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rename some examples folders

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This commit is contained in:
Axel Kohlmeyer
2021-06-29 20:21:53 -04:00
parent 878795e64a
commit 9d208c9ebd
396 changed files with 32 additions and 20 deletions
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12
examples/PACKAGES/dpd-react/README Normal file
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This directory contains input files for DPD simulations under
isothermal, isoenergetic, isobaric and isoenthalpic conditions. In
addition, there is also an example for a reaction DPD simulation under
isoenergetic conditions. All the DPD scenarios that are named with
*-shardlow use the Shardlow splitting algorithm to integrate the
equations of motion. All the DPD scenarious that are named with
*-vv utilize the velocity-Verlet integration scheme. The compute dpd
command is used in the isoenergetic and isenthalpic case to
demonstrate how one can access the particle internal energies.

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# Input File for DPD fluid under isothermal conditions using the VV-SSA integration scheme
boundary p p p
units metal
atom_style atomic # Can be either dpd or atomic
read_data data.dpd
comm_modify mode single vel yes
mass 1 100.0
pair_style dpd/fdt 300.0 10.0 234324
pair_coeff 1 1 0.075 0.022 10.0
neighbor 2.0 bin
neigh_modify every 1 delay 0 check no once no
timestep 0.001
thermo 1
thermo_style custom step temp pe ke etotal
thermo_modify format float %15.10f
fix 1 all shardlow
fix 2 all nve
run 100

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boundary p p p
units metal
atom_style atomic # Can be either dpd or atomic
read_data data.dpd
orthogonal box = (-5.36874 -4.6558 -6.56118) to (61.4618 53.2342 46.2472)
1 by 1 by 1 MPI processor grid
reading atoms ...
1000 atoms
reading velocities ...
1000 velocities
comm_modify mode single vel yes
mass 1 100.0
pair_style dpd/fdt 300.0 10.0 234324
pair_coeff 1 1 0.075 0.022 10.0
neighbor 2.0 bin
neigh_modify every 1 delay 0 check no once no
timestep 0.001
thermo 1
thermo_style custom step temp pe ke etotal
thermo_modify format float %15.10f
fix 1 all shardlow
fix 2 all nve
run 100
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6 -> bins = 12 10 9
Memory usage per processor = 2.04718 Mbytes
Step Temp PotEng KinEng TotEng
0 128.6667660382 263.2538386154 16.6148533499 279.8686919654
1 128.8781761686 263.2538784644 16.6421529271 279.8960313916
2 129.0263870902 263.2539595162 16.6612915346 279.9152510508
3 129.0944237374 263.2540669039 16.6700771671 279.9241440710
4 129.1614377649 263.2542208758 16.6787307477 279.9329516235
5 129.5099128271 263.2544124900 16.7237296409 279.9781421309
6 129.4373659800 263.2546219015 16.7143616023 279.9689835038
7 129.5468806805 263.2548644992 16.7285033325 279.9833678316
8 129.6703137794 263.2551528171 16.7444423578 279.9995951748
9 129.7536788486 263.2554888044 16.7552073629 280.0106961673
10 129.6933335128 263.2558687434 16.7474149163 280.0032836597
11 130.0493631708 263.2562775241 16.7933893411 280.0496668651
12 130.3213023474 263.2567180413 16.8285050876 280.0852231289
13 130.5593614920 263.2571985052 16.8592458756 280.1164443808
14 130.1135609854 263.2576988467 16.8016792617 280.0593781083
15 130.6547973821 263.2582286670 16.8715695965 280.1297982635
16 130.9755543830 263.2587957218 16.9129892318 280.1717849537
17 131.2014468453 263.2594089178 16.9421589254 280.2015678432
18 131.5359736858 263.2600714133 16.9853566723 280.2454280856
19 131.5639698309 263.2607714057 16.9889718393 280.2497432450
20 131.8466997826 263.2615003685 17.0254810081 280.2869813767
21 131.7458627362 263.2622725589 17.0124598311 280.2747323900
22 132.0934657725 263.2630837288 17.0573461188 280.3204298476
23 132.1061515433 263.2639293632 17.0589842436 280.3229136067
24 132.0864214418 263.2648176945 17.0564364781 280.3212541726
25 132.4555532557 263.2657363510 17.1041027959 280.3698391469
26 132.5425428008 263.2667037975 17.1153358328 280.3820396303
27 132.6414596131 263.2677249519 17.1281090483 280.3958340002
28 132.8195594744 263.2687722206 17.1511072410 280.4198794616
29 133.0651588574 263.2698776260 17.1828217066 280.4526993326
30 133.3017699525 263.2710083469 17.2133755067 280.4843838536
31 133.2181215134 263.2721789243 17.2025739097 280.4747528340
32 133.5618245607 263.2733947608 17.2469565884 280.5203513492
33 133.5661164951 263.2746603944 17.2475108097 280.5221712041
34 133.9344464424 263.2759722947 17.2950735817 280.5710458764
35 134.0251961976 263.2773346108 17.3067921779 280.5841267887
36 134.3358724267 263.2787485272 17.3469100742 280.6256586014
37 134.6482162324 263.2802008254 17.3872433062 280.6674441317
38 134.2954310490 263.2816753288 17.3416878433 280.6233631722
39 134.0354062280 263.2831892100 17.3081106081 280.5912998182
40 134.0661172306 263.2847313607 17.3120763471 280.5968077078
41 134.3213973561 263.2863160883 17.3450408956 280.6313569839
42 134.4478244006 263.2879405395 17.3613665317 280.6493070711
43 134.5229893434 263.2896079217 17.3710726473 280.6606805690
44 134.2978694888 263.2913074700 17.3420027212 280.6333101912
45 134.4286053741 263.2930392576 17.3588847618 280.6519240193
46 134.3890734684 263.2948065124 17.3537799718 280.6485864842
47 134.7017125938 263.2966099975 17.3941513387 280.6907613362
48 135.3432781257 263.2984784239 17.4769972635 280.7754756874
49 135.2888717576 263.3003986994 17.4699717211 280.7703704205
50 134.8400489486 263.3023526413 17.4120148346 280.7143674760
51 134.9125407886 263.3043622408 17.4213757701 280.7257380109
52 134.9445891203 263.3064156298 17.4255141995 280.7319298293
53 134.9641746234 263.3085208561 17.4280432929 280.7365641489
54 135.1512290376 263.3106740078 17.4521977949 280.7628718026
55 135.3892461150 263.3128611111 17.4829331507 280.7957942618
56 135.3265159462 263.3150960609 17.4748327485 280.7899288094
57 135.3024789894 263.3173668060 17.4717288350 280.7890956410
58 135.2521455389 263.3196730859 17.4652292320 280.7849023179
59 135.0019475213 263.3220166727 17.4329209406 280.7549376133
60 135.3361351967 263.3244052062 17.4760748908 280.8004800970
61 135.3139260237 263.3268337328 17.4732070006 280.8000407335
62 135.7430391011 263.3293105744 17.5286187520 280.8579293264
63 136.0382719607 263.3318402706 17.5667424324 280.8985827031
64 136.0795308896 263.3343895372 17.5720702344 280.9064597716
65 136.5429311056 263.3369791756 17.6319095144 280.9688886899
66 136.6748062200 263.3396069611 17.6489386646 280.9885456257
67 136.9345368547 263.3422798556 17.6824779113 281.0247577668
68 136.5691107745 263.3449827879 17.6352901182 280.9802729061
69 137.0307306394 263.3477331218 17.6948994998 281.0426326215
70 137.1049105513 263.3505262239 17.7044784174 281.0550046413
71 137.2866781802 263.3533590313 17.7279502322 281.0813092635
72 137.3465172948 263.3562278664 17.7356773100 281.0919051764
73 137.4268150510 263.3591375866 17.7460462303 281.1051838170
74 137.7032485805 263.3620734178 17.7817423366 281.1438157544
75 138.2326762937 263.3650595529 17.8501078057 281.2151673586
76 138.4007179077 263.3680954506 17.8718071680 281.2399026186
77 138.5404740065 263.3711820461 17.8898539967 281.2610360428
78 138.8912099732 263.3742923151 17.9351448424 281.3094371575
79 138.9741246994 263.3774486985 17.9458516944 281.3233003929
80 139.4197628632 263.3806611895 18.0033973448 281.3840585343
81 140.0251686765 263.3839130457 18.0815739332 281.4654869789
82 140.4343690117 263.3872054888 18.1344143345 281.5216198234
83 140.8339845433 263.3905429049 18.1860170417 281.5765599466
84 141.2138623100 263.3939327814 18.2350709939 281.6290037753
85 141.4316440060 263.3973682789 18.2631933370 281.6605616159
86 141.6165387841 263.4008469122 18.2870689633 281.6879158755
87 141.7511584697 263.4043736626 18.3044525224 281.7088261850
88 141.8992649298 263.4079464450 18.3235776407 281.7315240856
89 142.0701382121 263.4115664661 18.3456426588 281.7572091249
90 141.8941246854 263.4152285669 18.3229138764 281.7381424432
91 141.9603905137 263.4189393903 18.3314708414 281.7504102317
92 142.2257908954 263.4226844171 18.3657422275 281.7884266446
93 142.5513186924 263.4264738040 18.4077779200 281.8342517239
94 142.6488079657 263.4303196853 18.4203667961 281.8506864814
95 142.7997830804 263.4342276788 18.4398623463 281.8740900251
96 143.4667875851 263.4381892468 18.5259932282 281.9641824750
97 143.4616614838 263.4421960775 18.5253312902 281.9675273677
98 143.3138701934 263.4462347092 18.5062468701 281.9524815793
99 143.5996902366 263.4503180925 18.5431550652 281.9934731576
100 143.4332992914 263.4544359567 18.5216688552 281.9761048118
Loop time of 0.350154 on 1 procs for 100 steps with 1000 atoms
Performance: 24.675 ns/day, 0.973 hours/ns, 285.589 timesteps/s
99.4% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.041961 | 0.041961 | 0.041961 | 0.0 | 11.98
Neigh | 0.16181 | 0.16181 | 0.16181 | 0.0 | 46.21
Comm | 0.0074215 | 0.0074215 | 0.0074215 | 0.0 | 2.12
Output | 0.00099516 | 0.00099516 | 0.00099516 | 0.0 | 0.28
Modify | 0.13485 | 0.13485 | 0.13485 | 0.0 | 38.51
Other | | 0.003124 | | | 0.89
Nlocal: 1000 ave 1000 max 1000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1728 ave 1728 max 1728 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 18783 ave 18783 max 18783 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 18783
Ave neighs/atom = 18.783
Neighbor list builds = 100
Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:00

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# INPUT FILE FOR DPD_Fluid
boundary p p p
units metal # ev, ps
atom_style dpd # atomic atom style can also be used
read_data data.dpd
comm_modify mode single vel yes
mass 1 125.9
pair_style dpd/fdt 300.0 8.6 245455
pair_coeff 1 1 0.075 0.022 8.60
neighbor 2.0 bin
neigh_modify every 1 delay 0 check no once no
timestep 0.001
fix 2 all nve
variable totEnergy equal pe+ke
thermo 10
thermo_style custom step temp press pe ke v_totEnergy
thermo_modify format float %24.16f
run 1000

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boundary p p p
units metal # ev, ps
atom_style dpd # atomic atom style can also be used
read_data data.dpd
orthogonal box = (-64.5 -64.5 -64.5) to (64.5 64.5 64.5)
1 by 1 by 1 MPI processor grid
reading atoms ...
10125 atoms
reading velocities ...
10125 velocities
comm_modify mode single vel yes
mass 1 125.9
pair_style dpd/fdt 300.0 8.6 245455
pair_coeff 1 1 0.075 0.022 8.60
neighbor 2.0 bin
neigh_modify every 1 delay 0 check no once no
timestep 0.001
fix 2 all nve
variable totEnergy equal pe+ke
thermo 10
thermo_style custom step temp press pe ke v_totEnergy
thermo_modify format float %24.16f
run 1000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.6
ghost atom cutoff = 10.6
binsize = 5.3 -> bins = 25 25 25
Memory usage per processor = 3.36353 Mbytes
Step Temp Press PotEng KinEng v_totEnergy
0 301.4391322267262012 1549.5478087303108623 1188.6488072196075336 394.4722035796053206 1583.1210107992128542
10 301.1781716844517973 1472.5220704074272362 1188.7073118945888837 394.1307028613744592 1582.8380147559632860
20 301.3348035346627398 1561.5334938481948939 1188.7674931713575006 394.3356759537763878 1583.1031691251339453
30 301.2401656988171226 1589.1590400358682018 1188.8329522652118158 394.2118300702898637 1583.0447823355016226
40 301.2467282647567117 1612.7005954259220744 1188.8998661625830664 394.2204180390389752 1583.1202842016220984
50 301.3868530330685758 1538.2867560691233848 1188.9661306187101673 394.4037894736757153 1583.3699200923858825
60 301.2473566745931635 1442.8478446697065465 1189.0327863162424364 394.2212403948197448 1583.2540267110621244
70 301.3817325834245366 1449.9468021148002208 1189.0958917710283913 394.3970887011532795 1583.4929804721816708
80 301.6350661579102166 1528.7144337987854215 1189.1603115791012897 394.7286085427540456 1583.8889201218553353
90 301.1547075640817752 1512.1770835959378019 1189.2223449446209997 394.0999970163866237 1583.3223419610076235
100 301.1746038085076975 1564.5706067669673303 1189.2844219062417324 394.1260338329196315 1583.4104557391613071
110 301.2018622721547558 1515.4879381876448861 1189.3504251156646205 394.1617050682420427 1583.5121301839067200
120 301.0009801124808178 1557.0329613835117470 1189.4208319594404202 393.8988247062895880 1583.3196566657300082
130 301.0638502637480656 1548.3634383875796630 1189.4951157625748692 393.9810984539830656 1583.4762142165579917
140 301.0311113459680428 1495.2262845183092850 1189.5675481417179071 393.9382553335690318 1583.5058034752869389
150 300.8177209477242400 1428.8898919254613702 1189.6378084330838192 393.6590063190295155 1583.2968147521132778
160 300.8119775481491160 1570.2720283468329399 1189.7083716809172529 393.6514903357206663 1583.3598620166378623
170 300.9335106840651406 1557.4332901198370109 1189.7769958158935424 393.8105322078843642 1583.5875280237778497
180 300.5874591455081486 1520.5298514112455450 1189.8453389121095825 393.3576788840364884 1583.2030177961460140
190 300.4011803057076122 1519.7398182018539501 1189.9061296006261728 393.1139088603054574 1583.0200384609315734
200 300.2169140033789745 1458.2437505784337191 1189.9657655046762557 392.8727725028986129 1582.8385380075749254
210 300.2545970072604860 1496.2729155341944534 1190.0262935280240981 392.9220856012638592 1582.9483791292880142
220 300.3703364838470407 1606.0230144299605399 1190.0833027226285594 393.0735457187111024 1583.1568484413396618
230 300.2033407044385172 1459.9549740461736747 1190.1416131684936772 392.8550100806698424 1582.9966232491635765
240 300.4842762279440080 1670.3474276721599381 1190.2009109755040299 393.2226506527560446 1583.4235616282601313
250 300.2564573977281270 1557.2460328592953829 1190.2596238049020485 392.9245201634982436 1583.1841439684003490
260 300.0449762246657883 1505.0192578442308786 1190.3199416408031084 392.6477696177504413 1582.9677112585536634
270 300.0116460395994977 1509.1981340752856795 1190.3755696034054381 392.6041527474002351 1582.9797223508057868
280 300.3512486599618114 1518.9752783067131077 1190.4261072017084189 393.0485668253141966 1583.4746740270225018
290 300.3552418223667360 1555.5638176571358144 1190.4711084084597132 393.0537923962660898 1583.5249008047258030
300 300.1459940856700541 1599.6176002364238684 1190.5119834703855304 392.7799645916971940 1583.2919480620826107
310 300.0728060417839629 1641.1130631848714074 1190.5527862243700383 392.6841885431988999 1583.2369747675688814
320 300.2437004299284808 1480.0125150324981860 1190.5921170370866093 392.9078260164519065 1583.4999430535385727
330 300.0598571495680176 1558.1995284077863744 1190.6308838646664299 392.6672432381596991 1583.2981271028261290
340 300.2932457229409806 1504.8291140224332594 1190.6648789420762569 392.9726624587786432 1583.6375414008548432
350 300.0508025680157402 1578.6970748006153826 1190.6930603315840926 392.6553941437470598 1583.3484544753312093
360 300.2273424995200344 1514.2714360556162774 1190.7166098654090547 392.8864195427583468 1583.6030294081674583
370 300.1967941947077634 1511.8859175802745085 1190.7410406890937793 392.8464431235526035 1583.5874838126464965
380 300.4506922864079002 1551.8880937733540577 1190.7641303867108036 393.1787017091508005 1583.9428320958616041
390 300.6154615731481954 1491.6540598720923754 1190.7833472426696062 393.3943236927418070 1584.1776709354114701
400 300.4131888226039564 1518.2806993851902462 1190.8000216950690628 393.1296235622648396 1583.9296452573339593
410 300.2164206099614603 1492.4202869919304248 1190.8161806634459481 392.8721268336147432 1583.6883074970605776
420 299.9241651579524728 1437.1178040001384488 1190.8321211036075056 392.4896726667966504 1583.3217937704041560
430 300.1750324308378595 1592.1759851574131517 1190.8470728579757179 392.8179650328543744 1583.6650378908300354
440 300.3203232687657760 1610.5956304714268299 1190.8532393510404290 393.0080969396641422 1583.8613362907044575
450 300.3593377128640896 1514.2015724302684703 1190.8519495611071761 393.0591524002515484 1583.9111019613587814
460 300.2776675433437958 1593.6798981330243805 1190.8459747756926390 392.9522763901615008 1583.7982511658542535
470 299.8777606563147629 1525.3321416074672925 1190.8391264353913357 392.4289463573695116 1583.2680727927609041
480 300.0893325105251392 1577.2512023261467675 1190.8279401949503153 392.7058155711616223 1583.5337557661118808
490 299.7991035093194228 1480.4333732192599200 1190.8067847458821689 392.3260132780664549 1583.1327980239486806
500 299.9677949259065599 1495.0278787582656150 1190.7825410253908558 392.5467678772936324 1583.3293089026844882
510 300.0900811274784701 1639.6696686241473344 1190.7573430643653865 392.7067952335466430 1583.4641382979120863
520 299.9891246673825549 1600.2278532870598156 1190.7251960532676094 392.5746806106526492 1583.2998766639202586
530 300.1603400289337173 1539.5535066502900463 1190.6928984528919955 392.7987381192410226 1583.4916365721330749
540 300.3076269358370496 1595.8675994337252178 1190.6566703473422422 392.9914821412112360 1583.6481524885534782
550 300.4698674068499713 1466.7075904710529812 1190.6131481694715148 393.2037948414154016 1583.8169430108869165
560 300.7206981383458810 1630.2609903270986251 1190.5710873654240913 393.5320393883253018 1584.1031267537493932
570 300.8610815763000232 1556.2884022342987009 1190.5267109994711063 393.7157493257404326 1584.2424603252115958
580 300.8964633483231523 1554.3498972944137222 1190.4812222884627317 393.7620509637309283 1584.2432732521936032
590 300.9107621433563509 1547.4258400009323395 1190.4362818919200890 393.7807627916996580 1584.2170446836198607
600 301.3417451159046436 1536.4134563739603436 1190.3902887741262475 394.3447599132098844 1584.7350486873360751
610 301.6508989111560481 1593.7194612348341707 1190.3421610929228791 394.7493277540106646 1585.0914888469335438
620 301.5698128071562110 1576.1181463329294274 1190.2920606752038566 394.6432160694121194 1584.9352767446159760
630 301.3274041972169357 1509.2272524137147229 1190.2374741364669717 394.3259929609754408 1584.5634670974422988
640 301.3505920687090907 1592.1600851563935066 1190.1794204537054611 394.3563372984748980 1584.5357577521804160
650 301.5804461741749378 1544.9875554279790322 1190.1204065811848523 394.6571312093886377 1584.7775377905734331
660 301.3626783799006148 1580.4147481776212771 1190.0589205400185620 394.3721538043599821 1584.4310743443784304
670 301.3027587470089088 1570.9258836881758725 1189.9974183012859612 394.2937411926666869 1584.2911594939525912
680 301.1174106753824731 1503.7441951732287180 1189.9385560058665305 394.0511891998194756 1583.9897452056859493
690 301.1637317889510541 1485.4239754399416142 1189.8822999581352633 394.1118063851420743 1583.9941063432772808
700 300.7577284964789897 1497.3081311764312886 1189.8265818908062101 393.5804984150753967 1583.4070803058816637
710 300.7582337772330447 1443.2789996571248139 1189.7722579196470178 393.5811596404810757 1583.3534175601280367
720 300.7789291839182511 1480.1771366249440689 1189.7219401607021609 393.6082422644880126 1583.3301824251902872
730 300.2392032164642046 1573.9469162403461269 1189.6722050348253106 392.9019408293094102 1582.5741458641346071
740 300.1498721141534816 1495.8935024851559774 1189.6232009109407954 392.7850394949790029 1582.4082404059197415
750 299.7668955745960488 1587.0579224766690913 1189.5725329834676813 392.2838650178547937 1581.8563980013225319
760 300.1701246080039596 1476.2647356200661761 1189.5185800849978932 392.8115425100924085 1582.3301225950904154
770 300.0596917060459532 1476.9822776185721978 1189.4588693098098702 392.6670267338517419 1582.1258960436616690
780 300.0000978359947794 1656.0447969129193098 1189.3974011035754756 392.5890404250892516 1581.9864415286647272
790 299.8879395255003146 1498.3733949813793060 1189.3295612656791036 392.4422667279793586 1581.7718279936584622
800 299.5399296208984765 1536.5356907957796011 1189.2608026516975315 391.9868506281461009 1581.2476532798436892
810 299.7477702176125263 1527.7843172708669499 1189.1905997605726952 392.2588370075304169 1581.4494367681031690
820 299.6526441282851465 1520.2339634236550410 1189.1179282568577946 392.1343521810326251 1581.2522804378904766
830 299.7117040573267559 1519.3977355174756667 1189.0462571599482544 392.2116397587276992 1581.2578969186758968
840 299.8248393061855950 1492.9872520312869710 1188.9746922447459383 392.3596919064040662 1581.3343841511500614
850 299.8949042735604280 1548.8768511646294428 1188.9003206285553915 392.4513810041994475 1581.3517016327548390
860 299.8659753723547396 1612.8888123513665960 1188.8228698817265467 392.4135237846624591 1581.2363936663889490
870 299.4869644032468159 1501.1368986196648621 1188.7463971708887129 391.9175387708375524 1580.6639359417263222
880 299.4723145868704819 1610.5504771450589487 1188.6685353091816069 391.8983675859109894 1580.5669028950926531
890 299.4069994806970385 1463.6021272210480220 1188.5912631304522620 391.8128942975925497 1580.4041574280447549
900 299.3089704777128190 1566.2168185333516703 1188.5136206415770630 391.6846106320437571 1580.1982312736208769
910 299.5247041888713397 1495.6606753393330109 1188.4345654328317323 391.9669261754785907 1580.4014916083103799
920 298.9408951189174672 1640.3193219922013668 1188.3550783333537311 391.2029362827487944 1579.5580146161025823
930 299.1796032826329110 1446.8716230397405980 1188.2706215145828992 391.5153168773241532 1579.7859383919071661
940 299.3701987753103708 1492.9872751566551869 1188.1849188108449198 391.7647358012489462 1579.9496546120938092
950 299.2072786172182077 1562.8791943561973312 1188.0966113636363843 391.5515336423407575 1579.6481450059770850
960 299.3656085727831737 1560.6583667351615077 1188.0078929542073638 391.7587289258562464 1579.7666218800636670
970 299.3550703551496781 1470.6811691697550941 1187.9234716336209203 391.7449383011918940 1579.6684099348128711
980 299.3253482475718101 1439.7552468745370788 1187.8461953635626287 391.7060430682316792 1579.5522384317941942
990 299.5720628053319956 1537.8753917835106222 1187.7698518865308870 392.0289010679078388 1579.7987529544386689
1000 299.6565043425953263 1587.6003924665003524 1187.6939067472803799 392.1394037721581185 1579.8333105194385553
Loop time of 16.4015 on 1 procs for 1000 steps with 10125 atoms
Performance: 5.268 ns/day, 4.556 hours/ns, 60.970 timesteps/s
99.8% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.3216 | 5.3216 | 5.3216 | 0.0 | 32.45
Neigh | 10.155 | 10.155 | 10.155 | 0.0 | 61.91
Comm | 0.49085 | 0.49085 | 0.49085 | 0.0 | 2.99
Output | 0.0052254 | 0.0052254 | 0.0052254 | 0.0 | 0.03
Modify | 0.1345 | 0.1345 | 0.1345 | 0.0 | 0.82
Other | | 0.2945 | | | 1.80
Nlocal: 10125 ave 10125 max 10125 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5827 ave 5827 max 5827 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 114808 ave 114808 max 114808 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 114808
Ave neighs/atom = 11.3391
Neighbor list builds = 1000
Dangerous builds not checked
Total wall time: 0:00:16

2018
examples/PACKAGES/dpd-react/dpde-shardlow/data.dpde Normal file
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# Input File for DPD fluid under isoenergetic conditions using the VV-SSA integration scheme
boundary p p p
units metal # ev, ps
atom_style dpd
read_data data.dpde
comm_modify mode single vel yes
mass 1 100.0
pair_style dpd/fdt/energy 10.0 245455
pair_coeff 1 1 0.075 0.022 3.2E-5 10.00
neighbor 2.0 bin
neigh_modify every 1 delay 0 check no once no
timestep 0.001
compute dpdU all dpd
variable totEnergy equal pe+ke+c_dpdU[1]+c_dpdU[2]
thermo 1
thermo_style custom step temp pe ke v_totEnergy
thermo_modify format float %15.10f
fix 1 all shardlow
fix 2 all nve
fix 3 all eos/cv 0.0005
run 100

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LAMMPS (7 Dec 2015)
# Input File for DPD fluid under isoenergetic conditions using the VV-SSA integration scheme
boundary p p p
units metal # ev, ps
atom_style dpd
read_data data.dpde
orthogonal box = (-5.36874 -4.6558 -6.56118) to (61.4618 53.2342 46.2472)
1 by 1 by 1 MPI processor grid
reading atoms ...
1000 atoms
reading velocities ...
1000 velocities
comm_modify mode single vel yes
mass 1 100.0
pair_style dpd/fdt/energy 10.0 245455
pair_coeff 1 1 0.075 0.022 3.2E-5 10.00
neighbor 2.0 bin
neigh_modify every 1 delay 0 check no once no
timestep 0.001
compute dpdU all dpd
variable totEnergy equal pe+ke+c_dpdU[1]+c_dpdU[2]
thermo 1
thermo_style custom step temp pe ke v_totEnergy
thermo_modify format float %15.10f
fix 1 all shardlow
fix 2 all nve
fix 3 all eos/cv 0.0005
run 100
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6 -> bins = 12 10 9
Memory usage per processor = 3.33107 Mbytes
Step Temp PotEng KinEng totEnerg
0 128.6667660382 263.2538386154 16.6148533499 429.8686919654
1 128.9849917287 263.2538898270 16.6559461149 429.8686919651
2 128.8333822604 263.2539770413 16.6363686501 429.8686919650
3 128.7339619634 263.2541060527 16.6235304192 429.8686919618
4 129.0775205811 263.2542863822 16.6678944475 429.8686919618
5 129.4306564211 263.2545145142 16.7134951910 429.8686919618
6 129.4114326993 263.2547749062 16.7110128148 429.8686919619
7 129.3005442814 263.2550718076 16.6966936953 429.8686919620
8 129.3692785510 263.2554082313 16.7055694123 429.8686919600
9 129.2906385442 263.2557915576 16.6954145587 429.8686919569
10 129.4374487159 263.2562107913 16.7143722861 429.8686919571
11 129.8074096259 263.2566619501 16.7621456657 429.8686919573
12 129.5775408090 263.2571482272 16.7324625020 429.8686919571
13 129.6608210294 263.2576775975 16.7432165506 429.8686919575
14 129.9636716679 263.2582382637 16.7823239215 429.8686919579
15 130.1728562587 263.2588485908 16.8093361128 429.8686919584
16 130.5554484013 263.2595015423 16.8587405747 429.8686919589
17 130.8086711200 263.2602039738 16.8914394484 429.8686919594
18 130.7251703173 263.2609448717 16.8806569159 429.8686919601
19 130.7169772442 263.2617260879 16.8795989371 429.8686919607
20 130.6678547102 263.2625406124 16.8732557008 429.8686919615
21 130.7063354871 263.2634065120 16.8782247576 429.8686919588
22 130.5656594568 263.2643148354 16.8600591373 429.8686919597
23 130.4578862982 263.2652597956 16.8461422940 429.8686919607
24 130.3475082175 263.2662581744 16.8318890748 429.8686919720
25 130.7309020340 263.2672818391 16.8813970575 429.8686919730
26 130.8226651255 263.2683535129 16.8932465067 429.8686919741
27 131.1559504490 263.2694539874 16.9362839355 429.8686919752
28 130.9173143835 263.2705908027 16.9054686492 429.8686919764
29 130.9736783387 263.2717607897 16.9127469766 429.8686919776
30 131.3024002674 263.2729679272 16.9551951301 429.8686919788
31 131.2942351319 263.2742186164 16.9541407589 429.8686919802
32 131.4023576009 263.2755099256 16.9681027090 429.8686919815
33 131.4547155464 263.2768444460 16.9748637369 429.8686919829
34 131.4303370498 263.2782187473 16.9717157200 429.8686919837
35 131.4710774046 263.2796421696 16.9769765581 429.8686919852
36 131.5737878242 263.2811319228 16.9902396455 429.8686919868
37 131.6110752812 263.2826589472 16.9950546078 429.8686919885
38 131.9042344129 263.2842199274 17.0329105059 429.8686919902
39 132.0669342798 263.2858245296 17.0539200836 429.8686919920
40 132.4647311942 263.2874680226 17.1052879512 429.8686919938
41 132.3304988286 263.2891548913 17.0879544070 429.8686919958
42 132.4601608613 263.2908808074 17.1046977801 429.8686919977
43 132.5911192667 263.2926367821 17.1216085548 429.8686919997
44 132.9502496489 263.2944188749 17.1679833789 429.8686920018
45 133.2314174010 263.2962418787 17.2042908195 429.8686920038
46 133.5618716315 263.2981040572 17.2469626667 429.8686920092
47 133.3648452565 263.2999977400 17.2215204765 429.8686920114
48 133.7620566404 263.3019424135 17.2728127340 429.8686920135
49 133.5761903415 263.3039226506 17.2488116544 429.8686920157
50 134.0398067266 263.3059522378 17.3086788484 429.8686920179
51 134.3127295532 263.3080327254 17.3439216145 429.8686920202
52 134.5095010718 263.3101516100 17.3693308948 429.8686920226
53 134.4106524937 263.3123104304 17.3565664904 429.8686920250
54 134.5413426313 263.3145182049 17.3734426236 429.8686920372
55 134.9814060710 263.3167704551 17.4302684049 429.8686920397
56 135.2464345037 263.3190513823 17.4644917609 429.8686920423
57 135.2217801147 263.3213812604 17.4613081179 429.8686920514
58 135.0371058418 263.3237536703 17.4374609656 429.8686920608
59 135.6044115702 263.3261876951 17.5107176563 429.8686920635
60 135.5163441493 263.3286697175 17.4993454323 429.8686920569
61 135.8462618119 263.3312021764 17.5419479920 429.8686920687
62 135.5712784856 263.3337878822 17.5064391518 429.8686920716
63 135.8559007855 263.3364140640 17.5431926812 429.8686920745
64 136.0981737453 263.3390801144 17.5744776029 429.8686920774
65 136.3472745582 263.3417812091 17.6066442113 429.8686920804
66 136.4768377472 263.3445060776 17.6233748205 429.8686920834
67 136.5718905697 263.3472753966 17.6356490756 429.8686920864
68 136.9307096239 263.3500986538 17.6819836976 429.8686920895
69 137.0287267098 263.3529640934 17.6946407306 429.8686920926
70 136.9026056571 263.3558505535 17.6783546075 429.8686920958
71 137.1641950349 263.3587807400 17.7121338753 429.8686920990
72 137.2800166361 263.3617531068 17.7270900211 429.8686921022
73 137.2218820844 263.3647526848 17.7195830550 429.8686921055
74 137.8739569163 263.3678008786 17.8037860551 429.8686920969
75 138.3576399052 263.3708972702 17.8662444674 429.8686921004
76 138.5559886770 263.3740292943 17.8918574198 429.8686921075
77 138.7051387822 263.3772152758 17.9111173049 429.8686921111
78 138.7595627546 263.3804321606 17.9181451206 429.8686921146
79 138.5205847557 263.3836806479 17.8872856801 429.8686921182
80 138.5077707320 263.3869735635 17.8856309939 429.8686921218
81 138.4856534230 263.3903047682 17.8827749662 429.8686921254
82 138.3790174275 263.3936794953 17.8690049658 429.8686921292
83 138.4742465484 263.3970872458 17.8813019864 429.8686921329
84 138.4080000652 263.4005256415 17.8727475194 429.8686921390
85 138.3854698427 263.4040055268 17.8698381719 429.8686921429
86 138.4821447667 263.4075250866 17.8823218903 429.8686921527
87 138.7445878525 263.4110803475 17.9162113982 429.8686921573
88 138.7152775802 263.4146717535 17.9124265368 429.8686921613
89 138.7908881100 263.4183109427 17.9221901915 429.8686921653
90 138.8830632075 263.4219982501 17.9340928434 429.8686921694
91 139.5671118101 263.4257384011 18.0224246447 429.8686921736
92 139.9464913236 263.4295247461 18.0714142570 429.8686921778
93 139.9518374325 263.4333392965 18.0721046047 429.8686921820
94 139.9391743335 263.4371869424 18.0704694076 429.8686921863
95 139.8447896149 263.4410731790 18.0582814253 429.8686921964
96 140.0697631915 263.4449843697 18.0873324623 429.8686922001
97 140.3594611923 263.4489471179 18.1247414215 429.8686922046
98 140.8455519472 263.4529407598 18.1875107508 429.8686922091
99 140.8172402178 263.4569615862 18.1838548322 429.8686922137
100 140.7185453082 263.4610092311 18.1711102712 429.8686922182
Loop time of 0.844031 on 1 procs for 100 steps with 1000 atoms
Performance: 10.237 ns/day, 2.345 hours/ns, 118.479 timesteps/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.071503 | 0.071503 | 0.071503 | 0.0 | 8.47
Neigh | 0.26602 | 0.26602 | 0.26602 | 0.0 | 31.52
Comm | 0.013571 | 0.013571 | 0.013571 | 0.0 | 1.61
Output | 0.0046957 | 0.0046957 | 0.0046957 | 0.0 | 0.56
Modify | 0.48701 | 0.48701 | 0.48701 | 0.0 | 57.70
Other | | 0.001228 | | | 0.15
Nlocal: 1000 ave 1000 max 1000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1726 ave 1726 max 1726 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 18773 ave 18773 max 18773 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 18773
Ave neighs/atom = 18.773
Neighbor list builds = 100
Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:00

20266
examples/PACKAGES/dpd-react/dpde-vv/data.dpd Normal file
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# INPUT FILE FOR DPD_Fluid
boundary p p p
units metal # ev, ps
atom_style dpd
read_data data.dpd
comm_modify mode single vel yes
mass 1 125.9
pair_style dpd/fdt/energy 8.6 245455
pair_coeff 1 1 0.075 0.022 3.2E-05 8.60
neighbor 2.0 bin
neigh_modify every 1 delay 0 check no once no
timestep 0.001
fix 1 all dpd/energy
fix 2 all nve
fix 3 all eos/cv 0.00517041
compute dpdU all dpd
variable totEnergy equal pe+ke+c_dpdU[1]+c_dpdU[2]
thermo 10
thermo_style custom step temp press pe ke c_dpdU[1] c_dpdU[2] v_totEnergy c_dpdU[4]
thermo_modify format float %24.16f
run 1000

177
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boundary p p p
units metal # ev, ps
atom_style dpd
read_data data.dpd
orthogonal box = (-64.5 -64.5 -64.5) to (64.5 64.5 64.5)
1 by 1 by 1 MPI processor grid
reading atoms ...
10125 atoms
reading velocities ...
10125 velocities
comm_modify mode single vel yes
mass 1 125.9
pair_style dpd/fdt/energy 8.6 245455
pair_coeff 1 1 0.075 0.022 3.2E-05 8.60
neighbor 2.0 bin
neigh_modify every 1 delay 0 check no once no
timestep 0.001
fix 1 all dpd/energy
fix 2 all nve
fix 3 all eos/cv 0.00517041
compute dpdU all dpd
variable totEnergy equal pe+ke+c_dpdU[1]+c_dpdU[2]
thermo 10
thermo_style custom step temp press pe ke c_dpdU[1] c_dpdU[2] v_totEnergy c_dpdU[4]
thermo_modify format float %24.16f
run 1000
Neighbor list info ...
update every 1 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.6
ghost atom cutoff = 10.6
binsize = 5.3, bins = 25 25 25
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair dpd/fdt/energy, perpetual
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Memory usage per processor = 4.28221 Mbytes
Step Temp Press PotEng KinEng c_dpdU[1] c_dpdU[2] v_totEnergy c_dpdU[4]
0 301.4391322267262012 1636.1776395935080473 1188.6488072196075336 394.4722035796053206 0.0000000000000000 15705.1203749972210062 17288.2413857964347699 299.9999999999841407
10 301.4791572483523510 1486.4422375141214161 1188.7147620806101713 394.5245815119678241 0.0000000000000000 15704.9333817333845218 17288.1727253259632562 299.9960221120699089
20 301.4275643919337995 1677.9356110821622678 1188.7839634625399867 394.4570655673389865 -0.0000000000000000 15704.9313726932996360 17288.1724017231790640 299.9955485734552667
30 301.2240988054542186 1452.7304951528922174 1188.8550809767796181 394.1908044563202225 -0.0000000000000000 15705.1281541239713988 17288.1740395570705005 299.9988968405209562
40 301.1023506886409109 1527.9758363521384581 1188.9264527568634549 394.0314812537677085 -0.0000000000000000 15705.2176639573335706 17288.1755979679655866 300.0001694462812907
50 301.0409654880461972 1597.1737251233505503 1188.9944523606984603 393.9511507566391515 -0.0000000000000000 15705.2302422249904339 17288.1758453423281026 299.9999653064982112
60 301.2904978886138565 1610.8630327676828529 1189.0651026961211301 394.2776962691255562 -0.0000000000000000 15704.8336863976528548 17288.1764853628992569 299.9919857290491905
70 300.8575037843164068 1489.3259312130892340 1189.1295686642290548 393.7110673208617300 0.0000000000000000 15705.3309057198275696 17288.1715417049199459 300.0010992278232607
80 300.5955830326474825 1449.3896097889576140 1189.1880764967559116 393.3683100440913449 -0.0000000000000000 15705.6086113882302016 17288.1649979290777992 300.0059513551502164
90 301.0092332775843147 1553.9266324350371633 1189.2470037925056658 393.9096250433288446 -0.0000000000000000 15705.0053942113881931 17288.1620230472217372 299.9940347326859182
100 301.0478004479094238 1539.2270336322201274 1189.3010269201699884 393.9600951881690207 -0.0000000000000000 15704.9018111045588739 17288.1629332128977694 299.9916385566916119
110 300.9609384905550655 1500.0429484565015628 1189.3524514939088021 393.8464250502818231 -0.0000000000000000 15704.9716855356964516 17288.1705620798857126 299.9925626482006464
120 300.9625536631413070 1630.5065919443020448 1189.4006029528841282 393.8485387131116795 0.0000000000000000 15704.9202685123345873 17288.1694101783286897 299.9911580775880680
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Loop time of 17.0881 on 1 procs for 1000 steps with 10125 atoms
Performance: 5.056 ns/day, 4.747 hours/ns, 58.520 timesteps/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 8.0541 | 8.0541 | 8.0541 | 0.0 | 47.13
Neigh | 8.1306 | 8.1306 | 8.1306 | 0.0 | 47.58
Comm | 0.39415 | 0.39415 | 0.39415 | 0.0 | 2.31
Output | 0.01103 | 0.01103 | 0.01103 | 0.0 | 0.06
Modify | 0.24061 | 0.24061 | 0.24061 | 0.0 | 1.41
Other | | 0.2576 | | | 1.51
Nlocal: 10125 ave 10125 max 10125 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5824 ave 5824 max 5824 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 114682 ave 114682 max 114682 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 114682
Ave neighs/atom = 11.3266
Neighbor list builds = 1000
Dangerous builds not checked
Total wall time: 0:00:17

20266
examples/PACKAGES/dpd-react/dpdh-shardlow/data.dpdh Normal file
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31
examples/PACKAGES/dpd-react/dpdh-shardlow/in.dpdh-shardlow Normal file
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@ -0,0 +1,31 @@
# Input File for DPD fluid under isoenthalpic conditions using the VV-SSA integration scheme
boundary p p p
units metal # ev, ps
atom_style dpd
read_data data.dpdh
comm_modify mode single vel yes
mass 1 100.0
pair_style dpd/fdt/energy 10.0 234324
pair_coeff 1 1 0.075 0.022 3.2E-5 10.0
neighbor 2.0 bin
neigh_modify every 1 delay 0 check no once no
timestep 0.001
compute dpdU all dpd
variable totEnergy equal pe+ke+c_dpdU[1]+c_dpdU[2]+press*vol
thermo 1
thermo_style custom step temp press vol pe ke v_totEnergy cella cellb cellc
thermo_modify format float %15.10f
fix 1 all shardlow
fix 0 all nph iso 0.0 0.0 1000.0
fix 2 all eos/cv 0.0005
run 100

183
examples/PACKAGES/dpd-react/dpdh-shardlow/log.dpdh-shardlow.reference Normal file
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@ -0,0 +1,183 @@
boundary p p p
units metal # ev, ps
atom_style dpd
read_data data.dpdh
orthogonal box = (-64.5 -64.5 -64.5) to (64.5 64.5 64.5)
1 by 1 by 1 MPI processor grid
reading atoms ...
10125 atoms
reading velocities ...
10125 velocities
comm_modify mode single vel yes
mass 1 100.0
pair_style dpd/fdt/energy 10.0 234324
pair_coeff 1 1 0.075 0.022 3.2E-5 10.0
neighbor 2.0 bin
neigh_modify every 1 delay 0 check no once no
timestep 0.001
compute dpdU all dpd
variable totEnergy equal pe+ke+c_dpdU[1]+c_dpdU[2]+press*vol
thermo 1
thermo_style custom step temp press vol pe ke v_totEnergy cella cellb cellc
thermo_modify format float %15.10f
fix 1 all shardlow
fix 0 all nph iso 0.0 0.0 1000.0
fix 2 all eos/cv 0.0005
run 100
Neighbor list info ...
update every 1 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 22 22 22
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair dpd/fdt/energy, perpetual
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix shardlow, perpetual, ssa
pair build: half/bin/newton/ssa
stencil: half/bin/3d/newton/ssa
bin: ssa
Memory usage per processor = 8.55503 Mbytes
Step Temp Press Volume PotEng KinEng v_totEnergy Cella Cellb Cellc
0 239.4274282976 2817.4421750949 2146689.0000000000 2639.8225470740 313.3218455755 6048176597.3066034317 129.0000000000 129.0000000000 129.0000000000
1 239.4771405316 2817.4798146419 2146689.0000581890 2639.8304543632 313.3869004818 6048257397.8720483780 129.0000000012 129.0000000012 129.0000000012
2 239.5643955010 2817.5423194969 2146689.0002327557 2639.8379071907 313.5010849268 6048391576.8485937119 129.0000000047 129.0000000047 129.0000000047
3 239.6633839196 2817.6123662396 2146689.0005237064 2639.8445238058 313.6306241122 6048541946.2404479980 129.0000000105 129.0000000105 129.0000000105
4 239.5371222027 2817.5355424336 2146689.0009310376 2639.8505035043 313.4653942786 6048377030.5689325333 129.0000000186 129.0000000186 129.0000000186
5 239.6512678169 2817.6153097076 2146689.0014547524 2639.8561498340 313.6147686202 6048548267.5742130280 129.0000000291 129.0000000291 129.0000000291
6 239.5617886781 2817.5624195435 2146689.0020948485 2639.8617493725 313.4976735610 6048434730.6441593170 129.0000000420 129.0000000420 129.0000000420
7 239.5228587856 2817.5420009502 2146689.0028513218 2639.8666590407 313.4467287471 6048390900.4058599472 129.0000000571 129.0000000571 129.0000000571
8 239.6066877934 2817.6008649264 2146689.0037241788 2639.8710757645 313.5564298772 6048517265.5155982971 129.0000000746 129.0000000746 129.0000000746
9 239.5719861485 2817.5823530300 2146689.0047134170 2639.8752557893 313.5110182737 6048477529.0184717178 129.0000000944 129.0000000944 129.0000000944
10 239.5800176776 2817.5915671176 2146689.0058190385 2639.8793778438 313.5215285712 6048497311.9141387939 129.0000001166 129.0000001166 129.0000001166
11 239.6299830954 2817.6281223139 2146689.0070410441 2639.8829762049 313.5869148014 6048575787.9953098297 129.0000001410 129.0000001410 129.0000001410
12 239.6011995911 2817.6132377273 2146689.0083794324 2639.8860704236 313.5492478526 6048543839.1878814697 129.0000001678 129.0000001678 129.0000001678
13 239.6407681166 2817.6427924824 2146689.0098342048 2639.8889816934 313.6010284005 6048607288.1548709869 129.0000001970 129.0000001970 129.0000001970
14 239.6981172055 2817.6844100046 2146689.0114053637 2639.8913405110 313.6760771219 6048696632.4595127106 129.0000002285 129.0000002285 129.0000002285
15 239.8563971968 2817.7922519039 2146689.0130929090 2639.8934358481 313.8832070208 6048928140.2348766327 129.0000002623 129.0000002623 129.0000002623
16 239.8561894618 2817.7971208196 2146689.0148968464 2639.8950496967 313.8829351726 6048938597.3658657074 129.0000002984 129.0000002984 129.0000002984
17 239.8816520361 2817.8185621543 2146689.0168171758 2639.8961257823 313.9162562538 6048984630.6545839310 129.0000003369 129.0000003369 129.0000003369
18 239.9099966096 2817.8417368960 2146689.0188538977 2639.8965743204 313.9533488047 6049034385.3571958542 129.0000003777 129.0000003777 129.0000003777
19 240.0514024347 2817.9389205774 2146689.0210070144 2639.8966103811 314.1383966683 6049243014.5661621094 129.0000004208 129.0000004208 129.0000004208
20 239.8802541140 2817.8327386176 2146689.0232765260 2639.8962085210 313.9144268914 6049015081.3139505386 129.0000004662 129.0000004662 129.0000004662
21 239.8462621903 2817.8160306167 2146689.0256624296 2639.8953174755 313.8699440502 6048979221.1549577713 129.0000005140 129.0000005140 129.0000005140
22 240.0487944678 2817.9533849157 2146689.0281647225 2639.8938590354 314.1349838054 6049274085.1726217270 129.0000005642 129.0000005642 129.0000005642
23 240.0966314441 2817.9897873787 2146689.0307834130 2639.8918104774 314.1975846937 6049352237.3198652267 129.0000006166 129.0000006166 129.0000006166
24 240.1765312516 2818.0463843765 2146689.0335185044 2639.8891292321 314.3021439554 6049473741.1817827225 129.0000006714 129.0000006714 129.0000006714
25 240.1500705973 2818.0336048048 2146689.0363699966 2639.8858785483 314.2675167572 6049446315.4509468079 129.0000007285 129.0000007285 129.0000007285
26 240.2681423500 2818.1151708195 2146689.0393378921 2639.8825176506 314.4220289603 6049621420.6842966080 129.0000007880 129.0000007880 129.0000007880
27 240.4728815247 2818.2527327079 2146689.0424221945 2639.8784158747 314.6899567267 6049916731.9748563766 129.0000008498 129.0000008498 129.0000008498
28 240.4793027032 2818.2613348477 2146689.0456229053 2639.8736089473 314.6983596717 6049935207.1145420074 129.0000009139 129.0000009139 129.0000009139
29 240.5020619198 2818.2805472685 2146689.0489400285 2639.8681043704 314.7281430587 6049976459.5562763214 129.0000009803 129.0000009803 129.0000009803
30 240.5513721776 2818.3167157263 2146689.0523735629 2639.8623484053 314.7926719270 6050054111.6652946472 129.0000010491 129.0000010491 129.0000010491
31 240.7340393104 2818.4391703712 2146689.0559235099 2639.8563442170 315.0317155636 6050316993.7162160873 129.0000011202 129.0000011202 129.0000011202
32 240.8254719483 2818.5014640740 2146689.0595898777 2639.8498122053 315.1513670299 6050450729.2599506378 129.0000011936 129.0000011936 129.0000011936
33 240.9681573541 2818.5965480750 2146689.0633726656 2639.8425779528 315.3380893908 6050654855.7068986893 129.0000012694 129.0000012694 129.0000012694
34 241.0039494187 2818.6217008564 2146689.0672718794 2639.8347174393 315.3849279499 6050708861.8979463577 129.0000013475 129.0000013475 129.0000013475
35 241.0314566197 2818.6411150538 2146689.0712875174 2639.8262983643 315.4209246902 6050750549.4619541168 129.0000014279 129.0000014279 129.0000014279
36 241.0829173424 2818.6763455617 2146689.0754195810 2639.8174397481 315.4882677207 6050826190.0551443100 129.0000015107 129.0000015107 129.0000015107
37 241.2845682012 2818.8087982181 2146689.0796680767 2639.8080129872 315.7521540252 6051110536.7012710571 129.0000015958 129.0000015958 129.0000015958
38 241.3214712920 2818.8336260248 2146689.0840330068 2639.7981963574 315.8004465062 6051163846.5868301392 129.0000016833 129.0000016833 129.0000016833
39 241.3392127125 2818.8456991528 2146689.0885143690 2639.7879618658 315.8236634561 6051189776.4712991714 129.0000017730 129.0000017730 129.0000017730
40 241.5383770555 2818.9753950055 2146689.0931121684 2639.7769824244 316.0842958321 6051468206.1039972305 129.0000018651 129.0000018651 129.0000018651
41 241.5059730674 2818.9543817992 2146689.0978264087 2639.7656512498 316.0418910106 6051423110.5725250244 129.0000019595 129.0000019595 129.0000019595
42 241.3907605672 2818.8793800508 2146689.1026570834 2639.7541331920 315.8911205101 6051262118.7541017532 129.0000020563 129.0000020563 129.0000020563
43 241.5095917610 2818.9559595711 2146689.1076041958 2639.7424355740 316.0466265406 6051426525.1214485168 129.0000021554 129.0000021554 129.0000021554
44 241.6271631762 2819.0312325531 2146689.1126677482 2639.7297705654 316.2004839873 6051588127.0861988068 129.0000022568 129.0000022568 129.0000022568
45 241.5702411838 2818.9923790176 2146689.1178477411 2639.7163554760 316.1259941770 6051504735.2269029617 129.0000023606 129.0000023606 129.0000023606
46 241.7029985068 2819.0771124986 2146689.1231441777 2639.7024246704 316.2997243538 6051686646.5996389389 129.0000024667 129.0000024667 129.0000024667
47 241.7966144965 2819.1357830868 2146689.1285570571 2639.6882106593 316.4222330191 6051812609.3728218079 129.0000025751 129.0000025751 129.0000025751
48 241.8573480255 2819.1726205120 2146689.1340863821 2639.6735287925 316.5017107195 6051891703.4611186981 129.0000026859 129.0000026859 129.0000026859
49 241.9611147338 2819.2374095379 2146689.1397321564 2639.6583357477 316.6375029166 6052030801.2758235931 129.0000027990 129.0000027990 129.0000027990
50 242.1023518806 2819.3259059811 2146689.1454943856 2639.6424863169 316.8223300428 6052220791.8748512268 129.0000029144 129.0000029144 129.0000029144
51 242.1174105473 2819.3319633044 2146689.1513730693 2639.6264141131 316.8420362613 6052233811.6391019821 129.0000030321 129.0000030321 129.0000030321
52 242.2534914901 2819.4164594322 2146689.1573682069 2639.6098392671 317.0201158259 6052415215.4627037048 129.0000031522 129.0000031522 129.0000031522
53 242.3504633236 2819.4754119996 2146689.1634798055 2639.5930076506 317.1470160479 6052541785.5314817429 129.0000032746 129.0000032746 129.0000032746
54 242.2982323323 2819.4368568264 2146689.1697078613 2639.5756353782 317.0786650211 6052459037.1184797287 129.0000033994 129.0000033994 129.0000033994
55 242.3452896272 2819.4623310219 2146689.1760523771 2639.5575918586 317.1402455951 6052513740.1862611771 129.0000035265 129.0000035265 129.0000035265
56 242.4181903333 2819.5048897011 2146689.1825133534 2639.5390347547 317.2356456249 6052605118.6588287354 129.0000036559 129.0000036559 129.0000036559
57 242.5317091656 2819.5739975787 2146689.1890907930 2639.5199828249 317.3841997413 6052753490.3378009796 129.0000037876 129.0000037876 129.0000037876
58 242.5478978740 2819.5796954935 2146689.1957846982 2639.5006137388 317.4053847660 6052765740.8638200760 129.0000039217 129.0000039217 129.0000039217
59 242.6655316466 2819.6519225743 2146689.2025950695 2639.4808234811 317.5593238156 6052920809.1607065201 129.0000040582 129.0000040582 129.0000040582
60 242.8126131177 2819.7431588157 2146689.2095219092 2639.4607996998 317.7517989980 6053116684.5470046997 129.0000041969 129.0000041969 129.0000041969
61 242.7957124913 2819.7275989047 2146689.2165652174 2639.4406312730 317.7296823362 6053083302.1140241623 129.0000043380 129.0000043380 129.0000043380
62 242.9276177041 2819.8088790098 2146689.2237249981 2639.4201279058 317.9022974164 6053257805.4283437729 129.0000044814 129.0000044814 129.0000044814
63 243.0465445938 2819.8814758895 2146689.2310012528 2639.3991657500 318.0579286774 6053413668.8858547211 129.0000046272 129.0000046272 129.0000046272
64 242.9890585501 2819.8387587817 2146689.2383939880 2639.3781767844 317.9827007328 6053321989.3768787384 129.0000047752 129.0000047752 129.0000047752
65 242.9653746583 2819.8180104181 2146689.2459031967 2639.3568184374 317.9517072884 6053277470.2627182007 129.0000049256 129.0000049256 129.0000049256
66 243.0259297024 2819.8514334947 2146689.2535288804 2639.3352568621 318.0309514181 6053349240.7251205444 129.0000050784 129.0000050784 129.0000050784
67 242.9638979697 2819.8046112742 2146689.2612710390 2639.3134547096 317.9497748498 6053248749.7987766266 129.0000052335 129.0000052335 129.0000052335
68 243.0283540775 2819.8395632725 2146689.2691296688 2639.2912303374 318.0341240273 6053323803.0382738113 129.0000053909 129.0000053909 129.0000053909
69 243.2256418664 2819.9609646019 2146689.2771047787 2639.2684509205 318.2923006889 6053584436.4588871002 129.0000055506 129.0000055506 129.0000055506
70 243.2507495334 2819.9706145524 2146689.2851963686 2639.2450126010 318.3251573278 6053605174.7221174240 129.0000057127 129.0000057127 129.0000057127
71 243.4287155518 2820.0794853386 2146689.2934044413 2639.2213699915 318.5580489464 6053838909.6197280884 129.0000058771 129.0000058771 129.0000058771
72 243.5097518574 2820.1249498194 2146689.3017290002 2639.1971212009 318.6640954635 6053936531.2101163864 129.0000060439 129.0000060439 129.0000060439
73 243.5356790969 2820.1337977544 2146689.3101700447 2639.1723394661 318.6980246193 6053955548.7824945450 129.0000062130 129.0000062130 129.0000062130
74 243.5479180498 2820.1331964183 2146689.3187275808 2639.1473868749 318.7140408766 6053954282.0339813232 129.0000063844 129.0000063844 129.0000063844
75 243.7115573025 2820.2314361523 2146689.3274016059 2639.1220411207 318.9281840641 6054165196.6845111847 129.0000065581 129.0000065581 129.0000065581
76 243.7457279618 2820.2454531429 2146689.3361921217 2639.0963868224 318.9729008040 6054195311.5999307632 129.0000067342 129.0000067342 129.0000067342
77 243.8345031069 2820.2948644965 2146689.3450991292 2639.0700900389 319.0890745962 6054301407.5461502075 129.0000069126 129.0000069126 129.0000069126
78 244.0193931195 2820.4067881628 2146689.3541226317 2639.0435094409 319.3310271594 6054541698.3381366730 129.0000070934 129.0000070934 129.0000070934
79 243.9919100078 2820.3799166166 2146689.3632626338 2639.0164249037 319.2950619430 6054484039.2541246414 129.0000072765 129.0000072765 129.0000072765
80 244.0965612207 2820.4387335935 2146689.3725191355 2638.9888176882 319.4320116291 6054610327.1403293610 129.0000074619 129.0000074619 129.0000074619
81 244.1334315951 2820.4535208568 2146689.3818921377 2638.9608330195 319.4802612965 6054642097.2373485565 129.0000076496 129.0000076496 129.0000076496
82 244.3029520408 2820.5543485196 2146689.3913816395 2638.9318525796 319.7021007878 6054858569.6761827469 129.0000078397 129.0000078397 129.0000078397
83 244.3445761189 2820.5713690935 2146689.4009876498 2638.9021684795 319.7565712929 6054895134.6560049057 129.0000080321 129.0000080321 129.0000080321
84 244.2696671559 2820.5125763350 2146689.4107101629 2638.8720941742 319.6585431986 6054768952.2869329453 129.0000082269 129.0000082269 129.0000082269
85 244.5161919319 2820.6629431352 2146689.4205491822 2638.8415194387 319.9811528443 6055091770.8571672440 129.0000084240 129.0000084240 129.0000084240
86 244.5641090282 2820.6838080201 2146689.4305047127 2638.8103612394 320.0438585800 6055136589.3662166595 129.0000086234 129.0000086234 129.0000086234
87 244.5348240638 2820.6541129118 2146689.4405767513 2638.7789728309 320.0055354056 6055072871.6007261276 129.0000088251 129.0000088251 129.0000088251
88 244.6939431427 2820.7468233396 2146689.4507653015 2638.7470269267 320.2137633592 6055271920.8364210129 129.0000090292 129.0000090292 129.0000090292
89 244.8800201091 2820.8567117003 2146689.4610703662 2638.7147520097 320.4572692055 6055507846.0901927948 129.0000092356 129.0000092356 129.0000092356
90 244.8804280382 2820.8451141876 2146689.4714919478 2638.6820441173 320.4578030336 6055482979.2295818329 129.0000094444 129.0000094444 129.0000094444
91 244.9558851986 2820.8815975090 2146689.4820300462 2638.6491836104 320.5565485155 6055561327.3181543350 129.0000096555 129.0000096555 129.0000096555
92 244.9965893140 2820.8949614294 2146689.4926846647 2638.6159817170 320.6098151301 6055590045.5610351562 129.0000098689 129.0000098689 129.0000098689
93 245.1381056687 2820.9732811388 2146689.5034558061 2638.5824451870 320.7950076360 6055758204.0434722900 129.0000100846 129.0000100846 129.0000100846
94 245.2954807041 2821.0619342131 2146689.5143434699 2638.5485198222 321.0009532826 6055948545.3822879791 129.0000103027 129.0000103027 129.0000103027
95 245.3535822199 2821.0860553731 2146689.5253476589 2638.5144817512 321.0769866522 6056000357.0671482086 129.0000105232 129.0000105232 129.0000105232
96 245.5013476026 2821.1682908185 2146689.5364683764 2638.4801107361 321.2703568219 6056176922.4099712372 129.0000107459 129.0000107459 129.0000107459
97 245.4166531417 2821.0989038023 2146689.5477056229 2638.4453663061 321.1595231342 6056028001.7295455933 129.0000109710 129.0000109710 129.0000109710
98 245.4121937790 2821.0817490953 2146689.5590593945 2638.4097762390 321.1536874797 6055991207.9293851852 129.0000111984 129.0000111984 129.0000111984
99 245.4532592994 2821.0946353191 2146689.5705296928 2638.3738037546 321.2074270397 6056018903.0102539062 129.0000114282 129.0000114282 129.0000114282
100 245.7500657390 2821.2735939427 2146689.5821165247 2638.3375549051 321.5958367642 6056403104.3106222153 129.0000116603 129.0000116603 129.0000116603
Loop time of 5.22601 on 1 procs for 100 steps with 10125 atoms
Performance: 1.653 ns/day, 14.517 hours/ns, 19.135 timesteps/s
99.7% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.44045 | 0.44045 | 0.44045 | 0.0 | 8.43
Neigh | 2.669 | 2.669 | 2.669 | 0.0 | 51.07
Comm | 0.056143 | 0.056143 | 0.056143 | 0.0 | 1.07
Output | 0.012469 | 0.012469 | 0.012469 | 0.0 | 0.24
Modify | 2.0163 | 2.0163 | 2.0163 | 0.0 | 38.58
Other | | 0.03168 | | | 0.61
Nlocal: 10125 ave 10125 max 10125 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 6703 ave 6703 max 6703 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 166831 ave 166831 max 166831 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 166831
Ave neighs/atom = 16.4771
Neighbor list builds = 100
Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:05

2018
examples/PACKAGES/dpd-react/dpdp-shardlow/data.dpd Normal file
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27
examples/PACKAGES/dpd-react/dpdp-shardlow/in.dpdp-shardlow Normal file
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# Input File for DPD fluid under isobaric conditions using the VV-SSA integration scheme
boundary p p p
units metal
atom_style atomic # Can be either dpd or atomic
read_data data.dpd
comm_modify mode single vel yes
mass 1 100.0
pair_style dpd/fdt 300.0 10.0 234324
pair_coeff 1 1 0.075 0.022 10.0
neighbor 2.0 bin
neigh_modify every 1 delay 0 check no once no
timestep 0.001
thermo 1
thermo_style custom step temp press vol pe ke etotal enthalpy cella cellb cellc
thermo_modify format float %15.10f
fix 1 all shardlow
fix 0 all nph iso 0.0 0.0 1000.0
run 100

171
examples/PACKAGES/dpd-react/dpdp-shardlow/log.dpdp-shardlow.reference Normal file
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boundary p p p
units metal
atom_style atomic # Can be either dpd or atomic
read_data data.dpd
orthogonal box = (-5.36874 -4.6558 -6.56118) to (61.4618 53.2342 46.2472)
1 by 1 by 1 MPI processor grid
reading atoms ...
1000 atoms
reading velocities ...
1000 velocities
comm_modify mode single vel yes
mass 1 100.0
pair_style dpd/fdt 300.0 10.0 234324
pair_coeff 1 1 0.075 0.022 10.0
neighbor 2.0 bin
neigh_modify every 1 delay 0 check no once no
timestep 0.001
thermo 1
thermo_style custom step temp press vol pe ke etotal enthalpy cella cellb cellc
thermo_modify format float %15.10f
fix 1 all shardlow
fix 0 all nph iso 0.0 0.0 1000.0
run 100
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6 -> bins = 12 10 9
Memory usage per processor = 2.04718 Mbytes
Step Temp Press Volume PotEng KinEng TotEng Enthalpy Cella Cellb Cellc
0 128.6667660382 3065.7908751302 204306.2673181506 263.2538386154 16.6148533499 279.8686919654 670.8120681014 66.8305353589 57.8900140312 52.8084103339
1 128.8781761640 3065.9340218365 204306.2673289568 263.2538784443 16.6421529266 279.8960313709 670.8576613026 66.8305353600 57.8900140323 52.8084103348
2 129.0263870719 3066.0331169958 204306.2673613764 263.2539594358 16.6612915322 279.9152509680 670.8895173736 66.8305353636 57.8900140353 52.8084103376
3 129.0944236964 3066.0775853577 204306.2674154095 263.2540667231 16.6700771618 279.9241438848 670.9040809083 66.8305353695 57.8900140404 52.8084103423
4 129.1614376919 3066.1201695887 204306.2674910565 263.2542205543 16.6787307383 279.9329512926 670.9183187148 66.8305353777 57.8900140476 52.8084103488
5 129.5099127127 3066.3516291155 204306.2675883183 263.2544119877 16.7237296261 279.9781416138 670.9930244672 66.8305353883 57.8900140568 52.8084103572
6 129.4373658155 3066.2979832897 204306.2677071957 263.2546211781 16.7143615811 279.9689827592 670.9770250342 66.8305354013 57.8900140680 52.8084103674
7 129.5468804564 3066.3661894656 204306.2678476885 263.2548635146 16.7285033035 279.9833668181 671.0001068740 66.8305354166 57.8900140813 52.8084103795
8 129.6703134859 3066.4427527412 204306.2680097972 263.2551515311 16.7444423199 279.9995938510 671.0260974093 66.8305354343 57.8900140966 52.8084103935
9 129.7536784769 3066.4909380739 204306.2681935227 263.2554871768 16.7552073149 280.0106944917 671.0433428967 66.8305354543 57.8900141139 52.8084104093
10 129.6933330547 3066.4412060161 204306.2683988647 263.2558667340 16.7474148571 280.0032815912 671.0295886589 66.8305354767 57.8900141333 52.8084104270
11 130.0493626138 3066.6716229532 204306.2686258238 263.2562750927 16.7933892692 280.0496643619 671.1053541603 66.8305355014 57.8900141547 52.8084104465
12 130.3213016818 3066.8440489028 204306.2688744015 263.2567151478 16.8285050016 280.0852201494 671.1628978279 66.8305355285 57.8900141782 52.8084104680
13 130.5593607103 3066.9922169334 204306.2691445989 263.2571951093 16.8592457746 280.1164408840 671.2130131637 66.8305355580 57.8900142037 52.8084104912
14 130.1135600843 3066.6777117324 204306.2694364155 263.2576949083 16.8016791453 280.0593740536 671.1158418322 66.8305355898 57.8900142313 52.8084105164
15 130.6547963417 3067.0283008545 204306.2697498515 263.2582241459 16.8715694622 280.1297936080 671.2309683942 66.8305356240 57.8900142609 52.8084105434
16 130.9755531935 3067.2288355184 204306.2700849086 263.2587905777 16.9129890783 280.1717796560 671.2985268537 66.8305356605 57.8900142926 52.8084105723
17 131.2014454974 3067.3641769107 204306.2704415883 263.2594031106 16.9421587513 280.2015618620 671.3455682001 66.8305356994 57.8900143262 52.8084106030
18 131.5359721707 3067.5714631111 204306.2708198916 263.2600649028 16.9853564767 280.2454213795 671.4158611542 66.8305357407 57.8900143620 52.8084106356
19 131.5639681439 3067.5705655906 204306.2712198192 263.2607641517 16.9889716215 280.2497357731 671.4200618636 66.8305357843 57.8900143997 52.8084106700
20 131.8466979060 3067.7405506504 204306.2716413717 263.2614923308 17.0254807658 280.2869730966 671.4789761415 66.8305358302 57.8900144396 52.8084107064
21 131.7458606698 3067.6501610601 204306.2720845494 263.2622636973 17.0124595643 280.2747232616 671.4552008593 66.8305358786 57.8900144814 52.8084107445
22 132.0934634942 3067.8611721914 204306.2725493530 263.2630740031 17.0573458246 280.3204198277 671.5278060235 66.8305359292 57.8900145253 52.8084107846
23 132.1061490539 3067.8452272408 204306.2730357830 263.2639187332 17.0589839221 280.3229026553 671.5282565150 66.8305359823 57.8900145713 52.8084108265
24 132.0864187320 3067.8064692879 204306.2735438391 263.2648061201 17.0564361282 280.3212422483 671.5216547458 66.8305360377 57.8900146193 52.8084108703
25 132.4555503012 3068.0294628610 204306.2740735220 263.2657237919 17.1041024143 280.3698262063 671.5986754029 66.8305360954 57.8900146693 52.8084109159
26 132.5425396026 3068.0605856855 204306.2746248327 263.2666902136 17.1153354198 280.3820256334 671.6148446047 66.8305361555 57.8900147214 52.8084109634
27 132.6414561712 3068.0981288018 204306.2751977713 263.2677103029 17.1281086038 280.3958189068 671.6334263968 66.8305362180 57.8900147755 52.8084110128
28 132.8195557714 3068.1880757315 204306.2757923383 263.2687564664 17.1511067628 280.4198632292 671.6689417066 66.8305362828 57.8900148316 52.8084110640
29 133.0651548752 3068.3224074813 204306.2764085347 263.2698607264 17.1828211924 280.4526819188 671.7188912867 66.8305363500 57.8900148898 52.8084111171
30 133.3017656825 3068.4496355722 204306.2770463612 263.2709902617 17.2133749553 280.4843652170 671.7667996729 66.8305364196 57.8900149501 52.8084111721
31 133.2181169549 3068.3592522301 204306.2777058180 263.2721596133 17.2025733211 280.4747329344 671.7456431539 66.8305364915 57.8900150123 52.8084112289
32 133.5618196837 3068.5561657520 204306.2783869054 263.2733741839 17.2469559586 280.5203301425 671.8163516770 66.8305365658 57.8900150767 52.8084112875
33 133.5661113072 3068.5225231843 204306.2790896240 263.2746385114 17.2475101397 280.5221486512 671.8138814999 66.8305366424 57.8900151430 52.8084113481
34 133.9344409280 3068.7332886556 204306.2798139747 263.2759490654 17.2950728696 280.5710219350 671.8896325541 66.8305367214 57.8900152115 52.8084114105
35 134.0251903481 3068.7554422023 204306.2805599582 263.2773099950 17.3067914225 280.5841014175 671.9055384405 66.8305368027 57.8900152819 52.8084114748
36 134.3358662330 3068.9247619878 204306.2813275750 263.2787224847 17.3469092744 280.6256317591 671.9686615663 66.8305368864 57.8900153544 52.8084115409
37 134.6482096693 3069.0939486549 204306.2821168264 263.2801733161 17.3872424587 280.6674157749 672.0320214328 66.8305369724 57.8900154290 52.8084116089
38 134.2954241696 3068.8129844727 204306.2829277119 263.2816463125 17.3416869550 280.6233332675 671.9521124987 66.8305370609 57.8900155056 52.8084116788
39 134.0353990053 3068.5937480649 204306.2837602301 263.2831586466 17.3081096754 280.5912683220 671.8920925677 66.8305371516 57.8900155842 52.8084117505
40 134.0661096287 3068.5695889226 204306.2846143798 263.2846992099 17.3120753654 280.5967745753 671.8945197323 66.8305372448 57.8900156649 52.8084118241
41 134.3213893449 3068.6956839852 204306.2854901617 263.2862823101 17.3450398611 280.6313221711 671.9451483911 66.8305373403 57.8900157476 52.8084118996
42 134.4478159847 3068.7334555670 204306.2863875760 263.2879050936 17.3613654449 280.6492705385 671.9679150326 66.8305374381 57.8900158323 52.8084119769
43 134.5229805032 3068.7357045585 204306.2873066230 263.2895707681 17.3710715057 280.6606422738 671.9795753149 66.8305375383 57.8900159191 52.8084120561
44 134.2978602830 3068.5344030900 204306.2882473019 263.2912685684 17.3420015325 280.6332701009 671.9265353900 66.8305376409 57.8900160080 52.8084121371
45 134.4285957415 3068.5722177449 204306.2892096124 263.2929985679 17.3588835179 280.6518820858 671.9499712659 66.8305377458 57.8900160989 52.8084122200
46 134.3890633912 3068.4939450711 204306.2901935542 263.2947639946 17.3537786705 280.6485426651 671.9366525574 66.8305378531 57.8900161918 52.8084123048
47 134.7017020134 3068.6523501535 204306.2911991276 263.2965656113 17.3941499725 280.6907155838 671.9990268961 66.8305379628 57.8900162868 52.8084123914
48 135.3432669980 3069.0313768964 204306.2922263342 263.2984321292 17.4769958266 280.7754279559 672.1320739558 66.8305380748 57.8900163838 52.8084124799
49 135.2888601690 3068.9393187512 204306.2932751755 263.3003504562 17.4699702247 280.7703206808 672.1152296222 66.8305381891 57.8900164829 52.8084125703
50 134.8400369547 3068.5806102794 204306.2943456496 263.3023024093 17.4120132858 280.7143156952 672.0134849110 66.8305383058 57.8900165840 52.8084126625
51 134.9125282999 3068.5727411569 204306.2954377555 263.3043099800 17.4213741574 280.7256841374 672.0238519903 66.8305384249 57.8900166871 52.8084127566
52 134.9445761663 3068.5364265426 204306.2965514932 263.3063613000 17.4255125267 280.7318738267 672.0254130468 66.8305385464 57.8900167923 52.8084128526
53 134.9641611904 3068.4901429966 204306.2976868616 263.3084644171 17.4280415582 280.7365059753 672.0241453860 66.8305386702 57.8900168996 52.8084129504
54 135.1512150560 3068.5555596237 204306.2988438614 263.3106154196 17.4521959894 280.7628114090 672.0587948313 66.8305387963 57.8900170088 52.8084130501
55 135.3892315779 3068.6540323579 204306.3000224932 263.3128003337 17.4829312735 280.7957316072 672.1042743302 66.8305389248 57.8900171202 52.8084131516
56 135.3265008915 3068.5480189159 204306.3012227568 263.3150330541 17.4748308045 280.7898638585 672.0848902611 66.8305390557 57.8900172335 52.8084132551
57 135.3024634130 3068.4668168613 204306.3024446515 263.3173015297 17.4717268236 280.7890283533 672.0737023745 66.8305391889 57.8900173489 52.8084133603
58 135.2521293970 3068.3666950252 204306.3036881768 263.3196055001 17.4652271476 280.7848326476 672.0567417166 66.8305393245 57.8900174664 52.8084134675
59 135.0019308452 3068.1306120627 204306.3049533316 263.3219467372 17.4329187872 280.7548655243 671.9966721947 66.8305394625 57.8900175859 52.8084135765
60 135.3361178986 3068.2878435126 204306.3062401155 263.3243328810 17.4760726571 280.8004055381 672.0622645090 66.8305396028 57.8900177074 52.8084136874
61 135.3139081244 3068.2035774253 204306.3075485286 263.3267589778 17.4732046893 280.7999636671 672.0510797027 66.8305397454 57.8900178310 52.8084138001
62 135.7430205344 3068.4226983441 204306.3088785714 263.3292333495 17.5286163545 280.8578497040 672.1369101433 66.8305398905 57.8900179566 52.8084139147
63 136.0382527386 3068.5500741031 204306.3102302457 263.3317605359 17.5667399503 280.8985004861 672.1938062135 66.8305400378 57.8900180843 52.8084140311
64 136.0795110412 3068.5046583092 204306.3116035512 263.3343072525 17.5720676714 280.9063749238 672.1958919511 66.8305401876 57.8900182140 52.8084141495
65 136.5429104992 3068.7428965120 204306.3129984887 263.3368943008 17.6319068534 280.9688011542 672.2887005078 66.8305403397 57.8900183457 52.8084142696
66 136.6747848955 3068.7560934485 204306.3144150592 263.3395194563 17.6489359109 280.9884553672 672.3100402808 66.8305404941 57.8900184795 52.8084143917
67 136.9345148389 3068.8545703617 204306.3158532631 263.3421896806 17.6824750683 281.0246647490 672.3588099945 66.8305406510 57.8900186154 52.8084145156
68 136.5690881694 3068.5302814448 204306.3173130994 263.3448899028 17.6352871991 280.9801771020 672.2729724748 66.8305408101 57.8900187532 52.8084146414
69 137.0307072166 3068.7630696250 204306.3187945680 263.3476374865 17.6948964752 281.0425339617 672.3650168515 66.8305409717 57.8900188932 52.8084147690
70 137.1048864397 3068.7333916895 204306.3202976695 263.3504277984 17.7044753039 281.0549031023 672.3736044006 66.8305411356 57.8900190351 52.8084148985
71 137.2866532809 3068.7750522066 204306.3218224039 263.3532577755 17.7279470169 281.0812047925 672.4052214764 66.8305413018 57.8900191791 52.8084150299
72 137.3464916785 3068.7338430357 204306.3233687715 263.3561237403 17.7356740022 281.0917977425 672.4105624778 66.8305414704 57.8900193252 52.8084151631
73 137.4267886898 3068.7058777536 204306.3249367717 263.3590305503 17.7460428263 281.1050733766 672.4202750386 66.8305416414 57.8900194733 52.8084152982
74 137.7032214008 3068.8096995216 204306.3265264051 263.3619634311 17.7817388269 281.1437022580 672.4721461079 66.8305418147 57.8900196234 52.8084154352
75 138.2326481893 3069.0827847254 204306.3281376729 263.3649465758 17.8501041765 281.2150507524 672.5783209650 66.8305419904 57.8900197756 52.8084155740
76 138.4006889617 3069.1105563660 204306.3297705762 263.3679794432 17.8718034302 281.2397828734 672.6065975977 66.8305421684 57.8900199299 52.8084157147
77 138.5404442761 3069.1182683851 204306.3314251149 263.3710629684 17.8898501576 281.2609131260 672.6287144410 66.8305423489 57.8900200861 52.8084158573
78 138.8911793449 3069.2673604038 204306.3331012898 263.3741701271 17.9351408874 281.3093110144 672.6961274554 66.8305425316 57.8900202444 52.8084160017
79 138.9740932597 3069.2343926248 204306.3347991015 263.3773233601 17.9458476345 281.3231709947 672.7057867031 66.8305427167 57.8900204048 52.8084161480
80 139.4197304629 3069.4447568636 204306.3365185501 263.3805326609 18.0033931609 281.3839258218 672.7933700502 66.8305429042 57.8900205672 52.8084162961
81 140.0251352305 3069.7614239791 204306.3382596380 263.3837812869 18.0815696143 281.4653509011 672.9151792214 66.8305430941 57.8900207316 52.8084164461
82 140.4343345655 3069.9447540285 204306.3400223666 263.3870704597 18.1344098865 281.5214803462 672.9946899248 66.8305432863 57.8900208981 52.8084165980
83 140.8339491089 3070.1205252103 204306.3418067374 263.3904045656 18.1860124661 281.5764170317 673.0720440188 66.8305434808 57.8900210667 52.8084167517
84 141.2138258327 3070.2828678237 204306.3436127514 263.3937910919 18.2350662835 281.6288573754 673.1451894287 66.8305436777 57.8900212372 52.8084169073
85 141.4316065757 3070.3348892447 204306.3454404095 263.3972231992 18.2631885036 281.6604117028 673.1833809261 66.8305438770 57.8900214099 52.8084170648
86 141.6165004814 3070.3639126512 204306.3472897119 263.4006984023 18.2870640172 281.6877624195 673.2144361936 66.8305440787 57.8900215845 52.8084172241
87 141.7511192071 3070.3578486993 204306.3491606587 263.4042216826 18.3044474524 281.7086691350 673.2345732314 66.8305442827 57.8900217612 52.8084173853
88 141.8992247234 3070.3595802006 204306.3510532499 263.4077909549 18.3235724488 281.7313634037 673.2574919246 66.8305444890 57.8900219400 52.8084175484
89 142.0700970483 3070.3750740931 204306.3529674857 263.4114074261 18.3456373433 281.7570447694 673.2851527089 66.8305446978 57.8900221208 52.8084177133
90 141.8940825299 3070.1552595577 204306.3549033653 263.4150659370 18.3229084328 281.7379743697 673.2380557076 66.8305449088 57.8900223036 52.8084178801
91 141.9603474040 3070.0979256101 204306.3568608877 263.4187731305 18.3314652746 281.7502384052 673.2430123833 66.8305451223 57.8900224885 52.8084180488
92 142.2257467272 3070.1741170513 204306.3588400529 263.4225144876 18.3657365240 281.7882510116 673.2907445632 66.8305453381 57.8900226755 52.8084182193
93 142.5512734406 3070.2900234936 204306.3608408618 263.4263001648 18.4077720766 281.8340722414 673.3513497860 66.8305455562 57.8900228644 52.8084183917
94 142.6487617290 3070.2508281658 204306.3628633145 263.4301422965 18.4203608255 281.8505031221 673.3627864321 66.8305457768 57.8900230555 52.8084185659
95 142.7997358153 3070.2465681156 204306.3649074107 263.4340465006 18.4398562429 281.8739027435 673.3856467375 66.8305459996 57.8900232485 52.8084187421
96 143.4667389211 3070.5895488558 204306.3669731518 263.4380042392 18.5259869441 281.9639911833 673.5194753590 66.8305462249 57.8900234436 52.8084189200
97 143.4616118167 3070.4774890551 204306.3690605387 263.4420072006 18.5253248766 281.9673320772 673.5085306100 66.8305464525 57.8900236408 52.8084190999
98 143.3138195521 3070.2680530999 204306.3711695701 263.4460419232 18.5062403307 281.9522822539 673.4667779706 66.8305466824 57.8900238400 52.8084192816
99 143.5996384267 3070.3502690101 204306.3733002460 263.4501213575 18.5431483749 281.9932697324 673.5182535422 66.8305469148 57.8900240412 52.8084194652
100 143.4332465710 3070.1261458307 204306.3754525654 263.4542352328 18.5216620473 281.9758972802 673.4723054704 66.8305471495 57.8900242445 52.8084196506
Loop time of 0.363578 on 1 procs for 100 steps with 1000 atoms
Performance: 23.764 ns/day, 1.010 hours/ns, 275.044 timesteps/s
99.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.04388 | 0.04388 | 0.04388 | 0.0 | 12.07
Neigh | 0.16374 | 0.16374 | 0.16374 | 0.0 | 45.04
Comm | 0.0078104 | 0.0078104 | 0.0078104 | 0.0 | 2.15
Output | 0.0017376 | 0.0017376 | 0.0017376 | 0.0 | 0.48
Modify | 0.14291 | 0.14291 | 0.14291 | 0.0 | 39.31
Other | | 0.003504 | | | 0.96
Nlocal: 1000 ave 1000 max 1000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1728 ave 1728 max 1728 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 18783 ave 18783 max 18783 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 18783
Ave neighs/atom = 18.783
Neighbor list builds = 100
Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:00

58
examples/PACKAGES/dpd-react/dpdrx-shardlow/in.dpdrx-shardlow Normal file
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# Example for running DPD-RX
boundary p p p
units metal # ev, ps
atom_style dpd
atom_modify map array
fix 4 all rx kinetics.dpdrx none dense lammps_rk4 1
lattice hcp 6.6520898 origin 0.0833333333333 0.25 0.25 orient z 1 0 0 orient x 0 1 0 orient y 0 0 1
region box block 0 6.0 0 6.0 0.0 6.0 units lattice
create_box 2 box
region atoms block 0 6.0 0 6.0 0.0 6.0 units lattice
create_atoms 1 region atoms
comm_modify mode single vel yes
mass * 222.12
#Set concentrations
set atom * d_rdx 1.00
set atom * d_h2 0.0
set atom * d_no2 0.0
set atom * d_n2 0.0
set atom * d_hcn 0.0
set atom * d_no 0.0
set atom * d_h2o 0.0
set atom * d_co 0.0
set atom * d_co2 0.0
#Set the kinetic temperature of the particles
velocity all create 2065.0 875661 dist gaussian
#Set the internal temperature of the particles
set atom * dpd/theta 2065.00
timestep 0.001
pair_style hybrid/overlay dpd/fdt/energy 16.00 234324 exp6/rx 16.00
pair_coeff * * dpd/fdt/energy 0.0 0.05 10.0 16.00
pair_coeff * * exp6/rx params.exp6 1fluid 1fluid exponent 1.0 1.0 16.00
fix 1 all shardlow
fix 2 all nve
fix 3 all eos/table/rx linear table.eos 4001 KEYWORD thermo.dpdrx
compute dpdU all dpd
compute dpdUatom all dpd/atom
compute crdx all property/atom d_rdx
variable totEnergy equal pe+c_dpdU[1]+c_dpdU[2]+c_dpdU[3]
thermo 1
thermo_style custom step temp press vol pe ke c_dpdU[1] c_dpdU[2] c_dpdU[3] v_totEnergy c_dpdU[4]
thermo_modify format float %15.8f flush yes
dump 2 all custom 1 dump.dpdrx id x y z vx vy vz c_dpdUatom[1] c_dpdUatom[2] c_dpdUatom[3] c_dpdUatom[4] c_crdx
dump_modify 2 sort id
run 10

12
examples/PACKAGES/dpd-react/dpdrx-shardlow/kinetics.dpdrx Normal file
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# reaction equations and parameters
# multiple entries can be added to this file
# these entries are in LAMMPS "metal" units:
# Arr = 1/picosec or Angstroms^3/mol/picosec; Ern = eV
# format of a single entry (one or more lines):
# rxn equation, Arn, Ern
1.0 rdx = 3.0 hcn + 1.5 no2 + 1.5 no + 1.5 h2o 2.51000000000000E+04 0.0 1.912325921964536
1.0 hcn + 1.0 no2 = 1.0 no + 0.5 n2 + 0.5 h2 + 1.0 co 2.49081028001241E+01 0.0 1.344265387322009
1.0 hcn + 1.0 no = 1.0 co + 1.0 n2 + 0.5 h2 4.98162056E+00 0.0 1.517718985686140
1.0 no + 1.0 co = 0.5 n2 + 1.0 co2 1.66054018667494E+06 0.0 6.938245245

132
examples/PACKAGES/dpd-react/dpdrx-shardlow/log.dpdrx-shardlow.reference Normal file
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boundary p p p
units metal # ev, ps
atom_style dpd
atom_modify map array
fix 4 all rx kinetics.dpdrx none dense lammps_rk4 1
lattice hcp 6.6520898 origin 0.0833333333333 0.25 0.25 orient z 1 0 0 orient x 0 1 0 orient y 0 0 1
Lattice spacing in x,y,z = 11.5218 10.8628 6.65209
region box block 0 6.0 0 6.0 0.0 6.0 units lattice
create_box 2 box
Created orthogonal box = (0 0 0) to (69.1305 65.1769 39.9125)
1 by 1 by 1 MPI processor grid
region atoms block 0 6.0 0 6.0 0.0 6.0 units lattice
create_atoms 1 region atoms
Created 864 atoms
comm_modify mode single vel yes
mass * 222.12
#Set concentrations
set atom * d_rdx 1.00
864 settings made for d_rdx
set atom * d_h2 0.0
864 settings made for d_h2
set atom * d_no2 0.0
864 settings made for d_no2
set atom * d_n2 0.0
864 settings made for d_n2
set atom * d_hcn 0.0
864 settings made for d_hcn
set atom * d_no 0.0
864 settings made for d_no
set atom * d_h2o 0.0
864 settings made for d_h2o
set atom * d_co 0.0
864 settings made for d_co
set atom * d_co2 0.0
864 settings made for d_co2
#Set the kinetic temperature of the particles
velocity all create 2065.0 875661 dist gaussian
#Set the internal temperature of the particles
set atom * dpd/theta 2065.00
864 settings made for dpd/theta
timestep 0.001
pair_style hybrid/overlay dpd/fdt/energy 16.00 234324 exp6/rx 16.00
pair_coeff * * dpd/fdt/energy 0.0 0.05 10.0 16.00
pair_coeff * * exp6/rx params.exp6 1fluid 1fluid exponent 1.0 1.0 16.00
fix 1 all shardlow
fix 2 all nve
fix 3 all eos/table/rx linear table.eos 4001 KEYWORD thermo.dpdrx
compute dpdU all dpd
compute dpdUatom all dpd/atom
compute crdx all property/atom d_rdx
variable totEnergy equal pe+c_dpdU[1]+c_dpdU[2]+c_dpdU[3]
thermo 1
thermo_style custom step temp press vol pe ke c_dpdU[1] c_dpdU[2] c_dpdU[3] v_totEnergy c_dpdU[4]
thermo_modify format float %15.8f flush yes
dump 2 all custom 1 dump.dpdrx id x y z vx vy vz c_dpdUatom[1] c_dpdUatom[2] c_dpdUatom[3] c_dpdUatom[4] c_crdx
dump_modify 2 sort id
run 10
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 8 8 5
3 neighbor lists, perpetual/occasional/extra = 3 0 0
(1) pair dpd/fdt/energy, perpetual
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
(2) pair exp6/rx, perpetual, copy from (1)
pair build: copy
stencil: none
bin: none
(3) fix shardlow, perpetual, ssa
pair build: half/bin/newton/ssa
stencil: half/bin/3d/newton/ssa
bin: ssa
Memory usage per processor = 8.39564 Mbytes
Step Temp Press Volume PotEng KinEng c_dpdU[1] c_dpdU[2] c_dpdU[3] v_totEnergy c_dpdU[4]
0 2065.00000000 1368.17463335 179834.51777865 0.00000000 230.35385810 0.00000000 7682.84786557 0.00000000 7682.84786557 2065.00000000
1 2064.93210437 1368.12964881 179834.51777865 0.00000000 230.34628424 0.00000000 7682.85543943 0.00000000 7682.85543943 2065.20275230
2 2067.82089565 1370.04362990 179834.51777865 -0.00000000 230.66853326 0.00000000 7682.53319042 0.00000000 7682.53319042 2065.32453473
3 2070.45225169 1371.78704616 179834.51777865 -0.00000000 230.96206499 0.00000000 7682.23965869 0.00000000 7682.23965869 2065.45336917
4 2075.00241157 1374.80177416 179834.51777865 -0.00000000 231.46964217 0.00000000 7681.73208151 0.00000000 7681.73208151 2065.52973333
5 2073.96509212 1374.11449370 179834.51777865 -0.00000000 231.35392762 -0.00000000 7681.84779605 0.00000000 7681.84779605 2065.76011517
6 2074.26516936 1374.31331117 179834.51777865 -0.00000000 231.38740169 -0.00000000 7681.81432198 0.00000000 7681.81432198 2065.95399323
7 2071.41069700 1372.42206822 179834.51777865 -0.00000000 231.06898100 -0.00000000 7682.13274267 0.00000000 7682.13274267 2066.23407076
8 2071.35844957 1372.38745146 179834.51777865 -0.00000000 231.06315272 0.00000000 7682.13857095 0.00000000 7682.13857095 2066.43766287
9 2071.35676496 1372.38633532 179834.51777865 -0.00000000 231.06296480 0.00000000 7682.13875887 0.00000000 7682.13875887 2066.64001166
10 2066.53172340 1369.18948328 179834.51777865 -0.00000000 230.52472415 0.00000000 7682.67699952 0.00000000 7682.67699952 2066.97516855
Loop time of 0.611304 on 1 procs for 10 steps with 864 atoms
Performance: 1.413 ns/day, 16.981 hours/ns, 16.358 timesteps/s
98.2% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.34177 | 0.34177 | 0.34177 | 0.0 | 55.91
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0013342 | 0.0013342 | 0.0013342 | 0.0 | 0.22
Output | 0.083583 | 0.083583 | 0.083583 | 0.0 | 13.67
Modify | 0.18451 | 0.18451 | 0.18451 | 0.0 | 30.18
Other | | 0.0001087 | | | 0.02
Nlocal: 864 ave 864 max 864 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2700 ave 2700 max 2700 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 55296 ave 55296 max 55296 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 55296
Ave neighs/atom = 64
Neighbor list builds = 0
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:00

16
examples/PACKAGES/dpd-react/dpdrx-shardlow/params.exp6 Normal file
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@ -0,0 +1,16 @@
# rx parameters for various molecules
# multiple entries can be added to this file, LAMMPS reads the ones it needs
# these entries are in LAMMPS "metal" units:
# alpha = unitless; epsilon = eV; rho = Angstroms;
# format of a single entry (one or more lines):
# species, exp6, alpha, epsilon, rm
hcn exp6 13.57 0.030862657941745 5.3725
no2 exp6 13.57 0.029126283357001 4.2744
no exp6 13.10 0.013090454747817 3.7142
h2o exp6 11.01 0.022473771300313 3.5348
co exp6 13.24 0.0086353397713660428 4.1759
co2 exp6 14.09 0.019672305322873507 4.1757
h2 exp6 11.23 0.002618780329051 3.4925
n2 exp6 12.97 0.008635339808299 4.1778

4006
examples/PACKAGES/dpd-react/dpdrx-shardlow/table.eos Normal file
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File diff suppressed because it is too large Load Diff

17
examples/PACKAGES/dpd-react/dpdrx-shardlow/thermo.dpdrx Normal file
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@ -0,0 +1,17 @@
# rx heats of formation for various molecules
# multiple entries can be added to this file, LAMMPS reads the ones it needs
# the entries are in LAMMPS "metal" units (eV)
# Be sure the units are consistent with your input file
# format of a single entry (one or more lines):
# species DeltaHformation
rdx 1.989907438211819
h2 0.000000000000000
no2 0.343004076201018
n2 0.000000000000000
hcn 1.400635733970104
no 0.935781955892458
h2o -2.506184777415379
co -1.145533746031845
co2 -4.078501848437456

40
examples/PACKAGES/dpd-react/multi-lucy/in.multi-lucy Normal file
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@ -0,0 +1,40 @@
# RDX coarse-grain model
units metal # ev, ps
atom_style dpd
atom_modify map array
lattice hcp 6.6520898 origin 0.0833333333333 0.25 0.25 orient z 1 0 0 orient x 0 1 0 orient y 0 0 1
variable xrep equal 10.0
variable yrep equal 10.0
variable zrep equal 10.0
region box block 0 ${xrep} 0 ${yrep} 0.0 ${zrep} units lattice
create_box 2 box
region atoms block 0 ${xrep} 0 ${yrep} 0.0 ${zrep} units lattice
create_atoms 1 region atoms
variable newx equal xhi*0.99998623082367843
variable newy equal yhi*0.96972098958539854
change_box all x final 0.0 ${newx} y final 0.0 ${newy} remap units box
comm_modify vel yes
mass * 222.12
timestep 0.01
pair_style multi/lucy linear 74923
pair_coeff * * table.multibody KEYWORD 16.00
fix 2 all nve
neighbor 0.0 bin
neigh_modify every 1 delay 0 check no once no
variable totEnergy equal pe+ke
thermo 1
thermo_style custom step temp press vol pe ke v_totEnergy pxx pyy pzz lx ly lz
thermo_modify format float %15.8f flush yes
velocity all create 300.00 9198783 mom yes rot yes dist gaussian
run 100

192
examples/PACKAGES/dpd-react/multi-lucy/log.multi-lucy.reference Normal file
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@ -0,0 +1,192 @@
units metal # ev, ps
atom_style dpd
atom_modify map array
lattice hcp 6.6520898 origin 0.0833333333333 0.25 0.25 orient z 1 0 0 orient x 0 1 0 orient y 0 0 1
Lattice spacing in x,y,z = 11.5218 10.8628 6.65209
variable xrep equal 10.0
variable yrep equal 10.0
variable zrep equal 10.0
region box block 0 ${xrep} 0 ${yrep} 0.0 ${zrep} units lattice
region box block 0 10 0 ${yrep} 0.0 ${zrep} units lattice
region box block 0 10 0 10 0.0 ${zrep} units lattice
region box block 0 10 0 10 0.0 10 units lattice
create_box 2 box
Created orthogonal box = (0 0 0) to (115.218 108.628 66.5209)
1 by 1 by 1 MPI processor grid
region atoms block 0 ${xrep} 0 ${yrep} 0.0 ${zrep} units lattice
region atoms block 0 10 0 ${yrep} 0.0 ${zrep} units lattice
region atoms block 0 10 0 10 0.0 ${zrep} units lattice
region atoms block 0 10 0 10 0.0 10 units lattice
create_atoms 1 region atoms
Created 4000 atoms
variable newx equal xhi*0.99998623082367843
variable newy equal yhi*0.96972098958539854
change_box all x final 0.0 ${newx} y final 0.0 ${newy} remap units box
change_box all x final 0.0 115.21598865 y final 0.0 ${newy} remap units box
change_box all x final 0.0 115.21598865 y final 0.0 105.339018016667 remap units box
orthogonal box = (0 0 0) to (115.216 108.628 66.5209)
orthogonal box = (0 0 0) to (115.216 105.339 66.5209)
comm_modify vel yes
mass * 222.12
timestep 0.01
pair_style multi/lucy linear 74923
pair_coeff * * table.multibody KEYWORD 16.00
fix 2 all nve
neighbor 0.0 bin
neigh_modify every 1 delay 0 check no once no
variable totEnergy equal pe+ke
thermo 1
thermo_style custom step temp press vol pe ke v_totEnergy pxx pyy pzz lx ly lz
thermo_modify format float %15.8f flush yes
velocity all create 300.00 9198783 mom yes rot yes dist gaussian
run 100
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 16
ghost atom cutoff = 16
binsize = 8 -> bins = 15 14 9
Memory usage per processor = 3.86201 Mbytes
Step Temp Press Volume PotEng KinEng totEnerg Pxx Pyy Pzz Lx Ly Lz
0 300.00000000 1214.85216295 807346.78400379 -22.12267153 155.07339596 132.95072442 1220.12471110 1216.91825878 1207.51351897 115.21598865 105.33901802 66.52089800
1 299.98155049 1215.02568640 807346.78400379 -22.11313423 155.06385920 132.95072496 1220.29979706 1217.09227333 1207.68498882 115.21598865 105.33901802 66.52089800
2 299.92623729 1215.54625966 807346.78400379 -22.08453879 155.03526718 132.95072838 1220.82084147 1217.61430453 1208.20363298 115.21598865 105.33901802 66.52089800
3 299.83415613 1216.41405238 807346.78400379 -22.03693661 154.98766938 132.95073277 1221.68800899 1218.48449656 1209.06965158 115.21598865 105.33901802 66.52089800
4 299.70545314 1217.62933713 807346.78400379 -21.97040218 154.92114135 132.95073917 1222.90156854 1219.70309293 1210.28334991 115.21598865 105.33901802 66.52089800
5 299.54032469 1219.19252381 807346.78400379 -21.88503806 154.83578459 132.95074652 1224.46192758 1221.27047105 1211.84517279 115.21598865 105.33901802 66.52089800
6 299.33901717 1221.10411140 807346.78400379 -21.78097017 154.73172645 132.95075628 1226.36958369 1223.18709408 1213.75565644 115.21598865 105.33901802 66.52089800
7 299.10182669 1223.36472005 807346.78400379 -21.65835298 154.60912001 132.95076703 1228.62515623 1225.45354361 1216.01546031 115.21598865 105.33901802 66.52089800
8 298.82909869 1225.97503292 807346.78400379 -21.51736396 154.46814382 132.95077986 1231.22932809 1228.07046194 1218.62530873 115.21598865 105.33901802 66.52089800
9 298.52122747 1228.93581631 807346.78400379 -21.35820794 154.30900169 132.95079375 1234.18286483 1231.03857404 1221.58601007 115.21598865 105.33901802 66.52089800
10 298.17865561 1232.24787196 807346.78400379 -21.18111335 154.13192242 132.95080907 1237.48656650 1234.35864137 1224.89840803 115.21598865 105.33901802 66.52089800
11 297.80187339 1235.91202348 807346.78400379 -20.98633355 153.93715943 132.95082588 1241.14125365 1238.03144867 1228.56336813 115.21598865 105.33901802 66.52089800
12 297.39141808 1239.92908534 807346.78400379 -20.77414622 153.72499044 132.95084421 1245.14773653 1242.05777276 1232.58174674 115.21598865 105.33901802 66.52089800
13 296.94787317 1244.29983696 807346.78400379 -20.54485317 153.49571705 132.95086388 1249.50678888 1246.43835699 1236.95436501 115.21598865 105.33901802 66.52089800
14 296.47186749 1249.02497601 807346.78400379 -20.29877921 153.24966432 132.95088511 1254.21910126 1251.17386419 1241.68196256 115.21598865 105.33901802 66.52089800
15 295.96407431 1254.10509565 807346.78400379 -20.03627262 152.98718028 132.95090766 1259.28525845 1256.26485345 1246.76517504 115.21598865 105.33901802 66.52089800
16 295.42521029 1259.54064168 807346.78400379 -19.75770388 152.70863537 132.95093149 1264.70569635 1261.71173740 1252.20449129 115.21598865 105.33901802 66.52089800
17 294.85603433 1265.33187598 807346.78400379 -19.46346575 152.41442187 132.95095612 1270.48066555 1267.51474571 1258.00021668 115.21598865 105.33901802 66.52089800
18 294.25734640 1271.47883112 807346.78400379 -19.15397066 152.10495330 132.95098265 1276.61018593 1273.67387925 1264.15242818 115.21598865 105.33901802 66.52089800
19 293.62998623 1277.98128944 807346.78400379 -18.82965389 151.78066373 132.95100984 1283.09402558 1280.18888963 1270.66095310 115.21598865 105.33901802 66.52089800
20 292.97483191 1284.83872635 807346.78400379 -18.49096827 151.44200705 132.95103877 1289.93164440 1287.05922263 1277.52531201 115.21598865 105.33901802 66.52089800
21 292.29279840 1292.05029131 807346.78400379 -18.13838752 151.08945620 132.95106869 1297.12217493 1294.28399932 1284.74469966 115.21598865 105.33901802 66.52089800
22 291.58483599 1299.61476577 807346.78400379 -17.77240299 150.72350242 132.95109943 1304.66438055 1301.86197418 1292.31794256 115.21598865 105.33901802 66.52089800
23 290.85192865 1307.53051634 807346.78400379 -17.39352373 150.34465432 132.95113059 1312.55660811 1309.79148860 1300.24345231 115.21598865 105.33901802 66.52089800
24 290.09509230 1315.79547784 807346.78400379 -17.00227296 149.95343704 132.95116409 1320.79677086 1318.07045430 1308.51920836 115.21598865 105.33901802 66.52089800
25 289.31537304 1324.40713625 807346.78400379 -16.59919365 149.55039133 132.95119768 1329.38233222 1326.69633585 1317.14274068 115.21598865 105.33901802 66.52089800
26 288.51384364 1333.36102314 807346.78400379 -16.18484030 149.13607171 132.95123141 1338.30880774 1335.66464732 1326.10961436 115.21598865 105.33901802 66.52089800
27 287.69159987 1342.65187212 807346.78400379 -15.75977816 148.71104460 132.95126644 1347.57091685 1344.97010766 1335.41459186 115.21598865 105.33901802 66.52089800
28 286.84975866 1352.27397111 807346.78400379 -15.32458588 148.27588735 132.95130146 1357.16294383 1354.60697533 1345.05199418 115.21598865 105.33901802 66.52089800
29 285.98945385 1362.21810390 807346.78400379 -14.87984825 147.83118606 132.95133781 1367.07572944 1364.56591875 1355.01266352 115.21598865 105.33901802 66.52089800
30 285.11183157 1372.47402741 807346.78400379 -14.42615956 147.37753316 132.95137360 1377.29907470 1374.83660611 1365.28640141 115.21598865 105.33901802 66.52089800
31 284.21805121 1383.03399379 807346.78400379 -13.96411808 146.91552798 132.95140990 1387.82524185 1385.41127290 1375.86546663 115.21598865 105.33901802 66.52089800
32 283.30928639 1393.88949451 807346.78400379 -13.49433043 146.44577716 132.95144673 1398.64569849 1396.28141986 1386.74136518 115.21598865 105.33901802 66.52089800
33 282.38672308 1405.03145788 807346.78400379 -13.01741017 145.96889373 132.95148357 1409.75134678 1407.43799592 1397.90503094 115.21598865 105.33901802 66.52089800
34 281.45155812 1416.45050120 807346.78400379 -12.53397537 145.48549639 132.95152102 1421.13275266 1418.87162072 1409.34713021 115.21598865 105.33901802 66.52089800
35 280.50499797 1428.13709818 807346.78400379 -12.04465038 144.99620873 132.95155835 1432.78036207 1430.57277039 1421.05816207 115.21598865 105.33901802 66.52089800
36 279.54825705 1440.08125112 807346.78400379 -11.55006192 144.50165852 132.95159659 1444.68414393 1442.53147451 1433.02813492 115.21598865 105.33901802 66.52089800
37 278.58255618 1452.27309145 807346.78400379 -11.05084284 144.00247680 132.95163396 1456.83420615 1454.73786920 1445.24719900 115.21598865 105.33901802 66.52089800
38 277.60911953 1464.70025824 807346.78400379 -10.54762439 143.49929638 132.95167199 1469.21819177 1467.17955926 1457.70302368 115.21598865 105.33901802 66.52089800
39 276.62917178 1477.35076005 807346.78400379 -10.04104004 142.99275030 132.95171026 1481.82412322 1479.84454102 1470.38361590 115.21598865 105.33901802 66.52089800
40 275.64393717 1490.21272152 807346.78400379 -9.53172384 142.48347137 132.95174753 1494.64011882 1492.72094171 1483.27710402 115.21598865 105.33901802 66.52089800
41 274.65463761 1503.27360751 807346.78400379 -9.02030627 141.97209123 132.95178496 1507.65362511 1505.79619250 1496.37100491 115.21598865 105.33901802 66.52089800
42 273.66249069 1516.52078349 807346.78400379 -8.50741664 141.45923926 132.95182261 1520.85199536 1519.05762536 1509.65272975 115.21598865 105.33901802 66.52089800
43 272.66870760 1529.94104125 807346.78400379 -7.99368165 140.94554153 132.95185988 1534.22199310 1532.49203870 1523.10909195 115.21598865 105.33901802 66.52089800
44 271.67449075 1543.52061095 807346.78400379 -7.47972338 140.43161959 132.95189621 1547.74984313 1546.08566531 1536.72632440 115.21598865 105.33901802 66.52089800
45 270.68103146 1557.24551051 807346.78400379 -6.96615672 139.91808923 132.95193252 1561.42155306 1559.82447888 1550.49049959 115.21598865 105.33901802 66.52089800
46 269.68950826 1571.10240735 807346.78400379 -6.45359109 139.40555967 132.95196858 1575.22376775 1573.69514129 1564.38831301 115.21598865 105.33901802 66.52089800
47 268.70108495 1585.07761675 807346.78400379 -5.94262870 138.89463247 132.95200377 1589.14276538 1587.68396538 1578.40611949 115.21598865 105.33901802 66.52089800
48 267.71690840 1599.15793895 807346.78400379 -5.43386213 138.38590047 132.95203834 1603.16532146 1601.77776906 1592.53072631 115.21598865 105.33901802 66.52089800
49 266.73810668 1613.33033790 807346.78400379 -4.92787412 137.87994678 132.95207265 1617.27836120 1615.96354286 1606.74910964 115.21598865 105.33901802 66.52089800
50 265.76578715 1627.58258742 807346.78400379 -4.42523789 137.37734381 132.95210592 1631.46963718 1630.22908130 1621.04904378 115.21598865 105.33901802 66.52089800
51 264.80103448 1641.90248933 807346.78400379 -3.92651400 136.87865223 132.95213823 1645.72692666 1644.56220766 1635.41833366 115.21598865 105.33901802 66.52089800
52 263.84490793 1656.27734653 807346.78400379 -3.43224999 136.38441959 132.95216960 1660.03745892 1658.95026436 1649.84431631 115.21598865 105.33901802 66.52089800
53 262.89843908 1670.69551125 807346.78400379 -2.94297816 135.89517913 132.95220097 1674.38956673 1673.38163368 1664.31533334 115.21598865 105.33901802 66.52089800
54 261.96262992 1685.14553889 807346.78400379 -2.45921853 135.41144879 132.95223026 1688.77180510 1687.84489681 1678.81991477 115.21598865 105.33901802 66.52089800
55 261.03845044 1699.61620399 807346.78400379 -1.98147065 134.93372995 132.95225930 1703.17294770 1702.32885467 1693.34680961 115.21598865 105.33901802 66.52089800
56 260.12683635 1714.09662971 807346.78400379 -1.51021929 134.46250631 132.95228702 1717.58211523 1716.82266053 1707.88511338 115.21598865 105.33901802 66.52089800
57 259.22868684 1728.57618816 807346.78400379 -1.04592921 133.99824266 132.95231345 1731.98868431 1731.31571575 1722.42416441 115.21598865 105.33901802 66.52089800
58 258.34486232 1743.04444894 807346.78400379 -0.58904565 133.54138376 132.95233811 1746.38222948 1745.79761712 1736.95350021 115.21598865 105.33901802 66.52089800
59 257.47618217 1757.49110140 807346.78400379 -0.13999165 133.09235316 132.95236151 1760.75245090 1760.25807844 1751.46277487 115.21598865 105.33901802 66.52089800
60 256.62342270 1771.90631323 807346.78400379 0.30083203 132.65155213 132.95238416 1775.08953474 1774.68729658 1765.94210837 115.21598865 105.33901802 66.52089800
61 255.78731525 1786.28069085 807346.78400379 0.73304602 132.21935873 132.95240475 1789.38411899 1789.07590440 1780.38204916 115.21598865 105.33901802 66.52089800
62 254.96854444 1800.60528382 807346.78400379 1.15629768 131.79612683 132.95242450 1803.62728580 1803.41497663 1794.77358903 115.21598865 105.33901802 66.52089800
63 254.16774635 1814.87155477 807346.78400379 1.57025695 131.38218523 132.95244218 1817.81053503 1817.69599898 1809.10813030 115.21598865 105.33901802 66.52089800
64 253.38550694 1829.07117079 807346.78400379 1.97462094 130.97783682 132.95245777 1831.92557869 1831.91064783 1823.37728584 115.21598865 105.33901802 66.52089800
65 252.62236055 1843.19638891 807346.78400379 2.36911429 130.58335782 132.95247211 1845.96472133 1846.05119798 1837.57324742 115.21598865 105.33901802 66.52089800
66 251.87878865 1857.23990728 807346.78400379 2.75348779 130.19899708 132.95248487 1859.92071310 1860.11036576 1851.68864298 115.21598865 105.33901802 66.52089800
67 251.15521863 1871.19480215 807346.78400379 3.12752004 129.82497555 132.95249559 1873.78668892 1874.08124305 1865.71647448 115.21598865 105.33901802 66.52089800
68 250.45202285 1885.05459361 807346.78400379 3.49101896 129.46148569 132.95250466 1887.55623377 1887.95736166 1879.65018540 115.21598865 105.33901802 66.52089800
69 249.76951782 1898.81325923 807346.78400379 3.84382067 129.10869111 132.95251178 1901.22339385 1901.73270901 1893.48367484 115.21598865 105.33901802 66.52089800
70 249.10796351 1912.46515304 807346.78400379 4.18579091 128.76672621 132.95251712 1914.78259878 1915.40164433 1907.21121600 115.21598865 105.33901802 66.52089800
71 248.46756299 1926.00504201 807346.78400379 4.51682490 128.43569592 132.95252082 1928.22869236 1928.95893947 1920.82749418 115.21598865 105.33901802 66.52089800
72 247.84846207 1939.42810753 807346.78400379 4.83684677 128.11567565 132.95252243 1941.55693966 1942.39977558 1934.32760734 115.21598865 105.33901802 66.52089800
73 247.25074937 1952.72996785 807346.78400379 5.14581129 127.80671119 132.95252249 1954.76304891 1955.71976556 1947.70708909 115.21598865 105.33901802 66.52089800
74 246.67445640 1965.90663684 807346.78400379 5.44370154 127.50881883 132.95252037 1967.84312671 1968.91491617 1960.96186765 115.21598865 105.33901802 66.52089800
75 246.11955792 1978.95453145 807346.78400379 5.73053087 127.22198553 132.95251640 1980.79368722 1981.98163382 1974.08827333 115.21598865 105.33901802 66.52089800
76 245.58597254 1991.87045924 807346.78400379 6.00634144 126.94616920 132.95251065 1993.61163792 1994.91671290 1987.08302690 115.21598865 105.33901802 66.52089800
77 245.07356341 2004.65154721 807346.78400379 6.27120386 126.68129912 132.95250299 2006.29421214 2007.71726040 1999.94316910 115.21598865 105.33901802 66.52089800
78 244.58213918 2017.29539001 807346.78400379 6.52521809 126.42727638 132.95249447 2018.83910878 2020.38085546 2012.66620579 115.21598865 105.33901802 66.52089800
79 244.11145502 2029.80010784 807346.78400379 6.76850879 126.18397441 132.95248320 2031.24454685 2032.90560846 2025.25016823 115.21598865 105.33901802 66.52089800
80 243.66121397 2042.16407902 807346.78400379 7.00123097 125.95123971 132.95247068 2043.50902489 2045.28986433 2037.69334784 115.21598865 105.33901802 66.52089800
81 243.23106832 2054.38629348 807346.78400379 7.22356428 125.72889256 132.95245683 2055.63164607 2057.53258357 2049.99465079 115.21598865 105.33901802 66.52089800
82 242.82062122 2066.46613485 807346.78400379 7.43571312 125.51672780 132.95244092 2067.61189529 2069.63311930 2062.15338995 115.21598865 105.33901802 66.52089800
83 242.42942848 2078.40298107 807346.78400379 7.63790833 125.31451585 132.95242417 2079.44926149 2081.59081527 2074.16886644 115.21598865 105.33901802 66.52089800
84 242.05700073 2090.19639662 807346.78400379 7.83040181 125.12200373 132.95240554 2091.14342286 2093.40519773 2086.04056927 115.21598865 105.33901802 66.52089800
85 241.70280558 2101.84628378 807346.78400379 8.01346897 124.93891625 132.95238522 2102.69439895 2105.07612228 2097.76833012 115.21598865 105.33901802 66.52089800
86 241.36626994 2113.35269396 807346.78400379 8.18740712 124.76495716 132.95236428 2114.10235681 2116.60359480 2109.35213027 115.21598865 105.33901802 66.52089800
87 241.04678236 2124.71610357 807346.78400379 8.35253195 124.59981042 132.95234236 2125.36789014 2127.98804410 2120.79237645 115.21598865 105.33901802 66.52089800
88 240.74369534 2135.93768680 807346.78400379 8.50917742 124.44314130 132.95231873 2136.49230457 2139.23058407 2132.09017177 115.21598865 105.33901802 66.52089800
89 240.45632785 2147.01830215 807346.78400379 8.65769642 124.29459780 132.95229422 2147.47657315 2150.33201661 2143.24631669 115.21598865 105.33901802 66.52089800
90 240.18396823 2157.95915624 807346.78400379 8.79845686 124.15381203 132.95226889 2158.32202287 2161.29347731 2154.26196855 115.21598865 105.33901802 66.52089800
91 239.92587635 2168.76249542 807346.78400379 8.93184124 124.02040141 132.95224265 2169.03104691 2172.11712586 2165.13931349 115.21598865 105.33901802 66.52089800
92 239.68128636 2179.42956414 807346.78400379 9.05824571 123.89397007 132.95221578 2179.60501383 2182.80414124 2175.87953734 115.21598865 105.33901802 66.52089800
93 239.44941012 2189.96207637 807346.78400379 9.17807756 123.77411062 132.95218818 2190.04575379 2193.35616035 2186.48431497 115.21598865 105.33901802 66.52089800
94 239.22944006 2200.36210822 807346.78400379 9.29175459 123.66040561 132.95216020 2200.35545716 2203.77517672 2196.95569079 115.21598865 105.33901802 66.52089800
95 239.02055215 2210.63160393 807346.78400379 9.39970237 123.55242908 132.95213145 2210.53616675 2214.06307395 2207.29557110 115.21598865 105.33901802 66.52089800
96 238.82190903 2220.77267205 807346.78400379 9.50235468 123.44974821 132.95210289 2220.59008680 2224.22189558 2217.50603377 115.21598865 105.33901802 66.52089800
97 238.63266294 2230.78766339 807346.78400379 9.60014892 123.35192476 132.95207367 2230.51965356 2234.25392247 2227.58941414 115.21598865 105.33901802 66.52089800
98 238.45195842 2240.67914734 807346.78400379 9.69352820 123.25851655 132.95204475 2240.32755079 2244.16160081 2237.54829041 115.21598865 105.33901802 66.52089800
99 238.27893540 2250.44940329 807346.78400379 9.78293616 123.16907899 132.95201516 2250.01616090 2253.94710729 2247.38494167 115.21598865 105.33901802 66.52089800
100 238.11273236 2260.10079587 807346.78400379 9.86881920 123.08316676 132.95198596 2259.58791653 2263.61274057 2257.10173052 115.21598865 105.33901802 66.52089800
Loop time of 2.42086 on 1 procs for 100 steps with 4000 atoms
Performance: 35.690 ns/day, 0.672 hours/ns, 41.308 timesteps/s
99.6% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.4967 | 1.4967 | 1.4967 | 0.0 | 61.83
Neigh | 0.85998 | 0.85998 | 0.85998 | 0.0 | 35.52
Comm | 0.035836 | 0.035836 | 0.035836 | 0.0 | 1.48
Output | 0.0091844 | 0.0091844 | 0.0091844 | 0.0 | 0.38
Modify | 0.0055444 | 0.0055444 | 0.0055444 | 0.0 | 0.23
Other | | 0.01357 | | | 0.56
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5840 ave 5840 max 5840 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 165860 ave 165860 max 165860 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 165860
Ave neighs/atom = 41.465
Neighbor list builds = 100
Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:02

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