From 2f32fb7f8bda59f8044dda41bd86ab1a6f5db515 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Thu, 13 Apr 2017 11:19:48 -0600 Subject: [PATCH] patch 13Apr17 --- doc/src/Manual.txt | 4 +- examples/cmap/log.11Apr17.cmap.g++.1 | 205 +++++++++++++++++++++++++++ examples/cmap/log.11Apr17.cmap.g++.4 | 205 +++++++++++++++++++++++++++ src/KOKKOS/verlet_kokkos.cpp | 15 +- src/KOKKOS/verlet_kokkos.h | 2 +- src/MC/fix_gcmc.cpp | 9 +- src/MC/fix_gcmc.h | 2 +- src/version.h | 2 +- 8 files changed, 429 insertions(+), 15 deletions(-) create mode 100644 examples/cmap/log.11Apr17.cmap.g++.1 create mode 100644 examples/cmap/log.11Apr17.cmap.g++.4 diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt index a5a874fa8b..a6bc459530 100644 --- a/doc/src/Manual.txt +++ b/doc/src/Manual.txt @@ -1,7 +1,7 @@ LAMMPS Users Manual - + @@ -21,7 +21,7 @@

LAMMPS Documentation :c,h3 -11 Apr 2017 version :c,h4 +13 Apr 2017 version :c,h4 Version info: :h4 diff --git a/examples/cmap/log.11Apr17.cmap.g++.1 b/examples/cmap/log.11Apr17.cmap.g++.1 new file mode 100644 index 0000000000..9b4fc29991 --- /dev/null +++ b/examples/cmap/log.11Apr17.cmap.g++.1 @@ -0,0 +1,205 @@ +LAMMPS (31 Mar 2017) +# Created by charmm2lammps v1.8.2.6 beta on Thu Mar 3 20:56:57 EST 2016 + +units real +neigh_modify delay 2 every 1 +#newton off + +boundary p p p + +atom_style full +bond_style harmonic +angle_style charmm +dihedral_style charmmfsw +improper_style harmonic + +pair_style lj/charmmfsw/coul/charmmfsh 8 12 +pair_modify mix arithmetic + +fix cmap all cmap charmm22.cmap +Reading potential file charmm22.cmap with DATE: 2016-09-26 +fix_modify cmap energy yes + +read_data gagg.data fix cmap crossterm CMAP + orthogonal box = (-34.4147 -36.1348 -39.3491) to (45.5853 43.8652 40.6509) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 34 atoms + scanning bonds ... + 4 = max bonds/atom + scanning angles ... + 6 = max angles/atom + scanning dihedrals ... + 12 = max dihedrals/atom + scanning impropers ... + 1 = max impropers/atom + reading bonds ... + 33 bonds + reading angles ... + 57 angles + reading dihedrals ... + 75 dihedrals + reading impropers ... + 7 impropers + 4 = max # of 1-2 neighbors + 7 = max # of 1-3 neighbors + 13 = max # of 1-4 neighbors + 16 = max # of special neighbors + +special_bonds charmm +fix 1 all nve + +#fix 1 all nvt temp 300 300 100.0 +#fix 2 all shake 1e-9 500 0 m 1.0 + +velocity all create 0.0 12345678 dist uniform + +thermo 1000 +thermo_style custom step ecoul evdwl ebond eangle edihed f_cmap eimp +timestep 2.0 + +run 100000 +Neighbor list info ... + update every 1 steps, delay 2 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 12 12 12 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/charmmfsw/coul/charmmfsh, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 14.96 | 14.96 | 14.96 Mbytes +Step E_coul E_vdwl E_bond E_angle E_dihed f_cmap E_impro + 0 16.287573 -0.85933785 1.2470497 4.8441789 4.5432816 -1.473352 0.10453023 + 1000 18.816462 -0.84379243 0.78931817 2.7554247 4.4371421 -2.7762038 0.12697656 + 2000 18.091571 -1.045888 0.72306589 3.0951524 4.6725102 -2.3580092 0.22712496 + 3000 17.835596 -1.2171641 0.72666403 2.6696491 5.4373798 -2.0737041 0.075101693 + 4000 16.211232 -0.42713611 0.99472642 3.8961462 5.2009895 -2.5626866 0.17356243 + 5000 17.72183 -0.57081189 0.90733068 3.4376382 4.5457582 -2.3727543 0.12354518 + 6000 18.753977 -1.5772499 0.81468321 2.9236782 4.6033216 -2.3380859 0.12835782 + 7000 18.186024 -0.84205608 0.58996182 3.0329585 4.7221473 -2.5733243 0.10047631 + 8000 18.214306 -1.1360938 0.72597611 3.7493028 4.7319958 -2.8957969 0.2006046 + 9000 17.248408 -0.48641993 0.90266229 2.9721743 4.7651056 -2.1473354 0.1302043 + 10000 17.760655 -1.2968444 0.92384663 3.7007455 4.7378947 -2.2147779 0.06940579 + 11000 17.633929 -0.57368413 0.84872849 3.4277114 4.285393 -2.236944 0.17204973 + 12000 18.305835 -1.0675148 0.75879532 2.8853173 4.685027 -2.409087 0.087538866 + 13000 17.391558 -0.9975291 0.66671947 3.8065638 5.2285578 -2.4198822 0.06253594 + 14000 17.483387 -0.67727643 0.91966477 3.7317031 4.7770445 -2.6080027 0.11487095 + 15000 18.131749 -1.1918751 1.0025684 3.1238131 4.789742 -2.2546745 0.13782813 + 16000 16.972343 -0.43926531 0.60644597 3.7551592 4.8658618 -2.2627659 0.12353145 + 17000 18.080785 -1.2073565 0.7867072 3.5671106 4.43754 -2.5092904 0.17429146 + 18000 17.474576 -0.97836065 0.8678524 3.7961537 4.3409032 -1.8922572 0.134048 + 19000 17.000911 -1.2286864 0.83615834 3.9322908 4.9319492 -2.3281576 0.056689619 + 20000 17.043286 -0.8506561 0.80966589 3.5087339 4.8603878 -2.3365263 0.096794824 + 21000 17.314495 -1.1430889 0.95363892 4.2446032 4.2756745 -2.1829483 0.17119518 + 22000 18.954881 -0.998673 0.58688334 2.71536 4.6634319 -2.6862804 0.20328442 + 23000 17.160427 -0.97803282 0.86894041 4.0897736 4.3146238 -2.1962289 0.075339092 + 24000 17.602026 -1.0833323 0.94888776 3.7341878 4.3084335 -2.1640414 0.081493681 + 25000 17.845584 -1.3432612 0.93497086 3.8911043 4.468032 -2.3475883 0.093204333 + 26000 17.833261 -1.1020534 0.77931087 3.7628141 4.512381 -2.3134761 0.15568465 + 27000 17.68607 -1.3222026 1.1985872 3.5817624 4.6360755 -2.3492774 0.08427906 + 28000 18.326649 -1.2669291 0.74809075 3.2624429 4.4698564 -2.3679076 0.14677293 + 29000 17.720933 -1.0773886 0.83099482 3.7652834 4.6584594 -2.8255303 0.23092596 + 30000 18.201999 -1.0168706 1.0637455 3.453095 4.3738593 -2.8063214 0.18658217 + 31000 17.823502 -1.2685768 0.84805585 3.8600661 4.2195821 -2.1169716 0.12517101 + 32000 16.883133 -0.62062648 0.84434922 3.5042683 5.1264906 -2.2674699 0.030138165 + 33000 17.805715 -1.679553 1.2430372 4.314677 4.2523894 -2.3008321 0.18591872 + 34000 16.723767 -0.54189072 1.1282827 3.8542159 4.3026559 -2.2186336 0.05392425 + 35000 17.976909 -0.72092075 0.5876319 2.9726396 5.0881439 -2.491692 0.17356291 + 36000 18.782492 -1.514246 0.63237955 3.2777164 4.6077164 -2.502574 0.082537318 + 37000 17.247716 -0.6344626 0.79885976 3.452491 4.7618281 -2.3902444 0.11450271 + 38000 17.996494 -1.6712877 1.0111769 4.1689136 4.46963 -2.4076725 0.11875756 + 39000 17.586857 -0.74508086 0.95970486 3.7395038 4.6011357 -2.9854953 0.30143284 + 40000 17.494879 -0.30772446 0.72047991 3.2604877 4.7283734 -2.3812495 0.16399034 + 41000 15.855772 -0.49642605 0.82496448 4.5139653 4.76884 -2.214141 0.10899661 + 42000 17.898568 -1.3078863 1.1505144 4.0429873 4.3889581 -2.8696559 0.23336417 + 43000 19.014372 -1.6325979 1.1553166 3.5660772 4.4047997 -2.9302044 0.13672127 + 44000 18.250782 -0.97211613 0.72714301 3.2258362 4.7257298 -2.5533613 0.11968073 + 45000 17.335174 0.24746331 1.0415866 3.3220992 4.5251095 -3.0415216 0.24453084 + 46000 17.72846 -0.9541418 0.88153841 3.7893452 4.5251883 -2.4003613 0.051809816 + 47000 18.226762 -0.67057787 0.84352989 3.0609522 4.5449078 -2.4694254 0.073703949 + 48000 17.838074 -0.88768441 1.3812262 3.5890492 4.5827868 -3.0137515 0.21417113 + 49000 17.973733 -0.75118705 0.69667886 3.3989025 4.7058886 -2.8243945 0.26665792 + 50000 17.461583 -0.65040016 0.68943524 2.9374743 5.6971777 -2.4438011 0.1697603 + 51000 16.79766 -0.010684434 0.89795555 3.959039 4.56763 -2.5101098 0.15048853 + 52000 17.566543 -0.7262764 0.74354418 3.3423185 4.8426523 -2.4187649 0.16908776 + 53000 17.964274 -0.9270914 1.065952 3.0397181 4.4682262 -2.2179503 0.07873406 + 54000 17.941256 -0.5807578 0.76516121 3.7262371 4.6975126 -3.179899 0.24433708 + 55000 17.079478 -0.48559832 0.95364453 3.0414645 5.2811414 -2.7064882 0.30102814 + 56000 17.632179 -0.75403299 0.97577942 3.3672363 4.4851336 -2.3683659 0.051117638 + 57000 16.17128 -0.44699325 0.76341543 4.267716 5.0881056 -2.4122329 0.16671692 + 58000 16.899276 -0.76481024 1.0400825 3.973493 4.8823309 -2.4270284 0.048716383 + 59000 18.145412 -0.84968335 0.71698306 3.2024358 4.6115739 -2.2520353 0.19466966 + 60000 17.578258 -1.0067331 0.72822527 3.5375208 4.9110255 -2.2319607 0.11922362 + 61000 17.434762 -1.0244393 0.90593099 3.8446915 4.8571191 -2.6228357 0.23259208 + 62000 17.580489 -1.1135917 0.79577432 3.7043524 4.6058114 -2.351492 0.042904152 + 63000 18.207335 -1.1512268 0.82684507 3.4114738 4.351069 -2.1878441 0.082922105 + 64000 18.333083 -1.1182287 0.74058959 3.6905164 4.3226172 -2.7110393 0.14721704 + 65000 16.271579 -0.7122151 1.0200168 4.6983643 4.3681131 -2.194921 0.12831024 + 66000 17.316444 -0.5729385 0.85254108 3.5769963 4.5526705 -2.3321328 0.040452643 + 67000 17.19011 -0.8814312 1.1381258 3.8605789 4.4183813 -2.299607 0.091527355 + 68000 18.223367 -1.362189 0.74472056 3.259165 4.486512 -2.2181134 0.048952796 + 69000 17.646348 -0.91647162 0.73990335 3.9313692 5.2663097 -3.3816778 0.27769877 + 70000 18.173493 -1.3107718 0.96484426 3.219728 4.5045124 -2.3349534 0.082327407 + 71000 17.0627 -0.58509083 0.85964129 3.8490884 4.437895 -2.1673348 0.24151404 + 72000 17.809764 -0.35128902 0.65479258 3.3945008 4.6160508 -2.5486166 0.10829531 + 73000 18.27769 -1.0739758 0.80890957 3.6070901 4.6256762 -2.4576547 0.080025736 + 74000 18.109437 -1.0691837 0.66679323 3.5923203 4.4825716 -2.5048169 0.21372319 + 75000 17.914569 -1.3500765 1.2993494 3.362421 4.4160377 -2.1278163 0.19397641 + 76000 16.563928 -0.16539261 1.0067302 3.5742755 4.8581915 -2.1362429 0.059822408 + 77000 18.130477 -0.38361279 0.43406954 3.4725995 4.7005855 -2.8836242 0.11958174 + 78000 16.746204 -1.1732959 0.7455507 3.6296638 5.6344113 -2.459208 0.16099803 + 79000 18.243999 -1.5850155 1.0108545 3.4727867 4.3367411 -2.316686 0.070480814 + 80000 16.960715 -0.84100929 0.91604996 3.862215 4.780949 -2.3711596 0.073916605 + 81000 17.697722 -1.1126605 0.952804 3.7114455 4.4216316 -2.2770085 0.091372066 + 82000 17.835901 -1.3091474 0.71867629 3.8168122 5.0150205 -2.4730634 0.062592852 + 83000 19.168418 -1.476938 0.75592316 3.2304519 4.3946471 -2.2991395 0.13083324 + 84000 17.945778 -1.5223622 1.0859941 3.4334011 5.0286682 -2.7550892 0.2476269 + 85000 17.950251 -0.85843846 0.86888218 3.3101287 4.5511879 -2.3640013 0.12080834 + 86000 17.480699 -0.97493649 0.85049761 3.4973085 4.6344922 -2.343121 0.2009677 + 87000 17.980244 -1.114983 0.88796989 3.4113329 4.3535853 -2.2535412 0.14494917 + 88000 18.023866 -1.226683 0.62339706 3.7649269 4.5923973 -2.3923523 0.10464375 + 89000 16.362829 -0.311462 1.0265375 4.0101723 4.4184777 -2.0314129 0.056570704 + 90000 17.533149 -0.41526788 1.0362029 3.4247412 4.2734431 -2.4776658 0.16960663 + 91000 17.719099 -1.1956801 1.0069945 3.2380672 4.8982805 -2.2154906 0.12950936 + 92000 17.762654 -1.170027 0.95814525 3.5217717 4.5405343 -2.5983677 0.15037754 + 93000 17.393958 -0.45641026 0.6579069 3.6002204 4.5942053 -2.5559641 0.12026544 + 94000 16.8182 -0.92962066 0.86801362 4.2914398 4.659848 -2.5251987 0.18000415 + 95000 17.642086 -0.7994896 0.7003756 3.8036697 4.5252487 -2.4166307 0.15686517 + 96000 18.114292 -1.5102104 1.2635908 3.2764427 5.0659496 -2.2777806 0.054309645 + 97000 18.575765 -1.6015311 0.69500699 3.1649317 4.9945742 -2.4012125 0.067373724 + 98000 16.578893 -0.78030229 0.91524222 4.4429655 4.4622392 -2.4052655 0.15355705 + 99000 17.26063 -0.57832833 0.7098846 3.9000046 4.5576484 -2.5333026 0.25517222 + 100000 18.377235 -0.89109577 0.68988617 2.8751751 4.4115591 -2.3560731 0.12185212 +Loop time of 2.96043 on 1 procs for 100000 steps with 34 atoms + +Performance: 5836.990 ns/day, 0.004 hours/ns, 33778.875 timesteps/s +99.9% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.074 | 1.074 | 1.074 | 0.0 | 36.28 +Bond | 1.6497 | 1.6497 | 1.6497 | 0.0 | 55.72 +Neigh | 0.007576 | 0.007576 | 0.007576 | 0.0 | 0.26 +Comm | 0.012847 | 0.012847 | 0.012847 | 0.0 | 0.43 +Output | 0.0010746 | 0.0010746 | 0.0010746 | 0.0 | 0.04 +Modify | 0.16485 | 0.16485 | 0.16485 | 0.0 | 5.57 +Other | | 0.05037 | | | 1.70 + +Nlocal: 34 ave 34 max 34 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 395 ave 395 max 395 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 395 +Ave neighs/atom = 11.6176 +Ave special neighs/atom = 9.52941 +Neighbor list builds = 253 +Dangerous builds = 0 +Total wall time: 0:00:02 diff --git a/examples/cmap/log.11Apr17.cmap.g++.4 b/examples/cmap/log.11Apr17.cmap.g++.4 new file mode 100644 index 0000000000..ec471d5a7e --- /dev/null +++ b/examples/cmap/log.11Apr17.cmap.g++.4 @@ -0,0 +1,205 @@ +LAMMPS (31 Mar 2017) +# Created by charmm2lammps v1.8.2.6 beta on Thu Mar 3 20:56:57 EST 2016 + +units real +neigh_modify delay 2 every 1 +#newton off + +boundary p p p + +atom_style full +bond_style harmonic +angle_style charmm +dihedral_style charmmfsw +improper_style harmonic + +pair_style lj/charmmfsw/coul/charmmfsh 8 12 +pair_modify mix arithmetic + +fix cmap all cmap charmm22.cmap +Reading potential file charmm22.cmap with DATE: 2016-09-26 +fix_modify cmap energy yes + +read_data gagg.data fix cmap crossterm CMAP + orthogonal box = (-34.4147 -36.1348 -39.3491) to (45.5853 43.8652 40.6509) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 34 atoms + scanning bonds ... + 4 = max bonds/atom + scanning angles ... + 6 = max angles/atom + scanning dihedrals ... + 12 = max dihedrals/atom + scanning impropers ... + 1 = max impropers/atom + reading bonds ... + 33 bonds + reading angles ... + 57 angles + reading dihedrals ... + 75 dihedrals + reading impropers ... + 7 impropers + 4 = max # of 1-2 neighbors + 7 = max # of 1-3 neighbors + 13 = max # of 1-4 neighbors + 16 = max # of special neighbors + +special_bonds charmm +fix 1 all nve + +#fix 1 all nvt temp 300 300 100.0 +#fix 2 all shake 1e-9 500 0 m 1.0 + +velocity all create 0.0 12345678 dist uniform + +thermo 1000 +thermo_style custom step ecoul evdwl ebond eangle edihed f_cmap eimp +timestep 2.0 + +run 100000 +Neighbor list info ... + update every 1 steps, delay 2 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 12 12 12 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/charmmfsw/coul/charmmfsh, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 14.94 | 15.57 | 16.2 Mbytes +Step E_coul E_vdwl E_bond E_angle E_dihed f_cmap E_impro + 0 16.287573 -0.85933785 1.2470497 4.8441789 4.5432816 -1.473352 0.10453023 + 1000 18.816462 -0.84379243 0.78931817 2.7554247 4.4371421 -2.7762038 0.12697656 + 2000 18.091571 -1.045888 0.72306589 3.0951524 4.6725102 -2.3580092 0.22712496 + 3000 17.835596 -1.2171641 0.72666403 2.6696491 5.4373798 -2.0737041 0.075101693 + 4000 16.211232 -0.42713611 0.99472642 3.8961462 5.2009895 -2.5626866 0.17356243 + 5000 17.72183 -0.57081189 0.90733068 3.4376382 4.5457582 -2.3727543 0.12354518 + 6000 18.753977 -1.5772499 0.81468321 2.9236782 4.6033216 -2.3380859 0.12835782 + 7000 18.186024 -0.84205609 0.58996181 3.0329584 4.7221473 -2.5733244 0.10047631 + 8000 18.214306 -1.1360934 0.72597583 3.7493032 4.7319959 -2.8957975 0.20060467 + 9000 17.248415 -0.48642024 0.90266262 2.9721744 4.7651003 -2.1473349 0.13020438 + 10000 17.760663 -1.2968458 0.92384687 3.7007432 4.7378917 -2.2147799 0.06940514 + 11000 17.63395 -0.57366075 0.84871737 3.4276851 4.2853865 -2.2369491 0.17205075 + 12000 18.305713 -1.0672299 0.75876262 2.8852171 4.6850229 -2.4090072 0.087568888 + 13000 17.383367 -0.99678627 0.66712651 3.8060954 5.233865 -2.4180629 0.062014239 + 14000 17.510901 -0.68723297 0.92448551 3.7550867 4.7321218 -2.6059088 0.11504409 + 15000 18.080165 -1.13316 0.99982253 3.09947 4.8171402 -2.2713372 0.14580371 + 16000 17.383245 -0.4535296 0.57826268 3.6453593 4.6541138 -2.2434512 0.13285609 + 17000 17.111153 -0.3414839 0.73667584 3.7485311 4.6262965 -2.6166049 0.12635815 + 18000 16.862046 -1.3592061 1.2371142 4.4878937 4.2937117 -2.2112584 0.066145125 + 19000 18.313891 -1.654238 0.90644101 3.3934089 4.550735 -2.1862171 0.081267736 + 20000 19.083561 -1.3081747 0.56257812 2.7633848 4.6211438 -2.5196707 0.13763071 + 21000 18.23741 -1.051353 0.64408722 3.1735565 4.6912533 -2.2491947 0.099394904 + 22000 17.914515 -0.89769621 0.61793801 3.1224992 4.8683543 -2.282475 0.14524537 + 23000 16.756122 -0.98277883 1.2554905 3.7916115 4.7301443 -2.3094994 0.10226772 + 24000 16.109857 -0.54593177 0.86934462 4.4293574 4.926985 -2.2652264 0.11414331 + 25000 18.590559 -1.497327 1.1898361 2.9134403 4.7854107 -2.4437918 0.067416154 + 26000 18.493391 -1.0533797 0.4889578 3.6563013 4.6171721 -2.3240835 0.11607829 + 27000 18.646522 -1.1229601 0.67956815 2.7937638 4.8991207 -2.4068997 0.10109147 + 28000 18.545103 -1.7237438 0.72488022 3.8041665 4.6459974 -2.4339333 0.21943258 + 29000 17.840505 -1.0909667 0.88133248 3.3698456 5.0311644 -2.5116617 0.08102693 + 30000 17.649527 -0.65409177 0.86781692 3.24112 4.9903073 -2.6234925 0.14799777 + 31000 18.156812 -0.77476556 0.83192789 2.9620784 4.9160635 -2.8571635 0.22283201 + 32000 18.251583 -1.3384075 0.8059007 3.2588176 4.4365328 -2.1875071 0.087883637 + 33000 17.702785 -0.88311587 0.98573641 3.4645713 4.2650091 -2.0909158 0.14233004 + 34000 17.123413 -1.4873429 1.0419563 4.2628178 4.6318762 -2.2292095 0.105354 + 35000 18.162061 -1.0136007 0.82436129 3.6365024 4.5801677 -2.6856989 0.28648222 + 36000 17.65618 -1.094718 0.8872444 3.5075241 4.6382423 -2.3895134 0.18116961 + 37000 17.336475 -1.0657995 0.98869254 3.9252927 4.4383632 -2.2048244 0.22285949 + 38000 17.369467 -0.97623132 0.6712095 4.1349304 4.597754 -2.4088341 0.14608514 + 39000 18.170206 -1.2344285 0.77546195 3.6451049 4.7482287 -2.9895286 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17.839632 -1.0221781 0.76425017 3.3331547 4.5368437 -2.0988773 0.21098435 + 53000 18.693035 -1.4231915 0.76333082 3.1612761 4.583242 -2.4485762 0.089191206 + 54000 16.334672 -0.36309884 1.0200365 4.6700448 4.1628702 -2.1713841 0.11431995 + 55000 17.33842 -0.61522682 0.89847366 3.4970659 4.673495 -2.4743036 0.068004878 + 56000 17.790294 -1.0150845 0.73697112 3.6000297 4.5988343 -2.4822509 0.11434632 + 57000 18.913486 -1.0985507 1.0231848 2.7483267 4.4421755 -2.574424 0.1763388 + 58000 17.586896 -0.98284126 0.96965633 3.3330357 4.5325543 -2.1936869 0.083230915 + 59000 17.77788 -1.1649953 0.83092298 3.8004148 4.3940176 -2.3136642 0.017207608 + 60000 17.013042 -0.21728023 1.1688832 3.5374476 4.5462244 -2.4425301 0.15028297 + 61000 17.236242 -1.1342147 1.0301086 3.685948 4.6842331 -2.328108 0.070210812 + 62000 17.529852 -1.2961547 1.0323133 3.4474598 5.1435839 -2.4553423 0.060842687 + 63000 18.754704 -1.1816999 0.51806039 3.140172 4.5832701 -2.2713213 0.06327871 + 64000 17.54594 -1.3592836 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4.8031296 -2.2777895 0.063015508 + 77000 16.679231 -0.080955983 0.7253398 3.4203454 5.0987608 -2.379614 0.12961874 + 78000 18.164524 -1.3115525 0.92526408 3.5764487 4.3814882 -2.3712488 0.073436724 + 79000 17.738686 -1.0697859 1.2186866 3.0593848 4.6551053 -2.2505871 0.075340661 + 80000 16.767483 -0.84777477 1.03128 4.1982958 4.6992227 -2.4146425 0.079774219 + 81000 16.257265 0.62803774 0.84032194 3.3873471 5.0961071 -2.7219776 0.20467848 + 82000 18.232082 -1.2129302 0.50746051 3.9207128 4.5073437 -2.599371 0.094522372 + 83000 16.618985 -0.60917055 0.8825847 3.805497 4.9560959 -2.2194726 0.14852687 + 84000 17.90762 -0.82336075 0.90504161 3.0324198 4.7444271 -2.5036073 0.15860682 + 85000 16.699883 -0.50297228 0.83405307 3.8598996 4.7971968 -2.2427788 0.10338668 + 86000 16.353038 -0.0096880616 0.80705167 4.0865115 4.5364338 -2.4548873 0.098456203 + 87000 17.887331 -0.75281219 1.0030148 4.0117123 4.3443074 -2.9774392 0.16190152 + 88000 18.583708 -1.4867053 0.86324814 3.3971237 4.3526221 -2.221239 0.14459352 + 89000 17.684828 -1.283764 1.0021118 3.5426808 4.9057005 -2.3921967 0.05844702 + 90000 17.2597 -0.84306489 0.99797936 3.8896866 4.4315457 -2.5662899 0.18270206 + 91000 16.705581 -0.44704047 0.75239556 3.470805 4.976868 -2.1894571 0.12312848 + 92000 17.548071 -1.2222664 0.92898812 4.0813773 4.3432647 -2.1631158 0.14071343 + 93000 17.163675 -0.94994776 0.96876981 3.9137692 4.4388666 -2.1260232 0.13187968 + 94000 18.842071 -1.2822113 0.58767049 3.1393475 4.5820965 -2.7264682 0.10406266 + 95000 18.112287 -1.1011381 0.63546648 3.4672667 4.486275 -2.2991936 0.041589685 + 96000 17.102713 -0.6877313 0.8389032 3.6892719 4.5676004 -2.1905327 0.13507011 + 97000 16.778253 -1.2902153 1.1588744 4.2820083 4.9537657 -2.4798159 0.35696636 + 98000 18.34638 -1.2908146 1.185356 3.0739807 4.4575453 -2.3959144 0.22407922 + 99000 17.995148 -1.3939639 0.7727299 3.8774144 4.4345458 -2.1142776 0.13550099 + 100000 18.444746 -1.2456693 0.86061526 3.468696 4.5264336 -2.4239851 0.074369539 +Loop time of 2.52011 on 4 procs for 100000 steps with 34 atoms + +Performance: 6856.851 ns/day, 0.004 hours/ns, 39680.850 timesteps/s +98.8% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.072506 | 0.28131 | 0.69088 | 46.2 | 11.16 +Bond | 0.050544 | 0.45307 | 0.9416 | 57.6 | 17.98 +Neigh | 0.0060885 | 0.0061619 | 0.0062056 | 0.1 | 0.24 +Comm | 0.44686 | 1.3679 | 2.0111 | 53.5 | 54.28 +Output | 0.0028057 | 0.0029956 | 0.003264 | 0.3 | 0.12 +Modify | 0.028202 | 0.095174 | 0.15782 | 19.8 | 3.78 +Other | | 0.3135 | | | 12.44 + +Nlocal: 8.5 ave 14 max 2 min +Histogram: 1 0 1 0 0 0 0 0 0 2 +Nghost: 25.5 ave 32 max 20 min +Histogram: 2 0 0 0 0 0 0 1 0 1 +Neighs: 98.75 ave 242 max 31 min +Histogram: 2 0 1 0 0 0 0 0 0 1 + +Total # of neighbors = 395 +Ave neighs/atom = 11.6176 +Ave special neighs/atom = 9.52941 +Neighbor list builds = 246 +Dangerous builds = 0 +Total wall time: 0:00:02 diff --git a/src/KOKKOS/verlet_kokkos.cpp b/src/KOKKOS/verlet_kokkos.cpp index 53b4042376..e4a3f857d3 100644 --- a/src/KOKKOS/verlet_kokkos.cpp +++ b/src/KOKKOS/verlet_kokkos.cpp @@ -64,14 +64,17 @@ VerletKokkos::VerletKokkos(LAMMPS *lmp, int narg, char **arg) : setup before run ------------------------------------------------------------------------- */ -void VerletKokkos::setup() +void VerletKokkos::setup(int flag) { if (comm->me == 0 && screen) { fprintf(screen,"Setting up Verlet run ...\n"); - fprintf(screen," Unit style : %s\n", update->unit_style); - fprintf(screen," Current step : " BIGINT_FORMAT "\n", update->ntimestep); - fprintf(screen," Time step : %g\n", update->dt); - timer->print_timeout(screen); + if (flag) { + fprintf(screen," Unit style : %s\n", update->unit_style); + fprintf(screen," Current step : " BIGINT_FORMAT "\n", + update->ntimestep); + fprintf(screen," Time step : %g\n", update->dt); + timer->print_timeout(screen); + } } update->setupflag = 1; @@ -169,7 +172,7 @@ void VerletKokkos::setup() if (force->newton) comm->reverse_comm(); modify->setup(vflag); - output->setup(); + output->setup(flag); lmp->kokkos->auto_sync = 1; update->setupflag = 1; } diff --git a/src/KOKKOS/verlet_kokkos.h b/src/KOKKOS/verlet_kokkos.h index 03a9383324..6455239204 100644 --- a/src/KOKKOS/verlet_kokkos.h +++ b/src/KOKKOS/verlet_kokkos.h @@ -29,7 +29,7 @@ class VerletKokkos : public Verlet { public: VerletKokkos(class LAMMPS *, int, char **); ~VerletKokkos() {} - void setup(); + void setup(int flag=1); void setup_minimal(int); void run(int); diff --git a/src/MC/fix_gcmc.cpp b/src/MC/fix_gcmc.cpp index cba5a0a176..73758e3628 100644 --- a/src/MC/fix_gcmc.cpp +++ b/src/MC/fix_gcmc.cpp @@ -260,7 +260,7 @@ void FixGCMC::options(int narg, char **arg) grouptypebits = NULL; energy_intra = 0.0; tfac_insert = 1.0; - overlap_cutoff = 0.0; + overlap_cutoffsq = 0.0; overlap_flag = 0; int iarg = 0; @@ -366,7 +366,8 @@ void FixGCMC::options(int narg, char **arg) iarg += 2; } else if (strcmp(arg[iarg],"overlap_cutoff") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal fix gcmc command"); - overlap_cutoff = force->numeric(FLERR,arg[iarg+1]); + double rtmp = force->numeric(FLERR,arg[iarg+1]); + overlap_cutoffsq = rtmp*rtmp; overlap_flag = 1; iarg += 2; } else error->all(FLERR,"Illegal fix gcmc command"); @@ -2146,7 +2147,7 @@ double FixGCMC::energy(int i, int itype, tagint imolecule, double *coord) // if overlap check requested, if overlap, // return signal value for energy - if (overlap_flag && rsq < overlap_cutoff) + if (overlap_flag && rsq < overlap_cutoffsq) return MAXENERGYSIGNAL; if (rsq < cutsq[itype][jtype]) @@ -2216,7 +2217,7 @@ double FixGCMC::energy_full() delz = x[i][2] - x[j][2]; rsq = delx*delx + dely*dely + delz*delz; - if (rsq < overlap_cutoff) { + if (rsq < overlap_cutoffsq) { overlaptest = 1; break; } diff --git a/src/MC/fix_gcmc.h b/src/MC/fix_gcmc.h index 2519c00965..8a5375eed7 100644 --- a/src/MC/fix_gcmc.h +++ b/src/MC/fix_gcmc.h @@ -112,7 +112,7 @@ class FixGCMC : public Fix { double **cutsq; double **atom_coord; imageint imagezero; - double overlap_cutoff; + double overlap_cutoffsq; // square distance cutoff for overlap int overlap_flag; double energy_intra; diff --git a/src/version.h b/src/version.h index e6ffb22dc0..2068d64573 100644 --- a/src/version.h +++ b/src/version.h @@ -1 +1 @@ -#define LAMMPS_VERSION "11 Apr 2017" +#define LAMMPS_VERSION "13 Apr 2017"