: 0.83125 8.98919
Mpole time: 1.66803 18.0382
Induce time: 3.2846 35.5199
Polar time: 2.12371 22.9659
Qxfer time: 0.282486 3.05482
Total time: 9.24722
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 9.7915 | 9.7915 | 9.7915 | 0.0 | 99.74
Bond | 0.0024566 | 0.0024566 | 0.0024566 | 0.0 | 0.03
Neigh | 0.0056616 | 0.0056616 | 0.0056616 | 0.0 | 0.06
Comm | 0.0022387 | 0.0022387 | 0.0022387 | 0.0 | 0.02
Output | 0.013878 | 0.013878 | 0.013878 | 0.0 | 0.14
Modify | 0.00062189 | 0.00062189 | 0.00062189 | 0.0 | 0.01
Other | | 0.0007035 | | | 0.01
Pair | 9.2473 | 9.2473 | 9.2473 | 0.0 | 99.70
Bond | 0.0023727 | 0.0023727 | 0.0023727 | 0.0 | 0.03
Neigh | 0.0055338 | 0.0055338 | 0.0055338 | 0.0 | 0.06
Comm | 0.0021428 | 0.0021428 | 0.0021428 | 0.0 | 0.02
Output | 0.016044 | 0.016044 | 0.016044 | 0.0 | 0.17
Modify | 0.00059122 | 0.00059122 | 0.00059122 | 0.0 | 0.01
Other | | 0.0006893 | | | 0.01
Nlocal: 648 ave 648 max 648 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -150,4 +149,4 @@ Ave neighs/atom = 151.99074
Ave special neighs/atom = 2
Neighbor list builds = 2
Dangerous builds = 0
Total wall time: 0:00:10
Total wall time: 0:00:09

152
examples/amoeba/log.water_box.hippo.1.test
View File

@ -1,152 +0,0 @@
LAMMPS (24 Mar 2022)
# water box with AMOEBA or HIPPO
units real
boundary p p p
atom_style amoeba
bond_style class2
angle_style amoeba
dihedral_style none
# per-atom properties required by AMOEBA or HIPPO
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom i_amgroup d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
# read data file
read_data data.water_box.hippo fix amtype NULL "Tinker Types"
Reading data file ...
orthogonal box = (0 0 0) to (18.643 18.643 18.643)
1 by 1 by 1 MPI processor grid
reading atoms ...
648 atoms
scanning bonds ...
2 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
432 bonds
reading angles ...
216 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.012 seconds
# force field
pair_style hippo
pair_coeff * * hippo_water.prm hippo_water_box.key
special_bonds lj/coul 0.5 0.5 0.5 one/five yes
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0.5 0.5 0.5
special bond factors coul: 0.5 0.5 0.5
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of 1-5 neighbors
2 = max # of special neighbors
special bonds CPU = 0.001 seconds
# thermo output
compute virial all pressure NULL virial
thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*]
dump 1 all custom 10 dump.water_box id type x y z fx fy fz
dump_modify 1 sort id
# zero step run
#run 0
# dynamics
fix 1 all nve
thermo 10
run 100
AMOEBA/HIPPO force field settings
repulsion: cut 7 taper 6 rscale 0 0 1 1
qxfer: cut 7 taper 6 mscale 0 0 0.4 1
dispersion: cut 7 aewald 0.45 bsorder 4 FFT 16 16 16 dspscale 0 0 0.4 1
multipole: cut 7 aewald 0.4 bsorder 5 FFT 24 24 24 mscale 0 0 0.4 1
polar: cut 7 aewald 0.5 bsorder 5 FFT 24 24 24
pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 0.2 1 1 1 d/u scale 0 1
precondition: cut 4.5
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 9
ghost atom cutoff = 9
binsize = 4.5, bins = 5 5 5
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair hippo, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
AMOEBA/HIPPO group count: 216
Per MPI rank memory allocation (min/avg/max) = 57.8 | 57.8 | 57.8 Mbytes
Step Temp E_pair E_bond E_angle E_dihed E_impro E_mol TotEng Press c_virial[1] c_virial[2] c_virial[3] c_virial[4] c_virial[5] c_virial[6]
0 0 -2188.594 166.82637 77.478353 0 0 244.30473 -1944.2893 -10859.589 -9285.4645 -11598.049 -11695.254 -282.7072 3164.4148 2495.2578
10 100.94691 -2350.192 116.13156 88.56605 0 0 204.69761 -1950.8098 -11480.919 -13574.139 -12190.797 -12798.212 -263.77028 280.62864 1974.1486
20 153.91622 -2358.3058 36.396961 66.22466 0 0 102.62162 -1958.8438 -7778.4529 -8492.3868 -11999.431 -9125.9998 -917.99962 589.09064 1788.2094
30 145.5951 -2343.9956 39.651541 65.833248 0 0 105.48479 -1957.7184 -288.79965 -2574.4466 -3820.4824 -414.28285 -347.51491 -1147.3995 -126.71025
40 126.87801 -2340.2623 102.93951 43.896946 0 0 146.83646 -1948.7309 6766.15 5908.7048 1280.0961 7930.8191 -1085.6811 -1596.6859 -714.82888
50 134.52078 -2358.9232 107.49288 44.253826 0 0 151.74671 -1947.7419 8762.4348 6023.4661 5377.0189 9396.0316 -1629.1364 -1663.1666 -2381.51
60 173.10181 -2374.3854 51.097314 33.03646 0 0 84.133774 -1956.4102 4614.2907 1719.1989 505.79149 4552.3167 -1661.1714 -587.92108 -1380.6732
70 184.86849 -2391.6106 39.916931 35.978152 0 0 75.895083 -1959.1811 -2146.9339 -4993.4021 -4095.6729 -4897.5768 -833.09046 1542.411 -1539.5266
80 164.75795 -2406.3017 101.94229 33.067832 0 0 135.01013 -1953.542 -8779.3265 -10545.409 -10418.702 -12098.858 -1319.194 1750.3511 -275.1272
90 151.17491 -2434.6876 152.21826 41.301673 0 0 193.51993 -1949.6141 -13330.691 -15436.505 -13791.461 -16934.674 149.25497 2289.1026 976.14333
100 166.99163 -2452.5298 143.57768 35.341459 0 0 178.91914 -1951.5533 -14918.51 -16077.49 -17353.738 -18140.466 19.009088 1487.0469 1084.0231
Loop time of 9.27469 on 1 procs for 100 steps with 648 atoms
Performance: 0.932 ns/day, 25.763 hours/ns, 10.782 timesteps/s
99.0% CPU use with 1 MPI tasks x no OpenMP threads
AMEOBA/HIPPO timing breakdown:
Init time: 0.012403 0.00134127
Repulse time: 1.04474 11.2979
Disp time: 0.83125 8.98919
Mpole time: 1.66803 18.0382
Induce time: 3.2846 35.5199
Polar time: 2.12371 22.9659
Qxfer time: 0.282486 3.05482
Total time: 9.24722
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 9.2473 | 9.2473 | 9.2473 | 0.0 | 99.70
Bond | 0.0023727 | 0.0023727 | 0.0023727 | 0.0 | 0.03
Neigh | 0.0055338 | 0.0055338 | 0.0055338 | 0.0 | 0.06
Comm | 0.0021428 | 0.0021428 | 0.0021428 | 0.0 | 0.02
Output | 0.016044 | 0.016044 | 0.016044 | 0.0 | 0.17
Modify | 0.00059122 | 0.00059122 | 0.00059122 | 0.0 | 0.01
Other | | 0.0006893 | | | 0.01
Nlocal: 648 ave 648 max 648 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4282 ave 4282 max 4282 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 98490 ave 98490 max 98490 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 98490
Ave neighs/atom = 151.99074
Ave special neighs/atom = 2
Neighbor list builds = 2
Dangerous builds = 0
Total wall time: 0:00:09

49
examples/amoeba/log.water_box.hippo.32
View File

@ -12,8 +12,8 @@ dihedral_style none
# per-atom properties required by AMOEBA or HIPPO
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom i_amgroup d_redID d_xaxis d_yaxis d_zaxis d_pval ghost yes
fix extra2 all property/atom i_polaxe
fix extra all property/atom i_amgroup d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
# read data file
@ -39,7 +39,7 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.002 seconds
read_data CPU = 0.027 seconds
read_data CPU = 0.020 seconds
# force field
@ -98,7 +98,7 @@ Neighbor list info ...
stencil: half/bin/3d
bin: standard
AMOEBA/HIPPO group count: 216
Per MPI rank memory allocation (min/avg/max) = 10.07 | 10.08 | 10.34 Mbytes
Per MPI rank memory allocation (min/avg/max) = 57.03 | 57.04 | 57.3 Mbytes
Step Temp E_pair E_bond E_angle E_dihed E_impro E_mol TotEng Press c_virial[1] c_virial[2] c_virial[3] c_virial[4] c_virial[5] c_virial[6]
0 0 -2188.594 166.82637 77.478353 0 0 244.30473 -1944.2893 -10859.589 -9285.4645 -11598.049 -11695.254 -282.7072 3164.4148 2495.2578
10 100.94691 -2350.192 116.13156 88.56605 0 0 204.69761 -1950.8098 -11480.919 -13574.139 -12190.797 -12798.212 -263.77028 280.62864 1974.1486
@ -110,33 +110,32 @@ Per MPI rank memory allocation (min/avg/max) = 10.07 | 10.08 | 10.34 Mbytes
70 184.86849 -2391.6106 39.916931 35.978152 0 0 75.895083 -1959.1811 -2146.9339 -4993.4021 -4095.6729 -4897.5768 -833.09046 1542.411 -1539.5266
80 164.75795 -2406.3017 101.94229 33.067832 0 0 135.01013 -1953.542 -8779.3265 -10545.409 -10418.702 -12098.858 -1319.194 1750.3511 -275.1272
90 151.17491 -2434.6876 152.21826 41.301673 0 0 193.51993 -1949.6141 -13330.691 -15436.505 -13791.461 -16934.674 149.25497 2289.1026 976.14333
AMEOBA/HIPPO timing info:
Init time: 0.0225211 0.0138448
Repls time: 0.0710727 4.36919
Disp time: 0.147228 9.05085
Mpole time: 0.271419 16.6855
Induce time: 0.760323 46.7408
Polar time: 0.341361 20.9851
Qxfer time: 0.0127489 0.783737
Total time: 1.62668
100 166.99163 -2452.5298 143.57768 35.341459 0 0 178.91914 -1951.5533 -14918.51 -16077.49 -17353.738 -18140.466 19.009088 1487.0469 1084.0231
Loop time of 1.65072 on 32 procs for 100 steps with 648 atoms
Loop time of 1.60312 on 32 procs for 100 steps with 648 atoms
Performance: 5.234 ns/day, 4.585 hours/ns, 60.579 timesteps/s
99.7% CPU use with 32 MPI tasks x no OpenMP threads
Performance: 5.389 ns/day, 4.453 hours/ns, 62.378 timesteps/s
99.8% CPU use with 32 MPI tasks x no OpenMP threads
AMEOBA/HIPPO timing breakdown:
Init time: 0.019742 0.012493
Repulse time: 0.0675395 4.27399
Disp time: 0.142632 9.02596
Mpole time: 0.265051 16.7728
Induce time: 0.740525 46.8614
Polar time: 0.332551 21.0442
Qxfer time: 0.0121995 0.772001
Total time: 1.58025
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.6233 | 1.6277 | 1.632 | 0.2 | 98.61
Bond | 0.0001841 | 0.00025145 | 0.00041274 | 0.0 | 0.02
Neigh | 0.00046301 | 0.00052361 | 0.00059181 | 0.0 | 0.03
Comm | 0.013032 | 0.017446 | 0.021961 | 1.7 | 1.06
Output | 0.0035779 | 0.0036051 | 0.0038143 | 0.1 | 0.22
Modify | 0.00011362 | 0.00018386 | 0.0002631 | 0.0 | 0.01
Other | | 0.0009717 | | | 0.06
Pair | 1.5773 | 1.5814 | 1.5855 | 0.2 | 98.65
Bond | 0.00015755 | 0.00023663 | 0.0003199 | 0.0 | 0.01
Neigh | 0.00036065 | 0.00038248 | 0.00042908 | 0.0 | 0.02
Comm | 0.01209 | 0.016226 | 0.020477 | 1.7 | 1.01
Output | 0.0037797 | 0.0038027 | 0.0040217 | 0.1 | 0.24
Modify | 0.00010094 | 0.00013624 | 0.00018983 | 0.0 | 0.01
Other | | 0.0008996 | | | 0.06
Nlocal: 20.25 ave 27 max 12 min
Histogram: 1 1 3 1 6 2 10 4 2 2

152
examples/amoeba/log.water_box.hippo.32.test
View File

@ -1,152 +0,0 @@
LAMMPS (24 Mar 2022)
# water box with AMOEBA or HIPPO
units real
boundary p p p
atom_style amoeba
bond_style class2
angle_style amoeba
dihedral_style none
# per-atom properties required by AMOEBA or HIPPO
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom i_amgroup d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
# read data file
read_data data.water_box.hippo fix amtype NULL "Tinker Types"
Reading data file ...
orthogonal box = (0 0 0) to (18.643 18.643 18.643)
2 by 4 by 4 MPI processor grid
reading atoms ...
648 atoms
scanning bonds ...
2 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
432 bonds
reading angles ...
216 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.002 seconds
read_data CPU = 0.020 seconds
# force field
pair_style hippo
pair_coeff * * hippo_water.prm hippo_water_box.key
special_bonds lj/coul 0.5 0.5 0.5 one/five yes
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0.5 0.5 0.5
special bond factors coul: 0.5 0.5 0.5
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of 1-5 neighbors
2 = max # of special neighbors
special bonds CPU = 0.002 seconds
# thermo output
compute virial all pressure NULL virial
thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*]
dump 1 all custom 10 dump.water_box id type x y z fx fy fz
dump_modify 1 sort id
# zero step run
#run 0
# dynamics
fix 1 all nve
thermo 10
run 100
AMOEBA/HIPPO force field settings
repulsion: cut 7 taper 6 rscale 0 0 1 1
qxfer: cut 7 taper 6 mscale 0 0 0.4 1
dispersion: cut 7 aewald 0.45 bsorder 4 FFT 16 16 16 dspscale 0 0 0.4 1
multipole: cut 7 aewald 0.4 bsorder 5 FFT 24 24 24 mscale 0 0 0.4 1
polar: cut 7 aewald 0.5 bsorder 5 FFT 24 24 24
pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 0.2 1 1 1 d/u scale 0 1
precondition: cut 4.5
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 9
ghost atom cutoff = 9
binsize = 4.5, bins = 5 5 5
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair hippo, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
AMOEBA/HIPPO group count: 216
Per MPI rank memory allocation (min/avg/max) = 57.03 | 57.04 | 57.3 Mbytes
Step Temp E_pair E_bond E_angle E_dihed E_impro E_mol TotEng Press c_virial[1] c_virial[2] c_virial[3] c_virial[4] c_virial[5] c_virial[6]
0 0 -2188.594 166.82637 77.478353 0 0 244.30473 -1944.2893 -10859.589 -9285.4645 -11598.049 -11695.254 -282.7072 3164.4148 2495.2578
10 100.94691 -2350.192 116.13156 88.56605 0 0 204.69761 -1950.8098 -11480.919 -13574.139 -12190.797 -12798.212 -263.77028 280.62864 1974.1486
20 153.91622 -2358.3058 36.396961 66.22466 0 0 102.62162 -1958.8438 -7778.4529 -8492.3868 -11999.431 -9125.9998 -917.99962 589.09064 1788.2094
30 145.5951 -2343.9956 39.651541 65.833248 0 0 105.48479 -1957.7184 -288.79965 -2574.4466 -3820.4824 -414.28285 -347.51491 -1147.3995 -126.71025
40 126.87801 -2340.2623 102.93951 43.896946 0 0 146.83646 -1948.7309 6766.15 5908.7048 1280.0961 7930.8191 -1085.6811 -1596.6859 -714.82888
50 134.52078 -2358.9232 107.49288 44.253826 0 0 151.74671 -1947.7419 8762.4348 6023.4661 5377.0189 9396.0316 -1629.1364 -1663.1666 -2381.51
60 173.10181 -2374.3854 51.097314 33.03646 0 0 84.133774 -1956.4102 4614.2907 1719.1989 505.79149 4552.3167 -1661.1714 -587.92108 -1380.6732
70 184.86849 -2391.6106 39.916931 35.978152 0 0 75.895083 -1959.1811 -2146.9339 -4993.4021 -4095.6729 -4897.5768 -833.09046 1542.411 -1539.5266
80 164.75795 -2406.3017 101.94229 33.067832 0 0 135.01013 -1953.542 -8779.3265 -10545.409 -10418.702 -12098.858 -1319.194 1750.3511 -275.1272
90 151.17491 -2434.6876 152.21826 41.301673 0 0 193.51993 -1949.6141 -13330.691 -15436.505 -13791.461 -16934.674 149.25497 2289.1026 976.14333
100 166.99163 -2452.5298 143.57768 35.341459 0 0 178.91914 -1951.5533 -14918.51 -16077.49 -17353.738 -18140.466 19.009088 1487.0469 1084.0231
Loop time of 1.60312 on 32 procs for 100 steps with 648 atoms
Performance: 5.389 ns/day, 4.453 hours/ns, 62.378 timesteps/s
99.8% CPU use with 32 MPI tasks x no OpenMP threads
AMEOBA/HIPPO timing breakdown:
Init time: 0.019742 0.012493
Repulse time: 0.0675395 4.27399
Disp time: 0.142632 9.02596
Mpole time: 0.265051 16.7728
Induce time: 0.740525 46.8614
Polar time: 0.332551 21.0442
Qxfer time: 0.0121995 0.772001
Total time: 1.58025
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.5773 | 1.5814 | 1.5855 | 0.2 | 98.65
Bond | 0.00015755 | 0.00023663 | 0.0003199 | 0.0 | 0.01
Neigh | 0.00036065 | 0.00038248 | 0.00042908 | 0.0 | 0.02
Comm | 0.01209 | 0.016226 | 0.020477 | 1.7 | 1.01
Output | 0.0037797 | 0.0038027 | 0.0040217 | 0.1 | 0.24
Modify | 0.00010094 | 0.00013624 | 0.00018983 | 0.0 | 0.01
Other | | 0.0008996 | | | 0.06
Nlocal: 20.25 ave 27 max 12 min
Histogram: 1 1 3 1 6 2 10 4 2 2
Nghost: 1379.75 ave 1408 max 1345 min
Histogram: 2 4 1 3 3 4 4 3 2 6
Neighs: 3077.81 ave 4233 max 1858 min
Histogram: 1 3 1 4 5 7 6 2 1 2
Total # of neighbors = 98490
Ave neighs/atom = 151.99074
Ave special neighs/atom = 2
Neighbor list builds = 2
Dangerous builds = 0
Total wall time: 0:00:01

43
examples/amoeba/log.water_dimer.amoeba.1
View File

@ -12,8 +12,8 @@ dihedral_style none
# per-atom properties required by AMOEBA or HIPPO
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom i_amgroup d_redID d_xaxis d_yaxis d_zaxis d_pval ghost yes
fix extra2 all property/atom i_polaxe
fix extra all property/atom i_amgroup d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
# read data file
@ -39,7 +39,7 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.007 seconds
read_data CPU = 0.008 seconds
# force field
@ -97,7 +97,7 @@ Neighbor list info ...
bin: standard
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:974)
AMOEBA/HIPPO group count: 2
Per MPI rank memory allocation (min/avg/max) = 9.855 | 9.855 | 9.855 Mbytes
Per MPI rank memory allocation (min/avg/max) = 49.59 | 49.59 | 49.59 Mbytes
Step Temp E_pair E_bond E_angle E_dihed E_impro E_mol TotEng Press c_virial[1] c_virial[2] c_virial[3] c_virial[4] c_virial[5] c_virial[6]
0 0 -5.1627563 0.025695395 0.71581114 0 0 0.74150653 -4.4212497 -12260.522 -43226.042 39448.214 -33003.739 -85.160886 -28101.905 -72.971988
10 1.1174766 -4.7928792 0.045080327 0.30848527 0 0 0.35356559 -4.4226587 -14728.416 11456.119 -52592.829 -3262.8454 70.868937 29494.268 57.977562
@ -109,31 +109,30 @@ Per MPI rank memory allocation (min/avg/max) = 9.855 | 9.855 | 9.855 Mbytes
70 10.385926 -4.8250769 0.022572262 0.22235766 0 0 0.24492992 -4.4253547 -1117.3665 19070.918 -36063.612 11648.813 61.067533 25754.59 53.919881
80 12.797691 -5.123735 0.023756795 0.48275385 0 0 0.50651065 -4.4264869 -6491.9826 -28436.037 20681.908 -14176.121 -64.024669 -35737.052 -52.583533
90 12.569481 -4.8303379 0.060369422 0.15670502 0 0 0.21707444 -4.4259273 -16762.536 1720.5855 -47624.986 -6793.7441 59.966729 30024.566 52.339671
AMEOBA/HIPPO timing info:
Init time: 0.000126119 0.0205557
Hal time: 0.000487693 7.94875
Mpole time: 0.00066233 10.7951
Induce time: 0.00328101 53.4761
Polar time: 0.0015627 25.4699
Total time: 0.00613547
100 17.750788 -5.1195235 0.039885925 0.38711474 0 0 0.42700067 -4.4279642 -10817.92 -21833.456 4186.8301 -18211.329 -43.11086 -32664.671 -41.508916
Loop time of 0.00720187 on 1 procs for 100 steps with 6 atoms
Loop time of 0.00655818 on 1 procs for 100 steps with 6 atoms
Performance: 1199.688 ns/day, 0.020 hours/ns, 13885.283 timesteps/s
83.0% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 1317.439 ns/day, 0.018 hours/ns, 15248.138 timesteps/s
98.5% CPU use with 1 MPI tasks x no OpenMP threads
AMEOBA/HIPPO timing breakdown:
Init time: 0.000126483 0.0233682
Hal time: 0.000471055 8.70292
Mpole time: 0.000619314 11.4421
Induce time: 0.00270856 50.0417
Polar time: 0.00147122 27.1814
Total time: 0.00541261
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0062208 | 0.0062208 | 0.0062208 | 0.0 | 86.38
Bond | 0.00010381 | 0.00010381 | 0.00010381 | 0.0 | 1.44
Pair | 0.005443 | 0.005443 | 0.005443 | 0.0 | 83.00
Bond | 9.6579e-05 | 9.6579e-05 | 9.6579e-05 | 0.0 | 1.47
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 1.4955e-05 | 1.4955e-05 | 1.4955e-05 | 0.0 | 0.21
Output | 0.00075216 | 0.00075216 | 0.00075216 | 0.0 | 10.44
Modify | 4.5409e-05 | 4.5409e-05 | 4.5409e-05 | 0.0 | 0.63
Other | | 6.472e-05 | | | 0.90
Comm | 1.7434e-05 | 1.7434e-05 | 1.7434e-05 | 0.0 | 0.27
Output | 0.0008951 | 0.0008951 | 0.0008951 | 0.0 | 13.65
Modify | 5.161e-05 | 5.161e-05 | 5.161e-05 | 0.0 | 0.79
Other | | 5.444e-05 | | | 0.83
Nlocal: 6 ave 6 max 6 min
Histogram: 1 0 0 0 0 0 0 0 0 0

149
examples/amoeba/log.water_dimer.amoeba.1.test
View File

@ -1,149 +0,0 @@
LAMMPS (24 Mar 2022)
# water dimer with AMOEBA or HIPPO
units real
boundary s s s
atom_style amoeba
bond_style class2
angle_style amoeba
dihedral_style none
# per-atom properties required by AMOEBA or HIPPO
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom i_amgroup d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
# read data file
read_data data.water_dimer.amoeba fix amtype NULL "Tinker Types"
Reading data file ...
orthogonal box = (-1.463996 -0.756549 -0.009705) to (0.933234 0.75612 2.935934)
1 by 1 by 1 MPI processor grid
reading atoms ...
6 atoms
scanning bonds ...
2 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
4 bonds
reading angles ...
2 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.008 seconds
# force field
pair_style amoeba
pair_coeff * * amoeba_water.prm amoeba_water.key
special_bonds lj/coul 0.5 0.5 0.5 one/five yes
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0.5 0.5 0.5
special bond factors coul: 0.5 0.5 0.5
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of 1-5 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
# thermo output
compute virial all pressure NULL virial
thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*]
dump 1 all custom 10 dump.water_dimer id type x y z fx fy fz
dump_modify 1 sort id
# zero step run
#run 0
# dynamics
fix 1 all nve
thermo 10
run 100
AMOEBA/HIPPO force field settings
hal: cut 10 taper 8 vscale 0 0 1 1
multipole: cut 10 aewald 0 mscale 0 0 0.4 1
polar: cut 10 aewald 0
pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 1 1 1 1 d/u scale 0 1
precondition: cut 4.5
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair amoeba, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:974)
AMOEBA/HIPPO group count: 2
Per MPI rank memory allocation (min/avg/max) = 49.59 | 49.59 | 49.59 Mbytes
Step Temp E_pair E_bond E_angle E_dihed E_impro E_mol TotEng Press c_virial[1] c_virial[2] c_virial[3] c_virial[4] c_virial[5] c_virial[6]
0 0 -5.1627563 0.025695395 0.71581114 0 0 0.74150653 -4.4212497 -12260.522 -43226.042 39448.214 -33003.739 -85.160886 -28101.905 -72.971988
10 1.1174766 -4.7928792 0.045080327 0.30848527 0 0 0.35356559 -4.4226587 -14728.416 11456.119 -52592.829 -3262.8454 70.868937 29494.268 57.977562
20 3.0821934 -5.1387316 0.013108182 0.65694692 0 0 0.6700551 -4.4227393 3007.4148 -25925.326 49641.41 -15284.933 -79.726771 -29005.234 -68.530079
30 3.461967 -4.8079248 0.013888863 0.31895667 0 0 0.33284554 -4.423482 8616.211 40027.877 -31134.295 16291.126 72.510013 23088.238 51.407946
40 4.2181367 -5.0535921 0.0099009766 0.55796811 0 0 0.56786908 -4.4228557 24239.885 -5761.6967 62095.735 15576.675 -76.240192 -33057.385 -58.850871
50 5.216657 -4.8012751 0.0053003148 0.29489399 0 0 0.30019431 -4.4233315 17728.056 44785.731 -21215.714 28613.715 66.24671 20292.137 51.010856
60 9.45101 -5.0818046 0.0043357361 0.5118733 0 0 0.51620903 -4.4247372 16893.135 -15068.961 50111.11 13824.77 -75.966047 -34809.168 -52.83183
70 10.385926 -4.8250769 0.022572262 0.22235766 0 0 0.24492992 -4.4253547 -1117.3665 19070.918 -36063.612 11648.813 61.067533 25754.59 53.919881
80 12.797691 -5.123735 0.023756795 0.48275385 0 0 0.50651065 -4.4264869 -6491.9826 -28436.037 20681.908 -14176.121 -64.024669 -35737.052 -52.583533
90 12.569481 -4.8303379 0.060369422 0.15670502 0 0 0.21707444 -4.4259273 -16762.536 1720.5855 -47624.986 -6793.7441 59.966729 30024.566 52.339671
100 17.750788 -5.1195235 0.039885925 0.38711474 0 0 0.42700067 -4.4279642 -10817.92 -21833.456 4186.8301 -18211.329 -43.11086 -32664.671 -41.508916
Loop time of 0.00655818 on 1 procs for 100 steps with 6 atoms
Performance: 1317.439 ns/day, 0.018 hours/ns, 15248.138 timesteps/s
98.5% CPU use with 1 MPI tasks x no OpenMP threads
AMEOBA/HIPPO timing breakdown:
Init time: 0.000126483 0.0233682
Hal time: 0.000471055 8.70292
Mpole time: 0.000619314 11.4421
Induce time: 0.00270856 50.0417
Polar time: 0.00147122 27.1814
Total time: 0.00541261
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.005443 | 0.005443 | 0.005443 | 0.0 | 83.00
Bond | 9.6579e-05 | 9.6579e-05 | 9.6579e-05 | 0.0 | 1.47
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 1.7434e-05 | 1.7434e-05 | 1.7434e-05 | 0.0 | 0.27
Output | 0.0008951 | 0.0008951 | 0.0008951 | 0.0 | 13.65
Modify | 5.161e-05 | 5.161e-05 | 5.161e-05 | 0.0 | 0.79
Other | | 5.444e-05 | | | 0.83
Nlocal: 6 ave 6 max 6 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 15 ave 15 max 15 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 15
Ave neighs/atom = 2.5
Ave special neighs/atom = 2
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

43
examples/amoeba/log.water_dimer.amoeba.4
View File

@ -12,8 +12,8 @@ dihedral_style none
# per-atom properties required by AMOEBA or HIPPO
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom i_amgroup d_redID d_xaxis d_yaxis d_zaxis d_pval ghost yes
fix extra2 all property/atom i_polaxe
fix extra all property/atom i_amgroup d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
# read data file
@ -55,7 +55,7 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-4 neighbors
2 = max # of 1-5 neighbors
2 = max # of special neighbors
special bonds CPU = 0.001 seconds
special bonds CPU = 0.000 seconds
# thermo output
@ -97,7 +97,7 @@ Neighbor list info ...
bin: standard
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:974)
AMOEBA/HIPPO group count: 2
Per MPI rank memory allocation (min/avg/max) = 9.883 | 10.02 | 10.15 Mbytes
Per MPI rank memory allocation (min/avg/max) = 49.61 | 49.75 | 49.88 Mbytes
Step Temp E_pair E_bond E_angle E_dihed E_impro E_mol TotEng Press c_virial[1] c_virial[2] c_virial[3] c_virial[4] c_virial[5] c_virial[6]
0 0 -5.1627563 0.025695395 0.71581114 0 0 0.74150653 -4.4212497 -12260.522 -43226.042 39448.214 -33003.739 -85.160886 -28101.905 -72.971988
10 1.1174766 -4.7928792 0.045080327 0.30848527 0 0 0.35356559 -4.4226587 -14728.416 11456.119 -52592.829 -3262.8454 70.868937 29494.268 57.977562
@ -109,31 +109,30 @@ Per MPI rank memory allocation (min/avg/max) = 9.883 | 10.02 | 10.15 Mbytes
70 10.385926 -4.8250769 0.022572262 0.22235766 0 0 0.24492992 -4.4253547 -1117.3665 19070.918 -36063.612 11648.813 61.067533 25754.59 53.919881
80 12.797691 -5.123735 0.023756795 0.48275385 0 0 0.50651065 -4.4264869 -6491.9826 -28436.037 20681.908 -14176.121 -64.024669 -35737.052 -52.583533
90 12.569481 -4.8303379 0.060369422 0.15670502 0 0 0.21707444 -4.4259273 -16762.536 1720.5855 -47624.986 -6793.7441 59.966729 30024.566 52.339671
AMEOBA/HIPPO timing info:
Init time: 0.000562834 0.0392455
Hal time: 0.000119032 0.829992
Mpole time: 0.000759989 5.29928
Induce time: 0.0118027 82.2984
Polar time: 0.00108262 7.54891
Total time: 0.0143414
100 17.750788 -5.1195235 0.039885925 0.38711474 0 0 0.42700067 -4.4279642 -10817.92 -21833.456 4186.8301 -18211.329 -43.11086 -32664.671 -41.508916
Loop time of 0.0169266 on 4 procs for 100 steps with 6 atoms
Loop time of 0.0167554 on 4 procs for 100 steps with 6 atoms
Performance: 510.439 ns/day, 0.047 hours/ns, 5907.863 timesteps/s
99.7% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 515.654 ns/day, 0.047 hours/ns, 5968.213 timesteps/s
99.4% CPU use with 4 MPI tasks x no OpenMP threads
AMEOBA/HIPPO timing breakdown:
Init time: 0.000555846 0.0390251
Hal time: 0.000129733 0.910835
Mpole time: 0.000783914 5.50375
Induce time: 0.0115771 81.2811
Polar time: 0.00118294 8.30522
Total time: 0.0142433
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.014229 | 0.01457 | 0.014803 | 0.2 | 86.08
Bond | 1.311e-05 | 4.1295e-05 | 6.8411e-05 | 0.0 | 0.24
Pair | 0.013911 | 0.014439 | 0.0147 | 0.3 | 86.18
Bond | 1.196e-05 | 4.4667e-05 | 8.5848e-05 | 0.0 | 0.27
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00067827 | 0.0008315 | 0.0011965 | 0.0 | 4.91
Output | 0.00094515 | 0.0010124 | 0.0011247 | 0.2 | 5.98
Modify | 2.1384e-05 | 4.0305e-05 | 5.4006e-05 | 0.0 | 0.24
Other | | 0.0004309 | | | 2.55
Comm | 0.00060682 | 0.00082002 | 0.001342 | 0.0 | 4.89
Output | 0.00098235 | 0.0010281 | 0.0011458 | 0.2 | 6.14
Modify | 2.2946e-05 | 3.473e-05 | 4.2983e-05 | 0.0 | 0.21
Other | | 0.0003885 | | | 2.32
Nlocal: 1.5 ave 3 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 2

149
examples/amoeba/log.water_dimer.amoeba.4.test
View File

@ -1,149 +0,0 @@
LAMMPS (24 Mar 2022)
# water dimer with AMOEBA or HIPPO
units real
boundary s s s
atom_style amoeba
bond_style class2
angle_style amoeba
dihedral_style none
# per-atom properties required by AMOEBA or HIPPO
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom i_amgroup d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
# read data file
read_data data.water_dimer.amoeba fix amtype NULL "Tinker Types"
Reading data file ...
orthogonal box = (-1.463996 -0.756549 -0.009705) to (0.933234 0.75612 2.935934)
2 by 1 by 2 MPI processor grid
reading atoms ...
6 atoms
scanning bonds ...
2 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
4 bonds
reading angles ...
2 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.009 seconds
# force field
pair_style amoeba
pair_coeff * * amoeba_water.prm amoeba_water.key
special_bonds lj/coul 0.5 0.5 0.5 one/five yes
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0.5 0.5 0.5
special bond factors coul: 0.5 0.5 0.5
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of 1-5 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
# thermo output
compute virial all pressure NULL virial
thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*]
dump 1 all custom 10 dump.water_dimer id type x y z fx fy fz
dump_modify 1 sort id
# zero step run
#run 0
# dynamics
fix 1 all nve
thermo 10
run 100
AMOEBA/HIPPO force field settings
hal: cut 10 taper 8 vscale 0 0 1 1
multipole: cut 10 aewald 0 mscale 0 0 0.4 1
polar: cut 10 aewald 0
pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 1 1 1 1 d/u scale 0 1
precondition: cut 4.5
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair amoeba, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:974)
AMOEBA/HIPPO group count: 2
Per MPI rank memory allocation (min/avg/max) = 49.61 | 49.75 | 49.88 Mbytes
Step Temp E_pair E_bond E_angle E_dihed E_impro E_mol TotEng Press c_virial[1] c_virial[2] c_virial[3] c_virial[4] c_virial[5] c_virial[6]
0 0 -5.1627563 0.025695395 0.71581114 0 0 0.74150653 -4.4212497 -12260.522 -43226.042 39448.214 -33003.739 -85.160886 -28101.905 -72.971988
10 1.1174766 -4.7928792 0.045080327 0.30848527 0 0 0.35356559 -4.4226587 -14728.416 11456.119 -52592.829 -3262.8454 70.868937 29494.268 57.977562
20 3.0821934 -5.1387316 0.013108182 0.65694692 0 0 0.6700551 -4.4227393 3007.4148 -25925.326 49641.41 -15284.933 -79.726771 -29005.234 -68.530079
30 3.461967 -4.8079248 0.013888863 0.31895667 0 0 0.33284554 -4.423482 8616.211 40027.877 -31134.295 16291.126 72.510013 23088.238 51.407946
40 4.2181367 -5.0535921 0.0099009766 0.55796811 0 0 0.56786908 -4.4228557 24239.885 -5761.6967 62095.735 15576.675 -76.240192 -33057.385 -58.850871
50 5.216657 -4.8012751 0.0053003148 0.29489399 0 0 0.30019431 -4.4233315 17728.056 44785.731 -21215.714 28613.715 66.24671 20292.137 51.010856
60 9.45101 -5.0818046 0.0043357361 0.5118733 0 0 0.51620903 -4.4247372 16893.135 -15068.961 50111.11 13824.77 -75.966047 -34809.168 -52.83183
70 10.385926 -4.8250769 0.022572262 0.22235766 0 0 0.24492992 -4.4253547 -1117.3665 19070.918 -36063.612 11648.813 61.067533 25754.59 53.919881
80 12.797691 -5.123735 0.023756795 0.48275385 0 0 0.50651065 -4.4264869 -6491.9826 -28436.037 20681.908 -14176.121 -64.024669 -35737.052 -52.583533
90 12.569481 -4.8303379 0.060369422 0.15670502 0 0 0.21707444 -4.4259273 -16762.536 1720.5855 -47624.986 -6793.7441 59.966729 30024.566 52.339671
100 17.750788 -5.1195235 0.039885925 0.38711474 0 0 0.42700067 -4.4279642 -10817.92 -21833.456 4186.8301 -18211.329 -43.11086 -32664.671 -41.508916
Loop time of 0.0167554 on 4 procs for 100 steps with 6 atoms
Performance: 515.654 ns/day, 0.047 hours/ns, 5968.213 timesteps/s
99.4% CPU use with 4 MPI tasks x no OpenMP threads
AMEOBA/HIPPO timing breakdown:
Init time: 0.000555846 0.0390251
Hal time: 0.000129733 0.910835
Mpole time: 0.000783914 5.50375
Induce time: 0.0115771 81.2811
Polar time: 0.00118294 8.30522
Total time: 0.0142433
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.013911 | 0.014439 | 0.0147 | 0.3 | 86.18
Bond | 1.196e-05 | 4.4667e-05 | 8.5848e-05 | 0.0 | 0.27
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00060682 | 0.00082002 | 0.001342 | 0.0 | 4.89
Output | 0.00098235 | 0.0010281 | 0.0011458 | 0.2 | 6.14
Modify | 2.2946e-05 | 3.473e-05 | 4.2983e-05 | 0.0 | 0.21
Other | | 0.0003885 | | | 2.32
Nlocal: 1.5 ave 3 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 4.5 ave 6 max 3 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 3.75 ave 12 max 0 min
Histogram: 2 0 1 0 0 0 0 0 0 1
Total # of neighbors = 15
Ave neighs/atom = 2.5
Ave special neighs/atom = 2
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

47
examples/amoeba/log.water_dimer.hippo.1
View File

@ -12,8 +12,8 @@ dihedral_style none
# per-atom properties required by AMOEBA or HIPPO
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom i_amgroup d_redID d_xaxis d_yaxis d_zaxis d_pval ghost yes
fix extra2 all property/atom i_polaxe
fix extra all property/atom i_amgroup d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
# read data file
@ -39,7 +39,7 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.007 seconds
read_data CPU = 0.008 seconds
# force field
@ -99,7 +99,7 @@ Neighbor list info ...
bin: standard
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:974)
AMOEBA/HIPPO group count: 2
Per MPI rank memory allocation (min/avg/max) = 9.855 | 9.855 | 9.855 Mbytes
Per MPI rank memory allocation (min/avg/max) = 49.15 | 49.15 | 49.15 Mbytes
Step Temp E_pair E_bond E_angle E_dihed E_impro E_mol TotEng Press c_virial[1] c_virial[2] c_virial[3] c_virial[4] c_virial[5] c_virial[6]
0 0 -5.0101954 0.025695395 0.51472748 0 0 0.54042288 -4.4697726 -11875.159 -38149.178 29162.678 -26638.977 -70.63422 -24614.614 -58.505595
10 0.75132894 -4.7952077 0.028216017 0.28494196 0 0 0.31315798 -4.4708519 -13243.822 12661.254 -49613.657 -2923.1497 69.449413 29456.684 56.087663
@ -111,33 +111,32 @@ Per MPI rank memory allocation (min/avg/max) = 9.855 | 9.855 | 9.855 Mbytes
70 5.3145827 -4.8748857 0.025797484 0.29875503 0 0 0.32455252 -4.4711244 -10208.876 26324.134 -49272.688 -8697.2875 84.479942 36185.667 57.000355
80 3.8409793 -5.0262066 0.027669388 0.47104466 0 0 0.49871405 -4.4702464 -9777.1809 -52088.554 28053.855 -6033.4555 -94.607853 -44638.417 -59.108505
90 3.0683704 -4.8369716 0.035455716 0.28466932 0 0 0.32012503 -4.4711155 -10626.245 31066.635 -49425.925 -14107.889 87.765958 34632.905 52.101981
AMEOBA/HIPPO timing info:
Init time: 0.000114914 0.0215289
Repls time: 0.000617533 11.5693
Disp time: 0.000365952 6.85603
Mpole time: 0.000944495 17.6949
Induce time: 0.00199722 37.4176
Polar time: 0.0011473 21.4944
Qxfer time: 0.000145366 2.7234
Total time: 0.00533767
100 3.5262799 -4.9906817 0.016687539 0.45011301 0 0 0.46680055 -4.4713252 5216.7691 -34991.221 43883.163 6082.1058 -95.830393 -48645.129 -64.784334
Loop time of 0.0063791 on 1 procs for 100 steps with 6 atoms
Loop time of 0.00568827 on 1 procs for 100 steps with 6 atoms
Performance: 1354.423 ns/day, 0.018 hours/ns, 15676.190 timesteps/s
98.9% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 1518.916 ns/day, 0.016 hours/ns, 17580.041 timesteps/s
76.9% CPU use with 1 MPI tasks x no OpenMP threads
AMEOBA/HIPPO timing breakdown:
Init time: 0.00011293 0.024348
Repulse time: 0.000604058 13.0236
Disp time: 0.000336908 7.26382
Mpole time: 0.000853828 18.4087
Induce time: 0.00158723 34.2211
Polar time: 0.000996193 21.4782
Qxfer time: 0.000142246 3.06686
Total time: 0.00463817
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.005435 | 0.005435 | 0.005435 | 0.0 | 85.20
Bond | 8.7439e-05 | 8.7439e-05 | 8.7439e-05 | 0.0 | 1.37
Pair | 0.0046663 | 0.0046663 | 0.0046663 | 0.0 | 82.03
Bond | 7.8168e-05 | 7.8168e-05 | 7.8168e-05 | 0.0 | 1.37
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 1.447e-05 | 1.447e-05 | 1.447e-05 | 0.0 | 0.23
Output | 0.00073302 | 0.00073302 | 0.00073302 | 0.0 | 11.49
Modify | 4.6662e-05 | 4.6662e-05 | 4.6662e-05 | 0.0 | 0.73
Other | | 6.248e-05 | | | 0.98
Comm | 1.3206e-05 | 1.3206e-05 | 1.3206e-05 | 0.0 | 0.23
Output | 0.00084402 | 0.00084402 | 0.00084402 | 0.0 | 14.84
Modify | 3.8896e-05 | 3.8896e-05 | 3.8896e-05 | 0.0 | 0.68
Other | | 4.77e-05 | | | 0.84
Nlocal: 6 ave 6 max 6 min
Histogram: 1 0 0 0 0 0 0 0 0 0

153
examples/amoeba/log.water_dimer.hippo.1.test
View File

@ -1,153 +0,0 @@
LAMMPS (24 Mar 2022)
# water dimer with AMOEBA or HIPPO
units real
boundary s s s
atom_style amoeba
bond_style class2
angle_style amoeba
dihedral_style none
# per-atom properties required by AMOEBA or HIPPO
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom i_amgroup d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
# read data file
read_data data.water_dimer.hippo fix amtype NULL "Tinker Types"
Reading data file ...
orthogonal box = (-1.463996 -0.756549 -0.009705) to (0.933234 0.75612 2.935934)
1 by 1 by 1 MPI processor grid
reading atoms ...
6 atoms
scanning bonds ...
2 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
4 bonds
reading angles ...
2 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.008 seconds
# force field
pair_style hippo
pair_coeff * * hippo_water.prm hippo_water.key
special_bonds lj/coul 0.5 0.5 0.5 one/five yes
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0.5 0.5 0.5
special bond factors coul: 0.5 0.5 0.5
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of 1-5 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
# thermo output
compute virial all pressure NULL virial
thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*]
dump 1 all custom 10 dump.water_dimer id type x y z fx fy fz
dump_modify 1 sort id
# zero step run
#run 0
# dynamics
fix 1 all nve
thermo 10
run 100
AMOEBA/HIPPO force field settings
repulsion: cut 10 taper 8 rscale 0 0 1 1
qxfer: cut 10 taper 8 mscale 0 0 0.4 1
dispersion: cut 10 aewald 0 dspscale 0 0 0.4 1
multipole: cut 10 aewald 0 mscale 0 0 0.4 1
polar: cut 10 aewald 0
pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 0.2 1 1 1 d/u scale 0 1
precondition: cut 4.5
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair hippo, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:974)
AMOEBA/HIPPO group count: 2
Per MPI rank memory allocation (min/avg/max) = 49.15 | 49.15 | 49.15 Mbytes
Step Temp E_pair E_bond E_angle E_dihed E_impro E_mol TotEng Press c_virial[1] c_virial[2] c_virial[3] c_virial[4] c_virial[5] c_virial[6]
0 0 -5.0101954 0.025695395 0.51472748 0 0 0.54042288 -4.4697726 -11875.159 -38149.178 29162.678 -26638.977 -70.63422 -24614.614 -58.505595
10 0.75132894 -4.7952077 0.028216017 0.28494196 0 0 0.31315798 -4.4708519 -13243.822 12661.254 -49613.657 -2923.1497 69.449413 29456.684 56.087663
20 2.1716525 -5.0036265 0.011809223 0.48875837 0 0 0.50056759 -4.4706925 4371.5298 -22102.532 47044.297 -12243.648 -74.588915 -28903.762 -64.48154
30 2.9930198 -4.8261906 0.0091463366 0.30162756 0 0 0.3107739 -4.4708086 9992.4549 41973.539 -20985.339 8415.1715 67.458145 25027.414 40.261795
40 3.312268 -4.9802484 0.010400667 0.45076258 0 0 0.46116325 -4.4697189 21565.307 -11602.414 65186.215 10476.902 -83.374203 -33222.094 -64.700001
50 4.3187397 -4.8535614 0.0060313545 0.31244652 0 0 0.31847788 -4.4707168 11344.244 45839.35 -21073.749 8438.8954 73.345039 29422.636 43.897876
60 4.9127902 -5.0035271 0.0070589202 0.45246538 0 0 0.4595243 -4.4707824 6529.9354 -37107.891 46740.24 9015.2973 -90.41111 -34402.095 -53.57079
70 5.3145827 -4.8748857 0.025797484 0.29875503 0 0 0.32455252 -4.4711244 -10208.876 26324.134 -49272.688 -8697.2875 84.479942 36185.667 57.000355
80 3.8409793 -5.0262066 0.027669388 0.47104466 0 0 0.49871405 -4.4702464 -9777.1809 -52088.554 28053.855 -6033.4555 -94.607853 -44638.417 -59.108505
90 3.0683704 -4.8369716 0.035455716 0.28466932 0 0 0.32012503 -4.4711155 -10626.245 31066.635 -49425.925 -14107.889 87.765958 34632.905 52.101981
100 3.5262799 -4.9906817 0.016687539 0.45011301 0 0 0.46680055 -4.4713252 5216.7691 -34991.221 43883.163 6082.1058 -95.830393 -48645.129 -64.784334
Loop time of 0.00568827 on 1 procs for 100 steps with 6 atoms
Performance: 1518.916 ns/day, 0.016 hours/ns, 17580.041 timesteps/s
76.9% CPU use with 1 MPI tasks x no OpenMP threads
AMEOBA/HIPPO timing breakdown:
Init time: 0.00011293 0.024348
Repulse time: 0.000604058 13.0236
Disp time: 0.000336908 7.26382
Mpole time: 0.000853828 18.4087
Induce time: 0.00158723 34.2211
Polar time: 0.000996193 21.4782
Qxfer time: 0.000142246 3.06686
Total time: 0.00463817
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0046663 | 0.0046663 | 0.0046663 | 0.0 | 82.03
Bond | 7.8168e-05 | 7.8168e-05 | 7.8168e-05 | 0.0 | 1.37
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 1.3206e-05 | 1.3206e-05 | 1.3206e-05 | 0.0 | 0.23
Output | 0.00084402 | 0.00084402 | 0.00084402 | 0.0 | 14.84
Modify | 3.8896e-05 | 3.8896e-05 | 3.8896e-05 | 0.0 | 0.68
Other | | 4.77e-05 | | | 0.84
Nlocal: 6 ave 6 max 6 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 15 ave 15 max 15 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 15
Ave neighs/atom = 2.5
Ave special neighs/atom = 2
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

45
examples/amoeba/log.water_dimer.hippo.4
View File

@ -12,8 +12,8 @@ dihedral_style none
# per-atom properties required by AMOEBA or HIPPO
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom i_amgroup d_redID d_xaxis d_yaxis d_zaxis d_pval ghost yes
fix extra2 all property/atom i_polaxe
fix extra all property/atom i_amgroup d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
# read data file
@ -99,7 +99,7 @@ Neighbor list info ...
bin: standard
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:974)
AMOEBA/HIPPO group count: 2
Per MPI rank memory allocation (min/avg/max) = 9.883 | 10.02 | 10.15 Mbytes
Per MPI rank memory allocation (min/avg/max) = 49.18 | 49.31 | 49.44 Mbytes
Step Temp E_pair E_bond E_angle E_dihed E_impro E_mol TotEng Press c_virial[1] c_virial[2] c_virial[3] c_virial[4] c_virial[5] c_virial[6]
0 0 -5.0101954 0.025695395 0.51472748 0 0 0.54042288 -4.4697726 -11875.159 -38149.178 29162.678 -26638.977 -70.63422 -24614.614 -58.505595
10 0.75132894 -4.7952077 0.028216017 0.28494196 0 0 0.31315798 -4.4708519 -13243.822 12661.254 -49613.657 -2923.1497 69.449413 29456.684 56.087663
@ -111,33 +111,32 @@ Per MPI rank memory allocation (min/avg/max) = 9.883 | 10.02 | 10.15 Mbytes
70 5.3145827 -4.8748857 0.025797484 0.29875503 0 0 0.32455252 -4.4711244 -10208.876 26324.134 -49272.688 -8697.2875 84.479942 36185.667 57.000355
80 3.8409793 -5.0262066 0.027669388 0.47104466 0 0 0.49871405 -4.4702464 -9777.1809 -52088.554 28053.855 -6033.4555 -94.607853 -44638.417 -59.108505
90 3.0683704 -4.8369716 0.035455716 0.28466932 0 0 0.32012503 -4.4711155 -10626.245 31066.635 -49425.925 -14107.889 87.765958 34632.905 52.101981
AMEOBA/HIPPO timing info:
Init time: 0.000628997 0.0480375
Repls time: 0.000859377 6.5632
Disp time: 0.00015718 1.20041
Mpole time: 0.00153385 11.7143
Induce time: 0.0085554 65.339
Polar time: 0.00127985 9.77439
Qxfer time: 7.40915e-05 0.565849
Total time: 0.0130939
100 3.5262799 -4.9906817 0.016687539 0.45011301 0 0 0.46680055 -4.4713252 5216.7691 -34991.221 43883.163 6082.1058 -95.830393 -48645.129 -64.784334
Loop time of 0.0163786 on 4 procs for 100 steps with 6 atoms
Loop time of 0.0133873 on 4 procs for 100 steps with 6 atoms
Performance: 527.519 ns/day, 0.045 hours/ns, 6105.545 timesteps/s
98.7% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 645.386 ns/day, 0.037 hours/ns, 7469.744 timesteps/s
98.4% CPU use with 4 MPI tasks x no OpenMP threads
AMEOBA/HIPPO timing breakdown:
Init time: 0.000581606 0.0545512
Repulse time: 0.000622984 5.84322
Disp time: 0.000115637 1.0846
Mpole time: 0.000994723 9.32991
Induce time: 0.00737161 69.1413
Polar time: 0.00091816 8.61179
Qxfer time: 5.1997e-05 0.487701
Total time: 0.0106617
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.012747 | 0.013356 | 0.013763 | 0.3 | 81.55
Bond | 1.4562e-05 | 5.3301e-05 | 0.00010757 | 0.0 | 0.33
Pair | 0.010579 | 0.010896 | 0.011085 | 0.2 | 81.39
Bond | 1.3578e-05 | 4.3855e-05 | 7.6592e-05 | 0.0 | 0.33
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00061214 | 0.001076 | 0.0015518 | 1.0 | 6.57
Output | 0.0011991 | 0.0013282 | 0.0015124 | 0.3 | 8.11
Modify | 2.2511e-05 | 3.8778e-05 | 5.1854e-05 | 0.0 | 0.24
Other | | 0.0005259 | | | 3.21
Comm | 0.00058533 | 0.00080957 | 0.0011064 | 0.0 | 6.05
Output | 0.0011175 | 0.0011761 | 0.0013051 | 0.2 | 8.78
Modify | 2.4304e-05 | 3.4805e-05 | 4.2149e-05 | 0.0 | 0.26
Other | | 0.0004266 | | | 3.19
Nlocal: 1.5 ave 3 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 2

153
examples/amoeba/log.water_dimer.hippo.4.test
View File

@ -1,153 +0,0 @@
LAMMPS (24 Mar 2022)
# water dimer with AMOEBA or HIPPO
units real
boundary s s s
atom_style amoeba
bond_style class2
angle_style amoeba
dihedral_style none
# per-atom properties required by AMOEBA or HIPPO
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom i_amgroup d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
# read data file
read_data data.water_dimer.hippo fix amtype NULL "Tinker Types"
Reading data file ...
orthogonal box = (-1.463996 -0.756549 -0.009705) to (0.933234 0.75612 2.935934)
2 by 1 by 2 MPI processor grid
reading atoms ...
6 atoms
scanning bonds ...
2 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
4 bonds
reading angles ...
2 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.009 seconds
# force field
pair_style hippo
pair_coeff * * hippo_water.prm hippo_water.key
special_bonds lj/coul 0.5 0.5 0.5 one/five yes
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0.5 0.5 0.5
special bond factors coul: 0.5 0.5 0.5
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of 1-5 neighbors
2 = max # of special neighbors
special bonds CPU = 0.001 seconds
# thermo output
compute virial all pressure NULL virial
thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*]
dump 1 all custom 10 dump.water_dimer id type x y z fx fy fz
dump_modify 1 sort id
# zero step run
#run 0
# dynamics
fix 1 all nve
thermo 10
run 100
AMOEBA/HIPPO force field settings
repulsion: cut 10 taper 8 rscale 0 0 1 1
qxfer: cut 10 taper 8 mscale 0 0 0.4 1
dispersion: cut 10 aewald 0 dspscale 0 0 0.4 1
multipole: cut 10 aewald 0 mscale 0 0 0.4 1
polar: cut 10 aewald 0
pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 0.2 1 1 1 d/u scale 0 1
precondition: cut 4.5
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair hippo, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:974)
AMOEBA/HIPPO group count: 2
Per MPI rank memory allocation (min/avg/max) = 49.18 | 49.31 | 49.44 Mbytes
Step Temp E_pair E_bond E_angle E_dihed E_impro E_mol TotEng Press c_virial[1] c_virial[2] c_virial[3] c_virial[4] c_virial[5] c_virial[6]
0 0 -5.0101954 0.025695395 0.51472748 0 0 0.54042288 -4.4697726 -11875.159 -38149.178 29162.678 -26638.977 -70.63422 -24614.614 -58.505595
10 0.75132894 -4.7952077 0.028216017 0.28494196 0 0 0.31315798 -4.4708519 -13243.822 12661.254 -49613.657 -2923.1497 69.449413 29456.684 56.087663
20 2.1716525 -5.0036265 0.011809223 0.48875837 0 0 0.50056759 -4.4706925 4371.5298 -22102.532 47044.297 -12243.648 -74.588915 -28903.762 -64.48154
30 2.9930198 -4.8261906 0.0091463366 0.30162756 0 0 0.3107739 -4.4708086 9992.4549 41973.539 -20985.339 8415.1715 67.458145 25027.414 40.261795
40 3.312268 -4.9802484 0.010400667 0.45076258 0 0 0.46116325 -4.4697189 21565.307 -11602.414 65186.215 10476.902 -83.374203 -33222.094 -64.700001
50 4.3187397 -4.8535614 0.0060313545 0.31244652 0 0 0.31847788 -4.4707168 11344.244 45839.35 -21073.749 8438.8954 73.345039 29422.636 43.897876
60 4.9127902 -5.0035271 0.0070589202 0.45246538 0 0 0.4595243 -4.4707824 6529.9354 -37107.891 46740.24 9015.2973 -90.41111 -34402.095 -53.57079
70 5.3145827 -4.8748857 0.025797484 0.29875503 0 0 0.32455252 -4.4711244 -10208.876 26324.134 -49272.688 -8697.2875 84.479942 36185.667 57.000355
80 3.8409793 -5.0262066 0.027669388 0.47104466 0 0 0.49871405 -4.4702464 -9777.1809 -52088.554 28053.855 -6033.4555 -94.607853 -44638.417 -59.108505
90 3.0683704 -4.8369716 0.035455716 0.28466932 0 0 0.32012503 -4.4711155 -10626.245 31066.635 -49425.925 -14107.889 87.765958 34632.905 52.101981
100 3.5262799 -4.9906817 0.016687539 0.45011301 0 0 0.46680055 -4.4713252 5216.7691 -34991.221 43883.163 6082.1058 -95.830393 -48645.129 -64.784334
Loop time of 0.0133873 on 4 procs for 100 steps with 6 atoms
Performance: 645.386 ns/day, 0.037 hours/ns, 7469.744 timesteps/s
98.4% CPU use with 4 MPI tasks x no OpenMP threads
AMEOBA/HIPPO timing breakdown:
Init time: 0.000581606 0.0545512
Repulse time: 0.000622984 5.84322
Disp time: 0.000115637 1.0846
Mpole time: 0.000994723 9.32991
Induce time: 0.00737161 69.1413
Polar time: 0.00091816 8.61179
Qxfer time: 5.1997e-05 0.487701
Total time: 0.0106617
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.010579 | 0.010896 | 0.011085 | 0.2 | 81.39
Bond | 1.3578e-05 | 4.3855e-05 | 7.6592e-05 | 0.0 | 0.33
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00058533 | 0.00080957 | 0.0011064 | 0.0 | 6.05
Output | 0.0011175 | 0.0011761 | 0.0013051 | 0.2 | 8.78
Modify | 2.4304e-05 | 3.4805e-05 | 4.2149e-05 | 0.0 | 0.26
Other | | 0.0004266 | | | 3.19
Nlocal: 1.5 ave 3 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 4.5 ave 6 max 3 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 3.75 ave 12 max 0 min
Histogram: 2 0 1 0 0 0 0 0 0 1
Total # of neighbors = 15
Ave neighs/atom = 2.5
Ave special neighs/atom = 2
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

43
examples/amoeba/log.water_hexamer.amoeba.1
View File

@ -12,8 +12,8 @@ dihedral_style none
# per-atom properties required by AMOEBA or HIPPO
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom i_amgroup d_redID d_xaxis d_yaxis d_zaxis d_pval ghost yes
fix extra2 all property/atom i_polaxe
fix extra all property/atom i_amgroup d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
# read data file
@ -39,7 +39,7 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.007 seconds
read_data CPU = 0.009 seconds
# force field
@ -96,7 +96,7 @@ Neighbor list info ...
stencil: half/bin/3d
bin: standard
AMOEBA/HIPPO group count: 6
Per MPI rank memory allocation (min/avg/max) = 9.804 | 9.804 | 9.804 Mbytes
Per MPI rank memory allocation (min/avg/max) = 49.53 | 49.53 | 49.53 Mbytes
Step Temp E_pair E_bond E_angle E_dihed E_impro E_mol TotEng Press c_virial[1] c_virial[2] c_virial[3] c_virial[4] c_virial[5] c_virial[6]
0 0 -48.469664 1.9820353 2.2499329 0 0 4.2319683 -44.237696 -26322.671 -28303.103 -27669.614 -22995.296 1312.6688 2624.8394 4042.0489
10 6.3616471 -46.626437 1.7910812 0.25704063 0 0 2.0481218 -44.255947 -23813.06 -24671.886 -17167.34 -30208.043 -474.208 -8339.5934 -5278.359
@ -108,31 +108,30 @@ Per MPI rank memory allocation (min/avg/max) = 9.804 | 9.804 | 9.804 Mbytes
70 11.272241 -45.411622 0.07431614 0.51778317 0 0 0.59209931 -44.248316 32055.564 39306.193 30181.52 25601.501 1373.4778 -4501.0686 -2570.4767
80 14.011502 -46.081444 0.089688317 1.006928 0 0 1.0966163 -44.274812 25661.838 38836.598 12603.734 24205.867 -867.36437 -4211.9639 -2820.6725
90 17.659498 -46.247295 0.21744649 0.82687716 0 0 1.0443237 -44.308098 12101.207 19426.995 14142.311 1046.299 -2157.5418 -2141.2454 -2621.456
AMEOBA/HIPPO timing info:
Init time: 0.000298703 0.00766228
Hal time: 0.00477252 12.2424
Mpole time: 0.00429886 11.0274
Induce time: 0.0189419 48.5895
Polar time: 0.0106573 27.338
Total time: 0.0389836
100 17.630532 -46.788272 0.61811601 0.9654966 0 0 1.5836126 -44.311254 -4455.3587 3961.5737 -11554.095 -7458.8012 -3120.9771 -1532.1706 -1499.0117
Loop time of 0.0403763 on 1 procs for 100 steps with 18 atoms
Loop time of 0.0438592 on 1 procs for 100 steps with 18 atoms
Performance: 213.987 ns/day, 0.112 hours/ns, 2476.699 timesteps/s
96.9% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 196.994 ns/day, 0.122 hours/ns, 2280.022 timesteps/s
95.1% CPU use with 1 MPI tasks x no OpenMP threads
AMEOBA/HIPPO timing breakdown:
Init time: 0.000324764 0.00770058
Hal time: 0.00500441 11.8661
Mpole time: 0.00442974 10.5035
Induce time: 0.0210286 49.8617
Polar time: 0.0113696 26.9588
Total time: 0.042174
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.039062 | 0.039062 | 0.039062 | 0.0 | 96.74
Bond | 0.00018661 | 0.00018661 | 0.00018661 | 0.0 | 0.46
Pair | 0.042221 | 0.042221 | 0.042221 | 0.0 | 96.26
Bond | 0.00021632 | 0.00021632 | 0.00021632 | 0.0 | 0.49
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 1.665e-05 | 1.665e-05 | 1.665e-05 | 0.0 | 0.04
Output | 0.0009741 | 0.0009741 | 0.0009741 | 0.0 | 2.41
Modify | 6.7026e-05 | 6.7026e-05 | 6.7026e-05 | 0.0 | 0.17
Other | | 7.005e-05 | | | 0.17
Comm | 1.6322e-05 | 1.6322e-05 | 1.6322e-05 | 0.0 | 0.04
Output | 0.0012472 | 0.0012472 | 0.0012472 | 0.0 | 2.84
Modify | 7.9638e-05 | 7.9638e-05 | 7.9638e-05 | 0.0 | 0.18
Other | | 7.889e-05 | | | 0.18
Nlocal: 18 ave 18 max 18 min
Histogram: 1 0 0 0 0 0 0 0 0 0

148
examples/amoeba/log.water_hexamer.amoeba.1.test
View File

@ -1,148 +0,0 @@
LAMMPS (24 Mar 2022)
# water hexamer with AMOEBA or HIPPO
units real
boundary s s s
atom_style amoeba
bond_style class2
angle_style amoeba
dihedral_style none
# per-atom properties required by AMOEBA or HIPPO
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom i_amgroup d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
# read data file
read_data data.water_hexamer.amoeba fix amtype NULL "Tinker Types"
Reading data file ...
orthogonal box = (-2.517835 -1.523041 -1.734766) to (2.675716 2.01883 2.220847)
1 by 1 by 1 MPI processor grid
reading atoms ...
18 atoms
scanning bonds ...
2 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
12 bonds
reading angles ...
6 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.009 seconds
# force field
pair_style amoeba
pair_coeff * * amoeba_water.prm amoeba_water.key
special_bonds lj/coul 0.5 0.5 0.5 one/five yes
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0.5 0.5 0.5
special bond factors coul: 0.5 0.5 0.5
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of 1-5 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
# thermo output
compute virial all pressure NULL virial
thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*]
dump 1 all custom 10 dump.water_hexamer id type x y z fx fy fz
dump_modify 1 sort id
# zero step run
#run 0
# dynamics
fix 1 all nve
thermo 10
run 100
AMOEBA/HIPPO force field settings
hal: cut 10 taper 8 vscale 0 0 1 1
multipole: cut 10 aewald 0 mscale 0 0 0.4 1
polar: cut 10 aewald 0
pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 1 1 1 1 d/u scale 0 1
precondition: cut 4.5
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair amoeba, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
AMOEBA/HIPPO group count: 6
Per MPI rank memory allocation (min/avg/max) = 49.53 | 49.53 | 49.53 Mbytes
Step Temp E_pair E_bond E_angle E_dihed E_impro E_mol TotEng Press c_virial[1] c_virial[2] c_virial[3] c_virial[4] c_virial[5] c_virial[6]
0 0 -48.469664 1.9820353 2.2499329 0 0 4.2319683 -44.237696 -26322.671 -28303.103 -27669.614 -22995.296 1312.6688 2624.8394 4042.0489
10 6.3616471 -46.626437 1.7910812 0.25704063 0 0 2.0481218 -44.255947 -23813.06 -24671.886 -17167.34 -30208.043 -474.208 -8339.5934 -5278.359
20 15.149798 -48.177533 1.1130818 2.007499 0 0 3.1205807 -44.289255 -16468.855 -20150.975 -18596.629 -12107.083 885.52697 6320.1867 3064.949
30 17.896968 -45.959274 0.54802739 0.19519937 0 0 0.74322676 -44.309141 -4749.0624 -9053.7792 -182.37209 -6721.7499 -2003.7641 -627.56998 -1658.1301
40 16.203813 -46.840973 0.1371751 1.5793326 0 0 1.7165077 -44.303357 9267.4858 6108.7966 4116.4548 16028.336 380.03787 8468.0648 4492.3331
50 11.584975 -45.166711 0.017120512 0.28622888 0 0 0.30334939 -44.276308 22189.511 21453.083 22339.471 21668.607 150.93139 1059.5253 200.0668
60 10.002055 -45.994946 0.037889337 1.1987062 0 0 1.2365956 -44.251509 30944.004 35801.925 19832.696 36241.326 2042.3054 2320.5193 1660.0834
70 11.272241 -45.411622 0.07431614 0.51778317 0 0 0.59209931 -44.248316 32055.564 39306.193 30181.52 25601.501 1373.4778 -4501.0686 -2570.4767
80 14.011502 -46.081444 0.089688317 1.006928 0 0 1.0966163 -44.274812 25661.838 38836.598 12603.734 24205.867 -867.36437 -4211.9639 -2820.6725
90 17.659498 -46.247295 0.21744649 0.82687716 0 0 1.0443237 -44.308098 12101.207 19426.995 14142.311 1046.299 -2157.5418 -2141.2454 -2621.456
100 17.630532 -46.788272 0.61811601 0.9654966 0 0 1.5836126 -44.311254 -4455.3587 3961.5737 -11554.095 -7458.8012 -3120.9771 -1532.1706 -1499.0117
Loop time of 0.0438592 on 1 procs for 100 steps with 18 atoms
Performance: 196.994 ns/day, 0.122 hours/ns, 2280.022 timesteps/s
95.1% CPU use with 1 MPI tasks x no OpenMP threads
AMEOBA/HIPPO timing breakdown:
Init time: 0.000324764 0.00770058
Hal time: 0.00500441 11.8661
Mpole time: 0.00442974 10.5035
Induce time: 0.0210286 49.8617
Polar time: 0.0113696 26.9588
Total time: 0.042174
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.042221 | 0.042221 | 0.042221 | 0.0 | 96.26
Bond | 0.00021632 | 0.00021632 | 0.00021632 | 0.0 | 0.49
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 1.6322e-05 | 1.6322e-05 | 1.6322e-05 | 0.0 | 0.04
Output | 0.0012472 | 0.0012472 | 0.0012472 | 0.0 | 2.84
Modify | 7.9638e-05 | 7.9638e-05 | 7.9638e-05 | 0.0 | 0.18
Other | | 7.889e-05 | | | 0.18
Nlocal: 18 ave 18 max 18 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 153 ave 153 max 153 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 153
Ave neighs/atom = 8.5
Ave special neighs/atom = 2
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

45
examples/amoeba/log.water_hexamer.amoeba.4
View File

@ -12,8 +12,8 @@ dihedral_style none
# per-atom properties required by AMOEBA or HIPPO
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom i_amgroup d_redID d_xaxis d_yaxis d_zaxis d_pval ghost yes
fix extra2 all property/atom i_polaxe
fix extra all property/atom i_amgroup d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
# read data file
@ -38,8 +38,8 @@ 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 = 0.009 seconds
special bonds CPU = 0.000 seconds
read_data CPU = 0.008 seconds
# force field
@ -55,7 +55,7 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-4 neighbors
2 = max # of 1-5 neighbors
2 = max # of special neighbors
special bonds CPU = 0.001 seconds
special bonds CPU = 0.000 seconds
# thermo output
@ -97,7 +97,7 @@ Neighbor list info ...
bin: standard
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:974)
AMOEBA/HIPPO group count: 6
Per MPI rank memory allocation (min/avg/max) = 9.833 | 9.833 | 9.833 Mbytes
Per MPI rank memory allocation (min/avg/max) = 49.56 | 49.56 | 49.56 Mbytes
Step Temp E_pair E_bond E_angle E_dihed E_impro E_mol TotEng Press c_virial[1] c_virial[2] c_virial[3] c_virial[4] c_virial[5] c_virial[6]
0 0 -48.469664 1.9820353 2.2499329 0 0 4.2319683 -44.237696 -26322.671 -28303.103 -27669.614 -22995.296 1312.6688 2624.8394 4042.0489
10 6.3616471 -46.626437 1.7910812 0.25704063 0 0 2.0481218 -44.255947 -23813.06 -24671.886 -17167.34 -30208.043 -474.208 -8339.5934 -5278.359
@ -109,31 +109,30 @@ Per MPI rank memory allocation (min/avg/max) = 9.833 | 9.833 | 9.833 Mbytes
70 11.272241 -45.411622 0.07431614 0.51778317 0 0 0.59209931 -44.248316 32055.564 39306.193 30181.52 25601.501 1373.4778 -4501.0686 -2570.4767
80 14.011502 -46.081444 0.089688317 1.006928 0 0 1.0966163 -44.274812 25661.838 38836.598 12603.734 24205.867 -867.36437 -4211.9639 -2820.6725
90 17.659498 -46.247295 0.21744649 0.82687716 0 0 1.0443237 -44.308098 12101.207 19426.995 14142.311 1046.299 -2157.5418 -2141.2454 -2621.456
AMEOBA/HIPPO timing info:
Init time: 0.000875735 0.0198199
Hal time: 0.00136658 3.09288
Mpole time: 0.0042176 9.5454
Induce time: 0.0311498 70.4992
Polar time: 0.00655957 14.8458
Total time: 0.0441847
100 17.630532 -46.788272 0.61811601 0.9654966 0 0 1.5836126 -44.311254 -4455.3587 3961.5737 -11554.095 -7458.8012 -3120.9771 -1532.1706 -1499.0117
Loop time of 0.0471312 on 4 procs for 100 steps with 18 atoms
Loop time of 0.0405754 on 4 procs for 100 steps with 18 atoms
Performance: 183.318 ns/day, 0.131 hours/ns, 2121.739 timesteps/s
Performance: 212.937 ns/day, 0.113 hours/ns, 2464.547 timesteps/s
98.9% CPU use with 4 MPI tasks x no OpenMP threads
AMEOBA/HIPPO timing breakdown:
Init time: 0.000756446 0.0198927
Hal time: 0.00120064 3.15739
Mpole time: 0.00338295 8.89637
Induce time: 0.0273688 71.9733
Polar time: 0.00530425 13.9489
Total time: 0.0380263
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.044346 | 0.044424 | 0.044557 | 0.0 | 94.26
Bond | 9.3929e-05 | 0.00010313 | 0.00011252 | 0.0 | 0.22
Pair | 0.03816 | 0.038221 | 0.038312 | 0.0 | 94.20
Bond | 7.0759e-05 | 8.5222e-05 | 0.00010449 | 0.0 | 0.21
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00071684 | 0.00091755 | 0.0010385 | 0.0 | 1.95
Output | 0.0011333 | 0.0012027 | 0.0013253 | 0.2 | 2.55
Modify | 4.2618e-05 | 5.1978e-05 | 6.2018e-05 | 0.0 | 0.11
Other | | 0.0004322 | | | 0.92
Comm | 0.00065721 | 0.00081724 | 0.00093857 | 0.0 | 2.01
Output | 0.0010275 | 0.0010663 | 0.0011758 | 0.2 | 2.63
Modify | 3.3884e-05 | 4.422e-05 | 5.7037e-05 | 0.0 | 0.11
Other | | 0.000341 | | | 0.84
Nlocal: 4.5 ave 6 max 3 min
Histogram: 1 0 0 1 0 0 1 0 0 1

149
examples/amoeba/log.water_hexamer.amoeba.4.test
View File

@ -1,149 +0,0 @@
LAMMPS (24 Mar 2022)
# water hexamer with AMOEBA or HIPPO
units real
boundary s s s
atom_style amoeba
bond_style class2
angle_style amoeba
dihedral_style none
# per-atom properties required by AMOEBA or HIPPO
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom i_amgroup d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
# read data file
read_data data.water_hexamer.amoeba fix amtype NULL "Tinker Types"
Reading data file ...
orthogonal box = (-2.517835 -1.523041 -1.734766) to (2.675716 2.01883 2.220847)
2 by 1 by 2 MPI processor grid
reading atoms ...
18 atoms
scanning bonds ...
2 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
12 bonds
reading angles ...
6 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.008 seconds
# force field
pair_style amoeba
pair_coeff * * amoeba_water.prm amoeba_water.key
special_bonds lj/coul 0.5 0.5 0.5 one/five yes
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0.5 0.5 0.5
special bond factors coul: 0.5 0.5 0.5
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of 1-5 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
# thermo output
compute virial all pressure NULL virial
thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*]
dump 1 all custom 10 dump.water_hexamer id type x y z fx fy fz
dump_modify 1 sort id
# zero step run
#run 0
# dynamics
fix 1 all nve
thermo 10
run 100
AMOEBA/HIPPO force field settings
hal: cut 10 taper 8 vscale 0 0 1 1
multipole: cut 10 aewald 0 mscale 0 0 0.4 1
polar: cut 10 aewald 0
pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 1 1 1 1 d/u scale 0 1
precondition: cut 4.5
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair amoeba, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:974)
AMOEBA/HIPPO group count: 6
Per MPI rank memory allocation (min/avg/max) = 49.56 | 49.56 | 49.56 Mbytes
Step Temp E_pair E_bond E_angle E_dihed E_impro E_mol TotEng Press c_virial[1] c_virial[2] c_virial[3] c_virial[4] c_virial[5] c_virial[6]
0 0 -48.469664 1.9820353 2.2499329 0 0 4.2319683 -44.237696 -26322.671 -28303.103 -27669.614 -22995.296 1312.6688 2624.8394 4042.0489
10 6.3616471 -46.626437 1.7910812 0.25704063 0 0 2.0481218 -44.255947 -23813.06 -24671.886 -17167.34 -30208.043 -474.208 -8339.5934 -5278.359
20 15.149798 -48.177533 1.1130818 2.007499 0 0 3.1205807 -44.289255 -16468.855 -20150.975 -18596.629 -12107.083 885.52697 6320.1867 3064.949
30 17.896968 -45.959274 0.54802739 0.19519937 0 0 0.74322676 -44.309141 -4749.0624 -9053.7792 -182.37209 -6721.7499 -2003.7641 -627.56998 -1658.1301
40 16.203813 -46.840973 0.1371751 1.5793326 0 0 1.7165077 -44.303357 9267.4858 6108.7966 4116.4548 16028.336 380.03787 8468.0648 4492.3331
50 11.584975 -45.166711 0.017120512 0.28622888 0 0 0.30334939 -44.276308 22189.511 21453.083 22339.471 21668.607 150.93139 1059.5253 200.0668
60 10.002055 -45.994946 0.037889337 1.1987062 0 0 1.2365956 -44.251509 30944.004 35801.925 19832.696 36241.326 2042.3054 2320.5193 1660.0834
70 11.272241 -45.411622 0.07431614 0.51778317 0 0 0.59209931 -44.248316 32055.564 39306.193 30181.52 25601.501 1373.4778 -4501.0686 -2570.4767
80 14.011502 -46.081444 0.089688317 1.006928 0 0 1.0966163 -44.274812 25661.838 38836.598 12603.734 24205.867 -867.36437 -4211.9639 -2820.6725
90 17.659498 -46.247295 0.21744649 0.82687716 0 0 1.0443237 -44.308098 12101.207 19426.995 14142.311 1046.299 -2157.5418 -2141.2454 -2621.456
100 17.630532 -46.788272 0.61811601 0.9654966 0 0 1.5836126 -44.311254 -4455.3587 3961.5737 -11554.095 -7458.8012 -3120.9771 -1532.1706 -1499.0117
Loop time of 0.0405754 on 4 procs for 100 steps with 18 atoms
Performance: 212.937 ns/day, 0.113 hours/ns, 2464.547 timesteps/s
98.9% CPU use with 4 MPI tasks x no OpenMP threads
AMEOBA/HIPPO timing breakdown:
Init time: 0.000756446 0.0198927
Hal time: 0.00120064 3.15739
Mpole time: 0.00338295 8.89637
Induce time: 0.0273688 71.9733
Polar time: 0.00530425 13.9489
Total time: 0.0380263
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.03816 | 0.038221 | 0.038312 | 0.0 | 94.20
Bond | 7.0759e-05 | 8.5222e-05 | 0.00010449 | 0.0 | 0.21
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00065721 | 0.00081724 | 0.00093857 | 0.0 | 2.01
Output | 0.0010275 | 0.0010663 | 0.0011758 | 0.2 | 2.63
Modify | 3.3884e-05 | 4.422e-05 | 5.7037e-05 | 0.0 | 0.11
Other | | 0.000341 | | | 0.84
Nlocal: 4.5 ave 6 max 3 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Nghost: 13.5 ave 15 max 12 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Neighs: 38.25 ave 77 max 9 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Total # of neighbors = 153
Ave neighs/atom = 8.5
Ave special neighs/atom = 2
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

45
examples/amoeba/log.water_hexamer.hippo.1
View File

@ -12,8 +12,8 @@ dihedral_style none
# per-atom properties required by AMOEBA or HIPPO
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom i_amgroup d_redID d_xaxis d_yaxis d_zaxis d_pval ghost yes
fix extra2 all property/atom i_polaxe
fix extra all property/atom i_amgroup d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
# read data file
@ -98,7 +98,7 @@ Neighbor list info ...
stencil: half/bin/3d
bin: standard
AMOEBA/HIPPO group count: 6
Per MPI rank memory allocation (min/avg/max) = 9.804 | 9.804 | 9.804 Mbytes
Per MPI rank memory allocation (min/avg/max) = 49.1 | 49.1 | 49.1 Mbytes
Step Temp E_pair E_bond E_angle E_dihed E_impro E_mol TotEng Press c_virial[1] c_virial[2] c_virial[3] c_virial[4] c_virial[5] c_virial[6]
0 0 -47.362156 1.9820353 1.6634749 0 0 3.6455102 -43.716646 -34513.768 -42206.078 -31383.641 -29951.584 2850.1184 3579.9253 5768.3698
10 11.52238 -45.959856 1.53397 0.085100522 0 0 1.6190706 -43.756903 -28644.676 -34867.94 -19324.955 -32842.522 -370.63233 -6452.0859 -4002.3535
@ -110,33 +110,32 @@ Per MPI rank memory allocation (min/avg/max) = 9.804 | 9.804 | 9.804 Mbytes
70 26.129957 -46.022729 0.30434543 0.56770169 0 0 0.87204711 -43.826579 3919.9866 -2755.6905 11500.428 517.54333 5626.9543 -2238.5786 86.305984
80 17.768494 -46.309777 1.1680612 0.45551823 0 0 1.6235794 -43.785801 -18335.898 -22168.789 -14488.992 -20048.346 7343.173 -2646.2196 -2525.6625
90 8.3822494 -47.063502 2.0182644 0.88875358 0 0 2.9070179 -43.731724 -33693.203 -43487.996 -15178.35 -43214.494 2412.6411 1993.0113 1780.7512
AMEOBA/HIPPO timing info:
Init time: 0.000305988 0.00772963
Repls time: 0.00615705 15.5535
Disp time: 0.00270421 6.83116
Mpole time: 0.00727575 18.3794
Induce time: 0.0137304 34.6848
Polar time: 0.00789202 19.9362
Qxfer time: 0.00151645 3.83073
Total time: 0.0395864
100 8.6486333 -46.517402 1.9551958 0.38696887 0 0 2.3421647 -43.736979 -34734.97 -34372.659 -28372.146 -42286.799 226.18821 40.353457 -755.93912
Loop time of 0.0411107 on 1 procs for 100 steps with 18 atoms
Loop time of 0.0399433 on 1 procs for 100 steps with 18 atoms
Performance: 210.164 ns/day, 0.114 hours/ns, 2432.456 timesteps/s
94.5% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 216.307 ns/day, 0.111 hours/ns, 2503.548 timesteps/s
92.6% CPU use with 1 MPI tasks x no OpenMP threads
AMEOBA/HIPPO timing breakdown:
Init time: 0.000295019 0.00770171
Repulse time: 0.00594736 15.5261
Disp time: 0.00261218 6.81931
Mpole time: 0.0069314 18.095
Induce time: 0.013694 35.7492
Polar time: 0.00744631 19.4392
Qxfer time: 0.001375 3.58954
Total time: 0.0383057
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.039681 | 0.039681 | 0.039681 | 0.0 | 96.52
Bond | 0.00018196 | 0.00018196 | 0.00018196 | 0.0 | 0.44
Pair | 0.038344 | 0.038344 | 0.038344 | 0.0 | 96.00
Bond | 0.00017707 | 0.00017707 | 0.00017707 | 0.0 | 0.44
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 1.8274e-05 | 1.8274e-05 | 1.8274e-05 | 0.0 | 0.04
Output | 0.0010806 | 0.0010806 | 0.0010806 | 0.0 | 2.63
Modify | 7.5438e-05 | 7.5438e-05 | 7.5438e-05 | 0.0 | 0.18
Other | | 7.382e-05 | | | 0.18
Comm | 1.5549e-05 | 1.5549e-05 | 1.5549e-05 | 0.0 | 0.04
Output | 0.0012682 | 0.0012682 | 0.0012682 | 0.0 | 3.18
Modify | 7.0869e-05 | 7.0869e-05 | 7.0869e-05 | 0.0 | 0.18
Other | | 6.745e-05 | | | 0.17
Nlocal: 18 ave 18 max 18 min
Histogram: 1 0 0 0 0 0 0 0 0 0

152
examples/amoeba/log.water_hexamer.hippo.1.test
View File

@ -1,152 +0,0 @@
LAMMPS (24 Mar 2022)
# water hexamer with AMOEBA or HIPPO
units real
boundary s s s
atom_style amoeba
bond_style class2
angle_style amoeba
dihedral_style none
# per-atom properties required by AMOEBA or HIPPO
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom i_amgroup d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
# read data file
read_data data.water_hexamer.hippo fix amtype NULL "Tinker Types"
Reading data file ...
orthogonal box = (-2.517835 -1.523041 -1.734766) to (2.675716 2.01883 2.220847)
1 by 1 by 1 MPI processor grid
reading atoms ...
18 atoms
scanning bonds ...
2 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
12 bonds
reading angles ...
6 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.007 seconds
# force field
pair_style hippo
pair_coeff * * hippo_water.prm hippo_water.key
special_bonds lj/coul 0.5 0.5 0.5 one/five yes
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0.5 0.5 0.5
special bond factors coul: 0.5 0.5 0.5
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of 1-5 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
# thermo output
compute virial all pressure NULL virial
thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*]
dump 1 all custom 10 dump.water_hexamer id type x y z fx fy fz
dump_modify 1 sort id
# zero step run
#run 0
# dynamics
fix 1 all nve
thermo 10
run 100
AMOEBA/HIPPO force field settings
repulsion: cut 10 taper 8 rscale 0 0 1 1
qxfer: cut 10 taper 8 mscale 0 0 0.4 1
dispersion: cut 10 aewald 0 dspscale 0 0 0.4 1
multipole: cut 10 aewald 0 mscale 0 0 0.4 1
polar: cut 10 aewald 0
pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 0.2 1 1 1 d/u scale 0 1
precondition: cut 4.5
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair hippo, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
AMOEBA/HIPPO group count: 6
Per MPI rank memory allocation (min/avg/max) = 49.1 | 49.1 | 49.1 Mbytes
Step Temp E_pair E_bond E_angle E_dihed E_impro E_mol TotEng Press c_virial[1] c_virial[2] c_virial[3] c_virial[4] c_virial[5] c_virial[6]
0 0 -47.362156 1.9820353 1.6634749 0 0 3.6455102 -43.716646 -34513.768 -42206.078 -31383.641 -29951.584 2850.1184 3579.9253 5768.3698
10 11.52238 -45.959856 1.53397 0.085100522 0 0 1.6190706 -43.756903 -28644.676 -34867.94 -19324.955 -32842.522 -370.63233 -6452.0859 -4002.3535
20 20.237283 -46.772008 0.54762833 1.3835192 0 0 1.9311476 -43.815361 -10546.356 -10116.359 -17063.425 -6393.701 -1166.7608 4243.6327 3493.9596
30 20.666374 -45.011106 0.086797459 0.071122604 0 0 0.15792006 -43.805943 13150.762 15882.022 10964.553 10630.278 -6754.7642 -432.29165 -3783.115
40 10.639014 -45.430939 0.18926921 0.96410995 0 0 1.1533792 -43.738441 33402.664 41252.58 19726.586 38211.875 -6166.03 6081.5692 1815.7739
50 10.992432 -44.741108 0.19575431 0.25851128 0 0 0.45426559 -43.729815 37696.923 41572.466 33299.43 37168.141 -3254.5134 2.9639226 -1017.3669
60 19.748633 -45.461264 0.035287281 0.63217389 0 0 0.66746117 -43.793065 26212.839 28825.788 16048.096 31876.925 3504.5461 135.3505 420.28566
70 26.129957 -46.022729 0.30434543 0.56770169 0 0 0.87204711 -43.826579 3919.9866 -2755.6905 11500.428 517.54333 5626.9543 -2238.5786 86.305984
80 17.768494 -46.309777 1.1680612 0.45551823 0 0 1.6235794 -43.785801 -18335.898 -22168.789 -14488.992 -20048.346 7343.173 -2646.2196 -2525.6625
90 8.3822494 -47.063502 2.0182644 0.88875358 0 0 2.9070179 -43.731724 -33693.203 -43487.996 -15178.35 -43214.494 2412.6411 1993.0113 1780.7512
100 8.6486333 -46.517402 1.9551958 0.38696887 0 0 2.3421647 -43.736979 -34734.97 -34372.659 -28372.146 -42286.799 226.18821 40.353457 -755.93912
Loop time of 0.0399433 on 1 procs for 100 steps with 18 atoms
Performance: 216.307 ns/day, 0.111 hours/ns, 2503.548 timesteps/s
92.6% CPU use with 1 MPI tasks x no OpenMP threads
AMEOBA/HIPPO timing breakdown:
Init time: 0.000295019 0.00770171
Repulse time: 0.00594736 15.5261
Disp time: 0.00261218 6.81931
Mpole time: 0.0069314 18.095
Induce time: 0.013694 35.7492
Polar time: 0.00744631 19.4392
Qxfer time: 0.001375 3.58954
Total time: 0.0383057
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.038344 | 0.038344 | 0.038344 | 0.0 | 96.00
Bond | 0.00017707 | 0.00017707 | 0.00017707 | 0.0 | 0.44
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 1.5549e-05 | 1.5549e-05 | 1.5549e-05 | 0.0 | 0.04
Output | 0.0012682 | 0.0012682 | 0.0012682 | 0.0 | 3.18
Modify | 7.0869e-05 | 7.0869e-05 | 7.0869e-05 | 0.0 | 0.18
Other | | 6.745e-05 | | | 0.17
Nlocal: 18 ave 18 max 18 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 153 ave 153 max 153 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 153
Ave neighs/atom = 8.5
Ave special neighs/atom = 2
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

47
examples/amoeba/log.water_hexamer.hippo.4
View File

@ -12,8 +12,8 @@ dihedral_style none
# per-atom properties required by AMOEBA or HIPPO
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom i_amgroup d_redID d_xaxis d_yaxis d_zaxis d_pval ghost yes
fix extra2 all property/atom i_polaxe
fix extra all property/atom i_amgroup d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
# read data file
@ -39,7 +39,7 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.007 seconds
read_data CPU = 0.008 seconds
# force field
@ -99,7 +99,7 @@ Neighbor list info ...
bin: standard
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:974)
AMOEBA/HIPPO group count: 6
Per MPI rank memory allocation (min/avg/max) = 9.833 | 9.833 | 9.833 Mbytes
Per MPI rank memory allocation (min/avg/max) = 49.13 | 49.13 | 49.13 Mbytes
Step Temp E_pair E_bond E_angle E_dihed E_impro E_mol TotEng Press c_virial[1] c_virial[2] c_virial[3] c_virial[4] c_virial[5] c_virial[6]
0 0 -47.362156 1.9820353 1.6634749 0 0 3.6455102 -43.716646 -34513.768 -42206.078 -31383.641 -29951.584 2850.1184 3579.9253 5768.3698
10 11.52238 -45.959856 1.53397 0.085100522 0 0 1.6190706 -43.756903 -28644.676 -34867.94 -19324.955 -32842.522 -370.63233 -6452.0859 -4002.3535
@ -111,33 +111,32 @@ Per MPI rank memory allocation (min/avg/max) = 9.833 | 9.833 | 9.833 Mbytes
70 26.129957 -46.022729 0.30434543 0.56770169 0 0 0.87204711 -43.826579 3919.9866 -2755.6905 11500.428 517.54333 5626.9543 -2238.5786 86.305984
80 17.768494 -46.309777 1.1680612 0.45551823 0 0 1.6235794 -43.785801 -18335.898 -22168.789 -14488.992 -20048.346 7343.173 -2646.2196 -2525.6625
90 8.3822494 -47.063502 2.0182644 0.88875358 0 0 2.9070179 -43.731724 -33693.203 -43487.996 -15178.35 -43214.494 2412.6411 1993.0113 1780.7512
AMEOBA/HIPPO timing info:
Init time: 0.000674024 0.0214167
Repls time: 0.00313927 9.97487
Disp time: 0.000678053 2.15448
Mpole time: 0.00411311 13.0692
Induce time: 0.018633 59.2054
Polar time: 0.00385369 12.2449
Qxfer time: 0.000376264 1.19556
Total time: 0.0314718
100 8.6486333 -46.517402 1.9551958 0.38696887 0 0 2.3421647 -43.736979 -34734.97 -34372.659 -28372.146 -42286.799 226.18821 40.353457 -755.93912
Loop time of 0.0345189 on 4 procs for 100 steps with 18 atoms
Loop time of 0.033787 on 4 procs for 100 steps with 18 atoms
Performance: 250.298 ns/day, 0.096 hours/ns, 2896.962 timesteps/s
97.4% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 255.719 ns/day, 0.094 hours/ns, 2959.715 timesteps/s
99.9% CPU use with 4 MPI tasks x no OpenMP threads
AMEOBA/HIPPO timing breakdown:
Init time: 0.000724905 0.0236438
Repulse time: 0.00306516 9.99746
Disp time: 0.000637502 2.07931
Mpole time: 0.00397577 12.9676
Induce time: 0.0181268 59.123
Polar time: 0.00377543 12.3141
Qxfer time: 0.000349256 1.13915
Total time: 0.0306594
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.031394 | 0.031738 | 0.032246 | 0.2 | 91.94
Bond | 5.8552e-05 | 7.4876e-05 | 9.4475e-05 | 0.0 | 0.22
Pair | 0.030576 | 0.030875 | 0.031306 | 0.2 | 91.38
Bond | 6.4191e-05 | 7.956e-05 | 0.0001014 | 0.0 | 0.24
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00068606 | 0.0012736 | 0.0016838 | 1.2 | 3.69
Output | 0.00098398 | 0.0010248 | 0.0011389 | 0.2 | 2.97
Modify | 3.693e-05 | 4.5649e-05 | 5.4845e-05 | 0.0 | 0.13
Other | | 0.0003625 | | | 1.05
Comm | 0.00072972 | 0.0012341 | 0.0015501 | 1.0 | 3.65
Output | 0.0011293 | 0.0011806 | 0.0012922 | 0.2 | 3.49
Modify | 4.0541e-05 | 4.5677e-05 | 5.4304e-05 | 0.0 | 0.14
Other | | 0.0003717 | | | 1.10
Nlocal: 4.5 ave 6 max 3 min
Histogram: 1 0 0 1 0 0 1 0 0 1

153
examples/amoeba/log.water_hexamer.hippo.4.test
View File

@ -1,153 +0,0 @@
LAMMPS (24 Mar 2022)
# water hexamer with AMOEBA or HIPPO
units real
boundary s s s
atom_style amoeba
bond_style class2
angle_style amoeba
dihedral_style none
# per-atom properties required by AMOEBA or HIPPO
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom i_amgroup d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
# read data file
read_data data.water_hexamer.hippo fix amtype NULL "Tinker Types"
Reading data file ...
orthogonal box = (-2.517835 -1.523041 -1.734766) to (2.675716 2.01883 2.220847)
2 by 1 by 2 MPI processor grid
reading atoms ...
18 atoms
scanning bonds ...
2 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
12 bonds
reading angles ...
6 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.008 seconds
# force field
pair_style hippo
pair_coeff * * hippo_water.prm hippo_water.key
special_bonds lj/coul 0.5 0.5 0.5 one/five yes
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0.5 0.5 0.5
special bond factors coul: 0.5 0.5 0.5
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of 1-5 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
# thermo output
compute virial all pressure NULL virial
thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*]
dump 1 all custom 10 dump.water_hexamer id type x y z fx fy fz
dump_modify 1 sort id
# zero step run
#run 0
# dynamics
fix 1 all nve
thermo 10
run 100
AMOEBA/HIPPO force field settings
repulsion: cut 10 taper 8 rscale 0 0 1 1
qxfer: cut 10 taper 8 mscale 0 0 0.4 1
dispersion: cut 10 aewald 0 dspscale 0 0 0.4 1
multipole: cut 10 aewald 0 mscale 0 0 0.4 1
polar: cut 10 aewald 0
pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 0.2 1 1 1 d/u scale 0 1
precondition: cut 4.5
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair hippo, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:974)
AMOEBA/HIPPO group count: 6
Per MPI rank memory allocation (min/avg/max) = 49.13 | 49.13 | 49.13 Mbytes
Step Temp E_pair E_bond E_angle E_dihed E_impro E_mol TotEng Press c_virial[1] c_virial[2] c_virial[3] c_virial[4] c_virial[5] c_virial[6]
0 0 -47.362156 1.9820353 1.6634749 0 0 3.6455102 -43.716646 -34513.768 -42206.078 -31383.641 -29951.584 2850.1184 3579.9253 5768.3698
10 11.52238 -45.959856 1.53397 0.085100522 0 0 1.6190706 -43.756903 -28644.676 -34867.94 -19324.955 -32842.522 -370.63233 -6452.0859 -4002.3535
20 20.237283 -46.772008 0.54762833 1.3835192 0 0 1.9311476 -43.815361 -10546.356 -10116.359 -17063.425 -6393.701 -1166.7608 4243.6327 3493.9596
30 20.666374 -45.011106 0.086797459 0.071122604 0 0 0.15792006 -43.805943 13150.762 15882.022 10964.553 10630.278 -6754.7642 -432.29165 -3783.115
40 10.639014 -45.430939 0.18926921 0.96410995 0 0 1.1533792 -43.738441 33402.664 41252.58 19726.586 38211.875 -6166.03 6081.5692 1815.7739
50 10.992432 -44.741108 0.19575431 0.25851128 0 0 0.45426559 -43.729815 37696.923 41572.466 33299.43 37168.141 -3254.5134 2.9639226 -1017.3669
60 19.748633 -45.461264 0.035287281 0.63217389 0 0 0.66746117 -43.793065 26212.839 28825.788 16048.096 31876.925 3504.5461 135.3505 420.28566
70 26.129957 -46.022729 0.30434543 0.56770169 0 0 0.87204711 -43.826579 3919.9866 -2755.6905 11500.428 517.54333 5626.9543 -2238.5786 86.305984
80 17.768494 -46.309777 1.1680612 0.45551823 0 0 1.6235794 -43.785801 -18335.898 -22168.789 -14488.992 -20048.346 7343.173 -2646.2196 -2525.6625
90 8.3822494 -47.063502 2.0182644 0.88875358 0 0 2.9070179 -43.731724 -33693.203 -43487.996 -15178.35 -43214.494 2412.6411 1993.0113 1780.7512
100 8.6486333 -46.517402 1.9551958 0.38696887 0 0 2.3421647 -43.736979 -34734.97 -34372.659 -28372.146 -42286.799 226.18821 40.353457 -755.93912
Loop time of 0.033787 on 4 procs for 100 steps with 18 atoms
Performance: 255.719 ns/day, 0.094 hours/ns, 2959.715 timesteps/s
99.9% CPU use with 4 MPI tasks x no OpenMP threads
AMEOBA/HIPPO timing breakdown:
Init time: 0.000724905 0.0236438
Repulse time: 0.00306516 9.99746
Disp time: 0.000637502 2.07931
Mpole time: 0.00397577 12.9676
Induce time: 0.0181268 59.123
Polar time: 0.00377543 12.3141
Qxfer time: 0.000349256 1.13915
Total time: 0.0306594
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.030576 | 0.030875 | 0.031306 | 0.2 | 91.38
Bond | 6.4191e-05 | 7.956e-05 | 0.0001014 | 0.0 | 0.24
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00072972 | 0.0012341 | 0.0015501 | 1.0 | 3.65
Output | 0.0011293 | 0.0011806 | 0.0012922 | 0.2 | 3.49
Modify | 4.0541e-05 | 4.5677e-05 | 5.4304e-05 | 0.0 | 0.14
Other | | 0.0003717 | | | 1.10
Nlocal: 4.5 ave 6 max 3 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Nghost: 13.5 ave 15 max 12 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Neighs: 38.25 ave 77 max 9 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Total # of neighbors = 153
Ave neighs/atom = 8.5
Ave special neighs/atom = 2
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00