Updated tests to contain full stdout
This commit is contained in:
Oliver Henrich
@ -1,6 +1,27 @@
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LAMMPS (17 Apr 2024)
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LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-174-g749e259294-modified)
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using 1 OpenMP thread(s) per MPI task
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# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19
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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)
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variable number equal 1
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variable ofreq equal 1000
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variable efreq equal 1000
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variable T equal 300.0
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units real
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dimension 3
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newton on
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boundary p p p
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atom_style hybrid bond ellipsoid oxdna
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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)
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atom_modify sort 0 8.518
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# Pair interactions require lists of neighbours to be calculated
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neighbor 17.036 bin
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neigh_modify every 1 delay 0 check yes
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read_data data.duplex1
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Reading data file ...
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Reading data file ...
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orthogonal box = (-170 -170 -170) to (170 170 170)
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orthogonal box = (-170 -170 -170) to (170 170 170)
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1 by 1 by 1 MPI processor grid
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1 by 1 by 1 MPI processor grid
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@ -23,10 +44,19 @@ Finding 1-2 1-3 1-4 neighbors ...
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2 = max # of 1-4 neighbors
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2 = max # of 1-4 neighbors
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4 = max # of special neighbors
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4 = max # of special neighbors
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special bonds CPU = 0.000 seconds
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special bonds CPU = 0.000 seconds
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read_data CPU = 0.005 seconds
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read_data CPU = 0.009 seconds
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set atom * mass 315.8376
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Setting atom values ...
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Setting atom values ...
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10 settings made for mass
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10 settings made for mass
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group all type 1 4
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10 atoms in group all
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10 atoms in group all
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# oxDNA bond interactions - FENE backbone
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bond_style oxdna/fene
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bond_coeff * 11.92337812042065 2.1295 6.409795
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special_bonds lj 0 1 1
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Finding 1-2 1-3 1-4 neighbors ...
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 1 1
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special bond factors lj: 0 1 1
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special bond factors coul: 0 0 0
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special bond factors coul: 0 0 0
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@ -35,6 +65,47 @@ Finding 1-2 1-3 1-4 neighbors ...
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2 = max # of 1-4 neighbors
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2 = max # of 1-4 neighbors
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4 = max # of special neighbors
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4 = max # of special neighbors
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special bonds CPU = 0.000 seconds
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special bonds CPU = 0.000 seconds
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# oxDNA pair interactions
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pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
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pair_coeff * * oxdna/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576
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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
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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
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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
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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
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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
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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
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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
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# NVE ensemble
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fix 1 all nve/asphere
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#fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10
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timestep 0.01706
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#comm_style tiled
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fix 3 all balance 1000 1.03 shift xyz 10 1.03
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comm_modify cutoff 32.4
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compute quat all property/atom quatw quati quatj quatk
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compute erot all erotate/asphere
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compute ekin all ke
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compute epot all pe
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variable erot equal c_erot
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variable ekin equal c_ekin
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variable epot equal c_epot
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variable etot equal c_erot+c_ekin+c_epot
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fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
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fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
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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
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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
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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
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dump_modify out sort id
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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"
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run 1000000
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Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
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Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
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Neighbor list info ...
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Neighbor list info ...
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update: every = 1 steps, delay = 0 steps, check = yes
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update: every = 1 steps, delay = 0 steps, check = yes
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@ -63,10 +134,6 @@ Neighbor list info ...
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pair build: copy
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pair build: copy
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stencil: none
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stencil: none
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bin: none
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bin: none
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Setting up Verlet run ...
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Unit style : real
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Current step : 0
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Time step : 0.01706
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0 ekin = 6.60687273927977 | erot = 16.7817849122513 | epot = -77.8453746587949 | etot = -54.4567170072638
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0 ekin = 6.60687273927977 | erot = 16.7817849122513 | epot = -77.8453746587949 | etot = -54.4567170072638
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Per MPI rank memory allocation (min/avg/max) = 7.196 | 7.196 | 7.196 Mbytes
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Per MPI rank memory allocation (min/avg/max) = 7.196 | 7.196 | 7.196 Mbytes
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Step Temp E_pair E_mol TotEng Press Volume
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Step Temp E_pair E_mol TotEng Press Volume
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@ -1072,21 +1139,21 @@ Per MPI rank memory allocation (min/avg/max) = 7.196 | 7.196 | 7.196 Mbytes
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999000 ekin = 9.43365149698941 | erot = 9.73053828894017 | epot = -73.6209070698904 | etot = -54.4567172839608
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999000 ekin = 9.43365149698941 | erot = 9.73053828894017 | epot = -73.6209070698904 | etot = -54.4567172839608
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1000000 ekin = 9.45092723111945 | erot = 9.62486149925983 | epot = -73.532506015067 | etot = -54.4567172846877
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1000000 ekin = 9.45092723111945 | erot = 9.62486149925983 | epot = -73.532506015067 | etot = -54.4567172846877
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1000000 352.2878 -75.545604 2.0130979 -64.081579 -0.0098473389 39304000
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1000000 352.2878 -75.545604 2.0130979 -64.081579 -0.0098473389 39304000
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Loop time of 9.76856 on 1 procs for 1000000 steps with 10 atoms
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Loop time of 16.8981 on 1 procs for 1000000 steps with 10 atoms
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Performance: 150.891 ns/day, 0.159 hours/ns, 102369.234 timesteps/s, 1.024 Matom-step/s
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Performance: 87.228 ns/day, 0.275 hours/ns, 59178.314 timesteps/s, 591.783 katom-step/s
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99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
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99.6% CPU use with 1 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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---------------------------------------------------------------
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Pair | 7.5788 | 7.5788 | 7.5788 | 0.0 | 77.58
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Pair | 13.505 | 13.505 | 13.505 | 0.0 | 79.92
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Bond | 0.42182 | 0.42182 | 0.42182 | 0.0 | 4.32
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Bond | 0.61276 | 0.61276 | 0.61276 | 0.0 | 3.63
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Neigh | 0.012447 | 0.012447 | 0.012447 | 0.0 | 0.13
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Neigh | 0.038787 | 0.038787 | 0.038787 | 0.0 | 0.23
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Comm | 0.24821 | 0.24821 | 0.24821 | 0.0 | 2.54
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Comm | 0.46975 | 0.46975 | 0.46975 | 0.0 | 2.78
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Output | 0.10868 | 0.10868 | 0.10868 | 0.0 | 1.11
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Output | 0.12918 | 0.12918 | 0.12918 | 0.0 | 0.76
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Modify | 1.1076 | 1.1076 | 1.1076 | 0.0 | 11.34
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Modify | 1.6798 | 1.6798 | 1.6798 | 0.0 | 9.94
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Other | | 0.291 | | | 2.98
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Other | | 0.4627 | | | 2.74
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Nlocal: 10 ave 10 max 10 min
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Nlocal: 10 ave 10 max 10 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Histogram: 1 0 0 0 0 0 0 0 0 0
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@ -1100,6 +1167,10 @@ Ave neighs/atom = 3.7
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Ave special neighs/atom = 3.6
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Ave special neighs/atom = 3.6
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Neighbor list builds = 1000
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Neighbor list builds = 1000
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Dangerous builds = 0
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Dangerous builds = 0
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write_data last_config.${number}.* nocoeff
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write_data last_config.1.* nocoeff
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System init for write_data ...
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System init for write_data ...
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Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
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Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
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Total wall time: 0:00:09
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#write_restart last_config.${number}.*
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Total wall time: 0:00:16
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@ -1,6 +1,27 @@
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LAMMPS (17 Apr 2024)
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LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-174-g749e259294-modified)
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using 1 OpenMP thread(s) per MPI task
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# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19
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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)
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variable number equal 1
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variable ofreq equal 1000
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variable efreq equal 1000
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variable T equal 300.0
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units real
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dimension 3
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newton on
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boundary p p p
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atom_style hybrid bond ellipsoid oxdna
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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)
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atom_modify sort 0 8.518
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# Pair interactions require lists of neighbours to be calculated
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neighbor 17.036 bin
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neigh_modify every 1 delay 0 check yes
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read_data data.duplex1
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Reading data file ...
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Reading data file ...
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orthogonal box = (-170 -170 -170) to (170 170 170)
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orthogonal box = (-170 -170 -170) to (170 170 170)
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1 by 2 by 2 MPI processor grid
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1 by 2 by 2 MPI processor grid
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@ -23,10 +44,19 @@ Finding 1-2 1-3 1-4 neighbors ...
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2 = max # of 1-4 neighbors
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2 = max # of 1-4 neighbors
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4 = max # of special neighbors
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4 = max # of special neighbors
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special bonds CPU = 0.000 seconds
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special bonds CPU = 0.000 seconds
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read_data CPU = 0.007 seconds
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read_data CPU = 0.011 seconds
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set atom * mass 315.8376
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Setting atom values ...
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Setting atom values ...
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10 settings made for mass
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10 settings made for mass
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group all type 1 4
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10 atoms in group all
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10 atoms in group all
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# oxDNA bond interactions - FENE backbone
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bond_style oxdna/fene
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bond_coeff * 11.92337812042065 2.1295 6.409795
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special_bonds lj 0 1 1
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Finding 1-2 1-3 1-4 neighbors ...
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 1 1
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special bond factors lj: 0 1 1
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special bond factors coul: 0 0 0
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special bond factors coul: 0 0 0
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@ -35,6 +65,47 @@ Finding 1-2 1-3 1-4 neighbors ...
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2 = max # of 1-4 neighbors
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2 = max # of 1-4 neighbors
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4 = max # of special neighbors
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4 = max # of special neighbors
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special bonds CPU = 0.000 seconds
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special bonds CPU = 0.000 seconds
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# oxDNA pair interactions
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pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
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pair_coeff * * oxdna/excv 11.92337812042065 5.9626 5.74965 11.92337812042065 4.38677 4.259 11.92337812042065 2.81094 2.72576
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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
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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
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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
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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
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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
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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
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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
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# NVE ensemble
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fix 1 all nve/asphere
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#fix 2 all langevin ${T} ${T} 4265.0 457145 angmom 10
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timestep 0.01706
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#comm_style tiled
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fix 3 all balance 1000 1.03 shift xyz 10 1.03
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comm_modify cutoff 32.4
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||||||
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compute quat all property/atom quatw quati quatj quatk
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compute erot all erotate/asphere
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compute ekin all ke
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||||||
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compute epot all pe
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variable erot equal c_erot
|
||||||
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variable ekin equal c_ekin
|
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variable epot equal c_epot
|
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variable etot equal c_erot+c_ekin+c_epot
|
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fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||||
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fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||||
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|
||||||
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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
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||||||
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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
|
||||||
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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
|
||||||
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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
|
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
|
||||||
Neighbor list info ...
|
Neighbor list info ...
|
||||||
update: every = 1 steps, delay = 0 steps, check = yes
|
update: every = 1 steps, delay = 0 steps, check = yes
|
||||||
@ -63,10 +134,6 @@ Neighbor list info ...
|
|||||||
pair build: copy
|
pair build: copy
|
||||||
stencil: none
|
stencil: none
|
||||||
bin: 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
|
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
|
Per MPI rank memory allocation (min/avg/max) = 7.105 | 7.11 | 7.116 Mbytes
|
||||||
Step Temp E_pair E_mol TotEng Press Volume
|
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
|
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 ekin = 9.45092723106241 | erot = 9.62486149933323 | epot = -73.5325060150984 | etot = -54.4567172847028
|
||||||
1000000 352.2878 -75.545604 2.0130979 -64.081579 -0.0098473389 39304000
|
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
|
Performance: 87.763 ns/day, 0.273 hours/ns, 59541.025 timesteps/s, 595.410 katom-step/s
|
||||||
99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
|
99.4% CPU use with 4 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
MPI task timing breakdown:
|
MPI task timing breakdown:
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
---------------------------------------------------------------
|
---------------------------------------------------------------
|
||||||
Pair | 3.3362 | 4.003 | 5.7128 | 49.6 | 39.66
|
Pair | 5.5941 | 6.7707 | 9.5516 | 62.7 | 40.31
|
||||||
Bond | 0.12031 | 0.17704 | 0.23635 | 10.9 | 1.75
|
Bond | 0.2092 | 0.2872 | 0.38189 | 13.0 | 1.71
|
||||||
Neigh | 0.00676 | 0.006813 | 0.006854 | 0.0 | 0.07
|
Neigh | 0.018433 | 0.018502 | 0.018552 | 0.0 | 0.11
|
||||||
Comm | 2.2652 | 4.2367 | 5.0428 | 55.8 | 41.98
|
Comm | 3.8835 | 7.1053 | 8.5337 | 70.8 | 42.31
|
||||||
Output | 0.062416 | 0.073606 | 0.1045 | 6.6 | 0.73
|
Output | 0.073525 | 0.077664 | 0.085514 | 1.7 | 0.46
|
||||||
Modify | 0.36934 | 0.44375 | 0.5325 | 11.1 | 4.40
|
Modify | 0.58013 | 0.70982 | 0.8931 | 15.7 | 4.23
|
||||||
Other | | 1.152 | | | 11.41
|
Other | | 1.826 | | | 10.87
|
||||||
|
|
||||||
Nlocal: 2.5 ave 4 max 1 min
|
Nlocal: 2.5 ave 4 max 1 min
|
||||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
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
|
Ave special neighs/atom = 3.6
|
||||||
Neighbor list builds = 1000
|
Neighbor list builds = 1000
|
||||||
Dangerous builds = 0
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
write_data last_config.${number}.* nocoeff
|
||||||
|
write_data last_config.1.* nocoeff
|
||||||
System init for write_data ...
|
System init for write_data ...
|
||||||
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
|
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
|
||||||
@ -1,6 +1,27 @@
|
|||||||
LAMMPS (17 Apr 2024)
|
LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-174-g749e259294-modified)
|
||||||
using 1 OpenMP thread(s) per MPI task
|
# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19
|
||||||
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)
|
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 ...
|
Reading data file ...
|
||||||
orthogonal box = (-170 -170 -170) to (170 170 170)
|
orthogonal box = (-170 -170 -170) to (170 170 170)
|
||||||
1 by 1 by 1 MPI processor grid
|
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
|
4 = max # of 1-4 neighbors
|
||||||
6 = max # of special neighbors
|
6 = max # of special neighbors
|
||||||
special bonds CPU = 0.000 seconds
|
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 ...
|
Setting atom values ...
|
||||||
16 settings made for mass
|
16 settings made for mass
|
||||||
|
|
||||||
|
group all type 1 4
|
||||||
16 atoms in group all
|
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 ...
|
Finding 1-2 1-3 1-4 neighbors ...
|
||||||
special bond factors lj: 0 1 1
|
special bond factors lj: 0 1 1
|
||||||
special bond factors coul: 0 0 0
|
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
|
4 = max # of 1-4 neighbors
|
||||||
6 = max # of special neighbors
|
6 = max # of special neighbors
|
||||||
special bonds CPU = 0.000 seconds
|
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
|
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
|
||||||
Neighbor list info ...
|
Neighbor list info ...
|
||||||
update: every = 1 steps, delay = 0 steps, check = yes
|
update: every = 1 steps, delay = 0 steps, check = yes
|
||||||
@ -63,10 +136,6 @@ Neighbor list info ...
|
|||||||
pair build: copy
|
pair build: copy
|
||||||
stencil: none
|
stencil: none
|
||||||
bin: 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
|
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
|
Per MPI rank memory allocation (min/avg/max) = 7.322 | 7.322 | 7.322 Mbytes
|
||||||
Step Temp E_pair E_mol TotEng Press Volume
|
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
|
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 ekin = 18.6583620145008 | erot = 16.6848586754118 | epot = -128.346967556883 | etot = -93.0037468669704
|
||||||
1000000 417.29959 -129.94144 1.5944718 -109.68861 0.062656806 39304000
|
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
|
Performance: 42.738 ns/day, 0.562 hours/ns, 28994.847 timesteps/s, 463.918 katom-step/s
|
||||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
99.2% CPU use with 1 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
MPI task timing breakdown:
|
MPI task timing breakdown:
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
---------------------------------------------------------------
|
---------------------------------------------------------------
|
||||||
Pair | 17.105 | 17.105 | 17.105 | 0.0 | 77.59
|
Pair | 27.385 | 27.385 | 27.385 | 0.0 | 79.40
|
||||||
Bond | 0.67238 | 0.67238 | 0.67238 | 0.0 | 3.05
|
Bond | 0.89821 | 0.89821 | 0.89821 | 0.0 | 2.60
|
||||||
Neigh | 0.016373 | 0.016373 | 0.016373 | 0.0 | 0.07
|
Neigh | 0.043138 | 0.043138 | 0.043138 | 0.0 | 0.13
|
||||||
Comm | 0.29298 | 0.29298 | 0.29298 | 0.0 | 1.33
|
Comm | 0.47566 | 0.47566 | 0.47566 | 0.0 | 1.38
|
||||||
Output | 0.12608 | 0.12608 | 0.12608 | 0.0 | 0.57
|
Output | 0.20876 | 0.20876 | 0.20876 | 0.0 | 0.61
|
||||||
Modify | 3.5001 | 3.5001 | 3.5001 | 0.0 | 15.88
|
Modify | 5.0059 | 5.0059 | 5.0059 | 0.0 | 14.51
|
||||||
Other | | 0.3318 | | | 1.51
|
Other | | 0.4721 | | | 1.37
|
||||||
|
|
||||||
Nlocal: 16 ave 16 max 16 min
|
Nlocal: 16 ave 16 max 16 min
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
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
|
Ave special neighs/atom = 3.75
|
||||||
Neighbor list builds = 1000
|
Neighbor list builds = 1000
|
||||||
Dangerous builds = 0
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
write_data last_config.${number}.* nocoeff
|
||||||
|
write_data last_config.2.* nocoeff
|
||||||
System init for write_data ...
|
System init for write_data ...
|
||||||
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
|
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
|
||||||
@ -1,6 +1,27 @@
|
|||||||
LAMMPS (17 Apr 2024)
|
LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-174-g749e259294-modified)
|
||||||
using 1 OpenMP thread(s) per MPI task
|
# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19
|
||||||
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)
|
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 ...
|
Reading data file ...
|
||||||
orthogonal box = (-170 -170 -170) to (170 170 170)
|
orthogonal box = (-170 -170 -170) to (170 170 170)
|
||||||
1 by 2 by 2 MPI processor grid
|
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
|
4 = max # of 1-4 neighbors
|
||||||
6 = max # of special neighbors
|
6 = max # of special neighbors
|
||||||
special bonds CPU = 0.001 seconds
|
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 ...
|
Setting atom values ...
|
||||||
16 settings made for mass
|
16 settings made for mass
|
||||||
|
|
||||||
|
group all type 1 4
|
||||||
16 atoms in group all
|
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 ...
|
Finding 1-2 1-3 1-4 neighbors ...
|
||||||
special bond factors lj: 0 1 1
|
special bond factors lj: 0 1 1
|
||||||
special bond factors coul: 0 0 0
|
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
|
4 = max # of 1-4 neighbors
|
||||||
6 = max # of special neighbors
|
6 = max # of special neighbors
|
||||||
special bonds CPU = 0.000 seconds
|
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
|
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
|
||||||
Neighbor list info ...
|
Neighbor list info ...
|
||||||
update: every = 1 steps, delay = 0 steps, check = yes
|
update: every = 1 steps, delay = 0 steps, check = yes
|
||||||
@ -63,10 +136,6 @@ Neighbor list info ...
|
|||||||
pair build: copy
|
pair build: copy
|
||||||
stencil: none
|
stencil: none
|
||||||
bin: 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
|
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
|
Per MPI rank memory allocation (min/avg/max) = 7.232 | 7.264 | 7.344 Mbytes
|
||||||
Step Temp E_pair E_mol TotEng Press Volume
|
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
|
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 ekin = 16.4176868113516 | erot = 10.505891115617 | epot = -130.086633390017 | etot = -103.163055463049
|
||||||
1000000 367.18625 -134.96443 4.8777959 -113.66895 -0.029625089 39304000
|
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
|
Performance: 55.825 ns/day, 0.430 hours/ns, 37873.477 timesteps/s, 605.976 katom-step/s
|
||||||
99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
|
99.4% CPU use with 4 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
MPI task timing breakdown:
|
MPI task timing breakdown:
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
---------------------------------------------------------------
|
---------------------------------------------------------------
|
||||||
Pair | 5.4709 | 7.3456 | 10.788 | 75.7 | 41.18
|
Pair | 8.0347 | 10.957 | 16.143 | 93.9 | 41.50
|
||||||
Bond | 0.25222 | 0.29369 | 0.34982 | 7.2 | 1.65
|
Bond | 0.3256 | 0.38079 | 0.42679 | 6.8 | 1.44
|
||||||
Neigh | 0.009763 | 0.0099055 | 0.010039 | 0.1 | 0.06
|
Neigh | 0.021142 | 0.021313 | 0.021466 | 0.1 | 0.08
|
||||||
Comm | 3.6693 | 7.3401 | 9.3552 | 81.3 | 41.15
|
Comm | 5.5113 | 11.003 | 14.141 | 100.0 | 41.67
|
||||||
Output | 0.074481 | 0.079893 | 0.09183 | 2.5 | 0.45
|
Output | 0.091898 | 0.097995 | 0.11134 | 2.5 | 0.37
|
||||||
Modify | 1.0375 | 1.2928 | 1.4979 | 18.1 | 7.25
|
Modify | 1.3872 | 1.6961 | 1.9792 | 21.0 | 6.42
|
||||||
Other | | 1.475 | | | 8.27
|
Other | | 2.247 | | | 8.51
|
||||||
|
|
||||||
Nlocal: 4 ave 6 max 2 min
|
Nlocal: 4 ave 6 max 2 min
|
||||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
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
|
Ave special neighs/atom = 3.75
|
||||||
Neighbor list builds = 1000
|
Neighbor list builds = 1000
|
||||||
Dangerous builds = 0
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
write_data last_config.${number}.* nocoeff
|
||||||
|
write_data last_config.2.* nocoeff
|
||||||
System init for write_data ...
|
System init for write_data ...
|
||||||
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
|
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
|
||||||
@ -1,6 +1,28 @@
|
|||||||
LAMMPS (17 Apr 2024)
|
LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-174-g749e259294-modified)
|
||||||
using 1 OpenMP thread(s) per MPI task
|
# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19
|
||||||
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)
|
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 ...
|
Reading data file ...
|
||||||
orthogonal box = (0 0 0) to (851 851 851)
|
orthogonal box = (0 0 0) to (851 851 851)
|
||||||
1 by 1 by 1 MPI processor grid
|
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
|
4 = max # of 1-4 neighbors
|
||||||
6 = max # of special neighbors
|
6 = max # of special neighbors
|
||||||
special bonds CPU = 0.000 seconds
|
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 ...
|
Setting atom values ...
|
||||||
148 settings made for mass
|
148 settings made for mass
|
||||||
|
|
||||||
|
group all type 1 4
|
||||||
148 atoms in group all
|
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 ...
|
Finding 1-2 1-3 1-4 neighbors ...
|
||||||
special bond factors lj: 0 1 1
|
special bond factors lj: 0 1 1
|
||||||
special bond factors coul: 0 0 0
|
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
|
4 = max # of 1-4 neighbors
|
||||||
6 = max # of special neighbors
|
6 = max # of special neighbors
|
||||||
special bonds CPU = 0.000 seconds
|
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
|
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
|
||||||
Neighbor list info ...
|
Neighbor list info ...
|
||||||
update: every = 1 steps, delay = 0 steps, check = yes
|
update: every = 1 steps, delay = 0 steps, check = yes
|
||||||
@ -68,11 +143,7 @@ Neighbor list info ...
|
|||||||
pair build: copy
|
pair build: copy
|
||||||
stencil: none
|
stencil: none
|
||||||
bin: none
|
bin: none
|
||||||
Setting up Verlet run ...
|
WARNING: Communication cutoff adjusted to 48.03269686950012 (../comm.cpp:739)
|
||||||
Unit style : real
|
|
||||||
Current step : 0
|
|
||||||
Time step : 0.01706
|
|
||||||
WARNING: Communication cutoff adjusted to 48.03269686950012 (src/comm.cpp:739)
|
|
||||||
0 ekin = 122.015812851425 | erot = 125.402528675609 | epot = -1325.18559882055 | etot = -1077.76725729351
|
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
|
Per MPI rank memory allocation (min/avg/max) = 7.806 | 7.806 | 7.806 Mbytes
|
||||||
Step Temp E_pair E_mol TotEng Press Volume
|
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
|
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 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
|
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
|
Performance: 1.730 ns/day, 13.875 hours/ns, 1173.528 timesteps/s, 173.682 katom-step/s
|
||||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
99.8% CPU use with 1 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
MPI task timing breakdown:
|
MPI task timing breakdown:
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
---------------------------------------------------------------
|
---------------------------------------------------------------
|
||||||
Pair | 52.073 | 52.073 | 52.073 | 0.0 | 95.35
|
Pair | 81.71 | 81.71 | 81.71 | 0.0 | 95.89
|
||||||
Bond | 0.74079 | 0.74079 | 0.74079 | 0.0 | 1.36
|
Bond | 1.103 | 1.103 | 1.103 | 0.0 | 1.29
|
||||||
Neigh | 0.010107 | 0.010107 | 0.010107 | 0.0 | 0.02
|
Neigh | 0.017589 | 0.017589 | 0.017589 | 0.0 | 0.02
|
||||||
Comm | 0.040371 | 0.040371 | 0.040371 | 0.0 | 0.07
|
Comm | 0.055508 | 0.055508 | 0.055508 | 0.0 | 0.07
|
||||||
Output | 0.097636 | 0.097636 | 0.097636 | 0.0 | 0.18
|
Output | 0.1581 | 0.1581 | 0.1581 | 0.0 | 0.19
|
||||||
Modify | 1.5841 | 1.5841 | 1.5841 | 0.0 | 2.90
|
Modify | 2.0369 | 2.0369 | 2.0369 | 0.0 | 2.39
|
||||||
Other | | 0.06901 | | | 0.13
|
Other | | 0.132 | | | 0.15
|
||||||
|
|
||||||
Nlocal: 148 ave 148 max 148 min
|
Nlocal: 148 ave 148 max 148 min
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
@ -206,6 +277,10 @@ Ave neighs/atom = 28.371622
|
|||||||
Ave special neighs/atom = 6
|
Ave special neighs/atom = 6
|
||||||
Neighbor list builds = 100
|
Neighbor list builds = 100
|
||||||
Dangerous builds = 0
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
write_data last_config.${number}.* nocoeff
|
||||||
|
write_data last_config.5.* nocoeff
|
||||||
System init for write_data ...
|
System init for write_data ...
|
||||||
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
|
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
|
||||||
@ -1,6 +1,28 @@
|
|||||||
LAMMPS (17 Apr 2024)
|
LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-174-g749e259294-modified)
|
||||||
using 1 OpenMP thread(s) per MPI task
|
# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19
|
||||||
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)
|
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 ...
|
Reading data file ...
|
||||||
orthogonal box = (0 0 0) to (851 851 851)
|
orthogonal box = (0 0 0) to (851 851 851)
|
||||||
1 by 2 by 2 MPI processor grid
|
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
|
4 = max # of 1-4 neighbors
|
||||||
6 = max # of special neighbors
|
6 = max # of special neighbors
|
||||||
special bonds CPU = 0.001 seconds
|
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 ...
|
Setting atom values ...
|
||||||
148 settings made for mass
|
148 settings made for mass
|
||||||
|
|
||||||
|
group all type 1 4
|
||||||
148 atoms in group all
|
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 ...
|
Finding 1-2 1-3 1-4 neighbors ...
|
||||||
special bond factors lj: 0 1 1
|
special bond factors lj: 0 1 1
|
||||||
special bond factors coul: 0 0 0
|
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
|
4 = max # of 1-4 neighbors
|
||||||
6 = max # of special neighbors
|
6 = max # of special neighbors
|
||||||
special bonds CPU = 0.000 seconds
|
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
|
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
|
||||||
Neighbor list info ...
|
Neighbor list info ...
|
||||||
update: every = 1 steps, delay = 0 steps, check = yes
|
update: every = 1 steps, delay = 0 steps, check = yes
|
||||||
@ -68,11 +143,7 @@ Neighbor list info ...
|
|||||||
pair build: copy
|
pair build: copy
|
||||||
stencil: none
|
stencil: none
|
||||||
bin: none
|
bin: none
|
||||||
Setting up Verlet run ...
|
WARNING: Communication cutoff adjusted to 48.03269686950012 (../comm.cpp:739)
|
||||||
Unit style : real
|
|
||||||
Current step : 0
|
|
||||||
Time step : 0.01706
|
|
||||||
WARNING: Communication cutoff adjusted to 48.03269686950012 (src/comm.cpp:739)
|
|
||||||
0 ekin = 122.015812851425 | erot = 125.402528675609 | epot = -1325.18559882055 | etot = -1077.76725729351
|
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
|
Per MPI rank memory allocation (min/avg/max) = 7.619 | 7.668 | 7.742 Mbytes
|
||||||
Step Temp E_pair E_mol TotEng Press Volume
|
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
|
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 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
|
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
|
Performance: 4.877 ns/day, 4.921 hours/ns, 3308.461 timesteps/s, 489.652 katom-step/s
|
||||||
99.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
99.6% CPU use with 4 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
MPI task timing breakdown:
|
MPI task timing breakdown:
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
---------------------------------------------------------------
|
---------------------------------------------------------------
|
||||||
Pair | 11.553 | 15.593 | 18.744 | 74.9 | 74.65
|
Pair | 16.766 | 22.691 | 26.962 | 89.3 | 75.07
|
||||||
Bond | 0.22099 | 0.22585 | 0.22864 | 0.6 | 1.08
|
Bond | 0.28821 | 0.30757 | 0.32075 | 2.3 | 1.02
|
||||||
Neigh | 0.004397 | 0.0044708 | 0.004533 | 0.1 | 0.02
|
Neigh | 0.008451 | 0.008527 | 0.008607 | 0.1 | 0.03
|
||||||
Comm | 1.2201 | 4.3856 | 8.4421 | 141.8 | 21.00
|
Comm | 2.0101 | 6.3007 | 12.277 | 170.6 | 20.85
|
||||||
Output | 0.035571 | 0.037478 | 0.038787 | 0.7 | 0.18
|
Output | 0.051655 | 0.054646 | 0.056776 | 0.9 | 0.18
|
||||||
Modify | 0.45808 | 0.46752 | 0.47581 | 1.0 | 2.24
|
Modify | 0.53953 | 0.56983 | 0.63795 | 5.3 | 1.89
|
||||||
Other | | 0.1748 | | | 0.84
|
Other | | 0.2934 | | | 0.97
|
||||||
|
|
||||||
Nlocal: 37 ave 38 max 36 min
|
Nlocal: 37 ave 38 max 36 min
|
||||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||||
@ -206,6 +277,10 @@ Ave neighs/atom = 28.371622
|
|||||||
Ave special neighs/atom = 6
|
Ave special neighs/atom = 6
|
||||||
Neighbor list builds = 100
|
Neighbor list builds = 100
|
||||||
Dangerous builds = 0
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
write_data last_config.${number}.* nocoeff
|
||||||
|
write_data last_config.5.* nocoeff
|
||||||
System init for write_data ...
|
System init for write_data ...
|
||||||
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
|
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
|
||||||
@ -1,6 +1,28 @@
|
|||||||
LAMMPS (17 Apr 2024)
|
LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-174-g749e259294-modified)
|
||||||
using 1 OpenMP thread(s) per MPI task
|
# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19
|
||||||
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)
|
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 ...
|
Reading data file ...
|
||||||
orthogonal box = (-170 -170 -170) to (170 170 170)
|
orthogonal box = (-170 -170 -170) to (170 170 170)
|
||||||
1 by 1 by 1 MPI processor grid
|
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
|
2 = max # of 1-4 neighbors
|
||||||
4 = max # of special neighbors
|
4 = max # of special neighbors
|
||||||
special bonds CPU = 0.000 seconds
|
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 ...
|
Setting atom values ...
|
||||||
10 settings made for mass
|
10 settings made for mass
|
||||||
|
|
||||||
|
group all type 1 4
|
||||||
10 atoms in group all
|
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 ...
|
Finding 1-2 1-3 1-4 neighbors ...
|
||||||
special bond factors lj: 0 1 1
|
special bond factors lj: 0 1 1
|
||||||
special bond factors coul: 0 0 0
|
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
|
2 = max # of 1-4 neighbors
|
||||||
4 = max # of special neighbors
|
4 = max # of special neighbors
|
||||||
special bonds CPU = 0.000 seconds
|
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
|
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
|
||||||
Neighbor list info ...
|
Neighbor list info ...
|
||||||
update: every = 1 steps, delay = 0 steps, check = yes
|
update: every = 1 steps, delay = 0 steps, check = yes
|
||||||
@ -68,11 +143,7 @@ Neighbor list info ...
|
|||||||
pair build: copy
|
pair build: copy
|
||||||
stencil: none
|
stencil: none
|
||||||
bin: none
|
bin: none
|
||||||
Setting up Verlet run ...
|
WARNING: Communication cutoff adjusted to 48.03269686950012 (../comm.cpp:739)
|
||||||
Unit style : real
|
|
||||||
Current step : 0
|
|
||||||
Time step : 0.01706
|
|
||||||
WARNING: Communication cutoff adjusted to 48.03269686950012 (src/comm.cpp:739)
|
|
||||||
0 ekin = 6.60687273927977 | erot = 16.7817849122513 | epot = -73.3220946463642 | etot = -49.9334369948331
|
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
|
Per MPI rank memory allocation (min/avg/max) = 7.445 | 7.445 | 7.445 Mbytes
|
||||||
Step Temp E_pair E_mol TotEng Press Volume
|
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
|
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 ekin = 9.30950418584537 | erot = 13.3558388696135 | epot = -72.5987797643175 | etot = -49.9334367088586
|
||||||
1000000 347.01619 -80.374455 7.7756755 -63.289276 0.11518501 39304000
|
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
|
Performance: 76.341 ns/day, 0.314 hours/ns, 51792.277 timesteps/s, 517.923 katom-step/s
|
||||||
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
|
99.8% CPU use with 1 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
MPI task timing breakdown:
|
MPI task timing breakdown:
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
---------------------------------------------------------------
|
---------------------------------------------------------------
|
||||||
Pair | 10.471 | 10.471 | 10.471 | 0.0 | 80.68
|
Pair | 15.904 | 15.904 | 15.904 | 0.0 | 82.37
|
||||||
Bond | 0.50292 | 0.50292 | 0.50292 | 0.0 | 3.88
|
Bond | 0.68326 | 0.68326 | 0.68326 | 0.0 | 3.54
|
||||||
Neigh | 0.005498 | 0.005498 | 0.005498 | 0.0 | 0.04
|
Neigh | 0.011182 | 0.011182 | 0.011182 | 0.0 | 0.06
|
||||||
Comm | 0.29263 | 0.29263 | 0.29263 | 0.0 | 2.25
|
Comm | 0.45393 | 0.45393 | 0.45393 | 0.0 | 2.35
|
||||||
Output | 0.10128 | 0.10128 | 0.10128 | 0.0 | 0.78
|
Output | 0.12567 | 0.12567 | 0.12567 | 0.0 | 0.65
|
||||||
Modify | 1.2697 | 1.2697 | 1.2697 | 0.0 | 9.78
|
Modify | 1.6705 | 1.6705 | 1.6705 | 0.0 | 8.65
|
||||||
Other | | 0.3353 | | | 2.58
|
Other | | 0.459 | | | 2.38
|
||||||
|
|
||||||
Nlocal: 10 ave 10 max 10 min
|
Nlocal: 10 ave 10 max 10 min
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
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
|
Ave special neighs/atom = 3.6
|
||||||
Neighbor list builds = 1000
|
Neighbor list builds = 1000
|
||||||
Dangerous builds = 0
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
write_data last_config.${number}.* nocoeff
|
||||||
|
write_data last_config.1.* nocoeff
|
||||||
System init for write_data ...
|
System init for write_data ...
|
||||||
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
|
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
|
||||||
@ -1,6 +1,28 @@
|
|||||||
LAMMPS (17 Apr 2024)
|
LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-174-g749e259294-modified)
|
||||||
using 1 OpenMP thread(s) per MPI task
|
# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19
|
||||||
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)
|
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 ...
|
Reading data file ...
|
||||||
orthogonal box = (-170 -170 -170) to (170 170 170)
|
orthogonal box = (-170 -170 -170) to (170 170 170)
|
||||||
1 by 2 by 2 MPI processor grid
|
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
|
2 = max # of 1-4 neighbors
|
||||||
4 = max # of special neighbors
|
4 = max # of special neighbors
|
||||||
special bonds CPU = 0.001 seconds
|
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 ...
|
Setting atom values ...
|
||||||
10 settings made for mass
|
10 settings made for mass
|
||||||
|
|
||||||
|
group all type 1 4
|
||||||
10 atoms in group all
|
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 ...
|
Finding 1-2 1-3 1-4 neighbors ...
|
||||||
special bond factors lj: 0 1 1
|
special bond factors lj: 0 1 1
|
||||||
special bond factors coul: 0 0 0
|
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
|
2 = max # of 1-4 neighbors
|
||||||
4 = max # of special neighbors
|
4 = max # of special neighbors
|
||||||
special bonds CPU = 0.000 seconds
|
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
|
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
|
||||||
Neighbor list info ...
|
Neighbor list info ...
|
||||||
update: every = 1 steps, delay = 0 steps, check = yes
|
update: every = 1 steps, delay = 0 steps, check = yes
|
||||||
@ -68,11 +143,7 @@ Neighbor list info ...
|
|||||||
pair build: copy
|
pair build: copy
|
||||||
stencil: none
|
stencil: none
|
||||||
bin: none
|
bin: none
|
||||||
Setting up Verlet run ...
|
WARNING: Communication cutoff adjusted to 48.03269686950012 (../comm.cpp:739)
|
||||||
Unit style : real
|
|
||||||
Current step : 0
|
|
||||||
Time step : 0.01706
|
|
||||||
WARNING: Communication cutoff adjusted to 48.03269686950012 (src/comm.cpp:739)
|
|
||||||
0 ekin = 6.60687273927977 | erot = 16.7817849122513 | epot = -73.3220946463646 | etot = -49.9334369948335
|
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
|
Per MPI rank memory allocation (min/avg/max) = 7.443 | 7.444 | 7.445 Mbytes
|
||||||
Step Temp E_pair E_mol TotEng Press Volume
|
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
|
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 ekin = 9.30950418557169 | erot = 13.3558388695471 | epot = -72.5987797639821 | etot = -49.9334367088633
|
||||||
1000000 347.01619 -80.374455 7.7756755 -63.289276 0.11518501 39304000
|
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
|
Performance: 82.918 ns/day, 0.289 hours/ns, 56254.421 timesteps/s, 562.544 katom-step/s
|
||||||
99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
|
99.7% CPU use with 4 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
MPI task timing breakdown:
|
MPI task timing breakdown:
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
---------------------------------------------------------------
|
---------------------------------------------------------------
|
||||||
Pair | 4.1126 | 5.281 | 7.0829 | 48.1 | 42.66
|
Pair | 6.0475 | 7.6302 | 10.252 | 57.4 | 42.92
|
||||||
Bond | 0.14793 | 0.22282 | 0.2978 | 11.7 | 1.80
|
Bond | 0.22588 | 0.32246 | 0.42602 | 12.9 | 1.81
|
||||||
Neigh | 0.00393 | 0.0039655 | 0.004021 | 0.1 | 0.03
|
Neigh | 0.007601 | 0.007642 | 0.007702 | 0.0 | 0.04
|
||||||
Comm | 2.762 | 4.8726 | 6.048 | 56.9 | 39.36
|
Comm | 3.9938 | 7.0574 | 8.7017 | 68.2 | 39.70
|
||||||
Output | 0.063777 | 0.070646 | 0.088161 | 3.8 | 0.57
|
Output | 0.07165 | 0.07691 | 0.088092 | 2.4 | 0.43
|
||||||
Modify | 0.44561 | 0.5346 | 0.64233 | 11.9 | 4.32
|
Modify | 0.60223 | 0.70805 | 0.84637 | 11.9 | 3.98
|
||||||
Other | | 1.393 | | | 11.26
|
Other | | 1.974 | | | 11.10
|
||||||
|
|
||||||
Nlocal: 2.5 ave 3 max 2 min
|
Nlocal: 2.5 ave 3 max 2 min
|
||||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
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
|
Ave special neighs/atom = 3.6
|
||||||
Neighbor list builds = 1000
|
Neighbor list builds = 1000
|
||||||
Dangerous builds = 0
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
write_data last_config.${number}.* nocoeff
|
||||||
|
write_data last_config.1.* nocoeff
|
||||||
System init for write_data ...
|
System init for write_data ...
|
||||||
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
|
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
|
||||||
@ -1,6 +1,28 @@
|
|||||||
LAMMPS (17 Apr 2024)
|
LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-174-g749e259294-modified)
|
||||||
using 1 OpenMP thread(s) per MPI task
|
# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19
|
||||||
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)
|
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 ...
|
Reading data file ...
|
||||||
orthogonal box = (-170 -170 -170) to (170 170 170)
|
orthogonal box = (-170 -170 -170) to (170 170 170)
|
||||||
1 by 1 by 1 MPI processor grid
|
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
|
4 = max # of 1-4 neighbors
|
||||||
6 = max # of special neighbors
|
6 = max # of special neighbors
|
||||||
special bonds CPU = 0.000 seconds
|
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 ...
|
Setting atom values ...
|
||||||
16 settings made for mass
|
16 settings made for mass
|
||||||
|
|
||||||
|
group all type 1 4
|
||||||
16 atoms in group all
|
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 ...
|
Finding 1-2 1-3 1-4 neighbors ...
|
||||||
special bond factors lj: 0 1 1
|
special bond factors lj: 0 1 1
|
||||||
special bond factors coul: 0 0 0
|
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
|
4 = max # of 1-4 neighbors
|
||||||
6 = max # of special neighbors
|
6 = max # of special neighbors
|
||||||
special bonds CPU = 0.000 seconds
|
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
|
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
|
||||||
Neighbor list info ...
|
Neighbor list info ...
|
||||||
update: every = 1 steps, delay = 0 steps, check = yes
|
update: every = 1 steps, delay = 0 steps, check = yes
|
||||||
@ -68,11 +145,7 @@ Neighbor list info ...
|
|||||||
pair build: copy
|
pair build: copy
|
||||||
stencil: none
|
stencil: none
|
||||||
bin: none
|
bin: none
|
||||||
Setting up Verlet run ...
|
WARNING: Communication cutoff adjusted to 48.03269686950012 (../comm.cpp:739)
|
||||||
Unit style : real
|
|
||||||
Current step : 0
|
|
||||||
Time step : 0.01706
|
|
||||||
WARNING: Communication cutoff adjusted to 48.03269686950012 (src/comm.cpp:739)
|
|
||||||
0 ekin = 16.1203242878408 | erot = 16.6982509426318 | epot = -125.483166681887 | etot = -92.6645914514141
|
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
|
Per MPI rank memory allocation (min/avg/max) = 7.57 | 7.57 | 7.57 Mbytes
|
||||||
Step Temp E_pair E_mol TotEng Press Volume
|
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
|
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 ekin = 17.4266501863313 | erot = 15.93443523795 | epot = -121.571786609929 | etot = -88.2107011856477
|
||||||
1000000 389.752 -124.64554 3.0737557 -104.14514 0.13705163 39304000
|
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
|
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 1 OpenMP threads
|
99.8% CPU use with 1 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
MPI task timing breakdown:
|
MPI task timing breakdown:
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
---------------------------------------------------------------
|
---------------------------------------------------------------
|
||||||
Pair | 21.515 | 21.515 | 21.515 | 0.0 | 81.12
|
Pair | 33.133 | 33.133 | 33.133 | 0.0 | 82.29
|
||||||
Bond | 0.75114 | 0.75114 | 0.75114 | 0.0 | 2.83
|
Bond | 1.0208 | 1.0208 | 1.0208 | 0.0 | 2.54
|
||||||
Neigh | 0.007053 | 0.007053 | 0.007053 | 0.0 | 0.03
|
Neigh | 0.014956 | 0.014956 | 0.014956 | 0.0 | 0.04
|
||||||
Comm | 0.28128 | 0.28128 | 0.28128 | 0.0 | 1.06
|
Comm | 0.45341 | 0.45341 | 0.45341 | 0.0 | 1.13
|
||||||
Output | 0.13963 | 0.13963 | 0.13963 | 0.0 | 0.53
|
Output | 0.19799 | 0.19799 | 0.19799 | 0.0 | 0.49
|
||||||
Modify | 3.4968 | 3.4968 | 3.4968 | 0.0 | 13.18
|
Modify | 4.9747 | 4.9747 | 4.9747 | 0.0 | 12.35
|
||||||
Other | | 0.3331 | | | 1.26
|
Other | | 0.4711 | | | 1.17
|
||||||
|
|
||||||
Nlocal: 16 ave 16 max 16 min
|
Nlocal: 16 ave 16 max 16 min
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
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
|
Ave special neighs/atom = 3.75
|
||||||
Neighbor list builds = 1000
|
Neighbor list builds = 1000
|
||||||
Dangerous builds = 0
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
write_data last_config.${number}.* nocoeff
|
||||||
|
write_data last_config.2.* nocoeff
|
||||||
System init for write_data ...
|
System init for write_data ...
|
||||||
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
|
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
|
||||||
@ -1,6 +1,28 @@
|
|||||||
LAMMPS (17 Apr 2024)
|
LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-174-g749e259294-modified)
|
||||||
using 1 OpenMP thread(s) per MPI task
|
# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19
|
||||||
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)
|
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 ...
|
Reading data file ...
|
||||||
orthogonal box = (-170 -170 -170) to (170 170 170)
|
orthogonal box = (-170 -170 -170) to (170 170 170)
|
||||||
1 by 2 by 2 MPI processor grid
|
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
|
4 = max # of 1-4 neighbors
|
||||||
6 = max # of special neighbors
|
6 = max # of special neighbors
|
||||||
special bonds CPU = 0.001 seconds
|
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 ...
|
Setting atom values ...
|
||||||
16 settings made for mass
|
16 settings made for mass
|
||||||
|
|
||||||
|
group all type 1 4
|
||||||
16 atoms in group all
|
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 ...
|
Finding 1-2 1-3 1-4 neighbors ...
|
||||||
special bond factors lj: 0 1 1
|
special bond factors lj: 0 1 1
|
||||||
special bond factors coul: 0 0 0
|
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
|
4 = max # of 1-4 neighbors
|
||||||
6 = max # of special neighbors
|
6 = max # of special neighbors
|
||||||
special bonds CPU = 0.000 seconds
|
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
|
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
|
||||||
Neighbor list info ...
|
Neighbor list info ...
|
||||||
update: every = 1 steps, delay = 0 steps, check = yes
|
update: every = 1 steps, delay = 0 steps, check = yes
|
||||||
@ -68,11 +145,7 @@ Neighbor list info ...
|
|||||||
pair build: copy
|
pair build: copy
|
||||||
stencil: none
|
stencil: none
|
||||||
bin: none
|
bin: none
|
||||||
Setting up Verlet run ...
|
WARNING: Communication cutoff adjusted to 48.03269686950012 (../comm.cpp:739)
|
||||||
Unit style : real
|
|
||||||
Current step : 0
|
|
||||||
Time step : 0.01706
|
|
||||||
WARNING: Communication cutoff adjusted to 48.03269686950012 (src/comm.cpp:739)
|
|
||||||
0 ekin = 16.1203242878408 | erot = 16.6982509426318 | epot = -125.483166681887 | etot = -92.6645914514142
|
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
|
Per MPI rank memory allocation (min/avg/max) = 7.569 | 7.598 | 7.682 Mbytes
|
||||||
Step Temp E_pair E_mol TotEng Press Volume
|
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
|
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 ekin = 17.097105825142 | erot = 12.6179942372262 | epot = -129.692482442335 | etot = -99.977382379967
|
||||||
1000000 382.38165 -132.06191 2.3694293 -112.59538 0.043662828 39304000
|
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
|
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 1 OpenMP threads
|
99.8% CPU use with 4 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
MPI task timing breakdown:
|
MPI task timing breakdown:
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
---------------------------------------------------------------
|
---------------------------------------------------------------
|
||||||
Pair | 6.6389 | 9.0272 | 11.733 | 63.0 | 47.83
|
Pair | 9.5219 | 13.077 | 17.034 | 78.2 | 47.99
|
||||||
Bond | 0.25991 | 0.31216 | 0.34826 | 6.1 | 1.65
|
Bond | 0.38282 | 0.43293 | 0.48144 | 5.8 | 1.59
|
||||||
Neigh | 0.005375 | 0.0054547 | 0.005558 | 0.1 | 0.03
|
Neigh | 0.00956 | 0.0096418 | 0.009729 | 0.1 | 0.04
|
||||||
Comm | 3.8623 | 6.7331 | 8.8907 | 72.9 | 35.67
|
Comm | 5.6548 | 9.754 | 12.913 | 88.2 | 35.80
|
||||||
Output | 0.066898 | 0.071666 | 0.082232 | 2.3 | 0.38
|
Output | 0.086221 | 0.091692 | 0.10328 | 2.2 | 0.34
|
||||||
Modify | 1.173 | 1.3132 | 1.4562 | 9.6 | 6.96
|
Modify | 1.4663 | 1.6512 | 1.8474 | 13.1 | 6.06
|
||||||
Other | | 1.412 | | | 7.48
|
Other | | 2.231 | | | 8.19
|
||||||
|
|
||||||
Nlocal: 4 ave 5 max 3 min
|
Nlocal: 4 ave 5 max 3 min
|
||||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
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
|
Ave special neighs/atom = 3.75
|
||||||
Neighbor list builds = 1000
|
Neighbor list builds = 1000
|
||||||
Dangerous builds = 0
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
write_data last_config.${number}.* nocoeff
|
||||||
|
write_data last_config.2.* nocoeff
|
||||||
System init for write_data ...
|
System init for write_data ...
|
||||||
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
|
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
|
||||||
@ -1,6 +1,28 @@
|
|||||||
LAMMPS (17 Apr 2024)
|
LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-174-g749e259294-modified)
|
||||||
using 1 OpenMP thread(s) per MPI task
|
# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19
|
||||||
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)
|
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 ...
|
Reading data file ...
|
||||||
orthogonal box = (-170 -170 -170) to (170 170 170)
|
orthogonal box = (-170 -170 -170) to (170 170 170)
|
||||||
1 by 1 by 1 MPI processor grid
|
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
|
2 = max # of 1-4 neighbors
|
||||||
4 = max # of special neighbors
|
4 = max # of special neighbors
|
||||||
special bonds CPU = 0.000 seconds
|
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 ...
|
Setting atom values ...
|
||||||
10 settings made for mass
|
10 settings made for mass
|
||||||
|
|
||||||
|
group all type 1 4
|
||||||
10 atoms in group all
|
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 ...
|
Finding 1-2 1-3 1-4 neighbors ...
|
||||||
special bond factors lj: 0 1 1
|
special bond factors lj: 0 1 1
|
||||||
special bond factors coul: 0 0 0
|
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
|
2 = max # of 1-4 neighbors
|
||||||
4 = max # of special neighbors
|
4 = max # of special neighbors
|
||||||
special bonds CPU = 0.000 seconds
|
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
|
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
|
||||||
Neighbor list info ...
|
Neighbor list info ...
|
||||||
update: every = 1 steps, delay = 0 steps, check = yes
|
update: every = 1 steps, delay = 0 steps, check = yes
|
||||||
@ -68,11 +143,7 @@ Neighbor list info ...
|
|||||||
pair build: copy
|
pair build: copy
|
||||||
stencil: none
|
stencil: none
|
||||||
bin: none
|
bin: none
|
||||||
Setting up Verlet run ...
|
WARNING: Communication cutoff adjusted to 48.03269686950012 (../comm.cpp:739)
|
||||||
Unit style : real
|
|
||||||
Current step : 0
|
|
||||||
Time step : 0.01706
|
|
||||||
WARNING: Communication cutoff adjusted to 48.03269686950012 (src/comm.cpp:739)
|
|
||||||
0 ekin = 7.03429942525144 | erot = 12.9873344362494 | epot = -68.5183064451292 | etot = -48.4966725836283
|
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
|
Per MPI rank memory allocation (min/avg/max) = 7.445 | 7.445 | 7.445 Mbytes
|
||||||
Step Temp E_pair E_mol TotEng Press Volume
|
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
|
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 ekin = 6.56133020088365 | erot = 13.4950386916226 | epot = -68.5530411962168 | etot = -48.4966723037105
|
||||||
1000000 244.5767 -69.23317 0.68012891 -61.991711 -0.012778323 39304000
|
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
|
Performance: 78.272 ns/day, 0.307 hours/ns, 53102.168 timesteps/s, 531.022 katom-step/s
|
||||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
99.7% CPU use with 1 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
MPI task timing breakdown:
|
MPI task timing breakdown:
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
---------------------------------------------------------------
|
---------------------------------------------------------------
|
||||||
Pair | 8.9766 | 8.9766 | 8.9766 | 0.0 | 80.22
|
Pair | 15.43 | 15.43 | 15.43 | 0.0 | 81.93
|
||||||
Bond | 0.44821 | 0.44821 | 0.44821 | 0.0 | 4.01
|
Bond | 0.69466 | 0.69466 | 0.69466 | 0.0 | 3.69
|
||||||
Neigh | 0.004031 | 0.004031 | 0.004031 | 0.0 | 0.04
|
Neigh | 0.011044 | 0.011044 | 0.011044 | 0.0 | 0.06
|
||||||
Comm | 0.24442 | 0.24442 | 0.24442 | 0.0 | 2.18
|
Comm | 0.4431 | 0.4431 | 0.4431 | 0.0 | 2.35
|
||||||
Output | 0.11136 | 0.11136 | 0.11136 | 0.0 | 1.00
|
Output | 0.12591 | 0.12591 | 0.12591 | 0.0 | 0.67
|
||||||
Modify | 1.1158 | 1.1158 | 1.1158 | 0.0 | 9.97
|
Modify | 1.6795 | 1.6795 | 1.6795 | 0.0 | 8.92
|
||||||
Other | | 0.29 | | | 2.59
|
Other | | 0.4478 | | | 2.38
|
||||||
|
|
||||||
Nlocal: 10 ave 10 max 10 min
|
Nlocal: 10 ave 10 max 10 min
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
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
|
Ave special neighs/atom = 3.6
|
||||||
Neighbor list builds = 1000
|
Neighbor list builds = 1000
|
||||||
Dangerous builds = 0
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
write_data last_config.${number}.* nocoeff
|
||||||
|
write_data last_config.3.* nocoeff
|
||||||
System init for write_data ...
|
System init for write_data ...
|
||||||
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
|
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
|
||||||
@ -1,6 +1,28 @@
|
|||||||
LAMMPS (17 Apr 2024)
|
LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-174-g749e259294-modified)
|
||||||
using 1 OpenMP thread(s) per MPI task
|
# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19
|
||||||
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)
|
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 ...
|
Reading data file ...
|
||||||
orthogonal box = (-170 -170 -170) to (170 170 170)
|
orthogonal box = (-170 -170 -170) to (170 170 170)
|
||||||
1 by 2 by 2 MPI processor grid
|
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
|
2 = max # of 1-4 neighbors
|
||||||
4 = max # of special neighbors
|
4 = max # of special neighbors
|
||||||
special bonds CPU = 0.001 seconds
|
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 ...
|
Setting atom values ...
|
||||||
10 settings made for mass
|
10 settings made for mass
|
||||||
|
|
||||||
|
group all type 1 4
|
||||||
10 atoms in group all
|
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 ...
|
Finding 1-2 1-3 1-4 neighbors ...
|
||||||
special bond factors lj: 0 1 1
|
special bond factors lj: 0 1 1
|
||||||
special bond factors coul: 0 0 0
|
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
|
2 = max # of 1-4 neighbors
|
||||||
4 = max # of special neighbors
|
4 = max # of special neighbors
|
||||||
special bonds CPU = 0.000 seconds
|
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
|
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
|
||||||
Neighbor list info ...
|
Neighbor list info ...
|
||||||
update: every = 1 steps, delay = 0 steps, check = yes
|
update: every = 1 steps, delay = 0 steps, check = yes
|
||||||
@ -68,11 +143,7 @@ Neighbor list info ...
|
|||||||
pair build: copy
|
pair build: copy
|
||||||
stencil: none
|
stencil: none
|
||||||
bin: none
|
bin: none
|
||||||
Setting up Verlet run ...
|
WARNING: Communication cutoff adjusted to 48.03269686950012 (../comm.cpp:739)
|
||||||
Unit style : real
|
|
||||||
Current step : 0
|
|
||||||
Time step : 0.01706
|
|
||||||
WARNING: Communication cutoff adjusted to 48.03269686950012 (src/comm.cpp:739)
|
|
||||||
0 ekin = 7.03429942525144 | erot = 12.9873344362494 | epot = -68.5183064451292 | etot = -48.4966725836283
|
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
|
Per MPI rank memory allocation (min/avg/max) = 7.443 | 7.444 | 7.445 Mbytes
|
||||||
Step Temp E_pair E_mol TotEng Press Volume
|
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
|
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 ekin = 6.56133017801672 | erot = 13.4950387121477 | epot = -68.5530411938935 | etot = -48.4966723037291
|
||||||
1000000 244.5767 -69.23317 0.68012891 -61.991711 -0.012778323 39304000
|
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
|
Performance: 80.639 ns/day, 0.298 hours/ns, 54708.327 timesteps/s, 547.083 katom-step/s
|
||||||
99.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
99.7% CPU use with 4 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
MPI task timing breakdown:
|
MPI task timing breakdown:
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
---------------------------------------------------------------
|
---------------------------------------------------------------
|
||||||
Pair | 2.9984 | 4.6915 | 6.6489 | 59.9 | 41.12
|
Pair | 4.7489 | 7.413 | 10.648 | 77.4 | 40.56
|
||||||
Bond | 0.15743 | 0.20489 | 0.24566 | 8.9 | 1.80
|
Bond | 0.2292 | 0.30345 | 0.37909 | 12.0 | 1.66
|
||||||
Neigh | 0.003395 | 0.0034335 | 0.003477 | 0.1 | 0.03
|
Neigh | 0.00759 | 0.0076525 | 0.007698 | 0.0 | 0.04
|
||||||
Comm | 2.5981 | 4.8289 | 6.5413 | 64.5 | 42.32
|
Comm | 4.13 | 7.779 | 10.46 | 82.1 | 42.56
|
||||||
Output | 0.054733 | 0.058039 | 0.065343 | 1.8 | 0.51
|
Output | 0.072271 | 0.076746 | 0.085815 | 1.9 | 0.42
|
||||||
Modify | 0.4272 | 0.49029 | 0.54447 | 6.4 | 4.30
|
Modify | 0.63917 | 0.69264 | 0.75378 | 6.3 | 3.79
|
||||||
Other | | 1.132 | | | 9.93
|
Other | | 2.006 | | | 10.98
|
||||||
|
|
||||||
Nlocal: 2.5 ave 3 max 2 min
|
Nlocal: 2.5 ave 3 max 2 min
|
||||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
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
|
Ave special neighs/atom = 3.6
|
||||||
Neighbor list builds = 1000
|
Neighbor list builds = 1000
|
||||||
Dangerous builds = 0
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
write_data last_config.${number}.* nocoeff
|
||||||
|
write_data last_config.3.* nocoeff
|
||||||
System init for write_data ...
|
System init for write_data ...
|
||||||
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
|
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
|
||||||
@ -1,6 +1,30 @@
|
|||||||
LAMMPS (17 Apr 2024)
|
LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-174-g749e259294-modified)
|
||||||
using 1 OpenMP thread(s) per MPI task
|
variable number equal 4
|
||||||
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)
|
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 ...
|
Reading data file ...
|
||||||
orthogonal box = (-170 -170 -170) to (170 170 170)
|
orthogonal box = (-170 -170 -170) to (170 170 170)
|
||||||
1 by 1 by 1 MPI processor grid
|
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
|
4 = max # of 1-4 neighbors
|
||||||
6 = max # of special neighbors
|
6 = max # of special neighbors
|
||||||
special bonds CPU = 0.000 seconds
|
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 ...
|
Setting atom values ...
|
||||||
26 settings made for mass
|
26 settings made for mass
|
||||||
|
|
||||||
|
group all type 1 4
|
||||||
26 atoms in group all
|
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 ...
|
Finding 1-2 1-3 1-4 neighbors ...
|
||||||
special bond factors lj: 0 1 1
|
special bond factors lj: 0 1 1
|
||||||
special bond factors coul: 0 0 0
|
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
|
4 = max # of 1-4 neighbors
|
||||||
6 = max # of special neighbors
|
6 = max # of special neighbors
|
||||||
special bonds CPU = 0.000 seconds
|
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
|
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
|
||||||
Neighbor list info ...
|
Neighbor list info ...
|
||||||
update: every = 10 steps, delay = 0 steps, check = yes
|
update: every = 10 steps, delay = 0 steps, check = yes
|
||||||
@ -68,11 +191,7 @@ Neighbor list info ...
|
|||||||
pair build: copy
|
pair build: copy
|
||||||
stencil: none
|
stencil: none
|
||||||
bin: none
|
bin: none
|
||||||
Setting up Verlet run ...
|
WARNING: Communication cutoff adjusted to 48.03269686950012 (../comm.cpp:739)
|
||||||
Unit style : real
|
|
||||||
Current step : 0
|
|
||||||
Time step : 0.01706
|
|
||||||
WARNING: Communication cutoff adjusted to 48.03269686950012 (src/comm.cpp:739)
|
|
||||||
0 ekin = 22.349486974586 | erot = 20.578245994282 | epot = -222.813067990178 | etot = -179.88533502131
|
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
|
Per MPI rank memory allocation (min/avg/max) = 7.57 | 7.57 | 7.57 Mbytes
|
||||||
Step Temp E_pair E_mol TotEng Press Volume
|
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
|
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 ekin = 22.8867994582225 | erot = 20.7015166614267 | epot = -222.040127669769 | etot = -178.45181155012
|
||||||
1000000 307.12188 -227.88356 5.8434328 -199.15333 0.033370746 39304000
|
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
|
Performance: 17.147 ns/day, 1.400 hours/ns, 11633.421 timesteps/s, 302.469 katom-step/s
|
||||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
99.8% CPU use with 1 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
MPI task timing breakdown:
|
MPI task timing breakdown:
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
---------------------------------------------------------------
|
---------------------------------------------------------------
|
||||||
Pair | 42.93 | 42.93 | 42.93 | 0.0 | 85.86
|
Pair | 75.127 | 75.127 | 75.127 | 0.0 | 87.40
|
||||||
Bond | 1.1736 | 1.1736 | 1.1736 | 0.0 | 2.35
|
Bond | 1.8597 | 1.8597 | 1.8597 | 0.0 | 2.16
|
||||||
Neigh | 0.010656 | 0.010656 | 0.010656 | 0.0 | 0.02
|
Neigh | 0.023421 | 0.023421 | 0.023421 | 0.0 | 0.03
|
||||||
Comm | 0.2842 | 0.2842 | 0.2842 | 0.0 | 0.57
|
Comm | 0.47775 | 0.47775 | 0.47775 | 0.0 | 0.56
|
||||||
Output | 0.22398 | 0.22398 | 0.22398 | 0.0 | 0.45
|
Output | 0.31455 | 0.31455 | 0.31455 | 0.0 | 0.37
|
||||||
Modify | 5.1366 | 5.1366 | 5.1366 | 0.0 | 10.27
|
Modify | 7.8261 | 7.8261 | 7.8261 | 0.0 | 9.10
|
||||||
Other | | 0.2401 | | | 0.48
|
Other | | 0.3311 | | | 0.39
|
||||||
|
|
||||||
Nlocal: 26 ave 26 max 26 min
|
Nlocal: 26 ave 26 max 26 min
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
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
|
Ave special neighs/atom = 5.0769231
|
||||||
Neighbor list builds = 1000
|
Neighbor list builds = 1000
|
||||||
Dangerous builds = 0
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
write_data last_config.${number}.* nocoeff
|
||||||
|
write_data last_config.4.* nocoeff
|
||||||
System init for write_data ...
|
System init for write_data ...
|
||||||
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
|
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
|
||||||
@ -1,6 +1,30 @@
|
|||||||
LAMMPS (17 Apr 2024)
|
LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-174-g749e259294-modified)
|
||||||
using 1 OpenMP thread(s) per MPI task
|
variable number equal 4
|
||||||
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)
|
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 ...
|
Reading data file ...
|
||||||
orthogonal box = (-170 -170 -170) to (170 170 170)
|
orthogonal box = (-170 -170 -170) to (170 170 170)
|
||||||
1 by 2 by 2 MPI processor grid
|
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
|
4 = max # of 1-4 neighbors
|
||||||
6 = max # of special neighbors
|
6 = max # of special neighbors
|
||||||
special bonds CPU = 0.000 seconds
|
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 ...
|
Setting atom values ...
|
||||||
26 settings made for mass
|
26 settings made for mass
|
||||||
|
|
||||||
|
group all type 1 4
|
||||||
26 atoms in group all
|
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 ...
|
Finding 1-2 1-3 1-4 neighbors ...
|
||||||
special bond factors lj: 0 1 1
|
special bond factors lj: 0 1 1
|
||||||
special bond factors coul: 0 0 0
|
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
|
4 = max # of 1-4 neighbors
|
||||||
6 = max # of special neighbors
|
6 = max # of special neighbors
|
||||||
special bonds CPU = 0.000 seconds
|
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
|
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
|
||||||
Neighbor list info ...
|
Neighbor list info ...
|
||||||
update: every = 10 steps, delay = 0 steps, check = yes
|
update: every = 10 steps, delay = 0 steps, check = yes
|
||||||
@ -68,11 +191,7 @@ Neighbor list info ...
|
|||||||
pair build: copy
|
pair build: copy
|
||||||
stencil: none
|
stencil: none
|
||||||
bin: none
|
bin: none
|
||||||
Setting up Verlet run ...
|
WARNING: Communication cutoff adjusted to 48.03269686950012 (../comm.cpp:739)
|
||||||
Unit style : real
|
|
||||||
Current step : 0
|
|
||||||
Time step : 0.01706
|
|
||||||
WARNING: Communication cutoff adjusted to 48.03269686950012 (src/comm.cpp:739)
|
|
||||||
0 ekin = 22.349486974586 | erot = 20.578245994282 | epot = -222.813067990178 | etot = -179.88533502131
|
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
|
Per MPI rank memory allocation (min/avg/max) = 7.568 | 7.569 | 7.57 Mbytes
|
||||||
Step Temp E_pair E_mol TotEng Press Volume
|
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
|
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 ekin = 22.6406306102505 | erot = 22.5936369544571 | epot = -217.43832313152 | etot = -172.204055566812
|
||||||
1000000 303.8185 -221.63969 4.201369 -194.79769 -0.0039208577 39304000
|
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
|
Performance: 28.250 ns/day, 0.850 hours/ns, 19165.450 timesteps/s, 498.302 katom-step/s
|
||||||
99.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
99.7% CPU use with 4 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
MPI task timing breakdown:
|
MPI task timing breakdown:
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
---------------------------------------------------------------
|
---------------------------------------------------------------
|
||||||
Pair | 10.626 | 15.644 | 25.979 | 154.5 | 47.08
|
Pair | 16.653 | 24.637 | 41.068 | 196.4 | 47.22
|
||||||
Bond | 0.33928 | 0.43429 | 0.52964 | 14.4 | 1.31
|
Bond | 0.48356 | 0.63927 | 0.80015 | 17.6 | 1.23
|
||||||
Neigh | 0.007773 | 0.0079158 | 0.008061 | 0.1 | 0.02
|
Neigh | 0.014011 | 0.014287 | 0.01458 | 0.2 | 0.03
|
||||||
Comm | 4.0659 | 14.948 | 19.566 | 164.9 | 44.99
|
Comm | 6.7344 | 23.772 | 31.096 | 205.7 | 45.56
|
||||||
Output | 0.089356 | 0.10217 | 0.10917 | 2.4 | 0.31
|
Output | 0.12082 | 0.13899 | 0.14687 | 2.8 | 0.27
|
||||||
Modify | 1.2889 | 1.7411 | 2.1956 | 31.1 | 5.24
|
Modify | 1.8628 | 2.4412 | 3.0041 | 33.6 | 4.68
|
||||||
Other | | 0.3515 | | | 1.06
|
Other | | 0.5347 | | | 1.02
|
||||||
|
|
||||||
Nlocal: 6.5 ave 10 max 3 min
|
Nlocal: 6.5 ave 10 max 3 min
|
||||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
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
|
Ave special neighs/atom = 5.0769231
|
||||||
Neighbor list builds = 1000
|
Neighbor list builds = 1000
|
||||||
Dangerous builds = 0
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
write_data last_config.${number}.* nocoeff
|
||||||
|
write_data last_config.4.* nocoeff
|
||||||
System init for write_data ...
|
System init for write_data ...
|
||||||
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
|
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
|
||||||
@ -1,6 +1,30 @@
|
|||||||
LAMMPS (17 Apr 2024)
|
LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-174-g749e259294-modified)
|
||||||
using 1 OpenMP thread(s) per MPI task
|
variable number equal 8
|
||||||
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)
|
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 ...
|
Reading data file ...
|
||||||
orthogonal box = (-170 -170 -170) to (170 170 170)
|
orthogonal box = (-170 -170 -170) to (170 170 170)
|
||||||
1 by 1 by 1 MPI processor grid
|
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
|
4 = max # of 1-4 neighbors
|
||||||
6 = max # of special neighbors
|
6 = max # of special neighbors
|
||||||
special bonds CPU = 0.000 seconds
|
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 ...
|
Setting atom values ...
|
||||||
26 settings made for mass
|
26 settings made for mass
|
||||||
|
|
||||||
|
group all type 1 4
|
||||||
26 atoms in group all
|
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 ...
|
Finding 1-2 1-3 1-4 neighbors ...
|
||||||
special bond factors lj: 0 1 1
|
special bond factors lj: 0 1 1
|
||||||
special bond factors coul: 0 0 0
|
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
|
4 = max # of 1-4 neighbors
|
||||||
6 = max # of special neighbors
|
6 = max # of special neighbors
|
||||||
special bonds CPU = 0.000 seconds
|
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
|
Generated 0 of 28 mixed pair_coeff terms from geometric mixing rule
|
||||||
Neighbor list info ...
|
Neighbor list info ...
|
||||||
update: every = 10 steps, delay = 0 steps, check = yes
|
update: every = 10 steps, delay = 0 steps, check = yes
|
||||||
@ -68,11 +233,7 @@ Neighbor list info ...
|
|||||||
pair build: copy
|
pair build: copy
|
||||||
stencil: none
|
stencil: none
|
||||||
bin: none
|
bin: none
|
||||||
Setting up Verlet run ...
|
WARNING: Communication cutoff adjusted to 48.03269686950012 (../comm.cpp:739)
|
||||||
Unit style : real
|
|
||||||
Current step : 0
|
|
||||||
Time step : 0.01706
|
|
||||||
WARNING: Communication cutoff adjusted to 48.03269686950012 (src/comm.cpp:739)
|
|
||||||
0 ekin = 22.349486974586 | erot = 20.578245994282 | epot = -222.813067990178 | etot = -179.88533502131
|
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
|
Per MPI rank memory allocation (min/avg/max) = 7.57 | 7.57 | 7.57 Mbytes
|
||||||
Step Temp E_pair E_mol TotEng Press Volume
|
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
|
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 ekin = 22.8867994582225 | erot = 20.7015166614267 | epot = -222.040127669769 | etot = -178.45181155012
|
||||||
1000000 307.12188 -227.88356 5.8434328 -199.15333 0.033370746 39304000
|
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
|
Performance: 17.167 ns/day, 1.398 hours/ns, 11646.839 timesteps/s, 302.818 katom-step/s
|
||||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
99.7% CPU use with 1 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
MPI task timing breakdown:
|
MPI task timing breakdown:
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
---------------------------------------------------------------
|
---------------------------------------------------------------
|
||||||
Pair | 44.649 | 44.649 | 44.649 | 0.0 | 85.96
|
Pair | 75.033 | 75.033 | 75.033 | 0.0 | 87.39
|
||||||
Bond | 1.2217 | 1.2217 | 1.2217 | 0.0 | 2.35
|
Bond | 1.7719 | 1.7719 | 1.7719 | 0.0 | 2.06
|
||||||
Neigh | 0.011591 | 0.011591 | 0.011591 | 0.0 | 0.02
|
Neigh | 0.023059 | 0.023059 | 0.023059 | 0.0 | 0.03
|
||||||
Comm | 0.31411 | 0.31411 | 0.31411 | 0.0 | 0.60
|
Comm | 0.51625 | 0.51625 | 0.51625 | 0.0 | 0.60
|
||||||
Output | 0.2259 | 0.2259 | 0.2259 | 0.0 | 0.43
|
Output | 0.31488 | 0.31488 | 0.31488 | 0.0 | 0.37
|
||||||
Modify | 5.2451 | 5.2451 | 5.2451 | 0.0 | 10.10
|
Modify | 7.8149 | 7.8149 | 7.8149 | 0.0 | 9.10
|
||||||
Other | | 0.2734 | | | 0.53
|
Other | | 0.3861 | | | 0.45
|
||||||
|
|
||||||
Nlocal: 26 ave 26 max 26 min
|
Nlocal: 26 ave 26 max 26 min
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
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
|
Ave special neighs/atom = 5.0769231
|
||||||
Neighbor list builds = 1000
|
Neighbor list builds = 1000
|
||||||
Dangerous builds = 0
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
write_data last_config.${number}.* nocoeff
|
||||||
|
write_data last_config.8.* nocoeff
|
||||||
System init for write_data ...
|
System init for write_data ...
|
||||||
Generated 0 of 28 mixed pair_coeff terms from geometric mixing rule
|
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
|
||||||
@ -1,6 +1,30 @@
|
|||||||
LAMMPS (17 Apr 2024)
|
LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-174-g749e259294-modified)
|
||||||
using 1 OpenMP thread(s) per MPI task
|
variable number equal 8
|
||||||
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)
|
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 ...
|
Reading data file ...
|
||||||
orthogonal box = (-170 -170 -170) to (170 170 170)
|
orthogonal box = (-170 -170 -170) to (170 170 170)
|
||||||
1 by 2 by 2 MPI processor grid
|
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
|
4 = max # of 1-4 neighbors
|
||||||
6 = max # of special neighbors
|
6 = max # of special neighbors
|
||||||
special bonds CPU = 0.001 seconds
|
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 ...
|
Setting atom values ...
|
||||||
26 settings made for mass
|
26 settings made for mass
|
||||||
|
|
||||||
|
group all type 1 4
|
||||||
26 atoms in group all
|
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 ...
|
Finding 1-2 1-3 1-4 neighbors ...
|
||||||
special bond factors lj: 0 1 1
|
special bond factors lj: 0 1 1
|
||||||
special bond factors coul: 0 0 0
|
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
|
4 = max # of 1-4 neighbors
|
||||||
6 = max # of special neighbors
|
6 = max # of special neighbors
|
||||||
special bonds CPU = 0.000 seconds
|
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
|
Generated 0 of 28 mixed pair_coeff terms from geometric mixing rule
|
||||||
Neighbor list info ...
|
Neighbor list info ...
|
||||||
update: every = 10 steps, delay = 0 steps, check = yes
|
update: every = 10 steps, delay = 0 steps, check = yes
|
||||||
@ -68,11 +233,7 @@ Neighbor list info ...
|
|||||||
pair build: copy
|
pair build: copy
|
||||||
stencil: none
|
stencil: none
|
||||||
bin: none
|
bin: none
|
||||||
Setting up Verlet run ...
|
WARNING: Communication cutoff adjusted to 48.03269686950012 (../comm.cpp:739)
|
||||||
Unit style : real
|
|
||||||
Current step : 0
|
|
||||||
Time step : 0.01706
|
|
||||||
WARNING: Communication cutoff adjusted to 48.03269686950012 (src/comm.cpp:739)
|
|
||||||
0 ekin = 22.349486974586 | erot = 20.578245994282 | epot = -222.813067990178 | etot = -179.88533502131
|
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
|
Per MPI rank memory allocation (min/avg/max) = 7.568 | 7.569 | 7.57 Mbytes
|
||||||
Step Temp E_pair E_mol TotEng Press Volume
|
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
|
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 ekin = 22.6406306102505 | erot = 22.5936369544571 | epot = -217.43832313152 | etot = -172.204055566812
|
||||||
1000000 303.8185 -221.63969 4.201369 -194.79769 -0.0039208577 39304000
|
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
|
Performance: 27.729 ns/day, 0.866 hours/ns, 18812.191 timesteps/s, 489.117 katom-step/s
|
||||||
99.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
99.6% CPU use with 4 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
MPI task timing breakdown:
|
MPI task timing breakdown:
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
---------------------------------------------------------------
|
---------------------------------------------------------------
|
||||||
Pair | 11.103 | 15.989 | 27.026 | 161.4 | 46.27
|
Pair | 17.443 | 25.085 | 41.565 | 193.9 | 47.19
|
||||||
Bond | 0.3534 | 0.44646 | 0.54636 | 13.5 | 1.29
|
Bond | 0.47799 | 0.65467 | 0.81319 | 18.1 | 1.23
|
||||||
Neigh | 0.007879 | 0.0080685 | 0.008218 | 0.1 | 0.02
|
Neigh | 0.014771 | 0.014974 | 0.015145 | 0.1 | 0.03
|
||||||
Comm | 4.2767 | 15.803 | 20.415 | 168.6 | 45.73
|
Comm | 7.0561 | 24.213 | 31.359 | 204.1 | 45.55
|
||||||
Output | 0.084582 | 0.13406 | 0.15369 | 7.8 | 0.39
|
Output | 0.12434 | 0.14455 | 0.15308 | 3.1 | 0.27
|
||||||
Modify | 1.354 | 1.7988 | 2.2537 | 32.6 | 5.21
|
Modify | 1.8662 | 2.4548 | 3.0502 | 36.3 | 4.62
|
||||||
Other | | 0.378 | | | 1.09
|
Other | | 0.5899 | | | 1.11
|
||||||
|
|
||||||
Nlocal: 6.5 ave 10 max 3 min
|
Nlocal: 6.5 ave 10 max 3 min
|
||||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
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
|
Ave special neighs/atom = 5.0769231
|
||||||
Neighbor list builds = 1000
|
Neighbor list builds = 1000
|
||||||
Dangerous builds = 0
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
write_data last_config.${number}.* nocoeff
|
||||||
|
write_data last_config.8.* nocoeff
|
||||||
System init for write_data ...
|
System init for write_data ...
|
||||||
Generated 0 of 28 mixed pair_coeff terms from geometric mixing rule
|
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
|
||||||
@ -1,6 +1,28 @@
|
|||||||
LAMMPS (17 Apr 2024)
|
LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-174-g749e259294-modified)
|
||||||
using 1 OpenMP thread(s) per MPI task
|
# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19
|
||||||
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)
|
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 ...
|
Reading data file ...
|
||||||
orthogonal box = (-170 -170 -170) to (170 170 170)
|
orthogonal box = (-170 -170 -170) to (170 170 170)
|
||||||
1 by 1 by 1 MPI processor grid
|
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
|
4 = max # of 1-4 neighbors
|
||||||
6 = max # of special neighbors
|
6 = max # of special neighbors
|
||||||
special bonds CPU = 0.000 seconds
|
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 ...
|
Setting atom values ...
|
||||||
16 settings made for mass
|
16 settings made for mass
|
||||||
|
|
||||||
|
group all type 1 4
|
||||||
16 atoms in group all
|
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 ...
|
Finding 1-2 1-3 1-4 neighbors ...
|
||||||
special bond factors lj: 0 1 1
|
special bond factors lj: 0 1 1
|
||||||
special bond factors coul: 0 0 0
|
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
|
4 = max # of 1-4 neighbors
|
||||||
6 = max # of special neighbors
|
6 = max # of special neighbors
|
||||||
special bonds CPU = 0.000 seconds
|
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
|
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
|
||||||
Neighbor list info ...
|
Neighbor list info ...
|
||||||
update: every = 1 steps, delay = 0 steps, check = yes
|
update: every = 1 steps, delay = 0 steps, check = yes
|
||||||
@ -68,11 +144,7 @@ Neighbor list info ...
|
|||||||
pair build: copy
|
pair build: copy
|
||||||
stencil: none
|
stencil: none
|
||||||
bin: none
|
bin: none
|
||||||
Setting up Verlet run ...
|
WARNING: Communication cutoff adjusted to 36.640032409886274 (../comm.cpp:739)
|
||||||
Unit style : real
|
|
||||||
Current step : 0
|
|
||||||
Time step : 0.01706
|
|
||||||
WARNING: Communication cutoff adjusted to 36.640032409886274 (src/comm.cpp:739)
|
|
||||||
0 ekin = 16.1203242878408 | erot = 16.6982509426318 | epot = -66.3830249260541 | etot = -33.5644496955815
|
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
|
Per MPI rank memory allocation (min/avg/max) = 7.592 | 7.592 | 7.592 Mbytes
|
||||||
Step Temp E_pair E_mol TotEng Press Volume
|
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
|
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 ekin = 15.613660129969 | erot = 24.1382006023969 | epot = -73.3163115458147 | etot = -33.5644508134487
|
||||||
1000000 349.20396 -76.691733 3.375421 -57.702651 -0.00024160068 39304000
|
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
|
Performance: 47.324 ns/day, 0.507 hours/ns, 32106.084 timesteps/s, 513.697 katom-step/s
|
||||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
99.6% CPU use with 1 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
MPI task timing breakdown:
|
MPI task timing breakdown:
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
---------------------------------------------------------------
|
---------------------------------------------------------------
|
||||||
Pair | 16.095 | 16.095 | 16.095 | 0.0 | 83.79
|
Pair | 26.515 | 26.515 | 26.515 | 0.0 | 85.13
|
||||||
Bond | 0.6748 | 0.6748 | 0.6748 | 0.0 | 3.51
|
Bond | 1.0244 | 1.0244 | 1.0244 | 0.0 | 3.29
|
||||||
Neigh | 0.007855 | 0.007855 | 0.007855 | 0.0 | 0.04
|
Neigh | 0.019506 | 0.019506 | 0.019506 | 0.0 | 0.06
|
||||||
Comm | 0.27635 | 0.27635 | 0.27635 | 0.0 | 1.44
|
Comm | 0.45429 | 0.45429 | 0.45429 | 0.0 | 1.46
|
||||||
Output | 0.15161 | 0.15161 | 0.15161 | 0.0 | 0.79
|
Output | 0.22043 | 0.22043 | 0.22043 | 0.0 | 0.71
|
||||||
Modify | 1.7313 | 1.7313 | 1.7313 | 0.0 | 9.01
|
Modify | 2.4659 | 2.4659 | 2.4659 | 0.0 | 7.92
|
||||||
Other | | 0.2709 | | | 1.41
|
Other | | 0.4469 | | | 1.43
|
||||||
|
|
||||||
Nlocal: 16 ave 16 max 16 min
|
Nlocal: 16 ave 16 max 16 min
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
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
|
Ave special neighs/atom = 3.75
|
||||||
Neighbor list builds = 1000
|
Neighbor list builds = 1000
|
||||||
Dangerous builds = 0
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
write_data last_config.${number}.* nocoeff
|
||||||
|
write_data last_config.2.* nocoeff
|
||||||
System init for write_data ...
|
System init for write_data ...
|
||||||
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
|
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
|
||||||
@ -1,6 +1,28 @@
|
|||||||
LAMMPS (17 Apr 2024)
|
LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-174-g749e259294-modified)
|
||||||
using 1 OpenMP thread(s) per MPI task
|
# LAMMPS input file in real units via oxdna lj2real.py, date 2024-05-19
|
||||||
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)
|
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 ...
|
Reading data file ...
|
||||||
orthogonal box = (-170 -170 -170) to (170 170 170)
|
orthogonal box = (-170 -170 -170) to (170 170 170)
|
||||||
1 by 2 by 2 MPI processor grid
|
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
|
4 = max # of 1-4 neighbors
|
||||||
6 = max # of special neighbors
|
6 = max # of special neighbors
|
||||||
special bonds CPU = 0.001 seconds
|
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 ...
|
Setting atom values ...
|
||||||
16 settings made for mass
|
16 settings made for mass
|
||||||
|
|
||||||
|
group all type 1 4
|
||||||
16 atoms in group all
|
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 ...
|
Finding 1-2 1-3 1-4 neighbors ...
|
||||||
special bond factors lj: 0 1 1
|
special bond factors lj: 0 1 1
|
||||||
special bond factors coul: 0 0 0
|
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
|
4 = max # of 1-4 neighbors
|
||||||
6 = max # of special neighbors
|
6 = max # of special neighbors
|
||||||
special bonds CPU = 0.000 seconds
|
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
|
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
|
||||||
Neighbor list info ...
|
Neighbor list info ...
|
||||||
update: every = 1 steps, delay = 0 steps, check = yes
|
update: every = 1 steps, delay = 0 steps, check = yes
|
||||||
@ -68,11 +144,7 @@ Neighbor list info ...
|
|||||||
pair build: copy
|
pair build: copy
|
||||||
stencil: none
|
stencil: none
|
||||||
bin: none
|
bin: none
|
||||||
Setting up Verlet run ...
|
WARNING: Communication cutoff adjusted to 36.640032409886274 (../comm.cpp:739)
|
||||||
Unit style : real
|
|
||||||
Current step : 0
|
|
||||||
Time step : 0.01706
|
|
||||||
WARNING: Communication cutoff adjusted to 36.640032409886274 (src/comm.cpp:739)
|
|
||||||
0 ekin = 16.1203242878408 | erot = 16.6982509426318 | epot = -66.3830249260541 | etot = -33.5644496955815
|
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
|
Per MPI rank memory allocation (min/avg/max) = 7.577 | 7.606 | 7.69 Mbytes
|
||||||
Step Temp E_pair E_mol TotEng Press Volume
|
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
|
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 ekin = 15.6136601549948 | erot = 24.1382005377538 | epot = -73.31631150618 | etot = -33.5644508134314
|
||||||
1000000 349.20396 -76.691733 3.375421 -57.702651 -0.00024160018 39304000
|
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
|
Performance: 61.398 ns/day, 0.391 hours/ns, 41654.420 timesteps/s, 666.471 katom-step/s
|
||||||
99.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
99.4% CPU use with 4 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
MPI task timing breakdown:
|
MPI task timing breakdown:
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
---------------------------------------------------------------
|
---------------------------------------------------------------
|
||||||
Pair | 4.9563 | 7.0753 | 8.4914 | 52.5 | 48.03
|
Pair | 8.0729 | 11.462 | 13.699 | 68.6 | 47.74
|
||||||
Bond | 0.16693 | 0.26884 | 0.34644 | 12.5 | 1.82
|
Bond | 0.30957 | 0.43359 | 0.52757 | 12.0 | 1.81
|
||||||
Neigh | 0.004684 | 0.00475 | 0.004817 | 0.1 | 0.03
|
Neigh | 0.011335 | 0.011428 | 0.011526 | 0.1 | 0.05
|
||||||
Comm | 3.9378 | 5.5096 | 7.8538 | 63.4 | 37.40
|
Comm | 6.994 | 9.2216 | 12.853 | 77.8 | 38.41
|
||||||
Output | 0.065585 | 0.069947 | 0.079293 | 2.1 | 0.47
|
Output | 0.090149 | 0.096079 | 0.10876 | 2.4 | 0.40
|
||||||
Modify | 0.59102 | 0.65384 | 0.71706 | 6.6 | 4.44
|
Modify | 0.843 | 0.94516 | 1.0713 | 9.1 | 3.94
|
||||||
Other | | 1.15 | | | 7.81
|
Other | | 1.838 | | | 7.65
|
||||||
|
|
||||||
Nlocal: 4 ave 4 max 4 min
|
Nlocal: 4 ave 4 max 4 min
|
||||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
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
|
Ave special neighs/atom = 3.75
|
||||||
Neighbor list builds = 1000
|
Neighbor list builds = 1000
|
||||||
Dangerous builds = 0
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
write_data last_config.${number}.* nocoeff
|
||||||
|
write_data last_config.2.* nocoeff
|
||||||
System init for write_data ...
|
System init for write_data ...
|
||||||
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
|
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
|
||||||
Total wall time: 0:00:14
|
#write_restart last_config.${number}.*
|
||||||
|
Total wall time: 0:00:24
|
||||||
@ -1,11 +1,11 @@
|
|||||||
#! /bin/bash
|
#! /bin/bash
|
||||||
|
|
||||||
DATE='15May24'
|
DATE='22May24'
|
||||||
TOL=1e-8
|
TOL=1e-8
|
||||||
|
|
||||||
LMPDIR=/Users/ohenrich/Work/code/lammps
|
LMPDIR=/Users/ohenrich/Work/code/lammps
|
||||||
SRCDIR=$LMPDIR/src
|
SRCDIR=$LMPDIR/src
|
||||||
EXDIR=$LMPDIR/examples/PACKAGES/cgdna/examples
|
EXDIR=$LMPDIR/examples/PACKAGES/cgdna/examples/lj_units
|
||||||
|
|
||||||
if [ $# -eq 1 ] && [ $1 = run ]; then
|
if [ $# -eq 1 ] && [ $1 = run ]; then
|
||||||
echo '# Compiling executable in' $SRCDIR | tee -a $EXDIR/test.log
|
echo '# Compiling executable in' $SRCDIR | tee -a $EXDIR/test.log
|
||||||
|
|||||||
Reference in New Issue
Block a user