Updated tests and documentation, added warning message
This commit is contained in:
Oliver Henrich
@ -86,12 +86,11 @@ commands:
|
||||
|
||||
.. warning::
|
||||
|
||||
LAMMPS has per se no concept of bond directionality. This means the bond definition
|
||||
(i.e. the sequence of atom IDs) in data files produced with :doc:`write_data <write_data>`
|
||||
can be different from the one provided in your initial data file. If this is the case,
|
||||
then the correct 3' to 5' polarity needs to be restored before using the data file.
|
||||
This limitation does not apply to binary restart files produced with
|
||||
:doc:`write_restart <write_restart>`.
|
||||
If data files are produced with :doc:`write_data <write_data>`, then the
|
||||
:doc:`newton <newton>` command should be set to *newton on* or *newton off on*.
|
||||
Otherwise the data files will not have the same 3' to 5' polarity as the
|
||||
initial data file. This limitation does not apply to binary restart files
|
||||
produced with :doc:`write_restart <write_restart>`.
|
||||
|
||||
Example input and data files for DNA and RNA duplexes can be found in
|
||||
examples/PACKAGES/cgdna/examples/oxDNA/ , /oxDNA2/ and /oxRNA2/. A simple python
|
||||
|
||||
@ -72,6 +72,14 @@ between two individual nucleotides can be established.
|
||||
|
||||
/******************************************************************************/
|
||||
|
||||
/examples/oxDNA2/dsring:
|
||||
|
||||
This example uses a dsDNA ring of 74 base pairs. The bonds which close the ring
|
||||
are (in 3' to 5' direction) between nucleotide 74 and 1 and between nucleotide
|
||||
148 and 75, respectively.
|
||||
|
||||
/******************************************************************************/
|
||||
|
||||
/examples/oxRNA2/duplex2
|
||||
|
||||
This example uses the duplex2 with the oxRNA2 force field instead of oxDNA or
|
||||
|
||||
@ -7,7 +7,7 @@ units lj
|
||||
|
||||
dimension 3
|
||||
|
||||
newton off
|
||||
newton on
|
||||
|
||||
boundary p p p
|
||||
|
||||
@ -67,3 +67,4 @@ dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22
|
||||
run 1000000
|
||||
|
||||
write_data last_config.${number}.* nocoeff
|
||||
#write_restart last_config.${number}.*
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
@ -7,7 +7,7 @@ units lj
|
||||
|
||||
dimension 3
|
||||
|
||||
newton off
|
||||
newton on
|
||||
|
||||
boundary p p p
|
||||
|
||||
@ -67,3 +67,4 @@ dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22
|
||||
run 1000000
|
||||
|
||||
write_data last_config.${number}.* nocoeff
|
||||
#write_restart last_config.${number}.*
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
@ -8,7 +8,7 @@ units lj
|
||||
|
||||
dimension 3
|
||||
|
||||
newton off
|
||||
newton on
|
||||
|
||||
boundary p p p
|
||||
|
||||
@ -68,5 +68,5 @@ dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22
|
||||
|
||||
run 100000
|
||||
|
||||
#write_data last_config.${number}.* nocoeff
|
||||
write_data last_config.${number}.* nocoeff
|
||||
#write_restart last_config.${number}.*
|
||||
|
||||
@ -9,7 +9,7 @@ units lj
|
||||
|
||||
dimension 3
|
||||
|
||||
newton off
|
||||
newton on
|
||||
|
||||
boundary p p p
|
||||
|
||||
@ -30,7 +30,7 @@ Reading data file ...
|
||||
reading velocities ...
|
||||
148 velocities
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
1 = max bonds/atom
|
||||
148 ellipsoids
|
||||
reading bonds ...
|
||||
148 bonds
|
||||
@ -115,151 +115,151 @@ Neighbor list info ...
|
||||
binsize = 2.8194939, bins = 36 36 36
|
||||
5 neighbor lists, perpetual/occasional/extra = 5 0 0
|
||||
(1) pair oxdna2/excv, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: full/bin/3d
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
(2) pair oxdna2/hbond, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
attributes: half, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) pair oxdna2/xstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
attributes: half, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(4) pair oxdna2/coaxstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
attributes: half, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(5) pair oxdna2/dh, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
attributes: half, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
WARNING: Communication cutoff adjusted to 5.638987723814632 (../comm.cpp:739)
|
||||
0 ekin = 20.4724634226502 | erot = 21.0406985312466 | epot = -222.283862600785 | etot = -180.770700646889
|
||||
Per MPI rank memory allocation (min/avg/max) = 9.726 | 9.726 | 9.726 Mbytes
|
||||
Per MPI rank memory allocation (min/avg/max) = 9.601 | 9.601 | 9.601 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 0.092845639 -1.5501211 0.04820308 -1.3635905 -9.0052368e-06 1000000
|
||||
1000 ekin = 20.531989141805 | erot = 21.2158633183735 | epot = -222.518553109361 | etot = -180.770700649183
|
||||
2000 ekin = 20.585620972069 | erot = 21.3918594352261 | epot = -222.748181058335 | etot = -180.77070065104
|
||||
2000 ekin = 20.585620972069 | erot = 21.391859435226 | epot = -222.748181058335 | etot = -180.77070065104
|
||||
3000 ekin = 20.6239332104642 | erot = 21.5529389082728 | epot = -222.947572771312 | etot = -180.770700652575
|
||||
4000 ekin = 20.6395549184482 | erot = 21.6854113323895 | epot = -223.095666904229 | etot = -180.770700653391
|
||||
5000 ekin = 20.6295551742564 | erot = 21.7809539301805 | epot = -223.181209757876 | etot = -180.770700653439
|
||||
6000 ekin = 20.5959625511846 | erot = 21.8369756530727 | epot = -223.203638857302 | etot = -180.770700653045
|
||||
7000 ekin = 20.5431034482068 | erot = 21.8556844173875 | epot = -223.169488517717 | etot = -180.770700652122
|
||||
8000 ekin = 20.4774701419091 | erot = 21.8437134145374 | epot = -223.091884207389 | etot = -180.770700650943
|
||||
9000 ekin = 20.4074566554237 | erot = 21.8097283692398 | epot = -222.98788567426 | etot = -180.770700649597
|
||||
10000 ekin = 20.3427303660295 | erot = 21.7629575866663 | epot = -222.876388600949 | etot = -180.770700648253
|
||||
11000 ekin = 20.2927407149576 | erot = 21.7112100845349 | epot = -222.774651446682 | etot = -180.770700647189
|
||||
12000 ekin = 20.2665977502212 | erot = 21.6594999867139 | epot = -222.696798383221 | etot = -180.770700646286
|
||||
13000 ekin = 20.2733920359445 | erot = 21.6092715397933 | epot = -222.653364221616 | etot = -180.770700645878
|
||||
14000 ekin = 20.3196524789068 | erot = 21.5586630974992 | epot = -222.649016222075 | etot = -180.770700645669
|
||||
15000 ekin = 20.4104009374289 | erot = 21.5031572556306 | epot = -222.684258838857 | etot = -180.770700645798
|
||||
16000 ekin = 20.5472869005792 | erot = 21.4346177247041 | epot = -222.752605272036 | etot = -180.770700646753
|
||||
17000 ekin = 20.7266657908773 | erot = 21.3426631585217 | epot = -222.840029597232 | etot = -180.770700647833
|
||||
18000 ekin = 20.9417612759979 | erot = 21.2178611180927 | epot = -222.930323042997 | etot = -180.770700648907
|
||||
19000 ekin = 21.1819308659397 | erot = 21.0532289630294 | epot = -223.00586047892 | etot = -180.770700649951
|
||||
20000 ekin = 21.4358169889474 | erot = 20.8473069564707 | epot = -223.053824595387 | etot = -180.770700649969
|
||||
21000 ekin = 21.6968513750997 | erot = 20.6066744652586 | epot = -223.074226489837 | etot = -180.770700649479
|
||||
22000 ekin = 21.9614458442782 | erot = 20.3429420444511 | epot = -223.07508853737 | etot = -180.770700648641
|
||||
23000 ekin = 22.22760997557 | erot = 20.0703385165243 | epot = -223.068649139875 | etot = -180.770700647781
|
||||
24000 ekin = 22.4935893196671 | erot = 19.8020671721666 | epot = -223.066357139276 | etot = -180.770700647443
|
||||
25000 ekin = 22.7566064548224 | erot = 19.5464828008842 | epot = -223.073789902976 | etot = -180.770700647269
|
||||
26000 ekin = 23.0126717548395 | erot = 19.3065017718468 | epot = -223.089874174572 | etot = -180.770700647886
|
||||
27000 ekin = 23.255041706059 | erot = 19.0797753474573 | epot = -223.105517701933 | etot = -180.770700648417
|
||||
28000 ekin = 23.4774329734801 | erot = 18.864619729958 | epot = -223.112753352067 | etot = -180.770700648629
|
||||
29000 ekin = 23.674792772066 | erot = 18.662865341183 | epot = -223.108358761694 | etot = -180.770700648445
|
||||
30000 ekin = 23.8432321400243 | erot = 18.481221698364 | epot = -223.095154486375 | etot = -180.770700647987
|
||||
31000 ekin = 23.9793041752225 | erot = 18.3307845334023 | epot = -223.08078935577 | etot = -180.770700647145
|
||||
32000 ekin = 24.0810246040231 | erot = 18.2261577056005 | epot = -223.07788295592 | etot = -180.770700646296
|
||||
33000 ekin = 24.1468986449394 | erot = 18.1820705445407 | epot = -223.09966983514 | etot = -180.77070064566
|
||||
34000 ekin = 24.175661513286 | erot = 18.2103812210173 | epot = -223.156743379607 | etot = -180.770700645304
|
||||
35000 ekin = 24.1663193894648 | erot = 18.3185351073568 | epot = -223.25555514209 | etot = -180.770700645268
|
||||
36000 ekin = 24.1167205812961 | erot = 18.5091649894186 | epot = -223.396586216222 | etot = -180.770700645508
|
||||
37000 ekin = 24.0274860006133 | erot = 18.7785134320987 | epot = -223.576700078937 | etot = -180.770700646225
|
||||
38000 ekin = 23.8991479078982 | erot = 19.1166063146994 | epot = -223.78645486989 | etot = -180.770700647292
|
||||
39000 ekin = 23.7326911853235 | erot = 19.5069160952492 | epot = -224.010307929336 | etot = -180.770700648763
|
||||
40000 ekin = 23.529422307212 | erot = 19.9254673141826 | epot = -224.225590272293 | etot = -180.770700650898
|
||||
41000 ekin = 23.2899396141392 | erot = 20.340809778056 | epot = -224.401450045566 | etot = -180.770700653371
|
||||
42000 ekin = 23.0154529235023 | erot = 20.7165619564846 | epot = -224.502715535761 | etot = -180.770700655775
|
||||
43000 ekin = 22.7111536814278 | erot = 21.0163895622229 | epot = -224.498243901358 | etot = -180.770700657707
|
||||
44000 ekin = 22.3710575806355 | erot = 21.2060371289781 | epot = -224.347795365753 | etot = -180.770700656139
|
||||
45000 ekin = 22.0515843162891 | erot = 21.2588026881768 | epot = -224.081087646891 | etot = -180.770700642425
|
||||
46000 ekin = 21.7855632553136 | erot = 21.2036013766602 | epot = -223.759865260062 | etot = -180.770700628088
|
||||
47000 ekin = 21.5167766971458 | erot = 21.065636702367 | epot = -223.353114011015 | etot = -180.770700611502
|
||||
48000 ekin = 21.4540196107337 | erot = 20.8430832424325 | epot = -223.067803499525 | etot = -180.770700646359
|
||||
49000 ekin = 21.3647564765278 | erot = 20.5521507191688 | epot = -222.687607816921 | etot = -180.770700621224
|
||||
50000 ekin = 21.3125768184621 | erot = 20.2526464671332 | epot = -222.335923904309 | etot = -180.770700618714
|
||||
51000 ekin = 21.2949924810838 | erot = 19.9798421626043 | epot = -222.045535260404 | etot = -180.770700616716
|
||||
52000 ekin = 21.3137144249685 | erot = 19.7627691343687 | epot = -221.847184173962 | etot = -180.770700614625
|
||||
53000 ekin = 21.3664076685105 | erot = 19.6202359856899 | epot = -221.757344279694 | etot = -180.770700625493
|
||||
54000 ekin = 21.421424552406 | erot = 19.55882323195 | epot = -221.750948393747 | etot = -180.770700609391
|
||||
55000 ekin = 21.5995673396093 | erot = 19.5805214885678 | epot = -221.950789453583 | etot = -180.770700625406
|
||||
56000 ekin = 21.7643125668307 | erot = 19.6816042107778 | epot = -222.216617401429 | etot = -180.77070062382
|
||||
57000 ekin = 21.9221309084445 | erot = 19.8499880475953 | epot = -222.542819582064 | etot = -180.770700626024
|
||||
58000 ekin = 22.0666093644392 | erot = 20.0713856445716 | epot = -222.908695636277 | etot = -180.770700627266
|
||||
59000 ekin = 22.1910921687949 | erot = 20.328402409601 | epot = -223.290195207095 | etot = -180.770700628699
|
||||
60000 ekin = 22.2920682490237 | erot = 20.600331953154 | epot = -223.663100832376 | etot = -180.770700630198
|
||||
61000 ekin = 22.3680528265789 | erot = 20.864561419886 | epot = -224.003314878046 | etot = -180.770700631581
|
||||
62000 ekin = 22.4198570332632 | erot = 21.0983714926627 | epot = -224.288929158678 | etot = -180.770700632752
|
||||
63000 ekin = 22.4500800739919 | erot = 21.2815521440893 | epot = -224.502332851296 | etot = -180.770700633215
|
||||
64000 ekin = 22.4634052763981 | erot = 21.3990470998276 | epot = -224.633153009903 | etot = -180.770700633677
|
||||
65000 ekin = 22.4639885390962 | erot = 21.4413332838522 | epot = -224.676022456447 | etot = -180.770700633499
|
||||
66000 ekin = 22.4559522488541 | erot = 21.4074154510862 | epot = -224.634068332758 | etot = -180.770700632817
|
||||
67000 ekin = 22.4417384097823 | erot = 21.3051580893559 | epot = -224.517597130738 | etot = -180.770700631599
|
||||
68000 ekin = 22.4218785446456 | erot = 21.1490017805238 | epot = -224.341580956059 | etot = -180.77070063089
|
||||
69000 ekin = 22.3954651199574 | erot = 20.9555571676353 | epot = -224.121722917262 | etot = -180.77070062967
|
||||
70000 ekin = 22.3613349801191 | erot = 20.7433545871753 | epot = -223.875390195706 | etot = -180.770700628411
|
||||
71000 ekin = 22.3171019087139 | erot = 20.5301141425045 | epot = -223.617916679046 | etot = -180.770700627827
|
||||
72000 ekin = 22.2595195485148 | erot = 20.329630938296 | epot = -223.359851114099 | etot = -180.770700627288
|
||||
73000 ekin = 22.1869461213879 | erot = 20.1521902584585 | epot = -223.109837006429 | etot = -180.770700626583
|
||||
74000 ekin = 22.0990935565687 | erot = 20.0059494138148 | epot = -222.875743596757 | etot = -180.770700626373
|
||||
75000 ekin = 21.9959491639287 | erot = 19.8965902063256 | epot = -222.663239996049 | etot = -180.770700625795
|
||||
76000 ekin = 21.8806005890451 | erot = 19.8284243363261 | epot = -222.47972555068 | etot = -180.770700625309
|
||||
77000 ekin = 21.7590261899816 | erot = 19.8043252195866 | epot = -222.334052034218 | etot = -180.77070062465
|
||||
78000 ekin = 21.639241983951 | erot = 19.8262630279238 | epot = -222.236205635988 | etot = -180.770700624113
|
||||
79000 ekin = 21.5302317519724 | erot = 19.8938812521579 | epot = -222.19481362777 | etot = -180.77070062364
|
||||
80000 ekin = 21.4402276725665 | erot = 20.0060100278945 | epot = -222.216938324075 | etot = -180.770700623614
|
||||
81000 ekin = 21.3741486759864 | erot = 20.1585144791611 | epot = -222.30336377944 | etot = -180.770700624292
|
||||
82000 ekin = 21.3325013763512 | erot = 20.3431413542723 | epot = -222.446343355881 | etot = -180.770700625258
|
||||
83000 ekin = 21.3128808684044 | erot = 20.5483309907718 | epot = -222.63191248578 | etot = -180.770700626604
|
||||
84000 ekin = 21.3107661707936 | erot = 20.760791978517 | epot = -222.842258777119 | etot = -180.770700627809
|
||||
85000 ekin = 21.3216301567282 | erot = 20.967841853924 | epot = -223.060172639486 | etot = -180.770700628834
|
||||
86000 ekin = 21.3400295156728 | erot = 21.1566564817949 | epot = -223.267386627524 | etot = -180.770700630056
|
||||
87000 ekin = 21.3617783036996 | erot = 21.3170902458385 | epot = -223.449569179882 | etot = -180.770700630344
|
||||
88000 ekin = 21.3873913218412 | erot = 21.4454439910409 | epot = -223.603535942848 | etot = -180.770700629966
|
||||
89000 ekin = 21.4215740693991 | erot = 21.5439953706444 | epot = -223.736270068948 | etot = -180.770700628904
|
||||
90000 ekin = 21.4723781618092 | erot = 21.6216769093334 | epot = -223.864755698469 | etot = -180.770700627326
|
||||
91000 ekin = 21.5494066254721 | erot = 21.6927202486451 | epot = -224.012827499722 | etot = -180.770700625605
|
||||
92000 ekin = 21.6619209347598 | erot = 21.7730744492999 | epot = -224.205696008348 | etot = -180.770700624289
|
||||
93000 ekin = 21.8158778641473 | erot = 21.8756732628035 | epot = -224.462251750825 | etot = -180.770700623875
|
||||
94000 ekin = 22.0110275730999 | erot = 22.0060799403011 | epot = -224.787808138196 | etot = -180.770700624795
|
||||
95000 ekin = 22.2387555838385 | erot = 22.1596167137182 | epot = -225.16907292429 | etot = -180.770700626734
|
||||
96000 ekin = 22.4832444899363 | erot = 22.3220202374392 | epot = -225.575965356876 | etot = -180.7707006295
|
||||
97000 ekin = 22.7237276202696 | erot = 22.4720556690115 | epot = -225.966483921719 | etot = -180.770700632438
|
||||
98000 ekin = 22.9377647716045 | erot = 22.5858660312272 | epot = -226.294331437119 | etot = -180.770700634287
|
||||
99000 ekin = 23.1071231637242 | erot = 22.6457411046182 | epot = -226.523564904806 | etot = -180.770700636464
|
||||
100000 ekin = 23.2156001924317 | erot = 22.6390310936005 | epot = -226.625331923823 | etot = -180.770700637791
|
||||
6000 ekin = 20.5959625511847 | erot = 21.8369756530727 | epot = -223.203638857302 | etot = -180.770700653045
|
||||
7000 ekin = 20.5431034482068 | erot = 21.8556844173875 | epot = -223.169488517716 | etot = -180.770700652122
|
||||
8000 ekin = 20.4774701419092 | erot = 21.8437134145374 | epot = -223.091884207389 | etot = -180.770700650943
|
||||
9000 ekin = 20.4074566554238 | erot = 21.8097283692398 | epot = -222.987885674261 | etot = -180.770700649597
|
||||
10000 ekin = 20.3427303660296 | erot = 21.7629575866663 | epot = -222.876388600948 | etot = -180.770700648253
|
||||
11000 ekin = 20.2927407149577 | erot = 21.7112100845349 | epot = -222.774651446682 | etot = -180.770700647189
|
||||
12000 ekin = 20.2665977502213 | erot = 21.6594999867139 | epot = -222.696798383221 | etot = -180.770700646286
|
||||
13000 ekin = 20.2733920359447 | erot = 21.6092715397932 | epot = -222.653364221616 | etot = -180.770700645878
|
||||
14000 ekin = 20.319652478907 | erot = 21.558663097499 | epot = -222.649016222075 | etot = -180.770700645669
|
||||
15000 ekin = 20.4104009374291 | erot = 21.5031572556304 | epot = -222.684258838857 | etot = -180.770700645798
|
||||
16000 ekin = 20.5472869005793 | erot = 21.4346177247038 | epot = -222.752605272036 | etot = -180.770700646753
|
||||
17000 ekin = 20.7266657908775 | erot = 21.3426631585214 | epot = -222.840029597232 | etot = -180.770700647833
|
||||
18000 ekin = 20.9417612759981 | erot = 21.2178611180923 | epot = -222.930323042997 | etot = -180.770700648907
|
||||
19000 ekin = 21.1819308659399 | erot = 21.0532289630289 | epot = -223.00586047892 | etot = -180.770700649951
|
||||
20000 ekin = 21.4358169889477 | erot = 20.8473069564703 | epot = -223.053824595387 | etot = -180.770700649969
|
||||
21000 ekin = 21.6968513751 | erot = 20.6066744652581 | epot = -223.074226489837 | etot = -180.770700649478
|
||||
22000 ekin = 21.9614458442786 | erot = 20.3429420444505 | epot = -223.07508853737 | etot = -180.770700648641
|
||||
23000 ekin = 22.2276099755705 | erot = 20.0703385165238 | epot = -223.068649139875 | etot = -180.77070064778
|
||||
24000 ekin = 22.4935893196675 | erot = 19.802067172166 | epot = -223.066357139276 | etot = -180.770700647443
|
||||
25000 ekin = 22.7566064548228 | erot = 19.5464828008836 | epot = -223.073789902975 | etot = -180.770700647269
|
||||
26000 ekin = 23.0126717548399 | erot = 19.3065017718462 | epot = -223.089874174571 | etot = -180.770700647885
|
||||
27000 ekin = 23.2550417060594 | erot = 19.0797753474567 | epot = -223.105517701932 | etot = -180.770700648416
|
||||
28000 ekin = 23.4774329734805 | erot = 18.8646197299574 | epot = -223.112753352067 | etot = -180.770700648629
|
||||
29000 ekin = 23.6747927720663 | erot = 18.6628653411825 | epot = -223.108358761693 | etot = -180.770700648445
|
||||
30000 ekin = 23.8432321400247 | erot = 18.4812216983637 | epot = -223.095154486375 | etot = -180.770700647986
|
||||
31000 ekin = 23.9793041752229 | erot = 18.330784533402 | epot = -223.08078935577 | etot = -180.770700647145
|
||||
32000 ekin = 24.0810246040235 | erot = 18.2261577056003 | epot = -223.077882955919 | etot = -180.770700646295
|
||||
33000 ekin = 24.1468986449398 | erot = 18.1820705445406 | epot = -223.09966983514 | etot = -180.770700645659
|
||||
34000 ekin = 24.1756615132863 | erot = 18.2103812210172 | epot = -223.156743379607 | etot = -180.770700645303
|
||||
35000 ekin = 24.1663193894652 | erot = 18.3185351073568 | epot = -223.255555142089 | etot = -180.770700645267
|
||||
36000 ekin = 24.1167205812964 | erot = 18.5091649894187 | epot = -223.396586216223 | etot = -180.770700645508
|
||||
37000 ekin = 24.0274860006135 | erot = 18.7785134320989 | epot = -223.576700078937 | etot = -180.770700646225
|
||||
38000 ekin = 23.8991479078985 | erot = 19.1166063146995 | epot = -223.78645486989 | etot = -180.770700647292
|
||||
39000 ekin = 23.7326911853236 | erot = 19.5069160952493 | epot = -224.010307929336 | etot = -180.770700648763
|
||||
40000 ekin = 23.5294223072121 | erot = 19.9254673141826 | epot = -224.225590272292 | etot = -180.770700650897
|
||||
41000 ekin = 23.2899396141392 | erot = 20.340809778056 | epot = -224.401450045567 | etot = -180.770700653371
|
||||
42000 ekin = 23.0154529235024 | erot = 20.7165619564844 | epot = -224.502715535761 | etot = -180.770700655774
|
||||
43000 ekin = 22.7111536814278 | erot = 21.0163895622227 | epot = -224.498243901357 | etot = -180.770700657707
|
||||
44000 ekin = 22.3710575806356 | erot = 21.2060371289779 | epot = -224.347795365752 | etot = -180.770700656139
|
||||
45000 ekin = 22.0515843162889 | erot = 21.2588026881767 | epot = -224.08108764689 | etot = -180.770700642424
|
||||
46000 ekin = 21.7855632553132 | erot = 21.2036013766601 | epot = -223.75986526006 | etot = -180.770700628087
|
||||
47000 ekin = 21.5167766971454 | erot = 21.0656367023669 | epot = -223.353114011014 | etot = -180.770700611502
|
||||
48000 ekin = 21.4540196107332 | erot = 20.8430832424325 | epot = -223.067803499524 | etot = -180.770700646358
|
||||
49000 ekin = 21.3647564765273 | erot = 20.5521507191689 | epot = -222.68760781692 | etot = -180.770700621224
|
||||
50000 ekin = 21.3125768184616 | erot = 20.2526464671335 | epot = -222.335923904309 | etot = -180.770700618713
|
||||
51000 ekin = 21.2949924810833 | erot = 19.9798421626046 | epot = -222.045535260403 | etot = -180.770700616715
|
||||
52000 ekin = 21.313714424968 | erot = 19.762769134369 | epot = -221.847184173962 | etot = -180.770700614625
|
||||
53000 ekin = 21.3664076685101 | erot = 19.6202359856903 | epot = -221.757344279694 | etot = -180.770700625493
|
||||
54000 ekin = 21.4214245524056 | erot = 19.5588232319504 | epot = -221.750948393747 | etot = -180.770700609391
|
||||
55000 ekin = 21.5995673396088 | erot = 19.5805214885682 | epot = -221.950789453583 | etot = -180.770700625406
|
||||
56000 ekin = 21.7643125668302 | erot = 19.6816042107783 | epot = -222.216617401428 | etot = -180.77070062382
|
||||
57000 ekin = 21.922130908444 | erot = 19.8499880475958 | epot = -222.542819582063 | etot = -180.770700626024
|
||||
58000 ekin = 22.0666093644387 | erot = 20.0713856445721 | epot = -222.908695636277 | etot = -180.770700627266
|
||||
59000 ekin = 22.1910921687945 | erot = 20.3284024096015 | epot = -223.290195207095 | etot = -180.770700628699
|
||||
60000 ekin = 22.2920682490233 | erot = 20.6003319531545 | epot = -223.663100832376 | etot = -180.770700630198
|
||||
61000 ekin = 22.3680528265786 | erot = 20.8645614198866 | epot = -224.003314878046 | etot = -180.77070063158
|
||||
62000 ekin = 22.4198570332631 | erot = 21.0983714926633 | epot = -224.288929158679 | etot = -180.770700632752
|
||||
63000 ekin = 22.450080073992 | erot = 21.28155214409 | epot = -224.502332851296 | etot = -180.770700633215
|
||||
64000 ekin = 22.4634052763983 | erot = 21.3990470998282 | epot = -224.633153009903 | etot = -180.770700633676
|
||||
65000 ekin = 22.4639885390964 | erot = 21.4413332838528 | epot = -224.676022456447 | etot = -180.770700633498
|
||||
66000 ekin = 22.4559522488544 | erot = 21.4074154510867 | epot = -224.634068332758 | etot = -180.770700632817
|
||||
67000 ekin = 22.4417384097826 | erot = 21.3051580893564 | epot = -224.517597130738 | etot = -180.770700631599
|
||||
68000 ekin = 22.421878544646 | erot = 21.1490017805243 | epot = -224.34158095606 | etot = -180.77070063089
|
||||
69000 ekin = 22.3954651199576 | erot = 20.9555571676358 | epot = -224.121722917263 | etot = -180.770700629669
|
||||
70000 ekin = 22.3613349801193 | erot = 20.7433545871758 | epot = -223.875390195706 | etot = -180.770700628411
|
||||
71000 ekin = 22.3171019087139 | erot = 20.5301141425049 | epot = -223.617916679045 | etot = -180.770700627826
|
||||
72000 ekin = 22.2595195485147 | erot = 20.3296309382964 | epot = -223.359851114099 | etot = -180.770700627288
|
||||
73000 ekin = 22.1869461213877 | erot = 20.1521902584588 | epot = -223.109837006429 | etot = -180.770700626583
|
||||
74000 ekin = 22.0990935565683 | erot = 20.0059494138149 | epot = -222.875743596756 | etot = -180.770700626373
|
||||
75000 ekin = 21.9959491639282 | erot = 19.8965902063256 | epot = -222.663239996049 | etot = -180.770700625795
|
||||
76000 ekin = 21.8806005890445 | erot = 19.828424336326 | epot = -222.479725550679 | etot = -180.770700625308
|
||||
77000 ekin = 21.7590261899809 | erot = 19.8043252195864 | epot = -222.334052034216 | etot = -180.770700624649
|
||||
78000 ekin = 21.6392419839503 | erot = 19.8262630279236 | epot = -222.236205635986 | etot = -180.770700624113
|
||||
79000 ekin = 21.5302317519716 | erot = 19.8938812521576 | epot = -222.194813627769 | etot = -180.77070062364
|
||||
80000 ekin = 21.4402276725657 | erot = 20.0060100278943 | epot = -222.216938324074 | etot = -180.770700623614
|
||||
81000 ekin = 21.3741486759855 | erot = 20.158514479161 | epot = -222.303363779439 | etot = -180.770700624292
|
||||
82000 ekin = 21.3325013763505 | erot = 20.3431413542724 | epot = -222.44634335588 | etot = -180.770700625257
|
||||
83000 ekin = 21.3128808684037 | erot = 20.548330990772 | epot = -222.631912485779 | etot = -180.770700626604
|
||||
84000 ekin = 21.310766170793 | erot = 20.7607919785174 | epot = -222.842258777119 | etot = -180.770700627809
|
||||
85000 ekin = 21.3216301567277 | erot = 20.9678418539246 | epot = -223.060172639485 | etot = -180.770700628833
|
||||
86000 ekin = 21.3400295156723 | erot = 21.1566564817957 | epot = -223.267386627523 | etot = -180.770700630055
|
||||
87000 ekin = 21.3617783036992 | erot = 21.3170902458394 | epot = -223.449569179882 | etot = -180.770700630344
|
||||
88000 ekin = 21.3873913218409 | erot = 21.445443991042 | epot = -223.603535942848 | etot = -180.770700629965
|
||||
89000 ekin = 21.421574069399 | erot = 21.5439953706456 | epot = -223.736270068948 | etot = -180.770700628904
|
||||
90000 ekin = 21.4723781618091 | erot = 21.6216769093347 | epot = -223.86475569847 | etot = -180.770700627326
|
||||
91000 ekin = 21.549406625472 | erot = 21.6927202486463 | epot = -224.012827499723 | etot = -180.770700625604
|
||||
92000 ekin = 21.6619209347597 | erot = 21.7730744493012 | epot = -224.205696008348 | etot = -180.770700624287
|
||||
93000 ekin = 21.8158778641472 | erot = 21.8756732628048 | epot = -224.462251750825 | etot = -180.770700623873
|
||||
94000 ekin = 22.0110275730997 | erot = 22.0060799403022 | epot = -224.787808138196 | etot = -180.770700624794
|
||||
95000 ekin = 22.2387555838384 | erot = 22.1596167137192 | epot = -225.16907292429 | etot = -180.770700626733
|
||||
96000 ekin = 22.4832444899361 | erot = 22.3220202374401 | epot = -225.575965356875 | etot = -180.770700629499
|
||||
97000 ekin = 22.7237276202693 | erot = 22.4720556690122 | epot = -225.966483921719 | etot = -180.770700632437
|
||||
98000 ekin = 22.9377647716041 | erot = 22.5858660312277 | epot = -226.294331437118 | etot = -180.770700634287
|
||||
99000 ekin = 23.1071231637237 | erot = 22.6457411046184 | epot = -226.523564904806 | etot = -180.770700636464
|
||||
100000 ekin = 23.2156001924311 | erot = 22.6390310936006 | epot = -226.625331923822 | etot = -180.770700637791
|
||||
100000 0.10528617 -1.5761124 0.044860201 -1.3743901 -1.9205819e-05 1000000
|
||||
Loop time of 81.8713 on 1 procs for 100000 steps with 148 atoms
|
||||
Loop time of 83.9672 on 1 procs for 100000 steps with 148 atoms
|
||||
|
||||
Performance: 1055.315 tau/day, 1221.430 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
Performance: 1028.974 tau/day, 1190.942 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 | 78.718 | 78.718 | 78.718 | 0.0 | 96.15
|
||||
Bond | 0.97064 | 0.97064 | 0.97064 | 0.0 | 1.19
|
||||
Neigh | 0.016915 | 0.016915 | 0.016915 | 0.0 | 0.02
|
||||
Comm | 0.027127 | 0.027127 | 0.027127 | 0.0 | 0.03
|
||||
Output | 0.12162 | 0.12162 | 0.12162 | 0.0 | 0.15
|
||||
Modify | 1.9185 | 1.9185 | 1.9185 | 0.0 | 2.34
|
||||
Other | | 0.09845 | | | 0.12
|
||||
Pair | 80.885 | 80.885 | 80.885 | 0.0 | 96.33
|
||||
Bond | 0.94789 | 0.94789 | 0.94789 | 0.0 | 1.13
|
||||
Neigh | 0.011589 | 0.011589 | 0.011589 | 0.0 | 0.01
|
||||
Comm | 0.045979 | 0.045979 | 0.045979 | 0.0 | 0.05
|
||||
Output | 0.11973 | 0.11973 | 0.11973 | 0.0 | 0.14
|
||||
Modify | 1.8641 | 1.8641 | 1.8641 | 0.0 | 2.22
|
||||
Other | | 0.09239 | | | 0.11
|
||||
|
||||
Nlocal: 148.000 ave 148 max 148 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
@ -274,6 +274,8 @@ Ave special neighs/atom = 6.0000000
|
||||
Neighbor list builds = 100
|
||||
Dangerous builds = 0
|
||||
|
||||
#write_data last_config.${number}.* nocoeff
|
||||
write_data last_config.${number}.* nocoeff
|
||||
write_data last_config.5.* nocoeff
|
||||
System init for write_data ...
|
||||
#write_restart last_config.${number}.*
|
||||
Total wall time: 0:01:21
|
||||
Total wall time: 0:01:23
|
||||
|
||||
@ -9,7 +9,7 @@ units lj
|
||||
|
||||
dimension 3
|
||||
|
||||
newton off
|
||||
newton on
|
||||
|
||||
boundary p p p
|
||||
|
||||
@ -30,7 +30,7 @@ Reading data file ...
|
||||
reading velocities ...
|
||||
148 velocities
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
1 = max bonds/atom
|
||||
148 ellipsoids
|
||||
reading bonds ...
|
||||
148 bonds
|
||||
@ -115,33 +115,33 @@ Neighbor list info ...
|
||||
binsize = 2.8194939, bins = 36 36 36
|
||||
5 neighbor lists, perpetual/occasional/extra = 5 0 0
|
||||
(1) pair oxdna2/excv, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: full/bin/3d
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
(2) pair oxdna2/hbond, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
attributes: half, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) pair oxdna2/xstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
attributes: half, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(4) pair oxdna2/coaxstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
attributes: half, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(5) pair oxdna2/dh, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
attributes: half, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
WARNING: Communication cutoff adjusted to 5.638987723814632 (../comm.cpp:739)
|
||||
0 ekin = 20.4724634226502 | erot = 21.0406985312466 | epot = -222.283862600785 | etot = -180.770700646889
|
||||
Per MPI rank memory allocation (min/avg/max) = 9.508 | 9.558 | 9.632 Mbytes
|
||||
Per MPI rank memory allocation (min/avg/max) = 9.383 | 9.432 | 9.506 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 0.092845639 -1.5501211 0.04820308 -1.3635905 -9.0052368e-06 1000000
|
||||
1000 ekin = 20.531989141805 | erot = 21.2158633183735 | epot = -222.518553109361 | etot = -180.770700649183
|
||||
@ -150,130 +150,132 @@ Step Temp E_pair E_mol TotEng Press Volume
|
||||
4000 ekin = 20.6395549184482 | erot = 21.6854113323894 | epot = -223.095666904229 | etot = -180.770700653391
|
||||
5000 ekin = 20.6295551742564 | erot = 21.7809539301804 | epot = -223.181209757876 | etot = -180.770700653439
|
||||
6000 ekin = 20.5959625511847 | erot = 21.8369756530726 | epot = -223.203638857302 | etot = -180.770700653045
|
||||
7000 ekin = 20.5431034482068 | erot = 21.8556844173874 | epot = -223.169488517717 | etot = -180.770700652122
|
||||
8000 ekin = 20.4774701419092 | erot = 21.8437134145373 | epot = -223.091884207389 | etot = -180.770700650943
|
||||
9000 ekin = 20.4074566554239 | erot = 21.8097283692397 | epot = -222.987885674261 | etot = -180.770700649597
|
||||
10000 ekin = 20.3427303660297 | erot = 21.7629575866662 | epot = -222.876388600948 | etot = -180.770700648253
|
||||
7000 ekin = 20.5431034482069 | erot = 21.8556844173874 | epot = -223.169488517717 | etot = -180.770700652123
|
||||
8000 ekin = 20.4774701419093 | erot = 21.8437134145373 | epot = -223.09188420739 | etot = -180.770700650943
|
||||
9000 ekin = 20.4074566554239 | erot = 21.8097283692397 | epot = -222.987885674261 | etot = -180.770700649598
|
||||
10000 ekin = 20.3427303660297 | erot = 21.7629575866662 | epot = -222.876388600949 | etot = -180.770700648253
|
||||
11000 ekin = 20.2927407149578 | erot = 21.7112100845349 | epot = -222.774651446682 | etot = -180.77070064719
|
||||
12000 ekin = 20.2665977502213 | erot = 21.6594999867139 | epot = -222.696798383222 | etot = -180.770700646287
|
||||
13000 ekin = 20.2733920359447 | erot = 21.6092715397934 | epot = -222.653364221616 | etot = -180.770700645878
|
||||
14000 ekin = 20.3196524789069 | erot = 21.5586630974992 | epot = -222.649016222076 | etot = -180.770700645669
|
||||
15000 ekin = 20.410400937429 | erot = 21.5031572556308 | epot = -222.684258838858 | etot = -180.770700645798
|
||||
16000 ekin = 20.5472869005792 | erot = 21.4346177247042 | epot = -222.752605272036 | etot = -180.770700646753
|
||||
17000 ekin = 20.7266657908773 | erot = 21.3426631585219 | epot = -222.840029597232 | etot = -180.770700647833
|
||||
18000 ekin = 20.9417612759978 | erot = 21.2178611180929 | epot = -222.930323042998 | etot = -180.770700648907
|
||||
19000 ekin = 21.1819308659395 | erot = 21.0532289630295 | epot = -223.005860478921 | etot = -180.770700649952
|
||||
20000 ekin = 21.4358169889472 | erot = 20.8473069564709 | epot = -223.053824595387 | etot = -180.770700649969
|
||||
21000 ekin = 21.6968513750994 | erot = 20.6066744652587 | epot = -223.074226489837 | etot = -180.770700649479
|
||||
22000 ekin = 21.9614458442779 | erot = 20.3429420444511 | epot = -223.07508853737 | etot = -180.770700648641
|
||||
23000 ekin = 22.2276099755697 | erot = 20.0703385165243 | epot = -223.068649139875 | etot = -180.770700647781
|
||||
24000 ekin = 22.4935893196667 | erot = 19.8020671721665 | epot = -223.066357139277 | etot = -180.770700647443
|
||||
25000 ekin = 22.756606454822 | erot = 19.5464828008841 | epot = -223.073789902976 | etot = -180.77070064727
|
||||
26000 ekin = 23.0126717548392 | erot = 19.3065017718467 | epot = -223.089874174572 | etot = -180.770700647886
|
||||
27000 ekin = 23.2550417060587 | erot = 19.0797753474572 | epot = -223.105517701932 | etot = -180.770700648417
|
||||
28000 ekin = 23.4774329734798 | erot = 18.8646197299578 | epot = -223.112753352067 | etot = -180.770700648629
|
||||
29000 ekin = 23.6747927720656 | erot = 18.6628653411828 | epot = -223.108358761693 | etot = -180.770700648445
|
||||
30000 ekin = 23.843232140024 | erot = 18.4812216983639 | epot = -223.095154486375 | etot = -180.770700647987
|
||||
31000 ekin = 23.9793041752223 | erot = 18.330784533402 | epot = -223.08078935577 | etot = -180.770700647146
|
||||
32000 ekin = 24.081024604023 | erot = 18.2261577056003 | epot = -223.077882955919 | etot = -180.770700646296
|
||||
33000 ekin = 24.1468986449394 | erot = 18.1820705445404 | epot = -223.09966983514 | etot = -180.77070064566
|
||||
34000 ekin = 24.175661513286 | erot = 18.2103812210168 | epot = -223.156743379607 | etot = -180.770700645304
|
||||
35000 ekin = 24.166319389465 | erot = 18.3185351073562 | epot = -223.255555142089 | etot = -180.770700645268
|
||||
36000 ekin = 24.1167205812963 | erot = 18.509164989418 | epot = -223.396586216223 | etot = -180.770700645508
|
||||
37000 ekin = 24.0274860006135 | erot = 18.778513432098 | epot = -223.576700078937 | etot = -180.770700646225
|
||||
38000 ekin = 23.8991479078985 | erot = 19.1166063146986 | epot = -223.78645486989 | etot = -180.770700647293
|
||||
39000 ekin = 23.7326911853237 | erot = 19.5069160952483 | epot = -224.010307929335 | etot = -180.770700648763
|
||||
40000 ekin = 23.5294223072123 | erot = 19.9254673141817 | epot = -224.225590272292 | etot = -180.770700650898
|
||||
41000 ekin = 23.2899396141395 | erot = 20.3408097780551 | epot = -224.401450045567 | etot = -180.770700653372
|
||||
42000 ekin = 23.0154529235027 | erot = 20.7165619564837 | epot = -224.502715535762 | etot = -180.770700655775
|
||||
43000 ekin = 22.7111536814281 | erot = 21.0163895622221 | epot = -224.498243901358 | etot = -180.770700657708
|
||||
44000 ekin = 22.3710575806358 | erot = 21.2060371289775 | epot = -224.347795365753 | etot = -180.77070065614
|
||||
45000 ekin = 22.0515843162892 | erot = 21.2588026881763 | epot = -224.081087646891 | etot = -180.770700642425
|
||||
46000 ekin = 21.7855632553138 | erot = 21.2036013766598 | epot = -223.759865260062 | etot = -180.770700628088
|
||||
47000 ekin = 21.5167766971457 | erot = 21.0656367023666 | epot = -223.353114011016 | etot = -180.770700611503
|
||||
48000 ekin = 21.454019610733 | erot = 20.8430832424322 | epot = -223.067803499525 | etot = -180.77070064636
|
||||
49000 ekin = 21.3647564765269 | erot = 20.5521507191685 | epot = -222.687607816921 | etot = -180.770700621226
|
||||
50000 ekin = 21.312576818461 | erot = 20.252646467133 | epot = -222.335923904309 | etot = -180.770700618715
|
||||
51000 ekin = 21.2949924810824 | erot = 19.9798421626041 | epot = -222.045535260404 | etot = -180.770700616717
|
||||
52000 ekin = 21.3137144249669 | erot = 19.7627691343685 | epot = -221.847184173962 | etot = -180.770700614627
|
||||
53000 ekin = 21.3664076685088 | erot = 19.6202359856897 | epot = -221.757344279693 | etot = -180.770700625495
|
||||
54000 ekin = 21.4214245524042 | erot = 19.5588232319498 | epot = -221.750948393746 | etot = -180.770700609392
|
||||
55000 ekin = 21.5995673396072 | erot = 19.5805214885676 | epot = -221.950789453582 | etot = -180.770700625407
|
||||
56000 ekin = 21.7643125668285 | erot = 19.6816042107776 | epot = -222.216617401428 | etot = -180.770700623822
|
||||
57000 ekin = 21.9221309084424 | erot = 19.8499880475952 | epot = -222.542819582063 | etot = -180.770700626025
|
||||
58000 ekin = 22.0666093644371 | erot = 20.0713856445716 | epot = -222.908695636277 | etot = -180.770700627268
|
||||
59000 ekin = 22.191092168793 | erot = 20.3284024096011 | epot = -223.290195207095 | etot = -180.7707006287
|
||||
60000 ekin = 22.292068249022 | erot = 20.6003319531543 | epot = -223.663100832376 | etot = -180.7707006302
|
||||
61000 ekin = 22.3680528265774 | erot = 20.8645614198865 | epot = -224.003314878046 | etot = -180.770700631582
|
||||
62000 ekin = 22.4198570332621 | erot = 21.0983714926634 | epot = -224.288929158679 | etot = -180.770700632754
|
||||
63000 ekin = 22.450080073991 | erot = 21.2815521440901 | epot = -224.502332851297 | etot = -180.770700633216
|
||||
64000 ekin = 22.4634052763974 | erot = 21.3990470998285 | epot = -224.633153009904 | etot = -180.770700633678
|
||||
65000 ekin = 22.4639885390957 | erot = 21.4413332838532 | epot = -224.676022456449 | etot = -180.7707006335
|
||||
66000 ekin = 22.4559522488539 | erot = 21.4074154510872 | epot = -224.634068332759 | etot = -180.770700632818
|
||||
67000 ekin = 22.4417384097822 | erot = 21.3051580893569 | epot = -224.517597130739 | etot = -180.7707006316
|
||||
68000 ekin = 22.4218785446457 | erot = 21.1490017805248 | epot = -224.341580956061 | etot = -180.770700630891
|
||||
69000 ekin = 22.3954651199575 | erot = 20.9555571676363 | epot = -224.121722917264 | etot = -180.77070062967
|
||||
70000 ekin = 22.3613349801193 | erot = 20.7433545871763 | epot = -223.875390195707 | etot = -180.770700628412
|
||||
71000 ekin = 22.317101908714 | erot = 20.5301141425054 | epot = -223.617916679047 | etot = -180.770700627827
|
||||
72000 ekin = 22.2595195485149 | erot = 20.3296309382967 | epot = -223.3598511141 | etot = -180.770700627289
|
||||
73000 ekin = 22.186946121388 | erot = 20.1521902584591 | epot = -223.109837006431 | etot = -180.770700626584
|
||||
74000 ekin = 22.0990935565685 | erot = 20.0059494138152 | epot = -222.875743596758 | etot = -180.770700626374
|
||||
75000 ekin = 21.9959491639285 | erot = 19.8965902063258 | epot = -222.66323999605 | etot = -180.770700625796
|
||||
76000 ekin = 21.8806005890447 | erot = 19.8284243363262 | epot = -222.47972555068 | etot = -180.770700625309
|
||||
77000 ekin = 21.7590261899811 | erot = 19.8043252195865 | epot = -222.334052034218 | etot = -180.77070062465
|
||||
78000 ekin = 21.6392419839504 | erot = 19.8262630279235 | epot = -222.236205635988 | etot = -180.770700624114
|
||||
79000 ekin = 21.5302317519716 | erot = 19.8938812521573 | epot = -222.19481362777 | etot = -180.770700623641
|
||||
80000 ekin = 21.4402276725656 | erot = 20.0060100278937 | epot = -222.216938324074 | etot = -180.770700623615
|
||||
81000 ekin = 21.3741486759853 | erot = 20.1585144791602 | epot = -222.303363779439 | etot = -180.770700624293
|
||||
82000 ekin = 21.3325013763501 | erot = 20.3431413542714 | epot = -222.44634335588 | etot = -180.770700625258
|
||||
83000 ekin = 21.3128808684032 | erot = 20.5483309907707 | epot = -222.631912485778 | etot = -180.770700626604
|
||||
84000 ekin = 21.3107661707924 | erot = 20.7607919785161 | epot = -222.842258777118 | etot = -180.77070062781
|
||||
85000 ekin = 21.3216301567271 | erot = 20.9678418539233 | epot = -223.060172639485 | etot = -180.770700628834
|
||||
86000 ekin = 21.3400295156717 | erot = 21.1566564817944 | epot = -223.267386627523 | etot = -180.770700630057
|
||||
87000 ekin = 21.3617783036987 | erot = 21.3170902458384 | epot = -223.449569179882 | etot = -180.770700630345
|
||||
88000 ekin = 21.3873913218405 | erot = 21.4454439910411 | epot = -223.603535942848 | etot = -180.770700629967
|
||||
89000 ekin = 21.4215740693986 | erot = 21.5439953706449 | epot = -223.736270068949 | etot = -180.770700628906
|
||||
90000 ekin = 21.4723781618088 | erot = 21.6216769093341 | epot = -223.864755698471 | etot = -180.770700627328
|
||||
91000 ekin = 21.5494066254718 | erot = 21.6927202486458 | epot = -224.012827499724 | etot = -180.770700625606
|
||||
92000 ekin = 21.6619209347595 | erot = 21.7730744493006 | epot = -224.20569600835 | etot = -180.77070062429
|
||||
93000 ekin = 21.815877864147 | erot = 21.8756732628043 | epot = -224.462251750826 | etot = -180.770700623875
|
||||
94000 ekin = 22.0110275730996 | erot = 22.0060799403017 | epot = -224.787808138197 | etot = -180.770700624796
|
||||
95000 ekin = 22.2387555838383 | erot = 22.1596167137187 | epot = -225.169072924291 | etot = -180.770700626735
|
||||
96000 ekin = 22.483244489936 | erot = 22.3220202374395 | epot = -225.575965356877 | etot = -180.770700629501
|
||||
97000 ekin = 22.7237276202693 | erot = 22.4720556690117 | epot = -225.96648392172 | etot = -180.770700632439
|
||||
98000 ekin = 22.937764771604 | erot = 22.5858660312272 | epot = -226.29433143712 | etot = -180.770700634289
|
||||
99000 ekin = 23.1071231637235 | erot = 22.645741104618 | epot = -226.523564904807 | etot = -180.770700636466
|
||||
100000 ekin = 23.2156001924308 | erot = 22.6390310936003 | epot = -226.625331923823 | etot = -180.770700637792
|
||||
13000 ekin = 20.2733920359447 | erot = 21.6092715397933 | epot = -222.653364221617 | etot = -180.770700645879
|
||||
14000 ekin = 20.3196524789069 | erot = 21.5586630974992 | epot = -222.649016222076 | etot = -180.77070064567
|
||||
15000 ekin = 20.410400937429 | erot = 21.5031572556307 | epot = -222.684258838858 | etot = -180.770700645799
|
||||
16000 ekin = 20.5472869005792 | erot = 21.4346177247041 | epot = -222.752605272037 | etot = -180.770700646753
|
||||
17000 ekin = 20.7266657908773 | erot = 21.3426631585218 | epot = -222.840029597232 | etot = -180.770700647833
|
||||
18000 ekin = 20.9417612759978 | erot = 21.2178611180927 | epot = -222.930323042998 | etot = -180.770700648907
|
||||
19000 ekin = 21.1819308659396 | erot = 21.0532289630294 | epot = -223.005860478921 | etot = -180.770700649952
|
||||
20000 ekin = 21.4358169889472 | erot = 20.8473069564707 | epot = -223.053824595387 | etot = -180.77070064997
|
||||
21000 ekin = 21.6968513750995 | erot = 20.6066744652585 | epot = -223.074226489837 | etot = -180.770700649479
|
||||
22000 ekin = 21.9614458442779 | erot = 20.3429420444508 | epot = -223.075088537371 | etot = -180.770700648642
|
||||
23000 ekin = 22.2276099755697 | erot = 20.070338516524 | epot = -223.068649139875 | etot = -180.770700647781
|
||||
24000 ekin = 22.4935893196667 | erot = 19.8020671721661 | epot = -223.066357139277 | etot = -180.770700647444
|
||||
25000 ekin = 22.756606454822 | erot = 19.5464828008836 | epot = -223.073789902976 | etot = -180.77070064727
|
||||
26000 ekin = 23.0126717548391 | erot = 19.3065017718461 | epot = -223.089874174572 | etot = -180.770700647887
|
||||
27000 ekin = 23.2550417060586 | erot = 19.0797753474566 | epot = -223.105517701932 | etot = -180.770700648417
|
||||
28000 ekin = 23.4774329734797 | erot = 18.8646197299572 | epot = -223.112753352067 | etot = -180.77070064863
|
||||
29000 ekin = 23.6747927720654 | erot = 18.6628653411822 | epot = -223.108358761694 | etot = -180.770700648446
|
||||
30000 ekin = 23.8432321400238 | erot = 18.4812216983633 | epot = -223.095154486375 | etot = -180.770700647988
|
||||
31000 ekin = 23.979304175222 | erot = 18.3307845334015 | epot = -223.08078935577 | etot = -180.770700647146
|
||||
32000 ekin = 24.0810246040226 | erot = 18.2261577055998 | epot = -223.077882955919 | etot = -180.770700646297
|
||||
33000 ekin = 24.1468986449389 | erot = 18.1820705445401 | epot = -223.09966983514 | etot = -180.770700645661
|
||||
34000 ekin = 24.1756615132855 | erot = 18.2103812210167 | epot = -223.156743379607 | etot = -180.770700645304
|
||||
35000 ekin = 24.1663193894644 | erot = 18.3185351073563 | epot = -223.255555142089 | etot = -180.770700645269
|
||||
36000 ekin = 24.1167205812957 | erot = 18.5091649894184 | epot = -223.396586216223 | etot = -180.770700645509
|
||||
37000 ekin = 24.0274860006128 | erot = 18.7785134320987 | epot = -223.576700078937 | etot = -180.770700646226
|
||||
38000 ekin = 23.8991479078978 | erot = 19.1166063146994 | epot = -223.786454869891 | etot = -180.770700647293
|
||||
39000 ekin = 23.7326911853231 | erot = 19.5069160952493 | epot = -224.010307929336 | etot = -180.770700648764
|
||||
40000 ekin = 23.5294223072117 | erot = 19.9254673141828 | epot = -224.225590272293 | etot = -180.770700650899
|
||||
41000 ekin = 23.289939614139 | erot = 20.3408097780563 | epot = -224.401450045568 | etot = -180.770700653372
|
||||
42000 ekin = 23.0154529235022 | erot = 20.7165619564848 | epot = -224.502715535762 | etot = -180.770700655775
|
||||
43000 ekin = 22.7111536814277 | erot = 21.0163895622231 | epot = -224.498243901359 | etot = -180.770700657708
|
||||
44000 ekin = 22.3710575806355 | erot = 21.2060371289783 | epot = -224.347795365754 | etot = -180.77070065614
|
||||
45000 ekin = 22.0515843162889 | erot = 21.2588026881768 | epot = -224.081087646891 | etot = -180.770700642425
|
||||
46000 ekin = 21.7855632553133 | erot = 21.20360137666 | epot = -223.759865260062 | etot = -180.770700628089
|
||||
47000 ekin = 21.5167766971456 | erot = 21.0656367023667 | epot = -223.353114011016 | etot = -180.770700611503
|
||||
48000 ekin = 21.4540196107333 | erot = 20.8430832424321 | epot = -223.067803499525 | etot = -180.77070064636
|
||||
49000 ekin = 21.3647564765274 | erot = 20.5521507191682 | epot = -222.687607816922 | etot = -180.770700621226
|
||||
50000 ekin = 21.3125768184617 | erot = 20.2526464671325 | epot = -222.33592390431 | etot = -180.770700618715
|
||||
51000 ekin = 21.2949924810834 | erot = 19.9798421626035 | epot = -222.045535260404 | etot = -180.770700616717
|
||||
52000 ekin = 21.3137144249679 | erot = 19.7627691343679 | epot = -221.847184173963 | etot = -180.770700614627
|
||||
53000 ekin = 21.3664076685099 | erot = 19.6202359856891 | epot = -221.757344279695 | etot = -180.770700625496
|
||||
54000 ekin = 21.4214245524052 | erot = 19.5588232319492 | epot = -221.750948393748 | etot = -180.770700609393
|
||||
55000 ekin = 21.5995673396082 | erot = 19.580521488567 | epot = -221.950789453583 | etot = -180.770700625408
|
||||
56000 ekin = 21.7643125668294 | erot = 19.681604210777 | epot = -222.216617401429 | etot = -180.770700623823
|
||||
57000 ekin = 21.922130908443 | erot = 19.8499880475945 | epot = -222.542819582064 | etot = -180.770700626026
|
||||
58000 ekin = 22.0666093644375 | erot = 20.0713856445709 | epot = -222.908695636278 | etot = -180.770700627269
|
||||
59000 ekin = 22.1910921687932 | erot = 20.3284024096003 | epot = -223.290195207095 | etot = -180.770700628702
|
||||
60000 ekin = 22.2920682490219 | erot = 20.6003319531534 | epot = -223.663100832376 | etot = -180.770700630201
|
||||
61000 ekin = 22.3680528265772 | erot = 20.8645614198856 | epot = -224.003314878046 | etot = -180.770700631583
|
||||
62000 ekin = 22.4198570332617 | erot = 21.0983714926625 | epot = -224.288929158679 | etot = -180.770700632755
|
||||
63000 ekin = 22.4500800739905 | erot = 21.2815521440892 | epot = -224.502332851297 | etot = -180.770700633217
|
||||
64000 ekin = 22.4634052763968 | erot = 21.3990470998276 | epot = -224.633153009904 | etot = -180.770700633679
|
||||
65000 ekin = 22.463988539095 | erot = 21.4413332838523 | epot = -224.676022456448 | etot = -180.770700633501
|
||||
66000 ekin = 22.4559522488531 | erot = 21.4074154510864 | epot = -224.634068332759 | etot = -180.770700632819
|
||||
67000 ekin = 22.4417384097814 | erot = 21.3051580893563 | epot = -224.517597130739 | etot = -180.770700631601
|
||||
68000 ekin = 22.4218785446449 | erot = 21.1490017805243 | epot = -224.341580956061 | etot = -180.770700630892
|
||||
69000 ekin = 22.3954651199567 | erot = 20.9555571676359 | epot = -224.121722917264 | etot = -180.770700629671
|
||||
70000 ekin = 22.3613349801186 | erot = 20.743354587176 | epot = -223.875390195707 | etot = -180.770700628413
|
||||
71000 ekin = 22.3171019087134 | erot = 20.5301141425052 | epot = -223.617916679047 | etot = -180.770700627829
|
||||
72000 ekin = 22.2595195485144 | erot = 20.3296309382966 | epot = -223.3598511141 | etot = -180.77070062729
|
||||
73000 ekin = 22.1869461213875 | erot = 20.1521902584591 | epot = -223.109837006431 | etot = -180.770700626585
|
||||
74000 ekin = 22.0990935565682 | erot = 20.0059494138151 | epot = -222.875743596758 | etot = -180.770700626375
|
||||
75000 ekin = 21.9959491639282 | erot = 19.8965902063257 | epot = -222.663239996051 | etot = -180.770700625797
|
||||
76000 ekin = 21.8806005890446 | erot = 19.8284243363261 | epot = -222.479725550681 | etot = -180.77070062531
|
||||
77000 ekin = 21.759026189981 | erot = 19.8043252195865 | epot = -222.334052034218 | etot = -180.770700624651
|
||||
78000 ekin = 21.6392419839505 | erot = 19.8262630279235 | epot = -222.236205635988 | etot = -180.770700624114
|
||||
79000 ekin = 21.5302317519718 | erot = 19.8938812521574 | epot = -222.19481362777 | etot = -180.770700623641
|
||||
80000 ekin = 21.4402276725659 | erot = 20.0060100278939 | epot = -222.216938324075 | etot = -180.770700623615
|
||||
81000 ekin = 21.3741486759857 | erot = 20.1585144791605 | epot = -222.303363779439 | etot = -180.770700624293
|
||||
82000 ekin = 21.3325013763506 | erot = 20.3431413542717 | epot = -222.446343355881 | etot = -180.770700625259
|
||||
83000 ekin = 21.3128808684039 | erot = 20.5483309907712 | epot = -222.63191248578 | etot = -180.770700626605
|
||||
84000 ekin = 21.3107661707932 | erot = 20.7607919785166 | epot = -222.842258777119 | etot = -180.77070062781
|
||||
85000 ekin = 21.3216301567279 | erot = 20.9678418539237 | epot = -223.060172639486 | etot = -180.770700628834
|
||||
86000 ekin = 21.3400295156725 | erot = 21.1566564817949 | epot = -223.267386627524 | etot = -180.770700630057
|
||||
87000 ekin = 21.3617783036995 | erot = 21.3170902458388 | epot = -223.449569179883 | etot = -180.770700630345
|
||||
88000 ekin = 21.3873913218413 | erot = 21.4454439910414 | epot = -223.603535942849 | etot = -180.770700629967
|
||||
89000 ekin = 21.4215740693994 | erot = 21.5439953706451 | epot = -223.73627006895 | etot = -180.770700628906
|
||||
90000 ekin = 21.4723781618096 | erot = 21.6216769093343 | epot = -223.864755698472 | etot = -180.770700627328
|
||||
91000 ekin = 21.5494066254725 | erot = 21.6927202486459 | epot = -224.012827499725 | etot = -180.770700625606
|
||||
92000 ekin = 21.6619209347601 | erot = 21.7730744493007 | epot = -224.20569600835 | etot = -180.77070062429
|
||||
93000 ekin = 21.8158778641474 | erot = 21.8756732628043 | epot = -224.462251750827 | etot = -180.770700623875
|
||||
94000 ekin = 22.0110275730999 | erot = 22.0060799403016 | epot = -224.787808138198 | etot = -180.770700624796
|
||||
95000 ekin = 22.2387555838384 | erot = 22.1596167137185 | epot = -225.169072924291 | etot = -180.770700626735
|
||||
96000 ekin = 22.4832444899359 | erot = 22.3220202374394 | epot = -225.575965356876 | etot = -180.770700629501
|
||||
97000 ekin = 22.7237276202691 | erot = 22.4720556690115 | epot = -225.966483921719 | etot = -180.770700632439
|
||||
98000 ekin = 22.9377647716038 | erot = 22.5858660312271 | epot = -226.294331437119 | etot = -180.770700634288
|
||||
99000 ekin = 23.1071231637233 | erot = 22.645741104618 | epot = -226.523564904806 | etot = -180.770700636465
|
||||
100000 ekin = 23.2156001924307 | erot = 22.6390310936004 | epot = -226.625331923823 | etot = -180.770700637791
|
||||
100000 0.10528617 -1.5761124 0.044860201 -1.3743901 -1.9205819e-05 1000000
|
||||
Loop time of 39.1 on 4 procs for 100000 steps with 148 atoms
|
||||
Loop time of 28.0802 on 4 procs for 100000 steps with 148 atoms
|
||||
|
||||
Performance: 2209.721 tau/day, 2557.548 timesteps/s
|
||||
99.5% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
Performance: 3076.899 tau/day, 3561.226 timesteps/s
|
||||
99.7% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 33.685 | 34.998 | 35.676 | 13.1 | 89.51
|
||||
Bond | 0.30808 | 0.31468 | 0.31829 | 0.7 | 0.80
|
||||
Neigh | 0.008861 | 0.0089438 | 0.009012 | 0.1 | 0.02
|
||||
Comm | 0.79376 | 0.80216 | 0.8131 | 0.9 | 2.05
|
||||
Output | 0.054153 | 0.056983 | 0.058706 | 0.8 | 0.15
|
||||
Modify | 0.55623 | 0.5647 | 0.57239 | 0.9 | 1.44
|
||||
Other | | 2.354 | | | 6.02
|
||||
Pair | 16.209 | 21.356 | 25.248 | 81.3 | 76.05
|
||||
Bond | 0.26072 | 0.26526 | 0.27015 | 0.9 | 0.94
|
||||
Neigh | 0.005772 | 0.0058625 | 0.005932 | 0.1 | 0.02
|
||||
Comm | 1.7227 | 5.6246 | 10.79 | 158.9 | 20.03
|
||||
Output | 0.043943 | 0.046855 | 0.048664 | 0.9 | 0.17
|
||||
Modify | 0.54715 | 0.55336 | 0.55902 | 0.7 | 1.97
|
||||
Other | | 0.2279 | | | 0.81
|
||||
|
||||
Nlocal: 37.0000 ave 38 max 36 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Nghost: 111.000 ave 112 max 110 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Neighs: 1693.75 ave 1737 max 1653 min
|
||||
Histogram: 1 1 0 0 0 0 0 1 0 1
|
||||
Neighs: 1049.75 ave 1270 max 757 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 6775
|
||||
Ave neighs/atom = 45.777027
|
||||
Total # of neighbors = 4199
|
||||
Ave neighs/atom = 28.371622
|
||||
Ave special neighs/atom = 6.0000000
|
||||
Neighbor list builds = 100
|
||||
Dangerous builds = 0
|
||||
|
||||
#write_data last_config.${number}.* nocoeff
|
||||
write_data last_config.${number}.* nocoeff
|
||||
write_data last_config.5.* nocoeff
|
||||
System init for write_data ...
|
||||
#write_restart last_config.${number}.*
|
||||
Total wall time: 0:00:39
|
||||
Total wall time: 0:00:28
|
||||
|
||||
@ -8,7 +8,7 @@ units lj
|
||||
|
||||
dimension 3
|
||||
|
||||
newton off
|
||||
newton on
|
||||
|
||||
boundary p p p
|
||||
|
||||
@ -69,3 +69,4 @@ dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22
|
||||
run 1000000
|
||||
|
||||
write_data last_config.${number}.* nocoeff
|
||||
#write_restart last_config.${number}.*
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
@ -8,7 +8,7 @@ units lj
|
||||
|
||||
dimension 3
|
||||
|
||||
newton off
|
||||
newton on
|
||||
|
||||
boundary p p p
|
||||
|
||||
@ -69,3 +69,4 @@ dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22
|
||||
run 1000000
|
||||
|
||||
write_data last_config.${number}.* nocoeff
|
||||
#write_restart last_config.${number}.*
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
@ -8,7 +8,7 @@ units lj
|
||||
|
||||
dimension 3
|
||||
|
||||
newton off
|
||||
newton on
|
||||
|
||||
boundary p p p
|
||||
|
||||
@ -69,3 +69,4 @@ dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22
|
||||
run 1000000
|
||||
|
||||
write_data last_config.${number}.* nocoeff
|
||||
#write_restart last_config.${number}.*
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
@ -11,7 +11,7 @@ units lj
|
||||
|
||||
dimension 3
|
||||
|
||||
newton off
|
||||
newton on
|
||||
|
||||
boundary p p p
|
||||
|
||||
@ -84,3 +84,4 @@ dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22
|
||||
run 1000000
|
||||
|
||||
write_data last_config.${number}.* nocoeff
|
||||
#write_restart last_config.${number}.*
|
||||
|
||||
@ -11,7 +11,7 @@ units lj
|
||||
|
||||
dimension 3
|
||||
|
||||
newton off
|
||||
newton on
|
||||
|
||||
boundary p p p
|
||||
|
||||
@ -84,3 +84,4 @@ dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22
|
||||
run 1000000
|
||||
|
||||
write_data last_config.${number}.* nocoeff
|
||||
#write_restart last_config.${number}.*
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
@ -8,7 +8,7 @@ units lj
|
||||
|
||||
dimension 3
|
||||
|
||||
newton off
|
||||
newton on
|
||||
|
||||
boundary p p p
|
||||
|
||||
@ -70,3 +70,4 @@ dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22
|
||||
run 1000000
|
||||
|
||||
write_data last_config.${number}.* nocoeff
|
||||
#write_restart last_config.${number}.*
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
232
examples/PACKAGES/cgdna/examples/test.sh
Executable file
232
examples/PACKAGES/cgdna/examples/test.sh
Executable file
@ -0,0 +1,232 @@
|
||||
#! /bin/bash
|
||||
|
||||
DATE='2Jul21'
|
||||
LMPDIR=/Users/ohenrich/Work/code/lammps
|
||||
|
||||
SRCDIR=$LMPDIR/src
|
||||
EXDIR=$LMPDIR/examples/PACKAGES/cgdna/examples
|
||||
|
||||
if [ $# -eq 1 ] && [ $1 = run ]; then
|
||||
echo '# Compiling executable in' $SRCDIR
|
||||
|
||||
cd $SRCDIR
|
||||
make clean-all
|
||||
make -j8 mpi
|
||||
|
||||
######################################################
|
||||
echo '# Running oxDNA duplex1 test'
|
||||
cd $EXDIR/oxDNA/duplex1
|
||||
mkdir test
|
||||
cd test
|
||||
cp $SRCDIR/lmp_mpi .
|
||||
cp ../in.duplex1 .
|
||||
cp ../data.duplex1 .
|
||||
|
||||
mpirun -np 1 ./lmp_mpi < in.duplex1 > /dev/null
|
||||
mv log.lammps log.$DATE.duplex1.g++.1
|
||||
grep etot log.$DATE.duplex1.g++.1 > e_test.dat
|
||||
grep etot ../log*1 > e_old.dat
|
||||
ndiff -relerr 1e-8 e_test.dat e_old.dat
|
||||
|
||||
mpirun -np 4 ./lmp_mpi < in.duplex1 > /dev/null
|
||||
mv log.lammps log.$DATE.duplex1.g++.4
|
||||
grep etot log.$DATE.duplex1.g++.4 > e_test.dat
|
||||
grep etot ../log*4 > e_old.dat
|
||||
ndiff -relerr 1e-8 e_test.dat e_old.dat
|
||||
|
||||
######################################################
|
||||
|
||||
######################################################
|
||||
echo '# Running oxDNA duplex2 test'
|
||||
cd $EXDIR/oxDNA/duplex2
|
||||
mkdir test
|
||||
cd test
|
||||
cp $SRCDIR/lmp_mpi .
|
||||
cp ../in.duplex2 .
|
||||
cp ../data.duplex2 .
|
||||
|
||||
mpirun -np 1 ./lmp_mpi < in.duplex2 > /dev/null
|
||||
mv log.lammps log.$DATE.duplex2.g++.1
|
||||
grep etot log.$DATE.duplex2.g++.1 > e_test.dat
|
||||
grep etot ../log*1 > e_old.dat
|
||||
ndiff -relerr 1e-8 e_test.dat e_old.dat
|
||||
|
||||
mpirun -np 4 ./lmp_mpi < in.duplex2 > /dev/null
|
||||
mv log.lammps log.$DATE.duplex2.g++.4
|
||||
grep etot log.$DATE.duplex2.g++.4 > e_test.dat
|
||||
grep etot ../log*4 > e_old.dat
|
||||
ndiff -relerr 1e-8 e_test.dat e_old.dat
|
||||
|
||||
######################################################
|
||||
|
||||
######################################################
|
||||
echo '# Running oxDNA2 duplex1 test'
|
||||
cd $EXDIR/oxDNA2/duplex1
|
||||
mkdir test
|
||||
cd test
|
||||
cp $SRCDIR/lmp_mpi .
|
||||
cp ../in.duplex1 .
|
||||
cp ../data.duplex1 .
|
||||
|
||||
mpirun -np 1 ./lmp_mpi < in.duplex1 > /dev/null
|
||||
mv log.lammps log.$DATE.duplex1.g++.1
|
||||
grep etot log.$DATE.duplex1.g++.1 > e_test.dat
|
||||
grep etot ../log*1 > e_old.dat
|
||||
ndiff -relerr 1e-8 e_test.dat e_old.dat
|
||||
|
||||
mpirun -np 4 ./lmp_mpi < in.duplex1 > /dev/null
|
||||
mv log.lammps log.$DATE.duplex1.g++.4
|
||||
grep etot log.$DATE.duplex1.g++.4 > e_test.dat
|
||||
grep etot ../log*4 > e_old.dat
|
||||
ndiff -relerr 1e-8 e_test.dat e_old.dat
|
||||
|
||||
######################################################
|
||||
|
||||
######################################################
|
||||
echo '# Running oxDNA2 duplex2 test'
|
||||
cd $EXDIR/oxDNA2/duplex2
|
||||
mkdir test
|
||||
cd test
|
||||
cp $SRCDIR/lmp_mpi .
|
||||
cp ../in.duplex2 .
|
||||
cp ../data.duplex2 .
|
||||
|
||||
mpirun -np 1 ./lmp_mpi < in.duplex2 > /dev/null
|
||||
mv log.lammps log.$DATE.duplex2.g++.1
|
||||
grep etot log.$DATE.duplex2.g++.1 > e_test.dat
|
||||
grep etot ../log*1 > e_old.dat
|
||||
ndiff -relerr 1e-8 e_test.dat e_old.dat
|
||||
|
||||
mpirun -np 4 ./lmp_mpi < in.duplex2 > /dev/null
|
||||
mv log.lammps log.$DATE.duplex2.g++.4
|
||||
grep etot log.$DATE.duplex2.g++.4 > e_test.dat
|
||||
grep etot ../log*4 > e_old.dat
|
||||
ndiff -relerr 1e-8 e_test.dat e_old.dat
|
||||
|
||||
######################################################
|
||||
|
||||
######################################################
|
||||
echo '# Running oxDNA2 duplex3 test'
|
||||
cd $EXDIR/oxDNA2/duplex3
|
||||
mkdir test
|
||||
cd test
|
||||
cp $SRCDIR/lmp_mpi .
|
||||
cp ../in.duplex3 .
|
||||
cp ../data.duplex3 .
|
||||
|
||||
mpirun -np 1 ./lmp_mpi < in.duplex3 > /dev/null
|
||||
mv log.lammps log.$DATE.duplex3.g++.1
|
||||
grep etot log.$DATE.duplex3.g++.1 > e_test.dat
|
||||
grep etot ../log*1 > e_old.dat
|
||||
ndiff -relerr 1e-8 e_test.dat e_old.dat
|
||||
|
||||
mpirun -np 4 ./lmp_mpi < in.duplex3 > /dev/null
|
||||
mv log.lammps log.$DATE.duplex3.g++.4
|
||||
grep etot log.$DATE.duplex3.g++.4 > e_test.dat
|
||||
grep etot ../log*4 > e_old.dat
|
||||
ndiff -relerr 1e-8 e_test.dat e_old.dat
|
||||
|
||||
######################################################
|
||||
|
||||
######################################################
|
||||
echo '# Running oxDNA2 unique_bp test'
|
||||
cd $EXDIR/oxDNA2/unique_bp
|
||||
mkdir test
|
||||
cd test
|
||||
cp $SRCDIR/lmp_mpi .
|
||||
cp ../in.duplex4.4type .
|
||||
cp ../in.duplex4.8type .
|
||||
cp ../data.duplex4.4type .
|
||||
cp ../data.duplex4.8type .
|
||||
|
||||
mpirun -np 1 ./lmp_mpi < in.duplex4.4type > /dev/null
|
||||
mv log.lammps log.$DATE.duplex4.4type.g++.1
|
||||
grep etot log.$DATE.duplex4.4type.g++.1 > e_test.dat
|
||||
grep etot ../log*4type*1 > e_old.dat
|
||||
ndiff -relerr 1e-8 e_test.dat e_old.dat
|
||||
|
||||
mpirun -np 4 ./lmp_mpi < in.duplex4.4type > /dev/null
|
||||
mv log.lammps log.$DATE.duplex4.4type.g++.4
|
||||
grep etot log.$DATE.duplex4.4type.g++.4 > e_test.dat
|
||||
grep etot ../log*4type*4 > e_old.dat
|
||||
ndiff -relerr 1e-8 e_test.dat e_old.dat
|
||||
|
||||
mpirun -np 1 ./lmp_mpi < in.duplex4.8type > /dev/null
|
||||
mv log.lammps log.$DATE.duplex4.8type.g++.1
|
||||
grep etot log.$DATE.duplex4.8type.g++.1 > e_test.dat
|
||||
grep etot ../log*8type*1 > e_old.dat
|
||||
ndiff -relerr 1e-8 e_test.dat e_old.dat
|
||||
|
||||
mpirun -np 4 ./lmp_mpi < in.duplex4.8type > /dev/null
|
||||
mv log.lammps log.$DATE.duplex4.8type.g++.4
|
||||
grep etot log.$DATE.duplex4.8type.g++.4 > e_test.dat
|
||||
grep etot ../log*8type*4 > e_old.dat
|
||||
ndiff -relerr 1e-8 e_test.dat e_old.dat
|
||||
|
||||
######################################################
|
||||
|
||||
######################################################
|
||||
echo '# Running oxDNA2 dsring test'
|
||||
cd $EXDIR/oxDNA2/dsring
|
||||
mkdir test
|
||||
cd test
|
||||
cp $SRCDIR/lmp_mpi .
|
||||
cp ../in.dsring .
|
||||
cp ../data.dsring .
|
||||
|
||||
mpirun -np 1 ./lmp_mpi < in.dsring > /dev/null
|
||||
mv log.lammps log.$DATE.dsring.g++.1
|
||||
grep etot log.$DATE.dsring.g++.1 > e_test.dat
|
||||
grep etot ../log*1 > e_old.dat
|
||||
ndiff -relerr 1e-8 e_test.dat e_old.dat
|
||||
|
||||
mpirun -np 4 ./lmp_mpi < in.dsring > /dev/null
|
||||
mv log.lammps log.$DATE.dsring.g++.4
|
||||
grep etot log.$DATE.dsring.g++.4 > e_test.dat
|
||||
grep etot ../log*4 > e_old.dat
|
||||
ndiff -relerr 1e-8 e_test.dat e_old.dat
|
||||
|
||||
######################################################
|
||||
|
||||
######################################################
|
||||
echo '# Running oxRNA2 duplex2 test'
|
||||
cd $EXDIR/oxRNA2/duplex2
|
||||
mkdir test
|
||||
cd test
|
||||
cp $SRCDIR/lmp_mpi .
|
||||
cp ../in.duplex2 .
|
||||
cp ../data.duplex2 .
|
||||
|
||||
mpirun -np 1 ./lmp_mpi < in.duplex2 > /dev/null
|
||||
mv log.lammps log.$DATE.duplex2.g++.1
|
||||
grep etot log.$DATE.duplex2.g++.1 > e_test.dat
|
||||
grep etot ../log*1 > e_old.dat
|
||||
ndiff -relerr 1e-8 e_test.dat e_old.dat
|
||||
|
||||
mpirun -np 4 ./lmp_mpi < in.duplex2 > /dev/null
|
||||
mv log.lammps log.$DATE.duplex2.g++.4
|
||||
grep etot log.$DATE.duplex2.g++.4 > e_test.dat
|
||||
grep etot ../log*4 > e_old.dat
|
||||
ndiff -relerr 1e-8 e_test.dat e_old.dat
|
||||
|
||||
######################################################
|
||||
echo '# Done'
|
||||
|
||||
elif [ $# -eq 1 ] && [ $1 = clean ]; then
|
||||
echo '# Deleting test directories'
|
||||
rm -rf $EXDIR/oxDNA/duplex1/test
|
||||
rm -rf $EXDIR/oxDNA/duplex2/test
|
||||
rm -rf $EXDIR/oxDNA2/duplex1/test
|
||||
rm -rf $EXDIR/oxDNA2/duplex2/test
|
||||
rm -rf $EXDIR/oxDNA2/duplex3/test
|
||||
rm -rf $EXDIR/oxDNA2/unique_bp/test
|
||||
rm -rf $EXDIR/oxDNA2/dsring/test
|
||||
rm -rf $EXDIR/oxRNA2/duplex2/test
|
||||
echo '# Done'
|
||||
|
||||
else
|
||||
echo '# Usage:'
|
||||
echo '# ./test.sh run ... to run test suite'
|
||||
echo '# ./test.sh clean ... to delete test directories'
|
||||
|
||||
fi
|
||||
@ -15,6 +15,8 @@
|
||||
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "error.h"
|
||||
#include "force.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
@ -46,6 +48,11 @@ AtomVecOxdna::AtomVecOxdna(LAMMPS *lmp) : AtomVec(lmp)
|
||||
fields_data_vel = (char *) "id v";
|
||||
|
||||
setup_fields();
|
||||
|
||||
if(!force->newton_bond) {
|
||||
error->warning(FLERR,"Write_data command requires newton_bond on to preserve 3'->5' bond polarity");
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
Reference in New Issue
Block a user