Merge pull request #2210 from ohenrich/user-cgdna

Update of example input and log files

examples/USER/cgdna/examples/oxDNA/duplex1/in.duplex1

@@ -27,6 +27,7 @@ group all type 1 4
 # oxDNA bond interactions - FENE backbone
 bond_style oxdna/fene
 bond_coeff * 2.0 0.25 0.7525
+special_bonds lj 0 1 1
 
 # oxDNA pair interactions
 pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
@@ -48,6 +49,7 @@ timestep 1e-5
 
 #comm_style tiled
 #fix 3 all balance 10000 1.1 rcb
+comm_modify cutoff 2.5
 
 #compute mol all chunk/atom molecule
 #compute mychunk all vcm/chunk mol

examples/USER/cgdna/examples/oxDNA/duplex1/log.30Jun20.duplex1.g++.1

@@ -1,4 +1,4 @@
-LAMMPS (7 Aug 2019)
+LAMMPS (30 Jun 2020)
 variable number	equal 1
 variable ofreq	equal 1000
 variable efreq	equal 1000
@@ -12,7 +12,10 @@ newton off
 
 boundary  p p p
 
+
+
 atom_style hybrid bond ellipsoid
+WARNING: Atom_style hybrid defines both pertype and peratom masses - both must be set, only peratom masses will be used (../atom_vec_hybrid.cpp:156)
 atom_modify sort 0 1.0
 
 # Pair interactions require lists of neighbours to be calculated
@@ -35,9 +38,8 @@ read_data data.duplex1
   2 = max # of 1-3 neighbors
   2 = max # of 1-4 neighbors
   4 = max # of special neighbors
-  special bonds CPU = 9.5e-05 secs
+  special bonds CPU = 0.000 seconds
-  read_data CPU = 0.001865 secs
+  read_data CPU = 0.002 seconds
-
 set atom * mass 3.1575
   10 settings made for mass
 
@@ -47,6 +49,12 @@ group all type 1 4
 # oxDNA bond interactions - FENE backbone
 bond_style oxdna/fene
 bond_coeff * 2.0 0.25 0.7525
+special_bonds lj 0 1 1
+  2 = max # of 1-2 neighbors
+  2 = max # of 1-3 neighbors
+  2 = max # of 1-4 neighbors
+  4 = max # of special neighbors
+  special bonds CPU = 0.000 seconds
 
 # oxDNA pair interactions
 pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
@@ -69,6 +77,7 @@ timestep 1e-5
 
 #comm_style tiled
 #fix 3 all balance 10000 1.1 rcb
+comm_modify cutoff 2.5
 
 #compute mol all chunk/atom molecule
 #compute mychunk all vcm/chunk mol
@@ -99,9 +108,9 @@ run 1000000
 Neighbor list info ...
   update every 1 steps, delay 0 steps, check yes
   max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 1.956
+  master list distance cutoff = 1.9560004
-  ghost atom cutoff = 1.956
+  ghost atom cutoff = 2.5
-  binsize = 0.978, bins = 41 41 41
+  binsize = 0.97800022, bins = 41 41 41
   5 neighbor lists, perpetual/occasional/extra = 5 0 0
   (1) pair oxdna/excv, perpetual
       attributes: half, newton off
@@ -128,8 +137,8 @@ Neighbor list info ...
       pair build: copy
       stencil: none
       bin: none
-WARNING: Communication cutoff 1.956 is shorter than a bond length based estimate of 2.12875. This may lead to errors. (../comm.cpp:685)
+0  ekin = 0 |  erot = 0 | epot = -14.6424332448164 | etot = -14.6424332448164
-Per MPI rank memory allocation (min/avg/max) = 2.836 | 2.836 | 2.836 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 7.883 | 7.883 | 7.883 Mbytes
 Step Temp E_pair E_mol TotEng Press 
        0            0   -1.4711818 0.0069384985   -1.4642433 2.5836586e-06 
 1000  ekin = 0.00113448721737003 |  erot = 0.00413455947734281 | epot = -14.6477022915193 | etot = -14.6424332448246
@@ -1133,34 +1142,34 @@ Step Temp E_pair E_mol TotEng Press
 999000  ekin = 0.188315843917336 |  erot = 0.335221830001114 | epot = -15.1659709188676 | etot = -14.6424332449491
 1000000  ekin = 0.1816243230724 |  erot = 0.33096613964385 | epot = -15.155023707645 | etot = -14.6424332449287
  1000000  0.013453654   -1.5270261  0.011523695   -1.4973399 -8.4815516e-05 
-Loop time of 17.1797 on 1 procs for 1000000 steps with 10 atoms
+Loop time of 15.696 on 1 procs for 1000000 steps with 10 atoms
 
-Performance: 50291.944 tau/day, 58208.268 timesteps/s
+Performance: 55045.770 tau/day, 63710.382 timesteps/s
 99.6% CPU use with 1 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 13.871     | 13.871     | 13.871     |   0.0 | 80.74
+Pair    | 11.973     | 11.973     | 11.973     |   0.0 | 76.28
-Bond    | 0.52454    | 0.52454    | 0.52454    |   0.0 |  3.05
+Bond    | 0.57492    | 0.57492    | 0.57492    |   0.0 |  3.66
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.14987    | 0.14987    | 0.14987    |   0.0 |  0.87
+Comm    | 0.18391    | 0.18391    | 0.18391    |   0.0 |  1.17
-Output  | 7e-06      | 7e-06      | 7e-06      |   0.0 |  0.00
+Output  | 8e-06      | 8e-06      | 8e-06      |   0.0 |  0.00
-Modify  | 2.4075     | 2.4075     | 2.4075     |   0.0 | 14.01
+Modify  | 2.7068     | 2.7068     | 2.7068     |   0.0 | 17.25
-Other   |            | 0.227      |            |       |  1.32
+Other   |            | 0.2573     |            |       |  1.64
 
-Nlocal:    10 ave 10 max 10 min
+Nlocal:    10.0 ave 10.0 max 10.0 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    0 ave 0 max 0 min
+Nghost:    0.0 ave 0.0 max 0.0 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    45 ave 45 max 45 min
+Neighs:    37.0 ave 37.0 max 37.0 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
 
-Total # of neighbors = 45
+Total # of neighbors = 37
-Ave neighs/atom = 4.5
+Ave neighs/atom = 3.7
 Ave special neighs/atom = 3.6
 Neighbor list builds = 0
 Dangerous builds = 0
 
 #write_restart config.${number}.*
-Total wall time: 0:00:17
+Total wall time: 0:00:15

examples/USER/cgdna/examples/oxDNA/duplex1/log.30Jun20.duplex1.g++.4

@@ -1,4 +1,4 @@
-LAMMPS (7 Aug 2019)
+LAMMPS (30 Jun 2020)
 variable number	equal 1
 variable ofreq	equal 1000
 variable efreq	equal 1000
@@ -12,7 +12,10 @@ newton off
 
 boundary  p p p
 
+
+
 atom_style hybrid bond ellipsoid
+WARNING: Atom_style hybrid defines both pertype and peratom masses - both must be set, only peratom masses will be used (../atom_vec_hybrid.cpp:156)
 atom_modify sort 0 1.0
 
 # Pair interactions require lists of neighbours to be calculated
@@ -35,9 +38,8 @@ read_data data.duplex1
   2 = max # of 1-3 neighbors
   2 = max # of 1-4 neighbors
   4 = max # of special neighbors
-  special bonds CPU = 0.000216 secs
+  special bonds CPU = 0.001 seconds
-  read_data CPU = 0.003061 secs
+  read_data CPU = 0.003 seconds
-
 set atom * mass 3.1575
   10 settings made for mass
 
@@ -47,6 +49,12 @@ group all type 1 4
 # oxDNA bond interactions - FENE backbone
 bond_style oxdna/fene
 bond_coeff * 2.0 0.25 0.7525
+special_bonds lj 0 1 1
+  2 = max # of 1-2 neighbors
+  2 = max # of 1-3 neighbors
+  2 = max # of 1-4 neighbors
+  4 = max # of special neighbors
+  special bonds CPU = 0.000 seconds
 
 # oxDNA pair interactions
 pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
@@ -69,6 +77,7 @@ timestep 1e-5
 
 #comm_style tiled
 #fix 3 all balance 10000 1.1 rcb
+comm_modify cutoff 2.5
 
 #compute mol all chunk/atom molecule
 #compute mychunk all vcm/chunk mol
@@ -99,9 +108,9 @@ run 1000000
 Neighbor list info ...
   update every 1 steps, delay 0 steps, check yes
   max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 1.956
+  master list distance cutoff = 1.9560004
-  ghost atom cutoff = 1.956
+  ghost atom cutoff = 2.5
-  binsize = 0.978, bins = 41 41 41
+  binsize = 0.97800022, bins = 41 41 41
   5 neighbor lists, perpetual/occasional/extra = 5 0 0
   (1) pair oxdna/excv, perpetual
       attributes: half, newton off
@@ -128,8 +137,8 @@ Neighbor list info ...
       pair build: copy
       stencil: none
       bin: none
-WARNING: Communication cutoff 1.956 is shorter than a bond length based estimate of 2.12875. This may lead to errors. (../comm.cpp:685)
+0  ekin = 0 |  erot = 0 | epot = -14.6424332448164 | etot = -14.6424332448164
-Per MPI rank memory allocation (min/avg/max) = 7.33 | 7.512 | 7.694 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 7.605 | 7.662 | 7.719 Mbytes
 Step Temp E_pair E_mol TotEng Press 
        0            0   -1.4711818 0.0069384985   -1.4642433 2.5836586e-06 
 1000  ekin = 0.00113448721737009 |  erot = 0.0041345594773427 | epot = -14.6477022915193 | etot = -14.6424332448246
@@ -1133,34 +1142,34 @@ Step Temp E_pair E_mol TotEng Press
 999000  ekin = 0.18831584391307 |  erot = 0.335221830005501 | epot = -15.1659709188615 | etot = -14.642433244943
 1000000  ekin = 0.181624323067755 |  erot = 0.330966139649165 | epot = -15.1550237076395 | etot = -14.6424332449226
  1000000  0.013453654   -1.5270261  0.011523695   -1.4973399 -8.4815516e-05 
-Loop time of 18.6281 on 4 procs for 1000000 steps with 10 atoms
+Loop time of 16.5005 on 4 procs for 1000000 steps with 10 atoms
 
-Performance: 46381.610 tau/day, 53682.419 timesteps/s
+Performance: 52362.058 tau/day, 60604.234 timesteps/s
 99.5% CPU use with 4 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.50691    | 7.0285     | 12.641     | 197.6 | 37.73
+Pair    | 0.51373    | 5.7702     | 10.408     | 174.5 | 34.97
-Bond    | 0.081876   | 0.27627    | 0.44175    |  28.5 |  1.48
+Bond    | 0.084405   | 0.27056    | 0.44162    |  28.3 |  1.64
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 1.7692     | 2.0629     | 2.3468     |  17.0 | 11.07
+Comm    | 1.7403     | 2.0946     | 2.4247     |  18.8 | 12.69
-Output  | 1.8e-05    | 2.625e-05  | 3e-05      |   0.0 |  0.00
+Output  | 4e-05      | 6e-05      | 7.1e-05    |   0.0 |  0.00
-Modify  | 0.17309    | 0.88362    | 1.5352     |  58.4 |  4.74
+Modify  | 0.17451    | 0.87938    | 1.53       |  58.2 |  5.33
-Other   |            | 8.377      |            |       | 44.97
+Other   |            | 7.486      |            |       | 45.37
 
-Nlocal:    2.5 ave 5 max 0 min
+Nlocal:    2.5 ave 5.0 max 0.0 min
 Histogram: 1 0 1 0 0 0 0 0 1 1
-Nghost:    7.5 ave 10 max 5 min
+Nghost:    7.5 ave 10.0 max 5.0 min
 Histogram: 1 0 1 0 0 0 0 0 1 1
-Neighs:    18.5 ave 35 max 0 min
+Neighs:    16.0 ave 30.0 max 0.0 min
 Histogram: 1 0 1 0 0 0 0 0 1 1
 
-Total # of neighbors = 74
+Total # of neighbors = 64
-Ave neighs/atom = 7.4
+Ave neighs/atom = 6.4
 Ave special neighs/atom = 3.6
 Neighbor list builds = 0
 Dangerous builds = 0
 
 #write_restart config.${number}.*
-Total wall time: 0:00:18
+Total wall time: 0:00:16

examples/USER/cgdna/examples/oxDNA/duplex2/in.duplex2

@@ -27,6 +27,7 @@ group all type 1 4
 # oxDNA bond interactions - FENE backbone
 bond_style oxdna/fene
 bond_coeff * 2.0 0.25 0.7525
+special_bonds lj 0 1 1
 
 # oxDNA pair interactions
 pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
@@ -48,6 +49,7 @@ timestep 1e-5
 
 #comm_style tiled
 #fix 3 all balance 10000 1.1 rcb
+comm_modify cutoff 2.5
 
 #compute mol all chunk/atom molecule
 #compute mychunk all vcm/chunk mol

examples/USER/cgdna/examples/oxDNA2/duplex1/in.duplex1

@@ -27,6 +27,7 @@ group all type 1 4
 # oxDNA2 bond interactions - FENE backbone
 bond_style oxdna2/fene
 bond_coeff * 2.0 0.25 0.7564
+special_bonds lj 0 1 1
 
 # oxDNA2 pair interactions
 pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
@@ -49,6 +50,7 @@ timestep 1e-5
 
 #comm_style tiled
 #fix 3 all balance 10000 1.1 rcb
+comm_modify cutoff 2.5
 
 #compute mol all chunk/atom molecule
 #compute mychunk all vcm/chunk mol

examples/USER/cgdna/examples/oxDNA2/duplex1/log.30Jun20.duplex1.g++.1

@@ -1,4 +1,4 @@
-LAMMPS (7 Aug 2019)
+LAMMPS (30 Jun 2020)
 variable number	equal 1
 variable ofreq	equal 1000
 variable efreq	equal 1000
@@ -13,6 +13,7 @@ newton off
 boundary  p p p
 
 atom_style hybrid bond ellipsoid
+WARNING: Atom_style hybrid defines both pertype and peratom masses - both must be set, only peratom masses will be used (../atom_vec_hybrid.cpp:156)
 atom_modify sort 0 1.0
 
 # Pair interactions require lists of neighbours to be calculated
@@ -35,8 +36,8 @@ read_data data.duplex1
   2 = max # of 1-3 neighbors
   2 = max # of 1-4 neighbors
   4 = max # of special neighbors
-  special bonds CPU = 0.000116 secs
+  special bonds CPU = 0.000 seconds
-  read_data CPU = 0.002026 secs
+  read_data CPU = 0.003 seconds
 
 set atom * mass 3.1575
   10 settings made for mass
@@ -47,6 +48,12 @@ group all type 1 4
 # oxDNA2 bond interactions - FENE backbone
 bond_style oxdna2/fene
 bond_coeff * 2.0 0.25 0.7564
+special_bonds lj 0 1 1
+  2 = max # of 1-2 neighbors
+  2 = max # of 1-3 neighbors
+  2 = max # of 1-4 neighbors
+  4 = max # of special neighbors
+  special bonds CPU = 0.000 seconds
 
 # oxDNA2 pair interactions
 pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
@@ -71,6 +78,7 @@ timestep 1e-5
 
 #comm_style tiled
 #fix 3 all balance 10000 1.1 rcb
+comm_modify cutoff 2.5
 
 #compute mol all chunk/atom molecule
 #compute mychunk all vcm/chunk mol
@@ -101,9 +109,9 @@ run 1000000
 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
+  master list distance cutoff = 2.6274048
-  ghost atom cutoff = 2.6274
+  ghost atom cutoff = 2.6274048
-  binsize = 1.3137, bins = 31 31 31
+  binsize = 1.3137024, bins = 31 31 31
   6 neighbor lists, perpetual/occasional/extra = 6 0 0
   (1) pair oxdna2/excv, perpetual
       attributes: half, newton off
@@ -135,7 +143,9 @@ Neighbor list info ...
       pair build: copy
       stencil: none
       bin: none
-Per MPI rank memory allocation (min/avg/max) = 3.024 | 3.024 | 3.024 Mbytes
+WARNING: Communication cutoff adjusted to 2.627404783947349 (../comm.cpp:690)
+0  ekin = 0 |  erot = 0 | epot = -14.6175140343334 | etot = -14.6175140343334
+Per MPI rank memory allocation (min/avg/max) = 8.021 | 8.021 | 8.021 Mbytes
 Step Temp E_pair E_mol TotEng Press 
        0            0   -1.4712768  0.009525411   -1.4617514 4.663076e-06 
 1000  ekin = 0.00113086229080528 |  erot = 0.0043101016040658 | epot = -14.6229549982368 | etot = -14.617514034342
@@ -1139,34 +1149,34 @@ Step Temp E_pair E_mol TotEng Press
 999000  ekin = 0.190992053959174 |  erot = 0.320462575795008 | epot = -15.1289686644104 | etot = -14.6175140346562
 1000000  ekin = 0.179708146665509 |  erot = 0.311553394429298 | epot = -15.1087755756885 | etot = -14.6175140345937
  1000000  0.013311715   -1.5443684  0.033490821   -1.4929067 -3.7544839e-05 
-Loop time of 18.4193 on 1 procs for 1000000 steps with 10 atoms
+Loop time of 17.0535 on 1 procs for 1000000 steps with 10 atoms
 
-Performance: 46907.305 tau/day, 54290.862 timesteps/s
+Performance: 50663.947 tau/day, 58638.827 timesteps/s
 99.5% CPU use with 1 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 14.935     | 14.935     | 14.935     |   0.0 | 81.08
+Pair    | 13.135     | 13.135     | 13.135     |   0.0 | 77.02
-Bond    | 0.55556    | 0.55556    | 0.55556    |   0.0 |  3.02
+Bond    | 0.6362     | 0.6362     | 0.6362     |   0.0 |  3.73
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.16028    | 0.16028    | 0.16028    |   0.0 |  0.87
+Comm    | 0.18919    | 0.18919    | 0.18919    |   0.0 |  1.11
-Output  | 7e-06      | 7e-06      | 7e-06      |   0.0 |  0.00
+Output  | 8e-06      | 8e-06      | 8e-06      |   0.0 |  0.00
-Modify  | 2.5402     | 2.5402     | 2.5402     |   0.0 | 13.79
+Modify  | 2.8399     | 2.8399     | 2.8399     |   0.0 | 16.65
-Other   |            | 0.2285     |            |       |  1.24
+Other   |            | 0.2536     |            |       |  1.49
 
-Nlocal:    10 ave 10 max 10 min
+Nlocal:    10.0 ave 10.0 max 10.0 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    0 ave 0 max 0 min
+Nghost:    0.0 ave 0.0 max 0.0 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    45 ave 45 max 45 min
+Neighs:    37.0 ave 37.0 max 37.0 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
 
-Total # of neighbors = 45
+Total # of neighbors = 37
-Ave neighs/atom = 4.5
+Ave neighs/atom = 3.7
 Ave special neighs/atom = 3.6
 Neighbor list builds = 0
 Dangerous builds = 0
 
 #write_restart config.${number}.*
-Total wall time: 0:00:18
+Total wall time: 0:00:17

examples/USER/cgdna/examples/oxDNA2/duplex1/log.30Jun20.duplex1.g++.4

@@ -1,4 +1,4 @@
-LAMMPS (7 Aug 2019)
+LAMMPS (30 Jun 2020)
 variable number	equal 1
 variable ofreq	equal 1000
 variable efreq	equal 1000
@@ -13,6 +13,7 @@ newton off
 boundary  p p p
 
 atom_style hybrid bond ellipsoid
+WARNING: Atom_style hybrid defines both pertype and peratom masses - both must be set, only peratom masses will be used (../atom_vec_hybrid.cpp:156)
 atom_modify sort 0 1.0
 
 # Pair interactions require lists of neighbours to be calculated
@@ -35,8 +36,8 @@ read_data data.duplex1
   2 = max # of 1-3 neighbors
   2 = max # of 1-4 neighbors
   4 = max # of special neighbors
-  special bonds CPU = 0.000198 secs
+  special bonds CPU = 0.001 seconds
-  read_data CPU = 0.004522 secs
+  read_data CPU = 0.004 seconds
 
 set atom * mass 3.1575
   10 settings made for mass
@@ -47,6 +48,12 @@ group all type 1 4
 # oxDNA2 bond interactions - FENE backbone
 bond_style oxdna2/fene
 bond_coeff * 2.0 0.25 0.7564
+special_bonds lj 0 1 1
+  2 = max # of 1-2 neighbors
+  2 = max # of 1-3 neighbors
+  2 = max # of 1-4 neighbors
+  4 = max # of special neighbors
+  special bonds CPU = 0.000 seconds
 
 # oxDNA2 pair interactions
 pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
@@ -71,6 +78,7 @@ timestep 1e-5
 
 #comm_style tiled
 #fix 3 all balance 10000 1.1 rcb
+comm_modify cutoff 2.5
 
 #compute mol all chunk/atom molecule
 #compute mychunk all vcm/chunk mol
@@ -101,9 +109,9 @@ run 1000000
 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
+  master list distance cutoff = 2.6274048
-  ghost atom cutoff = 2.6274
+  ghost atom cutoff = 2.6274048
-  binsize = 1.3137, bins = 31 31 31
+  binsize = 1.3137024, bins = 31 31 31
   6 neighbor lists, perpetual/occasional/extra = 6 0 0
   (1) pair oxdna2/excv, perpetual
       attributes: half, newton off
@@ -135,7 +143,9 @@ Neighbor list info ...
       pair build: copy
       stencil: none
       bin: none
-Per MPI rank memory allocation (min/avg/max) = 7.653 | 7.835 | 8.018 Mbytes
+WARNING: Communication cutoff adjusted to 2.627404783947349 (../comm.cpp:690)
+0  ekin = 0 |  erot = 0 | epot = -14.6175140343334 | etot = -14.6175140343334
+Per MPI rank memory allocation (min/avg/max) = 7.903 | 7.96 | 8.018 Mbytes
 Step Temp E_pair E_mol TotEng Press 
        0            0   -1.4712768  0.009525411   -1.4617514 4.663076e-06 
 1000  ekin = 0.00113086229080478 |  erot = 0.00431010160406708 | epot = -14.6229549982368 | etot = -14.617514034342
@@ -1139,34 +1149,34 @@ Step Temp E_pair E_mol TotEng Press
 999000  ekin = 0.190992053959209 |  erot = 0.320462575794744 | epot = -15.1289686644103 | etot = -14.6175140346563
 1000000  ekin = 0.179708146665587 |  erot = 0.311553394428757 | epot = -15.1087755756882 | etot = -14.6175140345938
  1000000  0.013311715   -1.5443684  0.033490821   -1.4929067 -3.7544839e-05 
-Loop time of 20.7945 on 4 procs for 1000000 steps with 10 atoms
+Loop time of 17.7119 on 4 procs for 1000000 steps with 10 atoms
 
-Performance: 41549.361 tau/day, 48089.538 timesteps/s
+Performance: 48780.802 tau/day, 56459.261 timesteps/s
-99.6% CPU use with 4 MPI tasks x no OpenMP threads
+99.5% CPU use with 4 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.66725    | 7.9254     | 14.304     | 209.9 | 38.11
+Pair    | 0.59564    | 6.28       | 11.307     | 181.3 | 35.46
-Bond    | 0.095496   | 0.30973    | 0.49863    |  30.5 |  1.49
+Bond    | 0.083757   | 0.28777    | 0.47668    |  30.6 |  1.62
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 1.8943     | 2.1825     | 2.4604     |  15.6 | 10.50
+Comm    | 1.8539     | 2.1875     | 2.4877     |  17.3 | 12.35
-Output  | 2e-05      | 2.9e-05    | 3.2e-05    |   0.0 |  0.00
+Output  | 2.1e-05    | 3.85e-05   | 4.5e-05    |   0.0 |  0.00
-Modify  | 0.18231    | 0.95644    | 1.673      |  62.4 |  4.60
+Modify  | 0.18254    | 0.92719    | 1.638      |  61.5 |  5.23
-Other   |            | 9.421      |            |       | 45.30
+Other   |            | 8.029      |            |       | 45.33
 
-Nlocal:    2.5 ave 5 max 0 min
+Nlocal:    2.5 ave 5.0 max 0.0 min
 Histogram: 1 0 1 0 0 0 0 0 1 1
-Nghost:    7.5 ave 10 max 5 min
+Nghost:    7.5 ave 10.0 max 5.0 min
 Histogram: 1 0 1 0 0 0 0 0 1 1
-Neighs:    18.5 ave 35 max 0 min
+Neighs:    16.0 ave 30.0 max 0.0 min
 Histogram: 1 0 1 0 0 0 0 0 1 1
 
-Total # of neighbors = 74
+Total # of neighbors = 64
-Ave neighs/atom = 7.4
+Ave neighs/atom = 6.4
 Ave special neighs/atom = 3.6
 Neighbor list builds = 0
 Dangerous builds = 0
 
 #write_restart config.${number}.*
-Total wall time: 0:00:20
+Total wall time: 0:00:17

examples/USER/cgdna/examples/oxDNA2/duplex2/in.duplex2

@@ -27,6 +27,7 @@ group all type 1 4
 # oxDNA2 bond interactions - FENE backbone
 bond_style oxdna2/fene
 bond_coeff * 2.0 0.25 0.7564
+special_bonds lj 0 1 1
 
 # oxDNA2 pair interactions
 pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
@@ -49,6 +50,7 @@ timestep 1e-5
 
 #comm_style tiled
 #fix 3 all balance 10000 1.1 rcb
+comm_modify cutoff 2.5
 
 #compute mol all chunk/atom molecule
 #compute mychunk all vcm/chunk mol

examples/USER/cgdna/examples/oxDNA2/duplex3/in.duplex3

@@ -27,6 +27,7 @@ group all type 1 4
 # oxDNA2 bond interactions - FENE backbone
 bond_style oxdna2/fene
 bond_coeff * 2.0 0.25 0.7564
+special_bonds lj 0 1 1
 
 # oxDNA2 pair interactions
 pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
@@ -49,6 +50,7 @@ timestep 1e-5
 
 #comm_style tiled
 #fix 3 all balance 10000 1.1 rcb
+comm_modify cutoff 2.5
 
 #compute mol all chunk/atom molecule
 #compute mychunk all vcm/chunk mol

examples/USER/cgdna/examples/oxDNA2/duplex3/log.30Jun20.duplex3.g++.1

@@ -1,4 +1,4 @@
-LAMMPS (7 Aug 2019)
+LAMMPS (30 Jun 2020)
 variable number	equal 3
 variable ofreq	equal 1000
 variable efreq	equal 1000
@@ -13,6 +13,7 @@ newton off
 boundary  p p p
 
 atom_style hybrid bond ellipsoid
+WARNING: Atom_style hybrid defines both pertype and peratom masses - both must be set, only peratom masses will be used (../atom_vec_hybrid.cpp:156)
 atom_modify sort 0 1.0
 
 # Pair interactions require lists of neighbours to be calculated
@@ -35,8 +36,8 @@ read_data data.duplex3
   2 = max # of 1-3 neighbors
   2 = max # of 1-4 neighbors
   4 = max # of special neighbors
-  special bonds CPU = 0.000145 secs
+  special bonds CPU = 0.000 seconds
-  read_data CPU = 0.001965 secs
+  read_data CPU = 0.002 seconds
 
 set atom * mass 1.0
   10 settings made for mass
@@ -47,6 +48,12 @@ group all type 1 4
 # oxDNA2 bond interactions - FENE backbone
 bond_style oxdna2/fene
 bond_coeff * 2.0 0.25 0.7564
+special_bonds lj 0 1 1
+  2 = max # of 1-2 neighbors
+  2 = max # of 1-3 neighbors
+  2 = max # of 1-4 neighbors
+  4 = max # of special neighbors
+  special bonds CPU = 0.000 seconds
 
 # oxDNA2 pair interactions
 pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
@@ -71,6 +78,7 @@ timestep 1e-5
 
 #comm_style tiled
 #fix 3 all balance 10000 1.1 rcb
+comm_modify cutoff 2.5
 
 #compute mol all chunk/atom molecule
 #compute mychunk all vcm/chunk mol
@@ -101,9 +109,9 @@ run 1000000
 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
+  master list distance cutoff = 2.6274048
-  ghost atom cutoff = 2.6274
+  ghost atom cutoff = 2.6274048
-  binsize = 1.3137, bins = 31 31 31
+  binsize = 1.3137024, bins = 31 31 31
   6 neighbor lists, perpetual/occasional/extra = 6 0 0
   (1) pair oxdna2/excv, perpetual
       attributes: half, newton off
@@ -135,7 +143,9 @@ Neighbor list info ...
       pair build: copy
       stencil: none
       bin: none
-Per MPI rank memory allocation (min/avg/max) = 3.024 | 3.024 | 3.024 Mbytes
+WARNING: Communication cutoff adjusted to 2.627404783947349 (../comm.cpp:690)
+0  ekin = 0 |  erot = 0 | epot = -14.6249037416652 | etot = -14.6249037416652
+Per MPI rank memory allocation (min/avg/max) = 8.021 | 8.021 | 8.021 Mbytes
 Step Temp E_pair E_mol TotEng Press 
        0            0   -1.4720158  0.009525411   -1.4624904 3.1370518e-06 
 1000  ekin = 0.00366431201929618 |  erot = 0.00193726360267488 | epot = -14.630505317301 | etot = -14.624903741679
@@ -1139,34 +1149,34 @@ Step Temp E_pair E_mol TotEng Press
 999000  ekin = 0.330110494517114 |  erot = 0.658973630822449 | epot = -15.6139878677246 | etot = -14.624903742385
 1000000  ekin = 0.345190458650495 |  erot = 0.661138339466907 | epot = -15.6312325406154 | etot = -14.624903742498
  1000000  0.025569664   -1.5839232  0.020799898   -1.5286042 -3.5789082e-06 
-Loop time of 25.9663 on 1 procs for 1000000 steps with 10 atoms
+Loop time of 16.5683 on 1 procs for 1000000 steps with 10 atoms
 
-Performance: 33273.840 tau/day, 38511.388 timesteps/s
+Performance: 52147.644 tau/day, 60356.069 timesteps/s
-99.6% CPU use with 1 MPI tasks x no OpenMP threads
+99.7% CPU use with 1 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 21.428     | 21.428     | 21.428     |   0.0 | 82.52
+Pair    | 12.734     | 12.734     | 12.734     |   0.0 | 76.86
-Bond    | 0.76981    | 0.76981    | 0.76981    |   0.0 |  2.96
+Bond    | 0.62259    | 0.62259    | 0.62259    |   0.0 |  3.76
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.25709    | 0.25709    | 0.25709    |   0.0 |  0.99
+Comm    | 0.18386    | 0.18386    | 0.18386    |   0.0 |  1.11
-Output  | 9e-06      | 9e-06      | 9e-06      |   0.0 |  0.00
+Output  | 7e-06      | 7e-06      | 7e-06      |   0.0 |  0.00
-Modify  | 3.1584     | 3.1584     | 3.1584     |   0.0 | 12.16
+Modify  | 2.7788     | 2.7788     | 2.7788     |   0.0 | 16.77
-Other   |            | 0.3534     |            |       |  1.36
+Other   |            | 0.2491     |            |       |  1.50
 
-Nlocal:    10 ave 10 max 10 min
+Nlocal:    10.0 ave 10.0 max 10.0 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    0 ave 0 max 0 min
+Nghost:    0.0 ave 0.0 max 0.0 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    45 ave 45 max 45 min
+Neighs:    37.0 ave 37.0 max 37.0 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
 
-Total # of neighbors = 45
+Total # of neighbors = 37
-Ave neighs/atom = 4.5
+Ave neighs/atom = 3.7
 Ave special neighs/atom = 3.6
 Neighbor list builds = 0
 Dangerous builds = 0
 
 #write_restart config.${number}.*
-Total wall time: 0:00:25
+Total wall time: 0:00:16

examples/USER/cgdna/examples/oxDNA2/duplex3/log.30Jun20.duplex3.g++.4

@@ -1,4 +1,4 @@
-LAMMPS (7 Aug 2019)
+LAMMPS (30 Jun 2020)
 variable number	equal 3
 variable ofreq	equal 1000
 variable efreq	equal 1000
@@ -13,6 +13,7 @@ newton off
 boundary  p p p
 
 atom_style hybrid bond ellipsoid
+WARNING: Atom_style hybrid defines both pertype and peratom masses - both must be set, only peratom masses will be used (../atom_vec_hybrid.cpp:156)
 atom_modify sort 0 1.0
 
 # Pair interactions require lists of neighbours to be calculated
@@ -35,8 +36,8 @@ read_data data.duplex3
   2 = max # of 1-3 neighbors
   2 = max # of 1-4 neighbors
   4 = max # of special neighbors
-  special bonds CPU = 0.000188 secs
+  special bonds CPU = 0.001 seconds
-  read_data CPU = 0.002791 secs
+  read_data CPU = 0.004 seconds
 
 set atom * mass 1.0
   10 settings made for mass
@@ -47,6 +48,12 @@ group all type 1 4
 # oxDNA2 bond interactions - FENE backbone
 bond_style oxdna2/fene
 bond_coeff * 2.0 0.25 0.7564
+special_bonds lj 0 1 1
+  2 = max # of 1-2 neighbors
+  2 = max # of 1-3 neighbors
+  2 = max # of 1-4 neighbors
+  4 = max # of special neighbors
+  special bonds CPU = 0.000 seconds
 
 # oxDNA2 pair interactions
 pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
@@ -71,6 +78,7 @@ timestep 1e-5
 
 #comm_style tiled
 #fix 3 all balance 10000 1.1 rcb
+comm_modify cutoff 2.5
 
 #compute mol all chunk/atom molecule
 #compute mychunk all vcm/chunk mol
@@ -101,9 +109,9 @@ run 1000000
 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
+  master list distance cutoff = 2.6274048
-  ghost atom cutoff = 2.6274
+  ghost atom cutoff = 2.6274048
-  binsize = 1.3137, bins = 31 31 31
+  binsize = 1.3137024, bins = 31 31 31
   6 neighbor lists, perpetual/occasional/extra = 6 0 0
   (1) pair oxdna2/excv, perpetual
       attributes: half, newton off
@@ -135,7 +143,9 @@ Neighbor list info ...
       pair build: copy
       stencil: none
       bin: none
-Per MPI rank memory allocation (min/avg/max) = 7.653 | 7.835 | 8.018 Mbytes
+WARNING: Communication cutoff adjusted to 2.627404783947349 (../comm.cpp:690)
+0  ekin = 0 |  erot = 0 | epot = -14.6249037416652 | etot = -14.6249037416652
+Per MPI rank memory allocation (min/avg/max) = 7.903 | 7.96 | 8.018 Mbytes
 Step Temp E_pair E_mol TotEng Press 
        0            0   -1.4720158  0.009525411   -1.4624904 3.1370518e-06 
 1000  ekin = 0.00366431201929595 |  erot = 0.00193726360268106 | epot = -14.630505317301 | etot = -14.624903741679
@@ -1139,34 +1149,34 @@ Step Temp E_pair E_mol TotEng Press
 999000  ekin = 0.330110494517446 |  erot = 0.658973630822486 | epot = -15.613987867725 | etot = -14.6249037423851
 1000000  ekin = 0.345190458651126 |  erot = 0.66113833946702 | epot = -15.6312325406162 | etot = -14.624903742498
  1000000  0.025569664   -1.5839232  0.020799898   -1.5286042 -3.5789082e-06 
-Loop time of 20.0167 on 4 procs for 1000000 steps with 10 atoms
+Loop time of 17.6535 on 4 procs for 1000000 steps with 10 atoms
 
-Performance: 43164.007 tau/day, 49958.342 timesteps/s
+Performance: 48942.073 tau/day, 56645.918 timesteps/s
 99.5% CPU use with 4 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.59089    | 7.5652     | 13.908     | 205.5 | 37.79
+Pair    | 0.58208    | 6.2309     | 11.391     | 182.5 | 35.30
-Bond    | 0.090803   | 0.29363    | 0.47758    |  29.6 |  1.47
+Bond    | 0.087981   | 0.28429    | 0.45668    |  28.3 |  1.61
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 1.7298     | 2.0312     | 2.2983     |  16.6 | 10.15
+Comm    | 1.8415     | 2.1564     | 2.4456     |  17.3 | 12.21
-Output  | 1.4e-05    | 2.075e-05  | 2.3e-05    |   0.0 |  0.00
+Output  | 1.5e-05    | 2.275e-05  | 2.6e-05    |   0.0 |  0.00
-Modify  | 0.17638    | 0.90613    | 1.5893     |  60.1 |  4.53
+Modify  | 0.1751     | 0.91094    | 1.6034     |  60.5 |  5.16
-Other   |            | 9.22       |            |       | 46.06
+Other   |            | 8.071      |            |       | 45.72
 
-Nlocal:    2.5 ave 5 max 0 min
+Nlocal:    2.5 ave 5.0 max 0.0 min
 Histogram: 1 0 1 0 0 0 0 0 1 1
-Nghost:    7.5 ave 10 max 5 min
+Nghost:    7.5 ave 10.0 max 5.0 min
 Histogram: 1 0 1 0 0 0 0 0 1 1
-Neighs:    18.5 ave 35 max 0 min
+Neighs:    16.0 ave 30.0 max 0.0 min
 Histogram: 1 0 1 0 0 0 0 0 1 1
 
-Total # of neighbors = 74
+Total # of neighbors = 64
-Ave neighs/atom = 7.4
+Ave neighs/atom = 6.4
 Ave special neighs/atom = 3.6
 Neighbor list builds = 0
 Dangerous builds = 0
 
 #write_restart config.${number}.*
-Total wall time: 0:00:20
+Total wall time: 0:00:17

examples/USER/cgdna/examples/oxDNA2/unique_bp/in.duplex4.4type

@@ -18,17 +18,19 @@ atom_style hybrid bond ellipsoid
 atom_modify sort 0 1.0
 
 # Pair interactions require lists of neighbours to be calculated
-neighbor 2.0 bin 
+neighbor 1.0 bin 
 neigh_modify every 10 delay 0 check yes
 
 read_data data.duplex4.4type
-mass * 3.1575
+mass * 3.1575           # sets per-type mass if not in data file
+set atom * mass 3.1575  # sets per-atom mass
 
 group all type 1 4
 
 # oxDNA bond interactions - FENE backbone
 bond_style oxdna2/fene 
 bond_coeff * 2.0 0.25 0.7564
+special_bonds lj 0 1 1
 
 # oxDNA pair interactions
 pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh 
@@ -60,6 +62,7 @@ timestep 1e-4
 
 #comm_style tiled
 #fix 3 all balance 10000 1.1 rcb
+comm_modify cutoff 2.5
 
 #compute mol all chunk/atom molecule
 #compute mychunk all vcm/chunk mol

examples/USER/cgdna/examples/oxDNA2/unique_bp/in.duplex4.8type

@@ -10,7 +10,7 @@ units lj
 
 dimension 3
 
-newton on
+newton off
 
 boundary  p p p
 
@@ -22,13 +22,15 @@ neighbor 1.0 bin
 neigh_modify every 10 delay 0 check yes
 
 read_data data.duplex4.8type
-mass * 3.1575
+mass * 3.1575           # sets per-type mass if not in data file
+set atom * mass 3.1575  # sets per-atom mass
 
 group all type 1 8
 
 # oxDNA bond interactions - FENE backbone
 bond_style oxdna2/fene 
 bond_coeff * 2.0 0.25 0.7564
+special_bonds lj 0 1 1
 
 # oxDNA pair interactions
 pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh 
@@ -60,6 +62,7 @@ timestep 1e-4
 
 #comm_style tiled
 #fix 3 all balance 10000 1.1 rcb
+comm_modify cutoff 2.5
 
 #compute mol all chunk/atom molecule
 #compute mychunk all vcm/chunk mol

examples/USER/cgdna/examples/oxDNA2/unique_bp/log.30Jun20.duplex4.4type.g++1

@@ -1,4 +1,4 @@
-LAMMPS (7 Aug 2019)
+LAMMPS (30 Jun 2020)
 variable number	equal 1
 variable ofreq	equal 10000
 variable efreq	equal 10000
@@ -16,10 +16,11 @@ newton off
 boundary  p p p
 
 atom_style hybrid bond ellipsoid
+WARNING: Atom_style hybrid defines both pertype and peratom masses - both must be set, only peratom masses will be used (../atom_vec_hybrid.cpp:156)
 atom_modify sort 0 1.0
 
 # Pair interactions require lists of neighbours to be calculated
-neighbor 2.0 bin
+neighbor 1.0 bin
 neigh_modify every 10 delay 0 check yes
 
 read_data data.duplex4.4type
@@ -38,9 +39,11 @@ read_data data.duplex4.4type
   2 = max # of 1-3 neighbors
   4 = max # of 1-4 neighbors
   6 = max # of special neighbors
-  special bonds CPU = 6.2e-05 secs
+  special bonds CPU = 0.000 seconds
-  read_data CPU = 0.001124 secs
+  read_data CPU = 0.003 seconds
-mass * 3.1575
+mass * 3.1575           # sets per-type mass if not in data file
+set atom * mass 3.1575  # sets per-atom mass
+  26 settings made for mass
 
 group all type 1 4
 26 atoms in group all
@@ -48,6 +51,12 @@ group all type 1 4
 # oxDNA bond interactions - FENE backbone
 bond_style oxdna2/fene
 bond_coeff * 2.0 0.25 0.7564
+special_bonds lj 0 1 1
+  2 = max # of 1-2 neighbors
+  2 = max # of 1-3 neighbors
+  4 = max # of 1-4 neighbors
+  6 = max # of special neighbors
+  special bonds CPU = 0.000 seconds
 
 # oxDNA pair interactions
 pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
@@ -115,6 +124,7 @@ timestep 1e-4
 
 #comm_style tiled
 #fix 3 all balance 10000 1.1 rcb
+comm_modify cutoff 2.5
 
 #compute mol all chunk/atom molecule
 #compute mychunk all vcm/chunk mol
@@ -149,9 +159,9 @@ run 100000
 Neighbor list info ...
   update every 10 steps, delay 0 steps, check yes
   max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 5.63899
+  master list distance cutoff = 4.6389877
-  ghost atom cutoff = 5.63899
+  ghost atom cutoff = 4.6389877
-  binsize = 2.81949, bins = 15 15 15
+  binsize = 2.3194939, bins = 18 18 18
   6 neighbor lists, perpetual/occasional/extra = 6 0 0
   (1) pair oxdna2/excv, perpetual
       attributes: half, newton off
@@ -183,47 +193,49 @@ Neighbor list info ...
       pair build: copy
       stencil: none
       bin: none
-Per MPI rank memory allocation (min/avg/max) = 3.89 | 3.89 | 3.89 Mbytes
+WARNING: Communication cutoff adjusted to 4.638987723814632 (../comm.cpp:690)
+0  ekin = 0 |  erot = 0 | epot = -41.6285382417448 | etot = -41.6285382417448
+Per MPI rank memory allocation (min/avg/max) = 9.771 | 9.771 | 9.771 Mbytes
 Step Temp E_pair E_mol TotEng Press 
        0            0   -1.6384018  0.037304147   -1.6010976 6.7769766e-05 
-10000  ekin = 1.01296379553452 |  erot = 1.38476360245491 | epot = -41.9785360036035 | etot = -39.5808086056141
+10000  ekin = 0.876675896491307 |  erot = 3.01631310953192 | epot = -43.6949424313443 | etot = -39.8019534253211
-20000  ekin = 1.75607695499755 |  erot = 1.86620102096623 | epot = -41.9558496477913 | etot = -38.3335716718275
+20000  ekin = 1.02178060459022 |  erot = 1.54107635735041 | epot = -40.2257383206528 | etot = -37.6628813587121
-30000  ekin = 2.25878673688255 |  erot = 2.60035907744906 | epot = -41.2869827431736 | etot = -36.427836928842
+30000  ekin = 1.77819697871127 |  erot = 2.67180081099997 | epot = -40.9840548186678 | etot = -36.5340570289565
-40000  ekin = 2.11105717434601 |  erot = 3.16611217122795 | epot = -40.2762731426449 | etot = -34.999103797071
+40000  ekin = 2.55095642638533 |  erot = 2.97955929579275 | epot = -40.0756048400153 | etot = -34.5450891178372
-50000  ekin = 3.05379083545185 |  erot = 2.45050275456902 | epot = -40.3032957287999 | etot = -34.799002138779
+50000  ekin = 2.43321388920862 |  erot = 3.63137266285959 | epot = -39.3718897377946 | etot = -33.3073031857264
-60000  ekin = 3.05154113920288 |  erot = 2.52539576708931 | epot = -39.6800099891302 | etot = -34.103073082838
+60000  ekin = 2.51123200110303 |  erot = 3.95693243683571 | epot = -38.8877878920178 | etot = -32.4196234540791
-70000  ekin = 3.23212209366503 |  erot = 3.28914763888578 | epot = -40.1240667487288 | etot = -33.602797016178
+70000  ekin = 3.33444097207872 |  erot = 4.12593683683079 | epot = -38.7679893452499 | etot = -31.3076115363404
-80000  ekin = 2.82623224207568 |  erot = 2.91292948677805 | epot = -39.0983962904507 | etot = -33.3592345615969
+80000  ekin = 3.41969296989344 |  erot = 3.46589964095079 | epot = -37.5712487729465 | etot = -30.6856561621023
-90000  ekin = 3.05995314905566 |  erot = 3.5429982411034 | epot = -39.1646070343971 | etot = -32.561655644238
+90000  ekin = 3.53106755106414 |  erot = 3.40955821292295 | epot = -35.9319384430368 | etot = -28.9913126790497
-100000  ekin = 3.46139546969836 |  erot = 4.11704803295073 | epot = -38.5124679837256 | etot = -30.9340244810765
+100000  ekin = 3.47860763041501 |  erot = 3.95117534418391 | epot = -37.6128506757402 | etot = -30.1830677011413
-  100000  0.092303879   -1.5243833  0.043134544   -1.3481182 6.862374e-06 
+  100000   0.09276287   -1.4972391  0.050590991   -1.3128555 0.00017815014 
-Loop time of 7.99505 on 1 procs for 100000 steps with 26 atoms
+Loop time of 7.33046 on 1 procs for 100000 steps with 26 atoms
 
-Performance: 108066.893 tau/day, 12507.742 timesteps/s
+Performance: 117864.395 tau/day, 13641.712 timesteps/s
 99.8% CPU use with 1 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 7.2072     | 7.2072     | 7.2072     |   0.0 | 90.15
+Pair    | 6.4814     | 6.4814     | 6.4814     |   0.0 | 88.42
-Bond    | 0.14292    | 0.14292    | 0.14292    |   0.0 |  1.79
+Bond    | 0.16262    | 0.16262    | 0.16262    |   0.0 |  2.22
-Neigh   | 1.9e-05    | 1.9e-05    | 1.9e-05    |   0.0 |  0.00
+Neigh   | 4.2e-05    | 4.2e-05    | 4.2e-05    |   0.0 |  0.00
-Comm    | 0.015676   | 0.015676   | 0.015676   |   0.0 |  0.20
+Comm    | 0.019555   | 0.019555   | 0.019555   |   0.0 |  0.27
-Output  | 0.001372   | 0.001372   | 0.001372   |   0.0 |  0.02
+Output  | 0.00131    | 0.00131    | 0.00131    |   0.0 |  0.02
-Modify  | 0.61071    | 0.61071    | 0.61071    |   0.0 |  7.64
+Modify  | 0.64596    | 0.64596    | 0.64596    |   0.0 |  8.81
-Other   |            | 0.01714    |            |       |  0.21
+Other   |            | 0.01961    |            |       |  0.27
 
-Nlocal:    26 ave 26 max 26 min
+Nlocal:    26.0 ave 26.0 max 26.0 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    0 ave 0 max 0 min
+Nghost:    0.0 ave 0.0 max 0.0 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    325 ave 325 max 325 min
+Neighs:    299.0 ave 299.0 max 299.0 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
 
-Total # of neighbors = 325
+Total # of neighbors = 299
-Ave neighs/atom = 12.5
+Ave neighs/atom = 11.5
-Ave special neighs/atom = 5.07692
+Ave special neighs/atom = 5.076923076923077
-Neighbor list builds = 1
+Neighbor list builds = 2
 Dangerous builds = 0
 
 #write_restart config.${number}.*

examples/USER/cgdna/examples/oxDNA2/unique_bp/log.30Jun20.duplex4.4type.g++4

@@ -1,4 +1,4 @@
-LAMMPS (7 Aug 2019)
+LAMMPS (30 Jun 2020)
 variable number	equal 1
 variable ofreq	equal 10000
 variable efreq	equal 10000
@@ -16,10 +16,11 @@ newton off
 boundary  p p p
 
 atom_style hybrid bond ellipsoid
+WARNING: Atom_style hybrid defines both pertype and peratom masses - both must be set, only peratom masses will be used (../atom_vec_hybrid.cpp:156)
 atom_modify sort 0 1.0
 
 # Pair interactions require lists of neighbours to be calculated
-neighbor 2.0 bin
+neighbor 1.0 bin
 neigh_modify every 10 delay 0 check yes
 
 read_data data.duplex4.4type
@@ -38,9 +39,11 @@ read_data data.duplex4.4type
   2 = max # of 1-3 neighbors
   4 = max # of 1-4 neighbors
   6 = max # of special neighbors
-  special bonds CPU = 0.000173 secs
+  special bonds CPU = 0.001 seconds
-  read_data CPU = 0.00242 secs
+  read_data CPU = 0.004 seconds
-mass * 3.1575
+mass * 3.1575           # sets per-type mass if not in data file
+set atom * mass 3.1575  # sets per-atom mass
+  26 settings made for mass
 
 group all type 1 4
 26 atoms in group all
@@ -48,6 +51,12 @@ group all type 1 4
 # oxDNA bond interactions - FENE backbone
 bond_style oxdna2/fene
 bond_coeff * 2.0 0.25 0.7564
+special_bonds lj 0 1 1
+  2 = max # of 1-2 neighbors
+  2 = max # of 1-3 neighbors
+  4 = max # of 1-4 neighbors
+  6 = max # of special neighbors
+  special bonds CPU = 0.000 seconds
 
 # oxDNA pair interactions
 pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
@@ -115,6 +124,7 @@ timestep 1e-4
 
 #comm_style tiled
 #fix 3 all balance 10000 1.1 rcb
+comm_modify cutoff 2.5
 
 #compute mol all chunk/atom molecule
 #compute mychunk all vcm/chunk mol
@@ -149,9 +159,9 @@ run 100000
 Neighbor list info ...
   update every 10 steps, delay 0 steps, check yes
   max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 5.63899
+  master list distance cutoff = 4.6389877
-  ghost atom cutoff = 5.63899
+  ghost atom cutoff = 4.6389877
-  binsize = 2.81949, bins = 15 15 15
+  binsize = 2.3194939, bins = 18 18 18
   6 neighbor lists, perpetual/occasional/extra = 6 0 0
   (1) pair oxdna2/excv, perpetual
       attributes: half, newton off
@@ -183,50 +193,52 @@ Neighbor list info ...
       pair build: copy
       stencil: none
       bin: none
-Per MPI rank memory allocation (min/avg/max) = 9.499 | 9.682 | 9.864 Mbytes
+WARNING: Communication cutoff adjusted to 4.638987723814632 (../comm.cpp:690)
+0  ekin = 0 |  erot = 0 | epot = -41.6285382417448 | etot = -41.6285382417448
+Per MPI rank memory allocation (min/avg/max) = 9.756 | 9.813 | 9.871 Mbytes
 Step Temp E_pair E_mol TotEng Press 
        0            0   -1.6384018  0.037304147   -1.6010976 6.7769766e-05 
-10000  ekin = 1.20524984175817 |  erot = 1.2679122962101 | epot = -41.9183873815797 | etot = -39.4452252436114
+10000  ekin = 0.705506935391957 |  erot = 3.21864563172922 | epot = -44.0640899615318 | etot = -40.1399373944106
-20000  ekin = 1.60856540355485 |  erot = 2.64140880508964 | epot = -41.0106168994545 | etot = -36.76064269081
+20000  ekin = 1.16547426389222 |  erot = 1.69259899672632 | epot = -41.827511978894 | etot = -38.9694387182755
-30000  ekin = 2.821101638199 |  erot = 3.06373823252434 | epot = -40.9348041675027 | etot = -35.0499642967793
+30000  ekin = 2.07592540045025 |  erot = 2.81661265099434 | epot = -41.8258727293348 | etot = -36.9333346778902
-40000  ekin = 2.36296917392486 |  erot = 3.53353555114673 | epot = -39.5591676362755 | etot = -33.6626629112039
+40000  ekin = 3.0352692177735 |  erot = 2.43995587980307 | epot = -41.3155342467788 | etot = -35.8403091492022
-50000  ekin = 2.93383938780818 |  erot = 3.39920211088179 | epot = -40.3602175538497 | etot = -34.0271760551597
+50000  ekin = 2.69044710203348 |  erot = 2.86176633025683 | epot = -40.5544750556414 | etot = -35.0022616233511
-60000  ekin = 2.42811021532829 |  erot = 2.75130045540831 | epot = -39.3178531324554 | etot = -34.1384424617188
+60000  ekin = 2.90956639769978 |  erot = 2.84679944563592 | epot = -39.7474408128141 | etot = -33.9910749694784
-70000  ekin = 2.7282200818863 |  erot = 3.76502037022117 | epot = -40.5673105068195 | etot = -34.074070054712
+70000  ekin = 1.89941118514544 |  erot = 3.71508585194422 | epot = -38.9575890625426 | etot = -33.3430920254529
-80000  ekin = 2.90877851656705 |  erot = 2.43617899356904 | epot = -38.4099618426175 | etot = -33.0650043324814
+80000  ekin = 2.43472912058895 |  erot = 3.11589280920166 | epot = -39.844809532279 | etot = -34.2941876024883
-90000  ekin = 3.89203816080263 |  erot = 2.67194811393274 | epot = -39.1880466354802 | etot = -32.6240603607448
+90000  ekin = 2.3759389593227 |  erot = 3.25835921096947 | epot = -38.913072246407 | etot = -33.2787740761149
-100000  ekin = 3.98445325397832 |  erot = 2.77079124049636 | epot = -39.2805505658488 | etot = -32.5253060713741
+100000  ekin = 3.23901515322217 |  erot = 3.3464944524431 | epot = -38.6302041314432 | etot = -32.044694525778
-  100000   0.10625209   -1.5603519  0.049561514   -1.3575422 -1.7755557e-05 
+  100000  0.086373737   -1.5432369  0.057459797   -1.3611996 7.7958353e-05 
-Loop time of 7.14827 on 4 procs for 100000 steps with 26 atoms
+Loop time of 6.09292 on 4 procs for 100000 steps with 26 atoms
 
-Performance: 120868.376 tau/day, 13989.395 timesteps/s
+Performance: 141803.976 tau/day, 16412.497 timesteps/s
 99.7% CPU use with 4 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.047776   | 3.0726     | 6.3143     | 172.8 | 42.98
+Pair    | 0.047712   | 2.5625     | 5.2874     | 157.3 | 42.06
-Bond    | 0.00736    | 0.056846   | 0.10864    |  20.7 |  0.80
+Bond    | 0.007398   | 0.053166   | 0.10097    |  19.8 |  0.87
-Neigh   | 1.9e-05    | 1.9e-05    | 1.9e-05    |   0.0 |  0.00
+Neigh   | 1.8e-05    | 1.8e-05    | 1.8e-05    |   0.0 |  0.00
-Comm    | 0.30925    | 3.451      | 6.3739     | 157.5 | 48.28
+Comm    | 0.29205    | 2.9624     | 5.4188     | 143.0 | 48.62
-Output  | 0.000896   | 0.0010197  | 0.001301   |   0.5 |  0.01
+Output  | 0.000866   | 0.00099325 | 0.001303   |   0.0 |  0.02
-Modify  | 0.015512   | 0.18417    | 0.37845    |  39.4 |  2.58
+Modify  | 0.016247   | 0.18354    | 0.37524    |  39.2 |  3.01
-Other   |            | 0.3826     |            |       |  5.35
+Other   |            | 0.3303     |            |       |  5.42
 
-Nlocal:    6.5 ave 13 max 0 min
+Nlocal:    6.5 ave 14.0 max 0.0 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
+Histogram: 2 0 0 0 0 0 0 0 1 1
-Nghost:    19.5 ave 26 max 13 min
+Nghost:    18.5 ave 24.0 max 12.0 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
+Histogram: 1 1 0 0 0 0 0 0 0 2
-Neighs:    123.5 ave 247 max 0 min
+Neighs:    113.75 ave 239.0 max 0.0 min
 Histogram: 2 0 0 0 0 0 0 0 0 2
 
-Total # of neighbors = 494
+Total # of neighbors = 455
-Ave neighs/atom = 19
+Ave neighs/atom = 17.5
-Ave special neighs/atom = 5.07692
+Ave special neighs/atom = 5.076923076923077
 Neighbor list builds = 1
 Dangerous builds = 0
 
 #write_restart config.${number}.*
 
 
-Total wall time: 0:00:07
+Total wall time: 0:00:06

examples/USER/cgdna/examples/oxDNA2/unique_bp/log.30Jun20.duplex4.8type.g++1

@@ -1,4 +1,4 @@
-LAMMPS (7 Aug 2019)
+LAMMPS (30 Jun 2020)
 variable number	equal 1
 variable ofreq	equal 10000
 variable efreq	equal 10000
@@ -11,11 +11,12 @@ units lj
 
 dimension 3
 
-newton on
+newton off
 
 boundary  p p p
 
 atom_style hybrid bond ellipsoid
+WARNING: Atom_style hybrid defines both pertype and peratom masses - both must be set, only peratom masses will be used (../atom_vec_hybrid.cpp:156)
 atom_modify sort 0 1.0
 
 # Pair interactions require lists of neighbours to be calculated
@@ -31,16 +32,18 @@ read_data data.duplex4.8type
   26 velocities
   26 ellipsoids
   scanning bonds ...
-  1 = max bonds/atom
+  2 = max bonds/atom
   reading bonds ...
   24 bonds
   2 = max # of 1-2 neighbors
   2 = max # of 1-3 neighbors
   4 = max # of 1-4 neighbors
   6 = max # of special neighbors
-  special bonds CPU = 6.5e-05 secs
+  special bonds CPU = 0.000 seconds
-  read_data CPU = 0.001139 secs
+  read_data CPU = 0.002 seconds
-mass * 3.1575
+mass * 3.1575           # sets per-type mass if not in data file
+set atom * mass 3.1575  # sets per-atom mass
+  26 settings made for mass
 
 group all type 1 8
 26 atoms in group all
@@ -48,6 +51,12 @@ group all type 1 8
 # oxDNA bond interactions - FENE backbone
 bond_style oxdna2/fene
 bond_coeff * 2.0 0.25 0.7564
+special_bonds lj 0 1 1
+  2 = max # of 1-2 neighbors
+  2 = max # of 1-3 neighbors
+  4 = max # of 1-4 neighbors
+  6 = max # of special neighbors
+  special bonds CPU = 0.000 seconds
 
 # oxDNA pair interactions
 pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
@@ -157,6 +166,7 @@ timestep 1e-4
 
 #comm_style tiled
 #fix 3 all balance 10000 1.1 rcb
+comm_modify cutoff 2.5
 
 #compute mol all chunk/atom molecule
 #compute mychunk all vcm/chunk mol
@@ -191,81 +201,83 @@ run 100000
 Neighbor list info ...
   update every 10 steps, delay 0 steps, check yes
   max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 4.63899
+  master list distance cutoff = 4.6389877
-  ghost atom cutoff = 4.63899
+  ghost atom cutoff = 4.6389877
-  binsize = 2.31949, bins = 18 18 18
+  binsize = 2.3194939, bins = 18 18 18
   6 neighbor lists, perpetual/occasional/extra = 6 0 0
   (1) pair oxdna2/excv, perpetual
-      attributes: half, newton on
+      attributes: half, newton off
-      pair build: half/bin/newton
+      pair build: half/bin/newtoff
-      stencil: half/bin/3d/newton
+      stencil: half/bin/3d/newtoff
       bin: standard
   (2) pair oxdna2/stk, perpetual, copy from (1)
-      attributes: half, newton on
+      attributes: half, newton off
       pair build: copy
       stencil: none
       bin: none
   (3) pair oxdna2/hbond, perpetual, copy from (1)
-      attributes: half, newton on
+      attributes: half, newton off
       pair build: copy
       stencil: none
       bin: none
   (4) pair oxdna2/xstk, perpetual, copy from (1)
-      attributes: half, newton on
+      attributes: half, newton off
       pair build: copy
       stencil: none
       bin: none
   (5) pair oxdna2/coaxstk, perpetual, copy from (1)
-      attributes: half, newton on
+      attributes: half, newton off
       pair build: copy
       stencil: none
       bin: none
   (6) pair oxdna2/dh, perpetual, copy from (1)
-      attributes: half, newton on
+      attributes: half, newton off
       pair build: copy
       stencil: none
       bin: none
-Per MPI rank memory allocation (min/avg/max) = 3.905 | 3.905 | 3.905 Mbytes
+WARNING: Communication cutoff adjusted to 4.638987723814632 (../comm.cpp:690)
+0  ekin = 0 |  erot = 0 | epot = -41.6285382417448 | etot = -41.6285382417448
+Per MPI rank memory allocation (min/avg/max) = 9.771 | 9.771 | 9.771 Mbytes
 Step Temp E_pair E_mol TotEng Press 
        0            0   -1.6384018  0.037304147   -1.6010976 6.7769766e-05 
-10000  ekin = 1.0129637955345 |  erot = 1.38476360245492 | epot = -41.9785360036034 | etot = -39.580808605614
+10000  ekin = 0.876675896491307 |  erot = 3.01631310953192 | epot = -43.6949424313443 | etot = -39.8019534253211
-20000  ekin = 1.75607695499755 |  erot = 1.86620102096618 | epot = -41.9558496477911 | etot = -38.3335716718274
+20000  ekin = 1.02178060459022 |  erot = 1.54107635735041 | epot = -40.2257383206528 | etot = -37.6628813587121
-30000  ekin = 2.25878673688259 |  erot = 2.60035907744898 | epot = -41.2869827431736 | etot = -36.427836928842
+30000  ekin = 1.77819697871127 |  erot = 2.67180081099997 | epot = -40.9840548186678 | etot = -36.5340570289565
-40000  ekin = 2.11105717434584 |  erot = 3.16611217122799 | epot = -40.2762731426449 | etot = -34.9991037970711
+40000  ekin = 2.55095642638533 |  erot = 2.97955929579275 | epot = -40.0756048400153 | etot = -34.5450891178372
-50000  ekin = 3.05379083545187 |  erot = 2.45050275456888 | epot = -40.3032957287998 | etot = -34.7990021387791
+50000  ekin = 2.43321388920862 |  erot = 3.63137266285959 | epot = -39.3718897377946 | etot = -33.3073031857264
-60000  ekin = 3.05154113920291 |  erot = 2.5253957670889 | epot = -39.6800099891299 | etot = -34.1030730828381
+60000  ekin = 2.51123200110303 |  erot = 3.95693243683571 | epot = -38.8877878920178 | etot = -32.4196234540791
-70000  ekin = 3.23212209366464 |  erot = 3.28914763888543 | epot = -40.1240667487278 | etot = -33.6027970161777
+70000  ekin = 3.33444097207872 |  erot = 4.12593683683079 | epot = -38.7679893452499 | etot = -31.3076115363404
-80000  ekin = 2.82623224207591 |  erot = 2.91292948677732 | epot = -39.0983962904496 | etot = -33.3592345615963
+80000  ekin = 3.41969296989344 |  erot = 3.46589964095079 | epot = -37.5712487729465 | etot = -30.6856561621023
-90000  ekin = 3.05995314905694 |  erot = 3.54299824110274 | epot = -39.164607034397 | etot = -32.5616556442373
+90000  ekin = 3.53106755106414 |  erot = 3.40955821292295 | epot = -35.9319384430368 | etot = -28.9913126790497
-100000  ekin = 3.46139546969892 |  erot = 4.11704803295143 | epot = -38.512467983727 | etot = -30.9340244810767
+100000  ekin = 3.47860763041501 |  erot = 3.95117534418391 | epot = -37.6128506757402 | etot = -30.1830677011413
-  100000  0.092303879   -1.5243833  0.043134544   -1.3481182 6.862374e-06 
+  100000   0.09276287   -1.4972391  0.050590991   -1.3128555 0.00017815014 
-Loop time of 7.94086 on 1 procs for 100000 steps with 26 atoms
+Loop time of 7.44606 on 1 procs for 100000 steps with 26 atoms
 
-Performance: 108804.336 tau/day, 12593.094 timesteps/s
+Performance: 116034.458 tau/day, 13429.914 timesteps/s
-99.8% CPU use with 1 MPI tasks x no OpenMP threads
+99.7% CPU use with 1 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 7.1507     | 7.1507     | 7.1507     |   0.0 | 90.05
+Pair    | 6.5843     | 6.5843     | 6.5843     |   0.0 | 88.43
-Bond    | 0.14487    | 0.14487    | 0.14487    |   0.0 |  1.82
+Bond    | 0.16149    | 0.16149    | 0.16149    |   0.0 |  2.17
-Neigh   | 6.4e-05    | 6.4e-05    | 6.4e-05    |   0.0 |  0.00
+Neigh   | 4.3e-05    | 4.3e-05    | 4.3e-05    |   0.0 |  0.00
-Comm    | 0.032259   | 0.032259   | 0.032259   |   0.0 |  0.41
+Comm    | 0.022595   | 0.022595   | 0.022595   |   0.0 |  0.30
-Output  | 0.003484   | 0.003484   | 0.003484   |   0.0 |  0.04
+Output  | 0.001492   | 0.001492   | 0.001492   |   0.0 |  0.02
-Modify  | 0.59013    | 0.59013    | 0.59013    |   0.0 |  7.43
+Modify  | 0.65313    | 0.65313    | 0.65313    |   0.0 |  8.77
-Other   |            | 0.01934    |            |       |  0.24
+Other   |            | 0.02299    |            |       |  0.31
 
-Nlocal:    26 ave 26 max 26 min
+Nlocal:    26.0 ave 26.0 max 26.0 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    0 ave 0 max 0 min
+Nghost:    0.0 ave 0.0 max 0.0 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    323 ave 323 max 323 min
+Neighs:    299.0 ave 299.0 max 299.0 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
 
-Total # of neighbors = 323
+Total # of neighbors = 299
-Ave neighs/atom = 12.4231
+Ave neighs/atom = 11.5
-Ave special neighs/atom = 5.07692
+Ave special neighs/atom = 5.076923076923077
-Neighbor list builds = 4
+Neighbor list builds = 2
 Dangerous builds = 0
 
 #write_restart config.${number}.*

examples/USER/cgdna/examples/oxDNA2/unique_bp/log.30Jun20.duplex4.8type.g++4

@@ -1,4 +1,4 @@
-LAMMPS (7 Aug 2019)
+LAMMPS (30 Jun 2020)
 variable number	equal 1
 variable ofreq	equal 10000
 variable efreq	equal 10000
@@ -11,11 +11,12 @@ units lj
 
 dimension 3
 
-newton on
+newton off
 
 boundary  p p p
 
 atom_style hybrid bond ellipsoid
+WARNING: Atom_style hybrid defines both pertype and peratom masses - both must be set, only peratom masses will be used (../atom_vec_hybrid.cpp:156)
 atom_modify sort 0 1.0
 
 # Pair interactions require lists of neighbours to be calculated
@@ -31,16 +32,18 @@ read_data data.duplex4.8type
   26 velocities
   26 ellipsoids
   scanning bonds ...
-  1 = max bonds/atom
+  2 = max bonds/atom
   reading bonds ...
   24 bonds
   2 = max # of 1-2 neighbors
   2 = max # of 1-3 neighbors
   4 = max # of 1-4 neighbors
   6 = max # of special neighbors
-  special bonds CPU = 0.000232 secs
+  special bonds CPU = 0.001 seconds
-  read_data CPU = 0.002447 secs
+  read_data CPU = 0.004 seconds
-mass * 3.1575
+mass * 3.1575           # sets per-type mass if not in data file
+set atom * mass 3.1575  # sets per-atom mass
+  26 settings made for mass
 
 group all type 1 8
 26 atoms in group all
@@ -48,6 +51,12 @@ group all type 1 8
 # oxDNA bond interactions - FENE backbone
 bond_style oxdna2/fene
 bond_coeff * 2.0 0.25 0.7564
+special_bonds lj 0 1 1
+  2 = max # of 1-2 neighbors
+  2 = max # of 1-3 neighbors
+  4 = max # of 1-4 neighbors
+  6 = max # of special neighbors
+  special bonds CPU = 0.000 seconds
 
 # oxDNA pair interactions
 pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
@@ -157,6 +166,7 @@ timestep 1e-4
 
 #comm_style tiled
 #fix 3 all balance 10000 1.1 rcb
+comm_modify cutoff 2.5
 
 #compute mol all chunk/atom molecule
 #compute mychunk all vcm/chunk mol
@@ -191,84 +201,86 @@ run 100000
 Neighbor list info ...
   update every 10 steps, delay 0 steps, check yes
   max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 4.63899
+  master list distance cutoff = 4.6389877
-  ghost atom cutoff = 4.63899
+  ghost atom cutoff = 4.6389877
-  binsize = 2.31949, bins = 18 18 18
+  binsize = 2.3194939, bins = 18 18 18
   6 neighbor lists, perpetual/occasional/extra = 6 0 0
   (1) pair oxdna2/excv, perpetual
-      attributes: half, newton on
+      attributes: half, newton off
-      pair build: half/bin/newton
+      pair build: half/bin/newtoff
-      stencil: half/bin/3d/newton
+      stencil: half/bin/3d/newtoff
       bin: standard
   (2) pair oxdna2/stk, perpetual, copy from (1)
-      attributes: half, newton on
+      attributes: half, newton off
       pair build: copy
       stencil: none
       bin: none
   (3) pair oxdna2/hbond, perpetual, copy from (1)
-      attributes: half, newton on
+      attributes: half, newton off
       pair build: copy
       stencil: none
       bin: none
   (4) pair oxdna2/xstk, perpetual, copy from (1)
-      attributes: half, newton on
+      attributes: half, newton off
       pair build: copy
       stencil: none
       bin: none
   (5) pair oxdna2/coaxstk, perpetual, copy from (1)
-      attributes: half, newton on
+      attributes: half, newton off
       pair build: copy
       stencil: none
       bin: none
   (6) pair oxdna2/dh, perpetual, copy from (1)
-      attributes: half, newton on
+      attributes: half, newton off
       pair build: copy
       stencil: none
       bin: none
-Per MPI rank memory allocation (min/avg/max) = 9.381 | 9.563 | 9.746 Mbytes
+WARNING: Communication cutoff adjusted to 4.638987723814632 (../comm.cpp:690)
+0  ekin = 0 |  erot = 0 | epot = -41.6285382417448 | etot = -41.6285382417448
+Per MPI rank memory allocation (min/avg/max) = 9.756 | 9.813 | 9.871 Mbytes
 Step Temp E_pair E_mol TotEng Press 
        0            0   -1.6384018  0.037304147   -1.6010976 6.7769766e-05 
-10000  ekin = 1.20524984175816 |  erot = 1.26791229621008 | epot = -41.9183873815797 | etot = -39.4452252436115
+10000  ekin = 0.705506935391957 |  erot = 3.21864563172922 | epot = -44.0640899615318 | etot = -40.1399373944106
-20000  ekin = 1.6085654035548 |  erot = 2.6414088050897 | epot = -41.0106168994546 | etot = -36.7606426908101
+20000  ekin = 1.16547426389222 |  erot = 1.69259899672632 | epot = -41.827511978894 | etot = -38.9694387182755
-30000  ekin = 2.82110163819891 |  erot = 3.06373823252419 | epot = -40.9348041675026 | etot = -35.0499642967795
+30000  ekin = 2.07592540045025 |  erot = 2.81661265099434 | epot = -41.8258727293348 | etot = -36.9333346778902
-40000  ekin = 2.35553603700794 |  erot = 3.60405945883761 | epot = -39.5418687902286 | etot = -33.5822732943831
+40000  ekin = 3.0352692177735 |  erot = 2.43995587980307 | epot = -41.3155342467788 | etot = -35.8403091492022
-50000  ekin = 3.06061403125833 |  erot = 3.35548669087246 | epot = -40.3236585928169 | etot = -33.9075578706861
+50000  ekin = 2.69044710203348 |  erot = 2.86176633025683 | epot = -40.5544750556414 | etot = -35.0022616233511
-60000  ekin = 2.7347216991605 |  erot = 4.23926242244084 | epot = -39.5379959923263 | etot = -32.564011870725
+60000  ekin = 2.90956639769978 |  erot = 2.84679944563592 | epot = -39.7474408128141 | etot = -33.9910749694784
-70000  ekin = 3.46562604991873 |  erot = 2.8521307045909 | epot = -38.7237000550356 | etot = -32.4059433005259
+70000  ekin = 1.89941118514544 |  erot = 3.71508585194422 | epot = -38.9575890625426 | etot = -33.3430920254529
-80000  ekin = 3.17815543267806 |  erot = 3.11078099027451 | epot = -39.7525036398366 | etot = -33.463567216884
+80000  ekin = 2.43472912058895 |  erot = 3.11589280920166 | epot = -39.844809532279 | etot = -34.2941876024883
-90000  ekin = 3.51635117668857 |  erot = 2.58384069017333 | epot = -39.4762533092413 | etot = -33.3760614423795
+90000  ekin = 2.3759389593227 |  erot = 3.25835921096947 | epot = -38.913072246407 | etot = -33.2787740761149
-100000  ekin = 3.64218174280962 |  erot = 2.88607181210736 | epot = -37.6002449519119 | etot = -31.0719913969949
+100000  ekin = 3.23901515322217 |  erot = 3.3464944524431 | epot = -38.6302041314432 | etot = -32.044694525778
-  100000  0.097124846   -1.5164679  0.070304678   -1.3060794 -2.9111933e-05 
+  100000  0.086373737   -1.5432369  0.057459797   -1.3611996 7.7958353e-05 
-Loop time of 5.64462 on 4 procs for 100000 steps with 26 atoms
+Loop time of 6.15993 on 4 procs for 100000 steps with 26 atoms
 
-Performance: 153066.031 tau/day, 17715.976 timesteps/s
+Performance: 140261.437 tau/day, 16233.963 timesteps/s
-99.0% 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:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.069668   | 2.1601     | 4.2189     | 138.7 | 38.27
+Pair    | 0.049533   | 2.573      | 5.3124     | 157.6 | 41.77
-Bond    | 0.008542   | 0.052544   | 0.095929   |  18.7 |  0.93
+Bond    | 0.007709   | 0.055244   | 0.10383    |  20.2 |  0.90
-Neigh   | 4.8e-05    | 5.6e-05    | 6.4e-05    |   0.0 |  0.00
+Neigh   | 1.8e-05    | 1.875e-05  | 1.9e-05    |   0.0 |  0.00
-Comm    | 0.90402    | 3.1443     | 5.4155     | 124.9 | 55.70
+Comm    | 0.32774    | 3.0114     | 5.4815     | 142.5 | 48.89
-Output  | 0.001003   | 0.0011317  | 0.001468   |   0.6 |  0.02
+Output  | 0.000925   | 0.0010595  | 0.00137    |   0.6 |  0.02
-Modify  | 0.021098   | 0.20024    | 0.38154    |  39.2 |  3.55
+Modify  | 0.016369   | 0.18492    | 0.37491    |  39.3 |  3.00
-Other   |            | 0.0863     |            |       |  1.53
+Other   |            | 0.3343     |            |       |  5.43
 
-Nlocal:    6.5 ave 13 max 0 min
+Nlocal:    6.5 ave 14.0 max 0.0 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
+Histogram: 2 0 0 0 0 0 0 0 1 1
-Nghost:    17.5 ave 22 max 13 min
+Nghost:    18.5 ave 24.0 max 12.0 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
+Histogram: 1 1 0 0 0 0 0 0 0 2
-Neighs:    80.25 ave 167 max 0 min
+Neighs:    113.75 ave 239.0 max 0.0 min
 Histogram: 2 0 0 0 0 0 0 0 0 2
 
-Total # of neighbors = 321
+Total # of neighbors = 455
-Ave neighs/atom = 12.3462
+Ave neighs/atom = 17.5
-Ave special neighs/atom = 5.07692
+Ave special neighs/atom = 5.076923076923077
-Neighbor list builds = 3
+Neighbor list builds = 1
 Dangerous builds = 0
 
 #write_restart config.${number}.*
 
 
-Total wall time: 0:00:05
+Total wall time: 0:00:06

examples/USER/cgdna/examples/oxRNA2/duplex4/in.duplex4

@@ -27,6 +27,7 @@ group all type 1 4
 # oxRNA2 bond interactions - FENE backbone
 bond_style oxrna2/fene
 bond_coeff * 2.0 0.25 0.761070781051
+special_bonds lj 0 1 1
 
 # oxRNA2 pair interactions
 pair_style hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh
@@ -50,6 +51,7 @@ timestep 1e-5
 
 #comm_style tiled
 #fix 3 all balance 10000 1.1 rcb
+comm_modify cutoff 2.5
 
 #compute mol all chunk/atom molecule
 #compute mychunk all vcm/chunk mol

src/.gitignore

@@ -501,6 +501,8 @@
 /fix_bond_break.h
 /fix_bond_create.cpp
 /fix_bond_create.h
+/fix_bond_create_angle.cpp
+/fix_bond_create_angle.h
 /fix_bond_react.cpp
 /fix_bond_react.h
 /fix_bond_swap.cpp

src/USER-CGDNA/bond_oxdna_fene.cpp

@@ -328,9 +328,8 @@ void BondOxdnaFene::coeff(int narg, char **arg)
 
 void BondOxdnaFene::init_style()
 {
-  if (force->special_lj[1] != 0.0 || force->special_lj[2] != 1.0 || force->special_lj[3] != 1.0 ||
+  if (force->special_lj[1] != 0.0 || force->special_lj[2] != 1.0 || force->special_lj[3] != 1.0)
-      force->special_coul[1] != 1.0 || force->special_coul[2] != 1.0 || force->special_coul[3] != 1.0)
+    error->all(FLERR,"Must use 'special_bonds lj 0 1 1' with bond style oxdna/fene, oxdna2/fene or oxrna2/fene");
-    error->all(FLERR,"Must use 'special_bonds lj 0 1 1 coul 1 1 1' with bond style oxdna/fene");
 }
 
 /* ---------------------------------------------------------------------- */