From 378c5c168793e23cf585ab5eee8aea4c43908540 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 5 Jul 2022 11:03:48 -0400 Subject: [PATCH 1/2] silence compiler warnings --- src/AMOEBA/amoeba_file.cpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/AMOEBA/amoeba_file.cpp b/src/AMOEBA/amoeba_file.cpp index 77ea3ed774..ebedbc13d5 100644 --- a/src/AMOEBA/amoeba_file.cpp +++ b/src/AMOEBA/amoeba_file.cpp @@ -847,7 +847,7 @@ void PairAmoeba::file_ffield(const std::vector &words, int nline) /* ---------------------------------------------------------------------- */ -void PairAmoeba::file_literature(const std::vector &words, int /*nline*/) +void PairAmoeba::file_literature(const std::vector & /*words*/, int /*nline*/) { // do nothing, this section is skipped } @@ -1185,7 +1185,7 @@ void PairAmoeba::file_charge_penetration(const std::vector &words, void PairAmoeba::file_dippolar(const std::vector &words, int nline) { - const int ndipparams = amoeba ? 4 : 3; + const std::size_t ndipparams = amoeba ? 4 : 3; if (words[0] != "polarize") error->all(FLERR, "{} PRM file dipole polariability line {} has invalid format: {}", utils::uppercase(mystyle), nline, utils::join_words(words, " ")); From 67e29fc76683dc9cc846d47b89df8b6835f3e352 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 5 Jul 2022 11:20:15 -0400 Subject: [PATCH 2/2] add metadata tags to the .key files too. --- examples/amoeba/amoeba_ubiquitin.key | 1 + examples/amoeba/amoeba_water.key | 5 ++- examples/amoeba/amoeba_water_box.key | 4 +- examples/amoeba/hippo_water.key | 5 ++- examples/amoeba/hippo_water_box.key | 4 +- examples/amoeba/log.5Jul22.ubiquitin.g++.1 | 33 +++++++++-------- examples/amoeba/log.5Jul22.ubiquitin.g++.4 | 31 ++++++++-------- .../amoeba/log.5Jul22.water_box.amoeba.g++.1 | 37 ++++++++++--------- .../amoeba/log.5Jul22.water_box.amoeba.g++.4 | 33 +++++++++-------- .../amoeba/log.5Jul22.water_box.hippo.g++.1 | 33 +++++++++-------- .../amoeba/log.5Jul22.water_box.hippo.g++.4 | 37 ++++++++++--------- .../log.5Jul22.water_dimer.amoeba.g++.1 | 31 ++++++++-------- .../log.5Jul22.water_dimer.amoeba.g++.4 | 33 +++++++++-------- .../amoeba/log.5Jul22.water_dimer.hippo.g++.1 | 35 +++++++++--------- .../amoeba/log.5Jul22.water_dimer.hippo.g++.4 | 35 +++++++++--------- .../log.5Jul22.water_hexamer.amoeba.g++.1 | 31 ++++++++-------- .../log.5Jul22.water_hexamer.amoeba.g++.4 | 29 ++++++++------- .../log.5Jul22.water_hexamer.hippo.g++.1 | 35 +++++++++--------- .../log.5Jul22.water_hexamer.hippo.g++.4 | 35 +++++++++--------- 19 files changed, 252 insertions(+), 235 deletions(-) diff --git a/examples/amoeba/amoeba_ubiquitin.key b/examples/amoeba/amoeba_ubiquitin.key index db0a23c950..2870d071d4 100644 --- a/examples/amoeba/amoeba_ubiquitin.key +++ b/examples/amoeba/amoeba_ubiquitin.key @@ -1,3 +1,4 @@ +!! DATE: 2022-07-05 UNITS: real parameters ./amoeba.prm verbose neighbor-list diff --git a/examples/amoeba/amoeba_water.key b/examples/amoeba/amoeba_water.key index 8222179c52..9cfe063db1 100644 --- a/examples/amoeba/amoeba_water.key +++ b/examples/amoeba/amoeba_water.key @@ -1,4 +1,5 @@ -parameters ./amoeba.prm +!! DATE: 2022-07-05 UNITS: real +parameters ./amoeba.prm digits 8 @@ -6,4 +7,4 @@ cutoff 10 taper 8 polar-eps 1e-5 -usolve-diag 1.0 \ No newline at end of file +usolve-diag 1.0 diff --git a/examples/amoeba/amoeba_water_box.key b/examples/amoeba/amoeba_water_box.key index b74edf324a..94c9808875 100644 --- a/examples/amoeba/amoeba_water_box.key +++ b/examples/amoeba/amoeba_water_box.key @@ -1,4 +1,5 @@ -parameters ./amoeba.prm +!! DATE: 2022-07-05 UNITS: real +parameters ./amoeba.prm digits 10 openmp-threads 1 @@ -16,4 +17,3 @@ taper 6 polar-eps 1e-5 usolve-diag 1.0 - diff --git a/examples/amoeba/hippo_water.key b/examples/amoeba/hippo_water.key index a61b83875b..1b509c2276 100644 --- a/examples/amoeba/hippo_water.key +++ b/examples/amoeba/hippo_water.key @@ -1,4 +1,5 @@ -parameters ./hippo.prm +!! DATE: 2022-07-05 UNITS: real +parameters ./hippo.prm digits 8 @@ -6,4 +7,4 @@ cutoff 10 taper 8 polar-eps 1e-5 -usolve-diag 1.0 \ No newline at end of file +usolve-diag 1.0 diff --git a/examples/amoeba/hippo_water_box.key b/examples/amoeba/hippo_water_box.key index 1dd89919ed..24710cb465 100644 --- a/examples/amoeba/hippo_water_box.key +++ b/examples/amoeba/hippo_water_box.key @@ -1,4 +1,5 @@ -parameters ./hippo.prm +!! DATE: 2022-07-05 UNITS: real +parameters ./hippo.prm digits 8 verbose @@ -19,4 +20,3 @@ taper 6 polar-eps 1e-5 usolve-diag 1.0 - diff --git a/examples/amoeba/log.5Jul22.ubiquitin.g++.1 b/examples/amoeba/log.5Jul22.ubiquitin.g++.1 index 74019ccdf9..161b74167c 100644 --- a/examples/amoeba/log.5Jul22.ubiquitin.g++.1 +++ b/examples/amoeba/log.5Jul22.ubiquitin.g++.1 @@ -57,7 +57,7 @@ Finding 1-2 1-3 1-4 neighbors ... 19 = max # of 1-4 neighbors 21 = max # of special neighbors special bonds CPU = 0.003 seconds - read_data CPU = 0.077 seconds + read_data CPU = 0.040 seconds pair_style amoeba pair_coeff * * amoeba_ubiquitin.prm amoeba_ubiquitin.key @@ -65,6 +65,7 @@ Reading potential file amoeba_ubiquitin.prm with DATE: 2022-07-05 Skipping section: AMOEBA Protein Force Field Atom Classes Skipping section: Torsion-Torsion Parameters Skipping section: Biopolymer Atom Type Conversions +Reading potential file amoeba_ubiquitin.key with DATE: 2022-07-05 special_bonds lj/coul 0.5 0.5 0.5 one/five yes Finding 1-2 1-3 1-4 neighbors ... @@ -75,7 +76,7 @@ Finding 1-2 1-3 1-4 neighbors ... 19 = max # of 1-4 neighbors 58 = max # of 1-5 neighbors 21 = max # of special neighbors - special bonds CPU = 0.005 seconds + special bonds CPU = 0.004 seconds # thermo output @@ -124,29 +125,29 @@ Per MPI rank memory allocation (min/avg/max) = 258.3 | 258.3 | 258.3 Mbytes 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 -Loop time of 6.65546 on 1 procs for 5 steps with 9737 atoms +Loop time of 6.44802 on 1 procs for 5 steps with 9737 atoms -Performance: 0.065 ns/day, 369.748 hours/ns, 0.751 timesteps/s +Performance: 0.067 ns/day, 358.224 hours/ns, 0.775 timesteps/s 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads AMOEBA timing breakdown: - Init time: 0.0105468 0.16% - Hal time: 1.57051 23.62% - Mpole time: 0.805631 12.12% - Induce time: 2.69099 40.48% - Polar time: 1.57015 23.62% - Total time: 6.64783 + Init time: 0.0102334 0.16% + Hal time: 1.53439 23.82% + Mpole time: 0.799674 12.42% + Induce time: 2.57766 40.02% + Polar time: 1.51886 23.58% + Total time: 6.44082 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 6.6478 | 6.6478 | 6.6478 | 0.0 | 99.89 -Bond | 0.0052138 | 0.0052138 | 0.0052138 | 0.0 | 0.08 +Pair | 6.4408 | 6.4408 | 6.4408 | 0.0 | 99.89 +Bond | 0.0049681 | 0.0049681 | 0.0049681 | 0.0 | 0.08 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.0010535 | 0.0010535 | 0.0010535 | 0.0 | 0.02 -Output | 0.00033674 | 0.00033674 | 0.00033674 | 0.0 | 0.01 -Modify | 0.00085639 | 0.00085639 | 0.00085639 | 0.0 | 0.01 -Other | | 0.000145 | | | 0.00 +Comm | 0.00097251 | 0.00097251 | 0.00097251 | 0.0 | 0.02 +Output | 0.00031789 | 0.00031789 | 0.00031789 | 0.0 | 0.00 +Modify | 0.00080532 | 0.00080532 | 0.00080532 | 0.0 | 0.01 +Other | | 0.0001288 | | | 0.00 Nlocal: 9737 ave 9737 max 9737 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/amoeba/log.5Jul22.ubiquitin.g++.4 b/examples/amoeba/log.5Jul22.ubiquitin.g++.4 index fed3f9896e..b337dae759 100644 --- a/examples/amoeba/log.5Jul22.ubiquitin.g++.4 +++ b/examples/amoeba/log.5Jul22.ubiquitin.g++.4 @@ -57,7 +57,7 @@ Finding 1-2 1-3 1-4 neighbors ... 19 = max # of 1-4 neighbors 21 = max # of special neighbors special bonds CPU = 0.001 seconds - read_data CPU = 0.036 seconds + read_data CPU = 0.062 seconds pair_style amoeba pair_coeff * * amoeba_ubiquitin.prm amoeba_ubiquitin.key @@ -65,6 +65,7 @@ Reading potential file amoeba_ubiquitin.prm with DATE: 2022-07-05 Skipping section: AMOEBA Protein Force Field Atom Classes Skipping section: Torsion-Torsion Parameters Skipping section: Biopolymer Atom Type Conversions +Reading potential file amoeba_ubiquitin.key with DATE: 2022-07-05 special_bonds lj/coul 0.5 0.5 0.5 one/five yes Finding 1-2 1-3 1-4 neighbors ... @@ -124,29 +125,29 @@ Per MPI rank memory allocation (min/avg/max) = 144.2 | 144.7 | 145.4 Mbytes 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 -Loop time of 2.1516 on 4 procs for 5 steps with 9737 atoms +Loop time of 2.1567 on 4 procs for 5 steps with 9737 atoms -Performance: 0.201 ns/day, 119.533 hours/ns, 2.324 timesteps/s +Performance: 0.200 ns/day, 119.817 hours/ns, 2.318 timesteps/s 99.4% CPU use with 4 MPI tasks x 1 OpenMP threads AMOEBA timing breakdown: - Init time: 0.0116891 0.54% - Hal time: 0.423411 19.72% - Mpole time: 0.269917 12.57% - Induce time: 0.929983 43.30% - Polar time: 0.512586 23.87% - Total time: 2.14759 + Init time: 0.0115153 0.53% + Hal time: 0.445713 20.70% + Mpole time: 0.282302 13.11% + Induce time: 0.90538 42.06% + Polar time: 0.507821 23.59% + Total time: 2.15273 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 2.1477 | 2.1477 | 2.1477 | 0.0 | 99.82 -Bond | 0.001184 | 0.0014529 | 0.0016771 | 0.5 | 0.07 +Pair | 2.1527 | 2.1528 | 2.1529 | 0.0 | 99.82 +Bond | 0.0012019 | 0.0014482 | 0.0016726 | 0.4 | 0.07 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.0015356 | 0.0017027 | 0.001922 | 0.4 | 0.08 -Output | 0.00027025 | 0.0003219 | 0.00040484 | 0.0 | 0.01 -Modify | 0.00028633 | 0.00030716 | 0.00032386 | 0.0 | 0.01 -Other | | 0.0001328 | | | 0.01 +Comm | 0.0015211 | 0.0016953 | 0.0019541 | 0.4 | 0.08 +Output | 0.00024653 | 0.00030686 | 0.0003922 | 0.0 | 0.01 +Modify | 0.00028632 | 0.00030747 | 0.00033879 | 0.0 | 0.01 +Other | | 0.0001387 | | | 0.01 Nlocal: 2434.25 ave 2498 max 2390 min Histogram: 1 1 0 0 1 0 0 0 0 1 diff --git a/examples/amoeba/log.5Jul22.water_box.amoeba.g++.1 b/examples/amoeba/log.5Jul22.water_box.amoeba.g++.1 index 23b9fee06f..acf5cd5dba 100644 --- a/examples/amoeba/log.5Jul22.water_box.amoeba.g++.1 +++ b/examples/amoeba/log.5Jul22.water_box.amoeba.g++.1 @@ -40,14 +40,15 @@ 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 = 0.012 seconds + special bonds CPU = 0.000 seconds + read_data CPU = 0.004 seconds # force field pair_style amoeba pair_coeff * * amoeba_water.prm amoeba_water_box.key Reading potential file amoeba_water.prm with DATE: 2022-07-05 +Reading potential file amoeba_water_box.key with DATE: 2022-07-05 special_bonds lj/coul 0.5 0.5 0.5 one/five yes Finding 1-2 1-3 1-4 neighbors ... @@ -58,7 +59,7 @@ 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 @@ -112,29 +113,29 @@ Per MPI rank memory allocation (min/avg/max) = 56.94 | 56.94 | 56.94 Mbytes 80 171.83506 -2388.0612 76.465932 49.1299 0 0 125.59583 -1931.067 2210.3658 -318.23867 330.74353 -395.26693 -43.142216 252.53012 -1987.0412 90 175.73401 -2423.8154 90.786573 63.719496 0 0 154.50607 -1930.3915 -916.91571 -3942.3954 -2566.5361 -3414.8202 199.82369 2365.9443 -266.38604 100 173.72684 -2422.367 99.75941 57.294464 0 0 157.05387 -1930.2663 -3585.8356 -5734.1341 -5882.0146 -6232.4353 -227.79935 959.68225 404.47924 -Loop time of 9.23157 on 1 procs for 100 steps with 648 atoms +Loop time of 9.13006 on 1 procs for 100 steps with 648 atoms -Performance: 0.936 ns/day, 25.643 hours/ns, 10.832 timesteps/s +Performance: 0.946 ns/day, 25.361 hours/ns, 10.953 timesteps/s 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads AMOEBA timing breakdown: - Init time: 0.0194993 0.21% - Hal time: 0.383028 4.15% - Mpole time: 0.935775 10.15% - Induce time: 6.06306 65.76% - Polar time: 1.81839 19.72% - Total time: 9.21978 + Init time: 0.0195637 0.21% + Hal time: 0.383019 4.20% + Mpole time: 0.942757 10.34% + Induce time: 5.97653 65.54% + Polar time: 1.79658 19.70% + Total time: 9.11849 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 9.2201 | 9.2201 | 9.2201 | 0.0 | 99.88 -Bond | 0.0024949 | 0.0024949 | 0.0024949 | 0.0 | 0.03 -Neigh | 0.0046051 | 0.0046051 | 0.0046051 | 0.0 | 0.05 -Comm | 0.0023611 | 0.0023611 | 0.0023611 | 0.0 | 0.03 -Output | 0.00045516 | 0.00045516 | 0.00045516 | 0.0 | 0.00 -Modify | 0.00070554 | 0.00070554 | 0.00070554 | 0.0 | 0.01 -Other | | 0.0008327 | | | 0.01 +Pair | 9.1188 | 9.1188 | 9.1188 | 0.0 | 99.88 +Bond | 0.0025049 | 0.0025049 | 0.0025049 | 0.0 | 0.03 +Neigh | 0.0045289 | 0.0045289 | 0.0045289 | 0.0 | 0.05 +Comm | 0.0022625 | 0.0022625 | 0.0022625 | 0.0 | 0.02 +Output | 0.00044299 | 0.00044299 | 0.00044299 | 0.0 | 0.00 +Modify | 0.00069998 | 0.00069998 | 0.00069998 | 0.0 | 0.01 +Other | | 0.0008232 | | | 0.01 Nlocal: 648 ave 648 max 648 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/amoeba/log.5Jul22.water_box.amoeba.g++.4 b/examples/amoeba/log.5Jul22.water_box.amoeba.g++.4 index 1db1f9abee..a4ddd2f637 100644 --- a/examples/amoeba/log.5Jul22.water_box.amoeba.g++.4 +++ b/examples/amoeba/log.5Jul22.water_box.amoeba.g++.4 @@ -41,13 +41,14 @@ 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 = 0.005 seconds + read_data CPU = 0.008 seconds # force field pair_style amoeba pair_coeff * * amoeba_water.prm amoeba_water_box.key Reading potential file amoeba_water.prm with DATE: 2022-07-05 +Reading potential file amoeba_water_box.key with DATE: 2022-07-05 special_bonds lj/coul 0.5 0.5 0.5 one/five yes Finding 1-2 1-3 1-4 neighbors ... @@ -112,29 +113,29 @@ Per MPI rank memory allocation (min/avg/max) = 56.38 | 56.38 | 56.38 Mbytes 80 171.83506 -2388.0612 76.465932 49.1299 0 0 125.59583 -1931.067 2210.3658 -318.23867 330.74353 -395.26693 -43.142216 252.53012 -1987.0412 90 175.73401 -2423.8154 90.786573 63.719496 0 0 154.50607 -1930.3915 -916.91571 -3942.3954 -2566.5361 -3414.8202 199.82369 2365.9443 -266.38604 100 173.72684 -2422.367 99.75941 57.294464 0 0 157.05387 -1930.2663 -3585.8356 -5734.1341 -5882.0146 -6232.4353 -227.79935 959.68225 404.47924 -Loop time of 3.62992 on 4 procs for 100 steps with 648 atoms +Loop time of 3.55068 on 4 procs for 100 steps with 648 atoms -Performance: 2.380 ns/day, 10.083 hours/ns, 27.549 timesteps/s +Performance: 2.433 ns/day, 9.863 hours/ns, 28.164 timesteps/s 99.3% CPU use with 4 MPI tasks x 1 OpenMP threads AMOEBA timing breakdown: - Init time: 0.0211291 0.58% - Hal time: 0.114718 3.17% - Mpole time: 0.329891 9.11% - Induce time: 2.5339 69.99% - Polar time: 0.620639 17.14% - Total time: 3.6203 + Init time: 0.0212328 0.60% + Hal time: 0.112487 3.18% + Mpole time: 0.322738 9.11% + Induce time: 2.47321 69.83% + Polar time: 0.611925 17.28% + Total time: 3.54162 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 3.6209 | 3.621 | 3.6211 | 0.0 | 99.75 -Bond | 0.00085544 | 0.00087038 | 0.00090469 | 0.0 | 0.02 -Neigh | 0.0014354 | 0.0014405 | 0.0014453 | 0.0 | 0.04 -Comm | 0.004823 | 0.0048746 | 0.0049092 | 0.0 | 0.13 -Output | 0.00038727 | 0.00043628 | 0.00055233 | 0.0 | 0.01 -Modify | 0.00033814 | 0.0003491 | 0.00037267 | 0.0 | 0.01 -Other | | 0.0009691 | | | 0.03 +Pair | 3.5421 | 3.5423 | 3.5425 | 0.0 | 99.76 +Bond | 0.00080566 | 0.00088074 | 0.00099188 | 0.0 | 0.02 +Neigh | 0.0014246 | 0.0014359 | 0.0014469 | 0.0 | 0.04 +Comm | 0.0043463 | 0.0045083 | 0.0046393 | 0.2 | 0.13 +Output | 0.00035535 | 0.00039745 | 0.00051597 | 0.0 | 0.01 +Modify | 0.00034241 | 0.00035548 | 0.00036576 | 0.0 | 0.01 +Other | | 0.0008093 | | | 0.02 Nlocal: 162 ave 164 max 159 min Histogram: 1 0 0 0 0 0 1 0 1 1 diff --git a/examples/amoeba/log.5Jul22.water_box.hippo.g++.1 b/examples/amoeba/log.5Jul22.water_box.hippo.g++.1 index 1c998687f4..c398031b24 100644 --- a/examples/amoeba/log.5Jul22.water_box.hippo.g++.1 +++ b/examples/amoeba/log.5Jul22.water_box.hippo.g++.1 @@ -48,6 +48,7 @@ Finding 1-2 1-3 1-4 neighbors ... pair_style hippo pair_coeff * * hippo_water.prm hippo_water_box.key Reading potential file hippo_water.prm with DATE: 2022-07-05 +Reading potential file hippo_water_box.key with DATE: 2022-07-05 special_bonds lj/coul 0.5 0.5 0.5 one/five yes Finding 1-2 1-3 1-4 neighbors ... @@ -109,31 +110,31 @@ Per MPI rank memory allocation (min/avg/max) = 56.46 | 56.46 | 56.46 Mbytes 3 83.751912 -2189.1561 36.936027 32.349803 0 0 69.285831 -1958.3477 1505.3642 2789.4989 -1919.6532 227.71216 3.4467207 240.18575 -91.250567 4 59.186129 -2195.3882 116.40559 17.314099 0 0 133.71969 -1947.5231 7666.6109 9441.7634 4355.1915 6787.0543 329.33631 -768.83277 -966.66638 5 70.911532 -2215.1422 115.71443 14.75745 0 0 130.47188 -1947.9114 7292.9034 8506.6309 4019.0295 6458.6256 348.80878 -911.32703 -1060.6123 -Loop time of 0.326218 on 1 procs for 5 steps with 648 atoms +Loop time of 0.328535 on 1 procs for 5 steps with 648 atoms -Performance: 1.324 ns/day, 18.123 hours/ns, 15.327 timesteps/s +Performance: 1.315 ns/day, 18.252 hours/ns, 15.219 timesteps/s 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads HIPPO timing breakdown: - Init time: 0.000842282 0.26% - Repulse time: 0.0383544 11.78% - Disp time: 0.0173558 5.33% - Mpole time: 0.0613861 18.85% - Induce time: 0.121337 37.26% - Polar time: 0.0763061 23.43% - Qxfer time: 0.0101016 3.10% - Total time: 0.325683 + Init time: 0.000827146 0.25% + Repulse time: 0.0383201 11.68% + Disp time: 0.0174221 5.31% + Mpole time: 0.0612574 18.67% + Induce time: 0.123563 37.67% + Polar time: 0.076967 23.46% + Qxfer time: 0.00966432 2.95% + Total time: 0.328021 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.3257 | 0.3257 | 0.3257 | 0.0 | 99.84 -Bond | 0.00013737 | 0.00013737 | 0.00013737 | 0.0 | 0.04 +Pair | 0.32803 | 0.32803 | 0.32803 | 0.0 | 99.85 +Bond | 0.00013553 | 0.00013553 | 0.00013553 | 0.0 | 0.04 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.0001122 | 0.0001122 | 0.0001122 | 0.0 | 0.03 -Output | 0.00020981 | 0.00020981 | 0.00020981 | 0.0 | 0.06 -Modify | 3.4058e-05 | 3.4058e-05 | 3.4058e-05 | 0.0 | 0.01 -Other | | 2.595e-05 | | | 0.01 +Comm | 8.9842e-05 | 8.9842e-05 | 8.9842e-05 | 0.0 | 0.03 +Output | 0.00021433 | 0.00021433 | 0.00021433 | 0.0 | 0.07 +Modify | 3.4997e-05 | 3.4997e-05 | 3.4997e-05 | 0.0 | 0.01 +Other | | 2.511e-05 | | | 0.01 Nlocal: 648 ave 648 max 648 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/amoeba/log.5Jul22.water_box.hippo.g++.4 b/examples/amoeba/log.5Jul22.water_box.hippo.g++.4 index 80730c0301..35b8e2bd9b 100644 --- a/examples/amoeba/log.5Jul22.water_box.hippo.g++.4 +++ b/examples/amoeba/log.5Jul22.water_box.hippo.g++.4 @@ -41,13 +41,14 @@ 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 = 0.005 seconds # force field pair_style hippo pair_coeff * * hippo_water.prm hippo_water_box.key Reading potential file hippo_water.prm with DATE: 2022-07-05 +Reading potential file hippo_water_box.key with DATE: 2022-07-05 special_bonds lj/coul 0.5 0.5 0.5 one/five yes Finding 1-2 1-3 1-4 neighbors ... @@ -109,31 +110,31 @@ Per MPI rank memory allocation (min/avg/max) = 55.94 | 55.94 | 55.94 Mbytes 3 83.751912 -2189.1561 36.936027 32.349803 0 0 69.285831 -1958.3477 1505.3642 2789.4989 -1919.6532 227.71216 3.4467207 240.18575 -91.250567 4 59.186129 -2195.3882 116.40559 17.314099 0 0 133.71969 -1947.5231 7666.6109 9441.7634 4355.1915 6787.0543 329.33631 -768.83277 -966.66638 5 70.911532 -2215.1422 115.71443 14.75745 0 0 130.47188 -1947.9114 7292.9034 8506.6309 4019.0295 6458.6256 348.80878 -911.32703 -1060.6123 -Loop time of 0.122 on 4 procs for 5 steps with 648 atoms +Loop time of 0.122575 on 4 procs for 5 steps with 648 atoms -Performance: 3.541 ns/day, 6.778 hours/ns, 40.984 timesteps/s -98.6% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 3.524 ns/day, 6.810 hours/ns, 40.792 timesteps/s +99.2% CPU use with 4 MPI tasks x 1 OpenMP threads HIPPO timing breakdown: - Init time: 0.000810221 0.67% - Repulse time: 0.0125366 10.36% - Disp time: 0.00623213 5.15% - Mpole time: 0.0210595 17.40% - Induce time: 0.0506279 41.83% - Polar time: 0.026832 22.17% - Qxfer time: 0.00292863 2.42% - Total time: 0.121027 + Init time: 0.000860363 0.71% + Repulse time: 0.0125286 10.32% + Disp time: 0.00643959 5.30% + Mpole time: 0.0212485 17.50% + Induce time: 0.0494722 40.74% + Polar time: 0.0278425 22.93% + Qxfer time: 0.00305419 2.51% + Total time: 0.121446 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.12089 | 0.12109 | 0.12131 | 0.0 | 99.25 -Bond | 4.8642e-05 | 5.2114e-05 | 6.0555e-05 | 0.0 | 0.04 +Pair | 0.12142 | 0.12151 | 0.12158 | 0.0 | 99.13 +Bond | 6.0063e-05 | 6.7176e-05 | 7.9312e-05 | 0.0 | 0.05 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.00035781 | 0.00058015 | 0.00076608 | 0.0 | 0.48 -Output | 0.0001878 | 0.00022879 | 0.00026441 | 0.0 | 0.19 -Modify | 1.7668e-05 | 1.8481e-05 | 1.9751e-05 | 0.0 | 0.02 -Other | | 3.389e-05 | | | 0.03 +Comm | 0.00042855 | 0.00057228 | 0.00067923 | 0.0 | 0.47 +Output | 0.00031594 | 0.00036048 | 0.0004471 | 0.0 | 0.29 +Modify | 3.0303e-05 | 3.1698e-05 | 3.2468e-05 | 0.0 | 0.03 +Other | | 3.774e-05 | | | 0.03 Nlocal: 162 ave 166 max 159 min Histogram: 2 0 0 0 0 0 0 1 0 1 diff --git a/examples/amoeba/log.5Jul22.water_dimer.amoeba.g++.1 b/examples/amoeba/log.5Jul22.water_dimer.amoeba.g++.1 index c9aa2ba0a1..a6f5fd1f0d 100644 --- a/examples/amoeba/log.5Jul22.water_dimer.amoeba.g++.1 +++ b/examples/amoeba/log.5Jul22.water_dimer.amoeba.g++.1 @@ -48,6 +48,7 @@ Finding 1-2 1-3 1-4 neighbors ... pair_style amoeba pair_coeff * * amoeba_water.prm amoeba_water.key Reading potential file amoeba_water.prm with DATE: 2022-07-05 +Reading potential file amoeba_water.key with DATE: 2022-07-05 special_bonds lj/coul 0.5 0.5 0.5 one/five yes Finding 1-2 1-3 1-4 neighbors ... @@ -108,29 +109,29 @@ Per MPI rank memory allocation (min/avg/max) = 48.33 | 48.33 | 48.33 Mbytes 3 22.599529 -5.0641035 0.0093422156 0.28736734 0 0 0.29670956 -4.4305695 7832.024 -6436.638 34275.274 -8676.6339 -46.038158 -20245.105 -46.202354 4 30.447598 -5.0072832 0.0076827791 0.11282886 0 0 0.12051164 -4.432979 12374.854 6652.5061 24658.364 -25.4576 -23.025707 -13137.295 -27.801932 5 33.189086 -4.9523094 0.0086012541 0.015399005 0 0 0.024000259 -4.4336573 10023.674 11810.883 8754.5769 3140.658 0.25267021 -3546.6216 -6.83205 -Loop time of 0.000214688 on 1 procs for 5 steps with 6 atoms +Loop time of 0.000215006 on 1 procs for 5 steps with 6 atoms -Performance: 2012.222 ns/day, 0.012 hours/ns, 23289.611 timesteps/s -65.7% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 2009.246 ns/day, 0.012 hours/ns, 23255.165 timesteps/s +78.1% CPU use with 1 MPI tasks x 1 OpenMP threads AMOEBA timing breakdown: - Init time: 5.306e-06 4.54% - Hal time: 6.681e-06 5.72% - Mpole time: 1.6221e-05 13.88% - Induce time: 5.6723e-05 48.54% - Polar time: 3.1532e-05 26.98% - Total time: 0.000116854 + Init time: 5.213e-06 4.42% + Hal time: 6.546e-06 5.55% + Mpole time: 1.5909e-05 13.48% + Induce time: 5.8305e-05 49.39% + Polar time: 3.1695e-05 26.85% + Total time: 0.000118041 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.00011888 | 0.00011888 | 0.00011888 | 0.0 | 55.37 -Bond | 3.797e-06 | 3.797e-06 | 3.797e-06 | 0.0 | 1.77 +Pair | 0.00011999 | 0.00011999 | 0.00011999 | 0.0 | 55.81 +Bond | 3.429e-06 | 3.429e-06 | 3.429e-06 | 0.0 | 1.59 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 7.24e-07 | 7.24e-07 | 7.24e-07 | 0.0 | 0.34 -Output | 8.4738e-05 | 8.4738e-05 | 8.4738e-05 | 0.0 | 39.47 -Modify | 1.53e-06 | 1.53e-06 | 1.53e-06 | 0.0 | 0.71 -Other | | 5.022e-06 | | | 2.34 +Comm | 6.69e-07 | 6.69e-07 | 6.69e-07 | 0.0 | 0.31 +Output | 8.4574e-05 | 8.4574e-05 | 8.4574e-05 | 0.0 | 39.34 +Modify | 1.595e-06 | 1.595e-06 | 1.595e-06 | 0.0 | 0.74 +Other | | 4.744e-06 | | | 2.21 Nlocal: 6 ave 6 max 6 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/amoeba/log.5Jul22.water_dimer.amoeba.g++.4 b/examples/amoeba/log.5Jul22.water_dimer.amoeba.g++.4 index 94901fdf24..965cc5f5e5 100644 --- a/examples/amoeba/log.5Jul22.water_dimer.amoeba.g++.4 +++ b/examples/amoeba/log.5Jul22.water_dimer.amoeba.g++.4 @@ -41,13 +41,14 @@ 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 = 0.004 seconds + read_data CPU = 0.003 seconds # force field pair_style amoeba pair_coeff * * amoeba_water.prm amoeba_water.key Reading potential file amoeba_water.prm with DATE: 2022-07-05 +Reading potential file amoeba_water.key with DATE: 2022-07-05 special_bonds lj/coul 0.5 0.5 0.5 one/five yes Finding 1-2 1-3 1-4 neighbors ... @@ -108,29 +109,29 @@ Per MPI rank memory allocation (min/avg/max) = 48.35 | 48.48 | 48.62 Mbytes 3 22.599529 -5.0641035 0.0093422156 0.28736734 0 0 0.29670956 -4.4305695 7832.024 -6436.638 34275.274 -8676.6339 -46.038158 -20245.105 -46.202354 4 30.447598 -5.0072832 0.0076827791 0.11282886 0 0 0.12051164 -4.432979 12374.854 6652.5061 24658.364 -25.4576 -23.025707 -13137.295 -27.801932 5 33.189086 -4.9523094 0.0086012541 0.015399005 0 0 0.024000259 -4.4336573 10023.674 11810.883 8754.5769 3140.658 0.25267021 -3546.6216 -6.83205 -Loop time of 0.000598353 on 4 procs for 5 steps with 6 atoms +Loop time of 0.000514756 on 4 procs for 5 steps with 6 atoms -Performance: 721.982 ns/day, 0.033 hours/ns, 8356.278 timesteps/s -98.9% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 839.232 ns/day, 0.029 hours/ns, 9713.335 timesteps/s +99.0% CPU use with 4 MPI tasks x 1 OpenMP threads AMOEBA timing breakdown: - Init time: 1.3678e-05 3.81% - Hal time: 3.5045e-06 0.97% - Mpole time: 2.3748e-05 6.61% - Induce time: 0.000284514 79.15% - Polar time: 3.3521e-05 9.33% - Total time: 0.000359445 + Init time: 1.1899e-05 3.41% + Hal time: 2.53025e-06 0.73% + Mpole time: 1.78605e-05 5.12% + Induce time: 0.000291075 83.49% + Polar time: 2.47857e-05 7.11% + Total time: 0.000348626 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.00035282 | 0.00038565 | 0.00040584 | 0.0 | 64.45 -Bond | 1.637e-06 | 3.2485e-06 | 4.816e-06 | 0.0 | 0.54 +Pair | 0.00034972 | 0.00037431 | 0.00039297 | 0.0 | 72.72 +Bond | 1.243e-06 | 2.7775e-06 | 4.618e-06 | 0.0 | 0.54 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 1.4157e-05 | 3.2696e-05 | 5.1431e-05 | 0.0 | 5.46 -Output | 0.00014589 | 0.0001627 | 0.00018978 | 0.0 | 27.19 -Modify | 1.649e-06 | 2.0097e-06 | 2.209e-06 | 0.0 | 0.34 -Other | | 1.205e-05 | | | 2.01 +Comm | 1.4468e-05 | 2.4821e-05 | 4.155e-05 | 0.0 | 4.82 +Output | 9.2384e-05 | 0.00010253 | 0.0001268 | 0.0 | 19.92 +Modify | 1.439e-06 | 1.7457e-06 | 2.12e-06 | 0.0 | 0.34 +Other | | 8.573e-06 | | | 1.67 Nlocal: 1.5 ave 3 max 0 min Histogram: 2 0 0 0 0 0 0 0 0 2 diff --git a/examples/amoeba/log.5Jul22.water_dimer.hippo.g++.1 b/examples/amoeba/log.5Jul22.water_dimer.hippo.g++.1 index dccb8dee21..137b6f4123 100644 --- a/examples/amoeba/log.5Jul22.water_dimer.hippo.g++.1 +++ b/examples/amoeba/log.5Jul22.water_dimer.hippo.g++.1 @@ -48,6 +48,7 @@ Finding 1-2 1-3 1-4 neighbors ... pair_style hippo pair_coeff * * hippo_water.prm hippo_water.key Reading potential file hippo_water.prm with DATE: 2022-07-05 +Reading potential file hippo_water.key with DATE: 2022-07-05 special_bonds lj/coul 0.5 0.5 0.5 one/five yes Finding 1-2 1-3 1-4 neighbors ... @@ -110,31 +111,31 @@ Per MPI rank memory allocation (min/avg/max) = 47.9 | 47.9 | 47.9 Mbytes 3 18.15288 -4.9496234 0.010334146 0.19125791 0 0 0.20159205 -4.47748 7115.3453 -5853.149 32274.916 -8557.0355 -41.982111 -17374.865 -42.455978 4 24.248994 -4.9153331 0.0093063079 0.065238074 0 0 0.074544382 -4.4793805 11356.801 5716.9586 25838.412 -2135.3667 -22.820662 -10495.224 -28.045156 5 26.136423 -4.8829114 0.0095061937 0.0039834608 0 0 0.013489654 -4.4798832 9044.3732 10498.874 11345.536 276.34491 -1.1467483 -1185.8556 -8.820154 -Loop time of 0.000210439 on 1 procs for 5 steps with 6 atoms +Loop time of 0.000212779 on 1 procs for 5 steps with 6 atoms -Performance: 2052.851 ns/day, 0.012 hours/ns, 23759.854 timesteps/s -98.4% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 2030.276 ns/day, 0.012 hours/ns, 23498.560 timesteps/s +98.2% CPU use with 1 MPI tasks x 1 OpenMP threads HIPPO timing breakdown: - Init time: 5.006e-06 4.58% - Repulse time: 1.3587e-05 12.42% - Disp time: 5.471e-06 5.00% - Mpole time: 2.1321e-05 19.49% - Induce time: 3.7665e-05 34.43% - Polar time: 2.3919e-05 21.87% - Qxfer time: 2.295e-06 2.10% - Total time: 0.000109391 + Init time: 4.362e-06 3.79% + Repulse time: 1.3969e-05 12.14% + Disp time: 5.254e-06 4.57% + Mpole time: 2.6047e-05 22.64% + Induce time: 3.9053e-05 33.95% + Polar time: 2.3991e-05 20.86% + Qxfer time: 2.22e-06 1.93% + Total time: 0.000115031 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.00011125 | 0.00011125 | 0.00011125 | 0.0 | 52.86 -Bond | 3.062e-06 | 3.062e-06 | 3.062e-06 | 0.0 | 1.46 +Pair | 0.00011699 | 0.00011699 | 0.00011699 | 0.0 | 54.98 +Bond | 3.135e-06 | 3.135e-06 | 3.135e-06 | 0.0 | 1.47 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 6.3e-07 | 6.3e-07 | 6.3e-07 | 0.0 | 0.30 -Output | 8.8087e-05 | 8.8087e-05 | 8.8087e-05 | 0.0 | 41.86 -Modify | 1.664e-06 | 1.664e-06 | 1.664e-06 | 0.0 | 0.79 -Other | | 5.749e-06 | | | 2.73 +Comm | 5.59e-07 | 5.59e-07 | 5.59e-07 | 0.0 | 0.26 +Output | 8.5468e-05 | 8.5468e-05 | 8.5468e-05 | 0.0 | 40.17 +Modify | 1.509e-06 | 1.509e-06 | 1.509e-06 | 0.0 | 0.71 +Other | | 5.117e-06 | | | 2.40 Nlocal: 6 ave 6 max 6 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/amoeba/log.5Jul22.water_dimer.hippo.g++.4 b/examples/amoeba/log.5Jul22.water_dimer.hippo.g++.4 index 3758759b7a..0b1142db34 100644 --- a/examples/amoeba/log.5Jul22.water_dimer.hippo.g++.4 +++ b/examples/amoeba/log.5Jul22.water_dimer.hippo.g++.4 @@ -48,6 +48,7 @@ Finding 1-2 1-3 1-4 neighbors ... pair_style hippo pair_coeff * * hippo_water.prm hippo_water.key Reading potential file hippo_water.prm with DATE: 2022-07-05 +Reading potential file hippo_water.key with DATE: 2022-07-05 special_bonds lj/coul 0.5 0.5 0.5 one/five yes Finding 1-2 1-3 1-4 neighbors ... @@ -110,31 +111,31 @@ Per MPI rank memory allocation (min/avg/max) = 47.91 | 48.04 | 48.18 Mbytes 3 18.15288 -4.9496234 0.010334146 0.19125791 0 0 0.20159205 -4.47748 7115.3453 -5853.149 32274.916 -8557.0355 -41.982111 -17374.865 -42.455978 4 24.248994 -4.9153331 0.0093063079 0.065238074 0 0 0.074544382 -4.4793805 11356.801 5716.9586 25838.412 -2135.3667 -22.820662 -10495.224 -28.045156 5 26.136423 -4.8829114 0.0095061937 0.0039834608 0 0 0.013489654 -4.4798832 9044.3732 10498.874 11345.536 276.34491 -1.1467483 -1185.8556 -8.820154 -Loop time of 0.000488464 on 4 procs for 5 steps with 6 atoms +Loop time of 0.000517582 on 4 procs for 5 steps with 6 atoms -Performance: 884.405 ns/day, 0.027 hours/ns, 10236.169 timesteps/s -70.9% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 834.650 ns/day, 0.029 hours/ns, 9660.305 timesteps/s +99.1% CPU use with 4 MPI tasks x 1 OpenMP threads HIPPO timing breakdown: - Init time: 1.2924e-05 4.50% - Repulse time: 2.01283e-05 7.01% - Disp time: 3.04475e-06 1.06% - Mpole time: 3.51807e-05 12.25% - Induce time: 0.000183034 63.71% - Polar time: 3.13832e-05 10.92% - Qxfer time: 1.44475e-06 0.50% - Total time: 0.000287298 + Init time: 1.2878e-05 4.19% + Repulse time: 1.95775e-05 6.37% + Disp time: 3.19075e-06 1.04% + Mpole time: 3.54465e-05 11.54% + Induce time: 0.000202696 65.99% + Polar time: 3.1646e-05 10.30% + Qxfer time: 1.54075e-06 0.50% + Total time: 0.000307141 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.00028193 | 0.00030553 | 0.00032173 | 0.0 | 62.55 -Bond | 1.317e-06 | 2.7712e-06 | 4.847e-06 | 0.0 | 0.57 +Pair | 0.00030206 | 0.00032867 | 0.00034858 | 0.0 | 63.50 +Bond | 1.25e-06 | 2.9003e-06 | 5.069e-06 | 0.0 | 0.56 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 1.3015e-05 | 3.0698e-05 | 4.1342e-05 | 0.0 | 6.28 -Output | 0.00012315 | 0.00013964 | 0.00015356 | 0.0 | 28.59 -Modify | 1.445e-06 | 1.881e-06 | 2.366e-06 | 0.0 | 0.39 -Other | | 7.949e-06 | | | 1.63 +Comm | 1.2972e-05 | 3.2595e-05 | 4.1932e-05 | 0.0 | 6.30 +Output | 0.00012571 | 0.00014253 | 0.000161 | 0.0 | 27.54 +Modify | 1.414e-06 | 2.006e-06 | 2.581e-06 | 0.0 | 0.39 +Other | | 8.876e-06 | | | 1.71 Nlocal: 1.5 ave 3 max 0 min Histogram: 2 0 0 0 0 0 0 0 0 2 diff --git a/examples/amoeba/log.5Jul22.water_hexamer.amoeba.g++.1 b/examples/amoeba/log.5Jul22.water_hexamer.amoeba.g++.1 index 03224a076e..210672e638 100644 --- a/examples/amoeba/log.5Jul22.water_hexamer.amoeba.g++.1 +++ b/examples/amoeba/log.5Jul22.water_hexamer.amoeba.g++.1 @@ -48,6 +48,7 @@ Finding 1-2 1-3 1-4 neighbors ... pair_style amoeba pair_coeff * * amoeba_water.prm amoeba_water.key Reading potential file amoeba_water.prm with DATE: 2022-07-05 +Reading potential file amoeba_water.key with DATE: 2022-07-05 special_bonds lj/coul 0.5 0.5 0.5 one/five yes Finding 1-2 1-3 1-4 neighbors ... @@ -107,29 +108,29 @@ Per MPI rank memory allocation (min/avg/max) = 48.28 | 48.28 | 48.28 Mbytes 3 15.996484 -46.59119 0.087228651 1.3862662 0 0 1.4734948 -44.307093 15705.166 28374.161 4124.662 13087.621 -6242.1769 3159.6508 1787.4159 4 10.888785 -45.839064 0.062461924 0.96598997 0 0 1.0284519 -44.258837 30226.38 48920.372 15666.108 25051.837 -9443.9251 2603.8275 435.5257 5 10.58575 -45.503287 0.071817565 0.64254674 0 0 0.71436431 -44.252503 31899.04 51066.283 18170.57 25448.409 -9478.6752 638.72265 -1011.7679 -Loop time of 0.00100127 on 1 procs for 5 steps with 18 atoms +Loop time of 0.00102528 on 1 procs for 5 steps with 18 atoms -Performance: 431.450 ns/day, 0.056 hours/ns, 4993.633 timesteps/s -99.8% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 421.350 ns/day, 0.057 hours/ns, 4876.736 timesteps/s +97.8% CPU use with 1 MPI tasks x 1 OpenMP threads AMOEBA timing breakdown: - Init time: 1.2944e-05 1.45% - Hal time: 6.4578e-05 7.21% - Mpole time: 0.000124703 13.93% - Induce time: 0.000435232 48.60% - Polar time: 0.000257613 28.77% - Total time: 0.000895454 + Init time: 1.233e-05 1.38% + Hal time: 6.1298e-05 6.86% + Mpole time: 0.000124989 13.99% + Induce time: 0.000435176 48.70% + Polar time: 0.000259279 29.02% + Total time: 0.000893503 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.00089735 | 0.00089735 | 0.00089735 | 0.0 | 89.62 -Bond | 6.783e-06 | 6.783e-06 | 6.783e-06 | 0.0 | 0.68 +Pair | 0.0008955 | 0.0008955 | 0.0008955 | 0.0 | 87.34 +Bond | 6.723e-06 | 6.723e-06 | 6.723e-06 | 0.0 | 0.66 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 6.36e-07 | 6.36e-07 | 6.36e-07 | 0.0 | 0.06 -Output | 8.9119e-05 | 8.9119e-05 | 8.9119e-05 | 0.0 | 8.90 -Modify | 2.385e-06 | 2.385e-06 | 2.385e-06 | 0.0 | 0.24 -Other | | 4.998e-06 | | | 0.50 +Comm | 7.36e-07 | 7.36e-07 | 7.36e-07 | 0.0 | 0.07 +Output | 0.00011472 | 0.00011472 | 0.00011472 | 0.0 | 11.19 +Modify | 2.387e-06 | 2.387e-06 | 2.387e-06 | 0.0 | 0.23 +Other | | 5.206e-06 | | | 0.51 Nlocal: 18 ave 18 max 18 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/amoeba/log.5Jul22.water_hexamer.amoeba.g++.4 b/examples/amoeba/log.5Jul22.water_hexamer.amoeba.g++.4 index 1f5aff9134..d0813a0677 100644 --- a/examples/amoeba/log.5Jul22.water_hexamer.amoeba.g++.4 +++ b/examples/amoeba/log.5Jul22.water_hexamer.amoeba.g++.4 @@ -48,6 +48,7 @@ Finding 1-2 1-3 1-4 neighbors ... pair_style amoeba pair_coeff * * amoeba_water.prm amoeba_water.key Reading potential file amoeba_water.prm with DATE: 2022-07-05 +Reading potential file amoeba_water.key with DATE: 2022-07-05 special_bonds lj/coul 0.5 0.5 0.5 one/five yes Finding 1-2 1-3 1-4 neighbors ... @@ -108,29 +109,29 @@ Per MPI rank memory allocation (min/avg/max) = 48.3 | 48.3 | 48.3 Mbytes 3 15.996484 -46.59119 0.087228651 1.3862662 0 0 1.4734948 -44.307093 15705.166 28374.161 4124.662 13087.621 -6242.1769 3159.6508 1787.4159 4 10.888785 -45.839064 0.062461924 0.96598997 0 0 1.0284519 -44.258837 30226.38 48920.372 15666.108 25051.837 -9443.9251 2603.8275 435.5257 5 10.58575 -45.503287 0.071817565 0.64254674 0 0 0.71436431 -44.252503 31899.04 51066.283 18170.57 25448.409 -9478.6752 638.72265 -1011.7679 -Loop time of 0.00124102 on 4 procs for 5 steps with 18 atoms +Loop time of 0.00142392 on 4 procs for 5 steps with 18 atoms -Performance: 348.100 ns/day, 0.069 hours/ns, 4028.938 timesteps/s +Performance: 303.388 ns/day, 0.079 hours/ns, 3511.433 timesteps/s 99.4% CPU use with 4 MPI tasks x 1 OpenMP threads AMOEBA timing breakdown: - Init time: 1.93587e-05 1.89% - Hal time: 2.20198e-05 2.15% - Mpole time: 0.0001019 9.94% - Induce time: 0.000717017 69.95% - Polar time: 0.000164237 16.02% - Total time: 0.00102505 + Init time: 1.91963e-05 1.62% + Hal time: 2.47003e-05 2.08% + Mpole time: 0.000133592 11.24% + Induce time: 0.000773552 65.10% + Polar time: 0.000236616 19.91% + Total time: 0.00118822 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.0010331 | 0.0010362 | 0.0010375 | 0.0 | 83.50 -Bond | 3.723e-06 | 5.0355e-06 | 5.6e-06 | 0.0 | 0.41 +Pair | 0.0011966 | 0.0012002 | 0.0012035 | 0.0 | 84.29 +Bond | 3.666e-06 | 5.2103e-06 | 6.517e-06 | 0.0 | 0.37 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 1.7872e-05 | 4.1093e-05 | 6.4155e-05 | 0.0 | 3.31 -Output | 0.00012756 | 0.00014764 | 0.00016933 | 0.0 | 11.90 -Modify | 1.808e-06 | 2.4647e-06 | 2.74e-06 | 0.0 | 0.20 -Other | | 8.565e-06 | | | 0.69 +Comm | 1.5056e-05 | 5.6462e-05 | 7.9185e-05 | 0.0 | 3.97 +Output | 0.00012635 | 0.00014701 | 0.00018782 | 0.0 | 10.32 +Modify | 2.376e-06 | 2.7202e-06 | 3.086e-06 | 0.0 | 0.19 +Other | | 1.237e-05 | | | 0.87 Nlocal: 4.5 ave 6 max 3 min Histogram: 1 0 0 1 0 0 1 0 0 1 diff --git a/examples/amoeba/log.5Jul22.water_hexamer.hippo.g++.1 b/examples/amoeba/log.5Jul22.water_hexamer.hippo.g++.1 index e6a765c0e8..ab074128a4 100644 --- a/examples/amoeba/log.5Jul22.water_hexamer.hippo.g++.1 +++ b/examples/amoeba/log.5Jul22.water_hexamer.hippo.g++.1 @@ -48,6 +48,7 @@ Finding 1-2 1-3 1-4 neighbors ... pair_style hippo pair_coeff * * hippo_water.prm hippo_water.key Reading potential file hippo_water.prm with DATE: 2022-07-05 +Reading potential file hippo_water.key with DATE: 2022-07-05 special_bonds lj/coul 0.5 0.5 0.5 one/five yes Finding 1-2 1-3 1-4 neighbors ... @@ -109,31 +110,31 @@ Per MPI rank memory allocation (min/avg/max) = 47.84 | 47.84 | 47.84 Mbytes 3 19.013509 -45.750445 0.043880608 0.9336078 0 0 0.97748841 -43.809471 18351.549 29896.314 6275.5012 17065.39 -6055.8639 3664.6024 3015.6633 4 11.017518 -45.12347 0.24124811 0.58878104 0 0 0.83002915 -43.735142 35358.63 54252.632 19050.919 31719.21 -9822.7607 3160.7845 1520.1368 5 12.143149 -44.904245 0.22320916 0.3270434 0 0 0.55025256 -43.738653 35160.919 53395.572 20272.979 30653.482 -9511.0241 1392.4959 35.692826 -Loop time of 0.000984386 on 1 procs for 5 steps with 18 atoms +Loop time of 0.000973993 on 1 procs for 5 steps with 18 atoms -Performance: 438.852 ns/day, 0.055 hours/ns, 5079.308 timesteps/s -99.8% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 443.535 ns/day, 0.054 hours/ns, 5133.507 timesteps/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads HIPPO timing breakdown: - Init time: 1.2669e-05 1.45% - Repulse time: 0.000132325 15.15% - Disp time: 4.2534e-05 4.87% - Mpole time: 0.000177341 20.30% - Induce time: 0.000303723 34.77% - Polar time: 0.000179318 20.53% - Qxfer time: 2.5413e-05 2.91% - Total time: 0.000873466 + Init time: 1.2301e-05 1.42% + Repulse time: 0.000131627 15.20% + Disp time: 4.2386e-05 4.89% + Mpole time: 0.000181895 21.00% + Induce time: 0.000295778 34.15% + Polar time: 0.000178781 20.64% + Qxfer time: 2.3214e-05 2.68% + Total time: 0.00086611 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.00087559 | 0.00087559 | 0.00087559 | 0.0 | 88.95 -Bond | 6.455e-06 | 6.455e-06 | 6.455e-06 | 0.0 | 0.66 +Pair | 0.0008683 | 0.0008683 | 0.0008683 | 0.0 | 89.15 +Bond | 5.954e-06 | 5.954e-06 | 5.954e-06 | 0.0 | 0.61 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 7.87e-07 | 7.87e-07 | 7.87e-07 | 0.0 | 0.08 -Output | 9.3142e-05 | 9.3142e-05 | 9.3142e-05 | 0.0 | 9.46 -Modify | 2.351e-06 | 2.351e-06 | 2.351e-06 | 0.0 | 0.24 -Other | | 6.065e-06 | | | 0.62 +Comm | 6.69e-07 | 6.69e-07 | 6.69e-07 | 0.0 | 0.07 +Output | 9.1764e-05 | 9.1764e-05 | 9.1764e-05 | 0.0 | 9.42 +Modify | 2.34e-06 | 2.34e-06 | 2.34e-06 | 0.0 | 0.24 +Other | | 4.965e-06 | | | 0.51 Nlocal: 18 ave 18 max 18 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/amoeba/log.5Jul22.water_hexamer.hippo.g++.4 b/examples/amoeba/log.5Jul22.water_hexamer.hippo.g++.4 index 02d9b0f6f2..cea8fe5b53 100644 --- a/examples/amoeba/log.5Jul22.water_hexamer.hippo.g++.4 +++ b/examples/amoeba/log.5Jul22.water_hexamer.hippo.g++.4 @@ -48,6 +48,7 @@ Finding 1-2 1-3 1-4 neighbors ... pair_style hippo pair_coeff * * hippo_water.prm hippo_water.key Reading potential file hippo_water.prm with DATE: 2022-07-05 +Reading potential file hippo_water.key with DATE: 2022-07-05 special_bonds lj/coul 0.5 0.5 0.5 one/five yes Finding 1-2 1-3 1-4 neighbors ... @@ -110,31 +111,31 @@ Per MPI rank memory allocation (min/avg/max) = 47.86 | 47.86 | 47.86 Mbytes 3 19.013509 -45.750445 0.043880608 0.9336078 0 0 0.97748841 -43.809471 18351.549 29896.314 6275.5012 17065.39 -6055.8639 3664.6024 3015.6633 4 11.017518 -45.12347 0.24124811 0.58878104 0 0 0.83002915 -43.735142 35358.63 54252.632 19050.919 31719.21 -9822.7607 3160.7845 1520.1368 5 12.143149 -44.904245 0.22320916 0.3270434 0 0 0.55025256 -43.738653 35160.919 53395.572 20272.979 30653.482 -9511.0241 1392.4959 35.692826 -Loop time of 0.00126451 on 4 procs for 5 steps with 18 atoms +Loop time of 0.0010879 on 4 procs for 5 steps with 18 atoms -Performance: 341.634 ns/day, 0.070 hours/ns, 3954.096 timesteps/s -92.2% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 397.096 ns/day, 0.060 hours/ns, 4596.020 timesteps/s +97.6% CPU use with 4 MPI tasks x 1 OpenMP threads HIPPO timing breakdown: - Init time: 1.75712e-05 1.72% - Repulse time: 0.000116156 11.39% - Disp time: 1.69788e-05 1.66% - Mpole time: 0.000178714 17.52% - Induce time: 0.000515806 50.57% - Polar time: 0.0001659 16.27% - Qxfer time: 8.64975e-06 0.85% - Total time: 0.00101993 + Init time: 1.85215e-05 2.13% + Repulse time: 9.38538e-05 10.79% + Disp time: 1.49635e-05 1.72% + Mpole time: 0.000126348 14.53% + Induce time: 0.000481476 55.36% + Polar time: 0.000126323 14.53% + Qxfer time: 8.01125e-06 0.92% + Total time: 0.000869664 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.0010223 | 0.0010316 | 0.001045 | 0.0 | 81.58 -Bond | 3.062e-06 | 4.3805e-06 | 5.123e-06 | 0.0 | 0.35 +Pair | 0.00087311 | 0.00088213 | 0.00088962 | 0.0 | 81.09 +Bond | 3.358e-06 | 4.3378e-06 | 4.915e-06 | 0.0 | 0.40 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 1.4853e-05 | 6.5245e-05 | 9.2753e-05 | 0.0 | 5.16 -Output | 0.0001294 | 0.00014959 | 0.00018927 | 0.0 | 11.83 -Modify | 1.595e-06 | 2.2495e-06 | 2.798e-06 | 0.0 | 0.18 -Other | | 1.145e-05 | | | 0.91 +Comm | 2.4495e-05 | 4.3727e-05 | 6.9446e-05 | 0.0 | 4.02 +Output | 0.00012885 | 0.00014625 | 0.00016056 | 0.0 | 13.44 +Modify | 2.162e-06 | 2.5343e-06 | 2.766e-06 | 0.0 | 0.23 +Other | | 8.911e-06 | | | 0.82 Nlocal: 4.5 ave 6 max 3 min Histogram: 1 0 0 1 0 0 1 0 0 1