LAMMPS (28 Feb 2019) # REAX potential for AuO system # ..... units real # Bohr, a.u, femtosec, Hartree, force= Hartree/Bohr, charge=1e- , press= Pa , vitesse= Bohr/ atomic time unit (1.03275e-15 seconds) atom_style charge # atomic sysems with charge/ tester plutôt molecular: uncharged molecules (bonds, angles, dihedrals, impropers) ou full= molecular + charge #lattice hcp 1.0 origin 0.0 0.0 0.0 boundary p p p read_data data.surf #lecture de l'input avec géométrie et settings triclinic box = (0 0 0) to (29.88 25.86 300) with tilt (0 0 0) 1 by 1 by 16 MPI processor grid reading atoms ... 2448 atoms #group sublayers id 1:725 #group sublayers2 id 4351:5075 pair_style reax/c lmp_control # Type de potentiel pair_coeff * * ffield.montiAgAgSeem Ag S C H # valeurs des potentiels à utiliser avec les types d'atomes définis en interation neighbor 2.0 bin #rayon cutoff des pairs d'atomes considérées. neigh_modify every 1 delay 0 check no # communication entre procs pour les atomes switchant de proc pour calculs des forces. #fix 1 sublayers setforce 0.0 0.0 0.0 #fix 7 sublayers setforce NULL NULL NULL #fix 2 sublayers2 setforce 0.0 0.0 0.0 #fix 8 sublayers2 setforce NULL NULL NULL #fix 1 all box/relax tri 0.0 fix 2 all nve #un fix appliqué à un groupe d'atomes, ici l'ensemble nve fix 3 all reax/c/bonds 100000 bond.dat fix 4 all qeq/reax 1 0.0 20.0 1e-6 reax/c #Paramètres de charge, soit intrinsèque au Reax/c, soit un fichier avec eta=2eta(reax/c) PK ? format param.qeq = itype chi eta gamma (cf LAMMPS manual) fix 5 all temp/berendsen 0.0 300.0 5.0 compute reax all pair reax/c variable eb equal c_reax[1] variable ea equal c_reax[2] variable elp equal c_reax[3] variable emol equal c_reax[4] variable ev equal c_reax[5] variable epen equal c_reax[6] variable ecoa equal c_reax[7] variable ehb equal c_reax[8] variable et equal c_reax[9] variable eco equal c_reax[10] variable ew equal c_reax[11] variable ep equal c_reax[12] variable efi equal c_reax[13] variable eqeq equal c_reax[14] thermo 1000 thermo_style custom step temp etotal v_eb v_ea v_elp v_ev v_ehb v_et v_ew v_ep v_eqeq timestep 0.25 #Femtosec dump 1 all xyz 1000 toto_reax.xyz dump_modify 1 element Ag S C H #dump 3 all image 100 dump.*.jpg type type minimize 1.0e-10 1.0e-10 10000 10000 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 5 5 50 2 neighbor lists, perpetual/occasional/extra = 2 0 0 (1) pair reax/c, perpetual attributes: half, newton off, ghost pair build: half/bin/newtoff/ghost stencil: half/ghost/bin/3d/newtoff bin: standard (2) fix qeq/reax, perpetual, copy from (1) attributes: half, newton off, ghost pair build: copy stencil: none bin: none Per MPI rank memory allocation (min/avg/max) = 2.764 | 32.17 | 178.4 Mbytes Step Temp TotEng v_eb v_ea v_elp v_ev v_ehb v_et v_ew v_ep v_eqeq 0 0 -192969.58 -498179.62 239155.88 -0.00029151591 3206.3565 -3.3721209e-07 1280.4821 63340.124 -1251.0254 -139.41329 23 0 -194301.39 -494478.27 238231.39 -0.047822747 1924.2091 -6.0865689e-06 754.29775 60892.37 -1154.6444 -185.93181 Loop time of 38.1256 on 16 procs for 23 steps with 2448 atoms 90.1% CPU use with 16 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -192969.57881 -194301.39062 -194301.388875 Force two-norm initial, final = 1566.76 205.566 Force max component initial, final = 110.168 22.6541 Final line search alpha, max atom move = 4.60791e-05 0.00104388 Iterations, force evaluations = 23 80 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 27.126 | 27.132 | 27.14 | 0.1 | 71.16 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00033617 | 0.0060409 | 0.025881 | 12.1 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 10.95 | 10.955 | 10.956 | 0.1 | 28.73 Other | | 0.03308 | | | 0.09 Nlocal: 153 ave 864 max 0 min Histogram: 13 0 0 0 0 0 0 0 1 2 Nghost: 1050.62 ave 6470 max 0 min Histogram: 11 1 1 0 0 1 1 0 0 1 Neighs: 47001 ave 285313 max 0 min Histogram: 13 0 0 0 0 0 0 0 2 1 Total # of neighbors = 752016 Ave neighs/atom = 307.196 Neighbor list builds = 0 Dangerous builds not checked min_modify line quadratic #dump 1 all atom 30 dump.reax.auo run 300000 #femtosec Per MPI rank memory allocation (min/avg/max) = 2.747 | 32.26 | 176.8 Mbytes Step Temp TotEng v_eb v_ea v_elp v_ev v_ehb v_et v_ew v_ep v_eqeq 23 0 -194297.3 -494478.27 238231.39 -0.047822747 1924.2091 -6.0865689e-06 754.29775 60892.37 -1395.2874 58.803649 1000 1.2582565 -194386.67 -495085.03 238321.03 -0.0086974176 2054.3526 -5.2793576e-05 794.95317 61111.773 -1551.1751 241.68605 2000 2.166693 -194482.66 -496361.3 238968.71 -0.0028112403 2120.652 -8.9745044e-05 838.9382 61557.547 -1451.0048 111.91789 3000 3.2222622 -194531.65 -497565.69 239731.35 -0.0031316953 2075.4272 -0.00022715476 838.06216 61954.262 -1861.1488 556.36897 4000 4.1355217 -194593.57 -498604.06 240369.2 -0.0036025358 2031.2383 -0.00076991879 843.52376 62302.289 -2325.2339 1043.3917 5000 5.1282717 -194647.01 -499913.39 241196.48 -0.003464108 2003.1239 -0.0015152039 847.92175 62738.579 -2321.0469 1048.3138 6000 6.1387278 -194756.12 -501087.63 241966.25 -0.0034371047 1975.139 -0.0017755107 853.06187 63097.463 -1714.0359 393.23007 7000 6.9032492 -194710.53 -502255.36 242731.89 -0.0042685258 1972.4732 -0.0030151552 867.87792 63462.626 -1860.8118 604.86368 8000 7.834227 -194706.81 -503495.56 243534.92 -0.0045277685 1983.6276 -0.0032971174 865.09969 63920.193 -1620.0091 331.82173 9000 8.8030414 -194709.69 -504721.14 244295.56 -0.0042580812 1962.606 -0.0028801547 853.57698 64402.14 -1795.8323 513.26356 10000 10.129034 -194710.95 -504759.34 244326.22 -0.0046043284 1955.356 -0.0022987064 849.18129 64416.736 -2038.866 750.49899 11000 11.221718 -194748.62 -504100.45 243872.07 -0.0040512577 1974.3798 -0.0024230189 854.95098 64142.375 -1762.243 472.68666 12000 11.593384 -194647.13 -502818.82 243053.77 -0.0034197015 2054.1367 -0.0055740049 868.65942 63596.259 -2094.2327 892.93599 13000 12.797188 -194658.72 -501161.31 242050.51 -0.0040711111 2029.1551 -0.0052773574 869.62969 62980.697 -1780.93 544.70737 14000 14.052367 -194692.39 -500167.63 241196.65 -0.00049482478 2202.1967 -0.027856114 936.53414 62642.691 -1722.9274 403.12051 15000 15.082222 -194674.45 -500163.66 241286.26 -0.00064020675 2161.2204 -0.027742698 938.3202 62596.797 -1919.1276 600.38185 16000 16.078848 -194670.63 -501179.15 241944.45 -0.00056855819 2152.1913 -0.026616503 959.32149 62929.979 -2121.0302 810.0944 17000 17.024389 -194691.59 -502713.41 242928.54 -0.00042304481 2177.5817 -0.027181495 979.38657 63412.241 -2185.9026 870.57363 18000 17.864089 -194694.57 -504370.01 243954.33 -0.00057702478 2195.0855 -0.026474544 969.19421 64038.479 -1975.6655 648.30033 19000 18.851282 -194620.24 -505671.59 244783.57 -0.00086624693 2186.5254 -0.024965239 970.48909 64570.911 -2027.8342 715.33828 20000 20.145969 -194636.53 -505517.38 244762.92 -0.0010391835 2130.0986 -0.0255535 963.32066 64485.634 -1862.7395 538.72998 21000 20.99358 -194626.21 -504714.59 244192.64 -0.00078027512 2157.0893 -0.027523014 982.16239 64211.493 -1874.9956 551.88607 22000 22.025914 -194648.12 -503112.47 243214.28 -0.00072965927 2140.2958 -0.027006363 984.09807 63572.908 -1919.2753 596.1323 23000 22.81782 -194630.16 -501066.75 241905.73 -0.00081059747 2141.0188 -0.026621936 968.61088 62860.093 -1900.8653 579.24146 24000 23.673662 -194570.92 -499910.49 241185.7 -0.0007968325 2124.2028 -0.025612128 971.95802 62478.805 -1985.3587 676.02017 25000 25.030254 -194551.82 -499984.44 241231.59 -0.00088674797 2142.2062 -0.025316075 969.37752 62504.261 -2026.9272 713.63416 26000 25.878219 -194534.93 -500754.04 241747.53 -0.00099336818 2145.1127 -0.026162107 980.94667 62745.722 -2018.2655 713.53226 27000 27.361744 -194559.01 -502592.24 242841.43 -0.00067768859 2157.8052 -0.028113199 986.41257 63439.739 -2020.9736 714.96847 28000 27.865519 -194562.83 -504539.07 244153.04 -0.00087508961 2134.1657 -0.025531852 970.53693 64118.621 -1958.2804 638.67383 29000 28.284208 -194512.26 -505748.63 244846.67 -0.00054137053 2160.3819 -0.026710306 985.3819 64641.911 -1992.6023 673.72057 30000 30.326342 -194460.79 -505354.92 244696.08 -0.0014776458 2140.2449 -0.024838021 980.42506 64451.501 -2003.2267 691.99729 31000 30.737672 -194505.62 -504544.05 244155.98 -0.0013791558 2132.4507 -0.024790263 978.55872 64154.996 -1901.762 578.69716 32000 32.036813 -194484.01 -502701.7 243012.53 -0.0012040192 2119.4076 -0.022266081 972.08041 63478.949 -1937.9938 623.35546 33000 32.657053 -194499.12 -500398.82 241503.39 -0.00069064032 2140.3328 -0.024074129 962.22631 62659.941 -1870.7123 549.44188 34000 33.822859 -194399.8 -499827.74 241061.45 -0.0015610109 2177.6838 -0.026782543 990.2781 62536.664 -2011.0178 711.42496 35000 35.41859 -194382.24 -500087.99 241275.11 -0.00075426644 2166.0891 -0.026732128 995.77966 62601.882 -2019.718 713.93363 36000 36.288355 -194395.67 -500947.84 241808.62 -0.0012084795 2147.4599 -0.025115642 981.35343 62941.918 -2005.3315 698.15433 37000 36.69435 -194401.81 -502621.16 242941.04 -0.0018573261 2130.0133 -0.023973092 977.02086 63499.982 -2021.6136 710.0778 38000 37.211403 -194428.04 -504991.26 244438.84 -0.0011951313 2125.0224 -0.024308947 970.97116 64365.125 -1838.7946 515.23865 39000 38.896379 -194372.36 -505630.9 244830.06 -0.00092700747 2168.3676 -0.024937073 976.98839 64604.943 -1931.7218 609.79532 40000 40.120437 -194336.07 -505194.75 244529.59 -0.0016437996 2154.2917 -0.025149561 980.38567 64508.17 -1934.7154 613.05265 41000 41.014688 -194356.38 -503786.44 243673.55 -0.0010978036 2134.2369 -0.02282742 955.98627 63970.892 -1975.5398 655.10811 42000 42.025646 -194326.01 -502101.62 242585.31 -0.0011924399 2152.7975 -0.025406289 980.76008 63340.016 -2054.926 750.27882 43000 43.093582 -194335.05 -499964.06 241218.3 -0.00099811151 2148.9929 -0.025716596 993.18587 62555.325 -1959.927 644.26176 44000 43.476615 -194291.72 -499609.88 241051.93 -0.0012073591 2150.8925 -0.025390783 973.36193 62421.634 -1983.9582 671.49164 45000 45.271615 -194235.88 -500086.29 241328.39 -0.00086299014 2140.6937 -0.024196153 973.689 62665.723 -2033.1339 729.60033 46000 45.642969 -194251.78 -501384.09 242152.93 -0.0011984951 2161.5183 -0.025027958 974.10284 63111.309 -1937.5011 621.36335 47000 46.881324 -194260.92 -503302.39 243343.74 -0.00082912001 2159.6591 -0.024445997 980.19487 63827.809 -1913.8277 586.29232 48000 47.825035 -194276.58 -505409.09 244687.02 -0.00084991479 2156.0084 -0.024080956 988.7959 64566.388 -1966.5142 637.42779 49000 48.27948 -194231.14 -505310.5 244605.48 -0.0008611406 2191.4317 -0.02528827 981.14108 64543.662 -2121.0651 811.17201 50000 49.644127 -194200.81 -504587.6 244184.25 -0.0010165456 2173.9439 -0.024403829 982.74308 64283.153 -1964.6371 649.17321 51000 50.764511 -194182.88 -502780.62 243037.4 -0.0014363136 2165.2706 -0.023748175 979.80675 63639.517 -1889.6209 579.9174 52000 52.356444 -194173.74 -500964.82 241890.98 -0.00091765837 2167.3006 -0.023050389 985.97241 62957.962 -2026.5626 718.91879 53000 53.308502 -194145.53 -499192.75 240744.72 -0.0012696038 2165.2306 -0.024659205 974.73707 62358.758 -2080.0239 779.47896 54000 53.496134 -194156.62 -499478.61 240937.71 -0.0015114392 2167.4203 -0.023206866 964.48981 62465.555 -1905.5332 586.61543 55000 55.132637 -194137.17 -500472.62 241542.95 -0.0015603997 2175.6096 -0.024471284 972.32809 62843.205 -1891.6529 574.88056 56000 56.485432 -194120 -502564.6 242899.25 -0.00079212284 2185.0842 -0.025293554 1000.8549 63551.425 -1976.1039 657.34806 57000 57.02487 -194081.78 -504218.36 243932.78 -0.00085336522 2185.4418 -0.023393259 975.43008 64228.44 -1992.8436 676.02078 58000 57.990243 -194105.96 -505563.34 244881.75 -0.0012711463 2141.0977 -0.022530589 960.67277 64652.404 -1879.5763 561.86863 59000 59.362751 -194112.05 -505092.73 244504.21 -0.0016286556 2164.5158 -0.024979232 978.02205 64505.607 -1925.3569 605.68393 60000 59.409659 -194086.25 -503944.1 243792.22 -0.0011211678 2173.9266 -0.02478359 988.94566 64076.191 -1914.8757 592.83899 61000 60.748418 -194028.29 -501522.24 242213.54 -0.0020284192 2164.8339 -0.025598942 977.70966 63285.297 -2032.3304 725.17134 62000 62.517087 -194012.15 -499703.79 241051.98 -0.0012612103 2190.8682 -0.021940498 988.76021 62603.27 -1918.376 605.51536 63000 62.748999 -193979.83 -498650.08 240406.18 -0.001065449 2151.0108 -0.024465358 967.89802 62275.31 -2140.5519 835.69313 64000 63.905066 -194021.02 -499520.61 240932.49 -0.0010451689 2164.2015 -0.023634192 972.24502 62569.641 -1961.2017 640.83358 65000 65.162754 -194024.71 -500804.19 241776.62 -0.00070104574 2161.58 -0.023868639 975.82197 62991.544 -1919.7387 602.59696 66000 66.291738 -193972.7 -503439.73 243473.66 -0.00084388474 2181.407 -0.023568363 976.67647 63952.744 -1937.4506 620.97634 67000 66.909328 -193934.5 -505524.48 244723.16 -0.0011886075 2176.1446 -0.024208205 981.31991 64818.921 -2011.273 698.39333 68000 68.526206 -193926.82 -506045.51 245109.11 -0.0017870719 2166.7431 -0.023800769 978.69725 64971.798 -1982.8519 659.82709 69000 69.751777 -193973.56 -504955.99 244405.02 -0.0008769539 2173.6005 -0.023699085 972.30459 64517.387 -2044.6191 733.4165 70000 69.936323 -193990.98 -503341.77 243352.35 -0.0010951374 2179.113 -0.023771597 989.39714 63930.88 -1909.7663 584.26958 71000 72.030971 -193869.39 -500361.66 241481.19 -0.00083377952 2185.0284 -0.024488442 975.20582 62917.112 -1989.0818 680.78841 72000 71.679783 -193829.16 -498372.26 240244.52 -0.00098639489 2198.2522 -0.024122976 984.97511 62176.102 -2107.5652 806.71945 73000 72.839088 -193830.57 -498158.59 240126.95 -0.0011800054 2166.6766 -0.022477631 968.22632 62131.853 -1958.7094 645.12165 74000 74.201329 -193881.26 -499327.06 240894.99 -0.0017478412 2124.4451 -0.020889054 952.9493 62529.586 -1987.3134 672.52006 75000 75.347647 -193905.47 -501062.6 241989.09 -0.0020725964 2139.7102 -0.023718296 970.074 63106.048 -2033.1028 719.28582 76000 75.011401 -193833.49 -504189.93 243955.34 -0.0015459928 2193.8596 -0.023872021 976.18775 64283.643 -1976.9553 659.63457 77000 77.678197 -193774.54 -506240.5 245229.36 -0.0010335612 2175.9451 -0.023831439 982.58293 65109.666 -2050.6474 737.32797 78000 78.499607 -193763.57 -506077.71 245189.42 -0.0019209443 2121.8486 -0.018339236 960.70408 65072.04 -1918.5569 600.92264 79000 79.008574 -193821.4 -504782.77 244365.87 -0.0012966505 2146.3345 -0.021369709 991.37731 64480.988 -1960.0025 648.0566 80000 80.523089 -193848.95 -502648.33 242971.8 -0.0014355862 2172.709 -0.021559929 979.27284 63688.556 -1974.1211 658.24558 81000 80.74193 -193735.6 -499313.59 240872.94 -0.001787011 2177.732 -0.023614514 961.89892 62556.206 -2060.2559 764.88977 82000 81.48131 -193657.72 -497436.94 239673.22 -0.0025297775 2189.5648 -0.019419452 969.22777 61936.653 -1964.2726 664.76349 83000 83.198656 -193695.47 -497636.3 239804.91 -0.0022623217 2150.7756 -0.019840678 951.97398 62012.023 -2013.9011 711.63126 84000 84.211191 -193738.08 -499199.86 240835.43 -0.002299619 2156.4506 -0.022698417 975.14839 62476.503 -2004.4148 694.04308 85000 85.304476 -193771.05 -501439.27 242216.31 -0.0019528731 2181.4021 -0.022218037 974.06718 63270.842 -1983.5948 670.27599 86000 85.278779 -193691.36 -504732.13 244270.74 -0.0019901142 2218.0377 -0.022187086 973.01678 64557.319 -1960.9757 644.77777 87000 86.567831 -193597.22 -506783.7 245580.84 -0.0028293648 2168.5749 -0.02277172 976.57377 65415.922 -1969.9333 669.47031 88000 88.488929 -193597.72 -506214.11 245255.79 -0.0041782178 2160.4623 -0.018041398 963.44522 65180.77 -2017.9451 712.72749 89000 89.55217 -193695.06 -504375.11 244132.43 -0.0039832424 2138.6547 -0.017419521 954.21461 64386.79 -2032.0222 730.30811 90000 88.800452 -193699.78 -501836.93 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-497186.06 239494.82 -0.0043947632 2226.1091 -0.031673424 977.63991 63228.974 -2052.6296 794.43129 297000 295.63053 -190440.31 -493970 237508.76 -0.0050938203 2272.875 -0.025313461 946.85913 62175.591 -2286.9282 1043.9743 298000 295.61491 -190371.98 -492540.35 236600.17 -0.0054421287 2278.4215 -0.027466653 972.13893 61715.214 -1885.6271 617.687 299000 299.11908 -190382.72 -493625.54 237261.31 -0.0056366917 2267.6148 -0.026578827 964.89074 62080.463 -2322.9463 1095.591 300000 298.97584 -190452.72 -496188.85 238987.16 -0.0049002376 2255.787 -0.028600187 936.20065 62910.796 -2063.1851 810.90542 300023 299.37093 -190456.02 -496495.03 239133.8 -0.0058859867 2238.3107 -0.025938959 984.36613 63034.104 -2137.9482 892.44269 Loop time of 116540 on 16 procs for 300000 steps with 2448 atoms Performance: 0.056 ns/day, 431.631 hours/ns, 2.574 timesteps/s 91.2% CPU use with 16 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 59659 | 59678 | 59686 | 3.8 | 51.21 Neigh | 1.06 | 2455.3 | 17638 |10215.4 | 2.11 Comm | 8.5287 | 48.034 | 163.95 | 831.4 | 0.04 Output | 0.27945 | 0.28325 | 0.31974 | 1.8 | 0.00 Modify | 39069 | 54356 | 56855 |2191.1 | 46.64 Other | | 3.073 | | | 0.00 Nlocal: 153 ave 864 max 0 min Histogram: 13 0 0 0 0 0 0 0 1 2 Nghost: 1005.5 ave 6410 max 0 min Histogram: 12 0 1 0 0 1 1 0 0 1 Neighs: 49804.4 ave 305060 max 0 min Histogram: 13 0 0 0 0 0 0 1 1 1 Total # of neighbors = 796871 Ave neighs/atom = 325.519 Neighbor list builds = 300000 Dangerous builds not checked Please see the log.cite file for references relevant to this simulation Total wall time: 32:23:13