min latte partially fixed (2dcbc805) · Commits · 郑智淋 / lammps

examples/latte/data.sucrose_non_opt.lmp

0 → 100644

+63 −0

Original line number	Diff line number	Diff line
		LAMMPS Description

		45 atoms

		3 atom types

		0.0000000000000000 18.917000000000002 xlo xhi
		0.0000000000000000 17.350999999999999 ylo yhi
		0.0000000000000000 15.472000000000000 zlo zhi

		Masses

		1 15.994915008544922
		2 12.000000000000000
		3 1.0078250169754028

		Atoms

		1 1 1 0.0 11.47359 7.39174 7.26456
		2 1 2 0.0 12.66159 8.24474 7.53356
		3 1 3 0.0 13.49759 7.72474 7.00656
		4 1 2 0.0 12.92859 8.18374 9.02956
		5 1 1 0.0 13.69659 9.10274 10.46556
		6 1 2 0.0 12.83959 10.10474 6.64056
		7 1 3 0.0 13.24359 10.33074 7.58456
		8 1 1 0.0 13.17359 9.67874 5.60956
		9 1 2 0.0 11.20559 10.26374 6.86456
		10 1 3 0.0 11.22159 11.15674 6.18156
		11 1 1 0.0 10.78559 10.69674 8.19156
		12 1 2 0.0 10.23459 9.20474 6.34356
		13 1 3 0.0 9.23359 9.62574 6.11656
		14 1 1 0.0 10.73959 8.65074 5.08856
		15 1 2 0.0 10.18759 8.08774 7.38056
		16 1 3 0.0 10.03259 8.49174 8.42656
		17 1 1 0.0 9.22959 7.03374 7.08156
		18 1 2 0.0 7.79359 7.27874 7.34356
		19 1 1 0.0 7.44259 8.64274 6.96956
		20 1 2 0.0 7.01059 9.43674 8.13856
		21 1 3 0.0 5.95059 9.74974 7.96256
		22 1 2 0.0 7.08359 8.51474 9.35656
		23 1 3 0.0 8.19359 8.08474 9.80956
		24 1 1 0.0 5.86059 8.56174 10.14056
		25 1 2 0.0 7.34259 7.10674 8.80356
		26 1 3 0.0 6.37259 6.54074 8.80556
		27 1 1 0.0 8.32159 6.38474 9.58156
		28 1 2 0.0 7.89859 10.67174 8.17156
		29 1 1 0.0 6.06859 12.11474 7.59256
		30 1 2 0.0 7.47359 7.05174 5.99256
		31 1 1 0.0 5.66359 6.54374 6.50656
		32 1 3 0.0 12.00659 8.11374 9.61556
		33 1 3 0.0 13.35859 7.21774 9.30856
		34 1 3 0.0 13.67759 8.46774 11.22956
		35 1 3 0.0 12.44459 9.34474 5.00556
		36 1 3 0.0 11.54859 11.18274 8.59756
		37 1 3 0.0 11.00959 7.71574 5.30056
		38 1 3 0.0 5.09459 8.45474 9.52056
		39 1 3 0.0 7.92859 6.23074 10.47756
		40 1 3 0.0 8.53259 10.62974 7.23156
		41 1 3 0.0 8.58159 10.63874 9.05856
		42 1 3 0.0 6.42359 13.37374 7.86056
		43 1 3 0.0 7.58559 6.90074 4.62256
		44 1 3 0.0 7.35159 5.27974 6.61456
		45 1 3 0.0 5.22759 6.18974 5.69256

examples/latte/data.water

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+41 −0

Original line number	Diff line number	Diff line
		LAMMPS Description

		24 atoms

		2 atom types

		0.0000000000000000 6.2670000000000003 xlo xhi
		0.0000000000000000 6.2670000000000003 ylo yhi
		0.0000000000000000 6.2670000000000003 zlo zhi

		Masses

		1 15.994915008544922
		2 1.0078250169754028

		Atoms

		1 1 1 0.0 3.08800 3.70000 3.12400
		2 1 2 0.0 4.05800 3.70000 3.12400
		3 1 2 0.0 2.76400 3.13200 3.84100
		4 1 1 0.0 2.47000 0.39000 1.36000
		5 1 2 0.0 1.54000 0.37000 1.73000
		6 1 2 0.0 2.48000 0.00000 0.44000
		7 1 1 0.0 1.99300 0.41700 5.25000
		8 1 2 0.0 2.39300 1.32700 5.16000
		9 1 2 0.0 0.99300 0.49700 5.31000
		10 1 1 0.0 2.05300 6.09700 3.48000
		11 1 2 0.0 2.12300 5.20700 3.02000
		12 1 2 0.0 1.11300 0.17000 3.40000
		13 1 1 0.0 4.90000 5.37700 2.14000
		14 1 2 0.0 5.51000 6.17700 2.18000
		15 1 2 0.0 3.95000 5.68700 2.21000
		16 1 1 0.0 0.92000 3.82700 0.56000
		17 1 2 0.0 0.00000 3.54700 0.27000
		18 1 2 0.0 1.23000 4.59700 0.00000
		19 1 1 0.0 0.89000 2.03700 3.41000
		20 1 2 0.0 0.72000 2.86700 2.87000
		21 1 2 0.0 1.79000 1.66700 3.19000
		22 1 1 0.0 4.45000 4.61700 5.43000
		23 1 2 0.0 4.75000 3.89700 4.81000
		24 1 2 0.0 4.06000 4.21700 6.26000

examples/latte/in.latte.sucrose.min

0 → 100644

+42 −0

Original line number	Diff line number	Diff line
		# simple water model with LATTE

		units metal
		atom_style full
		atom_modify sort 0 0.0 # turn off sorting of the coordinates

		#read_data data.water
		read_data data.sucrose_non_opt.lmp

		# replicate system if requested

		variable x index 1
		variable y index 1
		variable z index 1

		variable nrep equal v_xv_yv_z
		if "${nrep} > 1" then "replicate $x $y $z"

		# initialize system

		velocity all create 0.0 87287 loop geom

		pair_style zero 1.0
		pair_coeff * *

		neighbor 1.0 bin
		neigh_modify every 1 delay 0 check yes

		timestep 0.00025

		fix 1 all nve

		fix 2 all latte NULL
		fix_modify 2 energy yes

		thermo_style custom step temp pe etotal

		# minimization

		thermo 1
		min_style cg
		minimize 1.0e-9 1.0e-9 1000 1000

examples/latte/in.latte.water

0 → 100644

+40 −0

Original line number	Diff line number	Diff line
		# simple water model with LATTE

		units metal
		atom_style full
		atom_modify sort 0 0.0 # turn off sorting of the coordinates

		read_data data.water

		# replicate system if requested

		variable x index 1
		variable y index 1
		variable z index 1

		variable nrep equal v_xv_yv_z
		if "${nrep} > 1" then "replicate $x $y $z"

		# initialize system

		velocity all create 0.0 87287 loop geom

		pair_style zero 1.0
		pair_coeff * *

		neighbor 1.0 bin
		neigh_modify every 1 delay 0 check yes

		timestep 0.00025

		fix 1 all nve

		fix 2 all latte NULL
		fix_modify 2 energy yes

		thermo_style custom step temp pe etotal

		# dynamics

		thermo 10
		run 100

examples/latte/in.latte.water.min

0 → 100644

+41 −0

Original line number	Diff line number	Diff line
		# simple water model with LATTE

		units metal
		atom_style full
		atom_modify sort 0 0.0 # turn off sorting of the coordinates

		read_data data.water

		# replicate system if requested

		variable x index 1
		variable y index 1
		variable z index 1

		variable nrep equal v_xv_yv_z
		if "${nrep} > 1" then "replicate $x $y $z"

		# initialize system

		velocity all create 0.0 87287 loop geom

		pair_style zero 1.0
		pair_coeff * *

		neighbor 1.0 bin
		neigh_modify every 1 delay 0 check yes

		timestep 0.00025

		fix 1 all nve

		fix 2 all latte NULL
		fix_modify 2 energy yes

		thermo_style custom step temp pe etotal

		# minimization

		thermo 1
		min_style fire
		minimize 1.0e-9 1.0e-9 1000 1000

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