diff --git a/doc/src/bond_oxdna.rst b/doc/src/bond_oxdna.rst index 80153d52b9..d11a0e54b9 100644 --- a/doc/src/bond_oxdna.rst +++ b/doc/src/bond_oxdna.rst @@ -84,6 +84,14 @@ commands: the bond topology in the data file. The first (second) atom in a bond definition is understood to point towards the 3'-end (5'-end) of the strand. +.. warning:: + + LAMMPS has per se no concept of bond directionality. This means the bond definition + (i.e. the sequence of atom IDs) in data files produced with :doc:`write_data ` + can be different from the one provided in your initial data file. If this is the case, + then the correct 3' to 5' polarity needs to be restored before using the data file. + This limitation does not apply to binary restart files produced with + :doc:`write_restart `. Example input and data files for DNA and RNA duplexes can be found in examples/PACKAGES/cgdna/examples/oxDNA/ , /oxDNA2/ and /oxRNA2/. A simple python diff --git a/examples/PACKAGES/cgdna/examples/oxDNA2/dsring/data.dsring b/examples/PACKAGES/cgdna/examples/oxDNA2/dsring/data.dsring new file mode 100644 index 0000000000..bc30aad2e4 --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/oxDNA2/dsring/data.dsring @@ -0,0 +1,622 @@ +LAMMPS data file via write_data, version 2 Jul 2021 + +148 atoms +4 atom types +148 bonds +1 bond types +148 ellipsoids + +0 100 xlo xhi +0 100 ylo yhi +0 100 zlo zhi + +Masses + +1 3.1575 +2 3.1575 +3 3.1575 +4 3.1575 + +Atoms # hybrid + +1 1 24.4563103076585 24.545468489552267 25.008405986404544 1 1 3.7269849963023267 0 0 0 +2 4 24.529799925849524 24.236299729034574 25.438869726984304 1 1 3.7269849963023267 0 0 0 +3 3 24.837268545282573 23.98498105692614 25.841653825869834 1 1 3.7269849963023267 0 0 0 +4 2 25.160243408748546 23.990448143707216 26.252262907702004 1 1 3.7269849963023267 0 0 0 +5 1 25.511800888983288 24.20297091581725 26.46953407064928 1 1 3.7269849963023267 0 0 0 +6 2 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1.173984503142341 -0.07853628249634757 0.6763776292711046 -0.7295609015799718 -0.06392375019562685 +147 1.173984503142341 1.173984503142341 1.173984503142341 0.18414802295685903 -0.34920401662445405 0.9187682994180332 0.0032973320918147885 +148 1.173984503142341 1.173984503142341 1.173984503142341 0.13019081328575915 -0.1370605858009623 0.9781659097238085 -0.08634929652338917 diff --git a/examples/PACKAGES/cgdna/examples/oxDNA2/dsring/in.dsring b/examples/PACKAGES/cgdna/examples/oxDNA2/dsring/in.dsring new file mode 100644 index 0000000000..68b77de981 --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/oxDNA2/dsring/in.dsring @@ -0,0 +1,72 @@ +variable number equal 5 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 0.1 +variable rhos equal 0.2 + +units lj + +dimension 3 + +newton off + +boundary p p p + +atom_style hybrid bond ellipsoid oxdna +atom_modify sort 0 1.0 + +# Pair interactions require lists of neighbours to be calculated +neighbor 2.0 bin +neigh_modify every 1 delay 0 check yes + +read_data data.dsring + +set atom * mass 3.1575 + +group all type 1 4 + +# oxDNA2 bond interactions - FENE backbone +bond_style oxdna2/fene +bond_coeff * 2.0 0.25 0.7564 +special_bonds lj 0 1 1 + +# oxDNA2 pair interactions +pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh +pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 +pair_coeff * * oxdna2/stk seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/hbond seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 1 4 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 2 3 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 +pair_coeff * * oxdna2/dh ${T} ${rhos} 0.815 + +# NVE ensemble +fix 1 all nve/asphere +#fix 2 all langevin ${T} ${T} 2.5 457145 angmom 10 + +timestep 1e-5 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 3.8 + +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 + +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_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 + +#write_data last_config.${number}.* nocoeff +#write_restart last_config.${number}.* diff --git a/examples/PACKAGES/cgdna/examples/oxDNA2/dsring/log.2Jul21.dsring.g++.1 b/examples/PACKAGES/cgdna/examples/oxDNA2/dsring/log.2Jul21.dsring.g++.1 new file mode 100644 index 0000000000..f1870c13e6 --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/oxDNA2/dsring/log.2Jul21.dsring.g++.1 @@ -0,0 +1,279 @@ +LAMMPS (2 Jul 2021) +variable number equal 5 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 0.1 +variable rhos equal 0.2 + +units lj + +dimension 3 + +newton off + +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:157) +atom_modify sort 0 1.0 + +# Pair interactions require lists of neighbours to be calculated +neighbor 2.0 bin +neigh_modify every 1 delay 0 check yes + +read_data data.dsring +Reading data file ... + orthogonal box = (0.0000000 0.0000000 0.0000000) to (100.00000 100.00000 100.00000) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 148 atoms + reading velocities ... + 148 velocities + scanning bonds ... + 2 = max bonds/atom + 148 ellipsoids + reading bonds ... + 148 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.004 seconds + +set atom * mass 3.1575 +Setting atom values ... + 148 settings made for mass + +group all type 1 4 +148 atoms in group all + +# oxDNA2 bond interactions - FENE backbone +bond_style oxdna2/fene +bond_coeff * 2.0 0.25 0.7564 +special_bonds lj 0 1 1 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000 seconds + +# oxDNA2 pair interactions +pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh +pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 +pair_coeff * * oxdna2/stk seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/hbond seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 1 4 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 2 3 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 +pair_coeff * * oxdna2/dh ${T} ${rhos} 0.815 +pair_coeff * * oxdna2/dh 0.1 ${rhos} 0.815 +pair_coeff * * oxdna2/dh 0.1 0.2 0.815 + +# NVE ensemble +fix 1 all nve/asphere +#fix 2 all langevin ${T} ${T} 2.5 457145 angmom 10 + +timestep 1e-5 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 3.8 + +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 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.6389877 + ghost atom cutoff = 5.6389877 + binsize = 2.8194939, bins = 36 36 36 + 5 neighbor lists, perpetual/occasional/extra = 5 0 0 + (1) pair oxdna2/excv, perpetual + attributes: half, newton off + pair build: half/bin/newtoff + stencil: full/bin/3d + bin: standard + (2) pair oxdna2/hbond, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (3) pair oxdna2/xstk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (4) pair oxdna2/coaxstk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (5) pair oxdna2/dh, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none +WARNING: Communication cutoff adjusted to 5.638987723814632 (../comm.cpp:739) +0 ekin = 20.4724634226502 | erot = 21.0406985312466 | epot = -222.283862600785 | etot = -180.770700646889 +Per MPI rank memory allocation (min/avg/max) = 9.726 | 9.726 | 9.726 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 0.092845639 -1.5501211 0.04820308 -1.3635905 -9.0052368e-06 1000000 +1000 ekin = 20.531989141805 | erot = 21.2158633183735 | epot = -222.518553109361 | etot = -180.770700649183 +2000 ekin = 20.585620972069 | erot = 21.3918594352261 | epot = -222.748181058335 | etot = -180.77070065104 +3000 ekin = 20.6239332104642 | erot = 21.5529389082728 | epot = -222.947572771312 | etot = -180.770700652575 +4000 ekin = 20.6395549184482 | erot = 21.6854113323895 | epot = -223.095666904229 | etot = -180.770700653391 +5000 ekin = 20.6295551742564 | erot = 21.7809539301805 | epot = -223.181209757876 | etot = -180.770700653439 +6000 ekin = 20.5959625511846 | erot = 21.8369756530727 | epot = -223.203638857302 | etot = -180.770700653045 +7000 ekin = 20.5431034482068 | erot = 21.8556844173875 | epot = -223.169488517717 | etot = -180.770700652122 +8000 ekin = 20.4774701419091 | erot = 21.8437134145374 | epot = -223.091884207389 | etot = -180.770700650943 +9000 ekin = 20.4074566554237 | erot = 21.8097283692398 | epot = -222.98788567426 | etot = -180.770700649597 +10000 ekin = 20.3427303660295 | erot = 21.7629575866663 | epot = -222.876388600949 | etot = -180.770700648253 +11000 ekin = 20.2927407149576 | erot = 21.7112100845349 | epot = -222.774651446682 | etot = -180.770700647189 +12000 ekin = 20.2665977502212 | erot = 21.6594999867139 | epot = -222.696798383221 | etot = -180.770700646286 +13000 ekin = 20.2733920359445 | erot = 21.6092715397933 | epot = -222.653364221616 | etot = -180.770700645878 +14000 ekin = 20.3196524789068 | erot = 21.5586630974992 | epot = -222.649016222075 | etot = -180.770700645669 +15000 ekin = 20.4104009374289 | erot = 21.5031572556306 | epot = -222.684258838857 | etot = -180.770700645798 +16000 ekin = 20.5472869005792 | erot = 21.4346177247041 | epot = -222.752605272036 | etot = -180.770700646753 +17000 ekin = 20.7266657908773 | erot = 21.3426631585217 | epot = -222.840029597232 | etot = -180.770700647833 +18000 ekin = 20.9417612759979 | erot = 21.2178611180927 | epot = -222.930323042997 | etot = -180.770700648907 +19000 ekin = 21.1819308659397 | erot = 21.0532289630294 | epot = -223.00586047892 | etot = -180.770700649951 +20000 ekin = 21.4358169889474 | erot = 20.8473069564707 | epot = -223.053824595387 | etot = -180.770700649969 +21000 ekin = 21.6968513750997 | erot = 20.6066744652586 | epot = -223.074226489837 | etot = -180.770700649479 +22000 ekin = 21.9614458442782 | erot = 20.3429420444511 | epot = -223.07508853737 | etot = -180.770700648641 +23000 ekin = 22.22760997557 | erot = 20.0703385165243 | epot = -223.068649139875 | etot = -180.770700647781 +24000 ekin = 22.4935893196671 | erot = 19.8020671721666 | epot = -223.066357139276 | etot = -180.770700647443 +25000 ekin = 22.7566064548224 | erot = 19.5464828008842 | epot = -223.073789902976 | etot = -180.770700647269 +26000 ekin = 23.0126717548395 | erot = 19.3065017718468 | epot = -223.089874174572 | etot = -180.770700647886 +27000 ekin = 23.255041706059 | erot = 19.0797753474573 | epot = -223.105517701933 | etot = -180.770700648417 +28000 ekin = 23.4774329734801 | erot = 18.864619729958 | epot = -223.112753352067 | etot = -180.770700648629 +29000 ekin = 23.674792772066 | erot = 18.662865341183 | epot = -223.108358761694 | etot = -180.770700648445 +30000 ekin = 23.8432321400243 | erot = 18.481221698364 | epot = -223.095154486375 | etot = -180.770700647987 +31000 ekin = 23.9793041752225 | erot = 18.3307845334023 | epot = -223.08078935577 | etot = -180.770700647145 +32000 ekin = 24.0810246040231 | erot = 18.2261577056005 | epot = -223.07788295592 | etot = -180.770700646296 +33000 ekin = 24.1468986449394 | erot = 18.1820705445407 | epot = -223.09966983514 | etot = -180.77070064566 +34000 ekin = 24.175661513286 | erot = 18.2103812210173 | epot = -223.156743379607 | etot = -180.770700645304 +35000 ekin = 24.1663193894648 | erot = 18.3185351073568 | epot = -223.25555514209 | etot = -180.770700645268 +36000 ekin = 24.1167205812961 | erot = 18.5091649894186 | epot = -223.396586216222 | etot = -180.770700645508 +37000 ekin = 24.0274860006133 | erot = 18.7785134320987 | epot = -223.576700078937 | etot = -180.770700646225 +38000 ekin = 23.8991479078982 | erot = 19.1166063146994 | epot = -223.78645486989 | etot = -180.770700647292 +39000 ekin = 23.7326911853235 | erot = 19.5069160952492 | epot = -224.010307929336 | etot = -180.770700648763 +40000 ekin = 23.529422307212 | erot = 19.9254673141826 | epot = -224.225590272293 | etot = -180.770700650898 +41000 ekin = 23.2899396141392 | erot = 20.340809778056 | epot = -224.401450045566 | etot = -180.770700653371 +42000 ekin = 23.0154529235023 | erot = 20.7165619564846 | epot = -224.502715535761 | etot = -180.770700655775 +43000 ekin = 22.7111536814278 | erot = 21.0163895622229 | epot = -224.498243901358 | etot = -180.770700657707 +44000 ekin = 22.3710575806355 | erot = 21.2060371289781 | epot = -224.347795365753 | etot = -180.770700656139 +45000 ekin = 22.0515843162891 | erot = 21.2588026881768 | epot = -224.081087646891 | etot = -180.770700642425 +46000 ekin = 21.7855632553136 | erot = 21.2036013766602 | epot = -223.759865260062 | etot = -180.770700628088 +47000 ekin = 21.5167766971458 | erot = 21.065636702367 | epot = -223.353114011015 | etot = -180.770700611502 +48000 ekin = 21.4540196107337 | erot = 20.8430832424325 | epot = -223.067803499525 | etot = -180.770700646359 +49000 ekin = 21.3647564765278 | erot = 20.5521507191688 | epot = -222.687607816921 | etot = -180.770700621224 +50000 ekin = 21.3125768184621 | erot = 20.2526464671332 | epot = -222.335923904309 | etot = -180.770700618714 +51000 ekin = 21.2949924810838 | erot = 19.9798421626043 | epot = -222.045535260404 | etot = -180.770700616716 +52000 ekin = 21.3137144249685 | erot = 19.7627691343687 | epot = -221.847184173962 | etot = -180.770700614625 +53000 ekin = 21.3664076685105 | erot = 19.6202359856899 | epot = -221.757344279694 | etot = -180.770700625493 +54000 ekin = 21.421424552406 | erot = 19.55882323195 | epot = -221.750948393747 | etot = -180.770700609391 +55000 ekin = 21.5995673396093 | erot = 19.5805214885678 | epot = -221.950789453583 | etot = -180.770700625406 +56000 ekin = 21.7643125668307 | erot = 19.6816042107778 | epot = -222.216617401429 | etot = -180.77070062382 +57000 ekin = 21.9221309084445 | erot = 19.8499880475953 | epot = -222.542819582064 | etot = -180.770700626024 +58000 ekin = 22.0666093644392 | erot = 20.0713856445716 | epot = -222.908695636277 | etot = -180.770700627266 +59000 ekin = 22.1910921687949 | erot = 20.328402409601 | epot = -223.290195207095 | etot = -180.770700628699 +60000 ekin = 22.2920682490237 | erot = 20.600331953154 | epot = -223.663100832376 | etot = -180.770700630198 +61000 ekin = 22.3680528265789 | erot = 20.864561419886 | epot = -224.003314878046 | etot = -180.770700631581 +62000 ekin = 22.4198570332632 | erot = 21.0983714926627 | epot = -224.288929158678 | etot = -180.770700632752 +63000 ekin = 22.4500800739919 | erot = 21.2815521440893 | epot = -224.502332851296 | etot = -180.770700633215 +64000 ekin = 22.4634052763981 | erot = 21.3990470998276 | epot = -224.633153009903 | etot = -180.770700633677 +65000 ekin = 22.4639885390962 | erot = 21.4413332838522 | epot = -224.676022456447 | etot = -180.770700633499 +66000 ekin = 22.4559522488541 | erot = 21.4074154510862 | epot = -224.634068332758 | etot = -180.770700632817 +67000 ekin = 22.4417384097823 | erot = 21.3051580893559 | epot = -224.517597130738 | etot = -180.770700631599 +68000 ekin = 22.4218785446456 | erot = 21.1490017805238 | epot = -224.341580956059 | etot = -180.77070063089 +69000 ekin = 22.3954651199574 | erot = 20.9555571676353 | epot = -224.121722917262 | etot = -180.77070062967 +70000 ekin = 22.3613349801191 | erot = 20.7433545871753 | epot = -223.875390195706 | etot = -180.770700628411 +71000 ekin = 22.3171019087139 | erot = 20.5301141425045 | epot = -223.617916679046 | etot = -180.770700627827 +72000 ekin = 22.2595195485148 | erot = 20.329630938296 | epot = -223.359851114099 | etot = -180.770700627288 +73000 ekin = 22.1869461213879 | erot = 20.1521902584585 | epot = -223.109837006429 | etot = -180.770700626583 +74000 ekin = 22.0990935565687 | erot = 20.0059494138148 | epot = -222.875743596757 | etot = -180.770700626373 +75000 ekin = 21.9959491639287 | erot = 19.8965902063256 | epot = -222.663239996049 | etot = -180.770700625795 +76000 ekin = 21.8806005890451 | erot = 19.8284243363261 | epot = -222.47972555068 | etot = -180.770700625309 +77000 ekin = 21.7590261899816 | erot = 19.8043252195866 | epot = -222.334052034218 | etot = -180.77070062465 +78000 ekin = 21.639241983951 | erot = 19.8262630279238 | epot = -222.236205635988 | etot = -180.770700624113 +79000 ekin = 21.5302317519724 | erot = 19.8938812521579 | epot = -222.19481362777 | etot = -180.77070062364 +80000 ekin = 21.4402276725665 | erot = 20.0060100278945 | epot = -222.216938324075 | etot = -180.770700623614 +81000 ekin = 21.3741486759864 | erot = 20.1585144791611 | epot = -222.30336377944 | etot = -180.770700624292 +82000 ekin = 21.3325013763512 | erot = 20.3431413542723 | epot = -222.446343355881 | etot = -180.770700625258 +83000 ekin = 21.3128808684044 | erot = 20.5483309907718 | epot = -222.63191248578 | etot = -180.770700626604 +84000 ekin = 21.3107661707936 | erot = 20.760791978517 | epot = -222.842258777119 | etot = -180.770700627809 +85000 ekin = 21.3216301567282 | erot = 20.967841853924 | epot = -223.060172639486 | etot = -180.770700628834 +86000 ekin = 21.3400295156728 | erot = 21.1566564817949 | epot = -223.267386627524 | etot = -180.770700630056 +87000 ekin = 21.3617783036996 | erot = 21.3170902458385 | epot = -223.449569179882 | etot = -180.770700630344 +88000 ekin = 21.3873913218412 | erot = 21.4454439910409 | epot = -223.603535942848 | etot = -180.770700629966 +89000 ekin = 21.4215740693991 | erot = 21.5439953706444 | epot = -223.736270068948 | etot = -180.770700628904 +90000 ekin = 21.4723781618092 | erot = 21.6216769093334 | epot = -223.864755698469 | etot = -180.770700627326 +91000 ekin = 21.5494066254721 | erot = 21.6927202486451 | epot = -224.012827499722 | etot = -180.770700625605 +92000 ekin = 21.6619209347598 | erot = 21.7730744492999 | epot = -224.205696008348 | etot = -180.770700624289 +93000 ekin = 21.8158778641473 | erot = 21.8756732628035 | epot = -224.462251750825 | etot = -180.770700623875 +94000 ekin = 22.0110275730999 | erot = 22.0060799403011 | epot = -224.787808138196 | etot = -180.770700624795 +95000 ekin = 22.2387555838385 | erot = 22.1596167137182 | epot = -225.16907292429 | etot = -180.770700626734 +96000 ekin = 22.4832444899363 | erot = 22.3220202374392 | epot = -225.575965356876 | etot = -180.7707006295 +97000 ekin = 22.7237276202696 | erot = 22.4720556690115 | epot = -225.966483921719 | etot = -180.770700632438 +98000 ekin = 22.9377647716045 | erot = 22.5858660312272 | epot = -226.294331437119 | etot = -180.770700634287 +99000 ekin = 23.1071231637242 | erot = 22.6457411046182 | epot = -226.523564904806 | etot = -180.770700636464 +100000 ekin = 23.2156001924317 | erot = 22.6390310936005 | epot = -226.625331923823 | etot = -180.770700637791 + 100000 0.10528617 -1.5761124 0.044860201 -1.3743901 -1.9205819e-05 1000000 +Loop time of 81.8713 on 1 procs for 100000 steps with 148 atoms + +Performance: 1055.315 tau/day, 1221.430 timesteps/s +99.8% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 78.718 | 78.718 | 78.718 | 0.0 | 96.15 +Bond | 0.97064 | 0.97064 | 0.97064 | 0.0 | 1.19 +Neigh | 0.016915 | 0.016915 | 0.016915 | 0.0 | 0.02 +Comm | 0.027127 | 0.027127 | 0.027127 | 0.0 | 0.03 +Output | 0.12162 | 0.12162 | 0.12162 | 0.0 | 0.15 +Modify | 1.9185 | 1.9185 | 1.9185 | 0.0 | 2.34 +Other | | 0.09845 | | | 0.12 + +Nlocal: 148.000 ave 148 max 148 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0.00000 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 4199.00 ave 4199 max 4199 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 4199 +Ave neighs/atom = 28.371622 +Ave special neighs/atom = 6.0000000 +Neighbor list builds = 100 +Dangerous builds = 0 + +#write_data last_config.${number}.* nocoeff +#write_restart last_config.${number}.* +Total wall time: 0:01:21 diff --git a/examples/PACKAGES/cgdna/examples/oxDNA2/dsring/log.2Jul21.dsring.g++.4 b/examples/PACKAGES/cgdna/examples/oxDNA2/dsring/log.2Jul21.dsring.g++.4 new file mode 100644 index 0000000000..1b2e2b23dc --- /dev/null +++ b/examples/PACKAGES/cgdna/examples/oxDNA2/dsring/log.2Jul21.dsring.g++.4 @@ -0,0 +1,279 @@ +LAMMPS (2 Jul 2021) +variable number equal 5 +variable ofreq equal 1000 +variable efreq equal 1000 +variable T equal 0.1 +variable rhos equal 0.2 + +units lj + +dimension 3 + +newton off + +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:157) +atom_modify sort 0 1.0 + +# Pair interactions require lists of neighbours to be calculated +neighbor 2.0 bin +neigh_modify every 1 delay 0 check yes + +read_data data.dsring +Reading data file ... + orthogonal box = (0.0000000 0.0000000 0.0000000) to (100.00000 100.00000 100.00000) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 148 atoms + reading velocities ... + 148 velocities + scanning bonds ... + 2 = max bonds/atom + 148 ellipsoids + reading bonds ... + 148 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.001 seconds + read_data CPU = 0.008 seconds + +set atom * mass 3.1575 +Setting atom values ... + 148 settings made for mass + +group all type 1 4 +148 atoms in group all + +# oxDNA2 bond interactions - FENE backbone +bond_style oxdna2/fene +bond_coeff * 2.0 0.25 0.7564 +special_bonds lj 0 1 1 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000 seconds + +# oxDNA2 pair interactions +pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh +pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 +pair_coeff * * oxdna2/stk seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/hbond seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 1 4 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 2 3 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 +pair_coeff * * oxdna2/dh ${T} ${rhos} 0.815 +pair_coeff * * oxdna2/dh 0.1 ${rhos} 0.815 +pair_coeff * * oxdna2/dh 0.1 0.2 0.815 + +# NVE ensemble +fix 1 all nve/asphere +#fix 2 all langevin ${T} ${T} 2.5 457145 angmom 10 + +timestep 1e-5 + +#comm_style tiled +fix 3 all balance 1000 1.03 shift xyz 10 1.03 +comm_modify cutoff 3.8 + +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 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.6389877 + ghost atom cutoff = 5.6389877 + binsize = 2.8194939, bins = 36 36 36 + 5 neighbor lists, perpetual/occasional/extra = 5 0 0 + (1) pair oxdna2/excv, perpetual + attributes: half, newton off + pair build: half/bin/newtoff + stencil: full/bin/3d + bin: standard + (2) pair oxdna2/hbond, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (3) pair oxdna2/xstk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (4) pair oxdna2/coaxstk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (5) pair oxdna2/dh, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none +WARNING: Communication cutoff adjusted to 5.638987723814632 (../comm.cpp:739) +0 ekin = 20.4724634226502 | erot = 21.0406985312466 | epot = -222.283862600785 | etot = -180.770700646889 +Per MPI rank memory allocation (min/avg/max) = 9.508 | 9.558 | 9.632 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 0.092845639 -1.5501211 0.04820308 -1.3635905 -9.0052368e-06 1000000 +1000 ekin = 20.531989141805 | erot = 21.2158633183735 | epot = -222.518553109361 | etot = -180.770700649183 +2000 ekin = 20.585620972069 | erot = 21.391859435226 | epot = -222.748181058335 | etot = -180.77070065104 +3000 ekin = 20.6239332104643 | erot = 21.5529389082727 | epot = -222.947572771312 | etot = -180.770700652575 +4000 ekin = 20.6395549184482 | erot = 21.6854113323894 | epot = -223.095666904229 | etot = -180.770700653391 +5000 ekin = 20.6295551742564 | erot = 21.7809539301804 | epot = -223.181209757876 | etot = -180.770700653439 +6000 ekin = 20.5959625511847 | erot = 21.8369756530726 | epot = -223.203638857302 | etot = -180.770700653045 +7000 ekin = 20.5431034482068 | erot = 21.8556844173874 | epot = -223.169488517717 | etot = -180.770700652122 +8000 ekin = 20.4774701419092 | erot = 21.8437134145373 | epot = -223.091884207389 | etot = -180.770700650943 +9000 ekin = 20.4074566554239 | erot = 21.8097283692397 | epot = -222.987885674261 | etot = -180.770700649597 +10000 ekin = 20.3427303660297 | erot = 21.7629575866662 | epot = -222.876388600948 | etot = -180.770700648253 +11000 ekin = 20.2927407149578 | erot = 21.7112100845349 | epot = -222.774651446682 | etot = -180.77070064719 +12000 ekin = 20.2665977502213 | erot = 21.6594999867139 | epot = -222.696798383222 | etot = -180.770700646287 +13000 ekin = 20.2733920359447 | erot = 21.6092715397934 | epot = -222.653364221616 | etot = -180.770700645878 +14000 ekin = 20.3196524789069 | erot = 21.5586630974992 | epot = -222.649016222076 | etot = -180.770700645669 +15000 ekin = 20.410400937429 | erot = 21.5031572556308 | epot = -222.684258838858 | etot = -180.770700645798 +16000 ekin = 20.5472869005792 | erot = 21.4346177247042 | epot = -222.752605272036 | etot = -180.770700646753 +17000 ekin = 20.7266657908773 | erot = 21.3426631585219 | epot = -222.840029597232 | etot = -180.770700647833 +18000 ekin = 20.9417612759978 | erot = 21.2178611180929 | epot = -222.930323042998 | etot = -180.770700648907 +19000 ekin = 21.1819308659395 | erot = 21.0532289630295 | epot = -223.005860478921 | etot = -180.770700649952 +20000 ekin = 21.4358169889472 | erot = 20.8473069564709 | epot = -223.053824595387 | etot = -180.770700649969 +21000 ekin = 21.6968513750994 | erot = 20.6066744652587 | epot = -223.074226489837 | etot = -180.770700649479 +22000 ekin = 21.9614458442779 | erot = 20.3429420444511 | epot = -223.07508853737 | etot = -180.770700648641 +23000 ekin = 22.2276099755697 | erot = 20.0703385165243 | epot = -223.068649139875 | etot = -180.770700647781 +24000 ekin = 22.4935893196667 | erot = 19.8020671721665 | epot = -223.066357139277 | etot = -180.770700647443 +25000 ekin = 22.756606454822 | erot = 19.5464828008841 | epot = -223.073789902976 | etot = -180.77070064727 +26000 ekin = 23.0126717548392 | erot = 19.3065017718467 | epot = -223.089874174572 | etot = -180.770700647886 +27000 ekin = 23.2550417060587 | erot = 19.0797753474572 | epot = -223.105517701932 | etot = -180.770700648417 +28000 ekin = 23.4774329734798 | erot = 18.8646197299578 | epot = -223.112753352067 | etot = -180.770700648629 +29000 ekin = 23.6747927720656 | erot = 18.6628653411828 | epot = -223.108358761693 | etot = -180.770700648445 +30000 ekin = 23.843232140024 | erot = 18.4812216983639 | epot = -223.095154486375 | etot = -180.770700647987 +31000 ekin = 23.9793041752223 | erot = 18.330784533402 | epot = -223.08078935577 | etot = -180.770700647146 +32000 ekin = 24.081024604023 | erot = 18.2261577056003 | epot = -223.077882955919 | etot = -180.770700646296 +33000 ekin = 24.1468986449394 | erot = 18.1820705445404 | epot = -223.09966983514 | etot = -180.77070064566 +34000 ekin = 24.175661513286 | erot = 18.2103812210168 | epot = -223.156743379607 | etot = -180.770700645304 +35000 ekin = 24.166319389465 | erot = 18.3185351073562 | epot = -223.255555142089 | etot = -180.770700645268 +36000 ekin = 24.1167205812963 | erot = 18.509164989418 | epot = -223.396586216223 | etot = -180.770700645508 +37000 ekin = 24.0274860006135 | erot = 18.778513432098 | epot = -223.576700078937 | etot = -180.770700646225 +38000 ekin = 23.8991479078985 | erot = 19.1166063146986 | epot = -223.78645486989 | etot = -180.770700647293 +39000 ekin = 23.7326911853237 | erot = 19.5069160952483 | epot = -224.010307929335 | etot = -180.770700648763 +40000 ekin = 23.5294223072123 | erot = 19.9254673141817 | epot = -224.225590272292 | etot = -180.770700650898 +41000 ekin = 23.2899396141395 | erot = 20.3408097780551 | epot = -224.401450045567 | etot = -180.770700653372 +42000 ekin = 23.0154529235027 | erot = 20.7165619564837 | epot = -224.502715535762 | etot = -180.770700655775 +43000 ekin = 22.7111536814281 | erot = 21.0163895622221 | epot = -224.498243901358 | etot = -180.770700657708 +44000 ekin = 22.3710575806358 | erot = 21.2060371289775 | epot = -224.347795365753 | etot = -180.77070065614 +45000 ekin = 22.0515843162892 | erot = 21.2588026881763 | epot = -224.081087646891 | etot = -180.770700642425 +46000 ekin = 21.7855632553138 | erot = 21.2036013766598 | epot = -223.759865260062 | etot = -180.770700628088 +47000 ekin = 21.5167766971457 | erot = 21.0656367023666 | epot = -223.353114011016 | etot = -180.770700611503 +48000 ekin = 21.454019610733 | erot = 20.8430832424322 | epot = -223.067803499525 | etot = -180.77070064636 +49000 ekin = 21.3647564765269 | erot = 20.5521507191685 | epot = -222.687607816921 | etot = -180.770700621226 +50000 ekin = 21.312576818461 | erot = 20.252646467133 | epot = -222.335923904309 | etot = -180.770700618715 +51000 ekin = 21.2949924810824 | erot = 19.9798421626041 | epot = -222.045535260404 | etot = -180.770700616717 +52000 ekin = 21.3137144249669 | erot = 19.7627691343685 | epot = -221.847184173962 | etot = -180.770700614627 +53000 ekin = 21.3664076685088 | erot = 19.6202359856897 | epot = -221.757344279693 | etot = -180.770700625495 +54000 ekin = 21.4214245524042 | erot = 19.5588232319498 | epot = -221.750948393746 | etot = -180.770700609392 +55000 ekin = 21.5995673396072 | erot = 19.5805214885676 | epot = -221.950789453582 | etot = -180.770700625407 +56000 ekin = 21.7643125668285 | erot = 19.6816042107776 | epot = -222.216617401428 | etot = -180.770700623822 +57000 ekin = 21.9221309084424 | erot = 19.8499880475952 | epot = -222.542819582063 | etot = -180.770700626025 +58000 ekin = 22.0666093644371 | erot = 20.0713856445716 | epot = -222.908695636277 | etot = -180.770700627268 +59000 ekin = 22.191092168793 | erot = 20.3284024096011 | epot = -223.290195207095 | etot = -180.7707006287 +60000 ekin = 22.292068249022 | erot = 20.6003319531543 | epot = -223.663100832376 | etot = -180.7707006302 +61000 ekin = 22.3680528265774 | erot = 20.8645614198865 | epot = -224.003314878046 | etot = -180.770700631582 +62000 ekin = 22.4198570332621 | erot = 21.0983714926634 | epot = -224.288929158679 | etot = -180.770700632754 +63000 ekin = 22.450080073991 | erot = 21.2815521440901 | epot = -224.502332851297 | etot = -180.770700633216 +64000 ekin = 22.4634052763974 | erot = 21.3990470998285 | epot = -224.633153009904 | etot = -180.770700633678 +65000 ekin = 22.4639885390957 | erot = 21.4413332838532 | epot = -224.676022456449 | etot = -180.7707006335 +66000 ekin = 22.4559522488539 | erot = 21.4074154510872 | epot = -224.634068332759 | etot = -180.770700632818 +67000 ekin = 22.4417384097822 | erot = 21.3051580893569 | epot = -224.517597130739 | etot = -180.7707006316 +68000 ekin = 22.4218785446457 | erot = 21.1490017805248 | epot = -224.341580956061 | etot = -180.770700630891 +69000 ekin = 22.3954651199575 | erot = 20.9555571676363 | epot = -224.121722917264 | etot = -180.77070062967 +70000 ekin = 22.3613349801193 | erot = 20.7433545871763 | epot = -223.875390195707 | etot = -180.770700628412 +71000 ekin = 22.317101908714 | erot = 20.5301141425054 | epot = -223.617916679047 | etot = -180.770700627827 +72000 ekin = 22.2595195485149 | erot = 20.3296309382967 | epot = -223.3598511141 | etot = -180.770700627289 +73000 ekin = 22.186946121388 | erot = 20.1521902584591 | epot = -223.109837006431 | etot = -180.770700626584 +74000 ekin = 22.0990935565685 | erot = 20.0059494138152 | epot = -222.875743596758 | etot = -180.770700626374 +75000 ekin = 21.9959491639285 | erot = 19.8965902063258 | epot = -222.66323999605 | etot = -180.770700625796 +76000 ekin = 21.8806005890447 | erot = 19.8284243363262 | epot = -222.47972555068 | etot = -180.770700625309 +77000 ekin = 21.7590261899811 | erot = 19.8043252195865 | epot = -222.334052034218 | etot = -180.77070062465 +78000 ekin = 21.6392419839504 | erot = 19.8262630279235 | epot = -222.236205635988 | etot = -180.770700624114 +79000 ekin = 21.5302317519716 | erot = 19.8938812521573 | epot = -222.19481362777 | etot = -180.770700623641 +80000 ekin = 21.4402276725656 | erot = 20.0060100278937 | epot = -222.216938324074 | etot = -180.770700623615 +81000 ekin = 21.3741486759853 | erot = 20.1585144791602 | epot = -222.303363779439 | etot = -180.770700624293 +82000 ekin = 21.3325013763501 | erot = 20.3431413542714 | epot = -222.44634335588 | etot = -180.770700625258 +83000 ekin = 21.3128808684032 | erot = 20.5483309907707 | epot = -222.631912485778 | etot = -180.770700626604 +84000 ekin = 21.3107661707924 | erot = 20.7607919785161 | epot = -222.842258777118 | etot = -180.77070062781 +85000 ekin = 21.3216301567271 | erot = 20.9678418539233 | epot = -223.060172639485 | etot = -180.770700628834 +86000 ekin = 21.3400295156717 | erot = 21.1566564817944 | epot = -223.267386627523 | etot = -180.770700630057 +87000 ekin = 21.3617783036987 | erot = 21.3170902458384 | epot = -223.449569179882 | etot = -180.770700630345 +88000 ekin = 21.3873913218405 | erot = 21.4454439910411 | epot = -223.603535942848 | etot = -180.770700629967 +89000 ekin = 21.4215740693986 | erot = 21.5439953706449 | epot = -223.736270068949 | etot = -180.770700628906 +90000 ekin = 21.4723781618088 | erot = 21.6216769093341 | epot = -223.864755698471 | etot = -180.770700627328 +91000 ekin = 21.5494066254718 | erot = 21.6927202486458 | epot = -224.012827499724 | etot = -180.770700625606 +92000 ekin = 21.6619209347595 | erot = 21.7730744493006 | epot = -224.20569600835 | etot = -180.77070062429 +93000 ekin = 21.815877864147 | erot = 21.8756732628043 | epot = -224.462251750826 | etot = -180.770700623875 +94000 ekin = 22.0110275730996 | erot = 22.0060799403017 | epot = -224.787808138197 | etot = -180.770700624796 +95000 ekin = 22.2387555838383 | erot = 22.1596167137187 | epot = -225.169072924291 | etot = -180.770700626735 +96000 ekin = 22.483244489936 | erot = 22.3220202374395 | epot = -225.575965356877 | etot = -180.770700629501 +97000 ekin = 22.7237276202693 | erot = 22.4720556690117 | epot = -225.96648392172 | etot = -180.770700632439 +98000 ekin = 22.937764771604 | erot = 22.5858660312272 | epot = -226.29433143712 | etot = -180.770700634289 +99000 ekin = 23.1071231637235 | erot = 22.645741104618 | epot = -226.523564904807 | etot = -180.770700636466 +100000 ekin = 23.2156001924308 | erot = 22.6390310936003 | epot = -226.625331923823 | etot = -180.770700637792 + 100000 0.10528617 -1.5761124 0.044860201 -1.3743901 -1.9205819e-05 1000000 +Loop time of 39.1 on 4 procs for 100000 steps with 148 atoms + +Performance: 2209.721 tau/day, 2557.548 timesteps/s +99.5% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 33.685 | 34.998 | 35.676 | 13.1 | 89.51 +Bond | 0.30808 | 0.31468 | 0.31829 | 0.7 | 0.80 +Neigh | 0.008861 | 0.0089438 | 0.009012 | 0.1 | 0.02 +Comm | 0.79376 | 0.80216 | 0.8131 | 0.9 | 2.05 +Output | 0.054153 | 0.056983 | 0.058706 | 0.8 | 0.15 +Modify | 0.55623 | 0.5647 | 0.57239 | 0.9 | 1.44 +Other | | 2.354 | | | 6.02 + +Nlocal: 37.0000 ave 38 max 36 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +Nghost: 111.000 ave 112 max 110 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +Neighs: 1693.75 ave 1737 max 1653 min +Histogram: 1 1 0 0 0 0 0 1 0 1 + +Total # of neighbors = 6775 +Ave neighs/atom = 45.777027 +Ave special neighs/atom = 6.0000000 +Neighbor list builds = 100 +Dangerous builds = 0 + +#write_data last_config.${number}.* nocoeff +#write_restart last_config.${number}.* +Total wall time: 0:00:39