Verified oxDNA with modified nucleotide layout (74350843) · Commits · 郑智淋 / lammps

doc/src/PDF/USER-CGDNA-overview.pdf

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

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Original line number	Diff line number	Diff line
		# 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

		# Atom masses for each atom type
		Masses

		1 3.1575
		2 3.1575
		3 3.1575
		4 3.1575

		# Atom-ID, type, position, molecule-ID, ellipsoid flag, density
		Atoms

		1 1 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 1 1 1
		2 1 1.3274493266864451e-01 -4.2912827978022683e-01 3.7506163469402809e-01 1 1 1
		3 1 4.8460810659772807e-01 -7.0834970533509178e-01 7.5012326938805618e-01 1 1 1
		4 1 9.3267359196674593e-01 -7.4012419946742802e-01 1.1251849040820843e+00 1 1 1
		5 1 1.3204192238113461e+00 -5.1335201721887447e-01 1.5002465387761124e+00 1 1 1
		6 4 1.9958077618865377e-01 5.1335201721887447e-01 1.5002465387761124e+00 1 1 1
		7 4 5.8732640803325409e-01 7.4012419946742802e-01 1.1251849040820843e+00 1 1 1
		8 4 1.0353918934022719e+00 7.0834970533509178e-01 7.5012326938805618e-01 1 1 1
		9 4 1.3872550673313555e+00 4.2912827978022683e-01 3.7506163469402809e-01 1 1 1
		10 4 1.5200000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 1 1 1

		# Atom-ID, translational, rotational velocity
		Velocities

		1 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
		2 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
		3 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
		4 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
		5 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
		6 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
		7 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
		8 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
		9 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
		10 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00

		# Atom-ID, shape, quaternion
		Ellipsoids

		1 1.1739845031423408e+00 1.1739845031423408e+00 1.1739845031423408e+00 1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
		2 1.1739845031423408e+00 1.1739845031423408e+00 1.1739845031423408e+00 9.5533648912560598e-01 0.0000000000000000e+00 0.0000000000000000e+00 2.9552020666133955e-01
		3 1.1739845031423408e+00 1.1739845031423408e+00 1.1739845031423408e+00 8.2533561490967822e-01 0.0000000000000000e+00 0.0000000000000000e+00 5.6464247339503526e-01
		4 1.1739845031423408e+00 1.1739845031423408e+00 1.1739845031423408e+00 6.2160996827066439e-01 0.0000000000000000e+00 0.0000000000000000e+00 7.8332690962748319e-01
		5 1.1739845031423408e+00 1.1739845031423408e+00 1.1739845031423408e+00 3.6235775447667351e-01 0.0000000000000000e+00 0.0000000000000000e+00 9.3203908596722607e-01
		6 1.1739845031423408e+00 1.1739845031423408e+00 1.1739845031423408e+00 0.0000000000000000e+00 9.3203908596722607e-01 -3.6235775447667351e-01 0.0000000000000000e+00
		7 1.1739845031423408e+00 1.1739845031423408e+00 1.1739845031423408e+00 0.0000000000000000e+00 7.8332690962748319e-01 -6.2160996827066439e-01 0.0000000000000000e+00
		8 1.1739845031423408e+00 1.1739845031423408e+00 1.1739845031423408e+00 0.0000000000000000e+00 5.6464247339503526e-01 -8.2533561490967822e-01 0.0000000000000000e+00
		9 1.1739845031423408e+00 1.1739845031423408e+00 1.1739845031423408e+00 0.0000000000000000e+00 2.9552020666133955e-01 -9.5533648912560598e-01 0.0000000000000000e+00
		10 1.1739845031423408e+00 1.1739845031423408e+00 1.1739845031423408e+00 0.0000000000000000e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+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

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Original line number	Diff line number	Diff line
		# LAMMPS data file
		16 atoms
		16 ellipsoids
		13 bonds

		4 atom types
		1 bond types

		# System size
		-20.0 20.0 xlo xhi
		-20.0 20.0 ylo yhi
		-20.0 20.0 zlo zhi

		# Atom masses for each atom type
		Masses

		1 3.1575
		2 3.1575
		3 3.1575
		4 3.1575

		# Atom-ID, type, position, molecule-ID, ellipsoid flag, density
		Atoms

		1 1 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 1 1 1
		2 1 1.327449326686445e-01 -4.291282797802268e-01 3.750616346940281e-01 1 1 1
		3 1 4.846081065977281e-01 -7.083497053350921e-01 7.501232693880562e-01 1 1 1
		4 1 9.326735919667459e-01 -7.401241994674285e-01 1.125184904082084e+00 1 1 1
		5 1 1.320419223811347e+00 -5.133520172188747e-01 1.500246538776112e+00 1 1 1
		6 1 1.512394297416339e+00 -1.072512061254991e-01 1.875308173470140e+00 1 1 1
		7 1 1.441536396413952e+00 3.363155369040876e-01 2.250369808164169e+00 1 1 1
		8 1 1.132598224218932e+00 6.623975870343269e-01 2.625431442858197e+00 1 1 1
		9 4 5.873264080332541e-01 7.401241994674285e-01 1.125184904082084e+00 1 1 1
		10 4 1.035391893402272e+00 7.083497053350921e-01 7.501232693880562e-01 1 1 1
		11 4 1.387255067331356e+00 4.291282797802267e-01 3.750616346940281e-01 1 1 1
		12 4 1.520000000000000e+00 1.260981291332700e-33 0.000000000000000e+00 1 1 1
		13 4 3.874017757810680e-01 -6.623975870343268e-01 2.625431442858197e+00 1 1 1
		14 4 7.846360358604798e-02 -3.363155369040874e-01 2.250369808164169e+00 1 1 1
		15 4 7.605702583661333e-03 1.072512061254995e-01 1.875308173470140e+00 1 1 1
		16 4 1.995807761886533e-01 5.133520172188748e-01 1.500246538776112e+00 1 1 1

		# Atom-ID, translational, rotational velocity
		Velocities

		1 0.0 0.0 0.0 0.0 0.0 0.0
		2 0.0 0.0 0.0 0.0 0.0 0.0
		3 0.0 0.0 0.0 0.0 0.0 0.0
		4 0.0 0.0 0.0 0.0 0.0 0.0
		5 0.0 0.0 0.0 0.0 0.0 0.0
		6 0.0 0.0 0.0 0.0 0.0 0.0
		7 0.0 0.0 0.0 0.0 0.0 0.0
		8 0.0 0.0 0.0 0.0 0.0 0.0
		9 0.0 0.0 0.0 0.0 0.0 0.0
		10 0.0 0.0 0.0 0.0 0.0 0.0
		11 0.0 0.0 0.0 0.0 0.0 0.0
		12 0.0 0.0 0.0 0.0 0.0 0.0
		13 0.0 0.0 0.0 0.0 0.0 0.0
		14 0.0 0.0 0.0 0.0 0.0 0.0
		15 0.0 0.0 0.0 0.0 0.0 0.0
		16 0.0 0.0 0.0 0.0 0.0 0.0

		# Atom-ID, shape, quaternion
		Ellipsoids

		1 1.1739845031423408 1.1739845031423408 1.1739845031423408 1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
		2 1.1739845031423408 1.1739845031423408 1.1739845031423408 9.553364891256060e-01 0.000000000000000e+00 0.000000000000000e+00 2.955202066613395e-01
		3 1.1739845031423408 1.1739845031423408 1.1739845031423408 8.253356149096783e-01 0.000000000000000e+00 0.000000000000000e+00 5.646424733950354e-01
		4 1.1739845031423408 1.1739845031423408 1.1739845031423408 6.216099682706646e-01 0.000000000000000e+00 0.000000000000000e+00 7.833269096274833e-01
		5 1.1739845031423408 1.1739845031423408 1.1739845031423408 3.623577544766736e-01 0.000000000000000e+00 0.000000000000000e+00 9.320390859672263e-01
		6 1.1739845031423408 1.1739845031423408 1.1739845031423408 7.073720166770291e-02 0.000000000000000e+00 0.000000000000000e+00 9.974949866040544e-01
		7 1.1739845031423408 1.1739845031423408 1.1739845031423408 -2.272020946930869e-01 -0.000000000000000e+00 0.000000000000000e+00 9.738476308781953e-01
		8 1.1739845031423408 1.1739845031423408 1.1739845031423408 -5.048461045998575e-01 -0.000000000000000e+00 0.000000000000000e+00 8.632093666488738e-01
		9 1.1739845031423408 1.1739845031423408 1.1739845031423408 4.796493962806427e-17 7.833269096274833e-01 -6.216099682706646e-01 3.806263289803786e-17
		10 1.1739845031423408 1.1739845031423408 1.1739845031423408 5.707093416549944e-17 5.646424733950354e-01 -8.253356149096784e-01 2.218801320830406e-17
		11 1.1739845031423408 1.1739845031423408 1.1739845031423408 6.107895212550935e-17 2.955202066613394e-01 -9.553364891256061e-01 4.331404380149668e-18
		12 1.1739845031423408 1.1739845031423408 1.1739845031423408 5.963096920061075e-17 0.000000000000000e+00 -1.000000000000000e+00 -1.391211590127312e-17
		13 1.1739845031423408 1.1739845031423408 1.1739845031423408 5.285632939302787e-17 8.632093666488739e-01 5.048461045998572e-01 -3.091290830301125e-17
		14 1.1739845031423408 1.1739845031423408 1.1739845031423408 4.136019110019290e-17 9.738476308781953e-01 2.272020946930868e-01 -4.515234267244800e-17
		15 1.1739845031423408 1.1739845031423408 1.1739845031423408 2.616947011741696e-17 9.974949866040544e-01 -7.073720166770313e-02 -5.535845274597425e-17
		16 1.1739845031423408 1.1739845031423408 1.1739845031423408 8.641108308308281e-18 9.320390859672264e-01 -3.623577544766736e-01 -6.061955710708163e-17

		# Bond-ID, type, atom pairs
		Bonds

		1 1 1 2
		2 1 2 3
		3 1 3 4
		4 1 4 5
		5 1 5 6
		6 1 6 7
		7 1 7 8
		8 1 13 14
		9 1 14 15
		10 1 15 16
		11 1 9 10
		12 1 10 11
		13 1 11 12

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