forked from lijiext/lammps
Updated input and log files, amended comment in data files
This commit is contained in:
Oliver Henrich
parent
3acb09e3b1
commit
7bf9757755
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@ -32,7 +32,7 @@ Atoms
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9 3 4.860249842674775e-01 3.518234140414733e-01 3.897628551303121e-01 2 1 1
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10 4 5.999999999999996e-01 -1.332267629550188e-16 -1.110223024625157e-16 2 1 1
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# Atom-ID, translational, rotational velocity
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# Atom-ID, translational velocity, angular momentum
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Velocities
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1 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
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@ -1,6 +1,7 @@
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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 0.1
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units lj
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@ -30,7 +31,7 @@ bond_coeff * 2.0 0.25 0.7525
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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 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
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pair_coeff * * oxdna/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
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pair_coeff * * oxdna/stk seqav ${T} 1.3448 2.6568 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
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pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
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pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
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pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
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@ -39,9 +40,9 @@ pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1
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# NVE ensemble
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fix 1 all nve/dot
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#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
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#fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10
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#fix 1 all nve/asphere
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#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
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#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10
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timestep 1e-5
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@ -72,6 +73,6 @@ fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${e
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#dump_modify out sort id
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#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
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run 10000
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run 1000000
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#write_restart config.${number}.*
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File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
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@ -1,172 +0,0 @@
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LAMMPS (27 Nov 2018)
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using 1 OpenMP thread(s) per MPI task
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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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units lj
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dimension 3
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newton off
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boundary p p p
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atom_style hybrid bond ellipsoid
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atom_modify sort 0 1.0
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# Pair interactions require lists of neighbours to be calculated
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neighbor 1.0 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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orthogonal box = (-20 -20 -20) to (20 20 20)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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10 atoms
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reading velocities ...
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10 velocities
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10 ellipsoids
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scanning bonds ...
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2 = max bonds/atom
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reading bonds ...
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8 bonds
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2 = max # of 1-2 neighbors
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2 = max # of 1-3 neighbors
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2 = max # of 1-4 neighbors
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4 = max # of special neighbors
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set atom * mass 3.1575
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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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# oxDNA bond interactions - FENE backbone
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bond_style oxdna/fene
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bond_coeff * 2.0 0.25 0.7525
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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 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
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pair_coeff * * oxdna/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
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pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
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pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
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pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
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pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
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pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
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# NVE ensemble
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fix 1 all nve/dot
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#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
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#fix 1 all nve/asphere
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#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
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timestep 1e-5
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#comm_style tiled
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#fix 3 all balance 10000 1.1 rcb
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#compute mol all chunk/atom molecule
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#compute mychunk all vcm/chunk mol
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#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
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#dump pos all xyz ${ofreq} traj.${number}.xyz
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#compute quat all property/atom quatw quati quatj quatk
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#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
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#dump_modify quat sort id
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#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
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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}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
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#dump_modify out sort id
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#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
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run 10000
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Neighbor list info ...
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update every 1 steps, delay 0 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 1.92828
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ghost atom cutoff = 1.92828
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binsize = 0.964142, bins = 42 42 42
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5 neighbor lists, perpetual/occasional/extra = 5 0 0
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(1) pair oxdna/excv, perpetual
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attributes: half, newton off
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pair build: half/bin/newtoff
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stencil: half/bin/3d/newtoff
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bin: standard
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(2) pair oxdna/stk, perpetual, copy from (1)
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attributes: half, newton off
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pair build: copy
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stencil: none
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bin: none
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(3) pair oxdna/hbond, perpetual, copy from (1)
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attributes: half, newton off
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pair build: copy
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stencil: none
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bin: none
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(4) pair oxdna/xstk, perpetual, copy from (1)
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attributes: half, newton off
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pair build: copy
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stencil: none
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bin: none
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(5) pair oxdna/coaxstk, perpetual, copy from (1)
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attributes: half, newton off
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pair build: copy
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stencil: none
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bin: none
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Per MPI rank memory allocation (min/avg/max) = 2.859 | 2.859 | 2.859 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 0 -1.4711818 0.0069384985 -1.4642433 -6.2745089e-05
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1000 ekin = 0.00113448721737003 | erot = 0.00413455947734281 | epot = -14.6477022915193 | etot = -14.6424332448246
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2000 ekin = 0.00449927223902336 | erot = 0.0164446434455805 | epot = -14.6633771605337 | etot = -14.6424332448491
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3000 ekin = 0.00997964450841065 | erot = 0.0366523356056461 | epot = -14.6890652250033 | etot = -14.6424332448892
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4000 ekin = 0.0173888111295073 | erot = 0.0643039804300221 | epot = -14.7241260365031 | etot = -14.6424332449436
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5000 ekin = 0.0264744514136619 | erot = 0.0987844033142066 | epot = -14.7676920997383 | etot = -14.6424332450104
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6000 ekin = 0.0369277948556079 | erot = 0.139336571052565 | epot = -14.8186976109956 | etot = -14.6424332450875
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7000 ekin = 0.04839505571915 | erot = 0.18508629569208 | epot = -14.8759145965832 | etot = -14.642433245172
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8000 ekin = 0.0604909336920643 | erot = 0.23507130752353 | epot = -14.9379954864767 | etot = -14.6424332452611
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9000 ekin = 0.0728137406440561 | erot = 0.288273694501537 | epot = -15.003520680497 | etot = -14.6424332453514
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10000 ekin = 0.0849615563085879 | erot = 0.343654369293472 | epot = -15.0710491710418 | etot = -14.6424332454398
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10000 0.0062934486 -1.5138305 0.0067255788 -1.4986088 -9.9021593e-05
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Loop time of 0.141929 on 1 procs for 10000 steps with 10 atoms
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Performance: 60875.649 tau/day, 70457.927 timesteps/s
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99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
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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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---------------------------------------------------------------
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Pair | 0.11467 | 0.11467 | 0.11467 | 0.0 | 80.79
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Bond | 0.0050094 | 0.0050094 | 0.0050094 | 0.0 | 3.53
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.0013616 | 0.0013616 | 0.0013616 | 0.0 | 0.96
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Output | 4.0531e-06 | 4.0531e-06 | 4.0531e-06 | 0.0 | 0.00
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Modify | 0.017901 | 0.017901 | 0.017901 | 0.0 | 12.61
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Other | | 0.002982 | | | 2.10
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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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Nghost: 0 ave 0 max 0 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 43 ave 43 max 43 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 43
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Ave neighs/atom = 4.3
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Ave special neighs/atom = 3.6
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Neighbor list builds = 0
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Dangerous builds = 0
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#write_restart config.${number}.*
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Total wall time: 0:00:00
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@ -1,172 +0,0 @@
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LAMMPS (27 Nov 2018)
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using 1 OpenMP thread(s) per MPI task
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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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units lj
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dimension 3
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newton off
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boundary p p p
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atom_style hybrid bond ellipsoid
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atom_modify sort 0 1.0
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# Pair interactions require lists of neighbours to be calculated
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neighbor 1.0 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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orthogonal box = (-20 -20 -20) to (20 20 20)
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1 by 2 by 2 MPI processor grid
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reading atoms ...
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10 atoms
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reading velocities ...
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10 velocities
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10 ellipsoids
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scanning bonds ...
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2 = max bonds/atom
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reading bonds ...
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8 bonds
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2 = max # of 1-2 neighbors
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2 = max # of 1-3 neighbors
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2 = max # of 1-4 neighbors
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4 = max # of special neighbors
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set atom * mass 3.1575
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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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# oxDNA bond interactions - FENE backbone
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bond_style oxdna/fene
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bond_coeff * 2.0 0.25 0.7525
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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 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
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pair_coeff * * oxdna/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
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pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
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pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
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pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
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pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
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pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
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# NVE ensemble
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fix 1 all nve/dot
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#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
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#fix 1 all nve/asphere
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#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
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timestep 1e-5
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#comm_style tiled
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#fix 3 all balance 10000 1.1 rcb
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#compute mol all chunk/atom molecule
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#compute mychunk all vcm/chunk mol
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#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
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#dump pos all xyz ${ofreq} traj.${number}.xyz
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#compute quat all property/atom quatw quati quatj quatk
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#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
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#dump_modify quat sort id
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#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
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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}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
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#dump_modify out sort id
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#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
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run 10000
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Neighbor list info ...
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update every 1 steps, delay 0 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 1.92828
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ghost atom cutoff = 1.92828
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binsize = 0.964142, bins = 42 42 42
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5 neighbor lists, perpetual/occasional/extra = 5 0 0
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(1) pair oxdna/excv, perpetual
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attributes: half, newton off
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pair build: half/bin/newtoff
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stencil: half/bin/3d/newtoff
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bin: standard
|
||||
(2) pair oxdna/stk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) pair oxdna/hbond, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(4) pair oxdna/xstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(5) pair oxdna/coaxstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.341 | 7.523 | 7.705 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -1.4711818 0.0069384985 -1.4642433 -6.2745089e-05
|
||||
1000 ekin = 0.00113448721737009 | erot = 0.0041345594773427 | epot = -14.6477022915193 | etot = -14.6424332448246
|
||||
2000 ekin = 0.00449927223902292 | erot = 0.0164446434455803 | epot = -14.6633771605337 | etot = -14.6424332448491
|
||||
3000 ekin = 0.00997964450840756 | erot = 0.0366523356056465 | epot = -14.6890652250033 | etot = -14.6424332448892
|
||||
4000 ekin = 0.017388811129498 | erot = 0.0643039804300254 | epot = -14.7241260365031 | etot = -14.6424332449436
|
||||
5000 ekin = 0.0264744514136422 | erot = 0.098784403314214 | epot = -14.7676920997383 | etot = -14.6424332450104
|
||||
6000 ekin = 0.0369277948555727 | erot = 0.139336571052581 | epot = -14.8186976109956 | etot = -14.6424332450875
|
||||
7000 ekin = 0.0483950557190949 | erot = 0.185086295692111 | epot = -14.8759145965832 | etot = -14.642433245172
|
||||
8000 ekin = 0.0604909336919856 | erot = 0.235071307523583 | epot = -14.9379954864767 | etot = -14.6424332452611
|
||||
9000 ekin = 0.0728137406439517 | erot = 0.288273694501617 | epot = -15.003520680497 | etot = -14.6424332453514
|
||||
10000 ekin = 0.0849615563084573 | erot = 0.34365436929359 | epot = -15.0710491710418 | etot = -14.6424332454398
|
||||
10000 0.0062934486 -1.5138305 0.0067255788 -1.4986088 -0.00010196899
|
||||
Loop time of 0.134536 on 4 procs for 10000 steps with 10 atoms
|
||||
|
||||
Performance: 64220.659 tau/day, 74329.466 timesteps/s
|
||||
97.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0030077 | 0.052212 | 0.093066 | 17.4 | 38.81
|
||||
Bond | 0.00061846 | 0.00234 | 0.0039451 | 2.8 | 1.74
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.013431 | 0.014091 | 0.014596 | 0.4 | 10.47
|
||||
Output | 5.0783e-05 | 5.1141e-05 | 5.1498e-05 | 0.0 | 0.04
|
||||
Modify | 0.0011578 | 0.0059478 | 0.010331 | 4.8 | 4.42
|
||||
Other | | 0.05989 | | | 44.52
|
||||
|
||||
Nlocal: 2.5 ave 5 max 0 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||
Nghost: 7.5 ave 10 max 5 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||
Neighs: 17.5 ave 33 max 0 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 70
|
||||
Ave neighs/atom = 7
|
||||
Ave special neighs/atom = 3.6
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
#write_restart config.${number}.*
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -38,7 +38,7 @@ Atoms
|
|||
15 3 4.860249842674773e-01 3.518234140414733e-01 3.897628551303119e-01 2 1 1
|
||||
16 4 5.999999999999995e-01 -3.330669073875470e-17 -3.330669073875470e-16 2 1 1
|
||||
|
||||
# Atom-ID, translational, rotational velocity
|
||||
# Atom-ID, translational velocity, angular momentum
|
||||
Velocities
|
||||
|
||||
1 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
|
|
|
|||
|
|
@ -1,6 +1,7 @@
|
|||
variable number equal 2
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
variable T equal 0.1
|
||||
|
||||
units lj
|
||||
|
||||
|
|
@ -30,7 +31,7 @@ bond_coeff * 2.0 0.25 0.7525
|
|||
# oxDNA pair interactions
|
||||
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
|
||||
pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna/stk seqav ${T} 1.3448 2.6568 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
|
|
@ -39,9 +40,9 @@ pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1
|
|||
|
||||
# NVE ensemble
|
||||
#fix 1 all nve/dot
|
||||
fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10
|
||||
#fix 1 all nve/asphere
|
||||
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10
|
||||
|
||||
timestep 1e-5
|
||||
|
||||
|
|
@ -72,6 +73,6 @@ fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${e
|
|||
#dump_modify out sort id
|
||||
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
run 10000
|
||||
run 1000000
|
||||
|
||||
#write_restart config.${number}.*
|
||||
|
|
|
|||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
|
|
@ -1,172 +0,0 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
variable number equal 2
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
|
||||
units lj
|
||||
|
||||
dimension 3
|
||||
|
||||
newton off
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid
|
||||
atom_modify sort 0 1.0
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
read_data data.duplex2
|
||||
orthogonal box = (-20 -20 -20) to (20 20 20)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
16 atoms
|
||||
reading velocities ...
|
||||
16 velocities
|
||||
16 ellipsoids
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
reading bonds ...
|
||||
13 bonds
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
4 = max # of 1-4 neighbors
|
||||
6 = max # of special neighbors
|
||||
|
||||
set atom * mass 3.1575
|
||||
16 settings made for mass
|
||||
|
||||
group all type 1 4
|
||||
16 atoms in group all
|
||||
|
||||
# oxDNA bond interactions - FENE backbone
|
||||
bond_style oxdna/fene
|
||||
bond_coeff * 2.0 0.25 0.7525
|
||||
|
||||
# oxDNA pair interactions
|
||||
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
|
||||
pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
|
||||
|
||||
# NVE ensemble
|
||||
#fix 1 all nve/dot
|
||||
fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
#fix 1 all nve/asphere
|
||||
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
|
||||
timestep 1e-5
|
||||
|
||||
#comm_style tiled
|
||||
#fix 3 all balance 10000 1.1 rcb
|
||||
|
||||
#compute mol all chunk/atom molecule
|
||||
#compute mychunk all vcm/chunk mol
|
||||
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
|
||||
|
||||
#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||
|
||||
#compute quat all property/atom quatw quati quatj quatk
|
||||
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
||||
#dump_modify quat sort id
|
||||
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
compute epot all pe
|
||||
variable erot equal c_erot
|
||||
variable ekin equal c_ekin
|
||||
variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
|
||||
#dump_modify out sort id
|
||||
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.92828
|
||||
ghost atom cutoff = 1.92828
|
||||
binsize = 0.964142, bins = 42 42 42
|
||||
5 neighbor lists, perpetual/occasional/extra = 5 0 0
|
||||
(1) pair oxdna/excv, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: half/bin/3d/newtoff
|
||||
bin: standard
|
||||
(2) pair oxdna/stk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) pair oxdna/hbond, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(4) pair oxdna/xstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(5) pair oxdna/coaxstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.861 | 2.861 | 2.861 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -1.5402493 0.0070469125 -1.5332024 -8.5641987e-05
|
||||
1000 ekin = 1.54234964773389 | erot = 1.71563526070267 | epot = -24.5477045187653 | etot = -21.2897196103287
|
||||
2000 ekin = 1.85988866919215 | erot = 1.9424302796508 | epot = -24.4843044999595 | etot = -20.6819855511165
|
||||
3000 ekin = 2.68354339452998 | erot = 2.14216528317607 | epot = -24.4019350693561 | etot = -19.57622639165
|
||||
4000 ekin = 2.04461800191989 | erot = 1.49015219763162 | epot = -24.2959428773347 | etot = -20.7611726777832
|
||||
5000 ekin = 1.76794859210155 | erot = 2.54289684465818 | epot = -24.2337587736863 | etot = -19.9229133369266
|
||||
6000 ekin = 3.1106424806079 | erot = 2.04409805200892 | epot = -24.1585729744133 | etot = -19.0038324417964
|
||||
7000 ekin = 3.21360097519306 | erot = 2.71941303605722 | epot = -24.0566262531609 | etot = -18.1236122419107
|
||||
8000 ekin = 2.82489935901743 | erot = 2.66790555575696 | epot = -24.0194805097633 | etot = -18.526675594989
|
||||
9000 ekin = 2.69381302856378 | erot = 2.59107820129446 | epot = -23.9216126050554 | etot = -18.6367213751972
|
||||
10000 ekin = 2.65765007662471 | erot = 1.95562671446597 | epot = -23.7978334881241 | etot = -19.1845566970334
|
||||
10000 0.11811778 -1.4992295 0.011864944 -1.3212615 -0.00013416809
|
||||
Loop time of 0.295538 on 1 procs for 10000 steps with 16 atoms
|
||||
|
||||
Performance: 29234.801 tau/day, 33836.575 timesteps/s
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.20959 | 0.20959 | 0.20959 | 0.0 | 70.92
|
||||
Bond | 0.0073669 | 0.0073669 | 0.0073669 | 0.0 | 2.49
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0016472 | 0.0016472 | 0.0016472 | 0.0 | 0.56
|
||||
Output | 5.0068e-06 | 5.0068e-06 | 5.0068e-06 | 0.0 | 0.00
|
||||
Modify | 0.073117 | 0.073117 | 0.073117 | 0.0 | 24.74
|
||||
Other | | 0.003813 | | | 1.29
|
||||
|
||||
Nlocal: 16 ave 16 max 16 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 88 ave 88 max 88 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 88
|
||||
Ave neighs/atom = 5.5
|
||||
Ave special neighs/atom = 3.75
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
#write_restart config.${number}.*
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -1,172 +0,0 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
variable number equal 2
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
|
||||
units lj
|
||||
|
||||
dimension 3
|
||||
|
||||
newton off
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid
|
||||
atom_modify sort 0 1.0
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
read_data data.duplex2
|
||||
orthogonal box = (-20 -20 -20) to (20 20 20)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
16 atoms
|
||||
reading velocities ...
|
||||
16 velocities
|
||||
16 ellipsoids
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
reading bonds ...
|
||||
13 bonds
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
4 = max # of 1-4 neighbors
|
||||
6 = max # of special neighbors
|
||||
|
||||
set atom * mass 3.1575
|
||||
16 settings made for mass
|
||||
|
||||
group all type 1 4
|
||||
16 atoms in group all
|
||||
|
||||
# oxDNA bond interactions - FENE backbone
|
||||
bond_style oxdna/fene
|
||||
bond_coeff * 2.0 0.25 0.7525
|
||||
|
||||
# oxDNA pair interactions
|
||||
pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
|
||||
pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65
|
||||
|
||||
# NVE ensemble
|
||||
#fix 1 all nve/dot
|
||||
fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
#fix 1 all nve/asphere
|
||||
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
|
||||
timestep 1e-5
|
||||
|
||||
#comm_style tiled
|
||||
#fix 3 all balance 10000 1.1 rcb
|
||||
|
||||
#compute mol all chunk/atom molecule
|
||||
#compute mychunk all vcm/chunk mol
|
||||
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
|
||||
|
||||
#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||
|
||||
#compute quat all property/atom quatw quati quatj quatk
|
||||
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
||||
#dump_modify quat sort id
|
||||
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
compute epot all pe
|
||||
variable erot equal c_erot
|
||||
variable ekin equal c_ekin
|
||||
variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
|
||||
#dump_modify out sort id
|
||||
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.92828
|
||||
ghost atom cutoff = 1.92828
|
||||
binsize = 0.964142, bins = 42 42 42
|
||||
5 neighbor lists, perpetual/occasional/extra = 5 0 0
|
||||
(1) pair oxdna/excv, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: half/bin/3d/newtoff
|
||||
bin: standard
|
||||
(2) pair oxdna/stk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) pair oxdna/hbond, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(4) pair oxdna/xstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(5) pair oxdna/coaxstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.466 | 7.648 | 7.83 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -1.5402493 0.0070469125 -1.5332024 -8.5641987e-05
|
||||
1000 ekin = 1.34565986428024 | erot = 2.31051421234078 | epot = -24.5061991591502 | etot = -20.8500250825292
|
||||
2000 ekin = 2.15911766687235 | erot = 2.16031365874707 | epot = -24.4723177103698 | etot = -20.1528863847504
|
||||
3000 ekin = 3.26561948796015 | erot = 2.75651822936604 | epot = -24.412573068346 | etot = -18.3904353510198
|
||||
4000 ekin = 1.92438809241066 | erot = 2.12016940074985 | epot = -24.3496233970111 | etot = -20.3050659038506
|
||||
5000 ekin = 1.35986357015476 | erot = 1.99413493074226 | epot = -24.2789445616949 | etot = -20.9249460607979
|
||||
6000 ekin = 2.19432475124593 | erot = 1.74281260409078 | epot = -24.2128064295788 | etot = -20.2756690742421
|
||||
7000 ekin = 2.65619274477635 | erot = 1.74094257048458 | epot = -24.1673462333493 | etot = -19.7702109180883
|
||||
8000 ekin = 2.51333548501168 | erot = 2.34649854571051 | epot = -24.0812769481836 | etot = -19.2214429174614
|
||||
9000 ekin = 2.24506493169711 | erot = 2.0652555461504 | epot = -23.9906736063989 | etot = -19.6803531285514
|
||||
10000 ekin = 2.36632635249862 | erot = 1.7959247176153 | epot = -23.9002627850602 | etot = -19.7380117149463
|
||||
10000 0.10517006 -1.5057137 0.011947302 -1.345871 -9.5924016e-05
|
||||
Loop time of 0.251867 on 4 procs for 10000 steps with 16 atoms
|
||||
|
||||
Performance: 34303.820 tau/day, 39703.495 timesteps/s
|
||||
97.8% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0035377 | 0.092047 | 0.17435 | 26.0 | 36.55
|
||||
Bond | 0.00065637 | 0.0031857 | 0.0053554 | 3.8 | 1.26
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.013929 | 0.01497 | 0.015733 | 0.6 | 5.94
|
||||
Output | 5.0783e-05 | 5.2691e-05 | 5.3883e-05 | 0.0 | 0.02
|
||||
Modify | 0.0013576 | 0.020825 | 0.040231 | 11.8 | 8.27
|
||||
Other | | 0.1208 | | | 47.96
|
||||
|
||||
Nlocal: 4 ave 8 max 0 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||
Nghost: 9 ave 10 max 8 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Neighs: 34.5 ave 67 max 0 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 138
|
||||
Ave neighs/atom = 8.625
|
||||
Ave special neighs/atom = 3.75
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
#write_restart config.${number}.*
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -32,7 +32,7 @@ Atoms
|
|||
9 3 4.860249842674775e-01 3.518234140414733e-01 3.897628551303121e-01 2 1 1
|
||||
10 4 5.999999999999996e-01 -1.332267629550188e-16 -1.110223024625157e-16 2 1 1
|
||||
|
||||
# Atom-ID, translational, rotational velocity
|
||||
# Atom-ID, translational velocity, angular momentum
|
||||
Velocities
|
||||
|
||||
1 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
|
|
|
|||
|
|
@ -1,6 +1,7 @@
|
|||
variable number equal 1
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
variable T equal 0.1
|
||||
|
||||
units lj
|
||||
|
||||
|
|
@ -30,19 +31,19 @@ bond_coeff * 2.0 0.25 0.7564
|
|||
# oxDNA pair interactions
|
||||
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna2/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/stk seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
|
||||
pair_coeff * * oxdna2/dh 0.1 1.0 0.815
|
||||
pair_coeff * * oxdna2/dh ${T} 1.0 0.815
|
||||
|
||||
# NVE ensemble
|
||||
fix 1 all nve/dot
|
||||
#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
#fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10
|
||||
#fix 1 all nve/asphere
|
||||
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10
|
||||
|
||||
timestep 1e-5
|
||||
|
||||
|
|
@ -73,6 +74,6 @@ fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${e
|
|||
#dump_modify out sort id
|
||||
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
run 10000
|
||||
run 1000000
|
||||
|
||||
#write_restart config.${number}.*
|
||||
|
|
|
|||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
|
|
@ -1,178 +0,0 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
variable number equal 1
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
|
||||
units lj
|
||||
|
||||
dimension 3
|
||||
|
||||
newton off
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid
|
||||
atom_modify sort 0 1.0
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
read_data data.duplex1
|
||||
orthogonal box = (-20 -20 -20) to (20 20 20)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
10 atoms
|
||||
reading velocities ...
|
||||
10 velocities
|
||||
10 ellipsoids
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
reading bonds ...
|
||||
8 bonds
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
2 = max # of 1-4 neighbors
|
||||
4 = max # of special neighbors
|
||||
|
||||
set atom * mass 3.1575
|
||||
10 settings made for mass
|
||||
|
||||
group all type 1 4
|
||||
10 atoms in group all
|
||||
|
||||
# oxDNA bond interactions - FENE backbone
|
||||
bond_style oxdna2/fene
|
||||
bond_coeff * 2.0 0.25 0.7564
|
||||
|
||||
# oxDNA pair interactions
|
||||
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna2/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
|
||||
pair_coeff * * oxdna2/dh 0.1 1.0 0.815
|
||||
|
||||
# NVE ensemble
|
||||
fix 1 all nve/dot
|
||||
#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
#fix 1 all nve/asphere
|
||||
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
|
||||
timestep 1e-5
|
||||
|
||||
#comm_style tiled
|
||||
#fix 3 all balance 10000 1.1 rcb
|
||||
|
||||
#compute mol all chunk/atom molecule
|
||||
#compute mychunk all vcm/chunk mol
|
||||
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
|
||||
|
||||
#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||
|
||||
#compute quat all property/atom quatw quati quatj quatk
|
||||
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
||||
#dump_modify quat sort id
|
||||
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
compute epot all pe
|
||||
variable erot equal c_erot
|
||||
variable ekin equal c_ekin
|
||||
variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
|
||||
#dump_modify out sort id
|
||||
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.6274
|
||||
ghost atom cutoff = 2.6274
|
||||
binsize = 1.3137, bins = 31 31 31
|
||||
6 neighbor lists, perpetual/occasional/extra = 6 0 0
|
||||
(1) pair oxdna2/excv, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: half/bin/3d/newtoff
|
||||
bin: standard
|
||||
(2) pair oxdna2/stk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) pair oxdna2/hbond, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(4) pair oxdna2/xstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(5) pair oxdna2/coaxstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(6) pair oxdna2/dh, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.023 | 3.023 | 3.023 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -1.4712768 0.009525411 -1.4617514 -5.8922361e-05
|
||||
1000 ekin = 0.00113086229080528 | erot = 0.0043101016040658 | epot = -14.6229549982368 | etot = -14.617514034342
|
||||
2000 ekin = 0.0044853322434243 | erot = 0.0171407706505008 | epot = -14.6391401372615 | etot = -14.6175140343675
|
||||
3000 ekin = 0.00995035259649284 | erot = 0.0381961780846485 | epot = -14.6656605650904 | etot = -14.6175140344093
|
||||
4000 ekin = 0.0173418024862054 | erot = 0.0669935184860634 | epot = -14.7018493554381 | etot = -14.6175140344659
|
||||
5000 ekin = 0.0264109356286075 | erot = 0.102878288094517 | epot = -14.7468032582586 | etot = -14.6175140345355
|
||||
6000 ekin = 0.0368533113591442 | erot = 0.14504542056987 | epot = -14.7994127665447 | etot = -14.6175140346157
|
||||
7000 ekin = 0.0483200640564843 | erot = 0.19256586251551 | epot = -14.8583999612756 | etot = -14.6175140347036
|
||||
8000 ekin = 0.0604312317605998 | erot = 0.24441787013151 | epot = -14.9223631366883 | etot = -14.6175140347962
|
||||
9000 ekin = 0.0727907119671751 | erot = 0.299521949931843 | epot = -14.989826696789 | etot = -14.6175140348899
|
||||
10000 ekin = 0.0850022498875221 | erot = 0.356777997217908 | epot = -15.0592942820869 | etot = -14.6175140349815
|
||||
10000 0.006296463 -1.5144685 0.0085391004 -1.4974292 -0.00010794792
|
||||
Loop time of 0.149406 on 1 procs for 10000 steps with 10 atoms
|
||||
|
||||
Performance: 57828.835 tau/day, 66931.522 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.11971 | 0.11971 | 0.11971 | 0.0 | 80.12
|
||||
Bond | 0.0051196 | 0.0051196 | 0.0051196 | 0.0 | 3.43
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0013614 | 0.0013614 | 0.0013614 | 0.0 | 0.91
|
||||
Output | 5.0068e-06 | 5.0068e-06 | 5.0068e-06 | 0.0 | 0.00
|
||||
Modify | 0.018941 | 0.018941 | 0.018941 | 0.0 | 12.68
|
||||
Other | | 0.004268 | | | 2.86
|
||||
|
||||
Nlocal: 10 ave 10 max 10 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 45 ave 45 max 45 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 45
|
||||
Ave neighs/atom = 4.5
|
||||
Ave special neighs/atom = 3.6
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
#write_restart config.${number}.*
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -1,178 +0,0 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
variable number equal 1
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
|
||||
units lj
|
||||
|
||||
dimension 3
|
||||
|
||||
newton off
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid
|
||||
atom_modify sort 0 1.0
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
read_data data.duplex1
|
||||
orthogonal box = (-20 -20 -20) to (20 20 20)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
10 atoms
|
||||
reading velocities ...
|
||||
10 velocities
|
||||
10 ellipsoids
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
reading bonds ...
|
||||
8 bonds
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
2 = max # of 1-4 neighbors
|
||||
4 = max # of special neighbors
|
||||
|
||||
set atom * mass 3.1575
|
||||
10 settings made for mass
|
||||
|
||||
group all type 1 4
|
||||
10 atoms in group all
|
||||
|
||||
# oxDNA bond interactions - FENE backbone
|
||||
bond_style oxdna2/fene
|
||||
bond_coeff * 2.0 0.25 0.7564
|
||||
|
||||
# oxDNA pair interactions
|
||||
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna2/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
|
||||
pair_coeff * * oxdna2/dh 0.1 1.0 0.815
|
||||
|
||||
# NVE ensemble
|
||||
fix 1 all nve/dot
|
||||
#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
#fix 1 all nve/asphere
|
||||
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
|
||||
timestep 1e-5
|
||||
|
||||
#comm_style tiled
|
||||
#fix 3 all balance 10000 1.1 rcb
|
||||
|
||||
#compute mol all chunk/atom molecule
|
||||
#compute mychunk all vcm/chunk mol
|
||||
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
|
||||
|
||||
#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||
|
||||
#compute quat all property/atom quatw quati quatj quatk
|
||||
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
||||
#dump_modify quat sort id
|
||||
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
compute epot all pe
|
||||
variable erot equal c_erot
|
||||
variable ekin equal c_ekin
|
||||
variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
|
||||
#dump_modify out sort id
|
||||
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.6274
|
||||
ghost atom cutoff = 2.6274
|
||||
binsize = 1.3137, bins = 31 31 31
|
||||
6 neighbor lists, perpetual/occasional/extra = 6 0 0
|
||||
(1) pair oxdna2/excv, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: half/bin/3d/newtoff
|
||||
bin: standard
|
||||
(2) pair oxdna2/stk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) pair oxdna2/hbond, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(4) pair oxdna2/xstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(5) pair oxdna2/coaxstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(6) pair oxdna2/dh, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.652 | 7.834 | 8.016 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -1.4712768 0.009525411 -1.4617514 -5.8922361e-05
|
||||
1000 ekin = 0.00113086229080478 | erot = 0.00431010160406708 | epot = -14.6229549982368 | etot = -14.617514034342
|
||||
2000 ekin = 0.00448533224342286 | erot = 0.0171407706505013 | epot = -14.6391401372615 | etot = -14.6175140343675
|
||||
3000 ekin = 0.0099503525964896 | erot = 0.0381961780846438 | epot = -14.6656605650904 | etot = -14.6175140344093
|
||||
4000 ekin = 0.0173418024861991 | erot = 0.0669935184860479 | epot = -14.7018493554381 | etot = -14.6175140344659
|
||||
5000 ekin = 0.0264109356285965 | erot = 0.102878288094482 | epot = -14.7468032582586 | etot = -14.6175140345355
|
||||
6000 ekin = 0.0368533113591268 | erot = 0.145045420569809 | epot = -14.7994127665446 | etot = -14.6175140346156
|
||||
7000 ekin = 0.0483200640564584 | erot = 0.192565862515413 | epot = -14.8583999612755 | etot = -14.6175140347036
|
||||
8000 ekin = 0.0604312317605635 | erot = 0.24441787013137 | epot = -14.9223631366881 | etot = -14.6175140347962
|
||||
9000 ekin = 0.072790711967127 | erot = 0.299521949931654 | epot = -14.9898266967887 | etot = -14.6175140348899
|
||||
10000 ekin = 0.0850022498874609 | erot = 0.356777997217666 | epot = -15.0592942820866 | etot = -14.6175140349815
|
||||
10000 0.006296463 -1.5144685 0.0085391004 -1.4974292 -0.00010794792
|
||||
Loop time of 0.14583 on 4 procs for 10000 steps with 10 atoms
|
||||
|
||||
Performance: 59247.054 tau/day, 68572.979 timesteps/s
|
||||
97.5% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0034175 | 0.055587 | 0.10059 | 17.9 | 38.12
|
||||
Bond | 0.00064635 | 0.002131 | 0.0035357 | 2.5 | 1.46
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.014538 | 0.014932 | 0.015271 | 0.2 | 10.24
|
||||
Output | 5.7459e-05 | 5.7697e-05 | 5.7936e-05 | 0.0 | 0.04
|
||||
Modify | 0.0012829 | 0.0063873 | 0.011321 | 5.2 | 4.38
|
||||
Other | | 0.06674 | | | 45.76
|
||||
|
||||
Nlocal: 2.5 ave 5 max 0 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||
Nghost: 7.5 ave 10 max 5 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||
Neighs: 18.5 ave 35 max 0 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 74
|
||||
Ave neighs/atom = 7.4
|
||||
Ave special neighs/atom = 3.6
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
#write_restart config.${number}.*
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -38,7 +38,7 @@ Atoms
|
|||
15 3 4.860249842674773e-01 3.518234140414733e-01 3.897628551303119e-01 2 1 1
|
||||
16 4 5.999999999999995e-01 -3.330669073875470e-17 -3.330669073875470e-16 2 1 1
|
||||
|
||||
# Atom-ID, translational, rotational velocity
|
||||
# Atom-ID, translational velocity, angular momentum
|
||||
Velocities
|
||||
|
||||
1 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
|
|
|
|||
|
|
@ -1,7 +1,7 @@
|
|||
variable number equal 2
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
|
||||
variable T equal 0.1
|
||||
units lj
|
||||
|
||||
dimension 3
|
||||
|
|
@ -30,19 +30,19 @@ bond_coeff * 2.0 0.25 0.7564
|
|||
# oxDNA pair interactions
|
||||
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna2/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/stk seqav ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
|
||||
pair_coeff * * oxdna2/dh 0.1 1.0 0.815
|
||||
pair_coeff * * oxdna2/dh ${T} 1.0 0.815
|
||||
|
||||
# NVE ensemble
|
||||
#fix 1 all nve/dot
|
||||
fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10
|
||||
#fix 1 all nve/asphere
|
||||
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10
|
||||
|
||||
timestep 1e-5
|
||||
|
||||
|
|
@ -73,6 +73,6 @@ fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${e
|
|||
#dump_modify out sort id
|
||||
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
run 10000
|
||||
run 1000000
|
||||
|
||||
#write_restart config.${number}.*
|
||||
|
|
|
|||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
|
|
@ -1,178 +0,0 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
variable number equal 2
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
|
||||
units lj
|
||||
|
||||
dimension 3
|
||||
|
||||
newton off
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid
|
||||
atom_modify sort 0 1.0
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
read_data data.duplex2
|
||||
orthogonal box = (-20 -20 -20) to (20 20 20)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
16 atoms
|
||||
reading velocities ...
|
||||
16 velocities
|
||||
16 ellipsoids
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
reading bonds ...
|
||||
13 bonds
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
4 = max # of 1-4 neighbors
|
||||
6 = max # of special neighbors
|
||||
|
||||
set atom * mass 3.1575
|
||||
16 settings made for mass
|
||||
|
||||
group all type 1 4
|
||||
16 atoms in group all
|
||||
|
||||
# oxDNA bond interactions - FENE backbone
|
||||
bond_style oxdna2/fene
|
||||
bond_coeff * 2.0 0.25 0.7564
|
||||
|
||||
# oxDNA pair interactions
|
||||
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna2/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
|
||||
pair_coeff * * oxdna2/dh 0.1 1.0 0.815
|
||||
|
||||
# NVE ensemble
|
||||
#fix 1 all nve/dot
|
||||
fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
#fix 1 all nve/asphere
|
||||
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
|
||||
timestep 1e-5
|
||||
|
||||
#comm_style tiled
|
||||
#fix 3 all balance 10000 1.1 rcb
|
||||
|
||||
#compute mol all chunk/atom molecule
|
||||
#compute mychunk all vcm/chunk mol
|
||||
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
|
||||
|
||||
#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||
|
||||
#compute quat all property/atom quatw quati quatj quatk
|
||||
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
||||
#dump_modify quat sort id
|
||||
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
compute epot all pe
|
||||
variable erot equal c_erot
|
||||
variable ekin equal c_ekin
|
||||
variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
|
||||
#dump_modify out sort id
|
||||
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.6274
|
||||
ghost atom cutoff = 2.6274
|
||||
binsize = 1.3137, bins = 31 31 31
|
||||
6 neighbor lists, perpetual/occasional/extra = 6 0 0
|
||||
(1) pair oxdna2/excv, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: half/bin/3d/newtoff
|
||||
bin: standard
|
||||
(2) pair oxdna2/stk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) pair oxdna2/hbond, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(4) pair oxdna2/xstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(5) pair oxdna2/coaxstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(6) pair oxdna2/dh, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.025 | 3.025 | 3.025 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -1.5358787 0.0096742456 -1.5262045 -7.9568629e-05
|
||||
1000 ekin = 1.54282272464468 | erot = 1.71757897250772 | epot = -24.4403527731341 | etot = -21.1799510759817
|
||||
2000 ekin = 1.86109566690716 | erot = 1.93804145796026 | epot = -24.3759816748265 | etot = -20.5768445499591
|
||||
3000 ekin = 2.68769182431188 | erot = 2.14559269500086 | epot = -24.2916556822451 | etot = -19.4583711629324
|
||||
4000 ekin = 2.04710303757243 | erot = 1.48774072590987 | epot = -24.190371461807 | etot = -20.6555276983247
|
||||
5000 ekin = 1.77654023802719 | erot = 2.534186505221 | epot = -24.1246365663843 | etot = -19.8139098231361
|
||||
6000 ekin = 3.12253137872527 | erot = 2.04028266818831 | epot = -24.0491248750916 | etot = -18.886310828178
|
||||
7000 ekin = 3.22418765752177 | erot = 2.72037570174023 | epot = -23.9458569915548 | etot = -18.0012936322928
|
||||
8000 ekin = 2.83204202112963 | erot = 2.67060276413777 | epot = -23.9211291529766 | etot = -18.4184843677092
|
||||
9000 ekin = 2.69585642754481 | erot = 2.59559820250212 | epot = -23.8340823338302 | etot = -18.5426277037833
|
||||
10000 ekin = 2.66058119525512 | erot = 1.95965933336077 | epot = -23.7132443170725 | etot = -19.0930037884566
|
||||
10000 0.11824805 -1.4953627 0.013284973 -1.3157914 -0.00012999454
|
||||
Loop time of 0.32781 on 1 procs for 10000 steps with 16 atoms
|
||||
|
||||
Performance: 26356.746 tau/day, 30505.493 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.24211 | 0.24211 | 0.24211 | 0.0 | 73.86
|
||||
Bond | 0.0075173 | 0.0075173 | 0.0075173 | 0.0 | 2.29
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0014515 | 0.0014515 | 0.0014515 | 0.0 | 0.44
|
||||
Output | 5.4836e-06 | 5.4836e-06 | 5.4836e-06 | 0.0 | 0.00
|
||||
Modify | 0.073331 | 0.073331 | 0.073331 | 0.0 | 22.37
|
||||
Other | | 0.003398 | | | 1.04
|
||||
|
||||
Nlocal: 16 ave 16 max 16 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 116 ave 116 max 116 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 116
|
||||
Ave neighs/atom = 7.25
|
||||
Ave special neighs/atom = 3.75
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
#write_restart config.${number}.*
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -1,178 +0,0 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
variable number equal 2
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
|
||||
units lj
|
||||
|
||||
dimension 3
|
||||
|
||||
newton off
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid
|
||||
atom_modify sort 0 1.0
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
read_data data.duplex2
|
||||
orthogonal box = (-20 -20 -20) to (20 20 20)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
16 atoms
|
||||
reading velocities ...
|
||||
16 velocities
|
||||
16 ellipsoids
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
reading bonds ...
|
||||
13 bonds
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
4 = max # of 1-4 neighbors
|
||||
6 = max # of special neighbors
|
||||
|
||||
set atom * mass 3.1575
|
||||
16 settings made for mass
|
||||
|
||||
group all type 1 4
|
||||
16 atoms in group all
|
||||
|
||||
# oxDNA bond interactions - FENE backbone
|
||||
bond_style oxdna2/fene
|
||||
bond_coeff * 2.0 0.25 0.7564
|
||||
|
||||
# oxDNA pair interactions
|
||||
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna2/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
|
||||
pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
|
||||
pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
|
||||
pair_coeff * * oxdna2/dh 0.1 1.0 0.815
|
||||
|
||||
# NVE ensemble
|
||||
#fix 1 all nve/dot
|
||||
fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
#fix 1 all nve/asphere
|
||||
#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10
|
||||
|
||||
timestep 1e-5
|
||||
|
||||
#comm_style tiled
|
||||
#fix 3 all balance 10000 1.1 rcb
|
||||
|
||||
#compute mol all chunk/atom molecule
|
||||
#compute mychunk all vcm/chunk mol
|
||||
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
|
||||
|
||||
#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||
|
||||
#compute quat all property/atom quatw quati quatj quatk
|
||||
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
||||
#dump_modify quat sort id
|
||||
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
compute epot all pe
|
||||
variable erot equal c_erot
|
||||
variable ekin equal c_ekin
|
||||
variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
|
||||
#dump_modify out sort id
|
||||
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.6274
|
||||
ghost atom cutoff = 2.6274
|
||||
binsize = 1.3137, bins = 31 31 31
|
||||
6 neighbor lists, perpetual/occasional/extra = 6 0 0
|
||||
(1) pair oxdna2/excv, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: half/bin/3d/newtoff
|
||||
bin: standard
|
||||
(2) pair oxdna2/stk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) pair oxdna2/hbond, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(4) pair oxdna2/xstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(5) pair oxdna2/coaxstk, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(6) pair oxdna2/dh, perpetual, copy from (1)
|
||||
attributes: half, newton off
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.777 | 7.959 | 8.142 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -1.5358787 0.0096742456 -1.5262045 -7.9568629e-05
|
||||
1000 ekin = 1.34554291364716 | erot = 2.30525041754444 | epot = -24.3924150888896 | etot = -20.741621757698
|
||||
2000 ekin = 2.15972469811184 | erot = 2.1628675965276 | epot = -24.3548203354875 | etot = -20.0322280408481
|
||||
3000 ekin = 3.26433550542939 | erot = 2.76107866472085 | epot = -24.2947953202752 | etot = -18.269381150125
|
||||
4000 ekin = 1.9203212531997 | erot = 2.13339438425299 | epot = -24.234098584123 | etot = -20.1803829466703
|
||||
5000 ekin = 1.35481075814721 | erot = 2.00854026688447 | epot = -24.1768963201279 | etot = -20.8135452950963
|
||||
6000 ekin = 2.18974627635306 | erot = 1.73271671162435 | epot = -24.1096616118305 | etot = -20.1871986238531
|
||||
7000 ekin = 2.65472853187395 | erot = 1.73258720631296 | epot = -24.0561118130561 | etot = -19.6687960748691
|
||||
8000 ekin = 2.51192327964357 | erot = 2.34132844779952 | epot = -23.9708695663488 | etot = -19.1176178389058
|
||||
9000 ekin = 2.24554900802464 | erot = 2.0522939078286 | epot = -23.874757758319 | etot = -19.5769148424658
|
||||
10000 ekin = 2.36227360512089 | erot = 1.80185994066737 | epot = -23.7793375260418 | etot = -19.6152039802535
|
||||
10000 0.10498994 -1.5020657 0.015857071 -1.3385665 -8.8930899e-05
|
||||
Loop time of 0.291642 on 4 procs for 10000 steps with 16 atoms
|
||||
|
||||
Performance: 29625.313 tau/day, 34288.557 timesteps/s
|
||||
96.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0035026 | 0.1107 | 0.20674 | 28.3 | 37.96
|
||||
Bond | 0.00062203 | 0.0029532 | 0.0049176 | 3.6 | 1.01
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.016712 | 0.018041 | 0.01914 | 0.7 | 6.19
|
||||
Output | 5.0306e-05 | 5.424e-05 | 5.579e-05 | 0.0 | 0.02
|
||||
Modify | 0.0013862 | 0.020914 | 0.039594 | 11.7 | 7.17
|
||||
Other | | 0.139 | | | 47.65
|
||||
|
||||
Nlocal: 4 ave 8 max 0 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||
Nghost: 11 ave 14 max 8 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||
Neighs: 46 ave 89 max 0 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 184
|
||||
Ave neighs/atom = 11.5
|
||||
Ave special neighs/atom = 3.75
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
#write_restart config.${number}.*
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -0,0 +1,73 @@
|
|||
# LAMMPS data file
|
||||
10 atoms
|
||||
10 ellipsoids
|
||||
8 bonds
|
||||
|
||||
4 atom types
|
||||
1 bond types
|
||||
|
||||
# System size
|
||||
-20.000000 20.000000 xlo xhi
|
||||
-20.000000 20.000000 ylo yhi
|
||||
-20.000000 20.000000 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 1.0
|
||||
2 1.0
|
||||
3 1.0
|
||||
4 1.0
|
||||
|
||||
# Atom-ID, type, position, molecule-ID, ellipsoid flag, density
|
||||
Atoms
|
||||
|
||||
1 1 -6.000000000000001e-01 0.000000000000000e+00 0.000000000000000e+00 1 1 1
|
||||
2 2 -4.860249842674776e-01 -3.518234140414736e-01 3.897628551303122e-01 1 1 1
|
||||
3 3 -1.874009511073395e-01 -5.699832309147915e-01 7.795257102606244e-01 1 1 1
|
||||
4 4 1.824198365552941e-01 -5.715968887521518e-01 1.169288565390937e+00 1 1 1
|
||||
5 1 4.829362784135484e-01 -3.560513319622209e-01 1.559051420521249e+00 1 1 1
|
||||
6 4 -4.829362784135484e-01 3.560513319622209e-01 1.559051420521249e+00 2 1 1
|
||||
7 1 -1.824198365552941e-01 5.715968887521516e-01 1.169288565390937e+00 2 1 1
|
||||
8 2 1.874009511073395e-01 5.699832309147913e-01 7.795257102606243e-01 2 1 1
|
||||
9 3 4.860249842674775e-01 3.518234140414733e-01 3.897628551303121e-01 2 1 1
|
||||
10 4 5.999999999999996e-01 -1.332267629550188e-16 -1.110223024625157e-16 2 1 1
|
||||
|
||||
# Atom-ID, translational velocity, angular momentum
|
||||
Velocities
|
||||
|
||||
1 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
2 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
3 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
4 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
5 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
6 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
7 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
8 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
9 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
10 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
|
||||
# Atom-ID, shape, quaternion
|
||||
Ellipsoids
|
||||
|
||||
1 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
|
||||
2 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 9.513258223252946e-01 0.000000000000000e+00 0.000000000000000e+00 3.081869234362515e-01
|
||||
3 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 8.100416404457962e-01 0.000000000000000e+00 0.000000000000000e+00 5.863723567357894e-01
|
||||
4 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 5.899012371043606e-01 0.000000000000000e+00 0.000000000000000e+00 8.074754054847398e-01
|
||||
5 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 3.123349185122326e-01 0.000000000000000e+00 0.000000000000000e+00 9.499720515246527e-01
|
||||
6 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 0.000000000000000e+00 9.499720515246527e-01 -3.123349185122326e-01 -0.000000000000000e+00
|
||||
7 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 0.000000000000000e+00 8.074754054847401e-01 -5.899012371043604e-01 0.000000000000000e+00
|
||||
8 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 0.000000000000000e+00 5.863723567357896e-01 -8.100416404457959e-01 0.000000000000000e+00
|
||||
9 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 -0.000000000000000e+00 -3.081869234362514e-01 9.513258223252947e-01 0.000000000000000e+00
|
||||
10 3.1622776601683795+00 3.1622776601683795+00 3.1622776601683795+00 -0.000000000000000e+00 1.110223024625157e-16 1.000000000000000e+00 -0.000000000000000e+00
|
||||
|
||||
# Bond topology
|
||||
Bonds
|
||||
|
||||
1 1 1 2
|
||||
2 1 2 3
|
||||
3 1 3 4
|
||||
4 1 4 5
|
||||
5 1 6 7
|
||||
6 1 7 8
|
||||
7 1 8 9
|
||||
8 1 9 10
|
||||
|
|
@ -0,0 +1,79 @@
|
|||
variable number equal 1
|
||||
variable ofreq equal 1000
|
||||
variable efreq equal 1000
|
||||
variable T equal 0.1
|
||||
|
||||
units lj
|
||||
|
||||
dimension 3
|
||||
|
||||
newton off
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style hybrid bond ellipsoid
|
||||
atom_modify sort 0 1.0
|
||||
|
||||
# Pair interactions require lists of neighbours to be calculated
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
read_data data.duplex3
|
||||
|
||||
set atom * mass 1.0
|
||||
|
||||
group all type 1 4
|
||||
|
||||
# oxDNA bond interactions - FENE backbone
|
||||
bond_style oxdna2/fene
|
||||
bond_coeff * 2.0 0.25 0.7564
|
||||
|
||||
# oxDNA pair interactions
|
||||
pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
|
||||
pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
|
||||
pair_coeff * * oxdna2/stk seqdep ${T} 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
|
||||
pair_coeff * * oxdna2/hbond 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} 1.0 0.815
|
||||
|
||||
# NVE ensemble
|
||||
fix 1 all nve/dot
|
||||
#fix 1 all nve/dotc/langevin ${T} ${T} 0.03 457145 angmom 10
|
||||
#fix 1 all nve/asphere
|
||||
#fix 2 all langevin ${T} ${T} 0.03 457145 angmom 10
|
||||
|
||||
timestep 1e-5
|
||||
|
||||
#comm_style tiled
|
||||
#fix 3 all balance 10000 1.1 rcb
|
||||
|
||||
#compute mol all chunk/atom molecule
|
||||
#compute mychunk all vcm/chunk mol
|
||||
#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector
|
||||
|
||||
#dump pos all xyz ${ofreq} traj.${number}.xyz
|
||||
|
||||
#compute quat all property/atom quatw quati quatj quatk
|
||||
#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4]
|
||||
#dump_modify quat sort id
|
||||
#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
compute erot all erotate/asphere
|
||||
compute ekin all ke
|
||||
compute epot all pe
|
||||
variable erot equal c_erot
|
||||
variable ekin equal c_ekin
|
||||
variable epot equal c_epot
|
||||
variable etot equal c_erot+c_ekin+c_epot
|
||||
fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes
|
||||
|
||||
#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz
|
||||
#dump_modify out sort id
|
||||
#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le"
|
||||
|
||||
run 1000000
|
||||
|
||||
#write_restart config.${number}.*
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
Loading…
Reference in New Issue