Commit 2f32fb7f authored by Steve Plimpton's avatar Steve Plimpton
Browse files

patch 13Apr17

parent cb867ea9
<!-- HTML_ONLY -->
<HEAD>
<TITLE>LAMMPS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="11 Apr 2017 version">
<META NAME="docnumber" CONTENT="13 Apr 2017 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD>
......@@ -21,7 +21,7 @@
<H1></H1>
LAMMPS Documentation :c,h3
11 Apr 2017 version :c,h4
13 Apr 2017 version :c,h4
Version info: :h4
......
LAMMPS (31 Mar 2017)
# Created by charmm2lammps v1.8.2.6 beta on Thu Mar 3 20:56:57 EST 2016
units real
neigh_modify delay 2 every 1
#newton off
boundary p p p
atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmmfsw
improper_style harmonic
pair_style lj/charmmfsw/coul/charmmfsh 8 12
pair_modify mix arithmetic
fix cmap all cmap charmm22.cmap
Reading potential file charmm22.cmap with DATE: 2016-09-26
fix_modify cmap energy yes
read_data gagg.data fix cmap crossterm CMAP
orthogonal box = (-34.4147 -36.1348 -39.3491) to (45.5853 43.8652 40.6509)
1 by 1 by 1 MPI processor grid
reading atoms ...
34 atoms
scanning bonds ...
4 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
12 = max dihedrals/atom
scanning impropers ...
1 = max impropers/atom
reading bonds ...
33 bonds
reading angles ...
57 angles
reading dihedrals ...
75 dihedrals
reading impropers ...
7 impropers
4 = max # of 1-2 neighbors
7 = max # of 1-3 neighbors
13 = max # of 1-4 neighbors
16 = max # of special neighbors
special_bonds charmm
fix 1 all nve
#fix 1 all nvt temp 300 300 100.0
#fix 2 all shake 1e-9 500 0 m 1.0
velocity all create 0.0 12345678 dist uniform
thermo 1000
thermo_style custom step ecoul evdwl ebond eangle edihed f_cmap eimp
timestep 2.0
run 100000
Neighbor list info ...
update every 1 steps, delay 2 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 12 12 12
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/charmmfsw/coul/charmmfsh, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 14.96 | 14.96 | 14.96 Mbytes
Step E_coul E_vdwl E_bond E_angle E_dihed f_cmap E_impro
0 16.287573 -0.85933785 1.2470497 4.8441789 4.5432816 -1.473352 0.10453023
1000 18.816462 -0.84379243 0.78931817 2.7554247 4.4371421 -2.7762038 0.12697656
2000 18.091571 -1.045888 0.72306589 3.0951524 4.6725102 -2.3580092 0.22712496
3000 17.835596 -1.2171641 0.72666403 2.6696491 5.4373798 -2.0737041 0.075101693
4000 16.211232 -0.42713611 0.99472642 3.8961462 5.2009895 -2.5626866 0.17356243
5000 17.72183 -0.57081189 0.90733068 3.4376382 4.5457582 -2.3727543 0.12354518
6000 18.753977 -1.5772499 0.81468321 2.9236782 4.6033216 -2.3380859 0.12835782
7000 18.186024 -0.84205608 0.58996182 3.0329585 4.7221473 -2.5733243 0.10047631
8000 18.214306 -1.1360938 0.72597611 3.7493028 4.7319958 -2.8957969 0.2006046
9000 17.248408 -0.48641993 0.90266229 2.9721743 4.7651056 -2.1473354 0.1302043
10000 17.760655 -1.2968444 0.92384663 3.7007455 4.7378947 -2.2147779 0.06940579
11000 17.633929 -0.57368413 0.84872849 3.4277114 4.285393 -2.236944 0.17204973
12000 18.305835 -1.0675148 0.75879532 2.8853173 4.685027 -2.409087 0.087538866
13000 17.391558 -0.9975291 0.66671947 3.8065638 5.2285578 -2.4198822 0.06253594
14000 17.483387 -0.67727643 0.91966477 3.7317031 4.7770445 -2.6080027 0.11487095
15000 18.131749 -1.1918751 1.0025684 3.1238131 4.789742 -2.2546745 0.13782813
16000 16.972343 -0.43926531 0.60644597 3.7551592 4.8658618 -2.2627659 0.12353145
17000 18.080785 -1.2073565 0.7867072 3.5671106 4.43754 -2.5092904 0.17429146
18000 17.474576 -0.97836065 0.8678524 3.7961537 4.3409032 -1.8922572 0.134048
19000 17.000911 -1.2286864 0.83615834 3.9322908 4.9319492 -2.3281576 0.056689619
20000 17.043286 -0.8506561 0.80966589 3.5087339 4.8603878 -2.3365263 0.096794824
21000 17.314495 -1.1430889 0.95363892 4.2446032 4.2756745 -2.1829483 0.17119518
22000 18.954881 -0.998673 0.58688334 2.71536 4.6634319 -2.6862804 0.20328442
23000 17.160427 -0.97803282 0.86894041 4.0897736 4.3146238 -2.1962289 0.075339092
24000 17.602026 -1.0833323 0.94888776 3.7341878 4.3084335 -2.1640414 0.081493681
25000 17.845584 -1.3432612 0.93497086 3.8911043 4.468032 -2.3475883 0.093204333
26000 17.833261 -1.1020534 0.77931087 3.7628141 4.512381 -2.3134761 0.15568465
27000 17.68607 -1.3222026 1.1985872 3.5817624 4.6360755 -2.3492774 0.08427906
28000 18.326649 -1.2669291 0.74809075 3.2624429 4.4698564 -2.3679076 0.14677293
29000 17.720933 -1.0773886 0.83099482 3.7652834 4.6584594 -2.8255303 0.23092596
30000 18.201999 -1.0168706 1.0637455 3.453095 4.3738593 -2.8063214 0.18658217
31000 17.823502 -1.2685768 0.84805585 3.8600661 4.2195821 -2.1169716 0.12517101
32000 16.883133 -0.62062648 0.84434922 3.5042683 5.1264906 -2.2674699 0.030138165
33000 17.805715 -1.679553 1.2430372 4.314677 4.2523894 -2.3008321 0.18591872
34000 16.723767 -0.54189072 1.1282827 3.8542159 4.3026559 -2.2186336 0.05392425
35000 17.976909 -0.72092075 0.5876319 2.9726396 5.0881439 -2.491692 0.17356291
36000 18.782492 -1.514246 0.63237955 3.2777164 4.6077164 -2.502574 0.082537318
37000 17.247716 -0.6344626 0.79885976 3.452491 4.7618281 -2.3902444 0.11450271
38000 17.996494 -1.6712877 1.0111769 4.1689136 4.46963 -2.4076725 0.11875756
39000 17.586857 -0.74508086 0.95970486 3.7395038 4.6011357 -2.9854953 0.30143284
40000 17.494879 -0.30772446 0.72047991 3.2604877 4.7283734 -2.3812495 0.16399034
41000 15.855772 -0.49642605 0.82496448 4.5139653 4.76884 -2.214141 0.10899661
42000 17.898568 -1.3078863 1.1505144 4.0429873 4.3889581 -2.8696559 0.23336417
43000 19.014372 -1.6325979 1.1553166 3.5660772 4.4047997 -2.9302044 0.13672127
44000 18.250782 -0.97211613 0.72714301 3.2258362 4.7257298 -2.5533613 0.11968073
45000 17.335174 0.24746331 1.0415866 3.3220992 4.5251095 -3.0415216 0.24453084
46000 17.72846 -0.9541418 0.88153841 3.7893452 4.5251883 -2.4003613 0.051809816
47000 18.226762 -0.67057787 0.84352989 3.0609522 4.5449078 -2.4694254 0.073703949
48000 17.838074 -0.88768441 1.3812262 3.5890492 4.5827868 -3.0137515 0.21417113
49000 17.973733 -0.75118705 0.69667886 3.3989025 4.7058886 -2.8243945 0.26665792
50000 17.461583 -0.65040016 0.68943524 2.9374743 5.6971777 -2.4438011 0.1697603
51000 16.79766 -0.010684434 0.89795555 3.959039 4.56763 -2.5101098 0.15048853
52000 17.566543 -0.7262764 0.74354418 3.3423185 4.8426523 -2.4187649 0.16908776
53000 17.964274 -0.9270914 1.065952 3.0397181 4.4682262 -2.2179503 0.07873406
54000 17.941256 -0.5807578 0.76516121 3.7262371 4.6975126 -3.179899 0.24433708
55000 17.079478 -0.48559832 0.95364453 3.0414645 5.2811414 -2.7064882 0.30102814
56000 17.632179 -0.75403299 0.97577942 3.3672363 4.4851336 -2.3683659 0.051117638
57000 16.17128 -0.44699325 0.76341543 4.267716 5.0881056 -2.4122329 0.16671692
58000 16.899276 -0.76481024 1.0400825 3.973493 4.8823309 -2.4270284 0.048716383
59000 18.145412 -0.84968335 0.71698306 3.2024358 4.6115739 -2.2520353 0.19466966
60000 17.578258 -1.0067331 0.72822527 3.5375208 4.9110255 -2.2319607 0.11922362
61000 17.434762 -1.0244393 0.90593099 3.8446915 4.8571191 -2.6228357 0.23259208
62000 17.580489 -1.1135917 0.79577432 3.7043524 4.6058114 -2.351492 0.042904152
63000 18.207335 -1.1512268 0.82684507 3.4114738 4.351069 -2.1878441 0.082922105
64000 18.333083 -1.1182287 0.74058959 3.6905164 4.3226172 -2.7110393 0.14721704
65000 16.271579 -0.7122151 1.0200168 4.6983643 4.3681131 -2.194921 0.12831024
66000 17.316444 -0.5729385 0.85254108 3.5769963 4.5526705 -2.3321328 0.040452643
67000 17.19011 -0.8814312 1.1381258 3.8605789 4.4183813 -2.299607 0.091527355
68000 18.223367 -1.362189 0.74472056 3.259165 4.486512 -2.2181134 0.048952796
69000 17.646348 -0.91647162 0.73990335 3.9313692 5.2663097 -3.3816778 0.27769877
70000 18.173493 -1.3107718 0.96484426 3.219728 4.5045124 -2.3349534 0.082327407
71000 17.0627 -0.58509083 0.85964129 3.8490884 4.437895 -2.1673348 0.24151404
72000 17.809764 -0.35128902 0.65479258 3.3945008 4.6160508 -2.5486166 0.10829531
73000 18.27769 -1.0739758 0.80890957 3.6070901 4.6256762 -2.4576547 0.080025736
74000 18.109437 -1.0691837 0.66679323 3.5923203 4.4825716 -2.5048169 0.21372319
75000 17.914569 -1.3500765 1.2993494 3.362421 4.4160377 -2.1278163 0.19397641
76000 16.563928 -0.16539261 1.0067302 3.5742755 4.8581915 -2.1362429 0.059822408
77000 18.130477 -0.38361279 0.43406954 3.4725995 4.7005855 -2.8836242 0.11958174
78000 16.746204 -1.1732959 0.7455507 3.6296638 5.6344113 -2.459208 0.16099803
79000 18.243999 -1.5850155 1.0108545 3.4727867 4.3367411 -2.316686 0.070480814
80000 16.960715 -0.84100929 0.91604996 3.862215 4.780949 -2.3711596 0.073916605
81000 17.697722 -1.1126605 0.952804 3.7114455 4.4216316 -2.2770085 0.091372066
82000 17.835901 -1.3091474 0.71867629 3.8168122 5.0150205 -2.4730634 0.062592852
83000 19.168418 -1.476938 0.75592316 3.2304519 4.3946471 -2.2991395 0.13083324
84000 17.945778 -1.5223622 1.0859941 3.4334011 5.0286682 -2.7550892 0.2476269
85000 17.950251 -0.85843846 0.86888218 3.3101287 4.5511879 -2.3640013 0.12080834
86000 17.480699 -0.97493649 0.85049761 3.4973085 4.6344922 -2.343121 0.2009677
87000 17.980244 -1.114983 0.88796989 3.4113329 4.3535853 -2.2535412 0.14494917
88000 18.023866 -1.226683 0.62339706 3.7649269 4.5923973 -2.3923523 0.10464375
89000 16.362829 -0.311462 1.0265375 4.0101723 4.4184777 -2.0314129 0.056570704
90000 17.533149 -0.41526788 1.0362029 3.4247412 4.2734431 -2.4776658 0.16960663
91000 17.719099 -1.1956801 1.0069945 3.2380672 4.8982805 -2.2154906 0.12950936
92000 17.762654 -1.170027 0.95814525 3.5217717 4.5405343 -2.5983677 0.15037754
93000 17.393958 -0.45641026 0.6579069 3.6002204 4.5942053 -2.5559641 0.12026544
94000 16.8182 -0.92962066 0.86801362 4.2914398 4.659848 -2.5251987 0.18000415
95000 17.642086 -0.7994896 0.7003756 3.8036697 4.5252487 -2.4166307 0.15686517
96000 18.114292 -1.5102104 1.2635908 3.2764427 5.0659496 -2.2777806 0.054309645
97000 18.575765 -1.6015311 0.69500699 3.1649317 4.9945742 -2.4012125 0.067373724
98000 16.578893 -0.78030229 0.91524222 4.4429655 4.4622392 -2.4052655 0.15355705
99000 17.26063 -0.57832833 0.7098846 3.9000046 4.5576484 -2.5333026 0.25517222
100000 18.377235 -0.89109577 0.68988617 2.8751751 4.4115591 -2.3560731 0.12185212
Loop time of 2.96043 on 1 procs for 100000 steps with 34 atoms
Performance: 5836.990 ns/day, 0.004 hours/ns, 33778.875 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.074 | 1.074 | 1.074 | 0.0 | 36.28
Bond | 1.6497 | 1.6497 | 1.6497 | 0.0 | 55.72
Neigh | 0.007576 | 0.007576 | 0.007576 | 0.0 | 0.26
Comm | 0.012847 | 0.012847 | 0.012847 | 0.0 | 0.43
Output | 0.0010746 | 0.0010746 | 0.0010746 | 0.0 | 0.04
Modify | 0.16485 | 0.16485 | 0.16485 | 0.0 | 5.57
Other | | 0.05037 | | | 1.70
Nlocal: 34 ave 34 max 34 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 395 ave 395 max 395 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 395
Ave neighs/atom = 11.6176
Ave special neighs/atom = 9.52941
Neighbor list builds = 253
Dangerous builds = 0
Total wall time: 0:00:02
LAMMPS (31 Mar 2017)
# Created by charmm2lammps v1.8.2.6 beta on Thu Mar 3 20:56:57 EST 2016
units real
neigh_modify delay 2 every 1
#newton off
boundary p p p
atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmmfsw
improper_style harmonic
pair_style lj/charmmfsw/coul/charmmfsh 8 12
pair_modify mix arithmetic
fix cmap all cmap charmm22.cmap
Reading potential file charmm22.cmap with DATE: 2016-09-26
fix_modify cmap energy yes
read_data gagg.data fix cmap crossterm CMAP
orthogonal box = (-34.4147 -36.1348 -39.3491) to (45.5853 43.8652 40.6509)
1 by 2 by 2 MPI processor grid
reading atoms ...
34 atoms
scanning bonds ...
4 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
12 = max dihedrals/atom
scanning impropers ...
1 = max impropers/atom
reading bonds ...
33 bonds
reading angles ...
57 angles
reading dihedrals ...
75 dihedrals
reading impropers ...
7 impropers
4 = max # of 1-2 neighbors
7 = max # of 1-3 neighbors
13 = max # of 1-4 neighbors
16 = max # of special neighbors
special_bonds charmm
fix 1 all nve
#fix 1 all nvt temp 300 300 100.0
#fix 2 all shake 1e-9 500 0 m 1.0
velocity all create 0.0 12345678 dist uniform
thermo 1000
thermo_style custom step ecoul evdwl ebond eangle edihed f_cmap eimp
timestep 2.0
run 100000
Neighbor list info ...
update every 1 steps, delay 2 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 12 12 12
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/charmmfsw/coul/charmmfsh, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 14.94 | 15.57 | 16.2 Mbytes
Step E_coul E_vdwl E_bond E_angle E_dihed f_cmap E_impro
0 16.287573 -0.85933785 1.2470497 4.8441789 4.5432816 -1.473352 0.10453023
1000 18.816462 -0.84379243 0.78931817 2.7554247 4.4371421 -2.7762038 0.12697656
2000 18.091571 -1.045888 0.72306589 3.0951524 4.6725102 -2.3580092 0.22712496
3000 17.835596 -1.2171641 0.72666403 2.6696491 5.4373798 -2.0737041 0.075101693
4000 16.211232 -0.42713611 0.99472642 3.8961462 5.2009895 -2.5626866 0.17356243
5000 17.72183 -0.57081189 0.90733068 3.4376382 4.5457582 -2.3727543 0.12354518
6000 18.753977 -1.5772499 0.81468321 2.9236782 4.6033216 -2.3380859 0.12835782
7000 18.186024 -0.84205609 0.58996181 3.0329584 4.7221473 -2.5733244 0.10047631
8000 18.214306 -1.1360934 0.72597583 3.7493032 4.7319959 -2.8957975 0.20060467
9000 17.248415 -0.48642024 0.90266262 2.9721744 4.7651003 -2.1473349 0.13020438
10000 17.760663 -1.2968458 0.92384687 3.7007432 4.7378917 -2.2147799 0.06940514
11000 17.63395 -0.57366075 0.84871737 3.4276851 4.2853865 -2.2369491 0.17205075
12000 18.305713 -1.0672299 0.75876262 2.8852171 4.6850229 -2.4090072 0.087568888
13000 17.383367 -0.99678627 0.66712651 3.8060954 5.233865 -2.4180629 0.062014239
14000 17.510901 -0.68723297 0.92448551 3.7550867 4.7321218 -2.6059088 0.11504409
15000 18.080165 -1.13316 0.99982253 3.09947 4.8171402 -2.2713372 0.14580371
16000 17.383245 -0.4535296 0.57826268 3.6453593 4.6541138 -2.2434512 0.13285609
17000 17.111153 -0.3414839 0.73667584 3.7485311 4.6262965 -2.6166049 0.12635815
18000 16.862046 -1.3592061 1.2371142 4.4878937 4.2937117 -2.2112584 0.066145125
19000 18.313891 -1.654238 0.90644101 3.3934089 4.550735 -2.1862171 0.081267736
20000 19.083561 -1.3081747 0.56257812 2.7633848 4.6211438 -2.5196707 0.13763071
21000 18.23741 -1.051353 0.64408722 3.1735565 4.6912533 -2.2491947 0.099394904
22000 17.914515 -0.89769621 0.61793801 3.1224992 4.8683543 -2.282475 0.14524537
23000 16.756122 -0.98277883 1.2554905 3.7916115 4.7301443 -2.3094994 0.10226772
24000 16.109857 -0.54593177 0.86934462 4.4293574 4.926985 -2.2652264 0.11414331
25000 18.590559 -1.497327 1.1898361 2.9134403 4.7854107 -2.4437918 0.067416154
26000 18.493391 -1.0533797 0.4889578 3.6563013 4.6171721 -2.3240835 0.11607829
27000 18.646522 -1.1229601 0.67956815 2.7937638 4.8991207 -2.4068997 0.10109147
28000 18.545103 -1.7237438 0.72488022 3.8041665 4.6459974 -2.4339333 0.21943258
29000 17.840505 -1.0909667 0.88133248 3.3698456 5.0311644 -2.5116617 0.08102693
30000 17.649527 -0.65409177 0.86781692 3.24112 4.9903073 -2.6234925 0.14799777
31000 18.156812 -0.77476556 0.83192789 2.9620784 4.9160635 -2.8571635 0.22283201
32000 18.251583 -1.3384075 0.8059007 3.2588176 4.4365328 -2.1875071 0.087883637
33000 17.702785 -0.88311587 0.98573641 3.4645713 4.2650091 -2.0909158 0.14233004
34000 17.123413 -1.4873429 1.0419563 4.2628178 4.6318762 -2.2292095 0.105354
35000 18.162061 -1.0136007 0.82436129 3.6365024 4.5801677 -2.6856989 0.28648222
36000 17.65618 -1.094718 0.8872444 3.5075241 4.6382423 -2.3895134 0.18116961
37000 17.336475 -1.0657995 0.98869254 3.9252927 4.4383632 -2.2048244 0.22285949
38000 17.369467 -0.97623132 0.6712095 4.1349304 4.597754 -2.4088341 0.14608514
39000 18.170206 -1.2344285 0.77546195 3.6451049 4.7482287 -2.9895286 0.25768859
40000 16.210866 -0.81407781 0.99246271 4.2676233 5.0253763 -2.2929865 0.13348624
41000 17.641798 -1.0868157 0.80119513 3.4302526 5.280872 -2.4025406 0.22747391
42000 18.349848 -1.613759 1.1497004 3.7800682 4.3237683 -2.8676401 0.2120425
43000 19.130245 -1.196778 0.71845659 2.9325758 4.3684415 -2.433424 0.12240982
44000 18.061321 -1.2410101 1.0329373 3.0751569 4.7138313 -2.2880904 0.075814461
45000 18.162713 -1.4414622 1.009159 4.2298758 4.589593 -2.8502298 0.21606844
46000 18.591574 -0.99730412 1.0955215 3.3965004 4.359466 -3.1049731 0.17322629
47000 18.380259 -1.2717381 0.72291269 3.3958016 4.6099628 -2.4605065 0.19825185
48000 18.130478 -1.5051279 1.2087492 3.2488529 4.6690881 -2.2518174 0.05633061
49000 16.419912 -0.89320635 0.98926144 4.0388252 4.9919488 -2.1699511 0.15646479
50000 16.453196 -1.0433497 0.778346 4.6078069 4.7320614 -2.3760788 0.17161976
51000 18.245221 -0.89550444 0.9310446 3.0758194 4.3944595 -2.3082379 0.19983428
52000 17.839632 -1.0221781 0.76425017 3.3331547 4.5368437 -2.0988773 0.21098435
53000 18.693035 -1.4231915 0.76333082 3.1612761 4.583242 -2.4485762 0.089191206
54000 16.334672 -0.36309884 1.0200365 4.6700448 4.1628702 -2.1713841 0.11431995
55000 17.33842 -0.61522682 0.89847366 3.4970659 4.673495 -2.4743036 0.068004878
56000 17.790294 -1.0150845 0.73697112 3.6000297 4.5988343 -2.4822509 0.11434632
57000 18.913486 -1.0985507 1.0231848 2.7483267 4.4421755 -2.574424 0.1763388
58000 17.586896 -0.98284126 0.96965633 3.3330357 4.5325543 -2.1936869 0.083230915
59000 17.77788 -1.1649953 0.83092298 3.8004148 4.3940176 -2.3136642 0.017207608
60000 17.013042 -0.21728023 1.1688832 3.5374476 4.5462244 -2.4425301 0.15028297
61000 17.236242 -1.1342147 1.0301086 3.685948 4.6842331 -2.328108 0.070210812
62000 17.529852 -1.2961547 1.0323133 3.4474598 5.1435839 -2.4553423 0.060842687
63000 18.754704 -1.1816999 0.51806039 3.140172 4.5832701 -2.2713213 0.06327871
64000 17.54594 -1.3592836 0.9694558 4.1363258 4.3547729 -2.3818433 0.12634448
65000 16.962312 -0.54192775 0.90321315 4.0788618 4.2008255 -2.1376711 0.039504515
66000 18.078619 -1.3552947 1.0716861 3.3285374 4.7229362 -2.3331115 0.21978698
67000 17.132732 -1.4376876 0.91486534 4.4461852 4.6894176 -2.3655045 0.068150385
68000 18.69286 -1.2856207 0.3895394 3.0620063 4.9922992 -2.3459189 0.079879643
69000 18.329552 -1.1545957 0.88632275 3.1741058 4.4562418 -2.7094867 0.25329613
70000 16.681168 -0.94434373 1.2450393 4.5737944 4.4902996 -2.4581775 0.15313095
71000 17.375032 -1.0514442 1.0741595 3.4896146 4.8407713 -2.5302576 0.13640847
72000 17.833013 -0.9047134 0.87067876 3.1658924 4.8825932 -2.4398117 0.2343991
73000 17.421411 -1.2190741 0.73706811 4.2895 4.6464636 -2.3872727 0.19696525
74000 17.383158 -0.34208984 0.71333984 3.2718891 4.2718495 -2.2484281 0.10827022
75000 17.20885 -1.2710479 1.125102 3.8414467 5.3222741 -2.375505 0.12910797
76000 16.811578 -0.545162 0.59076961 3.9118604 4.8031296 -2.2777895 0.063015508
77000 16.679231 -0.080955983 0.7253398 3.4203454 5.0987608 -2.379614 0.12961874
78000 18.164524 -1.3115525 0.92526408 3.5764487 4.3814882 -2.3712488 0.073436724
79000 17.738686 -1.0697859 1.2186866 3.0593848 4.6551053 -2.2505871 0.075340661
80000 16.767483 -0.84777477 1.03128 4.1982958 4.6992227 -2.4146425 0.079774219
81000 16.257265 0.62803774 0.84032194 3.3873471 5.0961071 -2.7219776 0.20467848
82000 18.232082 -1.2129302 0.50746051 3.9207128 4.5073437 -2.599371 0.094522372
83000 16.618985 -0.60917055 0.8825847 3.805497 4.9560959 -2.2194726 0.14852687
84000 17.90762 -0.82336075 0.90504161 3.0324198 4.7444271 -2.5036073 0.15860682
85000 16.699883 -0.50297228 0.83405307 3.8598996 4.7971968 -2.2427788 0.10338668
86000 16.353038 -0.0096880616 0.80705167 4.0865115 4.5364338 -2.4548873 0.098456203
87000 17.887331 -0.75281219 1.0030148 4.0117123 4.3443074 -2.9774392 0.16190152
88000 18.583708 -1.4867053 0.86324814 3.3971237 4.3526221 -2.221239 0.14459352
89000 17.684828 -1.283764 1.0021118 3.5426808 4.9057005 -2.3921967 0.05844702
90000 17.2597 -0.84306489 0.99797936 3.8896866 4.4315457 -2.5662899 0.18270206
91000 16.705581 -0.44704047 0.75239556 3.470805 4.976868 -2.1894571 0.12312848
92000 17.548071 -1.2222664 0.92898812 4.0813773 4.3432647 -2.1631158 0.14071343
93000 17.163675 -0.94994776 0.96876981 3.9137692 4.4388666 -2.1260232 0.13187968
94000 18.842071 -1.2822113 0.58767049 3.1393475 4.5820965 -2.7264682 0.10406266
95000 18.112287 -1.1011381 0.63546648 3.4672667 4.486275 -2.2991936 0.041589685
96000 17.102713 -0.6877313 0.8389032 3.6892719 4.5676004 -2.1905327 0.13507011
97000 16.778253 -1.2902153 1.1588744 4.2820083 4.9537657 -2.4798159 0.35696636
98000 18.34638 -1.2908146 1.185356 3.0739807 4.4575453 -2.3959144 0.22407922
99000 17.995148 -1.3939639 0.7727299 3.8774144 4.4345458 -2.1142776 0.13550099
100000 18.444746 -1.2456693 0.86061526 3.468696 4.5264336 -2.4239851 0.074369539
Loop time of 2.52011 on 4 procs for 100000 steps with 34 atoms
Performance: 6856.851 ns/day, 0.004 hours/ns, 39680.850 timesteps/s
98.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.072506 | 0.28131 | 0.69088 | 46.2 | 11.16
Bond | 0.050544 | 0.45307 | 0.9416 | 57.6 | 17.98
Neigh | 0.0060885 | 0.0061619 | 0.0062056 | 0.1 | 0.24
Comm | 0.44686 | 1.3679 | 2.0111 | 53.5 | 54.28
Output | 0.0028057 | 0.0029956 | 0.003264 | 0.3 | 0.12
Modify | 0.028202 | 0.095174 | 0.15782 | 19.8 | 3.78
Other | | 0.3135 | | | 12.44
Nlocal: 8.5 ave 14 max 2 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Nghost: 25.5 ave 32 max 20 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Neighs: 98.75 ave 242 max 31 min
Histogram: 2 0 1 0 0 0 0 0 0 1
Total # of neighbors = 395
Ave neighs/atom = 11.6176
Ave special neighs/atom = 9.52941
Neighbor list builds = 246
Dangerous builds = 0
Total wall time: 0:00:02
......@@ -64,14 +64,17 @@ VerletKokkos::VerletKokkos(LAMMPS *lmp, int narg, char **arg) :
setup before run
------------------------------------------------------------------------- */
void VerletKokkos::setup()
void VerletKokkos::setup(int flag)
{
if (comm->me == 0 && screen) {
fprintf(screen,"Setting up Verlet run ...\n");
fprintf(screen," Unit style : %s\n", update->unit_style);
fprintf(screen," Current step : " BIGINT_FORMAT "\n", update->ntimestep);
fprintf(screen," Time step : %g\n", update->dt);
timer->print_timeout(screen);
if (flag) {
fprintf(screen," Unit style : %s\n", update->unit_style);
fprintf(screen," Current step : " BIGINT_FORMAT "\n",
update->ntimestep);
fprintf(screen," Time step : %g\n", update->dt);
timer->print_timeout(screen);
}
}
update->setupflag = 1;
......@@ -169,7 +172,7 @@ void VerletKokkos::setup()
if (force->newton) comm->reverse_comm();
modify->setup(vflag);
output->setup();
output->setup(flag);
lmp->kokkos->auto_sync = 1;
update->setupflag = 1;
}
......
......@@ -29,7 +29,7 @@ class VerletKokkos : public Verlet {
public:
VerletKokkos(class LAMMPS *, int, char **);
~VerletKokkos() {}
void setup();
void setup(int flag=1);
void setup_minimal(int);
void run(int);
......
......@@ -260,7 +260,7 @@ void FixGCMC::options(int narg, char **arg)
grouptypebits = NULL;
energy_intra = 0.0;
tfac_insert = 1.0;
overlap_cutoff = 0.0;
overlap_cutoffsq = 0.0;
overlap_flag = 0;
int iarg = 0;
......@@ -366,7 +366,8 @@ void FixGCMC::options(int narg, char **arg)
iarg += 2;
} else if (strcmp(arg[iarg],"overlap_cutoff") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix gcmc command");
overlap_cutoff = force->numeric(FLERR,arg[iarg+1]);
double rtmp = force->numeric(FLERR,arg[iarg+1]);
overlap_cutoffsq = rtmp*rtmp;
overlap_flag = 1;
iarg += 2;
} else error->all(FLERR,"Illegal fix gcmc command");
......@@ -2146,7 +2147,7 @@ double FixGCMC::energy(int i, int itype, tagint imolecule, double *coord)
// if overlap check requested, if overlap,
// return signal value for energy
if (overlap_flag && rsq < overlap_cutoff)
if (overlap_flag && rsq < overlap_cutoffsq)
return MAXENERGYSIGNAL;
if (rsq < cutsq[itype][jtype])
......@@ -2216,7 +2217,7 @@ double FixGCMC::energy_full()
delz = x[i][2] - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < overlap_cutoff) {
if (rsq < overlap_cutoffsq) {
overlaptest = 1;
break;
}
......
......@@ -112,7 +112,7 @@ class FixGCMC : public Fix {
double **cutsq;
double **atom_coord;
imageint imagezero;
double overlap_cutoff;
double overlap_cutoffsq; // square distance cutoff for overlap
int overlap_flag;
double energy_intra;
......
#define LAMMPS_VERSION "11 Apr 2017"
#define LAMMPS_VERSION "13 Apr 2017"
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