diff --git a/examples/PACKAGES/cgdna/examples/real_units/oxDNA/duplex1/log.19May24.duplex1.g++.1 b/examples/PACKAGES/cgdna/examples/real_units/oxDNA/duplex1/log.22May24.duplex1.g++.1 similarity index 96% rename from examples/PACKAGES/cgdna/examples/real_units/oxDNA/duplex1/log.19May24.duplex1.g++.1 rename to examples/PACKAGES/cgdna/examples/real_units/oxDNA/duplex1/log.22May24.duplex1.g++.1 index 2b84f7c3ac..a8cb9b5d68 100644 --- a/examples/PACKAGES/cgdna/examples/real_units/oxDNA/duplex1/log.19May24.duplex1.g++.1 +++ b/examples/PACKAGES/cgdna/examples/real_units/oxDNA/duplex1/log.22May24.duplex1.g++.1 @@ -1,6 +1,27 @@ -LAMMPS (17 Apr 2024) - using 1 OpenMP thread(s) per MPI task -WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:132) +LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-174-g749e259294-modified) +# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19 +variable number equal 1 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 300.0 + +units real + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (../atom_vec_hybrid.cpp:132) +atom_modify sort 0 8.518 + +# Pair interactions require lists of neighbours to be calculated +neighbor 17.036 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex1 Reading data file ... orthogonal box = (-170 -170 -170) to (170 170 170) 1 by 1 by 1 MPI processor grid @@ -23,10 +44,19 @@ Finding 1-2 1-3 1-4 neighbors ... 2 = max # of 1-4 neighbors 4 = max # of special neighbors special bonds CPU = 0.000 seconds - read_data CPU = 0.005 seconds + read_data CPU = 0.009 seconds + +set atom * mass 315.8376 Setting atom values ... 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 * 11.92337812042065 2.1295 6.409795 +special_bonds lj 0 1 1 Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 1 1 special bond factors coul: 0 0 0 @@ -35,6 +65,47 @@ Finding 1-2 1-3 1-4 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 +pair_coeff * * oxdna/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576 +pair_coeff * * oxdna/stk seqav ${T} 8.01727944817084 0.005279604 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna/stk seqav 300 8.01727944817084 0.005279604 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna/hbond seqav 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 1 4 oxdna/hbond seqav 6.42073911784652 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 2 3 oxdna/hbond seqav 6.42073911784652 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff * * oxdna/xstk 3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 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 3.77965257404268 3.4072 5.1108 1.87396 4.94044 2.0 2.541592654 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2 -0.65 2 -0.65 + +# NVE ensemble +fix 1 all nve/asphere +#fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10 + +timestep 0.01706 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 32.4 + +compute quat all property/atom quatw quati quatj quatk + +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}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.1.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 1000000 Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes @@ -63,10 +134,6 @@ Neighbor list info ... pair build: copy stencil: none bin: none -Setting up Verlet run ... - Unit style : real - Current step : 0 - Time step : 0.01706 0 ekin = 6.60687273927977 | erot = 16.7817849122513 | epot = -77.8453746587949 | etot = -54.4567170072638 Per MPI rank memory allocation (min/avg/max) = 7.196 | 7.196 | 7.196 Mbytes Step Temp E_pair E_mol TotEng Press Volume @@ -1072,21 +1139,21 @@ Per MPI rank memory allocation (min/avg/max) = 7.196 | 7.196 | 7.196 Mbytes 999000 ekin = 9.43365149698941 | erot = 9.73053828894017 | epot = -73.6209070698904 | etot = -54.4567172839608 1000000 ekin = 9.45092723111945 | erot = 9.62486149925983 | epot = -73.532506015067 | etot = -54.4567172846877 1000000 352.2878 -75.545604 2.0130979 -64.081579 -0.0098473389 39304000 -Loop time of 9.76856 on 1 procs for 1000000 steps with 10 atoms +Loop time of 16.8981 on 1 procs for 1000000 steps with 10 atoms -Performance: 150.891 ns/day, 0.159 hours/ns, 102369.234 timesteps/s, 1.024 Matom-step/s -99.9% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 87.228 ns/day, 0.275 hours/ns, 59178.314 timesteps/s, 591.783 katom-step/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 | 7.5788 | 7.5788 | 7.5788 | 0.0 | 77.58 -Bond | 0.42182 | 0.42182 | 0.42182 | 0.0 | 4.32 -Neigh | 0.012447 | 0.012447 | 0.012447 | 0.0 | 0.13 -Comm | 0.24821 | 0.24821 | 0.24821 | 0.0 | 2.54 -Output | 0.10868 | 0.10868 | 0.10868 | 0.0 | 1.11 -Modify | 1.1076 | 1.1076 | 1.1076 | 0.0 | 11.34 -Other | | 0.291 | | | 2.98 +Pair | 13.505 | 13.505 | 13.505 | 0.0 | 79.92 +Bond | 0.61276 | 0.61276 | 0.61276 | 0.0 | 3.63 +Neigh | 0.038787 | 0.038787 | 0.038787 | 0.0 | 0.23 +Comm | 0.46975 | 0.46975 | 0.46975 | 0.0 | 2.78 +Output | 0.12918 | 0.12918 | 0.12918 | 0.0 | 0.76 +Modify | 1.6798 | 1.6798 | 1.6798 | 0.0 | 9.94 +Other | | 0.4627 | | | 2.74 Nlocal: 10 ave 10 max 10 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -1100,6 +1167,10 @@ Ave neighs/atom = 3.7 Ave special neighs/atom = 3.6 Neighbor list builds = 1000 Dangerous builds = 0 + +write_data last_config.${number}.* nocoeff +write_data last_config.1.* nocoeff System init for write_data ... Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule -Total wall time: 0:00:09 +#write_restart last_config.${number}.* +Total wall time: 0:00:16 diff --git a/examples/PACKAGES/cgdna/examples/real_units/oxDNA/duplex1/log.19May24.duplex1.g++.4 b/examples/PACKAGES/cgdna/examples/real_units/oxDNA/duplex1/log.22May24.duplex1.g++.4 similarity index 96% rename from examples/PACKAGES/cgdna/examples/real_units/oxDNA/duplex1/log.19May24.duplex1.g++.4 rename to examples/PACKAGES/cgdna/examples/real_units/oxDNA/duplex1/log.22May24.duplex1.g++.4 index b5766accaf..929e921b16 100644 --- a/examples/PACKAGES/cgdna/examples/real_units/oxDNA/duplex1/log.19May24.duplex1.g++.4 +++ b/examples/PACKAGES/cgdna/examples/real_units/oxDNA/duplex1/log.22May24.duplex1.g++.4 @@ -1,6 +1,27 @@ -LAMMPS (17 Apr 2024) - using 1 OpenMP thread(s) per MPI task -WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:132) +LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-174-g749e259294-modified) +# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19 +variable number equal 1 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 300.0 + +units real + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (../atom_vec_hybrid.cpp:132) +atom_modify sort 0 8.518 + +# Pair interactions require lists of neighbours to be calculated +neighbor 17.036 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex1 Reading data file ... orthogonal box = (-170 -170 -170) to (170 170 170) 1 by 2 by 2 MPI processor grid @@ -23,10 +44,19 @@ Finding 1-2 1-3 1-4 neighbors ... 2 = max # of 1-4 neighbors 4 = max # of special neighbors special bonds CPU = 0.000 seconds - read_data CPU = 0.007 seconds + read_data CPU = 0.011 seconds + +set atom * mass 315.8376 Setting atom values ... 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 * 11.92337812042065 2.1295 6.409795 +special_bonds lj 0 1 1 Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 1 1 special bond factors coul: 0 0 0 @@ -35,6 +65,47 @@ Finding 1-2 1-3 1-4 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 +pair_coeff * * oxdna/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576 +pair_coeff * * oxdna/stk seqav ${T} 8.01727944817084 0.005279604 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna/stk seqav 300 8.01727944817084 0.005279604 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna/hbond seqav 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 1 4 oxdna/hbond seqav 6.42073911784652 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 2 3 oxdna/hbond seqav 6.42073911784652 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff * * oxdna/xstk 3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 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 3.77965257404268 3.4072 5.1108 1.87396 4.94044 2.0 2.541592654 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2 -0.65 2 -0.65 + +# NVE ensemble +fix 1 all nve/asphere +#fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10 + +timestep 0.01706 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 32.4 + +compute quat all property/atom quatw quati quatj quatk + +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}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.1.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 1000000 Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes @@ -63,10 +134,6 @@ Neighbor list info ... pair build: copy stencil: none bin: none -Setting up Verlet run ... - Unit style : real - Current step : 0 - Time step : 0.01706 0 ekin = 6.60687273927977 | erot = 16.7817849122513 | epot = -77.8453746587951 | etot = -54.456717007264 Per MPI rank memory allocation (min/avg/max) = 7.105 | 7.11 | 7.116 Mbytes Step Temp E_pair E_mol TotEng Press Volume @@ -1072,21 +1139,21 @@ Per MPI rank memory allocation (min/avg/max) = 7.105 | 7.11 | 7.116 Mbytes 999000 ekin = 9.43365149694049 | erot = 9.73053828900897 | epot = -73.620907069925 | etot = -54.4567172839756 1000000 ekin = 9.45092723106241 | erot = 9.62486149933323 | epot = -73.5325060150984 | etot = -54.4567172847028 1000000 352.2878 -75.545604 2.0130979 -64.081579 -0.0098473389 39304000 -Loop time of 10.0925 on 4 procs for 1000000 steps with 10 atoms +Loop time of 16.7951 on 4 procs for 1000000 steps with 10 atoms -Performance: 146.047 ns/day, 0.164 hours/ns, 99083.127 timesteps/s, 990.831 katom-step/s -99.8% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 87.763 ns/day, 0.273 hours/ns, 59541.025 timesteps/s, 595.410 katom-step/s +99.4% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 3.3362 | 4.003 | 5.7128 | 49.6 | 39.66 -Bond | 0.12031 | 0.17704 | 0.23635 | 10.9 | 1.75 -Neigh | 0.00676 | 0.006813 | 0.006854 | 0.0 | 0.07 -Comm | 2.2652 | 4.2367 | 5.0428 | 55.8 | 41.98 -Output | 0.062416 | 0.073606 | 0.1045 | 6.6 | 0.73 -Modify | 0.36934 | 0.44375 | 0.5325 | 11.1 | 4.40 -Other | | 1.152 | | | 11.41 +Pair | 5.5941 | 6.7707 | 9.5516 | 62.7 | 40.31 +Bond | 0.2092 | 0.2872 | 0.38189 | 13.0 | 1.71 +Neigh | 0.018433 | 0.018502 | 0.018552 | 0.0 | 0.11 +Comm | 3.8835 | 7.1053 | 8.5337 | 70.8 | 42.31 +Output | 0.073525 | 0.077664 | 0.085514 | 1.7 | 0.46 +Modify | 0.58013 | 0.70982 | 0.8931 | 15.7 | 4.23 +Other | | 1.826 | | | 10.87 Nlocal: 2.5 ave 4 max 1 min Histogram: 2 0 0 0 0 0 0 0 0 2 @@ -1100,6 +1167,10 @@ Ave neighs/atom = 3.7 Ave special neighs/atom = 3.6 Neighbor list builds = 1000 Dangerous builds = 0 + +write_data last_config.${number}.* nocoeff +write_data last_config.1.* nocoeff System init for write_data ... Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule -Total wall time: 0:00:10 +#write_restart last_config.${number}.* +Total wall time: 0:00:16 diff --git a/examples/PACKAGES/cgdna/examples/real_units/oxDNA/duplex2/log.19May24.duplex1.g++.1 b/examples/PACKAGES/cgdna/examples/real_units/oxDNA/duplex2/log.22May24.duplex2.g++.1 similarity index 96% rename from examples/PACKAGES/cgdna/examples/real_units/oxDNA/duplex2/log.19May24.duplex1.g++.1 rename to examples/PACKAGES/cgdna/examples/real_units/oxDNA/duplex2/log.22May24.duplex2.g++.1 index caee1b298f..8254a5535a 100644 --- a/examples/PACKAGES/cgdna/examples/real_units/oxDNA/duplex2/log.19May24.duplex1.g++.1 +++ b/examples/PACKAGES/cgdna/examples/real_units/oxDNA/duplex2/log.22May24.duplex2.g++.1 @@ -1,6 +1,27 @@ -LAMMPS (17 Apr 2024) - using 1 OpenMP thread(s) per MPI task -WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:132) +LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-174-g749e259294-modified) +# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19 +variable number equal 2 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 300.0 + +units real + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (../atom_vec_hybrid.cpp:132) +atom_modify sort 0 8.518 + +# Pair interactions require lists of neighbours to be calculated +neighbor 17.036 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex2 Reading data file ... orthogonal box = (-170 -170 -170) to (170 170 170) 1 by 1 by 1 MPI processor grid @@ -23,10 +44,19 @@ Finding 1-2 1-3 1-4 neighbors ... 4 = max # of 1-4 neighbors 6 = max # of special neighbors special bonds CPU = 0.000 seconds - read_data CPU = 0.005 seconds + read_data CPU = 0.010 seconds + +set atom * mass 315.8376 Setting atom values ... 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 * 11.92337812042065 2.1295 6.409795 +special_bonds lj 0 1 1 Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 1 1 special bond factors coul: 0 0 0 @@ -35,6 +65,49 @@ Finding 1-2 1-3 1-4 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 oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk +pair_coeff * * oxdna/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576 +pair_coeff * * oxdna/stk seqav ${T} 8.01727944817084 0.005279604 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna/stk seqav 300 8.01727944817084 0.005279604 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna/hbond seqav 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 1 4 oxdna/hbond seqav 6.42073911784652 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 2 3 oxdna/hbond seqav 6.42073911784652 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff * * oxdna/xstk 3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 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 3.77965257404268 3.4072 5.1108 1.87396 4.94044 2.0 2.541592654 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2 -0.65 2 -0.65 + +# NVE ensemble +fix 1 all nve/asphere +fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10 +fix 2 all langevin 300 ${T} 4265.0 457145 angmom 10 +fix 2 all langevin 300 300 4265.0 457145 angmom 10 + +timestep 0.01706 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 32.4 + +compute quat all property/atom quatw quati quatj quatk + +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}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.2.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 1000000 Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes @@ -63,10 +136,6 @@ Neighbor list info ... pair build: copy stencil: none bin: none -Setting up Verlet run ... - Unit style : real - Current step : 0 - Time step : 0.01706 0 ekin = 16.1203242878408 | erot = 16.6982509426318 | epot = -131.137679785989 | etot = -98.3191045555159 Per MPI rank memory allocation (min/avg/max) = 7.322 | 7.322 | 7.322 Mbytes Step Temp E_pair E_mol TotEng Press Volume @@ -1072,21 +1141,21 @@ Per MPI rank memory allocation (min/avg/max) = 7.322 | 7.322 | 7.322 Mbytes 999000 ekin = 18.7341404690777 | erot = 19.3234540065288 | epot = -128.842851529638 | etot = -90.7852570540318 1000000 ekin = 18.6583620145008 | erot = 16.6848586754118 | epot = -128.346967556883 | etot = -93.0037468669704 1000000 417.29959 -129.94144 1.5944718 -109.68861 0.062656806 39304000 -Loop time of 22.0444 on 1 procs for 1000000 steps with 16 atoms +Loop time of 34.4889 on 1 procs for 1000000 steps with 16 atoms -Performance: 66.864 ns/day, 0.359 hours/ns, 45363.046 timesteps/s, 725.809 katom-step/s -99.9% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 42.738 ns/day, 0.562 hours/ns, 28994.847 timesteps/s, 463.918 katom-step/s +99.2% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 17.105 | 17.105 | 17.105 | 0.0 | 77.59 -Bond | 0.67238 | 0.67238 | 0.67238 | 0.0 | 3.05 -Neigh | 0.016373 | 0.016373 | 0.016373 | 0.0 | 0.07 -Comm | 0.29298 | 0.29298 | 0.29298 | 0.0 | 1.33 -Output | 0.12608 | 0.12608 | 0.12608 | 0.0 | 0.57 -Modify | 3.5001 | 3.5001 | 3.5001 | 0.0 | 15.88 -Other | | 0.3318 | | | 1.51 +Pair | 27.385 | 27.385 | 27.385 | 0.0 | 79.40 +Bond | 0.89821 | 0.89821 | 0.89821 | 0.0 | 2.60 +Neigh | 0.043138 | 0.043138 | 0.043138 | 0.0 | 0.13 +Comm | 0.47566 | 0.47566 | 0.47566 | 0.0 | 1.38 +Output | 0.20876 | 0.20876 | 0.20876 | 0.0 | 0.61 +Modify | 5.0059 | 5.0059 | 5.0059 | 0.0 | 14.51 +Other | | 0.4721 | | | 1.37 Nlocal: 16 ave 16 max 16 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -1100,6 +1169,10 @@ Ave neighs/atom = 6.5625 Ave special neighs/atom = 3.75 Neighbor list builds = 1000 Dangerous builds = 0 + +write_data last_config.${number}.* nocoeff +write_data last_config.2.* nocoeff System init for write_data ... Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule -Total wall time: 0:00:22 +#write_restart last_config.${number}.* +Total wall time: 0:00:34 diff --git a/examples/PACKAGES/cgdna/examples/real_units/oxDNA/duplex2/log.19May24.duplex1.g++.4 b/examples/PACKAGES/cgdna/examples/real_units/oxDNA/duplex2/log.22May24.duplex2.g++.4 similarity index 96% rename from examples/PACKAGES/cgdna/examples/real_units/oxDNA/duplex2/log.19May24.duplex1.g++.4 rename to examples/PACKAGES/cgdna/examples/real_units/oxDNA/duplex2/log.22May24.duplex2.g++.4 index 206baf6975..2397997895 100644 --- a/examples/PACKAGES/cgdna/examples/real_units/oxDNA/duplex2/log.19May24.duplex1.g++.4 +++ b/examples/PACKAGES/cgdna/examples/real_units/oxDNA/duplex2/log.22May24.duplex2.g++.4 @@ -1,6 +1,27 @@ -LAMMPS (17 Apr 2024) - using 1 OpenMP thread(s) per MPI task -WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:132) +LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-174-g749e259294-modified) +# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19 +variable number equal 2 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 300.0 + +units real + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (../atom_vec_hybrid.cpp:132) +atom_modify sort 0 8.518 + +# Pair interactions require lists of neighbours to be calculated +neighbor 17.036 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex2 Reading data file ... orthogonal box = (-170 -170 -170) to (170 170 170) 1 by 2 by 2 MPI processor grid @@ -23,10 +44,19 @@ Finding 1-2 1-3 1-4 neighbors ... 4 = max # of 1-4 neighbors 6 = max # of special neighbors special bonds CPU = 0.001 seconds - read_data CPU = 0.007 seconds + read_data CPU = 0.013 seconds + +set atom * mass 315.8376 Setting atom values ... 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 * 11.92337812042065 2.1295 6.409795 +special_bonds lj 0 1 1 Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 1 1 special bond factors coul: 0 0 0 @@ -35,6 +65,49 @@ Finding 1-2 1-3 1-4 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 oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk +pair_coeff * * oxdna/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576 +pair_coeff * * oxdna/stk seqav ${T} 8.01727944817084 0.005279604 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna/stk seqav 300 8.01727944817084 0.005279604 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna/hbond seqav 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 1 4 oxdna/hbond seqav 6.42073911784652 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 2 3 oxdna/hbond seqav 6.42073911784652 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff * * oxdna/xstk 3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 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 3.77965257404268 3.4072 5.1108 1.87396 4.94044 2.0 2.541592654 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2 -0.65 2 -0.65 + +# NVE ensemble +fix 1 all nve/asphere +fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10 +fix 2 all langevin 300 ${T} 4265.0 457145 angmom 10 +fix 2 all langevin 300 300 4265.0 457145 angmom 10 + +timestep 0.01706 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 32.4 + +compute quat all property/atom quatw quati quatj quatk + +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}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.2.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 1000000 Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes @@ -63,10 +136,6 @@ Neighbor list info ... pair build: copy stencil: none bin: none -Setting up Verlet run ... - Unit style : real - Current step : 0 - Time step : 0.01706 0 ekin = 16.1203242878408 | erot = 16.6982509426318 | epot = -131.137679785989 | etot = -98.3191045555159 Per MPI rank memory allocation (min/avg/max) = 7.232 | 7.264 | 7.344 Mbytes Step Temp E_pair E_mol TotEng Press Volume @@ -1072,21 +1141,21 @@ Per MPI rank memory allocation (min/avg/max) = 7.232 | 7.264 | 7.344 Mbytes 999000 ekin = 17.0511128282761 | erot = 11.8922913066054 | epot = -130.533301683943 | etot = -101.589897549061 1000000 ekin = 16.4176868113516 | erot = 10.505891115617 | epot = -130.086633390017 | etot = -103.163055463049 1000000 367.18625 -134.96443 4.8777959 -113.66895 -0.029625089 39304000 -Loop time of 17.8373 on 4 procs for 1000000 steps with 16 atoms +Loop time of 26.4037 on 4 procs for 1000000 steps with 16 atoms -Performance: 82.635 ns/day, 0.290 hours/ns, 56062.259 timesteps/s, 896.996 katom-step/s -99.8% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 55.825 ns/day, 0.430 hours/ns, 37873.477 timesteps/s, 605.976 katom-step/s +99.4% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 5.4709 | 7.3456 | 10.788 | 75.7 | 41.18 -Bond | 0.25222 | 0.29369 | 0.34982 | 7.2 | 1.65 -Neigh | 0.009763 | 0.0099055 | 0.010039 | 0.1 | 0.06 -Comm | 3.6693 | 7.3401 | 9.3552 | 81.3 | 41.15 -Output | 0.074481 | 0.079893 | 0.09183 | 2.5 | 0.45 -Modify | 1.0375 | 1.2928 | 1.4979 | 18.1 | 7.25 -Other | | 1.475 | | | 8.27 +Pair | 8.0347 | 10.957 | 16.143 | 93.9 | 41.50 +Bond | 0.3256 | 0.38079 | 0.42679 | 6.8 | 1.44 +Neigh | 0.021142 | 0.021313 | 0.021466 | 0.1 | 0.08 +Comm | 5.5113 | 11.003 | 14.141 | 100.0 | 41.67 +Output | 0.091898 | 0.097995 | 0.11134 | 2.5 | 0.37 +Modify | 1.3872 | 1.6961 | 1.9792 | 21.0 | 6.42 +Other | | 2.247 | | | 8.51 Nlocal: 4 ave 6 max 2 min Histogram: 2 0 0 0 0 0 0 0 0 2 @@ -1100,6 +1169,10 @@ Ave neighs/atom = 6.5625 Ave special neighs/atom = 3.75 Neighbor list builds = 1000 Dangerous builds = 0 + +write_data last_config.${number}.* nocoeff +write_data last_config.2.* nocoeff System init for write_data ... Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule -Total wall time: 0:00:17 +#write_restart last_config.${number}.* +Total wall time: 0:00:26 diff --git a/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/dsring/log.19May24.dsring.g++.1 b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/dsring/log.22May24.dsring.g++.1 similarity index 76% rename from examples/PACKAGES/cgdna/examples/real_units/oxDNA2/dsring/log.19May24.dsring.g++.1 rename to examples/PACKAGES/cgdna/examples/real_units/oxDNA2/dsring/log.22May24.dsring.g++.1 index bfc6e85a5a..e605409b1f 100644 --- a/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/dsring/log.19May24.dsring.g++.1 +++ b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/dsring/log.22May24.dsring.g++.1 @@ -1,6 +1,28 @@ -LAMMPS (17 Apr 2024) - using 1 OpenMP thread(s) per MPI task -WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:132) +LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-174-g749e259294-modified) +# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19 +variable number equal 5 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 300.0 +variable rhos equal 0.2 + +units real + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (../atom_vec_hybrid.cpp:132) +atom_modify sort 0 8.518 + +# Pair interactions require lists of neighbours to be calculated +neighbor 17.036 bin +neigh_modify every 1 delay 0 check yes + +read_data data.dsring Reading data file ... orthogonal box = (0 0 0) to (851 851 851) 1 by 1 by 1 MPI processor grid @@ -23,10 +45,19 @@ Finding 1-2 1-3 1-4 neighbors ... 4 = max # of 1-4 neighbors 6 = max # of special neighbors special bonds CPU = 0.000 seconds - read_data CPU = 0.007 seconds + read_data CPU = 0.012 seconds + +set atom * mass 315.8376 Setting atom values ... 148 settings made for mass + +group all type 1 4 148 atoms in group all + +# oxDNA2 bond interactions - FENE backbone +bond_style oxdna2/fene +bond_coeff * 11.92337812042065 2.1295 6.4430152 +special_bonds lj 0 1 1 Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 1 1 special bond factors coul: 0 0 0 @@ -35,6 +66,50 @@ Finding 1-2 1-3 1-4 neighbors ... 4 = max # of 1-4 neighbors 6 = 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 +pair_coeff * * oxdna2/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576 +pair_coeff * * oxdna2/stk seqdep ${T} 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/stk seqdep 300 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/hbond seqdep 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 1 4 oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 2 3 oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff * * oxdna2/xstk 3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 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 4.80673207785863 3.4072 5.1108 1.87396 4.94044 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 ${T} ${rhos} 0.815 +pair_coeff * * oxdna2/dh 300 ${rhos} 0.815 +pair_coeff * * oxdna2/dh 300 0.2 0.815 + +# NVE ensemble +fix 1 all nve/asphere +#fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10 + +timestep 0.01706 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 32.4 + +compute quat all property/atom quatw quati quatj quatk + +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}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.5.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 100000 Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes @@ -68,11 +143,7 @@ Neighbor list info ... pair build: copy stencil: none bin: none -Setting up Verlet run ... - Unit style : real - Current step : 0 - Time step : 0.01706 -WARNING: Communication cutoff adjusted to 48.03269686950012 (src/comm.cpp:739) +WARNING: Communication cutoff adjusted to 48.03269686950012 (../comm.cpp:739) 0 ekin = 122.015812851425 | erot = 125.402528675609 | epot = -1325.18559882055 | etot = -1077.76725729351 Per MPI rank memory allocation (min/avg/max) = 7.806 | 7.806 | 7.806 Mbytes Step Temp E_pair E_mol TotEng Press Volume @@ -178,21 +249,21 @@ Per MPI rank memory allocation (min/avg/max) = 7.806 | 7.806 | 7.806 Mbytes 99000 ekin = 137.752624159367 | erot = 134.99210077777 | epot = -1350.51198237554 | etot = -1077.7672574384 100000 ekin = 138.392477025647 | erot = 134.944608034508 | epot = -1351.10434250636 | etot = -1077.76725744621 100000 315.83543 -1390.6819 39.577599 -1212.7119 -0.012722464 6.1629505e+08 -Loop time of 54.6153 on 1 procs for 100000 steps with 148 atoms +Loop time of 85.2132 on 1 procs for 100000 steps with 148 atoms -Performance: 2.699 ns/day, 8.893 hours/ns, 1830.989 timesteps/s, 270.986 katom-step/s -99.9% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 1.730 ns/day, 13.875 hours/ns, 1173.528 timesteps/s, 173.682 katom-step/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 | 52.073 | 52.073 | 52.073 | 0.0 | 95.35 -Bond | 0.74079 | 0.74079 | 0.74079 | 0.0 | 1.36 -Neigh | 0.010107 | 0.010107 | 0.010107 | 0.0 | 0.02 -Comm | 0.040371 | 0.040371 | 0.040371 | 0.0 | 0.07 -Output | 0.097636 | 0.097636 | 0.097636 | 0.0 | 0.18 -Modify | 1.5841 | 1.5841 | 1.5841 | 0.0 | 2.90 -Other | | 0.06901 | | | 0.13 +Pair | 81.71 | 81.71 | 81.71 | 0.0 | 95.89 +Bond | 1.103 | 1.103 | 1.103 | 0.0 | 1.29 +Neigh | 0.017589 | 0.017589 | 0.017589 | 0.0 | 0.02 +Comm | 0.055508 | 0.055508 | 0.055508 | 0.0 | 0.07 +Output | 0.1581 | 0.1581 | 0.1581 | 0.0 | 0.19 +Modify | 2.0369 | 2.0369 | 2.0369 | 0.0 | 2.39 +Other | | 0.132 | | | 0.15 Nlocal: 148 ave 148 max 148 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -206,6 +277,10 @@ Ave neighs/atom = 28.371622 Ave special neighs/atom = 6 Neighbor list builds = 100 Dangerous builds = 0 + +write_data last_config.${number}.* nocoeff +write_data last_config.5.* nocoeff System init for write_data ... Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule -Total wall time: 0:00:54 +#write_restart last_config.${number}.* +Total wall time: 0:01:25 diff --git a/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/dsring/log.19May24.dsring.g++.4 b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/dsring/log.22May24.dsring.g++.4 similarity index 76% rename from examples/PACKAGES/cgdna/examples/real_units/oxDNA2/dsring/log.19May24.dsring.g++.4 rename to examples/PACKAGES/cgdna/examples/real_units/oxDNA2/dsring/log.22May24.dsring.g++.4 index fa68fac2c2..4701412063 100644 --- a/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/dsring/log.19May24.dsring.g++.4 +++ b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/dsring/log.22May24.dsring.g++.4 @@ -1,6 +1,28 @@ -LAMMPS (17 Apr 2024) - using 1 OpenMP thread(s) per MPI task -WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:132) +LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-174-g749e259294-modified) +# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19 +variable number equal 5 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 300.0 +variable rhos equal 0.2 + +units real + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (../atom_vec_hybrid.cpp:132) +atom_modify sort 0 8.518 + +# Pair interactions require lists of neighbours to be calculated +neighbor 17.036 bin +neigh_modify every 1 delay 0 check yes + +read_data data.dsring Reading data file ... orthogonal box = (0 0 0) to (851 851 851) 1 by 2 by 2 MPI processor grid @@ -23,10 +45,19 @@ Finding 1-2 1-3 1-4 neighbors ... 4 = max # of 1-4 neighbors 6 = max # of special neighbors special bonds CPU = 0.001 seconds - read_data CPU = 0.011 seconds + read_data CPU = 0.015 seconds + +set atom * mass 315.8376 Setting atom values ... 148 settings made for mass + +group all type 1 4 148 atoms in group all + +# oxDNA2 bond interactions - FENE backbone +bond_style oxdna2/fene +bond_coeff * 11.92337812042065 2.1295 6.4430152 +special_bonds lj 0 1 1 Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 1 1 special bond factors coul: 0 0 0 @@ -35,6 +66,50 @@ Finding 1-2 1-3 1-4 neighbors ... 4 = max # of 1-4 neighbors 6 = 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 +pair_coeff * * oxdna2/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576 +pair_coeff * * oxdna2/stk seqdep ${T} 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/stk seqdep 300 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/hbond seqdep 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 1 4 oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 2 3 oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff * * oxdna2/xstk 3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 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 4.80673207785863 3.4072 5.1108 1.87396 4.94044 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 ${T} ${rhos} 0.815 +pair_coeff * * oxdna2/dh 300 ${rhos} 0.815 +pair_coeff * * oxdna2/dh 300 0.2 0.815 + +# NVE ensemble +fix 1 all nve/asphere +#fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10 + +timestep 0.01706 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 32.4 + +compute quat all property/atom quatw quati quatj quatk + +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}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.5.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 100000 Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes @@ -68,11 +143,7 @@ Neighbor list info ... pair build: copy stencil: none bin: none -Setting up Verlet run ... - Unit style : real - Current step : 0 - Time step : 0.01706 -WARNING: Communication cutoff adjusted to 48.03269686950012 (src/comm.cpp:739) +WARNING: Communication cutoff adjusted to 48.03269686950012 (../comm.cpp:739) 0 ekin = 122.015812851425 | erot = 125.402528675609 | epot = -1325.18559882055 | etot = -1077.76725729351 Per MPI rank memory allocation (min/avg/max) = 7.619 | 7.668 | 7.742 Mbytes Step Temp E_pair E_mol TotEng Press Volume @@ -178,21 +249,21 @@ Per MPI rank memory allocation (min/avg/max) = 7.619 | 7.668 | 7.742 Mbytes 99000 ekin = 137.752624159367 | erot = 134.99210077777 | epot = -1350.51198237554 | etot = -1077.7672574384 100000 ekin = 138.392477025646 | erot = 134.94460803451 | epot = -1351.10434250636 | etot = -1077.76725744621 100000 315.83543 -1390.6819 39.577599 -1212.7119 -0.012722464 6.1629505e+08 -Loop time of 20.8885 on 4 procs for 100000 steps with 148 atoms +Loop time of 30.2255 on 4 procs for 100000 steps with 148 atoms -Performance: 7.056 ns/day, 3.401 hours/ns, 4787.333 timesteps/s, 708.525 katom-step/s -99.9% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 4.877 ns/day, 4.921 hours/ns, 3308.461 timesteps/s, 489.652 katom-step/s +99.6% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 11.553 | 15.593 | 18.744 | 74.9 | 74.65 -Bond | 0.22099 | 0.22585 | 0.22864 | 0.6 | 1.08 -Neigh | 0.004397 | 0.0044708 | 0.004533 | 0.1 | 0.02 -Comm | 1.2201 | 4.3856 | 8.4421 | 141.8 | 21.00 -Output | 0.035571 | 0.037478 | 0.038787 | 0.7 | 0.18 -Modify | 0.45808 | 0.46752 | 0.47581 | 1.0 | 2.24 -Other | | 0.1748 | | | 0.84 +Pair | 16.766 | 22.691 | 26.962 | 89.3 | 75.07 +Bond | 0.28821 | 0.30757 | 0.32075 | 2.3 | 1.02 +Neigh | 0.008451 | 0.008527 | 0.008607 | 0.1 | 0.03 +Comm | 2.0101 | 6.3007 | 12.277 | 170.6 | 20.85 +Output | 0.051655 | 0.054646 | 0.056776 | 0.9 | 0.18 +Modify | 0.53953 | 0.56983 | 0.63795 | 5.3 | 1.89 +Other | | 0.2934 | | | 0.97 Nlocal: 37 ave 38 max 36 min Histogram: 1 0 0 0 0 2 0 0 0 1 @@ -206,6 +277,10 @@ Ave neighs/atom = 28.371622 Ave special neighs/atom = 6 Neighbor list builds = 100 Dangerous builds = 0 + +write_data last_config.${number}.* nocoeff +write_data last_config.5.* nocoeff System init for write_data ... Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule -Total wall time: 0:00:20 +#write_restart last_config.${number}.* +Total wall time: 0:00:30 diff --git a/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex1/log.19May24.duplex1.g++.1 b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex1/log.22May24.duplex1.g++.1 similarity index 96% rename from examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex1/log.19May24.duplex1.g++.1 rename to examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex1/log.22May24.duplex1.g++.1 index a01079b1ec..031081bbc4 100644 --- a/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex1/log.19May24.duplex1.g++.1 +++ b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex1/log.22May24.duplex1.g++.1 @@ -1,6 +1,28 @@ -LAMMPS (17 Apr 2024) - using 1 OpenMP thread(s) per MPI task -WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:132) +LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-174-g749e259294-modified) +# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19 +variable number equal 1 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 300.0 +variable rhos equal 0.2 + +units real + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (../atom_vec_hybrid.cpp:132) +atom_modify sort 0 8.518 + +# Pair interactions require lists of neighbours to be calculated +neighbor 17.036 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex1 Reading data file ... orthogonal box = (-170 -170 -170) to (170 170 170) 1 by 1 by 1 MPI processor grid @@ -23,10 +45,19 @@ Finding 1-2 1-3 1-4 neighbors ... 2 = max # of 1-4 neighbors 4 = max # of special neighbors special bonds CPU = 0.000 seconds - read_data CPU = 0.005 seconds + read_data CPU = 0.009 seconds + +set atom * mass 315.8376 Setting atom values ... 10 settings made for mass + +group all type 1 4 10 atoms in group all + +# oxDNA2 bond interactions - FENE backbone +bond_style oxdna2/fene +bond_coeff * 11.92337812042065 2.1295 6.4430152 +special_bonds lj 0 1 1 Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 1 1 special bond factors coul: 0 0 0 @@ -35,6 +66,50 @@ Finding 1-2 1-3 1-4 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 +pair_coeff * * oxdna2/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576 +pair_coeff * * oxdna2/stk seqav ${T} 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/stk seqav 300 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/hbond seqav 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 1 4 oxdna2/hbond seqav 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 2 3 oxdna2/hbond seqav 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff * * oxdna2/xstk 3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 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 4.80673207785863 3.4072 5.1108 1.87396 4.94044 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 ${T} ${rhos} 0.815 +pair_coeff * * oxdna2/dh 300 ${rhos} 0.815 +pair_coeff * * oxdna2/dh 300 0.2 0.815 + +# NVE ensemble +fix 1 all nve/asphere +#fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10 + +timestep 0.01706 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 32.4 + +compute quat all property/atom quatw quati quatj quatk + +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}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.1.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 1000000 Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes @@ -68,11 +143,7 @@ Neighbor list info ... pair build: copy stencil: none bin: none -Setting up Verlet run ... - Unit style : real - Current step : 0 - Time step : 0.01706 -WARNING: Communication cutoff adjusted to 48.03269686950012 (src/comm.cpp:739) +WARNING: Communication cutoff adjusted to 48.03269686950012 (../comm.cpp:739) 0 ekin = 6.60687273927977 | erot = 16.7817849122513 | epot = -73.3220946463642 | etot = -49.9334369948331 Per MPI rank memory allocation (min/avg/max) = 7.445 | 7.445 | 7.445 Mbytes Step Temp E_pair E_mol TotEng Press Volume @@ -1078,21 +1149,21 @@ Per MPI rank memory allocation (min/avg/max) = 7.445 | 7.445 | 7.445 Mbytes 999000 ekin = 9.41957302295624 | erot = 13.2537863500049 | epot = -72.6067960815235 | etot = -49.9334367085624 1000000 ekin = 9.30950418584537 | erot = 13.3558388696135 | epot = -72.5987797643175 | etot = -49.9334367088586 1000000 347.01619 -80.374455 7.7756755 -63.289276 0.11518501 39304000 -Loop time of 12.9786 on 1 procs for 1000000 steps with 10 atoms +Loop time of 19.3079 on 1 procs for 1000000 steps with 10 atoms -Performance: 113.570 ns/day, 0.211 hours/ns, 77050.020 timesteps/s, 770.500 katom-step/s -99.5% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 76.341 ns/day, 0.314 hours/ns, 51792.277 timesteps/s, 517.923 katom-step/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 | 10.471 | 10.471 | 10.471 | 0.0 | 80.68 -Bond | 0.50292 | 0.50292 | 0.50292 | 0.0 | 3.88 -Neigh | 0.005498 | 0.005498 | 0.005498 | 0.0 | 0.04 -Comm | 0.29263 | 0.29263 | 0.29263 | 0.0 | 2.25 -Output | 0.10128 | 0.10128 | 0.10128 | 0.0 | 0.78 -Modify | 1.2697 | 1.2697 | 1.2697 | 0.0 | 9.78 -Other | | 0.3353 | | | 2.58 +Pair | 15.904 | 15.904 | 15.904 | 0.0 | 82.37 +Bond | 0.68326 | 0.68326 | 0.68326 | 0.0 | 3.54 +Neigh | 0.011182 | 0.011182 | 0.011182 | 0.0 | 0.06 +Comm | 0.45393 | 0.45393 | 0.45393 | 0.0 | 2.35 +Output | 0.12567 | 0.12567 | 0.12567 | 0.0 | 0.65 +Modify | 1.6705 | 1.6705 | 1.6705 | 0.0 | 8.65 +Other | | 0.459 | | | 2.38 Nlocal: 10 ave 10 max 10 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -1106,6 +1177,10 @@ Ave neighs/atom = 3.7 Ave special neighs/atom = 3.6 Neighbor list builds = 1000 Dangerous builds = 0 + +write_data last_config.${number}.* nocoeff +write_data last_config.1.* nocoeff System init for write_data ... Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule -Total wall time: 0:00:12 +#write_restart last_config.${number}.* +Total wall time: 0:00:19 diff --git a/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex1/log.19May24.duplex1.g++.4 b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex1/log.22May24.duplex1.g++.4 similarity index 96% rename from examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex1/log.19May24.duplex1.g++.4 rename to examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex1/log.22May24.duplex1.g++.4 index f9e95ed27a..36678a7103 100644 --- a/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex1/log.19May24.duplex1.g++.4 +++ b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex1/log.22May24.duplex1.g++.4 @@ -1,6 +1,28 @@ -LAMMPS (17 Apr 2024) - using 1 OpenMP thread(s) per MPI task -WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:132) +LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-174-g749e259294-modified) +# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19 +variable number equal 1 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 300.0 +variable rhos equal 0.2 + +units real + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (../atom_vec_hybrid.cpp:132) +atom_modify sort 0 8.518 + +# Pair interactions require lists of neighbours to be calculated +neighbor 17.036 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex1 Reading data file ... orthogonal box = (-170 -170 -170) to (170 170 170) 1 by 2 by 2 MPI processor grid @@ -23,10 +45,19 @@ Finding 1-2 1-3 1-4 neighbors ... 2 = max # of 1-4 neighbors 4 = max # of special neighbors special bonds CPU = 0.001 seconds - read_data CPU = 0.008 seconds + read_data CPU = 0.011 seconds + +set atom * mass 315.8376 Setting atom values ... 10 settings made for mass + +group all type 1 4 10 atoms in group all + +# oxDNA2 bond interactions - FENE backbone +bond_style oxdna2/fene +bond_coeff * 11.92337812042065 2.1295 6.4430152 +special_bonds lj 0 1 1 Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 1 1 special bond factors coul: 0 0 0 @@ -35,6 +66,50 @@ Finding 1-2 1-3 1-4 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 +pair_coeff * * oxdna2/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576 +pair_coeff * * oxdna2/stk seqav ${T} 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/stk seqav 300 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/hbond seqav 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 1 4 oxdna2/hbond seqav 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 2 3 oxdna2/hbond seqav 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff * * oxdna2/xstk 3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 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 4.80673207785863 3.4072 5.1108 1.87396 4.94044 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 ${T} ${rhos} 0.815 +pair_coeff * * oxdna2/dh 300 ${rhos} 0.815 +pair_coeff * * oxdna2/dh 300 0.2 0.815 + +# NVE ensemble +fix 1 all nve/asphere +#fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10 + +timestep 0.01706 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 32.4 + +compute quat all property/atom quatw quati quatj quatk + +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}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.1.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 1000000 Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes @@ -68,11 +143,7 @@ Neighbor list info ... pair build: copy stencil: none bin: none -Setting up Verlet run ... - Unit style : real - Current step : 0 - Time step : 0.01706 -WARNING: Communication cutoff adjusted to 48.03269686950012 (src/comm.cpp:739) +WARNING: Communication cutoff adjusted to 48.03269686950012 (../comm.cpp:739) 0 ekin = 6.60687273927977 | erot = 16.7817849122513 | epot = -73.3220946463646 | etot = -49.9334369948335 Per MPI rank memory allocation (min/avg/max) = 7.443 | 7.444 | 7.445 Mbytes Step Temp E_pair E_mol TotEng Press Volume @@ -1078,21 +1149,21 @@ Per MPI rank memory allocation (min/avg/max) = 7.443 | 7.444 | 7.445 Mbytes 999000 ekin = 9.4195730226422 | erot = 13.2537863498268 | epot = -72.6067960810353 | etot = -49.9334367085663 1000000 ekin = 9.30950418557169 | erot = 13.3558388695471 | epot = -72.5987797639821 | etot = -49.9334367088633 1000000 347.01619 -80.374455 7.7756755 -63.289276 0.11518501 39304000 -Loop time of 12.3789 on 4 procs for 1000000 steps with 10 atoms +Loop time of 17.7764 on 4 procs for 1000000 steps with 10 atoms -Performance: 119.072 ns/day, 0.202 hours/ns, 80782.753 timesteps/s, 807.828 katom-step/s -99.8% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 82.918 ns/day, 0.289 hours/ns, 56254.421 timesteps/s, 562.544 katom-step/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 | 4.1126 | 5.281 | 7.0829 | 48.1 | 42.66 -Bond | 0.14793 | 0.22282 | 0.2978 | 11.7 | 1.80 -Neigh | 0.00393 | 0.0039655 | 0.004021 | 0.1 | 0.03 -Comm | 2.762 | 4.8726 | 6.048 | 56.9 | 39.36 -Output | 0.063777 | 0.070646 | 0.088161 | 3.8 | 0.57 -Modify | 0.44561 | 0.5346 | 0.64233 | 11.9 | 4.32 -Other | | 1.393 | | | 11.26 +Pair | 6.0475 | 7.6302 | 10.252 | 57.4 | 42.92 +Bond | 0.22588 | 0.32246 | 0.42602 | 12.9 | 1.81 +Neigh | 0.007601 | 0.007642 | 0.007702 | 0.0 | 0.04 +Comm | 3.9938 | 7.0574 | 8.7017 | 68.2 | 39.70 +Output | 0.07165 | 0.07691 | 0.088092 | 2.4 | 0.43 +Modify | 0.60223 | 0.70805 | 0.84637 | 11.9 | 3.98 +Other | | 1.974 | | | 11.10 Nlocal: 2.5 ave 3 max 2 min Histogram: 2 0 0 0 0 0 0 0 0 2 @@ -1106,6 +1177,10 @@ Ave neighs/atom = 3.7 Ave special neighs/atom = 3.6 Neighbor list builds = 1000 Dangerous builds = 0 + +write_data last_config.${number}.* nocoeff +write_data last_config.1.* nocoeff System init for write_data ... Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule -Total wall time: 0:00:12 +#write_restart last_config.${number}.* +Total wall time: 0:00:17 diff --git a/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex2/log.19May24.duplex2.g++.1 b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex2/log.22May24.duplex2.g++.1 similarity index 96% rename from examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex2/log.19May24.duplex2.g++.1 rename to examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex2/log.22May24.duplex2.g++.1 index c070e4eaca..a0e4dabd93 100644 --- a/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex2/log.19May24.duplex2.g++.1 +++ b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex2/log.22May24.duplex2.g++.1 @@ -1,6 +1,28 @@ -LAMMPS (17 Apr 2024) - using 1 OpenMP thread(s) per MPI task -WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:132) +LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-174-g749e259294-modified) +# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19 +variable number equal 2 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 300.0 +variable rhos equal 0.2 + +units real + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (../atom_vec_hybrid.cpp:132) +atom_modify sort 0 8.518 + +# Pair interactions require lists of neighbours to be calculated +neighbor 17.036 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex2 Reading data file ... orthogonal box = (-170 -170 -170) to (170 170 170) 1 by 1 by 1 MPI processor grid @@ -23,10 +45,19 @@ Finding 1-2 1-3 1-4 neighbors ... 4 = max # of 1-4 neighbors 6 = max # of special neighbors special bonds CPU = 0.000 seconds - read_data CPU = 0.005 seconds + read_data CPU = 0.009 seconds + +set atom * mass 315.8376 Setting atom values ... 16 settings made for mass + +group all type 1 4 16 atoms in group all + +# oxDNA2 bond interactions - FENE backbone +bond_style oxdna2/fene +bond_coeff * 11.92337812042065 2.1295 6.4430152 +special_bonds lj 0 1 1 Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 1 1 special bond factors coul: 0 0 0 @@ -35,6 +66,52 @@ Finding 1-2 1-3 1-4 neighbors ... 4 = max # of 1-4 neighbors 6 = 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 +pair_coeff * * oxdna2/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576 +pair_coeff * * oxdna2/stk seqav ${T} 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/stk seqav 300 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/hbond seqav 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 1 4 oxdna2/hbond seqav 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 2 3 oxdna2/hbond seqav 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff * * oxdna2/xstk 3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 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 4.80673207785863 3.4072 5.1108 1.87396 4.94044 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 ${T} ${rhos} 0.815 +pair_coeff * * oxdna2/dh 300 ${rhos} 0.815 +pair_coeff * * oxdna2/dh 300 0.2 0.815 + +# NVE ensemble +fix 1 all nve/asphere +fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10 +fix 2 all langevin 300 ${T} 4265.0 457145 angmom 10 +fix 2 all langevin 300 300 4265.0 457145 angmom 10 + +timestep 0.01706 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 32.4 + +compute quat all property/atom quatw quati quatj quatk + +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}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.2.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 1000000 Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes @@ -68,11 +145,7 @@ Neighbor list info ... pair build: copy stencil: none bin: none -Setting up Verlet run ... - Unit style : real - Current step : 0 - Time step : 0.01706 -WARNING: Communication cutoff adjusted to 48.03269686950012 (src/comm.cpp:739) +WARNING: Communication cutoff adjusted to 48.03269686950012 (../comm.cpp:739) 0 ekin = 16.1203242878408 | erot = 16.6982509426318 | epot = -125.483166681887 | etot = -92.6645914514141 Per MPI rank memory allocation (min/avg/max) = 7.57 | 7.57 | 7.57 Mbytes Step Temp E_pair E_mol TotEng Press Volume @@ -1078,21 +1151,21 @@ Per MPI rank memory allocation (min/avg/max) = 7.57 | 7.57 | 7.57 Mbytes 999000 ekin = 17.3864595030106 | erot = 19.031153747846 | epot = -122.410040365131 | etot = -85.9924271142742 1000000 ekin = 17.4266501863313 | erot = 15.93443523795 | epot = -121.571786609929 | etot = -88.2107011856477 1000000 389.752 -124.64554 3.0737557 -104.14514 0.13705163 39304000 -Loop time of 26.5237 on 1 procs for 1000000 steps with 16 atoms +Loop time of 40.2662 on 1 procs for 1000000 steps with 16 atoms -Performance: 55.572 ns/day, 0.432 hours/ns, 37702.162 timesteps/s, 603.235 katom-step/s -99.8% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 36.606 ns/day, 0.656 hours/ns, 24834.718 timesteps/s, 397.355 katom-step/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 | 21.515 | 21.515 | 21.515 | 0.0 | 81.12 -Bond | 0.75114 | 0.75114 | 0.75114 | 0.0 | 2.83 -Neigh | 0.007053 | 0.007053 | 0.007053 | 0.0 | 0.03 -Comm | 0.28128 | 0.28128 | 0.28128 | 0.0 | 1.06 -Output | 0.13963 | 0.13963 | 0.13963 | 0.0 | 0.53 -Modify | 3.4968 | 3.4968 | 3.4968 | 0.0 | 13.18 -Other | | 0.3331 | | | 1.26 +Pair | 33.133 | 33.133 | 33.133 | 0.0 | 82.29 +Bond | 1.0208 | 1.0208 | 1.0208 | 0.0 | 2.54 +Neigh | 0.014956 | 0.014956 | 0.014956 | 0.0 | 0.04 +Comm | 0.45341 | 0.45341 | 0.45341 | 0.0 | 1.13 +Output | 0.19799 | 0.19799 | 0.19799 | 0.0 | 0.49 +Modify | 4.9747 | 4.9747 | 4.9747 | 0.0 | 12.35 +Other | | 0.4711 | | | 1.17 Nlocal: 16 ave 16 max 16 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -1106,6 +1179,10 @@ Ave neighs/atom = 6.6875 Ave special neighs/atom = 3.75 Neighbor list builds = 1000 Dangerous builds = 0 + +write_data last_config.${number}.* nocoeff +write_data last_config.2.* nocoeff System init for write_data ... Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule -Total wall time: 0:00:26 +#write_restart last_config.${number}.* +Total wall time: 0:00:40 diff --git a/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex2/log.19May24.duplex2.g++.4 b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex2/log.22May24.duplex2.g++.4 similarity index 96% rename from examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex2/log.19May24.duplex2.g++.4 rename to examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex2/log.22May24.duplex2.g++.4 index cd89d65300..3233f455ba 100644 --- a/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex2/log.19May24.duplex2.g++.4 +++ b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex2/log.22May24.duplex2.g++.4 @@ -1,6 +1,28 @@ -LAMMPS (17 Apr 2024) - using 1 OpenMP thread(s) per MPI task -WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:132) +LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-174-g749e259294-modified) +# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19 +variable number equal 2 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 300.0 +variable rhos equal 0.2 + +units real + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (../atom_vec_hybrid.cpp:132) +atom_modify sort 0 8.518 + +# Pair interactions require lists of neighbours to be calculated +neighbor 17.036 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex2 Reading data file ... orthogonal box = (-170 -170 -170) to (170 170 170) 1 by 2 by 2 MPI processor grid @@ -23,10 +45,19 @@ Finding 1-2 1-3 1-4 neighbors ... 4 = max # of 1-4 neighbors 6 = max # of special neighbors special bonds CPU = 0.001 seconds - read_data CPU = 0.008 seconds + read_data CPU = 0.011 seconds + +set atom * mass 315.8376 Setting atom values ... 16 settings made for mass + +group all type 1 4 16 atoms in group all + +# oxDNA2 bond interactions - FENE backbone +bond_style oxdna2/fene +bond_coeff * 11.92337812042065 2.1295 6.4430152 +special_bonds lj 0 1 1 Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 1 1 special bond factors coul: 0 0 0 @@ -35,6 +66,52 @@ Finding 1-2 1-3 1-4 neighbors ... 4 = max # of 1-4 neighbors 6 = 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 +pair_coeff * * oxdna2/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576 +pair_coeff * * oxdna2/stk seqav ${T} 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/stk seqav 300 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/hbond seqav 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 1 4 oxdna2/hbond seqav 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 2 3 oxdna2/hbond seqav 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff * * oxdna2/xstk 3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 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 4.80673207785863 3.4072 5.1108 1.87396 4.94044 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 ${T} ${rhos} 0.815 +pair_coeff * * oxdna2/dh 300 ${rhos} 0.815 +pair_coeff * * oxdna2/dh 300 0.2 0.815 + +# NVE ensemble +fix 1 all nve/asphere +fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10 +fix 2 all langevin 300 ${T} 4265.0 457145 angmom 10 +fix 2 all langevin 300 300 4265.0 457145 angmom 10 + +timestep 0.01706 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 32.4 + +compute quat all property/atom quatw quati quatj quatk + +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}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.2.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 1000000 Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes @@ -68,11 +145,7 @@ Neighbor list info ... pair build: copy stencil: none bin: none -Setting up Verlet run ... - Unit style : real - Current step : 0 - Time step : 0.01706 -WARNING: Communication cutoff adjusted to 48.03269686950012 (src/comm.cpp:739) +WARNING: Communication cutoff adjusted to 48.03269686950012 (../comm.cpp:739) 0 ekin = 16.1203242878408 | erot = 16.6982509426318 | epot = -125.483166681887 | etot = -92.6645914514142 Per MPI rank memory allocation (min/avg/max) = 7.569 | 7.598 | 7.682 Mbytes Step Temp E_pair E_mol TotEng Press Volume @@ -1078,21 +1151,21 @@ Per MPI rank memory allocation (min/avg/max) = 7.569 | 7.598 | 7.682 Mbytes 999000 ekin = 16.492584210326 | erot = 13.0108008173606 | epot = -129.709400513234 | etot = -100.206015485547 1000000 ekin = 17.097105825142 | erot = 12.6179942372262 | epot = -129.692482442335 | etot = -99.977382379967 1000000 382.38165 -132.06191 2.3694293 -112.59538 0.043662828 39304000 -Loop time of 18.875 on 4 procs for 1000000 steps with 16 atoms +Loop time of 27.2476 on 4 procs for 1000000 steps with 16 atoms -Performance: 78.092 ns/day, 0.307 hours/ns, 52980.236 timesteps/s, 847.684 katom-step/s -99.8% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 54.096 ns/day, 0.444 hours/ns, 36700.437 timesteps/s, 587.207 katom-step/s +99.8% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 6.6389 | 9.0272 | 11.733 | 63.0 | 47.83 -Bond | 0.25991 | 0.31216 | 0.34826 | 6.1 | 1.65 -Neigh | 0.005375 | 0.0054547 | 0.005558 | 0.1 | 0.03 -Comm | 3.8623 | 6.7331 | 8.8907 | 72.9 | 35.67 -Output | 0.066898 | 0.071666 | 0.082232 | 2.3 | 0.38 -Modify | 1.173 | 1.3132 | 1.4562 | 9.6 | 6.96 -Other | | 1.412 | | | 7.48 +Pair | 9.5219 | 13.077 | 17.034 | 78.2 | 47.99 +Bond | 0.38282 | 0.43293 | 0.48144 | 5.8 | 1.59 +Neigh | 0.00956 | 0.0096418 | 0.009729 | 0.1 | 0.04 +Comm | 5.6548 | 9.754 | 12.913 | 88.2 | 35.80 +Output | 0.086221 | 0.091692 | 0.10328 | 2.2 | 0.34 +Modify | 1.4663 | 1.6512 | 1.8474 | 13.1 | 6.06 +Other | | 2.231 | | | 8.19 Nlocal: 4 ave 5 max 3 min Histogram: 2 0 0 0 0 0 0 0 0 2 @@ -1106,6 +1179,10 @@ Ave neighs/atom = 6.6875 Ave special neighs/atom = 3.75 Neighbor list builds = 1000 Dangerous builds = 0 + +write_data last_config.${number}.* nocoeff +write_data last_config.2.* nocoeff System init for write_data ... Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule -Total wall time: 0:00:18 +#write_restart last_config.${number}.* +Total wall time: 0:00:27 diff --git a/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex3/log.19May24.duplex3.g++.1 b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex3/log.22May24.duplex3.g++.1 similarity index 96% rename from examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex3/log.19May24.duplex3.g++.1 rename to examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex3/log.22May24.duplex3.g++.1 index d78834f085..9db73c4b2d 100644 --- a/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex3/log.19May24.duplex3.g++.1 +++ b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex3/log.22May24.duplex3.g++.1 @@ -1,6 +1,28 @@ -LAMMPS (17 Apr 2024) - using 1 OpenMP thread(s) per MPI task -WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:132) +LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-174-g749e259294-modified) +# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19 +variable number equal 3 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 300.0 +variable rhos equal 0.2 + +units real + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (../atom_vec_hybrid.cpp:132) +atom_modify sort 0 8.518 + +# Pair interactions require lists of neighbours to be calculated +neighbor 17.036 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex3 Reading data file ... orthogonal box = (-170 -170 -170) to (170 170 170) 1 by 1 by 1 MPI processor grid @@ -23,10 +45,19 @@ Finding 1-2 1-3 1-4 neighbors ... 2 = max # of 1-4 neighbors 4 = max # of special neighbors special bonds CPU = 0.000 seconds - read_data CPU = 0.005 seconds + read_data CPU = 0.009 seconds + +set atom * mass 100.0278 Setting atom values ... 10 settings made for mass + +group all type 1 4 10 atoms in group all + +# oxDNA2 bond interactions - FENE backbone +bond_style oxdna2/fene +bond_coeff * 11.92337812042065 2.1295 6.4430152 +special_bonds lj 0 1 1 Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 1 1 special bond factors coul: 0 0 0 @@ -35,6 +66,50 @@ Finding 1-2 1-3 1-4 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 +pair_coeff * * oxdna2/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576 +pair_coeff * * oxdna2/stk seqdep ${T} 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/stk seqdep 300 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/hbond seqdep 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 1 4 oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 2 3 oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff * * oxdna2/xstk 3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 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 4.80673207785863 3.4072 5.1108 1.87396 4.94044 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 ${T} ${rhos} 0.815 +pair_coeff * * oxdna2/dh 300 ${rhos} 0.815 +pair_coeff * * oxdna2/dh 300 0.2 0.815 + +# NVE ensemble +fix 1 all nve/asphere +#fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10 + +timestep 0.01706 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 32.4 + +compute quat all property/atom quatw quati quatj quatk + +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}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.3.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 1000000 Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes @@ -68,11 +143,7 @@ Neighbor list info ... pair build: copy stencil: none bin: none -Setting up Verlet run ... - Unit style : real - Current step : 0 - Time step : 0.01706 -WARNING: Communication cutoff adjusted to 48.03269686950012 (src/comm.cpp:739) +WARNING: Communication cutoff adjusted to 48.03269686950012 (../comm.cpp:739) 0 ekin = 7.03429942525144 | erot = 12.9873344362494 | epot = -68.5183064451292 | etot = -48.4966725836283 Per MPI rank memory allocation (min/avg/max) = 7.445 | 7.445 | 7.445 Mbytes Step Temp E_pair E_mol TotEng Press Volume @@ -1078,21 +1149,21 @@ Per MPI rank memory allocation (min/avg/max) = 7.445 | 7.445 | 7.445 Mbytes 999000 ekin = 7.06575293322294 | erot = 13.1250004085097 | epot = -68.6874256472216 | etot = -48.496672305489 1000000 ekin = 6.56133020088365 | erot = 13.4950386916226 | epot = -68.5530411962168 | etot = -48.4966723037105 1000000 244.5767 -69.23317 0.68012891 -61.991711 -0.012778323 39304000 -Loop time of 11.1904 on 1 procs for 1000000 steps with 10 atoms +Loop time of 18.8316 on 1 procs for 1000000 steps with 10 atoms -Performance: 131.719 ns/day, 0.182 hours/ns, 89362.622 timesteps/s, 893.626 katom-step/s -99.9% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 78.272 ns/day, 0.307 hours/ns, 53102.168 timesteps/s, 531.022 katom-step/s +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 | 8.9766 | 8.9766 | 8.9766 | 0.0 | 80.22 -Bond | 0.44821 | 0.44821 | 0.44821 | 0.0 | 4.01 -Neigh | 0.004031 | 0.004031 | 0.004031 | 0.0 | 0.04 -Comm | 0.24442 | 0.24442 | 0.24442 | 0.0 | 2.18 -Output | 0.11136 | 0.11136 | 0.11136 | 0.0 | 1.00 -Modify | 1.1158 | 1.1158 | 1.1158 | 0.0 | 9.97 -Other | | 0.29 | | | 2.59 +Pair | 15.43 | 15.43 | 15.43 | 0.0 | 81.93 +Bond | 0.69466 | 0.69466 | 0.69466 | 0.0 | 3.69 +Neigh | 0.011044 | 0.011044 | 0.011044 | 0.0 | 0.06 +Comm | 0.4431 | 0.4431 | 0.4431 | 0.0 | 2.35 +Output | 0.12591 | 0.12591 | 0.12591 | 0.0 | 0.67 +Modify | 1.6795 | 1.6795 | 1.6795 | 0.0 | 8.92 +Other | | 0.4478 | | | 2.38 Nlocal: 10 ave 10 max 10 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -1106,6 +1177,10 @@ Ave neighs/atom = 3.7 Ave special neighs/atom = 3.6 Neighbor list builds = 1000 Dangerous builds = 0 + +write_data last_config.${number}.* nocoeff +write_data last_config.3.* nocoeff System init for write_data ... Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule -Total wall time: 0:00:11 +#write_restart last_config.${number}.* +Total wall time: 0:00:18 diff --git a/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex3/log.19May24.duplex3.g++.4 b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex3/log.22May24.duplex3.g++.4 similarity index 96% rename from examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex3/log.19May24.duplex3.g++.4 rename to examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex3/log.22May24.duplex3.g++.4 index a2ae24af6b..669a86a110 100644 --- a/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex3/log.19May24.duplex3.g++.4 +++ b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/duplex3/log.22May24.duplex3.g++.4 @@ -1,6 +1,28 @@ -LAMMPS (17 Apr 2024) - using 1 OpenMP thread(s) per MPI task -WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:132) +LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-174-g749e259294-modified) +# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19 +variable number equal 3 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 300.0 +variable rhos equal 0.2 + +units real + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (../atom_vec_hybrid.cpp:132) +atom_modify sort 0 8.518 + +# Pair interactions require lists of neighbours to be calculated +neighbor 17.036 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex3 Reading data file ... orthogonal box = (-170 -170 -170) to (170 170 170) 1 by 2 by 2 MPI processor grid @@ -23,10 +45,19 @@ Finding 1-2 1-3 1-4 neighbors ... 2 = max # of 1-4 neighbors 4 = max # of special neighbors special bonds CPU = 0.001 seconds - read_data CPU = 0.007 seconds + read_data CPU = 0.011 seconds + +set atom * mass 100.0278 Setting atom values ... 10 settings made for mass + +group all type 1 4 10 atoms in group all + +# oxDNA2 bond interactions - FENE backbone +bond_style oxdna2/fene +bond_coeff * 11.92337812042065 2.1295 6.4430152 +special_bonds lj 0 1 1 Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 1 1 special bond factors coul: 0 0 0 @@ -35,6 +66,50 @@ Finding 1-2 1-3 1-4 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 +pair_coeff * * oxdna2/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576 +pair_coeff * * oxdna2/stk seqdep ${T} 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/stk seqdep 300 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/hbond seqdep 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 1 4 oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 2 3 oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff * * oxdna2/xstk 3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 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 4.80673207785863 3.4072 5.1108 1.87396 4.94044 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 ${T} ${rhos} 0.815 +pair_coeff * * oxdna2/dh 300 ${rhos} 0.815 +pair_coeff * * oxdna2/dh 300 0.2 0.815 + +# NVE ensemble +fix 1 all nve/asphere +#fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10 + +timestep 0.01706 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 32.4 + +compute quat all property/atom quatw quati quatj quatk + +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}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.3.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 1000000 Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes @@ -68,11 +143,7 @@ Neighbor list info ... pair build: copy stencil: none bin: none -Setting up Verlet run ... - Unit style : real - Current step : 0 - Time step : 0.01706 -WARNING: Communication cutoff adjusted to 48.03269686950012 (src/comm.cpp:739) +WARNING: Communication cutoff adjusted to 48.03269686950012 (../comm.cpp:739) 0 ekin = 7.03429942525144 | erot = 12.9873344362494 | epot = -68.5183064451292 | etot = -48.4966725836283 Per MPI rank memory allocation (min/avg/max) = 7.443 | 7.444 | 7.445 Mbytes Step Temp E_pair E_mol TotEng Press Volume @@ -1078,21 +1149,21 @@ Per MPI rank memory allocation (min/avg/max) = 7.443 | 7.444 | 7.445 Mbytes 999000 ekin = 7.06575290471557 | erot = 13.1250004270275 | epot = -68.6874256372488 | etot = -48.4966723055057 1000000 ekin = 6.56133017801672 | erot = 13.4950387121477 | epot = -68.5530411938935 | etot = -48.4966723037291 1000000 244.5767 -69.23317 0.68012891 -61.991711 -0.012778323 39304000 -Loop time of 11.4095 on 4 procs for 1000000 steps with 10 atoms +Loop time of 18.2788 on 4 procs for 1000000 steps with 10 atoms -Performance: 129.189 ns/day, 0.186 hours/ns, 87646.083 timesteps/s, 876.461 katom-step/s -99.9% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 80.639 ns/day, 0.298 hours/ns, 54708.327 timesteps/s, 547.083 katom-step/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 | 2.9984 | 4.6915 | 6.6489 | 59.9 | 41.12 -Bond | 0.15743 | 0.20489 | 0.24566 | 8.9 | 1.80 -Neigh | 0.003395 | 0.0034335 | 0.003477 | 0.1 | 0.03 -Comm | 2.5981 | 4.8289 | 6.5413 | 64.5 | 42.32 -Output | 0.054733 | 0.058039 | 0.065343 | 1.8 | 0.51 -Modify | 0.4272 | 0.49029 | 0.54447 | 6.4 | 4.30 -Other | | 1.132 | | | 9.93 +Pair | 4.7489 | 7.413 | 10.648 | 77.4 | 40.56 +Bond | 0.2292 | 0.30345 | 0.37909 | 12.0 | 1.66 +Neigh | 0.00759 | 0.0076525 | 0.007698 | 0.0 | 0.04 +Comm | 4.13 | 7.779 | 10.46 | 82.1 | 42.56 +Output | 0.072271 | 0.076746 | 0.085815 | 1.9 | 0.42 +Modify | 0.63917 | 0.69264 | 0.75378 | 6.3 | 3.79 +Other | | 2.006 | | | 10.98 Nlocal: 2.5 ave 3 max 2 min Histogram: 2 0 0 0 0 0 0 0 0 2 @@ -1106,6 +1177,10 @@ Ave neighs/atom = 3.7 Ave special neighs/atom = 3.6 Neighbor list builds = 1000 Dangerous builds = 0 + +write_data last_config.${number}.* nocoeff +write_data last_config.3.* nocoeff System init for write_data ... Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule -Total wall time: 0:00:11 +#write_restart last_config.${number}.* +Total wall time: 0:00:18 diff --git a/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/unique_bp/log.19May24.duplex4.4type.g++.1 b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/unique_bp/log.22May24.duplex4.4type.g++.1 similarity index 93% rename from examples/PACKAGES/cgdna/examples/real_units/oxDNA2/unique_bp/log.19May24.duplex4.4type.g++.1 rename to examples/PACKAGES/cgdna/examples/real_units/oxDNA2/unique_bp/log.22May24.duplex4.4type.g++.1 index c468ee24ff..f454f2d2bf 100644 --- a/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/unique_bp/log.19May24.duplex4.4type.g++.1 +++ b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/unique_bp/log.22May24.duplex4.4type.g++.1 @@ -1,6 +1,30 @@ -LAMMPS (17 Apr 2024) - using 1 OpenMP thread(s) per MPI task -WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:132) +LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-174-g749e259294-modified) +variable number equal 4 +variable ofreq equal 1000 +variable efreq equal 1000 + +variable ntype equal 4 + +variable T equal 300.0 +variable rhos equal 0.2 + +units real + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (../atom_vec_hybrid.cpp:132) +atom_modify sort 0 8.518 + +# Pair interactions require lists of neighbours to be calculated +neighbor 17.036 bin +neigh_modify every 10 delay 0 check yes + +read_data data.duplex4.4type Reading data file ... orthogonal box = (-170 -170 -170) to (170 170 170) 1 by 1 by 1 MPI processor grid @@ -23,10 +47,20 @@ Finding 1-2 1-3 1-4 neighbors ... 4 = max # of 1-4 neighbors 6 = max # of special neighbors special bonds CPU = 0.000 seconds - read_data CPU = 0.005 seconds + read_data CPU = 0.009 seconds + +mass * 315.8376 # sets per-type mass if not in data file +set atom * mass 315.8376 # sets per-atom mass Setting atom values ... 26 settings made for mass + +group all type 1 4 26 atoms in group all + +# oxDNA2 bond interactions - FENE backbone +bond_style oxdna2/fene +bond_coeff * 11.92337812042065 2.1295 6.4430152 +special_bonds lj 0 1 1 Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 1 1 special bond factors coul: 0 0 0 @@ -35,6 +69,95 @@ Finding 1-2 1-3 1-4 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 +pair_coeff * * oxdna2/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576 +pair_coeff * * oxdna2/stk seqdep ${T} 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/stk seqdep 300 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/hbond seqdep 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 + +label loop +variable base loop ${ntype} +variable base loop 4 + variable basemod equal ${base}%4 + variable basemod equal 1%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" +variable comp equal ${base}+3 +variable comp equal 1+3 +pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 1 ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 1 4 oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" +next base +jump in.duplex4.4type loop +variable base loop ${ntype} +variable base loop 4 + variable basemod equal ${base}%4 + variable basemod equal 2%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" +variable comp equal ${base}+1 +variable comp equal 2+1 +pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 2 ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 2 3 oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +next base +jump in.duplex4.4type loop +variable base loop ${ntype} +variable base loop 4 + variable basemod equal ${base}%4 + variable basemod equal 3%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" +next base +jump in.duplex4.4type loop +variable base loop ${ntype} +variable base loop 4 + variable basemod equal ${base}%4 + variable basemod equal 4%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" +next base +jump in.duplex4.4type loop + +pair_coeff * * oxdna2/xstk 3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 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 4.80673207785863 3.4072 5.1108 1.87396 4.94044 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 ${T} ${rhos} 0.815 +pair_coeff * * oxdna2/dh 300 ${rhos} 0.815 +pair_coeff * * oxdna2/dh 300 0.2 0.815 + +# Langevin dynamics +fix 1 all nve/asphere +fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10 +fix 2 all langevin 300 ${T} 4265.0 457145 angmom 10 +fix 2 all langevin 300 300 4265.0 457145 angmom 10 + +timestep 0.01706 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 32.4 + +compute quat all property/atom quatw quati quatj quatk + +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}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.4.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 1000000 Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 10 steps, delay = 0 steps, check = yes @@ -68,11 +191,7 @@ Neighbor list info ... pair build: copy stencil: none bin: none -Setting up Verlet run ... - Unit style : real - Current step : 0 - Time step : 0.01706 -WARNING: Communication cutoff adjusted to 48.03269686950012 (src/comm.cpp:739) +WARNING: Communication cutoff adjusted to 48.03269686950012 (../comm.cpp:739) 0 ekin = 22.349486974586 | erot = 20.578245994282 | epot = -222.813067990178 | etot = -179.88533502131 Per MPI rank memory allocation (min/avg/max) = 7.57 | 7.57 | 7.57 Mbytes Step Temp E_pair E_mol TotEng Press Volume @@ -1078,21 +1197,21 @@ Per MPI rank memory allocation (min/avg/max) = 7.57 | 7.57 | 7.57 Mbytes 999000 ekin = 22.5781778653751 | erot = 21.7041052467461 | epot = -221.511725171924 | etot = -177.229442059803 1000000 ekin = 22.8867994582225 | erot = 20.7015166614267 | epot = -222.040127669769 | etot = -178.45181155012 1000000 307.12188 -227.88356 5.8434328 -199.15333 0.033370746 39304000 -Loop time of 49.9988 on 1 procs for 1000000 steps with 26 atoms +Loop time of 85.9592 on 1 procs for 1000000 steps with 26 atoms -Performance: 29.480 ns/day, 0.814 hours/ns, 20000.476 timesteps/s, 520.012 katom-step/s -99.9% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 17.147 ns/day, 1.400 hours/ns, 11633.421 timesteps/s, 302.469 katom-step/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 | 42.93 | 42.93 | 42.93 | 0.0 | 85.86 -Bond | 1.1736 | 1.1736 | 1.1736 | 0.0 | 2.35 -Neigh | 0.010656 | 0.010656 | 0.010656 | 0.0 | 0.02 -Comm | 0.2842 | 0.2842 | 0.2842 | 0.0 | 0.57 -Output | 0.22398 | 0.22398 | 0.22398 | 0.0 | 0.45 -Modify | 5.1366 | 5.1366 | 5.1366 | 0.0 | 10.27 -Other | | 0.2401 | | | 0.48 +Pair | 75.127 | 75.127 | 75.127 | 0.0 | 87.40 +Bond | 1.8597 | 1.8597 | 1.8597 | 0.0 | 2.16 +Neigh | 0.023421 | 0.023421 | 0.023421 | 0.0 | 0.03 +Comm | 0.47775 | 0.47775 | 0.47775 | 0.0 | 0.56 +Output | 0.31455 | 0.31455 | 0.31455 | 0.0 | 0.37 +Modify | 7.8261 | 7.8261 | 7.8261 | 0.0 | 9.10 +Other | | 0.3311 | | | 0.39 Nlocal: 26 ave 26 max 26 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -1106,6 +1225,10 @@ Ave neighs/atom = 11.576923 Ave special neighs/atom = 5.0769231 Neighbor list builds = 1000 Dangerous builds = 0 + +write_data last_config.${number}.* nocoeff +write_data last_config.4.* nocoeff System init for write_data ... Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule -Total wall time: 0:00:50 +#write_restart last_config.${number}.* +Total wall time: 0:01:25 diff --git a/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/unique_bp/log.19May24.duplex4.4type.g++.4 b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/unique_bp/log.22May24.duplex4.4type.g++.4 similarity index 93% rename from examples/PACKAGES/cgdna/examples/real_units/oxDNA2/unique_bp/log.19May24.duplex4.4type.g++.4 rename to examples/PACKAGES/cgdna/examples/real_units/oxDNA2/unique_bp/log.22May24.duplex4.4type.g++.4 index 17269a0e91..4c158da526 100644 --- a/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/unique_bp/log.19May24.duplex4.4type.g++.4 +++ b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/unique_bp/log.22May24.duplex4.4type.g++.4 @@ -1,6 +1,30 @@ -LAMMPS (17 Apr 2024) - using 1 OpenMP thread(s) per MPI task -WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:132) +LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-174-g749e259294-modified) +variable number equal 4 +variable ofreq equal 1000 +variable efreq equal 1000 + +variable ntype equal 4 + +variable T equal 300.0 +variable rhos equal 0.2 + +units real + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (../atom_vec_hybrid.cpp:132) +atom_modify sort 0 8.518 + +# Pair interactions require lists of neighbours to be calculated +neighbor 17.036 bin +neigh_modify every 10 delay 0 check yes + +read_data data.duplex4.4type Reading data file ... orthogonal box = (-170 -170 -170) to (170 170 170) 1 by 2 by 2 MPI processor grid @@ -23,10 +47,20 @@ Finding 1-2 1-3 1-4 neighbors ... 4 = max # of 1-4 neighbors 6 = max # of special neighbors special bonds CPU = 0.000 seconds - read_data CPU = 0.007 seconds + read_data CPU = 0.011 seconds + +mass * 315.8376 # sets per-type mass if not in data file +set atom * mass 315.8376 # sets per-atom mass Setting atom values ... 26 settings made for mass + +group all type 1 4 26 atoms in group all + +# oxDNA2 bond interactions - FENE backbone +bond_style oxdna2/fene +bond_coeff * 11.92337812042065 2.1295 6.4430152 +special_bonds lj 0 1 1 Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 1 1 special bond factors coul: 0 0 0 @@ -35,6 +69,95 @@ Finding 1-2 1-3 1-4 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 +pair_coeff * * oxdna2/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576 +pair_coeff * * oxdna2/stk seqdep ${T} 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/stk seqdep 300 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/hbond seqdep 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 + +label loop +variable base loop ${ntype} +variable base loop 4 + variable basemod equal ${base}%4 + variable basemod equal 1%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" +variable comp equal ${base}+3 +variable comp equal 1+3 +pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 1 ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 1 4 oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" +next base +jump in.duplex4.4type loop +variable base loop ${ntype} +variable base loop 4 + variable basemod equal ${base}%4 + variable basemod equal 2%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" +variable comp equal ${base}+1 +variable comp equal 2+1 +pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 2 ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 2 3 oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +next base +jump in.duplex4.4type loop +variable base loop ${ntype} +variable base loop 4 + variable basemod equal ${base}%4 + variable basemod equal 3%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" +next base +jump in.duplex4.4type loop +variable base loop ${ntype} +variable base loop 4 + variable basemod equal ${base}%4 + variable basemod equal 4%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" +next base +jump in.duplex4.4type loop + +pair_coeff * * oxdna2/xstk 3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 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 4.80673207785863 3.4072 5.1108 1.87396 4.94044 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 ${T} ${rhos} 0.815 +pair_coeff * * oxdna2/dh 300 ${rhos} 0.815 +pair_coeff * * oxdna2/dh 300 0.2 0.815 + +# Langevin dynamics +fix 1 all nve/asphere +fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10 +fix 2 all langevin 300 ${T} 4265.0 457145 angmom 10 +fix 2 all langevin 300 300 4265.0 457145 angmom 10 + +timestep 0.01706 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 32.4 + +compute quat all property/atom quatw quati quatj quatk + +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}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.4.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 1000000 Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 10 steps, delay = 0 steps, check = yes @@ -68,11 +191,7 @@ Neighbor list info ... pair build: copy stencil: none bin: none -Setting up Verlet run ... - Unit style : real - Current step : 0 - Time step : 0.01706 -WARNING: Communication cutoff adjusted to 48.03269686950012 (src/comm.cpp:739) +WARNING: Communication cutoff adjusted to 48.03269686950012 (../comm.cpp:739) 0 ekin = 22.349486974586 | erot = 20.578245994282 | epot = -222.813067990178 | etot = -179.88533502131 Per MPI rank memory allocation (min/avg/max) = 7.568 | 7.569 | 7.57 Mbytes Step Temp E_pair E_mol TotEng Press Volume @@ -1078,21 +1197,21 @@ Per MPI rank memory allocation (min/avg/max) = 7.568 | 7.569 | 7.57 Mbytes 999000 ekin = 22.1968344281123 | erot = 22.7999859685056 | epot = -216.784980184639 | etot = -171.788159788021 1000000 ekin = 22.6406306102505 | erot = 22.5936369544571 | epot = -217.43832313152 | etot = -172.204055566812 1000000 303.8185 -221.63969 4.201369 -194.79769 -0.0039208577 39304000 -Loop time of 33.2292 on 4 procs for 1000000 steps with 26 atoms +Loop time of 52.1772 on 4 procs for 1000000 steps with 26 atoms -Performance: 44.358 ns/day, 0.541 hours/ns, 30094.016 timesteps/s, 782.444 katom-step/s -99.9% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 28.250 ns/day, 0.850 hours/ns, 19165.450 timesteps/s, 498.302 katom-step/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 | 10.626 | 15.644 | 25.979 | 154.5 | 47.08 -Bond | 0.33928 | 0.43429 | 0.52964 | 14.4 | 1.31 -Neigh | 0.007773 | 0.0079158 | 0.008061 | 0.1 | 0.02 -Comm | 4.0659 | 14.948 | 19.566 | 164.9 | 44.99 -Output | 0.089356 | 0.10217 | 0.10917 | 2.4 | 0.31 -Modify | 1.2889 | 1.7411 | 2.1956 | 31.1 | 5.24 -Other | | 0.3515 | | | 1.06 +Pair | 16.653 | 24.637 | 41.068 | 196.4 | 47.22 +Bond | 0.48356 | 0.63927 | 0.80015 | 17.6 | 1.23 +Neigh | 0.014011 | 0.014287 | 0.01458 | 0.2 | 0.03 +Comm | 6.7344 | 23.772 | 31.096 | 205.7 | 45.56 +Output | 0.12082 | 0.13899 | 0.14687 | 2.8 | 0.27 +Modify | 1.8628 | 2.4412 | 3.0041 | 33.6 | 4.68 +Other | | 0.5347 | | | 1.02 Nlocal: 6.5 ave 10 max 3 min Histogram: 2 0 0 0 0 0 0 0 0 2 @@ -1106,6 +1225,10 @@ Ave neighs/atom = 11.576923 Ave special neighs/atom = 5.0769231 Neighbor list builds = 1000 Dangerous builds = 0 + +write_data last_config.${number}.* nocoeff +write_data last_config.4.* nocoeff System init for write_data ... Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule -Total wall time: 0:00:33 +#write_restart last_config.${number}.* +Total wall time: 0:00:52 diff --git a/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/unique_bp/log.19May24.duplex4.8type.g++.1 b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/unique_bp/log.22May24.duplex4.8type.g++.1 similarity index 90% rename from examples/PACKAGES/cgdna/examples/real_units/oxDNA2/unique_bp/log.19May24.duplex4.8type.g++.1 rename to examples/PACKAGES/cgdna/examples/real_units/oxDNA2/unique_bp/log.22May24.duplex4.8type.g++.1 index 29d38ba865..f812593d4d 100644 --- a/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/unique_bp/log.19May24.duplex4.8type.g++.1 +++ b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/unique_bp/log.22May24.duplex4.8type.g++.1 @@ -1,6 +1,30 @@ -LAMMPS (17 Apr 2024) - using 1 OpenMP thread(s) per MPI task -WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:132) +LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-174-g749e259294-modified) +variable number equal 8 +variable ofreq equal 1000 +variable efreq equal 1000 + +variable ntype equal 8 + +variable T equal 300.0 +variable rhos equal 0.2 + +units real + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (../atom_vec_hybrid.cpp:132) +atom_modify sort 0 8.518 + +# Pair interactions require lists of neighbours to be calculated +neighbor 17.036 bin +neigh_modify every 10 delay 0 check yes + +read_data data.duplex4.8type Reading data file ... orthogonal box = (-170 -170 -170) to (170 170 170) 1 by 1 by 1 MPI processor grid @@ -23,10 +47,20 @@ Finding 1-2 1-3 1-4 neighbors ... 4 = max # of 1-4 neighbors 6 = max # of special neighbors special bonds CPU = 0.000 seconds - read_data CPU = 0.005 seconds + read_data CPU = 0.009 seconds + +mass * 315.8376 # sets per-type mass if not in data file +set atom * mass 315.8376 # sets per-atom mass Setting atom values ... 26 settings made for mass + +group all type 1 4 26 atoms in group all + +# oxDNA2 bond interactions - FENE backbone +bond_style oxdna2/fene +bond_coeff * 11.92337812042065 2.1295 6.4430152 +special_bonds lj 0 1 1 Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 1 1 special bond factors coul: 0 0 0 @@ -35,6 +69,137 @@ Finding 1-2 1-3 1-4 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 +pair_coeff * * oxdna2/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576 +pair_coeff * * oxdna2/stk seqdep ${T} 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/stk seqdep 300 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/hbond seqdep 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 + +label loop +variable base loop ${ntype} +variable base loop 8 + variable basemod equal ${base}%4 + variable basemod equal 1%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" +variable comp equal ${base}+3 +variable comp equal 1+3 +pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 1 ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 1 4 oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" +next base +jump in.duplex4.8type loop +variable base loop ${ntype} +variable base loop 8 + variable basemod equal ${base}%4 + variable basemod equal 2%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" +variable comp equal ${base}+1 +variable comp equal 2+1 +pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 2 ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 2 3 oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +next base +jump in.duplex4.8type loop +variable base loop ${ntype} +variable base loop 8 + variable basemod equal ${base}%4 + variable basemod equal 3%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" +next base +jump in.duplex4.8type loop +variable base loop ${ntype} +variable base loop 8 + variable basemod equal ${base}%4 + variable basemod equal 4%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" +next base +jump in.duplex4.8type loop +variable base loop ${ntype} +variable base loop 8 + variable basemod equal ${base}%4 + variable basemod equal 5%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" +variable comp equal ${base}+3 +variable comp equal 5+3 +pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 5 ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 5 8 oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" +next base +jump in.duplex4.8type loop +variable base loop ${ntype} +variable base loop 8 + variable basemod equal ${base}%4 + variable basemod equal 6%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" +variable comp equal ${base}+1 +variable comp equal 6+1 +pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 6 ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 6 7 oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +next base +jump in.duplex4.8type loop +variable base loop ${ntype} +variable base loop 8 + variable basemod equal ${base}%4 + variable basemod equal 7%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" +next base +jump in.duplex4.8type loop +variable base loop ${ntype} +variable base loop 8 + variable basemod equal ${base}%4 + variable basemod equal 8%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" +next base +jump in.duplex4.8type loop + +pair_coeff * * oxdna2/xstk 3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 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 4.80673207785863 3.4072 5.1108 1.87396 4.94044 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 ${T} ${rhos} 0.815 +pair_coeff * * oxdna2/dh 300 ${rhos} 0.815 +pair_coeff * * oxdna2/dh 300 0.2 0.815 + +# Langevin dynamics +fix 1 all nve/asphere +fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10 +fix 2 all langevin 300 ${T} 4265.0 457145 angmom 10 +fix 2 all langevin 300 300 4265.0 457145 angmom 10 + +timestep 0.01706 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 32.4 + +compute quat all property/atom quatw quati quatj quatk + +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}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.8.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 1000000 Generated 0 of 28 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 10 steps, delay = 0 steps, check = yes @@ -68,11 +233,7 @@ Neighbor list info ... pair build: copy stencil: none bin: none -Setting up Verlet run ... - Unit style : real - Current step : 0 - Time step : 0.01706 -WARNING: Communication cutoff adjusted to 48.03269686950012 (src/comm.cpp:739) +WARNING: Communication cutoff adjusted to 48.03269686950012 (../comm.cpp:739) 0 ekin = 22.349486974586 | erot = 20.578245994282 | epot = -222.813067990178 | etot = -179.88533502131 Per MPI rank memory allocation (min/avg/max) = 7.57 | 7.57 | 7.57 Mbytes Step Temp E_pair E_mol TotEng Press Volume @@ -1078,21 +1239,21 @@ Per MPI rank memory allocation (min/avg/max) = 7.57 | 7.57 | 7.57 Mbytes 999000 ekin = 22.5781778653751 | erot = 21.7041052467461 | epot = -221.511725171924 | etot = -177.229442059803 1000000 ekin = 22.8867994582225 | erot = 20.7015166614267 | epot = -222.040127669769 | etot = -178.45181155012 1000000 307.12188 -227.88356 5.8434328 -199.15333 0.033370746 39304000 -Loop time of 51.9408 on 1 procs for 1000000 steps with 26 atoms +Loop time of 85.8602 on 1 procs for 1000000 steps with 26 atoms -Performance: 28.378 ns/day, 0.846 hours/ns, 19252.681 timesteps/s, 500.570 katom-step/s -99.9% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 17.167 ns/day, 1.398 hours/ns, 11646.839 timesteps/s, 302.818 katom-step/s +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 | 44.649 | 44.649 | 44.649 | 0.0 | 85.96 -Bond | 1.2217 | 1.2217 | 1.2217 | 0.0 | 2.35 -Neigh | 0.011591 | 0.011591 | 0.011591 | 0.0 | 0.02 -Comm | 0.31411 | 0.31411 | 0.31411 | 0.0 | 0.60 -Output | 0.2259 | 0.2259 | 0.2259 | 0.0 | 0.43 -Modify | 5.2451 | 5.2451 | 5.2451 | 0.0 | 10.10 -Other | | 0.2734 | | | 0.53 +Pair | 75.033 | 75.033 | 75.033 | 0.0 | 87.39 +Bond | 1.7719 | 1.7719 | 1.7719 | 0.0 | 2.06 +Neigh | 0.023059 | 0.023059 | 0.023059 | 0.0 | 0.03 +Comm | 0.51625 | 0.51625 | 0.51625 | 0.0 | 0.60 +Output | 0.31488 | 0.31488 | 0.31488 | 0.0 | 0.37 +Modify | 7.8149 | 7.8149 | 7.8149 | 0.0 | 9.10 +Other | | 0.3861 | | | 0.45 Nlocal: 26 ave 26 max 26 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -1106,6 +1267,10 @@ Ave neighs/atom = 11.576923 Ave special neighs/atom = 5.0769231 Neighbor list builds = 1000 Dangerous builds = 0 + +write_data last_config.${number}.* nocoeff +write_data last_config.8.* nocoeff System init for write_data ... Generated 0 of 28 mixed pair_coeff terms from geometric mixing rule -Total wall time: 0:00:51 +#write_restart last_config.${number}.* +Total wall time: 0:01:25 diff --git a/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/unique_bp/log.19May24.duplex4.8type.g++.4 b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/unique_bp/log.22May24.duplex4.8type.g++.4 similarity index 90% rename from examples/PACKAGES/cgdna/examples/real_units/oxDNA2/unique_bp/log.19May24.duplex4.8type.g++.4 rename to examples/PACKAGES/cgdna/examples/real_units/oxDNA2/unique_bp/log.22May24.duplex4.8type.g++.4 index 14e1c35e27..184462d373 100644 --- a/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/unique_bp/log.19May24.duplex4.8type.g++.4 +++ b/examples/PACKAGES/cgdna/examples/real_units/oxDNA2/unique_bp/log.22May24.duplex4.8type.g++.4 @@ -1,6 +1,30 @@ -LAMMPS (17 Apr 2024) - using 1 OpenMP thread(s) per MPI task -WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:132) +LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-174-g749e259294-modified) +variable number equal 8 +variable ofreq equal 1000 +variable efreq equal 1000 + +variable ntype equal 8 + +variable T equal 300.0 +variable rhos equal 0.2 + +units real + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (../atom_vec_hybrid.cpp:132) +atom_modify sort 0 8.518 + +# Pair interactions require lists of neighbours to be calculated +neighbor 17.036 bin +neigh_modify every 10 delay 0 check yes + +read_data data.duplex4.8type Reading data file ... orthogonal box = (-170 -170 -170) to (170 170 170) 1 by 2 by 2 MPI processor grid @@ -23,10 +47,20 @@ Finding 1-2 1-3 1-4 neighbors ... 4 = max # of 1-4 neighbors 6 = max # of special neighbors special bonds CPU = 0.001 seconds - read_data CPU = 0.007 seconds + read_data CPU = 0.011 seconds + +mass * 315.8376 # sets per-type mass if not in data file +set atom * mass 315.8376 # sets per-atom mass Setting atom values ... 26 settings made for mass + +group all type 1 4 26 atoms in group all + +# oxDNA2 bond interactions - FENE backbone +bond_style oxdna2/fene +bond_coeff * 11.92337812042065 2.1295 6.4430152 +special_bonds lj 0 1 1 Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 1 1 special bond factors coul: 0 0 0 @@ -35,6 +69,137 @@ Finding 1-2 1-3 1-4 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 +pair_coeff * * oxdna2/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576 +pair_coeff * * oxdna2/stk seqdep ${T} 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/stk seqdep 300 8.06199211612242 0.005309213 0.70439070204273 3.4072 7.6662 2.72576 6.3885 1.3 0.0 0.8 0.9 0.0 0.95 0.9 0.0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/hbond seqdep 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 + +label loop +variable base loop ${ntype} +variable base loop 8 + variable basemod equal ${base}%4 + variable basemod equal 1%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" +variable comp equal ${base}+3 +variable comp equal 1+3 +pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 1 ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 1 4 oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" +next base +jump in.duplex4.8type loop +variable base loop ${ntype} +variable base loop 8 + variable basemod equal ${base}%4 + variable basemod equal 2%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" +variable comp equal ${base}+1 +variable comp equal 2+1 +pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 2 ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 2 3 oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +next base +jump in.duplex4.8type loop +variable base loop ${ntype} +variable base loop 8 + variable basemod equal ${base}%4 + variable basemod equal 3%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" +next base +jump in.duplex4.8type loop +variable base loop ${ntype} +variable base loop 8 + variable basemod equal ${base}%4 + variable basemod equal 4%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" +next base +jump in.duplex4.8type loop +variable base loop ${ntype} +variable base loop 8 + variable basemod equal ${base}%4 + variable basemod equal 5%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" +variable comp equal ${base}+3 +variable comp equal 5+3 +pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 5 ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 5 8 oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" +next base +jump in.duplex4.8type loop +variable base loop ${ntype} +variable base loop 8 + variable basemod equal ${base}%4 + variable basemod equal 6%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" +variable comp equal ${base}+1 +variable comp equal 6+1 +pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 6 ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +pair_coeff 6 7 oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45 +next base +jump in.duplex4.8type loop +variable base loop ${ntype} +variable base loop 8 + variable basemod equal ${base}%4 + variable basemod equal 7%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" +next base +jump in.duplex4.8type loop +variable base loop ${ntype} +variable base loop 8 + variable basemod equal ${base}%4 + variable basemod equal 8%4 + if "${basemod} == 1" then "variable comp equal ${base}+3" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" + if "${basemod} == 2" then "variable comp equal ${base}+1" "pair_coeff ${base} ${comp} oxdna2/hbond seqdep 6.36589157849259 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0 0.7 1.5 0.0 0.7 1.5 0 0.7 0.46 3.141592654 0.7 4.0 1.570796327 0.45 4.0 1.570796327 0.45" +next base +jump in.duplex4.8type loop + +pair_coeff * * oxdna2/xstk 3.9029021145006 4.89785 5.74965 4.21641 5.57929 2.25 0.791592654 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 4.80673207785863 3.4072 5.1108 1.87396 4.94044 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 ${T} ${rhos} 0.815 +pair_coeff * * oxdna2/dh 300 ${rhos} 0.815 +pair_coeff * * oxdna2/dh 300 0.2 0.815 + +# Langevin dynamics +fix 1 all nve/asphere +fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10 +fix 2 all langevin 300 ${T} 4265.0 457145 angmom 10 +fix 2 all langevin 300 300 4265.0 457145 angmom 10 + +timestep 0.01706 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 32.4 + +compute quat all property/atom quatw quati quatj quatk + +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}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.8.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 1000000 Generated 0 of 28 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 10 steps, delay = 0 steps, check = yes @@ -68,11 +233,7 @@ Neighbor list info ... pair build: copy stencil: none bin: none -Setting up Verlet run ... - Unit style : real - Current step : 0 - Time step : 0.01706 -WARNING: Communication cutoff adjusted to 48.03269686950012 (src/comm.cpp:739) +WARNING: Communication cutoff adjusted to 48.03269686950012 (../comm.cpp:739) 0 ekin = 22.349486974586 | erot = 20.578245994282 | epot = -222.813067990178 | etot = -179.88533502131 Per MPI rank memory allocation (min/avg/max) = 7.568 | 7.569 | 7.57 Mbytes Step Temp E_pair E_mol TotEng Press Volume @@ -1078,21 +1239,21 @@ Per MPI rank memory allocation (min/avg/max) = 7.568 | 7.569 | 7.57 Mbytes 999000 ekin = 22.1968344281123 | erot = 22.7999859685056 | epot = -216.784980184639 | etot = -171.788159788021 1000000 ekin = 22.6406306102505 | erot = 22.5936369544571 | epot = -217.43832313152 | etot = -172.204055566812 1000000 303.8185 -221.63969 4.201369 -194.79769 -0.0039208577 39304000 -Loop time of 34.5573 on 4 procs for 1000000 steps with 26 atoms +Loop time of 53.157 on 4 procs for 1000000 steps with 26 atoms -Performance: 42.653 ns/day, 0.563 hours/ns, 28937.471 timesteps/s, 752.374 katom-step/s -99.9% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 27.729 ns/day, 0.866 hours/ns, 18812.191 timesteps/s, 489.117 katom-step/s +99.6% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 11.103 | 15.989 | 27.026 | 161.4 | 46.27 -Bond | 0.3534 | 0.44646 | 0.54636 | 13.5 | 1.29 -Neigh | 0.007879 | 0.0080685 | 0.008218 | 0.1 | 0.02 -Comm | 4.2767 | 15.803 | 20.415 | 168.6 | 45.73 -Output | 0.084582 | 0.13406 | 0.15369 | 7.8 | 0.39 -Modify | 1.354 | 1.7988 | 2.2537 | 32.6 | 5.21 -Other | | 0.378 | | | 1.09 +Pair | 17.443 | 25.085 | 41.565 | 193.9 | 47.19 +Bond | 0.47799 | 0.65467 | 0.81319 | 18.1 | 1.23 +Neigh | 0.014771 | 0.014974 | 0.015145 | 0.1 | 0.03 +Comm | 7.0561 | 24.213 | 31.359 | 204.1 | 45.55 +Output | 0.12434 | 0.14455 | 0.15308 | 3.1 | 0.27 +Modify | 1.8662 | 2.4548 | 3.0502 | 36.3 | 4.62 +Other | | 0.5899 | | | 1.11 Nlocal: 6.5 ave 10 max 3 min Histogram: 2 0 0 0 0 0 0 0 0 2 @@ -1106,6 +1267,10 @@ Ave neighs/atom = 11.576923 Ave special neighs/atom = 5.0769231 Neighbor list builds = 1000 Dangerous builds = 0 + +write_data last_config.${number}.* nocoeff +write_data last_config.8.* nocoeff System init for write_data ... Generated 0 of 28 mixed pair_coeff terms from geometric mixing rule -Total wall time: 0:00:34 +#write_restart last_config.${number}.* +Total wall time: 0:00:53 diff --git a/examples/PACKAGES/cgdna/examples/real_units/oxRNA2/duplex2/log.19May24.duplex2.g++.1 b/examples/PACKAGES/cgdna/examples/real_units/oxRNA2/duplex2/log.22May24.duplex2.g++.1 similarity index 95% rename from examples/PACKAGES/cgdna/examples/real_units/oxRNA2/duplex2/log.19May24.duplex2.g++.1 rename to examples/PACKAGES/cgdna/examples/real_units/oxRNA2/duplex2/log.22May24.duplex2.g++.1 index 4b03446769..1368ee307a 100644 --- a/examples/PACKAGES/cgdna/examples/real_units/oxRNA2/duplex2/log.19May24.duplex2.g++.1 +++ b/examples/PACKAGES/cgdna/examples/real_units/oxRNA2/duplex2/log.22May24.duplex2.g++.1 @@ -1,6 +1,28 @@ -LAMMPS (17 Apr 2024) - using 1 OpenMP thread(s) per MPI task -WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:132) +LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-174-g749e259294-modified) +# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19 +variable number equal 2 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 300.0 +variable rhos equal 0.5 + +units real + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (../atom_vec_hybrid.cpp:132) +atom_modify sort 0 8.518 + +# Pair interactions require lists of neighbours to be calculated +neighbor 17.036 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex2 Reading data file ... orthogonal box = (-170 -170 -170) to (170 170 170) 1 by 1 by 1 MPI processor grid @@ -23,10 +45,19 @@ Finding 1-2 1-3 1-4 neighbors ... 4 = max # of 1-4 neighbors 6 = max # of special neighbors special bonds CPU = 0.000 seconds - read_data CPU = 0.005 seconds + read_data CPU = 0.009 seconds + +set atom * mass 315.8376 Setting atom values ... 16 settings made for mass + +group all type 1 4 16 atoms in group all + +# oxRNA2 bond interactions - FENE backbone +bond_style oxrna2/fene +bond_coeff * 11.92337812042065 2.1295 6.482800913 +special_bonds lj 0 1 1 Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 1 1 special bond factors coul: 0 0 0 @@ -35,6 +66,51 @@ Finding 1-2 1-3 1-4 neighbors ... 4 = max # of 1-4 neighbors 6 = max # of special neighbors special bonds CPU = 0.000 seconds + +# oxRNA2 pair interactions +pair_style hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh +pair_coeff * * oxrna2/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576 +pair_coeff * * oxrna2/stk seqdep ${T} 8.35864576375849 0.005504556 0.70439070204273 3.66274 7.92174 2.9813 6.64404 0.9 0.0 0.95 0.9 0.0 0.95 1.3 0.0 0.8 1.3 0.0 0.8 2.0 0.65 2.0 0.65 +pair_coeff * * oxrna2/stk seqdep 300 8.35864576375849 0.005504556 0.70439070204273 3.66274 7.92174 2.9813 6.64404 0.9 0.0 0.95 0.9 0.0 0.95 1.3 0.0 0.8 1.3 0.0 0.8 2.0 0.65 2.0 0.65 +pair_coeff * * oxrna2/hbond seqdep 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 1 4 oxrna2/hbond seqdep 5.18928666388042 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 2 3 oxrna2/hbond seqdep 5.18928666388042 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 3 4 oxrna2/hbond seqdep 5.18928666388042 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff * * oxrna2/xstk 4.92690859644113 4.259 5.1108 3.57756 4.94044 2.25 0.505 0.58 1.7 1.266 0.68 1.7 1.266 0.68 1.7 0.309 0.68 1.7 0.309 0.68 +pair_coeff * * oxrna2/coaxstk 6.57330882442206 4.259 5.1108 3.57756 4.94044 2.0 2.592 0.65 1.3 0.151 0.8 0.9 0.685 0.95 0.9 0.685 0.95 2.0 -0.65 2.0 -0.65 +pair_coeff * * oxrna2/dh ${T} ${rhos} 1.02455 +pair_coeff * * oxrna2/dh 300 ${rhos} 1.02455 +pair_coeff * * oxrna2/dh 300 0.5 1.02455 + +# NVE ensemble +fix 1 all nve/asphere +#fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10 + +timestep 0.01706 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 32.4 + +compute quat all property/atom quatw quati quatj quatk + +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}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.2.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 1000000 Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes @@ -68,11 +144,7 @@ Neighbor list info ... pair build: copy stencil: none bin: none -Setting up Verlet run ... - Unit style : real - Current step : 0 - Time step : 0.01706 -WARNING: Communication cutoff adjusted to 36.640032409886274 (src/comm.cpp:739) +WARNING: Communication cutoff adjusted to 36.640032409886274 (../comm.cpp:739) 0 ekin = 16.1203242878408 | erot = 16.6982509426318 | epot = -66.3830249260541 | etot = -33.5644496955815 Per MPI rank memory allocation (min/avg/max) = 7.592 | 7.592 | 7.592 Mbytes Step Temp E_pair E_mol TotEng Press Volume @@ -1078,21 +1150,21 @@ Per MPI rank memory allocation (min/avg/max) = 7.592 | 7.592 | 7.592 Mbytes 999000 ekin = 15.0427312776222 | erot = 23.657392608768 | epot = -72.2645746968681 | etot = -33.5644508104779 1000000 ekin = 15.613660129969 | erot = 24.1382006023969 | epot = -73.3163115458147 | etot = -33.5644508134487 1000000 349.20396 -76.691733 3.375421 -57.702651 -0.00024160068 39304000 -Loop time of 19.2077 on 1 procs for 1000000 steps with 16 atoms +Loop time of 31.1467 on 1 procs for 1000000 steps with 16 atoms -Performance: 76.739 ns/day, 0.313 hours/ns, 52062.405 timesteps/s, 832.998 katom-step/s -99.8% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 47.324 ns/day, 0.507 hours/ns, 32106.084 timesteps/s, 513.697 katom-step/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 | 16.095 | 16.095 | 16.095 | 0.0 | 83.79 -Bond | 0.6748 | 0.6748 | 0.6748 | 0.0 | 3.51 -Neigh | 0.007855 | 0.007855 | 0.007855 | 0.0 | 0.04 -Comm | 0.27635 | 0.27635 | 0.27635 | 0.0 | 1.44 -Output | 0.15161 | 0.15161 | 0.15161 | 0.0 | 0.79 -Modify | 1.7313 | 1.7313 | 1.7313 | 0.0 | 9.01 -Other | | 0.2709 | | | 1.41 +Pair | 26.515 | 26.515 | 26.515 | 0.0 | 85.13 +Bond | 1.0244 | 1.0244 | 1.0244 | 0.0 | 3.29 +Neigh | 0.019506 | 0.019506 | 0.019506 | 0.0 | 0.06 +Comm | 0.45429 | 0.45429 | 0.45429 | 0.0 | 1.46 +Output | 0.22043 | 0.22043 | 0.22043 | 0.0 | 0.71 +Modify | 2.4659 | 2.4659 | 2.4659 | 0.0 | 7.92 +Other | | 0.4469 | | | 1.43 Nlocal: 16 ave 16 max 16 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -1106,6 +1178,10 @@ Ave neighs/atom = 6.6875 Ave special neighs/atom = 3.75 Neighbor list builds = 1000 Dangerous builds = 0 + +write_data last_config.${number}.* nocoeff +write_data last_config.2.* nocoeff System init for write_data ... Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule -Total wall time: 0:00:19 +#write_restart last_config.${number}.* +Total wall time: 0:00:31 diff --git a/examples/PACKAGES/cgdna/examples/real_units/oxRNA2/duplex2/log.19May24.duplex2.g++.4 b/examples/PACKAGES/cgdna/examples/real_units/oxRNA2/duplex2/log.22May24.duplex2.g++.4 similarity index 95% rename from examples/PACKAGES/cgdna/examples/real_units/oxRNA2/duplex2/log.19May24.duplex2.g++.4 rename to examples/PACKAGES/cgdna/examples/real_units/oxRNA2/duplex2/log.22May24.duplex2.g++.4 index 794ac22a91..81f7f1cafc 100644 --- a/examples/PACKAGES/cgdna/examples/real_units/oxRNA2/duplex2/log.19May24.duplex2.g++.4 +++ b/examples/PACKAGES/cgdna/examples/real_units/oxRNA2/duplex2/log.22May24.duplex2.g++.4 @@ -1,6 +1,28 @@ -LAMMPS (17 Apr 2024) - using 1 OpenMP thread(s) per MPI task -WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:132) +LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-174-g749e259294-modified) +# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19 +variable number equal 2 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 300.0 +variable rhos equal 0.5 + +units real + +dimension 3 + +newton on + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (../atom_vec_hybrid.cpp:132) +atom_modify sort 0 8.518 + +# Pair interactions require lists of neighbours to be calculated +neighbor 17.036 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex2 Reading data file ... orthogonal box = (-170 -170 -170) to (170 170 170) 1 by 2 by 2 MPI processor grid @@ -23,10 +45,19 @@ Finding 1-2 1-3 1-4 neighbors ... 4 = max # of 1-4 neighbors 6 = max # of special neighbors special bonds CPU = 0.001 seconds - read_data CPU = 0.008 seconds + read_data CPU = 0.011 seconds + +set atom * mass 315.8376 Setting atom values ... 16 settings made for mass + +group all type 1 4 16 atoms in group all + +# oxRNA2 bond interactions - FENE backbone +bond_style oxrna2/fene +bond_coeff * 11.92337812042065 2.1295 6.482800913 +special_bonds lj 0 1 1 Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 1 1 special bond factors coul: 0 0 0 @@ -35,6 +66,51 @@ Finding 1-2 1-3 1-4 neighbors ... 4 = max # of 1-4 neighbors 6 = max # of special neighbors special bonds CPU = 0.000 seconds + +# oxRNA2 pair interactions +pair_style hybrid/overlay oxrna2/excv oxrna2/stk oxrna2/hbond oxrna2/xstk oxrna2/coaxstk oxrna2/dh +pair_coeff * * oxrna2/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576 +pair_coeff * * oxrna2/stk seqdep ${T} 8.35864576375849 0.005504556 0.70439070204273 3.66274 7.92174 2.9813 6.64404 0.9 0.0 0.95 0.9 0.0 0.95 1.3 0.0 0.8 1.3 0.0 0.8 2.0 0.65 2.0 0.65 +pair_coeff * * oxrna2/stk seqdep 300 8.35864576375849 0.005504556 0.70439070204273 3.66274 7.92174 2.9813 6.64404 0.9 0.0 0.95 0.9 0.0 0.95 1.3 0.0 0.8 1.3 0.0 0.8 2.0 0.65 2.0 0.65 +pair_coeff * * oxrna2/hbond seqdep 0.0 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 1 4 oxrna2/hbond seqdep 5.18928666388042 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 2 3 oxrna2/hbond seqdep 5.18928666388042 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 3 4 oxrna2/hbond seqdep 5.18928666388042 0.93918760272364 3.4072 6.3885 2.89612 5.9626 1.5 0.0 0.7 1.5 0.0 0.7 1.5 0.0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff * * oxrna2/xstk 4.92690859644113 4.259 5.1108 3.57756 4.94044 2.25 0.505 0.58 1.7 1.266 0.68 1.7 1.266 0.68 1.7 0.309 0.68 1.7 0.309 0.68 +pair_coeff * * oxrna2/coaxstk 6.57330882442206 4.259 5.1108 3.57756 4.94044 2.0 2.592 0.65 1.3 0.151 0.8 0.9 0.685 0.95 0.9 0.685 0.95 2.0 -0.65 2.0 -0.65 +pair_coeff * * oxrna2/dh ${T} ${rhos} 1.02455 +pair_coeff * * oxrna2/dh 300 ${rhos} 1.02455 +pair_coeff * * oxrna2/dh 300 0.5 1.02455 + +# NVE ensemble +fix 1 all nve/asphere +#fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10 + +timestep 0.01706 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 32.4 + +compute quat all property/atom quatw quati quatj quatk + +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}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.${number}.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump out all custom 1000 out.2.lammpstrj id mol type x y z ix iy iz vx vy vz c_quat[1] c_quat[2] c_quat[3] c_quat[4] angmomx angmomy angmomz +dump_modify out sort id +dump_modify out format line "%d %d %d %22.15le %22.15le %22.15le %d %d %d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le" + +run 1000000 Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes @@ -68,11 +144,7 @@ Neighbor list info ... pair build: copy stencil: none bin: none -Setting up Verlet run ... - Unit style : real - Current step : 0 - Time step : 0.01706 -WARNING: Communication cutoff adjusted to 36.640032409886274 (src/comm.cpp:739) +WARNING: Communication cutoff adjusted to 36.640032409886274 (../comm.cpp:739) 0 ekin = 16.1203242878408 | erot = 16.6982509426318 | epot = -66.3830249260541 | etot = -33.5644496955815 Per MPI rank memory allocation (min/avg/max) = 7.577 | 7.606 | 7.69 Mbytes Step Temp E_pair E_mol TotEng Press Volume @@ -1078,21 +1150,21 @@ Per MPI rank memory allocation (min/avg/max) = 7.577 | 7.606 | 7.69 Mbytes 999000 ekin = 15.04273129669 | erot = 23.6573925697404 | epot = -72.2645746768899 | etot = -33.5644508104595 1000000 ekin = 15.6136601549948 | erot = 24.1382005377538 | epot = -73.31631150618 | etot = -33.5644508134314 1000000 349.20396 -76.691733 3.375421 -57.702651 -0.00024160018 39304000 -Loop time of 14.7322 on 4 procs for 1000000 steps with 16 atoms +Loop time of 24.0071 on 4 procs for 1000000 steps with 16 atoms -Performance: 100.052 ns/day, 0.240 hours/ns, 67878.359 timesteps/s, 1.086 Matom-step/s -99.9% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 61.398 ns/day, 0.391 hours/ns, 41654.420 timesteps/s, 666.471 katom-step/s +99.4% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 4.9563 | 7.0753 | 8.4914 | 52.5 | 48.03 -Bond | 0.16693 | 0.26884 | 0.34644 | 12.5 | 1.82 -Neigh | 0.004684 | 0.00475 | 0.004817 | 0.1 | 0.03 -Comm | 3.9378 | 5.5096 | 7.8538 | 63.4 | 37.40 -Output | 0.065585 | 0.069947 | 0.079293 | 2.1 | 0.47 -Modify | 0.59102 | 0.65384 | 0.71706 | 6.6 | 4.44 -Other | | 1.15 | | | 7.81 +Pair | 8.0729 | 11.462 | 13.699 | 68.6 | 47.74 +Bond | 0.30957 | 0.43359 | 0.52757 | 12.0 | 1.81 +Neigh | 0.011335 | 0.011428 | 0.011526 | 0.1 | 0.05 +Comm | 6.994 | 9.2216 | 12.853 | 77.8 | 38.41 +Output | 0.090149 | 0.096079 | 0.10876 | 2.4 | 0.40 +Modify | 0.843 | 0.94516 | 1.0713 | 9.1 | 3.94 +Other | | 1.838 | | | 7.65 Nlocal: 4 ave 4 max 4 min Histogram: 4 0 0 0 0 0 0 0 0 0 @@ -1106,6 +1178,10 @@ Ave neighs/atom = 6.6875 Ave special neighs/atom = 3.75 Neighbor list builds = 1000 Dangerous builds = 0 + +write_data last_config.${number}.* nocoeff +write_data last_config.2.* nocoeff System init for write_data ... Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule -Total wall time: 0:00:14 +#write_restart last_config.${number}.* +Total wall time: 0:00:24 diff --git a/examples/PACKAGES/cgdna/examples/test.sh b/examples/PACKAGES/cgdna/examples/test.sh index 2d03dd522b..11b02ac693 100755 --- a/examples/PACKAGES/cgdna/examples/test.sh +++ b/examples/PACKAGES/cgdna/examples/test.sh @@ -1,11 +1,11 @@ #! /bin/bash -DATE='15May24' +DATE='22May24' TOL=1e-8 LMPDIR=/Users/ohenrich/Work/code/lammps SRCDIR=$LMPDIR/src -EXDIR=$LMPDIR/examples/PACKAGES/cgdna/examples +EXDIR=$LMPDIR/examples/PACKAGES/cgdna/examples/lj_units if [ $# -eq 1 ] && [ $1 = run ]; then echo '# Compiling executable in' $SRCDIR | tee -a $EXDIR/test.log