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Merge pull request #1573 from ohenrich/user-cgdna 

Update for USER-CGDNA package
This commit is contained in:
Axel Kohlmeyer 2019-07-19 13:24:07 -04:00 committed by GitHub
parent 92b53c7bc2 c2643a519e
commit 67b74aea63
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GPG Key ID: 4AEE18F83AFDEB23
51 changed files with 12181 additions and 1610 deletions
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doc/src/pair_oxdna.txt
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@ -23,9 +23,11 @@ style1 = {hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxs
style2 = {oxdna/excv} or {oxdna/stk} or {oxdna/hbond} or {oxdna/xstk} or {oxdna/coaxstk}
args = list of arguments for these particular styles :ul
{oxdna/stk} args = seq T 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
{oxdna/stk} args = seq T xi kappa 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
seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength)
T = temperature (oxDNA units, 0.1 = 300 K)
xi = temperature-independent coefficient in stacking strength
kappa = coefficient of linear temperature dependence in stacking strength
{oxdna/hbond} args = seq eps 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
seq = seqav (for average sequence base-pairing strength) or seqdep (for sequence-dependent base-pairing strength)
eps = 1.077 (between base pairs A-T and C-G) or 0 (all other pairs) :pre
@ -34,7 +36,7 @@ args = list of arguments for these particular styles :ul
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 seqdep 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 seqdep 0.1 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 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 oxdna/hbond seqdep 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 seqdep 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
@ -62,7 +64,7 @@ NOTE: These pair styles have to be used together with the related oxDNA bond sty
{oxdna/fene} for the connectivity of the phosphate backbone (see also documentation of
"bond_style oxdna/fene"_bond_oxdna.html). Most of the coefficients
in the above example have to be kept fixed and cannot be changed without reparameterizing the entire model.
Exceptions are the first and second coefficient after {oxdna/stk} (seq=seqdep and T=0.1 in the above example)
Exceptions are the first four coefficients after {oxdna/stk} (seq=seqdep, T=0.1, xi=1.3448 and kappa=2.6568 in the above example)
and the first coefficient after {oxdna/hbond} (seq=seqdep in the above example).
When using a Langevin thermostat, e.g. through "fix langevin"_fix_langevin.html
or "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html

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doc/src/pair_oxdna2.txt
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@ -24,10 +24,12 @@ style1 = {hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/
style2 = {oxdna2/excv} or {oxdna2/stk} or {oxdna2/hbond} or {oxdna2/xstk} or {oxdna2/coaxstk} or {oxdna2/dh}
args = list of arguments for these particular styles :ul
{oxdna2/stk} args = seq T 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
{oxdna2/stk} args = seq T xi kappa 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
seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength)
T = temperature (oxDNA units, 0.1 = 300 K)
{oxdna/hbond} args = seq eps 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
xi = temperature-independent coefficient in stacking strength
kappa = coefficient of linear temperature dependence in stacking strength
{oxdna2/hbond} args = seq eps 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
seq = seqav (for average sequence base-pairing strength) or seqdep (for sequence-dependent base-pairing strength)
eps = 1.0678 (between base pairs A-T and C-G) or 0 (all other pairs)
{oxdna2/dh} args = T rhos qeff
@ -39,7 +41,7 @@ args = list of arguments for these particular styles :ul
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 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 seqdep 0.1 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
@ -68,8 +70,8 @@ NOTE: These pair styles have to be used together with the related oxDNA2 bond st
{oxdna2/fene} for the connectivity of the phosphate backbone (see also documentation of
"bond_style oxdna2/fene"_bond_oxdna.html). Most of the coefficients
in the above example have to be kept fixed and cannot be changed without reparameterizing the entire model.
Exceptions are the first and the second coefficient after {oxdna2/stk} (seq=seqdep and T=0.1 in the above example),
the first coefficient after {oxdna/hbond} (seq=seqdep in the above example) and the three coefficients
Exceptions are the first four coefficients after {oxdna2/stk} (seq=seqdep, T=0.1, xi=1.3523 and kappa=2.6717 in the above example),
the first coefficient after {oxdna2/hbond} (seq=seqdep in the above example) and the three coefficients
after {oxdna2/dh} (T=0.1, rhos=1.0, qeff=0.815 in the above example). When using a Langevin thermostat
e.g. through "fix langevin"_fix_langevin.html or "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html
the temperature coefficients have to be matched to the one used in the fix.

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examples/USER/cgdna/README
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@ -22,6 +22,17 @@ A - C - G - T - A - C - G - T
| | | | | | | |
T - G - C - A T - G - C - A
/examples/duplex3:
This is basically the duplex1 run with sequence-dependent stacking
and hydrogen-bonding strengths enabled and both nucleotide mass and
moment of inertia set to the value of the standalone implementation
of oxDNA (M = I = 1). To achieve this, the masses can be set directly
in the input and data file, whereas the moment of inertia is set via
the diameter of the ellipsoid in the data file and has a value of 3.16227766.
The change of mass and moment of inertia allows direct comparision of
e.g. trajectory data, energies or time-dependent observables on a per-timestep
basis until numerical noise causes deviations at later simulation times.
/util:
This directory contains a simple python setup tool which creates
single straight or helical DNA strands, DNA duplexes or arrays of DNA

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examples/USER/cgdna/examples/oxDNA/duplex1/data.duplex1
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@ -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

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examples/USER/cgdna/examples/oxDNA/duplex1/in.duplex1
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@ -1,6 +1,7 @@
variable number equal 1
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}.*

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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 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) = 2.859 | 2.859 | 2.859 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -1.4711818 0.0069384985 -1.4642433 -6.2745089e-05
1000 ekin = 0.00113448721737003 | erot = 0.00413455947734281 | epot = -14.6477022915193 | etot = -14.6424332448246
2000 ekin = 0.00449927223902336 | erot = 0.0164446434455805 | epot = -14.6633771605337 | etot = -14.6424332448491
3000 ekin = 0.00997964450841065 | erot = 0.0366523356056461 | epot = -14.6890652250033 | etot = -14.6424332448892
4000 ekin = 0.0173888111295073 | erot = 0.0643039804300221 | epot = -14.7241260365031 | etot = -14.6424332449436
5000 ekin = 0.0264744514136619 | erot = 0.0987844033142066 | epot = -14.7676920997383 | etot = -14.6424332450104
6000 ekin = 0.0369277948556079 | erot = 0.139336571052565 | epot = -14.8186976109956 | etot = -14.6424332450875
7000 ekin = 0.04839505571915 | erot = 0.18508629569208 | epot = -14.8759145965832 | etot = -14.642433245172
8000 ekin = 0.0604909336920643 | erot = 0.23507130752353 | epot = -14.9379954864767 | etot = -14.6424332452611
9000 ekin = 0.0728137406440561 | erot = 0.288273694501537 | epot = -15.003520680497 | etot = -14.6424332453514
10000 ekin = 0.0849615563085879 | erot = 0.343654369293472 | epot = -15.0710491710418 | etot = -14.6424332454398
10000 0.0062934486 -1.5138305 0.0067255788 -1.4986088 -9.9021593e-05
Loop time of 0.141929 on 1 procs for 10000 steps with 10 atoms
Performance: 60875.649 tau/day, 70457.927 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 | 0.11467 | 0.11467 | 0.11467 | 0.0 | 80.79
Bond | 0.0050094 | 0.0050094 | 0.0050094 | 0.0 | 3.53
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0013616 | 0.0013616 | 0.0013616 | 0.0 | 0.96
Output | 4.0531e-06 | 4.0531e-06 | 4.0531e-06 | 0.0 | 0.00
Modify | 0.017901 | 0.017901 | 0.017901 | 0.0 | 12.61
Other | | 0.002982 | | | 2.10
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: 43 ave 43 max 43 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 43
Ave neighs/atom = 4.3
Ave special neighs/atom = 3.6
Neighbor list builds = 0
Dangerous builds = 0
#write_restart config.${number}.*
Total wall time: 0:00:00

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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 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) = 7.341 | 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

2
examples/USER/cgdna/examples/oxDNA/duplex2/data.duplex2
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@ -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

9
examples/USER/cgdna/examples/oxDNA/duplex2/in.duplex2
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@ -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}.*

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@ -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

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examples/USER/cgdna/examples/oxDNA/duplex2/log.27Nov18.duplex2.g++.4
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@ -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

2
examples/USER/cgdna/examples/oxDNA2/duplex1/data.duplex1
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@ -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

11
examples/USER/cgdna/examples/oxDNA2/duplex1/in.duplex1
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@ -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}.*

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@ -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

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@ -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

2
examples/USER/cgdna/examples/oxDNA2/duplex2/data.duplex2
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@ -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

12
examples/USER/cgdna/examples/oxDNA2/duplex2/in.duplex2
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@ -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}.*

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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

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@ -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

73
examples/USER/cgdna/examples/oxDNA2/duplex3/data.duplex3 Normal file
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@ -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

79
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@ -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}.*

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examples/USER/cgdna/examples/oxDNA2/duplex3/log.18Jun19.duplex3.g++.1 Normal file
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examples/USER/cgdna/examples/oxDNA2/duplex3/log.18Jun19.duplex3.g++.4 Normal file
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2
src/USER-CGDNA/Install.sh
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@ -48,9 +48,7 @@ action pair_oxdna2_excv.h atom_vec_ellipsoid.h
action pair_oxdna_hbond.cpp atom_vec_ellipsoid.h
action pair_oxdna_hbond.h atom_vec_ellipsoid.h
action pair_oxdna_stk.cpp atom_vec_ellipsoid.h
action pair_oxdna2_stk.cpp atom_vec_ellipsoid.h
action pair_oxdna_stk.h atom_vec_ellipsoid.h
action pair_oxdna2_stk.h atom_vec_ellipsoid.h
action pair_oxdna_xstk.cpp atom_vec_ellipsoid.h
action pair_oxdna_xstk.h atom_vec_ellipsoid.h
action pair_oxdna2_dh.cpp atom_vec_ellipsoid.h

2
src/USER-CGDNA/README
View File

@ -73,7 +73,7 @@ pair_oxdna_xstk.cpp: cross-stacking interaction between nucleotides
pair_oxdna_coaxstk.cpp: coaxial stacking interaction between nucleotides
pair_oxdna2_excv.cpp, pair_oxdna2_stk.cpp, pair_oxdna2_coaxstk.cpp:
pair_oxdna2_excv.cpp, pair_oxdna2_coaxstk.cpp:
corresponding pair styles in oxDNA2 (see [3])
pair_oxdna2_dh.cpp: Debye-Hueckel electrostatic interaction between backbone

4
src/USER-CGDNA/bond_oxdna2_fene.cpp
View File

@ -37,8 +37,8 @@ BondOxdna2Fene::~BondOxdna2Fene()
/* ----------------------------------------------------------------------
compute vector COM-sugar-phosphate backbone interaction site in oxDNA2
------------------------------------------------------------------------- */
void BondOxdna2Fene::compute_interaction_sites(double e1[3],
double e2[3], double r[3])
void BondOxdna2Fene::compute_interaction_sites(double e1[3], double e2[3],
double /*e3*/[3], double r[3])
{
double d_cs_x=-0.34, d_cs_y=+0.3408;

3
src/USER-CGDNA/bond_oxdna2_fene.h
View File

@ -28,7 +28,8 @@ class BondOxdna2Fene : public BondOxdnaFene {
public:
BondOxdna2Fene(class LAMMPS *);
virtual ~BondOxdna2Fene();
virtual void compute_interaction_sites(double *, double *, double *);
virtual void compute_interaction_sites(double *, double *, double *,
double *);
};
}

98
src/USER-CGDNA/bond_oxdna_fene.cpp
View File

@ -55,8 +55,8 @@ BondOxdnaFene::~BondOxdnaFene()
/* ----------------------------------------------------------------------
compute vector COM-sugar-phosphate backbone interaction site in oxDNA
------------------------------------------------------------------------- */
void BondOxdnaFene::compute_interaction_sites(double e1[3],
double /*e2*/[3], double r[3])
void BondOxdnaFene::compute_interaction_sites(double e1[3], double /*e2*/[3],
double /*e3*/[3], double r[3])
{
double d_cs=-0.4;
@ -66,6 +66,90 @@ void BondOxdnaFene::compute_interaction_sites(double e1[3],
}
/* ----------------------------------------------------------------------
tally energy and virial into global and per-atom accumulators
------------------------------------------------------------------------- */
void BondOxdnaFene::ev_tally_xyz(int i, int j, int nlocal, int newton_bond,
double ebond,
double fx, double fy, double fz,
double delx, double dely, double delz)
{
double ebondhalf,v[6];
if (eflag_either) {
if (eflag_global) {
if (newton_bond) energy += ebond;
else {
ebondhalf = 0.5*ebond;
if (i < nlocal) energy += ebondhalf;
if (j < nlocal) energy += ebondhalf;
}
}
if (eflag_atom) {
ebondhalf = 0.5*ebond;
if (newton_bond || i < nlocal) eatom[i] += ebondhalf;
if (newton_bond || j < nlocal) eatom[j] += ebondhalf;
}
}
if (vflag_either) {
v[0] = delx*fx;
v[1] = dely*fy;
v[2] = delz*fz;
v[3] = delx*fy;
v[4] = delx*fz;
v[5] = dely*fz;
if (vflag_global) {
if (newton_bond) {
virial[0] += v[0];
virial[1] += v[1];
virial[2] += v[2];
virial[3] += v[3];
virial[4] += v[4];
virial[5] += v[5];
} else {
if (i < nlocal) {
virial[0] += 0.5*v[0];
virial[1] += 0.5*v[1];
virial[2] += 0.5*v[2];
virial[3] += 0.5*v[3];
virial[4] += 0.5*v[4];
virial[5] += 0.5*v[5];
}
if (j < nlocal) {
virial[0] += 0.5*v[0];
virial[1] += 0.5*v[1];
virial[2] += 0.5*v[2];
virial[3] += 0.5*v[3];
virial[4] += 0.5*v[4];
virial[5] += 0.5*v[5];
}
}
}
if (vflag_atom) {
if (newton_bond || i < nlocal) {
vatom[i][0] += 0.5*v[0];
vatom[i][1] += 0.5*v[1];
vatom[i][2] += 0.5*v[2];
vatom[i][3] += 0.5*v[3];
vatom[i][4] += 0.5*v[4];
vatom[i][5] += 0.5*v[5];
}
if (newton_bond || j < nlocal) {
vatom[j][0] += 0.5*v[0];
vatom[j][1] += 0.5*v[1];
vatom[j][2] += 0.5*v[2];
vatom[j][3] += 0.5*v[3];
vatom[j][4] += 0.5*v[4];
vatom[j][5] += 0.5*v[5];
}
}
}
}
/* ----------------------------------------------------------------------
compute function for oxDNA FENE-bond interaction
s=sugar-phosphate backbone site, b=base site, st=stacking site
@ -112,8 +196,8 @@ void BondOxdnaFene::compute(int eflag, int vflag)
MathExtra::q_to_exyz(qb,bx,by,bz);
// vector COM-backbone site a and b
compute_interaction_sites(ax,ay,ra_cs);
compute_interaction_sites(bx,by,rb_cs);
compute_interaction_sites(ax,ay,az,ra_cs);
compute_interaction_sites(bx,by,bz,rb_cs);
// vector backbone site b to a
delr[0] = x[a][0] + ra_cs[0] - x[b][0] - rb_cs[0];
@ -182,7 +266,11 @@ void BondOxdnaFene::compute(int eflag, int vflag)
}
// increment energy and virial
if (evflag) ev_tally(a,b,nlocal,newton_bond,ebond,fbond,delr[0],delr[1],delr[2]);
// NOTE: The virial is calculated on the 'molecular' basis.
// (see G. Ciccotti and J.P. Ryckaert, Comp. Phys. Rep. 4, 345-392 (1986))
if (evflag) ev_tally_xyz(a,b,nlocal,newton_bond,ebond,
delf[0],delf[1],delf[2],x[a][0]-x[b][0],x[a][1]-x[b][1],x[a][2]-x[b][2]);
}

4
src/USER-CGDNA/bond_oxdna_fene.h
View File

@ -28,7 +28,8 @@ class BondOxdnaFene : public Bond {
public:
BondOxdnaFene(class LAMMPS *);
virtual ~BondOxdnaFene();
virtual void compute_interaction_sites(double *, double *, double *);
virtual void compute_interaction_sites(double *, double *, double *,
double *);
virtual void compute(int, int);
void coeff(int, char **);
void init_style();
@ -42,6 +43,7 @@ class BondOxdnaFene : public Bond {
double *k,*Delta,*r0; // FENE
void allocate();
void ev_tally_xyz(int, int, int, int, double, double, double, double, double, double, double);
};
}

6
src/USER-CGDNA/pair_oxdna2_coaxstk.cpp
View File

@ -383,7 +383,11 @@ void PairOxdna2Coaxstk::compute(int eflag, int vflag)
}
// increment energy and virial
if (evflag) ev_tally(a,b,nlocal,newton_pair,evdwl,0.0,fpair,delr_st[0],delr_st[1],delr_st[2]);
// NOTE: The virial is calculated on the 'molecular' basis.
// (see G. Ciccotti and J.P. Ryckaert, Comp. Phys. Rep. 4, 345-392 (1986))
if (evflag) ev_tally_xyz(a,b,nlocal,newton_pair,evdwl,0.0,
delf[0],delf[1],delf[2],x[a][0]-x[b][0],x[a][1]-x[b][1],x[a][2]-x[b][2]);
// pure torques not expressible as r x f

10
src/USER-CGDNA/pair_oxdna2_dh.cpp
View File

@ -223,10 +223,14 @@ void PairOxdna2Dh::compute(int eflag, int vflag)
}
// increment energy and virial
if (evflag) ev_tally(a,b,nlocal,newton_pair,
evdwl,0.0,fpair,delr[0],delr[1],delr[2]);
// increment energy and virial
// NOTE: The virial is calculated on the 'molecular' basis.
// (see G. Ciccotti and J.P. Ryckaert, Comp. Phys. Rep. 4, 345-392 (1986))
if (evflag) ev_tally_xyz(a,b,nlocal,newton_pair,evdwl,0.0,
delf[0],delf[1],delf[2],x[a][0]-x[b][0],x[a][1]-x[b][1],x[a][2]-x[b][2]);
}
}

4
src/USER-CGDNA/pair_oxdna2_excv.cpp
View File

@ -39,8 +39,8 @@ PairOxdna2Excv::~PairOxdna2Excv()
/* ----------------------------------------------------------------------
compute vector COM-excluded volume interaction sites in oxDNA2
------------------------------------------------------------------------- */
void PairOxdna2Excv::compute_interaction_sites(double e1[3],
double e2[3], double rs[3], double rb[3])
void PairOxdna2Excv::compute_interaction_sites(double e1[3], double e2[3],
double /*e3*/[3], double rs[3], double rb[3])
{
double d_cs_x=-0.34, d_cs_y=+0.3408, d_cb=+0.4;

2
src/USER-CGDNA/pair_oxdna2_excv.h
View File

@ -28,7 +28,7 @@ class PairOxdna2Excv : public PairOxdnaExcv {
public:
PairOxdna2Excv(class LAMMPS *);
virtual ~PairOxdna2Excv();
virtual void compute_interaction_sites(double *,
virtual void compute_interaction_sites(double *, double *,
double *, double *, double *);
};

50
src/USER-CGDNA/pair_oxdna2_stk.cpp
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@ -1,50 +0,0 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Oliver Henrich (University of Strathclyde, Glasgow)
------------------------------------------------------------------------- */
#include <cmath>
#include <cstdio>
#include <cstdlib>
#include <cstring>
#include "pair_oxdna2_stk.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairOxdna2Stk::PairOxdna2Stk(LAMMPS *lmp) : PairOxdnaStk(lmp)
{
}
/* ---------------------------------------------------------------------- */
PairOxdna2Stk::~PairOxdna2Stk()
{
}
/* ----------------------------------------------------------------------
return temperature dependent oxDNA2 stacking strength
------------------------------------------------------------------------- */
double PairOxdna2Stk::stacking_strength(double T)
{
double eps;
eps = 1.3523 + 2.6717 * T;
return eps;
}

53
src/USER-CGDNA/pair_oxdna2_stk.h
View File

@ -1,53 +0,0 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef PAIR_CLASS
PairStyle(oxdna2/stk,PairOxdna2Stk)
#else
#ifndef LMP_PAIR_OXDNA2_STK_H
#define LMP_PAIR_OXDNA2_STK_H
#include "pair_oxdna_stk.h"
namespace LAMMPS_NS {
class PairOxdna2Stk : public PairOxdnaStk {
public:
PairOxdna2Stk(class LAMMPS *);
virtual ~PairOxdna2Stk();
protected:
virtual double stacking_strength(double);
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Illegal ... command
Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
E: Incorrect args for pair coefficients
Self-explanatory. Check the input script or data file.
*/

6
src/USER-CGDNA/pair_oxdna_coaxstk.cpp
View File

@ -450,7 +450,11 @@ void PairOxdnaCoaxstk::compute(int eflag, int vflag)
}
// increment energy and virial
if (evflag) ev_tally(a,b,nlocal,newton_pair,evdwl,0.0,fpair,delr_st[0],delr_st[1],delr_st[2]);
// NOTE: The virial is calculated on the 'molecular' basis.
// (see G. Ciccotti and J.P. Ryckaert, Comp. Phys. Rep. 4, 345-392 (1986))
if (evflag) ev_tally_xyz(a,b,nlocal,newton_pair,evdwl,0.0,
delf[0],delf[1],delf[2],x[a][0]-x[b][0],x[a][1]-x[b][1],x[a][2]-x[b][2]);
// pure torques not expressible as r x f

44
src/USER-CGDNA/pair_oxdna_excv.cpp
View File

@ -91,8 +91,8 @@ PairOxdnaExcv::~PairOxdnaExcv()
/* ----------------------------------------------------------------------
compute vector COM-excluded volume interaction sites in oxDNA
------------------------------------------------------------------------- */
void PairOxdnaExcv::compute_interaction_sites(double e1[3],
double /*e2*/[3], double rs[3], double rb[3])
void PairOxdnaExcv::compute_interaction_sites(double e1[3], double /*e2*/[3],
double /*e3*/[3], double rs[3], double rb[3])
{
double d_cs=-0.4, d_cb=+0.4;
@ -162,7 +162,7 @@ void PairOxdnaExcv::compute(int eflag, int vflag)
MathExtra::q_to_exyz(qa,ax,ay,az);
// vector COM - backbone and base site a
compute_interaction_sites(ax,ay,ra_cs,ra_cb);
compute_interaction_sites(ax,ay,az,ra_cs,ra_cb);
rtmp_s[0] = x[a][0] + ra_cs[0];
rtmp_s[1] = x[a][1] + ra_cs[1];
@ -187,7 +187,7 @@ void PairOxdnaExcv::compute(int eflag, int vflag)
MathExtra::q_to_exyz(qb,bx,by,bz);
// vector COM - backbone and base site b
compute_interaction_sites(bx,by,rb_cs,rb_cb);
compute_interaction_sites(bx,by,bz,rb_cs,rb_cb);
// vector backbone site b to a
delr_ss[0] = rtmp_s[0] - (x[b][0] + rb_cs[0]);
@ -225,14 +225,17 @@ void PairOxdnaExcv::compute(int eflag, int vflag)
fpair *= factor_lj;
evdwl *= factor_lj;
// increment energy and virial
if (evflag) ev_tally(a,b,nlocal,newton_pair,
evdwl,0.0,fpair,delr_ss[0],delr_ss[1],delr_ss[2]);
delf[0] = delr_ss[0]*fpair;
delf[1] = delr_ss[1]*fpair;
delf[2] = delr_ss[2]*fpair;
// increment energy and virial
// NOTE: The virial is calculated on the 'molecular' basis.
// (see G. Ciccotti and J.P. Ryckaert, Comp. Phys. Rep. 4, 345-392 (1986))
if (evflag) ev_tally_xyz(a,b,nlocal,newton_pair,evdwl,0.0,
delf[0],delf[1],delf[2],x[a][0]-x[b][0],x[a][1]-x[b][1],x[a][2]-x[b][2]);
f[a][0] += delf[0];
f[a][1] += delf[1];
f[a][2] += delf[2];
@ -259,21 +262,20 @@ void PairOxdnaExcv::compute(int eflag, int vflag)
}
// backbone-base
if (rsq_sb < cutsq_sb_c[atype][btype]) {
evdwl = F3(rsq_sb,cutsq_sb_ast[atype][btype],cut_sb_c[atype][btype],lj1_sb[atype][btype],
lj2_sb[atype][btype],epsilon_sb[atype][btype],b_sb[atype][btype],fpair);
// increment energy and virial
if (evflag) ev_tally(a,b,nlocal,newton_pair,
evdwl,0.0,fpair,delr_sb[0],delr_sb[1],delr_sb[2]);
delf[0] = delr_sb[0]*fpair;
delf[1] = delr_sb[1]*fpair;
delf[2] = delr_sb[2]*fpair;
// increment energy and virial
if (evflag) ev_tally_xyz(a,b,nlocal,newton_pair,evdwl,0.0,
delf[0],delf[1],delf[2],x[a][0]-x[b][0],x[a][1]-x[b][1],x[a][2]-x[b][2]);
f[a][0] += delf[0];
f[a][1] += delf[1];
f[a][2] += delf[2];
@ -306,14 +308,14 @@ void PairOxdnaExcv::compute(int eflag, int vflag)
evdwl = F3(rsq_bs,cutsq_sb_ast[atype][btype],cut_sb_c[atype][btype],lj1_sb[atype][btype],
lj2_sb[atype][btype],epsilon_sb[atype][btype],b_sb[atype][btype],fpair);
// increment energy and virial
if (evflag) ev_tally(a,b,nlocal,newton_pair,
evdwl,0.0,fpair,delr_bs[0],delr_bs[1],delr_bs[2]);
delf[0] = delr_bs[0]*fpair;
delf[1] = delr_bs[1]*fpair;
delf[2] = delr_bs[2]*fpair;
// increment energy and virial
if (evflag) ev_tally_xyz(a,b,nlocal,newton_pair,evdwl,0.0,
delf[0],delf[1],delf[2],x[a][0]-x[b][0],x[a][1]-x[b][1],x[a][2]-x[b][2]);
f[a][0] += delf[0];
f[a][1] += delf[1];
f[a][2] += delf[2];
@ -346,14 +348,14 @@ void PairOxdnaExcv::compute(int eflag, int vflag)
evdwl = F3(rsq_bb,cutsq_bb_ast[atype][btype],cut_bb_c[atype][btype],lj1_bb[atype][btype],
lj2_bb[atype][btype],epsilon_bb[atype][btype],b_bb[atype][btype],fpair);
// increment energy and virial
if (evflag) ev_tally(a,b,nlocal,newton_pair,
evdwl,0.0,fpair,delr_bb[0],delr_bb[1],delr_bb[2]);
delf[0] = delr_bb[0]*fpair;
delf[1] = delr_bb[1]*fpair;
delf[2] = delr_bb[2]*fpair;
// increment energy and virial
if (evflag) ev_tally_xyz(a,b,nlocal,newton_pair,evdwl,0.0,
delf[0],delf[1],delf[2],x[a][0]-x[b][0],x[a][1]-x[b][1],x[a][2]-x[b][2]);
f[a][0] += delf[0];
f[a][1] += delf[1];
f[a][2] += delf[2];

2
src/USER-CGDNA/pair_oxdna_excv.h
View File

@ -28,7 +28,7 @@ class PairOxdnaExcv : public Pair {
public:
PairOxdnaExcv(class LAMMPS *);
virtual ~PairOxdnaExcv();
virtual void compute_interaction_sites(double *, double *,
virtual void compute_interaction_sites(double *, double *, double *,
double *, double *);
virtual void compute(int, int);
void settings(int, char **);

6
src/USER-CGDNA/pair_oxdna_hbond.cpp
View File

@ -410,7 +410,11 @@ void PairOxdnaHbond::compute(int eflag, int vflag)
}
// increment energy and virial
if (evflag) ev_tally(a,b,nlocal,newton_pair,evdwl,0.0,fpair,delr_hb[0],delr_hb[1],delr_hb[2]);
// NOTE: The virial is calculated on the 'molecular' basis.
// (see G. Ciccotti and J.P. Ryckaert, Comp. Phys. Rep. 4, 345-392 (1986))
if (evflag) ev_tally_xyz(a,b,nlocal,newton_pair,evdwl,0.0,
delf[0],delf[1],delf[2],x[a][0]-x[b][0],x[a][1]-x[b][1],x[a][2]-x[b][2]);
// pure torques not expressible as r x f

155
src/USER-CGDNA/pair_oxdna_stk.cpp
View File

@ -106,6 +106,94 @@ PairOxdnaStk::~PairOxdnaStk()
}
}
/* ----------------------------------------------------------------------
tally energy and virial into global and per-atom accumulators
NOTE: Although this is a pair style interaction, the algorithm below
follows the virial incrementation of the bond style. This is because
the bond topology is used in the main compute loop.
------------------------------------------------------------------------- */
void PairOxdnaStk::ev_tally_xyz(int i, int j, int nlocal, int newton_bond,
double evdwl,
double fx, double fy, double fz,
double delx, double dely, double delz)
{
double evdwlhalf,v[6];
if (eflag_either) {
if (eflag_global) {
if (newton_bond) eng_vdwl += evdwl;
else {
evdwlhalf = 0.5*evdwl;
if (i < nlocal) eng_vdwl += evdwlhalf;
if (j < nlocal) eng_vdwl += evdwlhalf;
}
}
if (eflag_atom) {
evdwlhalf = 0.5*evdwl;
if (newton_bond || i < nlocal) eatom[i] += evdwlhalf;
if (newton_bond || j < nlocal) eatom[j] += evdwlhalf;
}
}
if (vflag_either) {
v[0] = delx*fx;
v[1] = dely*fy;
v[2] = delz*fz;
v[3] = delx*fy;
v[4] = delx*fz;
v[5] = dely*fz;
if (vflag_global) {
if (newton_bond) {
virial[0] += v[0];
virial[1] += v[1];
virial[2] += v[2];
virial[3] += v[3];
virial[4] += v[4];
virial[5] += v[5];
} else {
if (i < nlocal) {
virial[0] += 0.5*v[0];
virial[1] += 0.5*v[1];
virial[2] += 0.5*v[2];
virial[3] += 0.5*v[3];
virial[4] += 0.5*v[4];
virial[5] += 0.5*v[5];
}
if (j < nlocal) {
virial[0] += 0.5*v[0];
virial[1] += 0.5*v[1];
virial[2] += 0.5*v[2];
virial[3] += 0.5*v[3];
virial[4] += 0.5*v[4];
virial[5] += 0.5*v[5];
}
}
}
if (vflag_atom) {
if (newton_bond || i < nlocal) {
vatom[i][0] += 0.5*v[0];
vatom[i][1] += 0.5*v[1];
vatom[i][2] += 0.5*v[2];
vatom[i][3] += 0.5*v[3];
vatom[i][4] += 0.5*v[4];
vatom[i][5] += 0.5*v[5];
}
if (newton_bond || j < nlocal) {
vatom[j][0] += 0.5*v[0];
vatom[j][1] += 0.5*v[1];
vatom[j][2] += 0.5*v[2];
vatom[j][3] += 0.5*v[3];
vatom[j][4] += 0.5*v[4];
vatom[j][5] += 0.5*v[5];
}
}
}
}
/* ----------------------------------------------------------------------
compute function for oxDNA pair interactions
s=sugar-phosphate backbone site, b=base site, st=stacking site
@ -295,9 +383,6 @@ void PairOxdnaStk::compute(int eflag, int vflag)
// early rejection criterium
if (evdwl) {
// increment energy
if (evflag) ev_tally(a,b,nlocal,newton_bond,evdwl,0.0,0.0,0.0,0.0,0.0);
df1 = DF1(r_st, epsilon_st[atype][btype], a_st[atype][btype], cut_st_0[atype][btype],
cut_st_lc[atype][btype], cut_st_hc[atype][btype], cut_st_lo[atype][btype], cut_st_hi[atype][btype],
b_st_lo[atype][btype], b_st_hi[atype][btype]);
@ -366,7 +451,7 @@ void PairOxdnaStk::compute(int eflag, int vflag)
}
// increment forces, torques and virial
// increment forces and torques
if (newton_bond || a < nlocal) {
@ -402,7 +487,12 @@ void PairOxdnaStk::compute(int eflag, int vflag)
}
if (evflag) ev_tally(a,b,nlocal,newton_bond,0.0,0.0,fpair,delr_st[0],delr_st[1],delr_st[2]);
// increment energy and virial
// NOTE: The virial is calculated on the 'molecular' basis.
// (see G. Ciccotti and J.P. Ryckaert, Comp. Phys. Rep. 4, 345-392 (1986))
if (evflag) ev_tally_xyz(a,b,nlocal,newton_bond,evdwl,
delf[0],delf[1],delf[2],x[a][0]-x[b][0],x[a][1]-x[b][1],x[a][2]-x[b][2]);
// force, torque and virial contribution for forces between backbone sites
@ -444,7 +534,7 @@ void PairOxdnaStk::compute(int eflag, int vflag)
}
// increment forces, torques and virial
// increment forces and torques
if (newton_bond || a < nlocal) {
@ -480,8 +570,9 @@ void PairOxdnaStk::compute(int eflag, int vflag)
}
if (evflag) ev_tally(a,b,nlocal,newton_bond,0.0,0.0,fpair,delr_ss[0],delr_ss[1],delr_ss[2]);
// increment virial only
if (evflag) ev_tally_xyz(a,b,nlocal,newton_bond,0.0,
delf[0],delf[1],delf[2],x[a][0]-x[b][0],x[a][1]-x[b][1],x[a][2]-x[b][2]);
// pure torques not expressible as r x f
@ -656,11 +747,11 @@ void PairOxdnaStk::settings(int narg, char **/*arg*/)
return temperature dependent oxDNA stacking strength
------------------------------------------------------------------------- */
double PairOxdnaStk::stacking_strength(double T)
double PairOxdnaStk::stacking_strength(double xi_st, double kappa_st, double T)
{
double eps;
eps = 1.3448 + 2.6568 * T;
eps = xi_st + kappa_st * T;
return eps;
}
@ -673,7 +764,7 @@ void PairOxdnaStk::coeff(int narg, char **arg)
{
int count;
if (narg != 22) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/stk");
if (narg != 24) error->all(FLERR,"Incorrect args for pair coefficients in oxdna/stk");
if (!allocated) allocate();
int ilo,ihi,jlo,jhi;
@ -683,7 +774,7 @@ void PairOxdnaStk::coeff(int narg, char **arg)
// stacking interaction
count = 0;
double T, epsilon_st_one, a_st_one, b_st_lo_one, b_st_hi_one;
double T, epsilon_st_one, xi_st_one, kappa_st_one, a_st_one, b_st_lo_one, b_st_hi_one;
double cut_st_0_one, cut_st_c_one, cut_st_lo_one, cut_st_hi_one;
double cut_st_lc_one, cut_st_hc_one, tmp, shift_st_one;
@ -706,27 +797,29 @@ void PairOxdnaStk::coeff(int narg, char **arg)
if (strcmp(arg[2],"seqdep") == 0) seqdepflag = 1;
T = force->numeric(FLERR,arg[3]);
epsilon_st_one = stacking_strength(T);
xi_st_one = force->numeric(FLERR,arg[4]);
kappa_st_one = force->numeric(FLERR,arg[5]);
epsilon_st_one = stacking_strength(xi_st_one, kappa_st_one, T);
a_st_one = force->numeric(FLERR,arg[4]);
cut_st_0_one = force->numeric(FLERR,arg[5]);
cut_st_c_one = force->numeric(FLERR,arg[6]);
cut_st_lo_one = force->numeric(FLERR,arg[7]);
cut_st_hi_one = force->numeric(FLERR,arg[8]);
a_st_one = force->numeric(FLERR,arg[6]);
cut_st_0_one = force->numeric(FLERR,arg[7]);
cut_st_c_one = force->numeric(FLERR,arg[8]);
cut_st_lo_one = force->numeric(FLERR,arg[9]);
cut_st_hi_one = force->numeric(FLERR,arg[10]);
a_st4_one = force->numeric(FLERR,arg[9]);
theta_st4_0_one = force->numeric(FLERR,arg[10]);
dtheta_st4_ast_one = force->numeric(FLERR,arg[11]);
a_st5_one = force->numeric(FLERR,arg[12]);
theta_st5_0_one = force->numeric(FLERR,arg[13]);
dtheta_st5_ast_one = force->numeric(FLERR,arg[14]);
a_st6_one = force->numeric(FLERR,arg[15]);
theta_st6_0_one = force->numeric(FLERR,arg[16]);
dtheta_st6_ast_one = force->numeric(FLERR,arg[17]);
a_st1_one = force->numeric(FLERR,arg[18]);
cosphi_st1_ast_one = force->numeric(FLERR,arg[19]);
a_st2_one = force->numeric(FLERR,arg[20]);
cosphi_st2_ast_one = force->numeric(FLERR,arg[21]);
a_st4_one = force->numeric(FLERR,arg[11]);
theta_st4_0_one = force->numeric(FLERR,arg[12]);
dtheta_st4_ast_one = force->numeric(FLERR,arg[13]);
a_st5_one = force->numeric(FLERR,arg[14]);
theta_st5_0_one = force->numeric(FLERR,arg[15]);
dtheta_st5_ast_one = force->numeric(FLERR,arg[16]);
a_st6_one = force->numeric(FLERR,arg[17]);
theta_st6_0_one = force->numeric(FLERR,arg[18]);
dtheta_st6_ast_one = force->numeric(FLERR,arg[19]);
a_st1_one = force->numeric(FLERR,arg[20]);
cosphi_st1_ast_one = force->numeric(FLERR,arg[21]);
a_st2_one = force->numeric(FLERR,arg[22]);
cosphi_st2_ast_one = force->numeric(FLERR,arg[23]);
b_st_lo_one = 2*a_st_one*exp(-a_st_one*(cut_st_lo_one-cut_st_0_one))*
2*a_st_one*exp(-a_st_one*(cut_st_lo_one-cut_st_0_one))*

4
src/USER-CGDNA/pair_oxdna_stk.h
View File

@ -14,6 +14,7 @@
#ifdef PAIR_CLASS
PairStyle(oxdna/stk,PairOxdnaStk)
PairStyle(oxdna2/stk,PairOxdnaStk)
#else
@ -44,7 +45,7 @@ class PairOxdnaStk : public Pair {
protected:
// stacking interaction
virtual double stacking_strength(double);
double stacking_strength(double, double, double);
double **epsilon_st, **a_st, **cut_st_0, **cut_st_c;
double **cut_st_lo, **cut_st_hi;
double **cut_st_lc, **cut_st_hc, **b_st_lo, **b_st_hi, **shift_st;
@ -61,6 +62,7 @@ class PairOxdnaStk : public Pair {
int seqdepflag;
virtual void allocate();
void ev_tally_xyz(int, int, int, int, double, double, double, double, double, double, double);
};
}

6
src/USER-CGDNA/pair_oxdna_xstk.cpp
View File

@ -422,7 +422,11 @@ void PairOxdnaXstk::compute(int eflag, int vflag)
}
// increment energy and virial
if (evflag) ev_tally(a,b,nlocal,newton_pair,evdwl,0.0,fpair,delr_hb[0],delr_hb[1],delr_hb[2]);
// NOTE: The virial is calculated on the 'molecular' basis.
// (see G. Ciccotti and J.P. Ryckaert, Comp. Phys. Rep. 4, 345-392 (1986))
if (evflag) ev_tally_xyz(a,b,nlocal,newton_pair,evdwl,0.0,
delf[0],delf[1],delf[2],x[a][0]-x[b][0],x[a][1]-x[b][1],x[a][2]-x[b][2]);
// pure torques not expressible as r x f