| blob | de5d670073dd10a47f59634bf80160e5f4162a71 |
1 LAMMPS (5 Oct 2016)
2 # Created by charmm2lammps v1.8.2.6 beta on Thu Mar 3 20:56:57 EST 2016
4 units real
5 neigh_modify delay 2 every 1
6 #newton off
8 boundary p p p
10 atom_style full
11 bond_style harmonic
12 angle_style charmm
13 dihedral_style charmm
14 improper_style harmonic
16 pair_style lj/charmm/coul/charmm 8 12
17 #pair_style lj/charmmfsw/coul/charmmfsh 8 12
18 pair_modify mix arithmetic
20 fix cmap all cmap charmm22.cmap
21 Reading potential file charmm22.cmap with DATE: 2016-09-26
22 fix_modify cmap energy yes
24 read_data gagg.data fix cmap crossterm CMAP
25 orthogonal box = (-34.4147 -36.1348 -39.3491) to (45.5853 43.8652 40.6509)
26 1 by 2 by 2 MPI processor grid
27 reading atoms ...
28 34 atoms
29 scanning bonds ...
30 4 = max bonds/atom
31 scanning angles ...
32 6 = max angles/atom
33 scanning dihedrals ...
34 12 = max dihedrals/atom
35 scanning impropers ...
36 1 = max impropers/atom
37 reading bonds ...
38 33 bonds
39 reading angles ...
40 57 angles
41 reading dihedrals ...
42 75 dihedrals
43 reading impropers ...
44 7 impropers
45 4 = max # of 1-2 neighbors
46 7 = max # of 1-3 neighbors
47 13 = max # of 1-4 neighbors
48 16 = max # of special neighbors
50 special_bonds charmm
51 fix 1 all nve
53 #fix 1 all nvt temp 300 300 100.0
54 #fix 2 all shake 1e-9 500 0 m 1.0
56 velocity all create 0.0 12345678 dist uniform
58 thermo 1000
59 thermo_style custom step ecoul evdwl ebond eangle edihed f_cmap eimp
60 timestep 2.0
62 run 100000
63 Neighbor list info ...
64 1 neighbor list requests
65 update every 1 steps, delay 2 steps, check yes
66 max neighbors/atom: 2000, page size: 100000
67 master list distance cutoff = 14
68 ghost atom cutoff = 14
69 binsize = 7 -> bins = 12 12 12
70 Memory usage per processor = 15.9307 Mbytes
71 Step E_coul E_vdwl E_bond E_angle E_dihed f_cmap E_impro
72 0 26.542777 -0.93822087 1.2470497 4.8441789 4.5432816 -1.473352 0.10453023
73 1000 28.673005 -0.47724367 0.80029132 3.151679 4.4684446 -2.3928648 0.18604953
74 2000 27.67955 -1.170342 0.72018905 4.0400131 4.4713764 -2.5490207 0.21834436
75 3000 29.256656 -0.35856055 0.73303546 3.7411606 4.4710568 -2.8939692 0.37728884
76 4000 30.097549 -1.1353905 0.79007053 3.0688444 4.4091469 -2.3383587 0.20743631
77 5000 28.357525 -1.0723742 0.9180297 3.6579424 4.8792663 -2.3185572 0.088366962
78 6000 29.214175 -0.95299239 0.81926011 3.6805428 4.6742897 -2.9343578 0.26697816
79 7000 27.018614 -0.52423469 0.72502751 3.8840141 4.7780958 -2.3916014 0.24952572
80 8000 29.682494 -1.0940368 0.76113051 3.1089345 4.9357863 -2.5662256 0.14112613
81 9000 27.853918 -0.7913741 0.79503268 4.2177256 4.146792 -2.00475 0.090585666
82 10000 27.13754 -0.80551128 1.1325023 4.4718283 5.2460631 -3.4947725 0.11893125
83 11000 28.277434 -1.4897448 0.90075953 4.1895717 4.3594269 -1.9553119 0.090222212
84 12000 28.630973 -1.222206 0.67796385 3.3905661 4.9691334 -2.9052721 0.13897658
85 13000 28.593007 -0.95684026 0.75585196 3.7242568 4.7417932 -2.3893117 0.2074121
86 14000 26.147115 -0.6026921 0.93591488 5.1292829 4.9821952 -2.2571835 0.11872421
87 15000 26.29432 -0.82424162 1.048979 4.5569495 5.1189308 -2.9750422 0.16195676
88 16000 29.189992 -0.80998247 0.74093508 3.8299275 4.4536688 -2.5497538 0.19155639
89 17000 25.878012 -0.3519646 1.0988924 4.7359591 5.3923098 -2.7211029 0.13405223
90 18000 27.726135 -0.28229987 0.63072344 4.1777888 4.7237271 -2.2177157 0.15939372
91 19000 27.153504 -0.66477422 0.77910129 4.2036117 5.113851 -2.3494315 0.094793307
92 20000 28.044833 -1.2835827 0.88745367 3.9955526 4.5077788 -3.0116467 0.17197859
93 21000 27.205696 -0.74090037 1.0023251 4.3421733 4.912671 -2.3473271 0.26089356
94 22000 27.385785 -0.93740972 0.84554838 4.562743 4.883866 -2.2110955 0.11573301
95 23000 27.05534 -0.95605442 0.96719024 3.9277618 5.0359014 -2.6135949 0.21368061
96 24000 28.273378 -0.97543103 0.8983443 4.2067985 4.4782971 -2.4230505 0.30311692
97 25000 27.477789 -0.20383849 0.8380706 3.8037992 4.8312504 -2.5831791 0.093843746
98 26000 30.344199 -1.9773473 0.92882437 3.7821405 4.5176677 -2.3020968 0.2194307
99 27000 27.32767 -0.9803839 0.92988865 3.7611603 5.0328211 -2.4647656 0.18213622
100 28000 27.34208 -1.037938 0.74488346 4.1727342 4.7056812 -2.2718346 0.17741362
101 29000 27.682777 -0.51006495 0.57074224 4.7332237 4.7080462 -2.0491512 0.2130517
102 30000 24.925731 0.13670248 0.84976065 4.4143762 6.0677158 -3.5479173 0.28059419
103 31000 28.623419 -0.90725708 1.0710501 3.6930688 4.6639301 -2.2225373 0.20988139
104 32000 27.732286 -1.1948367 0.89230134 4.4398373 4.8923907 -3.5849327 0.49167488
105 33000 28.800772 -1.5319589 0.93455495 4.1634728 4.6107706 -2.3503486 0.22636535
106 34000 27.374398 -1.0957453 0.89450276 3.9829508 4.991786 -2.3548834 0.15869465
107 35000 28.38753 -0.89261166 0.90000776 3.536864 4.4293294 -2.4218118 0.10640557
108 36000 27.713974 0.088038031 0.85190574 3.8969601 4.6256355 -2.7935475 0.34671662
109 37000 29.13007 -1.378597 0.74412556 3.131538 4.6458653 -2.9373734 0.38035616
110 38000 28.556573 -1.4055344 1.139984 4.0035753 4.2938358 -2.489329 0.25338326
111 39000 26.447036 -1.1829705 0.87032438 5.0804461 4.5772023 -2.7346466 0.32165802
112 40000 27.991454 -0.64295679 0.61020872 4.165871 4.4623087 -2.2244194 0.13826991
113 41000 29.483296 -1.2400745 0.66926627 3.3473666 4.5766617 -2.3051145 0.12171554
114 42000 26.948627 -1.2162288 1.1440628 4.3993073 5.1176533 -2.4734485 0.15497709
115 43000 28.04459 -0.26543193 0.83647367 3.5160747 4.6964397 -2.2805068 0.12618821
116 44000 28.213608 -1.216128 0.9132792 4.0206483 4.9483599 -2.3387049 0.10132022
117 45000 28.283506 -1.0390766 0.86113772 4.504509 4.7209088 -2.3043085 0.14588362
118 46000 27.433853 -0.57912107 0.78448334 4.5998579 5.1181394 -2.6165094 0.18722528
119 47000 27.552939 -1.1128925 0.80087638 4.3448001 4.8062869 -2.4296883 0.2702479
120 48000 28.874034 -1.3242519 0.71770727 3.5648565 4.4671824 -2.2608958 0.16115978
121 49000 29.216186 -1.2210307 0.76937497 3.9260628 4.7550577 -2.7316081 0.085505664
122 50000 28.065856 -1.1545547 0.86953819 4.4137666 4.732157 -2.4450867 0.23320539
123 51000 26.308975 -0.99728352 0.90408444 4.2400186 5.6340425 -2.2090554 0.079882158
124 52000 28.517571 -1.5027398 0.83520278 3.8176552 4.3001251 -2.0731682 0.1665375
125 53000 28.77579 -1.3564268 0.97253881 3.6866407 4.8532347 -2.5330776 0.17668411
126 54000 29.135315 -1.0994106 0.67605671 3.6819254 4.3134408 -1.9796929 0.076951331
127 55000 26.168938 -0.76247492 0.88784685 4.6533473 6.0484793 -2.1334561 0.036876985
128 56000 27.471775 -0.68648837 1.0576168 4.0354311 4.4767052 -2.2368959 0.24950568
129 57000 29.787083 -1.4914384 1.0702944 3.5388133 4.5173097 -2.6694464 0.27937092
130 58000 28.705448 -1.3016617 0.63337853 3.9552713 4.4119825 -1.8774657 0.17540021
131 59000 29.130155 -0.91647363 0.84384883 3.1076903 4.5346348 -2.3457338 0.16674486
132 60000 26.874199 -0.81598034 1.3432151 5.1322624 4.9545484 -2.9566615 0.25950486
133 61000 27.401306 -0.82895856 1.1636949 4.020154 4.5745928 -2.601466 0.18061051
134 62000 28.930313 -1.5231967 0.85173243 4.3517328 4.4878662 -2.5859205 0.1755493
135 63000 26.56874 0.026147233 0.60836216 4.4231618 4.4390677 -2.1721849 0.08594237
136 64000 26.729023 -0.76953985 0.76734633 4.5104288 5.0886456 -2.2118551 0.11339216
137 65000 28.900471 -1.3901477 0.86194657 4.2774976 4.498325 -2.3672362 0.20668335
138 66000 26.884253 -0.21198879 0.98509625 4.0843117 4.4344172 -2.3289416 0.23631017
139 67000 27.210888 -0.84075559 1.0396559 4.7253607 4.4314589 -2.2985702 0.19326507
140 68000 28.042102 -1.1898715 1.053534 3.8748712 4.4358449 -2.3998723 0.2431659
141 69000 28.939141 -1.6968936 0.98155912 4.0460838 5.0075204 -2.5547087 0.28645131
142 70000 27.15577 -0.85202797 1.1469079 4.7645212 4.6133209 -2.3410451 0.086576572
143 71000 25.507417 -0.27780727 0.95157881 4.8759406 4.853401 -2.9598705 0.41011008
144 72000 29.804703 -1.4847015 0.96345767 3.6797304 4.3678377 -2.4594626 0.14480206
145 73000 28.602798 -1.4906143 0.72497266 4.2442974 4.5360598 -2.3621638 0.14385651
146 74000 28.4928 -0.91319873 1.0377472 3.8033127 4.3991601 -2.4051911 0.095567428
147 75000 26.38168 -0.70733237 1.1557817 5.697939 4.5935618 -2.4285007 0.058980519
148 76000 27.16626 -0.83631031 0.84844246 4.7460887 4.5801472 -2.1260014 0.12845946
149 77000 29.040661 -1.3089499 0.80285084 4.664804 4.5215895 -2.6861939 0.13215598
150 78000 27.477871 -1.0600977 0.88595045 4.6264017 5.4095605 -2.474411 0.10987174
151 79000 26.151797 -0.55779685 0.91382436 4.99964 4.9184022 -2.2547241 0.22854038
152 80000 28.14523 -0.54460026 0.8982411 3.5374555 4.3785673 -2.3196807 0.088567964
153 81000 29.029941 -1.6467789 0.79042284 3.7269899 4.7407998 -2.3795824 0.1408727
154 82000 27.920287 -0.72798032 1.0076975 3.4449461 4.5621371 -2.8239074 0.25103454
155 83000 29.131054 -1.114367 0.76887285 3.459639 4.5163922 -2.607825 0.19991648
156 84000 28.249768 -0.69944068 1.0510846 4.0436296 4.6430538 -2.4213355 0.077299966
157 85000 28.06888 -0.62132922 0.91829312 4.1294147 4.3099557 -2.354063 0.15866186
158 86000 28.664264 -1.1022906 0.87831695 4.5773522 4.6045802 -2.9206875 0.33950063
159 87000 27.960967 -1.2852756 0.77694253 3.9011301 4.9114139 -3.2374868 0.3068138
160 88000 27.190678 -1.2803268 1.1545301 4.5769709 5.2404761 -2.3825838 0.10356039
161 89000 26.792931 -0.44516641 1.0236244 4.2007253 4.7098685 -2.3608551 0.034447062
162 90000 27.173991 -0.87185611 1.065719 4.1953618 4.6856408 -2.6539232 0.16957757
163 91000 28.626528 -1.239257 0.89524651 4.7048012 4.6344201 -2.7367901 0.43534143
164 92000 27.661812 -1.109044 0.92817391 5.0294489 4.3890711 -2.4108669 0.12570139
165 93000 28.156793 -1.0820907 0.92812693 4.938385 4.4901426 -2.4023366 0.30135781
166 94000 28.842149 -1.3524969 1.1451109 4.3125908 4.6959035 -2.6747199 0.2254607
167 95000 27.862247 -1.2119045 1.0218976 4.2614082 4.4931316 -2.6902934 0.16345201
168 96000 27.084973 -0.93738328 1.3984324 4.5647189 4.4232205 -2.2834097 0.11217888
169 97000 27.587078 -0.89397255 0.78218462 3.8944421 4.3981479 -2.4205318 0.16570942
170 98000 27.981746 -1.2380545 0.84847869 4.311441 4.7340377 -2.4270441 0.023565612
171 99000 27.476625 -0.8569146 0.82550381 4.1656963 4.4064921 -2.4169708 0.160814
172 100000 26.121325 -0.63610855 1.0803389 4.9257118 4.7073263 -2.4010334 0.066303044
173 Loop time of 2.693 on 4 procs for 100000 steps with 34 atoms
175 Performance: 6416.646 ns/day, 0.004 hours/ns, 37133.367 timesteps/s
176 98.4% CPU use with 4 MPI tasks x no OpenMP threads
178 MPI task timing breakdown:
179 Section | min time | avg time | max time |%varavg| %total
180 ---------------------------------------------------------------
181 Pair | 0.065478 | 0.2501 | 0.63682 | 45.6 | 9.29
182 Bond | 0.066944 | 0.44772 | 0.88814 | 53.7 | 16.63
183 Neigh | 0.0076509 | 0.0077319 | 0.0078275 | 0.1 | 0.29
184 Comm | 0.57917 | 1.4166 | 1.9823 | 46.9 | 52.60
185 Output | 0.0033755 | 0.0035856 | 0.0037644 | 0.2 | 0.13
186 Modify | 0.03866 | 0.1366 | 0.23978 | 24.6 | 5.07
187 Other | | 0.4306 | | | 15.99
189 Nlocal: 8.5 ave 15 max 2 min
190 Histogram: 1 1 0 0 0 0 0 0 1 1
191 Nghost: 25.5 ave 32 max 19 min
192 Histogram: 1 1 0 0 0 0 0 0 1 1
193 Neighs: 98.75 ave 257 max 18 min
194 Histogram: 1 1 1 0 0 0 0 0 0 1
196 Total # of neighbors = 395
197 Ave neighs/atom = 11.6176
198 Ave special neighs/atom = 9.52941
199 Neighbor list builds = 294
200 Dangerous builds = 0
201 Total wall time: 0:00:02