From cc9632976c7d5282ca5356d8ae78ce7344328839 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 6 Dec 2023 08:32:11 -0500 Subject: [PATCH] recenter box to avoid issues with general triclinic --- tests/examples/USER/misc/flow_gauss/in.GD | 2 +- ...Apr22.linux.8.GD => log.6Dec23.linux.8.GD} | 186 +++++----- .../USER/phonon/2-1D-diatomic/data.pos | 2 +- .../2-1D-diatomic/log.06Jan19.linux.8.Ana | 305 ---------------- .../2-1D-diatomic/log.6Dec23.linux.8.Ana | 325 ++++++++++++++++++ 5 files changed, 422 insertions(+), 398 deletions(-) rename tests/examples/USER/misc/flow_gauss/{log.23Apr22.linux.8.GD => log.6Dec23.linux.8.GD} (88%) delete mode 100644 tests/examples/USER/phonon/2-1D-diatomic/log.06Jan19.linux.8.Ana create mode 100644 tests/examples/USER/phonon/2-1D-diatomic/log.6Dec23.linux.8.Ana diff --git a/tests/examples/USER/misc/flow_gauss/in.GD b/tests/examples/USER/misc/flow_gauss/in.GD index bcff4d4c..a22b440e 100644 --- a/tests/examples/USER/misc/flow_gauss/in.GD +++ b/tests/examples/USER/misc/flow_gauss/in.GD @@ -68,7 +68,7 @@ variable Lx1 equal round(${Lx}/${aWall})*${aWall} #create simulation box variable lx2 equal ${Lx1}/2 variable ly2 equal ${Ly1}/2 -region simbox block -${lx2} ${lx2} -${ly2} ${ly2} 0 0.1 units box +region simbox block -${lx2} ${lx2} -${ly2} ${ly2} -0.1 0.1 units box create_box 2 simbox ##################################################################### diff --git a/tests/examples/USER/misc/flow_gauss/log.23Apr22.linux.8.GD b/tests/examples/USER/misc/flow_gauss/log.6Dec23.linux.8.GD similarity index 88% rename from tests/examples/USER/misc/flow_gauss/log.23Apr22.linux.8.GD rename to tests/examples/USER/misc/flow_gauss/log.6Dec23.linux.8.GD index b4dd3dfb..5447fb7c 100644 --- a/tests/examples/USER/misc/flow_gauss/log.23Apr22.linux.8.GD +++ b/tests/examples/USER/misc/flow_gauss/log.6Dec23.linux.8.GD @@ -1,4 +1,6 @@ -LAMMPS (24 Mar 2022) +LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-132-g9edf553332) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task #LAMMPS input script #in.GD #see README for details @@ -6,6 +8,8 @@ LAMMPS (24 Mar 2022) ############################################################################### #initialize variables clear +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task #frequency for outputting info (timesteps) variable dump_rate equal 50 @@ -87,13 +91,13 @@ variable lx2 equal ${Lx1}/2 variable lx2 equal 100/2 variable ly2 equal ${Ly1}/2 variable ly2 equal 40/2 -region simbox block -${lx2} ${lx2} -${ly2} ${ly2} 0 0.1 units box -region simbox block -50 ${lx2} -${ly2} ${ly2} 0 0.1 units box -region simbox block -50 50 -${ly2} ${ly2} 0 0.1 units box -region simbox block -50 50 -20 ${ly2} 0 0.1 units box -region simbox block -50 50 -20 20 0 0.1 units box +region simbox block -${lx2} ${lx2} -${ly2} ${ly2} -0.1 0.1 units box +region simbox block -50 ${lx2} -${ly2} ${ly2} -0.1 0.1 units box +region simbox block -50 50 -${ly2} ${ly2} -0.1 0.1 units box +region simbox block -50 50 -20 ${ly2} -0.1 0.1 units box +region simbox block -50 50 -20 20 -0.1 0.1 units box create_box 2 simbox -Created orthogonal box = (-50 -20 0) to (50 20 0.1) +Created orthogonal box = (-50 -20 -0.1) to (50 20 0.1) 4 by 2 by 1 MPI processor grid ##################################################################### @@ -119,8 +123,8 @@ timestep 0.001 #create wall atoms everywhere create_atoms 2 box Created 4000 atoms - using lattice units in orthogonal box = (-50 -20 0) to (50 20 0.1) - create_atoms CPU = 0.001 seconds + using lattice units in orthogonal box = (-50 -20 -0.1) to (50 20 0.1) + create_atoms CPU = 0.000 seconds #define region which is "walled off" variable dhalf equal ${d1}/2 @@ -189,7 +193,7 @@ change_box all x final -${lx2} ${lx2} units box change_box all x final -50 ${lx2} units box change_box all x final -50 50 units box Changing box ... - orthogonal box = (-50 -20 0) to (50 20 0.1) + orthogonal box = (-50 -20 -0.1) to (50 20 0.1) #define new lattice lattice custom ${dens} a1 ${ax} 0.0 0.0 a2 0.0 ${ay} 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 @@ -219,8 +223,8 @@ region pipe block -15.001 15.001 -9.999 9.999 -0.1 0.1 region bulk union 3 left pipe right create_atoms 1 region bulk Created 2675 atoms - using lattice units in orthogonal box = (-50 -20 0) to (50 20 0.1) - create_atoms CPU = 0.001 seconds + using lattice units in orthogonal box = (-50 -20 -0.1) to (50 20 0.1) + create_atoms CPU = 0.000 seconds group bulk type 1 2675 atoms in group bulk @@ -230,9 +234,9 @@ group wall type 2 #remove atoms that are too close to wall delete_atoms overlap 0.9 bulk wall System init for delete_atoms ... - generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... - update every 1 steps, delay 10 steps, check yes + update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 2.8 ghost atom cutoff = 2.8 @@ -297,9 +301,9 @@ thermo_style custom step c_myT c_myTp etotal press # dump_modify 56 sort id run 0 WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) - generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... - update every 1 steps, delay 0 steps, check yes + update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 2.8 ghost atom cutoff = 2.8 @@ -313,9 +317,9 @@ Neighbor list info ... Per MPI rank memory allocation (min/avg/max) = 3.064 | 3.065 | 3.065 Mbytes Step c_myT c_myTp TotEng Press 0 2 2.054601 0.77892922 7.3417096 -Loop time of 7.88725e-06 on 8 procs for 0 steps with 2775 atoms +Loop time of 9.31262e-06 on 8 procs for 0 steps with 2775 atoms -42.8% CPU use with 8 MPI tasks x no OpenMP threads +38.9% CPU use with 8 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -325,7 +329,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 7.887e-06 | | |100.00 +Other | | 9.313e-06 | | |100.00 Nlocal: 346.875 ave 400 max 283 min Histogram: 2 2 0 0 0 0 0 0 0 4 @@ -349,12 +353,12 @@ fix nvt bulk nvt temp 2 $T ${tdamp} fix nvt bulk nvt temp 2 2 ${tdamp} fix nvt bulk nvt temp 2 2 0.1 fix_modify nvt temp myTp -WARNING: Temperature for fix modify is not for group all (src/fix_nh.cpp:1423) +WARNING: Temperature for fix modify is not for group all (src/fix_nh.cpp:1391) fix 2 bulk enforce2d run ${equil} run 1000 - generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule Per MPI rank memory allocation (min/avg/max) = 3.127 | 3.127 | 3.128 Mbytes Step c_myT c_myTp TotEng Press 0 2 2.054601 0.77892922 7.3417096 @@ -458,20 +462,20 @@ Per MPI rank memory allocation (min/avg/max) = 3.127 | 3.127 | 3.128 Mbytes 980 1.913512 1.9478848 0.45214528 6.7233279 990 1.9174938 1.9449699 0.44994026 6.6943867 1000 1.9365527 1.9663901 0.44852349 6.6101761 -Loop time of 0.295782 on 8 procs for 1000 steps with 2775 atoms +Loop time of 0.200772 on 8 procs for 1000 steps with 2775 atoms -Performance: 292107.425 tau/day, 3380.873 timesteps/s -99.5% CPU use with 8 MPI tasks x no OpenMP threads +Performance: 430339.469 tau/day, 4980.781 timesteps/s, 13.822 Matom-step/s +92.2% CPU use with 8 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.056246 | 0.080438 | 0.11102 | 7.4 | 27.20 -Neigh | 0.0071692 | 0.010037 | 0.012795 | 2.0 | 3.39 -Comm | 0.031381 | 0.059352 | 0.089142 | 8.0 | 20.07 -Output | 0.011791 | 0.012502 | 0.014989 | 0.9 | 4.23 -Modify | 0.10711 | 0.11621 | 0.13521 | 2.5 | 39.29 -Other | | 0.01724 | | | 5.83 +Pair | 0.029477 | 0.038641 | 0.049245 | 4.0 | 19.25 +Neigh | 0.0042291 | 0.0053815 | 0.0067742 | 1.3 | 2.68 +Comm | 0.028766 | 0.043621 | 0.060373 | 4.8 | 21.73 +Output | 0.01008 | 0.010541 | 0.013214 | 1.0 | 5.25 +Modify | 0.073404 | 0.08011 | 0.085186 | 1.2 | 39.90 +Other | | 0.02248 | | | 11.20 Nlocal: 346.875 ave 401 max 292 min Histogram: 4 0 0 0 0 0 0 0 0 4 @@ -507,7 +511,7 @@ CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: -- Gaussian dynamics package: +- Gaussian dynamics package: doi:10.1021/acs.jpcb.6b09387 @Article{strong_water_2017, title = {The Dynamics of Water in Porous Two-Dimensional Crystals}, @@ -516,7 +520,7 @@ number = {1}, url = {https://doi.org/10.1021/acs.jpcb.6b09387}, doi = {10.1021/acs.jpcb.6b09387}, urldate = {2016-12-07}, -journal = {J. Phys. Chem. B}, +journal = {J.~Phys.\ Chem.~B}, author = {Strong, Steven E. and Eaves, Joel D.}, year = {2017}, pages = {189--207} @@ -524,7 +528,7 @@ pages = {189--207} CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE - generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule Per MPI rank memory allocation (min/avg/max) = 3.127 | 3.127 | 3.128 Mbytes Step c_myT c_myTp TotEng Press 1000 1.9477212 1.9663901 0.45928547 6.6176422 @@ -628,20 +632,20 @@ Per MPI rank memory allocation (min/avg/max) = 3.127 | 3.127 | 3.128 Mbytes 1980 2.0143746 2.0524405 0.52221277 6.5687042 1990 2.0166553 2.0466885 0.5281276 6.5835144 2000 2.0130617 2.0424179 0.53381506 6.6234083 -Loop time of 0.293942 on 8 procs for 1000 steps with 2775 atoms +Loop time of 0.181497 on 8 procs for 1000 steps with 2775 atoms -Performance: 293935.846 tau/day, 3402.035 timesteps/s -99.9% CPU use with 8 MPI tasks x no OpenMP threads +Performance: 476041.666 tau/day, 5509.742 timesteps/s, 15.290 Matom-step/s +93.2% CPU use with 8 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.044173 | 0.075413 | 0.10295 | 7.3 | 25.66 -Neigh | 0.0055128 | 0.0088333 | 0.0111 | 2.0 | 3.01 -Comm | 0.035026 | 0.061235 | 0.087939 | 7.7 | 20.83 -Output | 0.011338 | 0.011931 | 0.013335 | 0.5 | 4.06 -Modify | 0.11197 | 0.11993 | 0.13666 | 2.0 | 40.80 -Other | | 0.0166 | | | 5.65 +Pair | 0.029481 | 0.03915 | 0.046666 | 3.5 | 21.57 +Neigh | 0.0039576 | 0.0049666 | 0.0057814 | 1.1 | 2.74 +Comm | 0.02662 | 0.038326 | 0.051356 | 4.5 | 21.12 +Output | 0.0045575 | 0.0058438 | 0.0067289 | 1.2 | 3.22 +Modify | 0.063771 | 0.073687 | 0.081049 | 2.1 | 40.60 +Other | | 0.01952 | | | 10.76 Nlocal: 346.875 ave 401 max 293 min Histogram: 4 0 0 0 0 0 0 0 0 4 @@ -704,7 +708,7 @@ fix velYprof bulk ave/chunk 1 1 50 chunkY vx file Vy run ${run} run 2000 - generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule Per MPI rank memory allocation (min/avg/max) = 5.135 | 5.136 | 5.136 Mbytes Step c_myT c_myTp TotEng Press 2000 2.0130617 2.0424179 0.53381506 6.6234083 @@ -808,7 +812,7 @@ Per MPI rank memory allocation (min/avg/max) = 5.135 | 5.136 | 5.136 Mbytes 2980 1.9556442 2.0212175 0.48459527 6.6731473 2990 1.9663638 2.0285202 0.49047217 6.667322 3000 1.976263 2.0326354 0.49540098 6.6601492 - 3010 1.9734917 2.0251301 0.49938916 6.6970878 + 3010 1.9734916 2.0251301 0.49938916 6.6970878 3020 1.955368 1.9974693 0.50265656 6.7865104 3030 1.9476644 1.9780945 0.50564273 6.8327176 3040 1.9584769 1.9887952 0.50867872 6.8046262 @@ -821,10 +825,10 @@ Per MPI rank memory allocation (min/avg/max) = 5.135 | 5.136 | 5.136 Mbytes 3110 2.0039819 2.0511266 0.52275172 6.6355886 3120 1.9958773 2.0457899 0.52253307 6.6565817 3130 1.9933925 2.04521 0.52158082 6.6543706 - 3140 1.9936643 2.0477262 0.51996279 6.6395641 + 3140 1.9936643 2.0477262 0.51996279 6.639564 3150 1.9921223 2.0455965 0.51768794 6.6291901 3160 1.9914788 2.0365842 0.51483187 6.6154874 - 3170 1.9922866 2.0422451 0.51144091 6.5976334 + 3170 1.9922866 2.0422451 0.51144092 6.5976334 3180 1.9872806 2.0376593 0.50747923 6.6043774 3190 1.9708577 2.0198422 0.50308657 6.6551127 3200 1.9534272 1.9982319 0.49857904 6.7093718 @@ -858,70 +862,70 @@ Per MPI rank memory allocation (min/avg/max) = 5.135 | 5.136 | 5.136 Mbytes 3480 1.9307395 1.98193 0.47840998 6.7307929 3490 1.9206678 1.9678856 0.47853003 6.7702613 3500 1.9139405 1.955324 0.47914241 6.7934071 - 3510 1.9206383 1.957176 0.48041531 6.763312 - 3520 1.9449301 1.9816996 0.4823109 6.6651453 + 3510 1.9206383 1.9571761 0.48041531 6.763312 + 3520 1.9449301 1.9816996 0.4823109 6.6651452 3530 1.9752924 2.0115126 0.48452681 6.5438659 3540 1.9951599 2.037759 0.48660439 6.463461 - 3550 2.00071 2.0413872 0.48813253 6.4405933 + 3550 2.00071 2.0413872 0.48813252 6.4405933 3560 1.9939017 2.0277566 0.48901382 6.4684771 3570 1.9766844 2.0031366 0.48946452 6.5392906 - 3580 1.9600495 1.9790718 0.48988281 6.6106542 + 3580 1.9600494 1.9790718 0.48988281 6.6106542 3590 1.9522334 1.9727673 0.49062615 6.6517495 3600 1.9522007 1.9829458 0.49183552 6.6635632 3610 1.9614098 1.9992781 0.49340617 6.6407777 3620 1.9739926 2.0159629 0.49511752 6.6062456 - 3630 1.9726539 2.0152219 0.49675446 6.625436 - 3640 1.9613098 2.0017247 0.49829012 6.6828523 + 3630 1.9726539 2.0152219 0.49675445 6.625436 + 3640 1.9613098 2.0017247 0.49829011 6.6828523 3650 1.9577727 2.0000723 0.49991877 6.7111789 3660 1.9626403 2.0037309 0.50175296 6.7072182 3670 1.9603974 1.9937256 0.50383808 6.7277465 3680 1.9532611 1.9846903 0.50638428 6.766139 - 3690 1.9541656 1.9798331 0.50962883 6.7752527 - 3700 1.9656726 1.9951191 0.51377056 6.7462001 - 3710 1.9834474 2.0193011 0.5187681 6.6957856 + 3690 1.9541656 1.9798331 0.50962883 6.7752528 + 3700 1.9656726 1.9951191 0.51377055 6.7462001 + 3710 1.9834474 2.019301 0.5187681 6.6957857 3720 2.0017372 2.0396413 0.52433682 6.6470375 - 3730 2.0109702 2.0469463 0.53011728 6.6363717 + 3730 2.0109702 2.0469463 0.53011727 6.6363717 3740 2.0096858 2.0458572 0.53588233 6.6682278 3750 2.0066189 2.0519842 0.54153098 6.7085484 3760 2.0096125 2.0561094 0.54689936 6.7250789 - 3770 2.0117777 2.0668795 0.55183558 6.7400961 - 3780 2.0154601 2.0763941 0.55607391 6.7423368 - 3790 2.0313954 2.0972106 0.55930714 6.6920108 - 3800 2.0496133 2.1176374 0.56110467 6.6271088 - 3810 2.0553084 2.1205041 0.56098738 6.6034667 - 3820 2.0478771 2.1131255 0.55870309 6.6239895 - 3830 2.0342107 2.0991257 0.55418077 6.663231 - 3840 2.0142205 2.0767164 0.5475632 6.7196408 - 3850 1.9879527 2.0516847 0.53919956 6.7932757 - 3860 1.9593315 2.0232738 0.52966135 6.8686985 - 3870 1.9362884 1.9952027 0.51970091 6.9156688 - 3880 1.9292998 1.9883081 0.50996281 6.8957696 - 3890 1.9372438 1.9978667 0.50073928 6.8160962 - 3900 1.949918 2.0107189 0.49208883 6.7186534 - 3910 1.9547594 2.0160936 0.48397838 6.6537347 - 3920 1.9543568 2.0191268 0.47640162 6.6136065 - 3930 1.9582199 2.020036 0.46933872 6.5629723 - 3940 1.9644632 2.0304626 0.46272219 6.5077174 - 3950 1.9645882 2.030183 0.4564441 6.4795256 - 3960 1.9546999 2.0197242 0.45050582 6.4943662 - 3970 1.9424307 2.0063452 0.44500623 6.5237707 - 3980 1.9281472 1.9910524 0.44010498 6.5640158 - 3990 1.9168821 1.976369 0.43594016 6.5926212 - 4000 1.9150055 1.9752501 0.43256473 6.5855643 -Loop time of 0.611475 on 8 procs for 2000 steps with 2775 atoms - -Performance: 282595.183 tau/day, 3270.778 timesteps/s -99.9% CPU use with 8 MPI tasks x no OpenMP threads + 3770 2.0117777 2.0668795 0.55183559 6.7400962 + 3780 2.0154601 2.0763941 0.55607392 6.7423369 + 3790 2.0313954 2.0972106 0.55930714 6.6920109 + 3800 2.0496133 2.1176374 0.56110468 6.6271089 + 3810 2.0553084 2.1205041 0.56098739 6.6034668 + 3820 2.0478771 2.1131255 0.55870311 6.6239896 + 3830 2.0342107 2.0991257 0.55418079 6.663231 + 3840 2.0142205 2.0767164 0.54756322 6.7196408 + 3850 1.9879527 2.0516847 0.53919958 6.7932758 + 3860 1.9593315 2.0232738 0.52966137 6.8686985 + 3870 1.9362884 1.9952027 0.51970093 6.9156688 + 3880 1.9292998 1.9883081 0.50996284 6.8957696 + 3890 1.9372438 1.9978668 0.50073931 6.8160962 + 3900 1.949918 2.0107189 0.49208885 6.7186535 + 3910 1.9547594 2.0160936 0.48397841 6.6537347 + 3920 1.9543568 2.0191268 0.47640164 6.6136066 + 3930 1.9582199 2.020036 0.46933874 6.5629724 + 3940 1.9644632 2.0304626 0.46272221 6.5077175 + 3950 1.9645882 2.030183 0.45644412 6.4795257 + 3960 1.9546999 2.0197242 0.45050583 6.4943664 + 3970 1.9424307 2.0063452 0.44500625 6.5237707 + 3980 1.9281472 1.9910524 0.440105 6.5640157 + 3990 1.9168821 1.976369 0.43594017 6.5926212 + 4000 1.9150055 1.9752501 0.43256475 6.5855643 +Loop time of 0.464374 on 8 procs for 2000 steps with 2775 atoms + +Performance: 372113.985 tau/day, 4306.875 timesteps/s, 11.952 Matom-step/s +91.4% CPU use with 8 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.097975 | 0.15488 | 0.20389 | 10.2 | 25.33 -Neigh | 0.012788 | 0.019074 | 0.023093 | 2.9 | 3.12 -Comm | 0.061464 | 0.11054 | 0.17136 | 12.3 | 18.08 -Output | 0.028843 | 0.035675 | 0.03718 | 1.4 | 5.83 -Modify | 0.24221 | 0.25693 | 0.2769 | 2.1 | 42.02 -Other | | 0.03438 | | | 5.62 +Pair | 0.061056 | 0.080029 | 0.095433 | 5.1 | 17.23 +Neigh | 0.0086591 | 0.01104 | 0.013647 | 1.8 | 2.38 +Comm | 0.052263 | 0.078317 | 0.10124 | 5.9 | 16.87 +Output | 0.037845 | 0.046447 | 0.052064 | 2.0 | 10.00 +Modify | 0.19166 | 0.20338 | 0.22105 | 2.0 | 43.80 +Other | | 0.04516 | | | 9.73 Nlocal: 346.875 ave 401 max 291 min Histogram: 4 0 0 0 0 0 0 0 0 4 @@ -934,4 +938,4 @@ Total # of neighbors = 24313 Ave neighs/atom = 8.7614414 Neighbor list builds = 75 Dangerous builds = 0 -Total wall time: 0:00:01 +Total wall time: 0:00:00 diff --git a/tests/examples/USER/phonon/2-1D-diatomic/data.pos b/tests/examples/USER/phonon/2-1D-diatomic/data.pos index cba35b49..3ab4033a 100644 --- a/tests/examples/USER/phonon/2-1D-diatomic/data.pos +++ b/tests/examples/USER/phonon/2-1D-diatomic/data.pos @@ -8,7 +8,7 @@ 0.00000000 64.00000000 xlo xhi 0.00000000 1.00000000 ylo yhi - 0.00000000 1.00000000 zlo zhi + -0.50000000 0.50000000 zlo zhi Atoms diff --git a/tests/examples/USER/phonon/2-1D-diatomic/log.06Jan19.linux.8.Ana b/tests/examples/USER/phonon/2-1D-diatomic/log.06Jan19.linux.8.Ana deleted file mode 100644 index 86d4494a..00000000 --- a/tests/examples/USER/phonon/2-1D-diatomic/log.06Jan19.linux.8.Ana +++ /dev/null @@ -1,305 +0,0 @@ -LAMMPS (4 Jan 2019) -# 3D simple cubic lattice simulation -dimension 2 -boundary p f p - -units lj -atom_style bond -atom_modify sort 0 1. -bond_style harmonic -pair_style none -comm_modify cutoff 2.0 - -# geometry -read_data data.pos - orthogonal box = (0 0 0) to (64 1 1) - 8 by 1 by 1 MPI processor grid - reading atoms ... - 64 atoms - scanning bonds ... - 2 = max bonds/atom - reading bonds ... - 64 bonds - 2 = max # of 1-2 neighbors - 2 = max # of 1-3 neighbors - 4 = max # of 1-4 neighbors - 6 = max # of special neighbors - -# -neighbor 1.0 nsq -neigh_modify delay 0 check no - -#Langevin random seed -variable r equal 571101 - -#Langevin Temperature -variable t equal 0.005 - -# Langevin Damping variable -variable d equal 0.5 - -# Create velocities and equilibrate -compute MyTemp all temp/partial 1 0 0 -velocity all create $t 28711 mom yes rot yes dist gaussian temp MyTemp -velocity all create 0.005 28711 mom yes rot yes dist gaussian temp MyTemp -velocity all set NULL 0.0 0.0 units box -# -fix 1 all langevin $t $t $d $r -fix 1 all langevin 0.005 $t $d $r -fix 1 all langevin 0.005 0.005 $d $r -fix 1 all langevin 0.005 0.005 0.5 $r -fix 1 all langevin 0.005 0.005 0.5 571101 -fix_modify 1 temp MyTemp -fix 2 all setforce NULL 0. 0. -fix 3 all nve -fix 4 all phonon 10 50000 500000 map.in phonon sysdim 1 -fix_modify 4 temp MyTemp - -# 1 2 3 4 -thermo_style custom step temp pe etotal -thermo_modify temp MyTemp -thermo 100 - -# -run 20000 -Neighbor list info ... - update every 1 steps, delay 0 steps, check no - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 0 - ghost atom cutoff = 2 - 0 neighbor lists, perpetual/occasional/extra = 0 0 0 -Per MPI rank memory allocation (min/avg/max) = 3.233 | 3.233 | 3.233 Mbytes -Step Temp PotEng TotEng - 0 0.005 0 0.0024609375 - 100 0.0040317698 0.00057611306 0.0025604997 - 200 0.0039466978 0.0014798375 0.0034223528 - 300 0.0049810321 0.0015344278 0.0039860295 - 400 0.0037348908 0.0016782267 0.0035164933 - 500 0.0037881177 0.0015677155 0.0034321796 - 600 0.0041689301 0.0017321518 0.0037840471 - 700 0.0058760646 0.0016058402 0.0044979658 - 800 0.0047107527 0.0015931496 0.0039117232 - 900 0.0043877843 0.0019178716 0.0040774842 - 1000 0.0025890269 0.0021471924 0.0034214791 - 1100 0.0038592006 0.0022346004 0.0041340507 - 1200 0.004387057 0.0024507654 0.00461002 - 1300 0.0048111907 0.0023009732 0.0046689811 - 1400 0.0040750613 0.0019856631 0.0039913573 - 1500 0.0054785426 0.0018574075 0.0045538776 - 1600 0.0042296974 0.0017625075 0.0038443117 - 1700 0.0053368425 0.0021909162 0.0048176434 - 1800 0.0047155011 0.002485385 0.0048062957 - 1900 0.0058375543 0.0027155715 0.0055887428 - 2000 0.0051879408 0.0028862341 0.0054396737 - 2100 0.0046916962 0.0025370381 0.0048462323 - 2200 0.0033521181 0.0023402854 0.003990156 - 2300 0.0049801639 0.0018232806 0.004274455 - 2400 0.0050811427 0.0018368938 0.0043377687 - 2500 0.0042478497 0.0019609695 0.004051708 - 2600 0.0062970026 0.0022437587 0.0053430646 - 2700 0.0059960596 0.0025439406 0.0054951262 - 2800 0.0063446105 0.0025248024 0.0056475404 - 2900 0.0060654889 0.002105717 0.0050910749 - 3000 0.0040624598 0.0022728422 0.0042723341 - 3100 0.0050390187 0.0025647466 0.0050448886 - 3200 0.005602116 0.002787116 0.0055444075 - 3300 0.0042929653 0.002781784 0.0048947278 - 3400 0.0066134583 0.0029329302 0.0061879917 - 3500 0.0063468439 0.0028931967 0.0060170339 - 3600 0.006017959 0.0027217173 0.0056836815 - 3700 0.0053175638 0.0025847578 0.0052019962 - 3800 0.0052680024 0.0022124533 0.0048052983 - 3900 0.005470927 0.0027146952 0.0054074171 - 4000 0.0056387931 0.0027104052 0.0054857487 - 4100 0.0045195513 0.0022641002 0.0044885669 - 4200 0.0030188033 0.0019143621 0.0034001793 - 4300 0.0064826856 0.0017180483 0.0049087451 - 4400 0.0037430095 0.0027018963 0.0045441588 - 4500 0.0046063907 0.0028447641 0.005111972 - 4600 0.0054743512 0.0021702013 0.0048646086 - 4700 0.004028283 0.001948861 0.0039315316 - 4800 0.005078026 0.0020112375 0.0045105784 - 4900 0.0044808181 0.0021876377 0.0043930404 - 5000 0.0054682534 0.0024186264 0.0051100324 - 5100 0.0039524207 0.0024300354 0.0043753675 - 5200 0.0054651391 0.0023352584 0.0050251315 - 5300 0.0042802074 0.0023567677 0.0044634323 - 5400 0.0052282133 0.0021414153 0.0047146765 - 5500 0.0051670461 0.0019601609 0.0045033165 - 5600 0.0042548158 0.0021833764 0.0042775435 - 5700 0.0065919467 0.0023731587 0.0056176325 - 5800 0.0056629728 0.0021464685 0.0049337129 - 5900 0.0048028421 0.0020022955 0.0043661943 - 6000 0.0040232417 0.0018899295 0.0038701188 - 6100 0.0066009682 0.0018757268 0.0051246408 - 6200 0.0038893329 0.002165131 0.004079412 - 6300 0.0045644486 0.0023343887 0.0045809533 - 6400 0.0054516489 0.0022265175 0.004909751 - 6500 0.0054579579 0.001923252 0.0046095906 - 6600 0.005248124 0.0022589614 0.0048420224 - 6700 0.0073402378 0.0025768098 0.006189583 - 6800 0.0062693704 0.0029554422 0.0060411479 - 6900 0.0059127809 0.0023761519 0.0052863487 - 7000 0.0043903813 0.0018805407 0.0040414315 - 7100 0.0064692049 0.0014238462 0.004607908 - 7200 0.0067438425 0.0016114404 0.0049306754 - 7300 0.0039799918 0.0020904108 0.0040493131 - 7400 0.0077346428 0.0019930186 0.0057999131 - 7500 0.0058797138 0.0015593511 0.0044532728 - 7600 0.0040191429 0.0018672418 0.0038454137 - 7700 0.0039342019 0.0017630444 0.0036994093 - 7800 0.003693069 0.0018600394 0.0036777218 - 7900 0.0045467714 0.0018814723 0.0041193363 - 8000 0.0071366715 0.0019307057 0.0054432862 - 8100 0.0053134895 0.0019695553 0.0045847884 - 8200 0.0039451994 0.0025648908 0.0045066686 - 8300 0.0060010431 0.0023961043 0.0053497427 - 8400 0.0061549258 0.0023176221 0.0053469997 - 8500 0.0042619034 0.0023784736 0.0044761292 - 8600 0.0049493025 0.0025288018 0.0049647866 - 8700 0.0059442009 0.0025678062 0.0054934676 - 8800 0.0059890199 0.0028485272 0.0057962479 - 8900 0.0058196199 0.0029027136 0.0057670578 - 9000 0.0039073692 0.0028440115 0.0047671698 - 9100 0.0055731882 0.0024231007 0.0051661543 - 9200 0.006115157 0.0022834159 0.0052932197 - 9300 0.0037989013 0.002231824 0.0041015957 - 9400 0.005020721 0.0020809508 0.0045520869 - 9500 0.0037841915 0.0021453576 0.0040078893 - 9600 0.0064431036 0.0018965958 0.0050678108 - 9700 0.0062930554 0.0022137654 0.0053111286 - 9800 0.00346704 0.0021389496 0.0038453833 - 9900 0.0056712706 0.0017413773 0.0045327057 - 10000 0.004721313 0.0022513152 0.0045750864 - 10100 0.0050400459 0.0022557677 0.0047364153 - 10200 0.006386415 0.0018911503 0.0050344639 - 10300 0.0045078219 0.0028018432 0.0050205368 - 10400 0.0048063429 0.0021738471 0.004539469 - 10500 0.00537903 0.0018457553 0.0044932467 - 10600 0.0041890109 0.0019266016 0.0039883804 - 10700 0.005443143 0.0020939606 0.0047730075 - 10800 0.0050528278 0.0020492432 0.0045361819 - 10900 0.005769596 0.0016270627 0.0044667858 - 11000 0.0056733394 0.0017745252 0.004566872 - 11100 0.0052934221 0.0019894313 0.0045947875 - 11200 0.0044870893 0.0018164736 0.0040249629 - 11300 0.0053161354 0.0017951342 0.0044116697 - 11400 0.005259404 0.0017022739 0.0042908868 - 11500 0.0042197805 0.002096343 0.0041732662 - 11600 0.0050229323 0.0022651745 0.004737399 - 11700 0.0052706698 0.0022179931 0.0048121508 - 11800 0.006160635 0.0021756981 0.0052078856 - 11900 0.0035528892 0.0024710812 0.0042197688 - 12000 0.0058424856 0.0026953604 0.0055709588 - 12100 0.0061898245 0.0025188692 0.0055654234 - 12200 0.006831648 0.002170524 0.0055329757 - 12300 0.0035095309 0.002067062 0.0037944092 - 12400 0.0044682302 0.0024620271 0.0046612341 - 12500 0.0048661249 0.0027292712 0.0051243171 - 12600 0.0056244803 0.0024880727 0.0052563715 - 12700 0.0054933101 0.0018814342 0.0045851727 - 12800 0.0055651513 0.0019585684 0.0046976664 - 12900 0.0032487726 0.0024590263 0.0040580316 - 13000 0.006542736 0.0022764878 0.0054967407 - 13100 0.0046951427 0.0022041085 0.0045149991 - 13200 0.0064950854 0.0016414374 0.0048382373 - 13300 0.0042674494 0.0018852606 0.0039856459 - 13400 0.0053467575 0.0021467875 0.0047783947 - 13500 0.0054076368 0.0022546674 0.0049162386 - 13600 0.0047325869 0.0028583272 0.0051876473 - 13700 0.0049967211 0.0022623977 0.0047217214 - 13800 0.0060452058 0.0017945719 0.0047699467 - 13900 0.0053914404 0.0019985338 0.0046521334 - 14000 0.0038540387 0.0025482084 0.0044451181 - 14100 0.0048951011 0.0026749967 0.0050843043 - 14200 0.0047756809 0.0019877947 0.0043383252 - 14300 0.0051096077 0.0018631064 0.0043779914 - 14400 0.0057812762 0.0017694286 0.0046149005 - 14500 0.0056121936 0.0017261963 0.0044884478 - 14600 0.0058210314 0.001989082 0.0048541209 - 14700 0.005186483 0.0025778738 0.0051305959 - 14800 0.0041351683 0.0023327863 0.0043680644 - 14900 0.004305324 0.0024104247 0.0045294514 - 15000 0.0054904198 0.002323945 0.0050262609 - 15100 0.0055249952 0.0023875783 0.0051069119 - 15200 0.0046056582 0.0022511493 0.0045179967 - 15300 0.0069335372 0.0022229056 0.0056355059 - 15400 0.0061379998 0.0020399043 0.005060951 - 15500 0.0040218515 0.0024960325 0.0044755375 - 15600 0.0044245533 0.0023778495 0.0045555594 - 15700 0.0054357019 0.002334036 0.0050094205 - 15800 0.0050325279 0.0022926191 0.0047695664 - 15900 0.0068350459 0.0017613576 0.0051254818 - 16000 0.0043537231 0.0026397702 0.0047826183 - 16100 0.0062948757 0.0026681887 0.0057664479 - 16200 0.0048455857 0.002381603 0.0047665397 - 16300 0.0056432303 0.0023998654 0.0051773928 - 16400 0.0044684105 0.0027800699 0.0049793657 - 16500 0.0059661504 0.0029200866 0.0058565513 - 16600 0.0069573771 0.0026528611 0.0060771951 - 16700 0.0054694778 0.0032303884 0.005922397 - 16800 0.0047425987 0.0032413648 0.0055756127 - 16900 0.0045441118 0.0029243397 0.0051608947 - 17000 0.0054294546 0.0026243849 0.0052966946 - 17100 0.0038026024 0.0021776854 0.0040492788 - 17200 0.0056089724 0.0015755028 0.0043361689 - 17300 0.005163097 0.0019157689 0.0044569807 - 17400 0.0041711402 0.0022300707 0.0042830538 - 17500 0.0046863457 0.0018701361 0.0041766968 - 17600 0.0038006416 0.001795451 0.0036660793 - 17700 0.0062488598 0.0022363257 0.0053119364 - 17800 0.0063191541 0.0027846283 0.005894837 - 17900 0.0058737541 0.002700107 0.0055910954 - 18000 0.0057721618 0.0024534552 0.0052944411 - 18100 0.0061951884 0.0028344746 0.0058836689 - 18200 0.0048230864 0.0033880583 0.0057619211 - 18300 0.0044808561 0.0034652449 0.0056706662 - 18400 0.0075139088 0.0027807761 0.006479028 - 18500 0.005555126 0.0024207514 0.005154915 - 18600 0.0056004285 0.0022551893 0.0050116502 - 18700 0.0053077569 0.002349624 0.0049620356 - 18800 0.0055811689 0.0024244994 0.0051714809 - 18900 0.0043818222 0.0025569507 0.0047136288 - 19000 0.0040143327 0.0024028413 0.0043786457 - 19100 0.0070578223 0.0021099546 0.0055837265 - 19200 0.0037928503 0.0023082214 0.0041750149 - 19300 0.0048818228 0.0022283322 0.0046311044 - 19400 0.0037943219 0.002917794 0.0047853118 - 19500 0.0042177805 0.0028149483 0.0048908871 - 19600 0.0043524695 0.0025860053 0.0047282364 - 19700 0.0058013866 0.0027400475 0.0055954175 - 19800 0.0047681786 0.0034511924 0.0057980303 - 19900 0.0055118425 0.0030527188 0.0057655788 - 20000 0.0066763605 0.0027926431 0.0060786643 -Loop time of 0.390598 on 8 procs for 20000 steps with 64 atoms - -Performance: 22119917.358 tau/day, 51203.512 timesteps/s -99.9% CPU use with 8 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Bond | 0.0041523 | 0.004827 | 0.0057615 | 0.8 | 1.24 -Neigh | 0.0583 | 0.064393 | 0.070362 | 1.4 | 16.49 -Comm | 0.22944 | 0.23781 | 0.24809 | 1.3 | 60.88 -Output | 0.0020355 | 0.0021165 | 0.0025374 | 0.3 | 0.54 -Modify | 0.073112 | 0.07647 | 0.079733 | 0.9 | 19.58 -Other | | 0.004977 | | | 1.27 - -Nlocal: 8 ave 9 max 7 min -Histogram: 2 0 0 0 0 4 0 0 0 2 -Nghost: 3.75 ave 5 max 2 min -Histogram: 1 0 0 1 0 0 5 0 0 1 -Neighs: 0 ave 0 max 0 min -Histogram: 8 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 0 -Ave neighs/atom = 0 -Ave special neighs/atom = 6 -Neighbor list builds = 20000 -Dangerous builds not checked - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:00 diff --git a/tests/examples/USER/phonon/2-1D-diatomic/log.6Dec23.linux.8.Ana b/tests/examples/USER/phonon/2-1D-diatomic/log.6Dec23.linux.8.Ana new file mode 100644 index 00000000..ac6bd0c8 --- /dev/null +++ b/tests/examples/USER/phonon/2-1D-diatomic/log.6Dec23.linux.8.Ana @@ -0,0 +1,325 @@ +LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-132-g9edf553332) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# 3D simple cubic lattice simulation +dimension 2 +boundary p f p + +units lj +atom_style bond +atom_modify sort 0 1. +bond_style harmonic +pair_style none +comm_modify cutoff 2.0 + +# geometry +read_data data.pos +Reading data file ... + orthogonal box = (0 0 -0.5) to (64 1 0.5) + 8 by 1 by 1 MPI processor grid + reading atoms ... + 64 atoms + scanning bonds ... + 2 = max bonds/atom + reading bonds ... + 64 bonds +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 + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.001 seconds + read_data CPU = 0.002 seconds + +# +neighbor 1.0 nsq +neigh_modify delay 0 check no + +#Langevin random seed +variable r equal 571101 + +#Langevin Temperature +variable t equal 0.005 + +# Langevin Damping variable +variable d equal 0.5 + +# Create velocities and equilibrate +compute MyTemp all temp/partial 1 0 0 +velocity all create $t 28711 mom yes rot yes dist gaussian temp MyTemp +velocity all create 0.005 28711 mom yes rot yes dist gaussian temp MyTemp +velocity all set NULL 0.0 0.0 units box +# +fix 1 all langevin $t $t $d $r +fix 1 all langevin 0.005 $t $d $r +fix 1 all langevin 0.005 0.005 $d $r +fix 1 all langevin 0.005 0.005 0.5 $r +fix 1 all langevin 0.005 0.005 0.5 571101 +fix_modify 1 temp MyTemp +fix 2 all setforce NULL 0. 0. +fix 3 all nve +fix 4 all phonon 10 50000 500000 map.in phonon sysdim 1 +fix_modify 4 temp MyTemp + +# 1 2 3 4 +thermo_style custom step temp pe etotal +thermo_modify temp MyTemp +thermo 100 + +# +run 20000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix phonon command: doi:10.1016/j.cpc.2011.04.019 + +@Article{Kong11, + author = {L. T. Kong}, + title = {Phonon Dispersion Measured Directly from Molecular Dynamics Simulations}, + journal = {Comput.\ Phys.\ Commun.}, + year = 2011, + volume = 182, + pages = {2201--2207} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +WARNING: Communication cutoff 2 is shorter than a bond length based estimate of 2.5. This may lead to errors. (src/comm.cpp:723) +WARNING: Communication cutoff 2 is shorter than a bond length based estimate of 2.5. This may lead to errors. (src/comm.cpp:723) +WARNING: Inconsistent image flags (src/domain.cpp:815) +Per MPI rank memory allocation (min/avg/max) = 3.234 | 3.234 | 3.234 Mbytes + Step Temp PotEng TotEng + 0 0.005 0 0.0024609375 + 100 0.0040317698 0.00057611306 0.0025604997 + 200 0.0039466978 0.0014798375 0.0034223528 + 300 0.0049810321 0.0015344278 0.0039860295 + 400 0.0037348908 0.0016782267 0.0035164933 + 500 0.0037881177 0.0015677155 0.0034321796 + 600 0.0041689301 0.0017321518 0.0037840471 + 700 0.0058760646 0.0016058402 0.0044979658 + 800 0.0047107527 0.0015931496 0.0039117232 + 900 0.0043877843 0.0019178716 0.0040774842 + 1000 0.0025890269 0.0021471924 0.0034214791 + 1100 0.0038592006 0.0022346004 0.0041340507 + 1200 0.004387057 0.0024507654 0.00461002 + 1300 0.0048111907 0.0023009732 0.0046689811 + 1400 0.0040750613 0.0019856631 0.0039913573 + 1500 0.0054785426 0.0018574075 0.0045538776 + 1600 0.0042296974 0.0017625075 0.0038443117 + 1700 0.0053368425 0.0021909162 0.0048176434 + 1800 0.0047155011 0.002485385 0.0048062957 + 1900 0.0058375543 0.0027155715 0.0055887428 + 2000 0.0051879408 0.0028862341 0.0054396737 + 2100 0.0046916962 0.0025370381 0.0048462323 + 2200 0.0033521181 0.0023402854 0.003990156 + 2300 0.0049801639 0.0018232806 0.004274455 + 2400 0.0050811427 0.0018368938 0.0043377687 + 2500 0.0042478497 0.0019609695 0.004051708 + 2600 0.0062970026 0.0022437587 0.0053430646 + 2700 0.0059960596 0.0025439406 0.0054951262 + 2800 0.0063446105 0.0025248024 0.0056475404 + 2900 0.0060654889 0.002105717 0.0050910749 + 3000 0.0040624598 0.0022728422 0.0042723341 + 3100 0.0050390187 0.0025647466 0.0050448886 + 3200 0.005602116 0.002787116 0.0055444075 + 3300 0.0042929653 0.002781784 0.0048947278 + 3400 0.0066134583 0.0029329302 0.0061879917 + 3500 0.0063468439 0.0028931967 0.0060170339 + 3600 0.006017959 0.0027217173 0.0056836815 + 3700 0.0053175638 0.0025847578 0.0052019962 + 3800 0.0052680024 0.0022124533 0.0048052983 + 3900 0.005470927 0.0027146952 0.0054074171 + 4000 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0.20028 | 3.3 | 49.50 +Output | 0.0023346 | 0.0039064 | 0.010653 | 4.1 | 1.07 +Modify | 0.0638 | 0.086832 | 0.10556 | 3.9 | 23.87 +Other | | 0.02304 | | | 6.33 + +Nlocal: 8 ave 9 max 7 min +Histogram: 2 0 0 0 0 4 0 0 0 2 +Nghost: 3.75 ave 5 max 2 min +Histogram: 1 0 0 1 0 0 5 0 0 1 +Neighs: 0 ave 0 max 0 min +Histogram: 8 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Ave special neighs/atom = 6 +Neighbor list builds = 20000 +Dangerous builds not checked +Total wall time: 0:00:00