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update or add logs for USER-AWPMD, USER-BOCS, and USER-CGDNA

This commit is contained in:
Axel Kohlmeyer 2018-12-07 04:32:46 -05:00
parent cd0924ca4c
commit 685a8bfc62
24 changed files with 1481 additions and 9397 deletions
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3
examples/USER/awpmd/in.h_atom
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@ -1,5 +1,4 @@
variable sname index h_atom
log ${sname}.spe.log
units real
newton on
@ -37,4 +36,4 @@ variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
thermo 1
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
run 0
run 10

3
examples/USER/awpmd/in.h_molecule
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@ -1,5 +1,4 @@
variable sname index h_molecule
log ${sname}.spe.log
units real
newton on
@ -37,4 +36,4 @@ variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
thermo 1
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
run 0
run 10

71
examples/USER/bocs/log.20Apr18.methanol.g++.1 → examples/USER/bocs/log.27Nov18.methanol.g++.1
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@ -1,5 +1,4 @@
LAMMPS (20 Apr 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
units real
dimension 3
@ -21,7 +20,7 @@ pair_style table spline 15000
pair_coeff 1 1 lammps_nb_MET-MET.table nb_METMET 12.0
WARNING: 78 of 2500 force values in table are inconsistent with -dE/dr.
Should only be flagged at inflection points (../pair_table.cpp:481)
Should only be flagged at inflection points (src/pair_table.cpp:481)
neigh_modify delay 0 every 1 check yes one 10000
neighbor 12.0 bin
@ -90,54 +89,54 @@ Neighbor list info ...
Per MPI rank memory allocation (min/avg/max) = 4.691 | 4.691 | 4.691 Mbytes
Step Temp PotEng TotEng Press Volume
0 300 1061.5961 1926.3291 107.006 66250.679
500 314.54728 1034.1091 1940.7738 194.42689 65660.282
1000 301.41603 1030.7027 1899.5173 -91.966709 66262.543
1500 298.8308 1014.8276 1876.1905 -80.178606 67053.605
2000 294.78476 1046.8207 1896.521 50.592942 66316.735
2500 301.18564 1033.9214 1902.0719 40.48255 66607.667
3000 301.06632 1022.0381 1889.8447 47.582344 66341.947
3500 297.98361 989.80983 1848.7307 -204.69879 67462.078
4000 299.03493 1034.6571 1896.6083 89.188888 66457.385
4500 306.03351 985.4121 1867.5363 -51.102407 67519.446
5000 305.6903 1013.8613 1894.9963 -141.13704 67240.467
5500 292.23444 1029.5558 1871.905 20.764579 66683.876
6000 287.87735 1017.7325 1847.5226 -35.288049 66630.031
6500 305.26461 960.08118 1839.9891 -352.42596 67612.317
7000 300.34449 1055.0664 1920.7923 22.04027 66187.27
7500 305.48612 1038.6651 1919.2115 17.807254 66324.168
8000 316.03232 1034.6809 1945.6262 27.482857 66502.198
8500 294.28636 1038.8213 1887.085 -72.840559 66851.661
9000 316.69029 1065.7481 1978.5899 245.61677 65678.385
9500 297.46127 1034.5547 1891.97 54.23428 66892.627
10000 301.24799 1036.5432 1904.8735 7.7134029 66150.506
Loop time of 34.426 on 1 procs for 10000 steps with 968 atoms
500 314.70267 1036.3305 1943.4431 205.83301 65603.85
1000 304.99804 1034.15 1913.2896 -79.521176 66268.87
1500 305.2621 996.9303 1876.831 -97.93992 67090.442
2000 311.29317 1083.9171 1981.2021 119.28085 65589.674
2500 305.51905 1051.59 1932.2314 -34.076658 66487.327
3000 291.76224 1053.524 1894.5121 45.522865 65879.535
3500 297.65795 1017.1028 1875.085 -79.41965 67185.19
4000 285.98779 1042.3622 1866.7058 88.549172 66357.051
4500 295.35 1071.4505 1922.7801 -16.75965 65378.949
5000 293.20958 1009.9943 1855.1543 -270.58058 67555.38
5500 292.40422 1085.3901 1928.2287 161.88502 65677.644
6000 318.79663 1012.4832 1931.3964 -65.692451 67458.05
6500 308.03807 1046.1413 1934.0436 249.70237 66052.045
7000 289.33716 1037.9657 1871.9636 47.662734 66782.578
7500 297.3092 1032.356 1889.3329 -24.049617 66129.95
8000 298.27827 1044.118 1903.8882 -26.61809 66720.381
8500 299.52706 1026.7068 1890.0766 -128.14995 67695.559
9000 304.67694 1018.2095 1896.4236 -61.360724 65942.4
9500 293.81117 1019.2221 1866.1162 -47.726496 66843.848
10000 309.9256 1043.5321 1936.875 -103.81403 66222.21
Loop time of 42.5056 on 1 procs for 10000 steps with 968 atoms
Performance: 25.097 ns/day, 0.956 hours/ns, 290.478 timesteps/s
Performance: 20.327 ns/day, 1.181 hours/ns, 235.263 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 33.324 | 33.324 | 33.324 | 0.0 | 96.80
Neigh | 0.12198 | 0.12198 | 0.12198 | 0.0 | 0.35
Comm | 0.42865 | 0.42865 | 0.42865 | 0.0 | 1.25
Output | 0.00059938 | 0.00059938 | 0.00059938 | 0.0 | 0.00
Modify | 0.42553 | 0.42553 | 0.42553 | 0.0 | 1.24
Other | | 0.1252 | | | 0.36
Pair | 40.972 | 40.972 | 40.972 | 0.0 | 96.39
Neigh | 0.18576 | 0.18576 | 0.18576 | 0.0 | 0.44
Comm | 0.71338 | 0.71338 | 0.71338 | 0.0 | 1.68
Output | 0.00050306 | 0.00050306 | 0.00050306 | 0.0 | 0.00
Modify | 0.52926 | 0.52926 | 0.52926 | 0.0 | 1.25
Other | | 0.1042 | | | 0.25
Nlocal: 968 ave 968 max 968 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 9112 ave 9112 max 9112 min
Nghost: 9215 ave 9215 max 9215 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 404392 ave 404392 max 404392 min
Neighs: 411837 ave 411837 max 411837 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 404392
Ave neighs/atom = 417.76
Total # of neighbors = 411837
Ave neighs/atom = 425.451
Neighbor list builds = 13
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:34
Total wall time: 0:00:42

81
examples/USER/bocs/log.20Apr18.methanol.g++.4 → examples/USER/bocs/log.27Nov18.methanol.g++.4
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@ -1,5 +1,4 @@
LAMMPS (20 Apr 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
units real
dimension 3
@ -21,7 +20,7 @@ pair_style table spline 15000
pair_coeff 1 1 lammps_nb_MET-MET.table nb_METMET 12.0
WARNING: 78 of 2500 force values in table are inconsistent with -dE/dr.
Should only be flagged at inflection points (../pair_table.cpp:481)
Should only be flagged at inflection points (src/pair_table.cpp:481)
neigh_modify delay 0 every 1 check yes one 10000
neighbor 12.0 bin
@ -90,54 +89,54 @@ Neighbor list info ...
Per MPI rank memory allocation (min/avg/max) = 3.37 | 3.37 | 3.371 Mbytes
Step Temp PotEng TotEng Press Volume
0 300 1061.5961 1926.3291 107.006 66250.679
500 314.54728 1034.1091 1940.7738 194.42689 65660.282
1000 301.41603 1030.7027 1899.5173 -91.966709 66262.543
1500 298.8308 1014.8276 1876.1905 -80.178606 67053.605
2000 294.78476 1046.8207 1896.521 50.592942 66316.735
2500 301.18564 1033.9214 1902.0719 40.482557 66607.667
3000 301.06631 1022.0381 1889.8447 47.582403 66341.947
3500 297.98353 989.81011 1848.7308 -204.69823 67462.076
4000 299.03465 1034.6603 1896.6108 89.196235 66457.338
4500 306.04532 985.37017 1867.5285 -51.094929 67519.735
5000 304.72903 1014.9543 1893.3184 -127.04402 67238.517
5500 292.52622 1025.6599 1868.8502 -19.753932 66716.551
6000 296.82719 1031.5184 1887.1059 -1.2609328 66368.611
6500 298.63312 1018.4299 1879.2229 -24.75835 66524.898
7000 303.25389 1005.9283 1880.0404 -96.273504 67349.674
7500 292.45089 1068.2863 1911.2595 103.23295 65778.08
8000 301.22765 1040.6294 1908.9011 -0.83635353 66831.038
8500 300.19765 1047.5856 1912.8883 -31.582343 66316.305
9000 295.1108 1023.8234 1874.4635 -88.165532 67192.344
9500 302.1087 1003.6348 1874.4459 -18.707065 66369.361
10000 296.3083 1004.126 1858.2178 -28.293045 66862.576
Loop time of 28.8053 on 4 procs for 10000 steps with 968 atoms
500 314.70267 1036.3305 1943.4431 205.83301 65603.85
1000 304.99804 1034.15 1913.2896 -79.521176 66268.87
1500 305.2621 996.9303 1876.831 -97.93992 67090.442
2000 311.29317 1083.9171 1981.2021 119.28085 65589.674
2500 305.51905 1051.59 1932.2314 -34.076657 66487.327
3000 291.76224 1053.524 1894.5121 45.522919 65879.535
3500 297.65792 1017.1041 1875.0862 -79.411904 67185.183
4000 285.99141 1042.379 1866.733 88.735986 66356.756
4500 295.34218 1071.2977 1922.6048 -17.479073 65381.597
5000 292.47 1012.3769 1855.405 -255.07433 67527.215
5500 294.04431 1080.4547 1928.0208 192.6588 65811.742
6000 300.45893 986.16669 1852.2225 -167.3405 67858.175
6500 305.59738 1022.5276 1903.3947 -116.41298 66612.704
7000 312.11968 1032.7392 1932.4065 152.17956 66016.299
7500 306.80585 1032.1157 1916.4662 51.07705 66875.727
8000 292.30957 1048.9003 1891.4661 61.280503 65894.103
8500 297.79592 1013.4061 1871.786 -133.01136 66842.574
9000 290.36753 1043.7732 1880.7412 65.208248 66010.86
9500 288.92211 1077.8835 1910.6851 46.291982 65674.639
10000 311.51608 1015.3567 1913.2842 -146.49492 66882.692
Loop time of 13.9823 on 4 procs for 10000 steps with 968 atoms
Performance: 29.994 ns/day, 0.800 hours/ns, 347.159 timesteps/s
95.2% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 61.792 ns/day, 0.388 hours/ns, 715.190 timesteps/s
98.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 19.929 | 21.765 | 23.391 | 27.8 | 75.56
Neigh | 0.067397 | 0.071231 | 0.077313 | 1.5 | 0.25
Comm | 3.9226 | 5.5183 | 7.3214 | 53.7 | 19.16
Output | 0.00069928 | 0.0016099 | 0.0043275 | 3.9 | 0.01
Modify | 1.0874 | 1.1376 | 1.1888 | 4.2 | 3.95
Other | | 0.3112 | | | 1.08
Pair | 10.131 | 11.235 | 12.333 | 23.2 | 80.35
Neigh | 0.044854 | 0.046303 | 0.047541 | 0.5 | 0.33
Comm | 1.1939 | 2.2964 | 3.4087 | 51.7 | 16.42
Output | 0.0004735 | 0.0032033 | 0.01137 | 8.3 | 0.02
Modify | 0.30542 | 0.31846 | 0.32508 | 1.4 | 2.28
Other | | 0.08323 | | | 0.60
Nlocal: 242 ave 244 max 239 min
Nlocal: 242 ave 248 max 232 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Nghost: 5718.5 ave 5736 max 5702 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Neighs: 100703 ave 108064 max 93454 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Nghost: 5845.75 ave 5877 max 5808 min
Histogram: 1 0 0 0 1 0 0 1 0 1
Neighs: 104313 ave 113860 max 95507 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Total # of neighbors = 402813
Ave neighs/atom = 416.129
Neighbor list builds = 14
Total # of neighbors = 417252
Ave neighs/atom = 431.045
Neighbor list builds = 13
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:28
Total wall time: 0:00:14

2
examples/USER/cgdna/examples/oxDNA/duplex1/input.duplex1 → examples/USER/cgdna/examples/oxDNA/duplex1/in.duplex1
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@ -72,6 +72,6 @@ fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${e
#dump_modify out sort id
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
run 1000000
run 10000
#write_restart config.${number}.*

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examples/USER/cgdna/examples/oxDNA/duplex1/log.24Mar17.duplex1.g++.1
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examples/USER/cgdna/examples/oxDNA/duplex1/log.24Mar17.duplex1.g++.4
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examples/USER/cgdna/examples/oxDNA/duplex1/log.27Nov18.duplex1.g++.1 Normal file
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LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
variable number equal 1
variable ofreq equal 1000
variable efreq equal 1000
units lj
dimension 3
newton off
boundary p p p
atom_style hybrid bond ellipsoid
atom_modify sort 0 1.0
# Pair interactions require lists of neighbours to be calculated
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
read_data data.duplex1
orthogonal box = (-20 -20 -20) to (20 20 20)
1 by 1 by 1 MPI processor grid
reading atoms ...
10 atoms
reading velocities ...
10 velocities
10 ellipsoids
scanning bonds ...
2 = max bonds/atom
reading bonds ...
8 bonds
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
2 = max # of 1-4 neighbors
4 = max # of special neighbors
set atom * mass 3.1575
10 settings made for mass
group all type 1 4
10 atoms in group all
# oxDNA bond interactions - FENE backbone
bond_style oxdna/fene
bond_coeff * 2.0 0.25 0.7525
# oxDNA pair interactions
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
pair_coeff * * oxdna/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
# NVE ensemble
fix 1 all nve/dot
#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
#fix 1 all nve/asphere
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
timestep 1e-5
#comm_style tiled
#fix 3 all balance 10000 1.1 rcb
#compute mol all chunk/atom molecule
#compute mychunk all vcm/chunk mol
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
#dump pos all xyz ${ofreq} traj.${number}.xyz
#compute quat all property/atom quatw quati quatj quatk
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
#dump_modify quat sort id
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
compute erot all erotate/asphere
compute ekin all ke
compute epot all pe
variable erot equal c_erot
variable ekin equal c_ekin
variable epot equal c_epot
variable etot equal c_erot+c_ekin+c_epot
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
#dump_modify out sort id
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
run 10000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.92828
ghost atom cutoff = 1.92828
binsize = 0.964142, bins = 42 42 42
5 neighbor lists, perpetual/occasional/extra = 5 0 0
(1) pair oxdna/excv, perpetual
attributes: half, newton off
pair build: half/bin/newtoff
stencil: half/bin/3d/newtoff
bin: standard
(2) pair oxdna/stk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(3) pair oxdna/hbond, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(4) pair oxdna/xstk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(5) pair oxdna/coaxstk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 2.859 | 2.859 | 2.859 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -1.4711818 0.0069384985 -1.4642433 -6.2745089e-05
1000 ekin = 0.00113448721737003 | erot = 0.00413455947734281 | epot = -14.6477022915193 | etot = -14.6424332448246
2000 ekin = 0.00449927223902336 | erot = 0.0164446434455805 | epot = -14.6633771605337 | etot = -14.6424332448491
3000 ekin = 0.00997964450841065 | erot = 0.0366523356056461 | epot = -14.6890652250033 | etot = -14.6424332448892
4000 ekin = 0.0173888111295073 | erot = 0.0643039804300221 | epot = -14.7241260365031 | etot = -14.6424332449436
5000 ekin = 0.0264744514136619 | erot = 0.0987844033142066 | epot = -14.7676920997383 | etot = -14.6424332450104
6000 ekin = 0.0369277948556079 | erot = 0.139336571052565 | epot = -14.8186976109956 | etot = -14.6424332450875
7000 ekin = 0.04839505571915 | erot = 0.18508629569208 | epot = -14.8759145965832 | etot = -14.642433245172
8000 ekin = 0.0604909336920643 | erot = 0.23507130752353 | epot = -14.9379954864767 | etot = -14.6424332452611
9000 ekin = 0.0728137406440561 | erot = 0.288273694501537 | epot = -15.003520680497 | etot = -14.6424332453514
10000 ekin = 0.0849615563085879 | erot = 0.343654369293472 | epot = -15.0710491710418 | etot = -14.6424332454398
10000 0.0062934486 -1.5138305 0.0067255788 -1.4986088 -9.9021593e-05
Loop time of 0.141929 on 1 procs for 10000 steps with 10 atoms
Performance: 60875.649 tau/day, 70457.927 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.11467 | 0.11467 | 0.11467 | 0.0 | 80.79
Bond | 0.0050094 | 0.0050094 | 0.0050094 | 0.0 | 3.53
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0013616 | 0.0013616 | 0.0013616 | 0.0 | 0.96
Output | 4.0531e-06 | 4.0531e-06 | 4.0531e-06 | 0.0 | 0.00
Modify | 0.017901 | 0.017901 | 0.017901 | 0.0 | 12.61
Other | | 0.002982 | | | 2.10
Nlocal: 10 ave 10 max 10 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 43 ave 43 max 43 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 43
Ave neighs/atom = 4.3
Ave special neighs/atom = 3.6
Neighbor list builds = 0
Dangerous builds = 0
#write_restart config.${number}.*
Total wall time: 0:00:00

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examples/USER/cgdna/examples/oxDNA/duplex1/log.27Nov18.duplex1.g++.4 Normal file
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LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
variable number equal 1
variable ofreq equal 1000
variable efreq equal 1000
units lj
dimension 3
newton off
boundary p p p
atom_style hybrid bond ellipsoid
atom_modify sort 0 1.0
# Pair interactions require lists of neighbours to be calculated
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
read_data data.duplex1
orthogonal box = (-20 -20 -20) to (20 20 20)
1 by 2 by 2 MPI processor grid
reading atoms ...
10 atoms
reading velocities ...
10 velocities
10 ellipsoids
scanning bonds ...
2 = max bonds/atom
reading bonds ...
8 bonds
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
2 = max # of 1-4 neighbors
4 = max # of special neighbors
set atom * mass 3.1575
10 settings made for mass
group all type 1 4
10 atoms in group all
# oxDNA bond interactions - FENE backbone
bond_style oxdna/fene
bond_coeff * 2.0 0.25 0.7525
# oxDNA pair interactions
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
pair_coeff * * oxdna/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
# NVE ensemble
fix 1 all nve/dot
#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
#fix 1 all nve/asphere
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
timestep 1e-5
#comm_style tiled
#fix 3 all balance 10000 1.1 rcb
#compute mol all chunk/atom molecule
#compute mychunk all vcm/chunk mol
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
#dump pos all xyz ${ofreq} traj.${number}.xyz
#compute quat all property/atom quatw quati quatj quatk
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
#dump_modify quat sort id
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
compute erot all erotate/asphere
compute ekin all ke
compute epot all pe
variable erot equal c_erot
variable ekin equal c_ekin
variable epot equal c_epot
variable etot equal c_erot+c_ekin+c_epot
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
#dump_modify out sort id
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
run 10000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.92828
ghost atom cutoff = 1.92828
binsize = 0.964142, bins = 42 42 42
5 neighbor lists, perpetual/occasional/extra = 5 0 0
(1) pair oxdna/excv, perpetual
attributes: half, newton off
pair build: half/bin/newtoff
stencil: half/bin/3d/newtoff
bin: standard
(2) pair oxdna/stk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(3) pair oxdna/hbond, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(4) pair oxdna/xstk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(5) pair oxdna/coaxstk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 7.341 | 7.523 | 7.705 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -1.4711818 0.0069384985 -1.4642433 -6.2745089e-05
1000 ekin = 0.00113448721737009 | erot = 0.0041345594773427 | epot = -14.6477022915193 | etot = -14.6424332448246
2000 ekin = 0.00449927223902292 | erot = 0.0164446434455803 | epot = -14.6633771605337 | etot = -14.6424332448491
3000 ekin = 0.00997964450840756 | erot = 0.0366523356056465 | epot = -14.6890652250033 | etot = -14.6424332448892
4000 ekin = 0.017388811129498 | erot = 0.0643039804300254 | epot = -14.7241260365031 | etot = -14.6424332449436
5000 ekin = 0.0264744514136422 | erot = 0.098784403314214 | epot = -14.7676920997383 | etot = -14.6424332450104
6000 ekin = 0.0369277948555727 | erot = 0.139336571052581 | epot = -14.8186976109956 | etot = -14.6424332450875
7000 ekin = 0.0483950557190949 | erot = 0.185086295692111 | epot = -14.8759145965832 | etot = -14.642433245172
8000 ekin = 0.0604909336919856 | erot = 0.235071307523583 | epot = -14.9379954864767 | etot = -14.6424332452611
9000 ekin = 0.0728137406439517 | erot = 0.288273694501617 | epot = -15.003520680497 | etot = -14.6424332453514
10000 ekin = 0.0849615563084573 | erot = 0.34365436929359 | epot = -15.0710491710418 | etot = -14.6424332454398
10000 0.0062934486 -1.5138305 0.0067255788 -1.4986088 -0.00010196899
Loop time of 0.134536 on 4 procs for 10000 steps with 10 atoms
Performance: 64220.659 tau/day, 74329.466 timesteps/s
97.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0030077 | 0.052212 | 0.093066 | 17.4 | 38.81
Bond | 0.00061846 | 0.00234 | 0.0039451 | 2.8 | 1.74
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.013431 | 0.014091 | 0.014596 | 0.4 | 10.47
Output | 5.0783e-05 | 5.1141e-05 | 5.1498e-05 | 0.0 | 0.04
Modify | 0.0011578 | 0.0059478 | 0.010331 | 4.8 | 4.42
Other | | 0.05989 | | | 44.52
Nlocal: 2.5 ave 5 max 0 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Nghost: 7.5 ave 10 max 5 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Neighs: 17.5 ave 33 max 0 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Total # of neighbors = 70
Ave neighs/atom = 7
Ave special neighs/atom = 3.6
Neighbor list builds = 0
Dangerous builds = 0
#write_restart config.${number}.*
Total wall time: 0:00:00

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@ -72,6 +72,6 @@ fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${e
#dump_modify out sort id
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
run 1000000
run 10000
#write_restart config.${number}.*

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LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
variable number equal 2
variable ofreq equal 1000
variable efreq equal 1000
units lj
dimension 3
newton off
boundary p p p
atom_style hybrid bond ellipsoid
atom_modify sort 0 1.0
# Pair interactions require lists of neighbours to be calculated
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
read_data data.duplex2
orthogonal box = (-20 -20 -20) to (20 20 20)
1 by 1 by 1 MPI processor grid
reading atoms ...
16 atoms
reading velocities ...
16 velocities
16 ellipsoids
scanning bonds ...
2 = max bonds/atom
reading bonds ...
13 bonds
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of 1-4 neighbors
6 = max # of special neighbors
set atom * mass 3.1575
16 settings made for mass
group all type 1 4
16 atoms in group all
# oxDNA bond interactions - FENE backbone
bond_style oxdna/fene
bond_coeff * 2.0 0.25 0.7525
# oxDNA pair interactions
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
pair_coeff * * oxdna/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
# NVE ensemble
#fix 1 all nve/dot
fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
#fix 1 all nve/asphere
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
timestep 1e-5
#comm_style tiled
#fix 3 all balance 10000 1.1 rcb
#compute mol all chunk/atom molecule
#compute mychunk all vcm/chunk mol
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
#dump pos all xyz ${ofreq} traj.${number}.xyz
#compute quat all property/atom quatw quati quatj quatk
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
#dump_modify quat sort id
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
compute erot all erotate/asphere
compute ekin all ke
compute epot all pe
variable erot equal c_erot
variable ekin equal c_ekin
variable epot equal c_epot
variable etot equal c_erot+c_ekin+c_epot
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
#dump_modify out sort id
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
run 10000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.92828
ghost atom cutoff = 1.92828
binsize = 0.964142, bins = 42 42 42
5 neighbor lists, perpetual/occasional/extra = 5 0 0
(1) pair oxdna/excv, perpetual
attributes: half, newton off
pair build: half/bin/newtoff
stencil: half/bin/3d/newtoff
bin: standard
(2) pair oxdna/stk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(3) pair oxdna/hbond, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(4) pair oxdna/xstk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(5) pair oxdna/coaxstk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 2.861 | 2.861 | 2.861 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -1.5402493 0.0070469125 -1.5332024 -8.5641987e-05
1000 ekin = 1.54234964773389 | erot = 1.71563526070267 | epot = -24.5477045187653 | etot = -21.2897196103287
2000 ekin = 1.85988866919215 | erot = 1.9424302796508 | epot = -24.4843044999595 | etot = -20.6819855511165
3000 ekin = 2.68354339452998 | erot = 2.14216528317607 | epot = -24.4019350693561 | etot = -19.57622639165
4000 ekin = 2.04461800191989 | erot = 1.49015219763162 | epot = -24.2959428773347 | etot = -20.7611726777832
5000 ekin = 1.76794859210155 | erot = 2.54289684465818 | epot = -24.2337587736863 | etot = -19.9229133369266
6000 ekin = 3.1106424806079 | erot = 2.04409805200892 | epot = -24.1585729744133 | etot = -19.0038324417964
7000 ekin = 3.21360097519306 | erot = 2.71941303605722 | epot = -24.0566262531609 | etot = -18.1236122419107
8000 ekin = 2.82489935901743 | erot = 2.66790555575696 | epot = -24.0194805097633 | etot = -18.526675594989
9000 ekin = 2.69381302856378 | erot = 2.59107820129446 | epot = -23.9216126050554 | etot = -18.6367213751972
10000 ekin = 2.65765007662471 | erot = 1.95562671446597 | epot = -23.7978334881241 | etot = -19.1845566970334
10000 0.11811778 -1.4992295 0.011864944 -1.3212615 -0.00013416809
Loop time of 0.295538 on 1 procs for 10000 steps with 16 atoms
Performance: 29234.801 tau/day, 33836.575 timesteps/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.20959 | 0.20959 | 0.20959 | 0.0 | 70.92
Bond | 0.0073669 | 0.0073669 | 0.0073669 | 0.0 | 2.49
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0016472 | 0.0016472 | 0.0016472 | 0.0 | 0.56
Output | 5.0068e-06 | 5.0068e-06 | 5.0068e-06 | 0.0 | 0.00
Modify | 0.073117 | 0.073117 | 0.073117 | 0.0 | 24.74
Other | | 0.003813 | | | 1.29
Nlocal: 16 ave 16 max 16 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 88 ave 88 max 88 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 88
Ave neighs/atom = 5.5
Ave special neighs/atom = 3.75
Neighbor list builds = 0
Dangerous builds = 0
#write_restart config.${number}.*
Total wall time: 0:00:00

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LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
variable number equal 2
variable ofreq equal 1000
variable efreq equal 1000
units lj
dimension 3
newton off
boundary p p p
atom_style hybrid bond ellipsoid
atom_modify sort 0 1.0
# Pair interactions require lists of neighbours to be calculated
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
read_data data.duplex2
orthogonal box = (-20 -20 -20) to (20 20 20)
1 by 2 by 2 MPI processor grid
reading atoms ...
16 atoms
reading velocities ...
16 velocities
16 ellipsoids
scanning bonds ...
2 = max bonds/atom
reading bonds ...
13 bonds
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of 1-4 neighbors
6 = max # of special neighbors
set atom * mass 3.1575
16 settings made for mass
group all type 1 4
16 atoms in group all
# oxDNA bond interactions - FENE backbone
bond_style oxdna/fene
bond_coeff * 2.0 0.25 0.7525
# oxDNA pair interactions
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
pair_coeff * * oxdna/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
# NVE ensemble
#fix 1 all nve/dot
fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
#fix 1 all nve/asphere
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
timestep 1e-5
#comm_style tiled
#fix 3 all balance 10000 1.1 rcb
#compute mol all chunk/atom molecule
#compute mychunk all vcm/chunk mol
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
#dump pos all xyz ${ofreq} traj.${number}.xyz
#compute quat all property/atom quatw quati quatj quatk
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
#dump_modify quat sort id
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
compute erot all erotate/asphere
compute ekin all ke
compute epot all pe
variable erot equal c_erot
variable ekin equal c_ekin
variable epot equal c_epot
variable etot equal c_erot+c_ekin+c_epot
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
#dump_modify out sort id
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
run 10000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.92828
ghost atom cutoff = 1.92828
binsize = 0.964142, bins = 42 42 42
5 neighbor lists, perpetual/occasional/extra = 5 0 0
(1) pair oxdna/excv, perpetual
attributes: half, newton off
pair build: half/bin/newtoff
stencil: half/bin/3d/newtoff
bin: standard
(2) pair oxdna/stk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(3) pair oxdna/hbond, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(4) pair oxdna/xstk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(5) pair oxdna/coaxstk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 7.466 | 7.648 | 7.83 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -1.5402493 0.0070469125 -1.5332024 -8.5641987e-05
1000 ekin = 1.34565986428024 | erot = 2.31051421234078 | epot = -24.5061991591502 | etot = -20.8500250825292
2000 ekin = 2.15911766687235 | erot = 2.16031365874707 | epot = -24.4723177103698 | etot = -20.1528863847504
3000 ekin = 3.26561948796015 | erot = 2.75651822936604 | epot = -24.412573068346 | etot = -18.3904353510198
4000 ekin = 1.92438809241066 | erot = 2.12016940074985 | epot = -24.3496233970111 | etot = -20.3050659038506
5000 ekin = 1.35986357015476 | erot = 1.99413493074226 | epot = -24.2789445616949 | etot = -20.9249460607979
6000 ekin = 2.19432475124593 | erot = 1.74281260409078 | epot = -24.2128064295788 | etot = -20.2756690742421
7000 ekin = 2.65619274477635 | erot = 1.74094257048458 | epot = -24.1673462333493 | etot = -19.7702109180883
8000 ekin = 2.51333548501168 | erot = 2.34649854571051 | epot = -24.0812769481836 | etot = -19.2214429174614
9000 ekin = 2.24506493169711 | erot = 2.0652555461504 | epot = -23.9906736063989 | etot = -19.6803531285514
10000 ekin = 2.36632635249862 | erot = 1.7959247176153 | epot = -23.9002627850602 | etot = -19.7380117149463
10000 0.10517006 -1.5057137 0.011947302 -1.345871 -9.5924016e-05
Loop time of 0.251867 on 4 procs for 10000 steps with 16 atoms
Performance: 34303.820 tau/day, 39703.495 timesteps/s
97.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0035377 | 0.092047 | 0.17435 | 26.0 | 36.55
Bond | 0.00065637 | 0.0031857 | 0.0053554 | 3.8 | 1.26
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.013929 | 0.01497 | 0.015733 | 0.6 | 5.94
Output | 5.0783e-05 | 5.2691e-05 | 5.3883e-05 | 0.0 | 0.02
Modify | 0.0013576 | 0.020825 | 0.040231 | 11.8 | 8.27
Other | | 0.1208 | | | 47.96
Nlocal: 4 ave 8 max 0 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Nghost: 9 ave 10 max 8 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Neighs: 34.5 ave 67 max 0 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Total # of neighbors = 138
Ave neighs/atom = 8.625
Ave special neighs/atom = 3.75
Neighbor list builds = 0
Dangerous builds = 0
#write_restart config.${number}.*
Total wall time: 0:00:00

2
examples/USER/cgdna/examples/oxDNA2/duplex1/input.duplex1 → examples/USER/cgdna/examples/oxDNA2/duplex1/in.duplex1
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@ -73,6 +73,6 @@ fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${e
#dump_modify out sort id
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
run 1000000
run 10000
#write_restart config.${number}.*

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LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
variable number equal 1
variable ofreq equal 1000
variable efreq equal 1000
units lj
dimension 3
newton off
boundary p p p
atom_style hybrid bond ellipsoid
atom_modify sort 0 1.0
# Pair interactions require lists of neighbours to be calculated
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
read_data data.duplex1
orthogonal box = (-20 -20 -20) to (20 20 20)
1 by 1 by 1 MPI processor grid
reading atoms ...
10 atoms
reading velocities ...
10 velocities
10 ellipsoids
scanning bonds ...
2 = max bonds/atom
reading bonds ...
8 bonds
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
2 = max # of 1-4 neighbors
4 = max # of special neighbors
set atom * mass 3.1575
10 settings made for mass
group all type 1 4
10 atoms in group all
# oxDNA bond interactions - FENE backbone
bond_style oxdna2/fene
bond_coeff * 2.0 0.25 0.7564
# oxDNA pair interactions
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
pair_coeff * * oxdna2/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
pair_coeff * * oxdna2/dh 0.1 1.0 0.815
# NVE ensemble
fix 1 all nve/dot
#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
#fix 1 all nve/asphere
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
timestep 1e-5
#comm_style tiled
#fix 3 all balance 10000 1.1 rcb
#compute mol all chunk/atom molecule
#compute mychunk all vcm/chunk mol
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
#dump pos all xyz ${ofreq} traj.${number}.xyz
#compute quat all property/atom quatw quati quatj quatk
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
#dump_modify quat sort id
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
compute erot all erotate/asphere
compute ekin all ke
compute epot all pe
variable erot equal c_erot
variable ekin equal c_ekin
variable epot equal c_epot
variable etot equal c_erot+c_ekin+c_epot
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
#dump_modify out sort id
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
run 10000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.6274
ghost atom cutoff = 2.6274
binsize = 1.3137, bins = 31 31 31
6 neighbor lists, perpetual/occasional/extra = 6 0 0
(1) pair oxdna2/excv, perpetual
attributes: half, newton off
pair build: half/bin/newtoff
stencil: half/bin/3d/newtoff
bin: standard
(2) pair oxdna2/stk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(3) pair oxdna2/hbond, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(4) pair oxdna2/xstk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(5) pair oxdna2/coaxstk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(6) pair oxdna2/dh, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 3.023 | 3.023 | 3.023 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -1.4712768 0.009525411 -1.4617514 -5.8922361e-05
1000 ekin = 0.00113086229080528 | erot = 0.0043101016040658 | epot = -14.6229549982368 | etot = -14.617514034342
2000 ekin = 0.0044853322434243 | erot = 0.0171407706505008 | epot = -14.6391401372615 | etot = -14.6175140343675
3000 ekin = 0.00995035259649284 | erot = 0.0381961780846485 | epot = -14.6656605650904 | etot = -14.6175140344093
4000 ekin = 0.0173418024862054 | erot = 0.0669935184860634 | epot = -14.7018493554381 | etot = -14.6175140344659
5000 ekin = 0.0264109356286075 | erot = 0.102878288094517 | epot = -14.7468032582586 | etot = -14.6175140345355
6000 ekin = 0.0368533113591442 | erot = 0.14504542056987 | epot = -14.7994127665447 | etot = -14.6175140346157
7000 ekin = 0.0483200640564843 | erot = 0.19256586251551 | epot = -14.8583999612756 | etot = -14.6175140347036
8000 ekin = 0.0604312317605998 | erot = 0.24441787013151 | epot = -14.9223631366883 | etot = -14.6175140347962
9000 ekin = 0.0727907119671751 | erot = 0.299521949931843 | epot = -14.989826696789 | etot = -14.6175140348899
10000 ekin = 0.0850022498875221 | erot = 0.356777997217908 | epot = -15.0592942820869 | etot = -14.6175140349815
10000 0.006296463 -1.5144685 0.0085391004 -1.4974292 -0.00010794792
Loop time of 0.149406 on 1 procs for 10000 steps with 10 atoms
Performance: 57828.835 tau/day, 66931.522 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.11971 | 0.11971 | 0.11971 | 0.0 | 80.12
Bond | 0.0051196 | 0.0051196 | 0.0051196 | 0.0 | 3.43
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0013614 | 0.0013614 | 0.0013614 | 0.0 | 0.91
Output | 5.0068e-06 | 5.0068e-06 | 5.0068e-06 | 0.0 | 0.00
Modify | 0.018941 | 0.018941 | 0.018941 | 0.0 | 12.68
Other | | 0.004268 | | | 2.86
Nlocal: 10 ave 10 max 10 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 45 ave 45 max 45 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 45
Ave neighs/atom = 4.5
Ave special neighs/atom = 3.6
Neighbor list builds = 0
Dangerous builds = 0
#write_restart config.${number}.*
Total wall time: 0:00:00

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LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
variable number equal 1
variable ofreq equal 1000
variable efreq equal 1000
units lj
dimension 3
newton off
boundary p p p
atom_style hybrid bond ellipsoid
atom_modify sort 0 1.0
# Pair interactions require lists of neighbours to be calculated
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
read_data data.duplex1
orthogonal box = (-20 -20 -20) to (20 20 20)
1 by 2 by 2 MPI processor grid
reading atoms ...
10 atoms
reading velocities ...
10 velocities
10 ellipsoids
scanning bonds ...
2 = max bonds/atom
reading bonds ...
8 bonds
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
2 = max # of 1-4 neighbors
4 = max # of special neighbors
set atom * mass 3.1575
10 settings made for mass
group all type 1 4
10 atoms in group all
# oxDNA bond interactions - FENE backbone
bond_style oxdna2/fene
bond_coeff * 2.0 0.25 0.7564
# oxDNA pair interactions
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
pair_coeff * * oxdna2/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
pair_coeff * * oxdna2/dh 0.1 1.0 0.815
# NVE ensemble
fix 1 all nve/dot
#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
#fix 1 all nve/asphere
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
timestep 1e-5
#comm_style tiled
#fix 3 all balance 10000 1.1 rcb
#compute mol all chunk/atom molecule
#compute mychunk all vcm/chunk mol
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
#dump pos all xyz ${ofreq} traj.${number}.xyz
#compute quat all property/atom quatw quati quatj quatk
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
#dump_modify quat sort id
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
compute erot all erotate/asphere
compute ekin all ke
compute epot all pe
variable erot equal c_erot
variable ekin equal c_ekin
variable epot equal c_epot
variable etot equal c_erot+c_ekin+c_epot
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
#dump_modify out sort id
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
run 10000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.6274
ghost atom cutoff = 2.6274
binsize = 1.3137, bins = 31 31 31
6 neighbor lists, perpetual/occasional/extra = 6 0 0
(1) pair oxdna2/excv, perpetual
attributes: half, newton off
pair build: half/bin/newtoff
stencil: half/bin/3d/newtoff
bin: standard
(2) pair oxdna2/stk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(3) pair oxdna2/hbond, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(4) pair oxdna2/xstk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(5) pair oxdna2/coaxstk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(6) pair oxdna2/dh, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 7.652 | 7.834 | 8.016 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -1.4712768 0.009525411 -1.4617514 -5.8922361e-05
1000 ekin = 0.00113086229080478 | erot = 0.00431010160406708 | epot = -14.6229549982368 | etot = -14.617514034342
2000 ekin = 0.00448533224342286 | erot = 0.0171407706505013 | epot = -14.6391401372615 | etot = -14.6175140343675
3000 ekin = 0.0099503525964896 | erot = 0.0381961780846438 | epot = -14.6656605650904 | etot = -14.6175140344093
4000 ekin = 0.0173418024861991 | erot = 0.0669935184860479 | epot = -14.7018493554381 | etot = -14.6175140344659
5000 ekin = 0.0264109356285965 | erot = 0.102878288094482 | epot = -14.7468032582586 | etot = -14.6175140345355
6000 ekin = 0.0368533113591268 | erot = 0.145045420569809 | epot = -14.7994127665446 | etot = -14.6175140346156
7000 ekin = 0.0483200640564584 | erot = 0.192565862515413 | epot = -14.8583999612755 | etot = -14.6175140347036
8000 ekin = 0.0604312317605635 | erot = 0.24441787013137 | epot = -14.9223631366881 | etot = -14.6175140347962
9000 ekin = 0.072790711967127 | erot = 0.299521949931654 | epot = -14.9898266967887 | etot = -14.6175140348899
10000 ekin = 0.0850022498874609 | erot = 0.356777997217666 | epot = -15.0592942820866 | etot = -14.6175140349815
10000 0.006296463 -1.5144685 0.0085391004 -1.4974292 -0.00010794792
Loop time of 0.14583 on 4 procs for 10000 steps with 10 atoms
Performance: 59247.054 tau/day, 68572.979 timesteps/s
97.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0034175 | 0.055587 | 0.10059 | 17.9 | 38.12
Bond | 0.00064635 | 0.002131 | 0.0035357 | 2.5 | 1.46
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.014538 | 0.014932 | 0.015271 | 0.2 | 10.24
Output | 5.7459e-05 | 5.7697e-05 | 5.7936e-05 | 0.0 | 0.04
Modify | 0.0012829 | 0.0063873 | 0.011321 | 5.2 | 4.38
Other | | 0.06674 | | | 45.76
Nlocal: 2.5 ave 5 max 0 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Nghost: 7.5 ave 10 max 5 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Neighs: 18.5 ave 35 max 0 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Total # of neighbors = 74
Ave neighs/atom = 7.4
Ave special neighs/atom = 3.6
Neighbor list builds = 0
Dangerous builds = 0
#write_restart config.${number}.*
Total wall time: 0:00:00

2
examples/USER/cgdna/examples/oxDNA2/duplex2/input.duplex2 → examples/USER/cgdna/examples/oxDNA2/duplex2/in.duplex2
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@ -73,6 +73,6 @@ fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${e
#dump_modify out sort id
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
run 1000000
run 10000
#write_restart config.${number}.*

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LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
variable number equal 2
variable ofreq equal 1000
variable efreq equal 1000
units lj
dimension 3
newton off
boundary p p p
atom_style hybrid bond ellipsoid
atom_modify sort 0 1.0
# Pair interactions require lists of neighbours to be calculated
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
read_data data.duplex2
orthogonal box = (-20 -20 -20) to (20 20 20)
1 by 1 by 1 MPI processor grid
reading atoms ...
16 atoms
reading velocities ...
16 velocities
16 ellipsoids
scanning bonds ...
2 = max bonds/atom
reading bonds ...
13 bonds
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of 1-4 neighbors
6 = max # of special neighbors
set atom * mass 3.1575
16 settings made for mass
group all type 1 4
16 atoms in group all
# oxDNA bond interactions - FENE backbone
bond_style oxdna2/fene
bond_coeff * 2.0 0.25 0.7564
# oxDNA pair interactions
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
pair_coeff * * oxdna2/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
pair_coeff * * oxdna2/dh 0.1 1.0 0.815
# NVE ensemble
#fix 1 all nve/dot
fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
#fix 1 all nve/asphere
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
timestep 1e-5
#comm_style tiled
#fix 3 all balance 10000 1.1 rcb
#compute mol all chunk/atom molecule
#compute mychunk all vcm/chunk mol
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
#dump pos all xyz ${ofreq} traj.${number}.xyz
#compute quat all property/atom quatw quati quatj quatk
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
#dump_modify quat sort id
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
compute erot all erotate/asphere
compute ekin all ke
compute epot all pe
variable erot equal c_erot
variable ekin equal c_ekin
variable epot equal c_epot
variable etot equal c_erot+c_ekin+c_epot
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
#dump_modify out sort id
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
run 10000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.6274
ghost atom cutoff = 2.6274
binsize = 1.3137, bins = 31 31 31
6 neighbor lists, perpetual/occasional/extra = 6 0 0
(1) pair oxdna2/excv, perpetual
attributes: half, newton off
pair build: half/bin/newtoff
stencil: half/bin/3d/newtoff
bin: standard
(2) pair oxdna2/stk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(3) pair oxdna2/hbond, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(4) pair oxdna2/xstk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(5) pair oxdna2/coaxstk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(6) pair oxdna2/dh, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 3.025 | 3.025 | 3.025 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -1.5358787 0.0096742456 -1.5262045 -7.9568629e-05
1000 ekin = 1.54282272464468 | erot = 1.71757897250772 | epot = -24.4403527731341 | etot = -21.1799510759817
2000 ekin = 1.86109566690716 | erot = 1.93804145796026 | epot = -24.3759816748265 | etot = -20.5768445499591
3000 ekin = 2.68769182431188 | erot = 2.14559269500086 | epot = -24.2916556822451 | etot = -19.4583711629324
4000 ekin = 2.04710303757243 | erot = 1.48774072590987 | epot = -24.190371461807 | etot = -20.6555276983247
5000 ekin = 1.77654023802719 | erot = 2.534186505221 | epot = -24.1246365663843 | etot = -19.8139098231361
6000 ekin = 3.12253137872527 | erot = 2.04028266818831 | epot = -24.0491248750916 | etot = -18.886310828178
7000 ekin = 3.22418765752177 | erot = 2.72037570174023 | epot = -23.9458569915548 | etot = -18.0012936322928
8000 ekin = 2.83204202112963 | erot = 2.67060276413777 | epot = -23.9211291529766 | etot = -18.4184843677092
9000 ekin = 2.69585642754481 | erot = 2.59559820250212 | epot = -23.8340823338302 | etot = -18.5426277037833
10000 ekin = 2.66058119525512 | erot = 1.95965933336077 | epot = -23.7132443170725 | etot = -19.0930037884566
10000 0.11824805 -1.4953627 0.013284973 -1.3157914 -0.00012999454
Loop time of 0.32781 on 1 procs for 10000 steps with 16 atoms
Performance: 26356.746 tau/day, 30505.493 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.24211 | 0.24211 | 0.24211 | 0.0 | 73.86
Bond | 0.0075173 | 0.0075173 | 0.0075173 | 0.0 | 2.29
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0014515 | 0.0014515 | 0.0014515 | 0.0 | 0.44
Output | 5.4836e-06 | 5.4836e-06 | 5.4836e-06 | 0.0 | 0.00
Modify | 0.073331 | 0.073331 | 0.073331 | 0.0 | 22.37
Other | | 0.003398 | | | 1.04
Nlocal: 16 ave 16 max 16 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 116 ave 116 max 116 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 116
Ave neighs/atom = 7.25
Ave special neighs/atom = 3.75
Neighbor list builds = 0
Dangerous builds = 0
#write_restart config.${number}.*
Total wall time: 0:00:00

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LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
variable number equal 2
variable ofreq equal 1000
variable efreq equal 1000
units lj
dimension 3
newton off
boundary p p p
atom_style hybrid bond ellipsoid
atom_modify sort 0 1.0
# Pair interactions require lists of neighbours to be calculated
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
read_data data.duplex2
orthogonal box = (-20 -20 -20) to (20 20 20)
1 by 2 by 2 MPI processor grid
reading atoms ...
16 atoms
reading velocities ...
16 velocities
16 ellipsoids
scanning bonds ...
2 = max bonds/atom
reading bonds ...
13 bonds
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of 1-4 neighbors
6 = max # of special neighbors
set atom * mass 3.1575
16 settings made for mass
group all type 1 4
16 atoms in group all
# oxDNA bond interactions - FENE backbone
bond_style oxdna2/fene
bond_coeff * 2.0 0.25 0.7564
# oxDNA pair interactions
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
pair_coeff * * oxdna2/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
pair_coeff * * oxdna2/dh 0.1 1.0 0.815
# NVE ensemble
#fix 1 all nve/dot
fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
#fix 1 all nve/asphere
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
timestep 1e-5
#comm_style tiled
#fix 3 all balance 10000 1.1 rcb
#compute mol all chunk/atom molecule
#compute mychunk all vcm/chunk mol
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
#dump pos all xyz ${ofreq} traj.${number}.xyz
#compute quat all property/atom quatw quati quatj quatk
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
#dump_modify quat sort id
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
compute erot all erotate/asphere
compute ekin all ke
compute epot all pe
variable erot equal c_erot
variable ekin equal c_ekin
variable epot equal c_epot
variable etot equal c_erot+c_ekin+c_epot
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
#dump_modify out sort id
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
run 10000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.6274
ghost atom cutoff = 2.6274
binsize = 1.3137, bins = 31 31 31
6 neighbor lists, perpetual/occasional/extra = 6 0 0
(1) pair oxdna2/excv, perpetual
attributes: half, newton off
pair build: half/bin/newtoff
stencil: half/bin/3d/newtoff
bin: standard
(2) pair oxdna2/stk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(3) pair oxdna2/hbond, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(4) pair oxdna2/xstk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(5) pair oxdna2/coaxstk, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
(6) pair oxdna2/dh, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 7.777 | 7.959 | 8.142 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -1.5358787 0.0096742456 -1.5262045 -7.9568629e-05
1000 ekin = 1.34554291364716 | erot = 2.30525041754444 | epot = -24.3924150888896 | etot = -20.741621757698
2000 ekin = 2.15972469811184 | erot = 2.1628675965276 | epot = -24.3548203354875 | etot = -20.0322280408481
3000 ekin = 3.26433550542939 | erot = 2.76107866472085 | epot = -24.2947953202752 | etot = -18.269381150125
4000 ekin = 1.9203212531997 | erot = 2.13339438425299 | epot = -24.234098584123 | etot = -20.1803829466703
5000 ekin = 1.35481075814721 | erot = 2.00854026688447 | epot = -24.1768963201279 | etot = -20.8135452950963
6000 ekin = 2.18974627635306 | erot = 1.73271671162435 | epot = -24.1096616118305 | etot = -20.1871986238531
7000 ekin = 2.65472853187395 | erot = 1.73258720631296 | epot = -24.0561118130561 | etot = -19.6687960748691
8000 ekin = 2.51192327964357 | erot = 2.34132844779952 | epot = -23.9708695663488 | etot = -19.1176178389058
9000 ekin = 2.24554900802464 | erot = 2.0522939078286 | epot = -23.874757758319 | etot = -19.5769148424658
10000 ekin = 2.36227360512089 | erot = 1.80185994066737 | epot = -23.7793375260418 | etot = -19.6152039802535
10000 0.10498994 -1.5020657 0.015857071 -1.3385665 -8.8930899e-05
Loop time of 0.291642 on 4 procs for 10000 steps with 16 atoms
Performance: 29625.313 tau/day, 34288.557 timesteps/s
96.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0035026 | 0.1107 | 0.20674 | 28.3 | 37.96
Bond | 0.00062203 | 0.0029532 | 0.0049176 | 3.6 | 1.01
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.016712 | 0.018041 | 0.01914 | 0.7 | 6.19
Output | 5.0306e-05 | 5.424e-05 | 5.579e-05 | 0.0 | 0.02
Modify | 0.0013862 | 0.020914 | 0.039594 | 11.7 | 7.17
Other | | 0.139 | | | 47.65
Nlocal: 4 ave 8 max 0 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Nghost: 11 ave 14 max 8 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Neighs: 46 ave 89 max 0 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Total # of neighbors = 184
Ave neighs/atom = 11.5
Ave special neighs/atom = 3.75
Neighbor list builds = 0
Dangerous builds = 0
#write_restart config.${number}.*
Total wall time: 0:00:00