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Updated tests and documentation, added warning message

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This commit is contained in:
Oliver Henrich
2021-07-19 11:22:06 +01:00
parent b7a17dc25d
commit 15b3b6445e
47 changed files with 19656 additions and 19382 deletions
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11
doc/src/bond_oxdna.rst
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@ -86,12 +86,11 @@ commands:
.. warning:: .. warning::
LAMMPS has per se no concept of bond directionality. This means the bond definition If data files are produced with :doc:`write_data <write_data>`, then the
(i.e. the sequence of atom IDs) in data files produced with :doc:`write_data <write_data>` :doc:`newton <newton>` command should be set to *newton on* or *newton off on*.
can be different from the one provided in your initial data file. If this is the case, Otherwise the data files will not have the same 3' to 5' polarity as the
then the correct 3' to 5' polarity needs to be restored before using the data file. initial data file. This limitation does not apply to binary restart files
This limitation does not apply to binary restart files produced with produced with :doc:`write_restart <write_restart>`.
:doc:`write_restart <write_restart>`.
Example input and data files for DNA and RNA duplexes can be found in 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 examples/PACKAGES/cgdna/examples/oxDNA/ , /oxDNA2/ and /oxRNA2/. A simple python

8
examples/PACKAGES/cgdna/README
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@ -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 /examples/oxRNA2/duplex2
This example uses the duplex2 with the oxRNA2 force field instead of oxDNA or This example uses the duplex2 with the oxRNA2 force field instead of oxDNA or

3
examples/PACKAGES/cgdna/examples/oxDNA/duplex1/in.duplex1
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@ -7,7 +7,7 @@ units lj
dimension 3 dimension 3
newton off newton on
boundary p p p 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 run 1000000
write_data last_config.${number}.* nocoeff write_data last_config.${number}.* nocoeff
#write_restart last_config.${number}.*

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examples/PACKAGES/cgdna/examples/oxDNA/duplex1/log.27May21.duplex1.g++.1
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examples/PACKAGES/cgdna/examples/oxDNA/duplex2/in.duplex2
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@ -7,7 +7,7 @@ units lj
dimension 3 dimension 3
newton off newton on
boundary p p p 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 run 1000000
write_data last_config.${number}.* nocoeff write_data last_config.${number}.* nocoeff
#write_restart last_config.${number}.*

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examples/PACKAGES/cgdna/examples/oxDNA/duplex2/log.27May21.duplex2.g++.1
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examples/PACKAGES/cgdna/examples/oxDNA2/dsring/in.dsring
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@ -8,7 +8,7 @@ units lj
dimension 3 dimension 3
newton off newton on
boundary p p p 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 run 100000
#write_data last_config.${number}.* nocoeff write_data last_config.${number}.* nocoeff
#write_restart last_config.${number}.* #write_restart last_config.${number}.*

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examples/PACKAGES/cgdna/examples/oxDNA2/dsring/log.2Jul21.dsring.g++.1
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@ -9,7 +9,7 @@ units lj
dimension 3 dimension 3
newton off newton on
boundary p p p boundary p p p
@ -30,7 +30,7 @@ Reading data file ...
reading velocities ... reading velocities ...
148 velocities 148 velocities
scanning bonds ... scanning bonds ...
2 = max bonds/atom 1 = max bonds/atom
148 ellipsoids 148 ellipsoids
reading bonds ... reading bonds ...
148 bonds 148 bonds
@ -115,151 +115,151 @@ Neighbor list info ...
binsize = 2.8194939, bins = 36 36 36 binsize = 2.8194939, bins = 36 36 36
5 neighbor lists, perpetual/occasional/extra = 5 0 0 5 neighbor lists, perpetual/occasional/extra = 5 0 0
(1) pair oxdna2/excv, perpetual (1) pair oxdna2/excv, perpetual
attributes: half, newton off attributes: half, newton on
pair build: half/bin/newtoff pair build: half/bin/newton
stencil: full/bin/3d stencil: half/bin/3d
bin: standard bin: standard
(2) pair oxdna2/hbond, perpetual, copy from (1) (2) pair oxdna2/hbond, perpetual, copy from (1)
attributes: half, newton off attributes: half, newton on
pair build: copy pair build: copy
stencil: none stencil: none
bin: none bin: none
(3) pair oxdna2/xstk, perpetual, copy from (1) (3) pair oxdna2/xstk, perpetual, copy from (1)
attributes: half, newton off attributes: half, newton on
pair build: copy pair build: copy
stencil: none stencil: none
bin: none bin: none
(4) pair oxdna2/coaxstk, perpetual, copy from (1) (4) pair oxdna2/coaxstk, perpetual, copy from (1)
attributes: half, newton off attributes: half, newton on
pair build: copy pair build: copy
stencil: none stencil: none
bin: none bin: none
(5) pair oxdna2/dh, perpetual, copy from (1) (5) pair oxdna2/dh, perpetual, copy from (1)
attributes: half, newton off attributes: half, newton on
pair build: copy pair build: copy
stencil: none stencil: none
bin: none bin: none
WARNING: Communication cutoff adjusted to 5.638987723814632 (../comm.cpp:739) WARNING: Communication cutoff adjusted to 5.638987723814632 (../comm.cpp:739)
0 ekin = 20.4724634226502 | erot = 21.0406985312466 | epot = -222.283862600785 | etot = -180.770700646889 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 Step Temp E_pair E_mol TotEng Press Volume
0 0.092845639 -1.5501211 0.04820308 -1.3635905 -9.0052368e-06 1000000 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 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 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 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 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 6000 ekin = 20.5959625511847 | erot = 21.8369756530727 | epot = -223.203638857302 | etot = -180.770700653045
7000 ekin = 20.5431034482068 | erot = 21.8556844173875 | epot = -223.169488517717 | etot = -180.770700652122 7000 ekin = 20.5431034482068 | erot = 21.8556844173875 | epot = -223.169488517716 | etot = -180.770700652122
8000 ekin = 20.4774701419091 | erot = 21.8437134145374 | epot = -223.091884207389 | etot = -180.770700650943 8000 ekin = 20.4774701419092 | erot = 21.8437134145374 | epot = -223.091884207389 | etot = -180.770700650943
9000 ekin = 20.4074566554237 | erot = 21.8097283692398 | epot = -222.98788567426 | etot = -180.770700649597 9000 ekin = 20.4074566554238 | erot = 21.8097283692398 | epot = -222.987885674261 | etot = -180.770700649597
10000 ekin = 20.3427303660295 | erot = 21.7629575866663 | epot = -222.876388600949 | etot = -180.770700648253 10000 ekin = 20.3427303660296 | erot = 21.7629575866663 | epot = -222.876388600948 | etot = -180.770700648253
11000 ekin = 20.2927407149576 | erot = 21.7112100845349 | epot = -222.774651446682 | etot = -180.770700647189 11000 ekin = 20.2927407149577 | erot = 21.7112100845349 | epot = -222.774651446682 | etot = -180.770700647189
12000 ekin = 20.2665977502212 | erot = 21.6594999867139 | epot = -222.696798383221 | etot = -180.770700646286 12000 ekin = 20.2665977502213 | erot = 21.6594999867139 | epot = -222.696798383221 | etot = -180.770700646286
13000 ekin = 20.2733920359445 | erot = 21.6092715397933 | epot = -222.653364221616 | etot = -180.770700645878 13000 ekin = 20.2733920359447 | erot = 21.6092715397932 | epot = -222.653364221616 | etot = -180.770700645878
14000 ekin = 20.3196524789068 | erot = 21.5586630974992 | epot = -222.649016222075 | etot = -180.770700645669 14000 ekin = 20.319652478907 | erot = 21.558663097499 | epot = -222.649016222075 | etot = -180.770700645669
15000 ekin = 20.4104009374289 | erot = 21.5031572556306 | epot = -222.684258838857 | etot = -180.770700645798 15000 ekin = 20.4104009374291 | erot = 21.5031572556304 | epot = -222.684258838857 | etot = -180.770700645798
16000 ekin = 20.5472869005792 | erot = 21.4346177247041 | epot = -222.752605272036 | etot = -180.770700646753 16000 ekin = 20.5472869005793 | erot = 21.4346177247038 | epot = -222.752605272036 | etot = -180.770700646753
17000 ekin = 20.7266657908773 | erot = 21.3426631585217 | epot = -222.840029597232 | etot = -180.770700647833 17000 ekin = 20.7266657908775 | erot = 21.3426631585214 | epot = -222.840029597232 | etot = -180.770700647833
18000 ekin = 20.9417612759979 | erot = 21.2178611180927 | epot = -222.930323042997 | etot = -180.770700648907 18000 ekin = 20.9417612759981 | erot = 21.2178611180923 | epot = -222.930323042997 | etot = -180.770700648907
19000 ekin = 21.1819308659397 | erot = 21.0532289630294 | epot = -223.00586047892 | etot = -180.770700649951 19000 ekin = 21.1819308659399 | erot = 21.0532289630289 | epot = -223.00586047892 | etot = -180.770700649951
20000 ekin = 21.4358169889474 | erot = 20.8473069564707 | epot = -223.053824595387 | etot = -180.770700649969 20000 ekin = 21.4358169889477 | erot = 20.8473069564703 | epot = -223.053824595387 | etot = -180.770700649969
21000 ekin = 21.6968513750997 | erot = 20.6066744652586 | epot = -223.074226489837 | etot = -180.770700649479 21000 ekin = 21.6968513751 | erot = 20.6066744652581 | epot = -223.074226489837 | etot = -180.770700649478
22000 ekin = 21.9614458442782 | erot = 20.3429420444511 | epot = -223.07508853737 | etot = -180.770700648641 22000 ekin = 21.9614458442786 | erot = 20.3429420444505 | epot = -223.07508853737 | etot = -180.770700648641
23000 ekin = 22.22760997557 | erot = 20.0703385165243 | epot = -223.068649139875 | etot = -180.770700647781 23000 ekin = 22.2276099755705 | erot = 20.0703385165238 | epot = -223.068649139875 | etot = -180.77070064778
24000 ekin = 22.4935893196671 | erot = 19.8020671721666 | epot = -223.066357139276 | etot = -180.770700647443 24000 ekin = 22.4935893196675 | erot = 19.802067172166 | epot = -223.066357139276 | etot = -180.770700647443
25000 ekin = 22.7566064548224 | erot = 19.5464828008842 | epot = -223.073789902976 | etot = -180.770700647269 25000 ekin = 22.7566064548228 | erot = 19.5464828008836 | epot = -223.073789902975 | etot = -180.770700647269
26000 ekin = 23.0126717548395 | erot = 19.3065017718468 | epot = -223.089874174572 | etot = -180.770700647886 26000 ekin = 23.0126717548399 | erot = 19.3065017718462 | epot = -223.089874174571 | etot = -180.770700647885
27000 ekin = 23.255041706059 | erot = 19.0797753474573 | epot = -223.105517701933 | etot = -180.770700648417 27000 ekin = 23.2550417060594 | erot = 19.0797753474567 | epot = -223.105517701932 | etot = -180.770700648416
28000 ekin = 23.4774329734801 | erot = 18.864619729958 | epot = -223.112753352067 | etot = -180.770700648629 28000 ekin = 23.4774329734805 | erot = 18.8646197299574 | epot = -223.112753352067 | etot = -180.770700648629
29000 ekin = 23.674792772066 | erot = 18.662865341183 | epot = -223.108358761694 | etot = -180.770700648445 29000 ekin = 23.6747927720663 | erot = 18.6628653411825 | epot = -223.108358761693 | etot = -180.770700648445
30000 ekin = 23.8432321400243 | erot = 18.481221698364 | epot = -223.095154486375 | etot = -180.770700647987 30000 ekin = 23.8432321400247 | erot = 18.4812216983637 | epot = -223.095154486375 | etot = -180.770700647986
31000 ekin = 23.9793041752225 | erot = 18.3307845334023 | epot = -223.08078935577 | etot = -180.770700647145 31000 ekin = 23.9793041752229 | erot = 18.330784533402 | epot = -223.08078935577 | etot = -180.770700647145
32000 ekin = 24.0810246040231 | erot = 18.2261577056005 | epot = -223.07788295592 | etot = -180.770700646296 32000 ekin = 24.0810246040235 | erot = 18.2261577056003 | epot = -223.077882955919 | etot = -180.770700646295
33000 ekin = 24.1468986449394 | erot = 18.1820705445407 | epot = -223.09966983514 | etot = -180.77070064566 33000 ekin = 24.1468986449398 | erot = 18.1820705445406 | epot = -223.09966983514 | etot = -180.770700645659
34000 ekin = 24.175661513286 | erot = 18.2103812210173 | epot = -223.156743379607 | etot = -180.770700645304 34000 ekin = 24.1756615132863 | erot = 18.2103812210172 | epot = -223.156743379607 | etot = -180.770700645303
35000 ekin = 24.1663193894648 | erot = 18.3185351073568 | epot = -223.25555514209 | etot = -180.770700645268 35000 ekin = 24.1663193894652 | erot = 18.3185351073568 | epot = -223.255555142089 | etot = -180.770700645267
36000 ekin = 24.1167205812961 | erot = 18.5091649894186 | epot = -223.396586216222 | etot = -180.770700645508 36000 ekin = 24.1167205812964 | erot = 18.5091649894187 | epot = -223.396586216223 | etot = -180.770700645508
37000 ekin = 24.0274860006133 | erot = 18.7785134320987 | epot = -223.576700078937 | etot = -180.770700646225 37000 ekin = 24.0274860006135 | erot = 18.7785134320989 | epot = -223.576700078937 | etot = -180.770700646225
38000 ekin = 23.8991479078982 | erot = 19.1166063146994 | epot = -223.78645486989 | etot = -180.770700647292 38000 ekin = 23.8991479078985 | erot = 19.1166063146995 | epot = -223.78645486989 | etot = -180.770700647292
39000 ekin = 23.7326911853235 | erot = 19.5069160952492 | epot = -224.010307929336 | etot = -180.770700648763 39000 ekin = 23.7326911853236 | erot = 19.5069160952493 | epot = -224.010307929336 | etot = -180.770700648763
40000 ekin = 23.529422307212 | erot = 19.9254673141826 | epot = -224.225590272293 | etot = -180.770700650898 40000 ekin = 23.5294223072121 | erot = 19.9254673141826 | epot = -224.225590272292 | etot = -180.770700650897
41000 ekin = 23.2899396141392 | erot = 20.340809778056 | epot = -224.401450045566 | etot = -180.770700653371 41000 ekin = 23.2899396141392 | erot = 20.340809778056 | epot = -224.401450045567 | etot = -180.770700653371
42000 ekin = 23.0154529235023 | erot = 20.7165619564846 | epot = -224.502715535761 | etot = -180.770700655775 42000 ekin = 23.0154529235024 | erot = 20.7165619564844 | epot = -224.502715535761 | etot = -180.770700655774
43000 ekin = 22.7111536814278 | erot = 21.0163895622229 | epot = -224.498243901358 | etot = -180.770700657707 43000 ekin = 22.7111536814278 | erot = 21.0163895622227 | epot = -224.498243901357 | etot = -180.770700657707
44000 ekin = 22.3710575806355 | erot = 21.2060371289781 | epot = -224.347795365753 | etot = -180.770700656139 44000 ekin = 22.3710575806356 | erot = 21.2060371289779 | epot = -224.347795365752 | etot = -180.770700656139
45000 ekin = 22.0515843162891 | erot = 21.2588026881768 | epot = -224.081087646891 | etot = -180.770700642425 45000 ekin = 22.0515843162889 | erot = 21.2588026881767 | epot = -224.08108764689 | etot = -180.770700642424
46000 ekin = 21.7855632553136 | erot = 21.2036013766602 | epot = -223.759865260062 | etot = -180.770700628088 46000 ekin = 21.7855632553132 | erot = 21.2036013766601 | epot = -223.75986526006 | etot = -180.770700628087
47000 ekin = 21.5167766971458 | erot = 21.065636702367 | epot = -223.353114011015 | etot = -180.770700611502 47000 ekin = 21.5167766971454 | erot = 21.0656367023669 | epot = -223.353114011014 | etot = -180.770700611502
48000 ekin = 21.4540196107337 | erot = 20.8430832424325 | epot = -223.067803499525 | etot = -180.770700646359 48000 ekin = 21.4540196107332 | erot = 20.8430832424325 | epot = -223.067803499524 | etot = -180.770700646358
49000 ekin = 21.3647564765278 | erot = 20.5521507191688 | epot = -222.687607816921 | etot = -180.770700621224 49000 ekin = 21.3647564765273 | erot = 20.5521507191689 | epot = -222.68760781692 | etot = -180.770700621224
50000 ekin = 21.3125768184621 | erot = 20.2526464671332 | epot = -222.335923904309 | etot = -180.770700618714 50000 ekin = 21.3125768184616 | erot = 20.2526464671335 | epot = -222.335923904309 | etot = -180.770700618713
51000 ekin = 21.2949924810838 | erot = 19.9798421626043 | epot = -222.045535260404 | etot = -180.770700616716 51000 ekin = 21.2949924810833 | erot = 19.9798421626046 | epot = -222.045535260403 | etot = -180.770700616715
52000 ekin = 21.3137144249685 | erot = 19.7627691343687 | epot = -221.847184173962 | etot = -180.770700614625 52000 ekin = 21.313714424968 | erot = 19.762769134369 | epot = -221.847184173962 | etot = -180.770700614625
53000 ekin = 21.3664076685105 | erot = 19.6202359856899 | epot = -221.757344279694 | etot = -180.770700625493 53000 ekin = 21.3664076685101 | erot = 19.6202359856903 | epot = -221.757344279694 | etot = -180.770700625493
54000 ekin = 21.421424552406 | erot = 19.55882323195 | epot = -221.750948393747 | etot = -180.770700609391 54000 ekin = 21.4214245524056 | erot = 19.5588232319504 | epot = -221.750948393747 | etot = -180.770700609391
55000 ekin = 21.5995673396093 | erot = 19.5805214885678 | epot = -221.950789453583 | etot = -180.770700625406 55000 ekin = 21.5995673396088 | erot = 19.5805214885682 | epot = -221.950789453583 | etot = -180.770700625406
56000 ekin = 21.7643125668307 | erot = 19.6816042107778 | epot = -222.216617401429 | etot = -180.77070062382 56000 ekin = 21.7643125668302 | erot = 19.6816042107783 | epot = -222.216617401428 | etot = -180.77070062382
57000 ekin = 21.9221309084445 | erot = 19.8499880475953 | epot = -222.542819582064 | etot = -180.770700626024 57000 ekin = 21.922130908444 | erot = 19.8499880475958 | epot = -222.542819582063 | etot = -180.770700626024
58000 ekin = 22.0666093644392 | erot = 20.0713856445716 | epot = -222.908695636277 | etot = -180.770700627266 58000 ekin = 22.0666093644387 | erot = 20.0713856445721 | epot = -222.908695636277 | etot = -180.770700627266
59000 ekin = 22.1910921687949 | erot = 20.328402409601 | epot = -223.290195207095 | etot = -180.770700628699 59000 ekin = 22.1910921687945 | erot = 20.3284024096015 | epot = -223.290195207095 | etot = -180.770700628699
60000 ekin = 22.2920682490237 | erot = 20.600331953154 | epot = -223.663100832376 | etot = -180.770700630198 60000 ekin = 22.2920682490233 | erot = 20.6003319531545 | epot = -223.663100832376 | etot = -180.770700630198
61000 ekin = 22.3680528265789 | erot = 20.864561419886 | epot = -224.003314878046 | etot = -180.770700631581 61000 ekin = 22.3680528265786 | erot = 20.8645614198866 | epot = -224.003314878046 | etot = -180.77070063158
62000 ekin = 22.4198570332632 | erot = 21.0983714926627 | epot = -224.288929158678 | etot = -180.770700632752 62000 ekin = 22.4198570332631 | erot = 21.0983714926633 | epot = -224.288929158679 | etot = -180.770700632752
63000 ekin = 22.4500800739919 | erot = 21.2815521440893 | epot = -224.502332851296 | etot = -180.770700633215 63000 ekin = 22.450080073992 | erot = 21.28155214409 | epot = -224.502332851296 | etot = -180.770700633215
64000 ekin = 22.4634052763981 | erot = 21.3990470998276 | epot = -224.633153009903 | etot = -180.770700633677 64000 ekin = 22.4634052763983 | erot = 21.3990470998282 | epot = -224.633153009903 | etot = -180.770700633676
65000 ekin = 22.4639885390962 | erot = 21.4413332838522 | epot = -224.676022456447 | etot = -180.770700633499 65000 ekin = 22.4639885390964 | erot = 21.4413332838528 | epot = -224.676022456447 | etot = -180.770700633498
66000 ekin = 22.4559522488541 | erot = 21.4074154510862 | epot = -224.634068332758 | etot = -180.770700632817 66000 ekin = 22.4559522488544 | erot = 21.4074154510867 | epot = -224.634068332758 | etot = -180.770700632817
67000 ekin = 22.4417384097823 | erot = 21.3051580893559 | epot = -224.517597130738 | etot = -180.770700631599 67000 ekin = 22.4417384097826 | erot = 21.3051580893564 | epot = -224.517597130738 | etot = -180.770700631599
68000 ekin = 22.4218785446456 | erot = 21.1490017805238 | epot = -224.341580956059 | etot = -180.77070063089 68000 ekin = 22.421878544646 | erot = 21.1490017805243 | epot = -224.34158095606 | etot = -180.77070063089
69000 ekin = 22.3954651199574 | erot = 20.9555571676353 | epot = -224.121722917262 | etot = -180.77070062967 69000 ekin = 22.3954651199576 | erot = 20.9555571676358 | epot = -224.121722917263 | etot = -180.770700629669
70000 ekin = 22.3613349801191 | erot = 20.7433545871753 | epot = -223.875390195706 | etot = -180.770700628411 70000 ekin = 22.3613349801193 | erot = 20.7433545871758 | epot = -223.875390195706 | etot = -180.770700628411
71000 ekin = 22.3171019087139 | erot = 20.5301141425045 | epot = -223.617916679046 | etot = -180.770700627827 71000 ekin = 22.3171019087139 | erot = 20.5301141425049 | epot = -223.617916679045 | etot = -180.770700627826
72000 ekin = 22.2595195485148 | erot = 20.329630938296 | epot = -223.359851114099 | etot = -180.770700627288 72000 ekin = 22.2595195485147 | erot = 20.3296309382964 | epot = -223.359851114099 | etot = -180.770700627288
73000 ekin = 22.1869461213879 | erot = 20.1521902584585 | epot = -223.109837006429 | etot = -180.770700626583 73000 ekin = 22.1869461213877 | erot = 20.1521902584588 | epot = -223.109837006429 | etot = -180.770700626583
74000 ekin = 22.0990935565687 | erot = 20.0059494138148 | epot = -222.875743596757 | etot = -180.770700626373 74000 ekin = 22.0990935565683 | erot = 20.0059494138149 | epot = -222.875743596756 | etot = -180.770700626373
75000 ekin = 21.9959491639287 | erot = 19.8965902063256 | epot = -222.663239996049 | etot = -180.770700625795 75000 ekin = 21.9959491639282 | erot = 19.8965902063256 | epot = -222.663239996049 | etot = -180.770700625795
76000 ekin = 21.8806005890451 | erot = 19.8284243363261 | epot = -222.47972555068 | etot = -180.770700625309 76000 ekin = 21.8806005890445 | erot = 19.828424336326 | epot = -222.479725550679 | etot = -180.770700625308
77000 ekin = 21.7590261899816 | erot = 19.8043252195866 | epot = -222.334052034218 | etot = -180.77070062465 77000 ekin = 21.7590261899809 | erot = 19.8043252195864 | epot = -222.334052034216 | etot = -180.770700624649
78000 ekin = 21.639241983951 | erot = 19.8262630279238 | epot = -222.236205635988 | etot = -180.770700624113 78000 ekin = 21.6392419839503 | erot = 19.8262630279236 | epot = -222.236205635986 | etot = -180.770700624113
79000 ekin = 21.5302317519724 | erot = 19.8938812521579 | epot = -222.19481362777 | etot = -180.77070062364 79000 ekin = 21.5302317519716 | erot = 19.8938812521576 | epot = -222.194813627769 | etot = -180.77070062364
80000 ekin = 21.4402276725665 | erot = 20.0060100278945 | epot = -222.216938324075 | etot = -180.770700623614 80000 ekin = 21.4402276725657 | erot = 20.0060100278943 | epot = -222.216938324074 | etot = -180.770700623614
81000 ekin = 21.3741486759864 | erot = 20.1585144791611 | epot = -222.30336377944 | etot = -180.770700624292 81000 ekin = 21.3741486759855 | erot = 20.158514479161 | epot = -222.303363779439 | etot = -180.770700624292
82000 ekin = 21.3325013763512 | erot = 20.3431413542723 | epot = -222.446343355881 | etot = -180.770700625258 82000 ekin = 21.3325013763505 | erot = 20.3431413542724 | epot = -222.44634335588 | etot = -180.770700625257
83000 ekin = 21.3128808684044 | erot = 20.5483309907718 | epot = -222.63191248578 | etot = -180.770700626604 83000 ekin = 21.3128808684037 | erot = 20.548330990772 | epot = -222.631912485779 | etot = -180.770700626604
84000 ekin = 21.3107661707936 | erot = 20.760791978517 | epot = -222.842258777119 | etot = -180.770700627809 84000 ekin = 21.310766170793 | erot = 20.7607919785174 | epot = -222.842258777119 | etot = -180.770700627809
85000 ekin = 21.3216301567282 | erot = 20.967841853924 | epot = -223.060172639486 | etot = -180.770700628834 85000 ekin = 21.3216301567277 | erot = 20.9678418539246 | epot = -223.060172639485 | etot = -180.770700628833
86000 ekin = 21.3400295156728 | erot = 21.1566564817949 | epot = -223.267386627524 | etot = -180.770700630056 86000 ekin = 21.3400295156723 | erot = 21.1566564817957 | epot = -223.267386627523 | etot = -180.770700630055
87000 ekin = 21.3617783036996 | erot = 21.3170902458385 | epot = -223.449569179882 | etot = -180.770700630344 87000 ekin = 21.3617783036992 | erot = 21.3170902458394 | epot = -223.449569179882 | etot = -180.770700630344
88000 ekin = 21.3873913218412 | erot = 21.4454439910409 | epot = -223.603535942848 | etot = -180.770700629966 88000 ekin = 21.3873913218409 | erot = 21.445443991042 | epot = -223.603535942848 | etot = -180.770700629965
89000 ekin = 21.4215740693991 | erot = 21.5439953706444 | epot = -223.736270068948 | etot = -180.770700628904 89000 ekin = 21.421574069399 | erot = 21.5439953706456 | epot = -223.736270068948 | etot = -180.770700628904
90000 ekin = 21.4723781618092 | erot = 21.6216769093334 | epot = -223.864755698469 | etot = -180.770700627326 90000 ekin = 21.4723781618091 | erot = 21.6216769093347 | epot = -223.86475569847 | etot = -180.770700627326
91000 ekin = 21.5494066254721 | erot = 21.6927202486451 | epot = -224.012827499722 | etot = -180.770700625605 91000 ekin = 21.549406625472 | erot = 21.6927202486463 | epot = -224.012827499723 | etot = -180.770700625604
92000 ekin = 21.6619209347598 | erot = 21.7730744492999 | epot = -224.205696008348 | etot = -180.770700624289 92000 ekin = 21.6619209347597 | erot = 21.7730744493012 | epot = -224.205696008348 | etot = -180.770700624287
93000 ekin = 21.8158778641473 | erot = 21.8756732628035 | epot = -224.462251750825 | etot = -180.770700623875 93000 ekin = 21.8158778641472 | erot = 21.8756732628048 | epot = -224.462251750825 | etot = -180.770700623873
94000 ekin = 22.0110275730999 | erot = 22.0060799403011 | epot = -224.787808138196 | etot = -180.770700624795 94000 ekin = 22.0110275730997 | erot = 22.0060799403022 | epot = -224.787808138196 | etot = -180.770700624794
95000 ekin = 22.2387555838385 | erot = 22.1596167137182 | epot = -225.16907292429 | etot = -180.770700626734 95000 ekin = 22.2387555838384 | erot = 22.1596167137192 | epot = -225.16907292429 | etot = -180.770700626733
96000 ekin = 22.4832444899363 | erot = 22.3220202374392 | epot = -225.575965356876 | etot = -180.7707006295 96000 ekin = 22.4832444899361 | erot = 22.3220202374401 | epot = -225.575965356875 | etot = -180.770700629499
97000 ekin = 22.7237276202696 | erot = 22.4720556690115 | epot = -225.966483921719 | etot = -180.770700632438 97000 ekin = 22.7237276202693 | erot = 22.4720556690122 | epot = -225.966483921719 | etot = -180.770700632437
98000 ekin = 22.9377647716045 | erot = 22.5858660312272 | epot = -226.294331437119 | etot = -180.770700634287 98000 ekin = 22.9377647716041 | erot = 22.5858660312277 | epot = -226.294331437118 | etot = -180.770700634287
99000 ekin = 23.1071231637242 | erot = 22.6457411046182 | epot = -226.523564904806 | etot = -180.770700636464 99000 ekin = 23.1071231637237 | erot = 22.6457411046184 | epot = -226.523564904806 | etot = -180.770700636464
100000 ekin = 23.2156001924317 | erot = 22.6390310936005 | epot = -226.625331923823 | etot = -180.770700637791 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 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 Performance: 1028.974 tau/day, 1190.942 timesteps/s
99.8% CPU use with 1 MPI tasks x no OpenMP threads 99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 78.718 | 78.718 | 78.718 | 0.0 | 96.15 Pair | 80.885 | 80.885 | 80.885 | 0.0 | 96.33
Bond | 0.97064 | 0.97064 | 0.97064 | 0.0 | 1.19 Bond | 0.94789 | 0.94789 | 0.94789 | 0.0 | 1.13
Neigh | 0.016915 | 0.016915 | 0.016915 | 0.0 | 0.02 Neigh | 0.011589 | 0.011589 | 0.011589 | 0.0 | 0.01
Comm | 0.027127 | 0.027127 | 0.027127 | 0.0 | 0.03 Comm | 0.045979 | 0.045979 | 0.045979 | 0.0 | 0.05
Output | 0.12162 | 0.12162 | 0.12162 | 0.0 | 0.15 Output | 0.11973 | 0.11973 | 0.11973 | 0.0 | 0.14
Modify | 1.9185 | 1.9185 | 1.9185 | 0.0 | 2.34 Modify | 1.8641 | 1.8641 | 1.8641 | 0.0 | 2.22
Other | | 0.09845 | | | 0.12 Other | | 0.09239 | | | 0.11
Nlocal: 148.000 ave 148 max 148 min Nlocal: 148.000 ave 148 max 148 min
Histogram: 1 0 0 0 0 0 0 0 0 0 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 Neighbor list builds = 100
Dangerous builds = 0 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.${number}.* #write_restart last_config.${number}.*
Total wall time: 0:01:21 Total wall time: 0:01:23

238
examples/PACKAGES/cgdna/examples/oxDNA2/dsring/log.2Jul21.dsring.g++.4
View File

@ -9,7 +9,7 @@ units lj
dimension 3 dimension 3
newton off newton on
boundary p p p boundary p p p
@ -30,7 +30,7 @@ Reading data file ...
reading velocities ... reading velocities ...
148 velocities 148 velocities
scanning bonds ... scanning bonds ...
2 = max bonds/atom 1 = max bonds/atom
148 ellipsoids 148 ellipsoids
reading bonds ... reading bonds ...
148 bonds 148 bonds
@ -115,33 +115,33 @@ Neighbor list info ...
binsize = 2.8194939, bins = 36 36 36 binsize = 2.8194939, bins = 36 36 36
5 neighbor lists, perpetual/occasional/extra = 5 0 0 5 neighbor lists, perpetual/occasional/extra = 5 0 0
(1) pair oxdna2/excv, perpetual (1) pair oxdna2/excv, perpetual
attributes: half, newton off attributes: half, newton on
pair build: half/bin/newtoff pair build: half/bin/newton
stencil: full/bin/3d stencil: half/bin/3d
bin: standard bin: standard
(2) pair oxdna2/hbond, perpetual, copy from (1) (2) pair oxdna2/hbond, perpetual, copy from (1)
attributes: half, newton off attributes: half, newton on
pair build: copy pair build: copy
stencil: none stencil: none
bin: none bin: none
(3) pair oxdna2/xstk, perpetual, copy from (1) (3) pair oxdna2/xstk, perpetual, copy from (1)
attributes: half, newton off attributes: half, newton on
pair build: copy pair build: copy
stencil: none stencil: none
bin: none bin: none
(4) pair oxdna2/coaxstk, perpetual, copy from (1) (4) pair oxdna2/coaxstk, perpetual, copy from (1)
attributes: half, newton off attributes: half, newton on
pair build: copy pair build: copy
stencil: none stencil: none
bin: none bin: none
(5) pair oxdna2/dh, perpetual, copy from (1) (5) pair oxdna2/dh, perpetual, copy from (1)
attributes: half, newton off attributes: half, newton on
pair build: copy pair build: copy
stencil: none stencil: none
bin: none bin: none
WARNING: Communication cutoff adjusted to 5.638987723814632 (../comm.cpp:739) WARNING: Communication cutoff adjusted to 5.638987723814632 (../comm.cpp:739)
0 ekin = 20.4724634226502 | erot = 21.0406985312466 | epot = -222.283862600785 | etot = -180.770700646889 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 Step Temp E_pair E_mol TotEng Press Volume
0 0.092845639 -1.5501211 0.04820308 -1.3635905 -9.0052368e-06 1000000 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 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 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 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 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 7000 ekin = 20.5431034482069 | erot = 21.8556844173874 | epot = -223.169488517717 | etot = -180.770700652123
8000 ekin = 20.4774701419092 | erot = 21.8437134145373 | epot = -223.091884207389 | etot = -180.770700650943 8000 ekin = 20.4774701419093 | erot = 21.8437134145373 | epot = -223.09188420739 | etot = -180.770700650943
9000 ekin = 20.4074566554239 | erot = 21.8097283692397 | epot = -222.987885674261 | etot = -180.770700649597 9000 ekin = 20.4074566554239 | erot = 21.8097283692397 | epot = -222.987885674261 | etot = -180.770700649598
10000 ekin = 20.3427303660297 | erot = 21.7629575866662 | epot = -222.876388600948 | etot = -180.770700648253 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 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 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 13000 ekin = 20.2733920359447 | erot = 21.6092715397933 | epot = -222.653364221617 | etot = -180.770700645879
14000 ekin = 20.3196524789069 | erot = 21.5586630974992 | epot = -222.649016222076 | etot = -180.770700645669 14000 ekin = 20.3196524789069 | erot = 21.5586630974992 | epot = -222.649016222076 | etot = -180.77070064567
15000 ekin = 20.410400937429 | erot = 21.5031572556308 | epot = -222.684258838858 | etot = -180.770700645798 15000 ekin = 20.410400937429 | erot = 21.5031572556307 | epot = -222.684258838858 | etot = -180.770700645799
16000 ekin = 20.5472869005792 | erot = 21.4346177247042 | epot = -222.752605272036 | etot = -180.770700646753 16000 ekin = 20.5472869005792 | erot = 21.4346177247041 | epot = -222.752605272037 | etot = -180.770700646753
17000 ekin = 20.7266657908773 | erot = 21.3426631585219 | epot = -222.840029597232 | etot = -180.770700647833 17000 ekin = 20.7266657908773 | erot = 21.3426631585218 | epot = -222.840029597232 | etot = -180.770700647833
18000 ekin = 20.9417612759978 | erot = 21.2178611180929 | epot = -222.930323042998 | etot = -180.770700648907 18000 ekin = 20.9417612759978 | erot = 21.2178611180927 | epot = -222.930323042998 | etot = -180.770700648907
19000 ekin = 21.1819308659395 | erot = 21.0532289630295 | epot = -223.005860478921 | etot = -180.770700649952 19000 ekin = 21.1819308659396 | erot = 21.0532289630294 | epot = -223.005860478921 | etot = -180.770700649952
20000 ekin = 21.4358169889472 | erot = 20.8473069564709 | epot = -223.053824595387 | etot = -180.770700649969 20000 ekin = 21.4358169889472 | erot = 20.8473069564707 | epot = -223.053824595387 | etot = -180.77070064997
21000 ekin = 21.6968513750994 | erot = 20.6066744652587 | epot = -223.074226489837 | etot = -180.770700649479 21000 ekin = 21.6968513750995 | erot = 20.6066744652585 | epot = -223.074226489837 | etot = -180.770700649479
22000 ekin = 21.9614458442779 | erot = 20.3429420444511 | epot = -223.07508853737 | etot = -180.770700648641 22000 ekin = 21.9614458442779 | erot = 20.3429420444508 | epot = -223.075088537371 | etot = -180.770700648642
23000 ekin = 22.2276099755697 | erot = 20.0703385165243 | epot = -223.068649139875 | etot = -180.770700647781 23000 ekin = 22.2276099755697 | erot = 20.070338516524 | epot = -223.068649139875 | etot = -180.770700647781
24000 ekin = 22.4935893196667 | erot = 19.8020671721665 | epot = -223.066357139277 | etot = -180.770700647443 24000 ekin = 22.4935893196667 | erot = 19.8020671721661 | epot = -223.066357139277 | etot = -180.770700647444
25000 ekin = 22.756606454822 | erot = 19.5464828008841 | epot = -223.073789902976 | etot = -180.77070064727 25000 ekin = 22.756606454822 | erot = 19.5464828008836 | epot = -223.073789902976 | etot = -180.77070064727
26000 ekin = 23.0126717548392 | erot = 19.3065017718467 | epot = -223.089874174572 | etot = -180.770700647886 26000 ekin = 23.0126717548391 | erot = 19.3065017718461 | epot = -223.089874174572 | etot = -180.770700647887
27000 ekin = 23.2550417060587 | erot = 19.0797753474572 | epot = -223.105517701932 | etot = -180.770700648417 27000 ekin = 23.2550417060586 | erot = 19.0797753474566 | epot = -223.105517701932 | etot = -180.770700648417
28000 ekin = 23.4774329734798 | erot = 18.8646197299578 | epot = -223.112753352067 | etot = -180.770700648629 28000 ekin = 23.4774329734797 | erot = 18.8646197299572 | epot = -223.112753352067 | etot = -180.77070064863
29000 ekin = 23.6747927720656 | erot = 18.6628653411828 | epot = -223.108358761693 | etot = -180.770700648445 29000 ekin = 23.6747927720654 | erot = 18.6628653411822 | epot = -223.108358761694 | etot = -180.770700648446
30000 ekin = 23.843232140024 | erot = 18.4812216983639 | epot = -223.095154486375 | etot = -180.770700647987 30000 ekin = 23.8432321400238 | erot = 18.4812216983633 | epot = -223.095154486375 | etot = -180.770700647988
31000 ekin = 23.9793041752223 | erot = 18.330784533402 | epot = -223.08078935577 | etot = -180.770700647146 31000 ekin = 23.979304175222 | erot = 18.3307845334015 | epot = -223.08078935577 | etot = -180.770700647146
32000 ekin = 24.081024604023 | erot = 18.2261577056003 | epot = -223.077882955919 | etot = -180.770700646296 32000 ekin = 24.0810246040226 | erot = 18.2261577055998 | epot = -223.077882955919 | etot = -180.770700646297
33000 ekin = 24.1468986449394 | erot = 18.1820705445404 | epot = -223.09966983514 | etot = -180.77070064566 33000 ekin = 24.1468986449389 | erot = 18.1820705445401 | epot = -223.09966983514 | etot = -180.770700645661
34000 ekin = 24.175661513286 | erot = 18.2103812210168 | epot = -223.156743379607 | etot = -180.770700645304 34000 ekin = 24.1756615132855 | erot = 18.2103812210167 | epot = -223.156743379607 | etot = -180.770700645304
35000 ekin = 24.166319389465 | erot = 18.3185351073562 | epot = -223.255555142089 | etot = -180.770700645268 35000 ekin = 24.1663193894644 | erot = 18.3185351073563 | epot = -223.255555142089 | etot = -180.770700645269
36000 ekin = 24.1167205812963 | erot = 18.509164989418 | epot = -223.396586216223 | etot = -180.770700645508 36000 ekin = 24.1167205812957 | erot = 18.5091649894184 | epot = -223.396586216223 | etot = -180.770700645509
37000 ekin = 24.0274860006135 | erot = 18.778513432098 | epot = -223.576700078937 | etot = -180.770700646225 37000 ekin = 24.0274860006128 | erot = 18.7785134320987 | epot = -223.576700078937 | etot = -180.770700646226
38000 ekin = 23.8991479078985 | erot = 19.1166063146986 | epot = -223.78645486989 | etot = -180.770700647293 38000 ekin = 23.8991479078978 | erot = 19.1166063146994 | epot = -223.786454869891 | etot = -180.770700647293
39000 ekin = 23.7326911853237 | erot = 19.5069160952483 | epot = -224.010307929335 | etot = -180.770700648763 39000 ekin = 23.7326911853231 | erot = 19.5069160952493 | epot = -224.010307929336 | etot = -180.770700648764
40000 ekin = 23.5294223072123 | erot = 19.9254673141817 | epot = -224.225590272292 | etot = -180.770700650898 40000 ekin = 23.5294223072117 | erot = 19.9254673141828 | epot = -224.225590272293 | etot = -180.770700650899
41000 ekin = 23.2899396141395 | erot = 20.3408097780551 | epot = -224.401450045567 | etot = -180.770700653372 41000 ekin = 23.289939614139 | erot = 20.3408097780563 | epot = -224.401450045568 | etot = -180.770700653372
42000 ekin = 23.0154529235027 | erot = 20.7165619564837 | epot = -224.502715535762 | etot = -180.770700655775 42000 ekin = 23.0154529235022 | erot = 20.7165619564848 | epot = -224.502715535762 | etot = -180.770700655775
43000 ekin = 22.7111536814281 | erot = 21.0163895622221 | epot = -224.498243901358 | etot = -180.770700657708 43000 ekin = 22.7111536814277 | erot = 21.0163895622231 | epot = -224.498243901359 | etot = -180.770700657708
44000 ekin = 22.3710575806358 | erot = 21.2060371289775 | epot = -224.347795365753 | etot = -180.77070065614 44000 ekin = 22.3710575806355 | erot = 21.2060371289783 | epot = -224.347795365754 | etot = -180.77070065614
45000 ekin = 22.0515843162892 | erot = 21.2588026881763 | epot = -224.081087646891 | etot = -180.770700642425 45000 ekin = 22.0515843162889 | erot = 21.2588026881768 | epot = -224.081087646891 | etot = -180.770700642425
46000 ekin = 21.7855632553138 | erot = 21.2036013766598 | epot = -223.759865260062 | etot = -180.770700628088 46000 ekin = 21.7855632553133 | erot = 21.20360137666 | epot = -223.759865260062 | etot = -180.770700628089
47000 ekin = 21.5167766971457 | erot = 21.0656367023666 | epot = -223.353114011016 | etot = -180.770700611503 47000 ekin = 21.5167766971456 | erot = 21.0656367023667 | epot = -223.353114011016 | etot = -180.770700611503
48000 ekin = 21.454019610733 | erot = 20.8430832424322 | epot = -223.067803499525 | etot = -180.77070064636 48000 ekin = 21.4540196107333 | erot = 20.8430832424321 | epot = -223.067803499525 | etot = -180.77070064636
49000 ekin = 21.3647564765269 | erot = 20.5521507191685 | epot = -222.687607816921 | etot = -180.770700621226 49000 ekin = 21.3647564765274 | erot = 20.5521507191682 | epot = -222.687607816922 | etot = -180.770700621226
50000 ekin = 21.312576818461 | erot = 20.252646467133 | epot = -222.335923904309 | etot = -180.770700618715 50000 ekin = 21.3125768184617 | erot = 20.2526464671325 | epot = -222.33592390431 | etot = -180.770700618715
51000 ekin = 21.2949924810824 | erot = 19.9798421626041 | epot = -222.045535260404 | etot = -180.770700616717 51000 ekin = 21.2949924810834 | erot = 19.9798421626035 | epot = -222.045535260404 | etot = -180.770700616717
52000 ekin = 21.3137144249669 | erot = 19.7627691343685 | epot = -221.847184173962 | etot = -180.770700614627 52000 ekin = 21.3137144249679 | erot = 19.7627691343679 | epot = -221.847184173963 | etot = -180.770700614627
53000 ekin = 21.3664076685088 | erot = 19.6202359856897 | epot = -221.757344279693 | etot = -180.770700625495 53000 ekin = 21.3664076685099 | erot = 19.6202359856891 | epot = -221.757344279695 | etot = -180.770700625496
54000 ekin = 21.4214245524042 | erot = 19.5588232319498 | epot = -221.750948393746 | etot = -180.770700609392 54000 ekin = 21.4214245524052 | erot = 19.5588232319492 | epot = -221.750948393748 | etot = -180.770700609393
55000 ekin = 21.5995673396072 | erot = 19.5805214885676 | epot = -221.950789453582 | etot = -180.770700625407 55000 ekin = 21.5995673396082 | erot = 19.580521488567 | epot = -221.950789453583 | etot = -180.770700625408
56000 ekin = 21.7643125668285 | erot = 19.6816042107776 | epot = -222.216617401428 | etot = -180.770700623822 56000 ekin = 21.7643125668294 | erot = 19.681604210777 | epot = -222.216617401429 | etot = -180.770700623823
57000 ekin = 21.9221309084424 | erot = 19.8499880475952 | epot = -222.542819582063 | etot = -180.770700626025 57000 ekin = 21.922130908443 | erot = 19.8499880475945 | epot = -222.542819582064 | etot = -180.770700626026
58000 ekin = 22.0666093644371 | erot = 20.0713856445716 | epot = -222.908695636277 | etot = -180.770700627268 58000 ekin = 22.0666093644375 | erot = 20.0713856445709 | epot = -222.908695636278 | etot = -180.770700627269
59000 ekin = 22.191092168793 | erot = 20.3284024096011 | epot = -223.290195207095 | etot = -180.7707006287 59000 ekin = 22.1910921687932 | erot = 20.3284024096003 | epot = -223.290195207095 | etot = -180.770700628702
60000 ekin = 22.292068249022 | erot = 20.6003319531543 | epot = -223.663100832376 | etot = -180.7707006302 60000 ekin = 22.2920682490219 | erot = 20.6003319531534 | epot = -223.663100832376 | etot = -180.770700630201
61000 ekin = 22.3680528265774 | erot = 20.8645614198865 | epot = -224.003314878046 | etot = -180.770700631582 61000 ekin = 22.3680528265772 | erot = 20.8645614198856 | epot = -224.003314878046 | etot = -180.770700631583
62000 ekin = 22.4198570332621 | erot = 21.0983714926634 | epot = -224.288929158679 | etot = -180.770700632754 62000 ekin = 22.4198570332617 | erot = 21.0983714926625 | epot = -224.288929158679 | etot = -180.770700632755
63000 ekin = 22.450080073991 | erot = 21.2815521440901 | epot = -224.502332851297 | etot = -180.770700633216 63000 ekin = 22.4500800739905 | erot = 21.2815521440892 | epot = -224.502332851297 | etot = -180.770700633217
64000 ekin = 22.4634052763974 | erot = 21.3990470998285 | epot = -224.633153009904 | etot = -180.770700633678 64000 ekin = 22.4634052763968 | erot = 21.3990470998276 | epot = -224.633153009904 | etot = -180.770700633679
65000 ekin = 22.4639885390957 | erot = 21.4413332838532 | epot = -224.676022456449 | etot = -180.7707006335 65000 ekin = 22.463988539095 | erot = 21.4413332838523 | epot = -224.676022456448 | etot = -180.770700633501
66000 ekin = 22.4559522488539 | erot = 21.4074154510872 | epot = -224.634068332759 | etot = -180.770700632818 66000 ekin = 22.4559522488531 | erot = 21.4074154510864 | epot = -224.634068332759 | etot = -180.770700632819
67000 ekin = 22.4417384097822 | erot = 21.3051580893569 | epot = -224.517597130739 | etot = -180.7707006316 67000 ekin = 22.4417384097814 | erot = 21.3051580893563 | epot = -224.517597130739 | etot = -180.770700631601
68000 ekin = 22.4218785446457 | erot = 21.1490017805248 | epot = -224.341580956061 | etot = -180.770700630891 68000 ekin = 22.4218785446449 | erot = 21.1490017805243 | epot = -224.341580956061 | etot = -180.770700630892
69000 ekin = 22.3954651199575 | erot = 20.9555571676363 | epot = -224.121722917264 | etot = -180.77070062967 69000 ekin = 22.3954651199567 | erot = 20.9555571676359 | epot = -224.121722917264 | etot = -180.770700629671
70000 ekin = 22.3613349801193 | erot = 20.7433545871763 | epot = -223.875390195707 | etot = -180.770700628412 70000 ekin = 22.3613349801186 | erot = 20.743354587176 | epot = -223.875390195707 | etot = -180.770700628413
71000 ekin = 22.317101908714 | erot = 20.5301141425054 | epot = -223.617916679047 | etot = -180.770700627827 71000 ekin = 22.3171019087134 | erot = 20.5301141425052 | epot = -223.617916679047 | etot = -180.770700627829
72000 ekin = 22.2595195485149 | erot = 20.3296309382967 | epot = -223.3598511141 | etot = -180.770700627289 72000 ekin = 22.2595195485144 | erot = 20.3296309382966 | epot = -223.3598511141 | etot = -180.77070062729
73000 ekin = 22.186946121388 | erot = 20.1521902584591 | epot = -223.109837006431 | etot = -180.770700626584 73000 ekin = 22.1869461213875 | erot = 20.1521902584591 | epot = -223.109837006431 | etot = -180.770700626585
74000 ekin = 22.0990935565685 | erot = 20.0059494138152 | epot = -222.875743596758 | etot = -180.770700626374 74000 ekin = 22.0990935565682 | erot = 20.0059494138151 | epot = -222.875743596758 | etot = -180.770700626375
75000 ekin = 21.9959491639285 | erot = 19.8965902063258 | epot = -222.66323999605 | etot = -180.770700625796 75000 ekin = 21.9959491639282 | erot = 19.8965902063257 | epot = -222.663239996051 | etot = -180.770700625797
76000 ekin = 21.8806005890447 | erot = 19.8284243363262 | epot = -222.47972555068 | etot = -180.770700625309 76000 ekin = 21.8806005890446 | erot = 19.8284243363261 | epot = -222.479725550681 | etot = -180.77070062531
77000 ekin = 21.7590261899811 | erot = 19.8043252195865 | epot = -222.334052034218 | etot = -180.77070062465 77000 ekin = 21.759026189981 | erot = 19.8043252195865 | epot = -222.334052034218 | etot = -180.770700624651
78000 ekin = 21.6392419839504 | erot = 19.8262630279235 | epot = -222.236205635988 | etot = -180.770700624114 78000 ekin = 21.6392419839505 | erot = 19.8262630279235 | epot = -222.236205635988 | etot = -180.770700624114
79000 ekin = 21.5302317519716 | erot = 19.8938812521573 | epot = -222.19481362777 | etot = -180.770700623641 79000 ekin = 21.5302317519718 | erot = 19.8938812521574 | epot = -222.19481362777 | etot = -180.770700623641
80000 ekin = 21.4402276725656 | erot = 20.0060100278937 | epot = -222.216938324074 | etot = -180.770700623615 80000 ekin = 21.4402276725659 | erot = 20.0060100278939 | epot = -222.216938324075 | etot = -180.770700623615
81000 ekin = 21.3741486759853 | erot = 20.1585144791602 | epot = -222.303363779439 | etot = -180.770700624293 81000 ekin = 21.3741486759857 | erot = 20.1585144791605 | epot = -222.303363779439 | etot = -180.770700624293
82000 ekin = 21.3325013763501 | erot = 20.3431413542714 | epot = -222.44634335588 | etot = -180.770700625258 82000 ekin = 21.3325013763506 | erot = 20.3431413542717 | epot = -222.446343355881 | etot = -180.770700625259
83000 ekin = 21.3128808684032 | erot = 20.5483309907707 | epot = -222.631912485778 | etot = -180.770700626604 83000 ekin = 21.3128808684039 | erot = 20.5483309907712 | epot = -222.63191248578 | etot = -180.770700626605
84000 ekin = 21.3107661707924 | erot = 20.7607919785161 | epot = -222.842258777118 | etot = -180.77070062781 84000 ekin = 21.3107661707932 | erot = 20.7607919785166 | epot = -222.842258777119 | etot = -180.77070062781
85000 ekin = 21.3216301567271 | erot = 20.9678418539233 | epot = -223.060172639485 | etot = -180.770700628834 85000 ekin = 21.3216301567279 | erot = 20.9678418539237 | epot = -223.060172639486 | etot = -180.770700628834
86000 ekin = 21.3400295156717 | erot = 21.1566564817944 | epot = -223.267386627523 | etot = -180.770700630057 86000 ekin = 21.3400295156725 | erot = 21.1566564817949 | epot = -223.267386627524 | etot = -180.770700630057
87000 ekin = 21.3617783036987 | erot = 21.3170902458384 | epot = -223.449569179882 | etot = -180.770700630345 87000 ekin = 21.3617783036995 | erot = 21.3170902458388 | epot = -223.449569179883 | etot = -180.770700630345
88000 ekin = 21.3873913218405 | erot = 21.4454439910411 | epot = -223.603535942848 | etot = -180.770700629967 88000 ekin = 21.3873913218413 | erot = 21.4454439910414 | epot = -223.603535942849 | etot = -180.770700629967
89000 ekin = 21.4215740693986 | erot = 21.5439953706449 | epot = -223.736270068949 | etot = -180.770700628906 89000 ekin = 21.4215740693994 | erot = 21.5439953706451 | epot = -223.73627006895 | etot = -180.770700628906
90000 ekin = 21.4723781618088 | erot = 21.6216769093341 | epot = -223.864755698471 | etot = -180.770700627328 90000 ekin = 21.4723781618096 | erot = 21.6216769093343 | epot = -223.864755698472 | etot = -180.770700627328
91000 ekin = 21.5494066254718 | erot = 21.6927202486458 | epot = -224.012827499724 | etot = -180.770700625606 91000 ekin = 21.5494066254725 | erot = 21.6927202486459 | epot = -224.012827499725 | etot = -180.770700625606
92000 ekin = 21.6619209347595 | erot = 21.7730744493006 | epot = -224.20569600835 | etot = -180.77070062429 92000 ekin = 21.6619209347601 | erot = 21.7730744493007 | epot = -224.20569600835 | etot = -180.77070062429
93000 ekin = 21.815877864147 | erot = 21.8756732628043 | epot = -224.462251750826 | etot = -180.770700623875 93000 ekin = 21.8158778641474 | erot = 21.8756732628043 | epot = -224.462251750827 | etot = -180.770700623875
94000 ekin = 22.0110275730996 | erot = 22.0060799403017 | epot = -224.787808138197 | etot = -180.770700624796 94000 ekin = 22.0110275730999 | erot = 22.0060799403016 | epot = -224.787808138198 | etot = -180.770700624796
95000 ekin = 22.2387555838383 | erot = 22.1596167137187 | epot = -225.169072924291 | etot = -180.770700626735 95000 ekin = 22.2387555838384 | erot = 22.1596167137185 | epot = -225.169072924291 | etot = -180.770700626735
96000 ekin = 22.483244489936 | erot = 22.3220202374395 | epot = -225.575965356877 | etot = -180.770700629501 96000 ekin = 22.4832444899359 | erot = 22.3220202374394 | epot = -225.575965356876 | etot = -180.770700629501
97000 ekin = 22.7237276202693 | erot = 22.4720556690117 | epot = -225.96648392172 | etot = -180.770700632439 97000 ekin = 22.7237276202691 | erot = 22.4720556690115 | epot = -225.966483921719 | etot = -180.770700632439
98000 ekin = 22.937764771604 | erot = 22.5858660312272 | epot = -226.29433143712 | etot = -180.770700634289 98000 ekin = 22.9377647716038 | erot = 22.5858660312271 | epot = -226.294331437119 | etot = -180.770700634288
99000 ekin = 23.1071231637235 | erot = 22.645741104618 | epot = -226.523564904807 | etot = -180.770700636466 99000 ekin = 23.1071231637233 | erot = 22.645741104618 | epot = -226.523564904806 | etot = -180.770700636465
100000 ekin = 23.2156001924308 | erot = 22.6390310936003 | epot = -226.625331923823 | etot = -180.770700637792 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 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 Performance: 3076.899 tau/day, 3561.226 timesteps/s
99.5% CPU use with 4 MPI tasks x no OpenMP threads 99.7% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 33.685 | 34.998 | 35.676 | 13.1 | 89.51 Pair | 16.209 | 21.356 | 25.248 | 81.3 | 76.05
Bond | 0.30808 | 0.31468 | 0.31829 | 0.7 | 0.80 Bond | 0.26072 | 0.26526 | 0.27015 | 0.9 | 0.94
Neigh | 0.008861 | 0.0089438 | 0.009012 | 0.1 | 0.02 Neigh | 0.005772 | 0.0058625 | 0.005932 | 0.1 | 0.02
Comm | 0.79376 | 0.80216 | 0.8131 | 0.9 | 2.05 Comm | 1.7227 | 5.6246 | 10.79 | 158.9 | 20.03
Output | 0.054153 | 0.056983 | 0.058706 | 0.8 | 0.15 Output | 0.043943 | 0.046855 | 0.048664 | 0.9 | 0.17
Modify | 0.55623 | 0.5647 | 0.57239 | 0.9 | 1.44 Modify | 0.54715 | 0.55336 | 0.55902 | 0.7 | 1.97
Other | | 2.354 | | | 6.02 Other | | 0.2279 | | | 0.81
Nlocal: 37.0000 ave 38 max 36 min Nlocal: 37.0000 ave 38 max 36 min
Histogram: 1 0 0 0 0 2 0 0 0 1 Histogram: 1 0 0 0 0 2 0 0 0 1
Nghost: 111.000 ave 112 max 110 min Nghost: 111.000 ave 112 max 110 min
Histogram: 1 0 0 0 0 2 0 0 0 1 Histogram: 1 0 0 0 0 2 0 0 0 1
Neighs: 1693.75 ave 1737 max 1653 min Neighs: 1049.75 ave 1270 max 757 min
Histogram: 1 1 0 0 0 0 0 1 0 1 Histogram: 1 0 0 1 0 0 0 0 0 2
Total # of neighbors = 6775 Total # of neighbors = 4199
Ave neighs/atom = 45.777027 Ave neighs/atom = 28.371622
Ave special neighs/atom = 6.0000000 Ave special neighs/atom = 6.0000000
Neighbor list builds = 100 Neighbor list builds = 100
Dangerous builds = 0 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.${number}.* #write_restart last_config.${number}.*
Total wall time: 0:00:39 Total wall time: 0:00:28

3
examples/PACKAGES/cgdna/examples/oxDNA2/duplex1/in.duplex1
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@ -8,7 +8,7 @@ units lj
dimension 3 dimension 3
newton off newton on
boundary p p p 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 run 1000000
write_data last_config.${number}.* nocoeff write_data last_config.${number}.* nocoeff
#write_restart last_config.${number}.*

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examples/PACKAGES/cgdna/examples/oxDNA2/duplex2/in.duplex2
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@ -8,7 +8,7 @@ units lj
dimension 3 dimension 3
newton off newton on
boundary p p p 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 run 1000000
write_data last_config.${number}.* nocoeff write_data last_config.${number}.* nocoeff
#write_restart last_config.${number}.*

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examples/PACKAGES/cgdna/examples/oxDNA2/duplex3/in.duplex3
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@ -8,7 +8,7 @@ units lj
dimension 3 dimension 3
newton off newton on
boundary p p p 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 run 1000000
write_data last_config.${number}.* nocoeff write_data last_config.${number}.* nocoeff
#write_restart last_config.${number}.*

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examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/in.duplex4.4type
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@ -11,7 +11,7 @@ units lj
dimension 3 dimension 3
newton off newton on
boundary p p p 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 run 1000000
write_data last_config.${number}.* nocoeff write_data last_config.${number}.* nocoeff
#write_restart last_config.${number}.*

3
examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/in.duplex4.8type
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@ -11,7 +11,7 @@ units lj
dimension 3 dimension 3
newton off newton on
boundary p p p 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 run 1000000
write_data last_config.${number}.* nocoeff write_data last_config.${number}.* nocoeff
#write_restart last_config.${number}.*

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examples/PACKAGES/cgdna/examples/oxRNA2/duplex2/in.duplex2
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dimension 3 dimension 3
newton off newton on
boundary p p p 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 run 1000000
write_data last_config.${number}.* nocoeff write_data last_config.${number}.* nocoeff
#write_restart last_config.${number}.*

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examples/PACKAGES/cgdna/examples/test.sh Executable file
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@ -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

7
src/CG-DNA/atom_vec_oxdna.cpp
View File

@ -15,6 +15,8 @@
#include "atom.h" #include "atom.h"
#include "comm.h" #include "comm.h"
#include "error.h"
#include "force.h"
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
@ -46,6 +48,11 @@ AtomVecOxdna::AtomVecOxdna(LAMMPS *lmp) : AtomVec(lmp)
fields_data_vel = (char *) "id v"; fields_data_vel = (char *) "id v";
setup_fields(); setup_fields();
if(!force->newton_bond) {
error->warning(FLERR,"Write_data command requires newton_bond on to preserve 3'->5' bond polarity");
}
} }
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */