From 5d02e140d467756260ff3510f65d4c0d2ecffee7 Mon Sep 17 00:00:00 2001 From: 3j <1310424077@qq.com> Date: Fri, 28 Feb 2025 17:43:54 +0800 Subject: [PATCH 1/2] There is a wrong equation in the line490, MY_4PI should be MY_PI*zt --- src/ASPHERE/pair_ylz.cpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/ASPHERE/pair_ylz.cpp b/src/ASPHERE/pair_ylz.cpp index 833dc8e3e4..d52765283c 100644 --- a/src/ASPHERE/pair_ylz.cpp +++ b/src/ASPHERE/pair_ylz.cpp @@ -32,7 +32,7 @@ #include using namespace LAMMPS_NS; -using MathConst::MY_4PI; +using MathConst::MY_PI; using MathConst::MY_PI2; using MathConst::MY_TWOBYSIXTH; @@ -487,7 +487,7 @@ double PairYLZ::ylz_analytic(const int i, const int j, double a1[3][3], double a uA = -energy_well * t1 * cos_t; U = uA * phi; - dUdr = MY_4PI / (rcut - rmin) * (t1) *sin(t) * phi * energy_well; + dUdr = MY_PI * zt / (rcut - rmin) * (t1) *sin(t) * phi * energy_well; dUdphi = uA; } From bc3aafd324dac5a8791180b4dcf3eb96f2c2ce5a Mon Sep 17 00:00:00 2001 From: megmcca Date: Mon, 3 Mar 2025 08:06:33 -0700 Subject: [PATCH 2/2] update log files after bugfix to pair_style ylz --- ...e.g++.1 => log.3Mar25.flat_membrane.g++.1} | 67 ++++++++--------- ...e.g++.4 => log.3Mar25.flat_membrane.g++.4} | 71 ++++++++++--------- 2 files changed, 70 insertions(+), 68 deletions(-) rename examples/ASPHERE/flat_membrane/{log.18Oct22.flat_membrane.g++.1 => log.3Mar25.flat_membrane.g++.1} (66%) rename examples/ASPHERE/flat_membrane/{log.18Oct22.flat_membrane.g++.4 => log.3Mar25.flat_membrane.g++.4} (65%) diff --git a/examples/ASPHERE/flat_membrane/log.18Oct22.flat_membrane.g++.1 b/examples/ASPHERE/flat_membrane/log.3Mar25.flat_membrane.g++.1 similarity index 66% rename from examples/ASPHERE/flat_membrane/log.18Oct22.flat_membrane.g++.1 rename to examples/ASPHERE/flat_membrane/log.3Mar25.flat_membrane.g++.1 index 750aa5328c..5c051bb725 100644 --- a/examples/ASPHERE/flat_membrane/log.18Oct22.flat_membrane.g++.1 +++ b/examples/ASPHERE/flat_membrane/log.3Mar25.flat_membrane.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (15 Sep 2022) +LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-106-g5d02e140d4) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99) using 1 OpenMP thread(s) per MPI task # flat membrane demo variable r0 equal 0.97 @@ -46,7 +47,7 @@ set type 1 mass 1.0 Setting atom values ... 1920 settings made for mass -set type 1 shape 1 1 1 +set type 1 shape 1 0.99 0.99 Setting atom values ... 1920 settings made for shape @@ -99,7 +100,7 @@ CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Generated 0 of 0 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 = 3.6 ghost atom cutoff = 3.6 @@ -113,47 +114,47 @@ Neighbor list info ... Per MPI rank memory allocation (min/avg/max) = 5.024 | 5.024 | 5.024 Mbytes Step Temp Press Pxx Pyy 0 0.23 -0.0073508785 -0.012283389 -0.012234574 - 200 0.20903886 -0.0010605951 -0.0011885957 -0.00198842 - 400 0.21898026 -0.00069250685 -0.0013217981 -0.00073225707 - 600 0.22689361 -0.00057919328 -0.00076880503 -0.0010242283 - 800 0.22983221 -0.00032145682 -0.00051928834 -0.00059337525 - 1000 0.23819392 -0.00027969126 -0.00088082301 -5.2666567e-05 - 1200 0.22053795 -0.00029571329 -0.0004446455 -0.00035529929 - 1400 0.22285021 -0.0002690371 -0.00068896571 -3.6258442e-05 - 1600 0.22687044 2.8599875e-05 -0.00032651798 0.0004056081 - 1800 0.23356905 -2.28742e-05 -0.00027073251 0.00025081131 - 2000 0.22499821 8.8230586e-06 -7.5750159e-05 0.0001988705 - 2200 0.23162995 -9.026855e-05 -0.00025832535 5.4904927e-05 - 2400 0.22920223 0.00016700455 3.5283125e-05 0.00034955857 - 2600 0.2260299 5.3095557e-05 0.00025691786 0.00013353467 - 2800 0.2296401 0.00043234854 0.00058344966 0.00063645193 - 3000 0.22564577 2.6423111e-05 8.9918406e-05 0.00022146229 -Loop time of 6.76659 on 1 procs for 3000 steps with 1920 atoms + 200 0.20906916 -0.0010610794 -0.0011895359 -0.00198968 + 400 0.21907691 -0.00068750897 -0.0013175111 -0.00072355516 + 600 0.22648739 -0.00057306694 -0.000831971 -0.00096776143 + 800 0.2368957 -0.00028517767 -0.00050638195 -0.00052670236 + 1000 0.22735705 -0.00032638104 -0.00037959812 -0.00071879257 + 1200 0.22910882 -0.00019457758 -0.00024451315 -0.00027807764 + 1400 0.22754022 -0.00033048317 -0.00010053263 -0.00075173132 + 1600 0.22503496 -7.593954e-05 5.2989168e-05 -0.00022521685 + 1800 0.22673577 -0.00017917699 1.0176667e-05 -0.00047893102 + 2000 0.22480858 9.318318e-05 0.00031024343 1.2738253e-05 + 2200 0.22387294 -6.9083174e-05 -4.6170865e-05 4.6682009e-05 + 2400 0.22686231 0.00022776785 0.00028204391 0.00030116273 + 2600 0.23055637 8.2778175e-05 0.00027137529 4.2254076e-05 + 2800 0.23126717 0.00044863024 0.00071654709 0.00057652233 + 3000 0.22234736 0.00031577792 0.00051797227 0.00039087282 +Loop time of 7.17991 on 1 procs for 3000 steps with 1920 atoms -Performance: 383058.431 tau/day, 443.355 timesteps/s -99.8% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 361007.348 tau/day, 417.833 timesteps/s, 802.239 katom-step/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 5.7968 | 5.7968 | 5.7968 | 0.0 | 85.67 -Neigh | 0.086077 | 0.086077 | 0.086077 | 0.0 | 1.27 -Comm | 0.034761 | 0.034761 | 0.034761 | 0.0 | 0.51 -Output | 0.00038014 | 0.00038014 | 0.00038014 | 0.0 | 0.01 -Modify | 0.8268 | 0.8268 | 0.8268 | 0.0 | 12.22 -Other | | 0.02181 | | | 0.32 +Pair | 6.2257 | 6.2257 | 6.2257 | 0.0 | 86.71 +Neigh | 0.11392 | 0.11392 | 0.11392 | 0.0 | 1.59 +Comm | 0.036614 | 0.036614 | 0.036614 | 0.0 | 0.51 +Output | 0.00052672 | 0.00052672 | 0.00052672 | 0.0 | 0.01 +Modify | 0.78577 | 0.78577 | 0.78577 | 0.0 | 10.94 +Other | | 0.01743 | | | 0.24 Nlocal: 1920 ave 1920 max 1920 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 772 ave 772 max 772 min +Nghost: 771 ave 771 max 771 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 46804 ave 46804 max 46804 min +Neighs: 46750 ave 46750 max 46750 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Total # of neighbors = 46804 -Ave neighs/atom = 24.377083 -Neighbor list builds = 99 +Total # of neighbors = 46750 +Ave neighs/atom = 24.348958 +Neighbor list builds = 98 Dangerous builds = 0 -Total wall time: 0:00:06 +Total wall time: 0:00:07 diff --git a/examples/ASPHERE/flat_membrane/log.18Oct22.flat_membrane.g++.4 b/examples/ASPHERE/flat_membrane/log.3Mar25.flat_membrane.g++.4 similarity index 65% rename from examples/ASPHERE/flat_membrane/log.18Oct22.flat_membrane.g++.4 rename to examples/ASPHERE/flat_membrane/log.3Mar25.flat_membrane.g++.4 index 7bbe99b58b..b695da500b 100644 --- a/examples/ASPHERE/flat_membrane/log.18Oct22.flat_membrane.g++.4 +++ b/examples/ASPHERE/flat_membrane/log.3Mar25.flat_membrane.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (15 Sep 2022) +LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-106-g5d02e140d4) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99) using 1 OpenMP thread(s) per MPI task # flat membrane demo variable r0 equal 0.97 @@ -46,7 +47,7 @@ set type 1 mass 1.0 Setting atom values ... 1920 settings made for mass -set type 1 shape 1 1 1 +set type 1 shape 1 0.99 0.99 Setting atom values ... 1920 settings made for shape @@ -99,7 +100,7 @@ CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Generated 0 of 0 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 = 3.6 ghost atom cutoff = 3.6 @@ -113,47 +114,47 @@ Neighbor list info ... Per MPI rank memory allocation (min/avg/max) = 4.182 | 4.794 | 5.472 Mbytes Step Temp Press Pxx Pyy 0 0.23 -0.0073508785 -0.012283389 -0.012234574 - 200 0.20647718 -0.0012368074 -0.0021167303 -0.0015343502 - 400 0.21648371 -0.00085695085 -0.0015627331 -0.0011177093 - 600 0.22929515 -0.00050218657 -0.0008332 -0.00062622609 - 800 0.22062664 -0.00049172378 -0.000611884 -0.00075089294 - 1000 0.22422425 -0.00039405068 -0.00037600355 -0.00070786572 - 1200 0.2298767 -0.00025939082 -0.00021616578 -0.00053125505 - 1400 0.2335927 5.8028332e-05 0.00017530192 -3.1675138e-05 - 1600 0.22884878 -0.0001733902 -0.0008056431 0.00014276754 - 1800 0.22813498 0.00019873459 0.00051040124 5.8860949e-05 - 2000 0.2273166 -3.3595127e-05 0.0001705632 -0.00026498213 - 2200 0.2251643 -2.4517311e-05 -4.0618888e-05 1.066658e-05 - 2400 0.22460629 -4.5661259e-05 -0.00019144039 -1.6649099e-05 - 2600 0.23085675 0.00014029405 0.00017983536 0.00017895001 - 2800 0.22364591 4.2999164e-05 -0.00011000466 0.00024363243 - 3000 0.23421357 0.00023505702 0.00020752013 0.00053567111 -Loop time of 4.68577 on 4 procs for 3000 steps with 1920 atoms + 200 0.21866566 -0.0011213114 -0.0017540296 -0.0017008786 + 400 0.22409469 -0.00055137604 -0.00050366017 -0.0012846672 + 600 0.21623646 -0.0004808564 -0.00063496522 -0.00071617302 + 800 0.22248339 -0.00066333806 -0.00093812145 -0.00099410261 + 1000 0.22367907 -0.0003439459 -0.00076259578 -0.00013354375 + 1200 0.23276206 8.5764334e-06 -0.00036165178 0.00038543803 + 1400 0.23129049 -5.1997966e-06 -0.00040514787 0.00017093646 + 1600 0.22074564 -0.0001604642 -0.00053959031 9.0463391e-05 + 1800 0.2276062 -0.00015655254 -0.00042925633 5.4938379e-05 + 2000 0.22469391 -3.6198836e-05 -1.8538296e-06 -0.00010464749 + 2200 0.22737515 -1.8967356e-05 0.0001341006 -0.00022739894 + 2400 0.22607533 0.00014650382 -2.4871789e-05 0.00058296255 + 2600 0.24044743 0.00045066449 0.00049153595 0.00078042437 + 2800 0.23346628 0.00017994019 -5.0897724e-05 0.00046011801 + 3000 0.22427206 0.00040437022 0.00049580531 0.00046259202 +Loop time of 5.04539 on 4 procs for 3000 steps with 1920 atoms -Performance: 553164.568 tau/day, 640.237 timesteps/s -95.6% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 513736.789 tau/day, 594.603 timesteps/s, 1.142 Matom-step/s +99.0% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.00015072 | 1.6029 | 3.8573 | 131.7 | 34.21 -Neigh | 0.00055747 | 0.025423 | 0.065858 | 17.0 | 0.54 -Comm | 0.0052259 | 0.48173 | 1.624 | 96.5 | 10.28 -Output | 0.0003894 | 0.023428 | 0.047223 | 15.0 | 0.50 -Modify | 0.00037337 | 0.2141 | 0.44595 | 46.3 | 4.57 -Other | | 2.338 | | | 49.90 +Pair | 4.1163 | 4.2634 | 4.4004 | 6.5 | 84.50 +Neigh | 0.00088605 | 0.032793 | 0.083516 | 19.1 | 0.65 +Comm | 0.006704 | 0.20003 | 0.40672 | 42.5 | 3.96 +Output | 0.00033812 | 0.0012192 | 0.0020905 | 2.3 | 0.02 +Modify | 0.00035967 | 0.20167 | 0.42535 | 45.0 | 4.00 +Other | | 0.3462 | | | 6.86 -Nlocal: 480 ave 1011 max 0 min +Nlocal: 480 ave 1052 max 0 min Histogram: 2 0 0 0 0 0 0 0 1 1 -Nghost: 860 ave 1771 max 0 min -Histogram: 2 0 0 0 0 0 0 0 0 2 -Neighs: 11697.8 ave 30095 max 0 min +Nghost: 854.5 ave 1801 max 0 min +Histogram: 2 0 0 0 0 0 0 0 1 1 +Neighs: 11684.2 ave 31145 max 0 min Histogram: 2 0 0 0 0 1 0 0 0 1 -Total # of neighbors = 46791 -Ave neighs/atom = 24.370313 -Neighbor list builds = 99 +Total # of neighbors = 46737 +Ave neighs/atom = 24.342188 +Neighbor list builds = 98 Dangerous builds = 0 -Total wall time: 0:00:04 +Total wall time: 0:00:05