(7d832b4d) · Commits · 郑智淋 / lammps

examples/USER/eff/Auger-Adamantane/README

deleted100644 → 0

+0 −3

Original line number	Diff line number	Diff line
		Valence electron ionization in adamantane, adamantane_ionized has one less electron.
		The full adamantane molecule is also included.
		Finite system.

examples/USER/eff/Auger-Adamantane/data.adamantane

deleted100644 → 0

+0 −119

Original line number	Diff line number	Diff line
		Created by AJB

		102 atoms
		3 atom types

		-500.0 500.0 xlo xhi
		-500.0 500.0 ylo yhi
		-500.0 500.0 zlo zhi

		Masses

		1 12.01070 # C nuclei
		2 1.000794 # H nuclei
		3 1.000000 # electron

		Atoms

		1 1 0.223271 2.836177 0.99547 6.00 0 0.00
		2 1 -0.611326 1.278041 3.303884 6.00 0 0.00
		3 1 -0.645795 -1.544681 2.608294 6.00 0 0.00
		4 1 -2.509122 -1.980433 0.419368 6.00 0 0.00
		5 1 -1.674732 -0.422977 -1.889518 6.00 0 0.00
		6 1 -1.640226 2.39965 -1.193097 6.00 0 0.00
		7 1 2.018681 -2.373515 1.79163 6.00 0 0.00
		8 1 2.887596 2.006776 0.178976 6.00 0 0.00
		9 1 0.98999 -1.251962 -2.705445 6.00 0 0.00
		10 1 2.853997 -0.815965 -0.517029 6.00 0 0.00
		11 2 -3.029741 -0.739677 -3.479893 1.00 0 0.00
		12 2 -4.456466 -1.425024 1.003463 1.00 0 0.00
		13 2 -2.581253 -4.027951 -0.074795 1.00 0 0.00
		14 2 -1.252983 -2.67657 4.28622 1.00 0 0.00
		15 2 -2.524731 1.891635 3.93955 1.00 0 0.00
		16 2 0.703394 1.61118 4.917143 1.00 0 0.00
		17 2 0.247516 4.887701 1.501501 1.00 0 0.00
		18 2 2.027034 -4.428006 1.321731 1.00 0 0.00
		19 2 3.379737 -2.105382 3.378244 1.00 0 0.00
		20 2 4.790758 -1.418428 -1.109855 1.00 0 0.00
		21 2 -1.077541 3.552194 -2.865467 1.00 0 0.00
		22 2 -3.572149 3.033181 -0.63782 1.00 0 0.00
		23 2 1.599389 -0.164293 -4.40463 1.00 0 0.00
		24 2 0.980069 -3.286423 -3.255167 1.00 0 0.00
		25 2 4.264224 2.353276 1.736734 1.00 0 0.00
		26 2 3.530575 3.152347 -1.469016 1.00 0 0.00
		27 3 0.223271 2.836177 0.99547 0.00 1 0.332948
		28 3 0.223271 2.836177 0.99547 0.00 -1 0.332948
		29 3 -0.611326 1.278041 3.303884 0.00 1 0.332948
		30 3 -0.611326 1.278041 3.303884 0.00 -1 0.332948
		31 3 -0.645795 -1.544681 2.608294 0.00 1 0.332948
		32 3 -0.645795 -1.544681 2.608294 0.00 -1 0.332948
		33 3 -2.509122 -1.980433 0.419368 0.00 1 0.332948
		34 3 -2.509122 -1.980433 0.419368 0.00 -1 0.332948
		35 3 -1.674732 -0.422977 -1.889518 0.00 1 0.332948
		36 3 -1.674732 -0.422977 -1.889518 0.00 -1 0.332948
		37 3 -1.640226 2.39965 -1.193097 0.00 1 0.332948
		38 3 -1.640226 2.39965 -1.193097 0.00 -1 0.332948
		39 3 2.018681 -2.373515 1.79163 0.00 1 0.332948
		40 3 2.018681 -2.373515 1.79163 0.00 -1 0.332948
		41 3 2.887596 2.006776 0.178976 0.00 1 0.332948
		42 3 2.887596 2.006776 0.178976 0.00 -1 0.332948
		43 3 0.98999 -1.251962 -2.705445 0.00 1 0.332948
		44 3 0.98999 -1.251962 -2.705445 0.00 -1 0.332948
		45 3 2.853997 -0.815965 -0.517029 0.00 1 0.332948
		46 3 2.853997 -0.815965 -0.517029 0.00 -1 0.332948
		47 3 -0.194028 2.057109 2.149677 0.00 1 1.258
		48 3 -0.194028 2.057109 2.149677 0.00 -1 1.258
		49 3 -0.628561 -0.13332 2.956089 0.00 1 1.258
		50 3 -0.628561 -0.13332 2.956089 0.00 -1 1.258
		51 3 -1.577458 -1.762557 1.513831 0.00 1 1.258
		52 3 -1.577458 -1.762557 1.513831 0.00 -1 1.258
		53 3 -2.091927 -1.201705 -0.735075 0.00 1 1.258
		54 3 -2.091927 -1.201705 -0.735075 0.00 -1 1.258
		55 3 -0.708477 2.617913 -0.098814 0.00 1 1.258
		56 3 -0.708477 2.617913 -0.098814 0.00 -1 1.258
		57 3 -1.657479 0.988336 -1.541308 0.00 1 1.258
		58 3 -1.657479 0.988336 -1.541308 0.00 -1 1.258
		59 3 0.686443 -1.959098 2.199962 0.00 1 1.258
		60 3 0.686443 -1.959098 2.199962 0.00 -1 1.258
		61 3 1.555434 2.421476 0.587223 0.00 1 1.258
		62 3 1.555434 2.421476 0.587223 0.00 -1 1.258
		63 3 -0.342371 -0.83747 -2.297482 0.00 1 1.258
		64 3 -0.342371 -0.83747 -2.297482 0.00 -1 1.258
		65 3 2.436339 -1.59474 0.637301 0.00 1 1.258
		66 3 2.436339 -1.59474 0.637301 0.00 -1 1.258
		67 3 2.870796 0.595405 -0.169027 0.00 1 1.258
		68 3 2.870796 0.595405 -0.169027 0.00 -1 1.258
		69 3 1.921993 -1.033964 -1.611237 0.00 1 1.258
		70 3 1.921993 -1.033964 -1.611237 0.00 -1 1.258
		71 3 -2.632724 -0.646884 -3.013913 0.00 1 1.543
		72 3 -2.632724 -0.646884 -3.013913 0.00 -1 1.543
		73 3 -3.885894 -1.587759 0.832324 0.00 1 1.543
		74 3 -3.885894 -1.587759 0.832324 0.00 -1 1.543
		75 3 -2.560118 -3.428028 0.069995 0.00 1 1.543
		76 3 -2.560118 -3.428028 0.069995 0.00 -1 1.543
		77 3 -1.075077 -2.344927 3.794588 0.00 1 1.543
		78 3 -1.075077 -2.344927 3.794588 0.00 -1 1.543
		79 3 -1.964103 1.711852 3.7533 0.00 1 1.543
		80 3 -1.964103 1.711852 3.7533 0.00 -1 1.543
		81 3 0.318181 1.513571 4.444458 0.00 1 1.543
		82 3 0.318181 1.513571 4.444458 0.00 -1 1.543
		83 3 0.240412 4.286604 1.353234 0.00 1 1.543
		84 3 0.240412 4.286604 1.353234 0.00 -1 1.543
		85 3 2.024586 -3.82604 1.459412 0.00 1 1.543
		86 3 2.024586 -3.82604 1.459412 0.00 -1 1.543
		87 3 2.980948 -2.183945 2.913367 0.00 1 1.543
		88 3 2.980948 -2.183945 2.913367 0.00 -1 1.543
		89 3 4.223287 -1.241907 -0.936157 0.00 1 1.543
		90 3 4.223287 -1.241907 -0.936157 0.00 -1 1.543
		91 3 -1.242407 3.214498 -2.375463 0.00 1 1.543
		92 3 -1.242407 3.214498 -2.375463 0.00 -1 1.543
		93 3 -3.006096 2.847556 -0.800517 0.00 1 1.543
		94 3 -3.006096 2.847556 -0.800517 0.00 -1 1.543
		95 3 1.420835 -0.48298 -3.906769 0.00 1 1.543
		96 3 1.420835 -0.48298 -3.906769 0.00 -1 1.543
		97 3 0.982976 -2.690326 -3.094098 0.00 1 1.543
		98 3 0.982976 -2.690326 -3.094098 0.00 -1 1.543
		99 3 3.860872 2.251751 1.280311 0.00 1 1.543
		100 3 3.860872 2.251751 1.280311 0.00 -1 1.543
		101 3 3.342182 2.816694 -0.986155 0.00 1 1.543
		102 3 3.342182 2.816694 -0.986155 0.00 -1 1.543

examples/USER/eff/Auger-Adamantane/data.adamantane_ionized

deleted100644 → 0

+0 −118

Original line number	Diff line number	Diff line
		Created by AJB

		101 atoms
		3 atom types

		-50.0 50.0 xlo xhi
		-50.0 50.0 ylo yhi
		-50.0 50.0 zlo zhi

		Masses

		1 12.01070 # C nuclei
		2 1.000794 # H nuclei
		3 1.000000 # electron

		Atoms

		1 1 0.22423 2.918607 1.015812 6 0 0.00
		2 1 -0.63445 1.31446 3.390303 6 0 0.00
		3 1 -0.670162 -1.590173 2.675707 6 0 0.00
		4 1 -2.586695 -2.037708 0.422846 6 0 0.00
		5 1 -1.729127 -0.435706 -1.953488 6 0 0.00
		6 1 -1.692867 2.468206 -1.236 6 0 0.00
		7 1 2.071281 -2.442011 1.834504 6 0 0.00
		8 1 2.965108 2.063979 0.175607 6 0 0.00
		9 1 1.013015 -1.288254 -2.791737 6 0 0.00
		10 1 2.931847 -0.84022 -0.540904 6 0 0.00
		11 2 -3.23707 -0.788493 -3.724286 1 0 0.00
		12 2 -4.691469 -1.429253 1.05608 1 0 0.00
		13 2 -2.657034 -4.253233 -0.113602 1 0 0.00
		14 2 -1.345725 -2.850372 4.543752 1 0 0.00
		15 2 -2.707861 1.976434 4.071194 1 0 0.00
		16 2 0.79423 1.672161 5.131751 1 0 0.00
		17 2 0.251667 5.202465 1.579125 1 0 0.00
		18 2 2.074796 -4.663951 1.320307 1 0 0.00
		19 2 3.542471 -2.144066 3.551451 1 0 0.00
		20 2 5.087753 -1.51102 -1.201338 1 0 0.00
		21 2 -1.077021 3.711707 -3.045901 1 0 0.00
		22 2 -3.783389 3.148492 -0.629227 1 0 0.00
		23 2 1.671766 -0.104421 -4.626344 1 0 0.00
		24 2 0.999815 -3.49189 -3.379184 1 0 0.00
		25 2 4.450647 2.434018 1.865941 1 0 0.00
		26 2 3.65466 3.300997 -1.612081 1 0 0.00
		27 3 -0.634804 1.31502 3.391634 0 -1 0.328405
		28 3 -0.670512 -1.590826 2.676675 0 -1 0.328107
		29 3 -2.587889 -2.038591 0.422899 0 -1 0.328405
		30 3 -1.729909 -0.435889 -1.954405 0 -1 0.328107
		31 3 -1.693676 2.469262 -1.236661 0 -1 0.328405
		32 3 2.072091 -2.443067 1.835165 0 -1 0.328405
		33 3 2.966303 2.064861 0.175553 0 -1 0.328405
		34 3 1.01337 -1.288814 -2.793067 0 -1 0.328405
		35 3 2.932965 -0.840567 -0.541247 0 -1 0.328108
		36 3 -0.210743 2.123398 2.223462 0 -1 1.326096
		37 3 -0.657351 -0.127988 3.052304 0 -1 1.326096
		38 3 -1.646634 -1.826737 1.548546 0 -1 1.326093
		39 3 -2.175416 -1.25026 -0.762988 0 -1 1.326095
		40 3 -0.747076 2.708081 -0.120938 0 -1 1.326093
		41 3 -1.722464 1.033139 -1.603613 0 -1 1.326095
		42 3 0.713852 -2.031645 2.263933 0 -1 1.326092
		43 3 1.613424 2.503259 0.59442 0 -1 1.326092
		44 3 -0.351222 -0.870483 -2.392027 0 -1 1.326098
		45 3 2.512477 -1.657113 0.657756 0 -1 1.3261
		46 3 2.965428 0.626295 -0.182887 0 -1 1.326099
		47 3 1.976186 -1.072464 -1.68666 0 -1 1.326101
		48 3 -2.952851 -0.722 -3.390526 0 -1 1.603792
		49 3 -4.265445 -1.534526 0.932369 0 -1 1.558563
		50 3 -2.625986 -3.810249 -0.010226 0 -1 1.558562
		51 3 -1.218394 -2.612849 4.191661 0 -1 1.603792
		52 3 -2.300135 1.839753 3.919625 0 -1 1.558507
		53 3 0.522041 1.594565 4.77431 0 -1 1.55862
		54 3 0.246496 4.772002 1.472951 0 -1 1.603792
		55 3 2.062319 -4.217199 1.410516 0 -1 1.558582
		56 3 3.245048 -2.186529 3.208486 0 -1 1.558537
		57 3 4.681408 -1.384588 -1.07686 0 -1 1.603791
		58 3 -1.184793 3.454906 -2.684898 0 -1 1.558565
		59 3 -3.365733 3.001032 -0.737405 0 -1 1.558559
		60 3 1.538708 -0.326106 -4.250794 0 -1 1.558551
		61 3 0.997214 -3.055912 -3.245768 0 -1 1.558563
		62 3 4.144833 2.349324 1.538532 0 -1 1.558524
		63 3 3.503398 3.047996 -1.264247 0 -1 1.558594
		64 3 0.224244 2.91979 1.016104 0 1 0.328107
		65 3 -0.634804 1.31502 3.391634 0 1 0.328405
		66 3 -0.670512 -1.590826 2.676675 0 1 0.328107
		67 3 -2.587889 -2.038591 0.422899 0 1 0.328405
		68 3 -1.729909 -0.435889 -1.954405 0 1 0.328107
		69 3 -1.693676 2.469262 -1.236661 0 1 0.328405
		70 3 2.072091 -2.443067 1.835165 0 1 0.328405
		71 3 2.966303 2.064861 0.175553 0 1 0.328405
		72 3 1.01337 -1.288814 -2.793067 0 1 0.328405
		73 3 2.932965 -0.840567 -0.541247 0 1 0.328108
		74 3 -0.210743 2.123398 2.223462 0 1 1.326096
		75 3 -0.657351 -0.127988 3.052304 0 1 1.326096
		76 3 -1.646634 -1.826737 1.548546 0 1 1.326093
		77 3 -2.175416 -1.250259 -0.762988 0 1 1.326094
		78 3 -0.747076 2.708081 -0.120938 0 1 1.326094
		79 3 -1.722464 1.033139 -1.603613 0 1 1.326096
		80 3 0.713852 -2.031645 2.263933 0 1 1.326092
		81 3 1.613424 2.503259 0.59442 0 1 1.326092
		82 3 -0.351222 -0.870483 -2.392027 0 1 1.326098
		83 3 2.512477 -1.657113 0.657756 0 1 1.3261
		84 3 2.965428 0.626295 -0.182887 0 1 1.326099
		85 3 1.976186 -1.072464 -1.68666 0 1 1.326101
		86 3 -2.952851 -0.722 -3.390526 0 1 1.603792
		87 3 -4.265445 -1.534526 0.932369 0 1 1.558563
		88 3 -2.625986 -3.810249 -0.010226 0 1 1.558562
		89 3 -1.218394 -2.612849 4.191661 0 1 1.603792
		90 3 -2.300135 1.839753 3.919625 0 1 1.558507
		91 3 0.522041 1.594565 4.77431 0 1 1.55862
		92 3 0.246496 4.772002 1.472951 0 1 1.603792
		93 3 2.062319 -4.217199 1.410516 0 1 1.558582
		94 3 3.245048 -2.186529 3.208486 0 1 1.558537
		95 3 4.681408 -1.384588 -1.07686 0 1 1.603791
		96 3 -1.184793 3.454906 -2.684898 0 1 1.558565
		97 3 -3.365733 3.001032 -0.737405 0 1 1.558559
		98 3 1.538708 -0.326106 -4.250794 0 1 1.558551
		99 3 0.997214 -3.055912 -3.245768 0 1 1.558563
		100 3 4.144833 2.349324 1.538532 0 1 1.558524
		101 3 3.503398 3.047996 -1.264247 0 1 1.558594

examples/USER/eff/Auger-Adamantane/in.adamantane.min

deleted100644 → 0

+0 −29

Original line number	Diff line number	Diff line
		variable sname index adamantane
		log ${sname}.min.log

		units electron
		newton on
		#boundary p p p
		boundary f f f

		atom_style hybrid charge electron

		read_data data.${sname}

		pair_style eff/cut 500.0
		pair_coeff * *

		communicate single vel yes

		thermo 1
		thermo_style multi

		dump 1 all xyz 1 ${sname}.min.xyz
		dump 2 all custom 1 ${sname}.min.lammpstrj id type x y z radius fx fy fz rf

		min_style cg
		#min_modify line quadratic
		minimize 0 1.0e-5 10000 100000

		undump 1
		undump 2

examples/USER/eff/Auger-Adamantane/in.adamantane.nvt

deleted100644 → 0

+0 −40

Original line number	Diff line number	Diff line
		variable sname index adamantane

		units electron
		newton on
		boundary f f f

		atom_style hybrid charge electron

		read_data data.${sname}

		pair_style eff/cut 500.0
		pair_coeff * *

		log ${sname}.min.log

		communicate single vel yes

		thermo 100
		thermo_style custom step etotal pe ke press vol temp

		min_style cg
		min_modify line quadratic
		minimize 0 1.0e-5 10000 100000

		velocity all create 300.0 4928459 rot yes dist gaussian

		reset_timestep 0
		log ${sname}.nvt.log

		timestep 0.001
		fix 1 all nvt/eff 300.0 300.0 1.0 chain yes
		compute eff_temp all temp/eff
		thermo_style custom step etotal pe ke press vol temp c_eff_temp
		dump 1 all custom 100 ${sname}.nvt.lammpstrj id type x y z spin radius vx vy vz vr

		run 1000000

		unfix 1
		undump 1

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