Updated input and log files, amended comment in data files (7bf97577) · Commits · 郑智淋 / lammps

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

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Original line number	Diff line number	Diff line
		@@ -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

examples/USER/cgdna/examples/oxDNA/duplex1/in.duplex1

+5 −4

Original line number	Diff line number	Diff line
		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}.*

examples/USER/cgdna/examples/oxDNA/duplex1/log.18Jun19.duplex1.g++.1

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examples/USER/cgdna/examples/oxDNA/duplex1/log.18Jun19.duplex1.g++.4

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examples/USER/cgdna/examples/oxDNA/duplex1/log.27Nov18.duplex1.g++.1

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Original line number	Diff line number	Diff line
		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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