(6ce7d466) · Commits · 郑智淋 / lammps

examples/USER/eff/Auger-Adamantane/README

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+9 −0

Original line number	Diff line number	Diff line
		In the Auger process, a valence electron falls in to a core hole, which
		releases enough energy to eject another valence electron. Thus a state with
		two valence holes is created. Using eFF it is possible to track, for the first
		time, the continuous evolution of a core-hole state into a two-valence hole state,
		with full electron and nuclear dynamics included (Adamantane case).
		To simulate the dissociation dynamics of core-ionized adamantane, we proceed
		by deleting a core electron from the data.adamantane structure.
		An complete Adamantane molecule is also provided.
		Finite system.

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

0 → 100644

+119 −0

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 6.00 0 0.000000 0.223271 2.836177 0.99547
		2 1 6.00 0 0.000000 -0.611326 1.278041 3.303884
		3 1 6.00 0 0.000000 -0.645795 -1.544681 2.608294
		4 1 6.00 0 0.000000 -2.509122 -1.980433 0.419368
		5 1 6.00 0 0.000000 -1.674732 -0.422977 -1.889518
		6 1 6.00 0 0.000000 -1.640226 2.39965 -1.193097
		7 1 6.00 0 0.000000 2.018681 -2.373515 1.79163
		8 1 6.00 0 0.000000 2.887596 2.006776 0.178976
		9 1 6.00 0 0.000000 0.98999 -1.251962 -2.705445
		10 1 6.00 0 0.000000 2.853997 -0.815965 -0.517029
		11 2 1.00 0 0.000000 -3.029741 -0.739677 -3.479893
		12 2 1.00 0 0.000000 -4.456466 -1.425024 1.003463
		13 2 1.00 0 0.000000 -2.581253 -4.027951 -0.074795
		14 2 1.00 0 0.000000 -1.252983 -2.67657 4.28622
		15 2 1.00 0 0.000000 -2.524731 1.891635 3.93955
		16 2 1.00 0 0.000000 0.703394 1.61118 4.917143
		17 2 1.00 0 0.000000 0.247516 4.887701 1.501501
		18 2 1.00 0 0.000000 2.027034 -4.428006 1.321731
		19 2 1.00 0 0.000000 3.379737 -2.105382 3.378244
		20 2 1.00 0 0.000000 4.790758 -1.418428 -1.109855
		21 2 1.00 0 0.000000 -1.077541 3.552194 -2.865467
		22 2 1.00 0 0.000000 -3.572149 3.033181 -0.63782
		23 2 1.00 0 0.000000 1.599389 -0.164293 -4.40463
		24 2 1.00 0 0.000000 0.980069 -3.286423 -3.255167
		25 2 1.00 0 0.000000 4.264224 2.353276 1.736734
		26 2 1.00 0 0.000000 3.530575 3.152347 -1.469016
		27 3 0.00 1 0.332948 0.223271 2.836177 0.99547
		28 3 0.00 -1 0.332948 0.223271 2.836177 0.99547
		29 3 0.00 1 0.332948 -0.611326 1.278041 3.303884
		30 3 0.00 -1 0.332948 -0.611326 1.278041 3.303884
		31 3 0.00 1 0.332948 -0.645795 -1.544681 2.608294
		32 3 0.00 -1 0.332948 -0.645795 -1.544681 2.608294
		33 3 0.00 1 0.332948 -2.509122 -1.980433 0.419368
		34 3 0.00 -1 0.332948 -2.509122 -1.980433 0.419368
		35 3 0.00 1 0.332948 -1.674732 -0.422977 -1.889518
		36 3 0.00 -1 0.332948 -1.674732 -0.422977 -1.889518
		37 3 0.00 1 0.332948 -1.640226 2.39965 -1.193097
		38 3 0.00 -1 0.332948 -1.640226 2.39965 -1.193097
		39 3 0.00 1 0.332948 2.018681 -2.373515 1.79163
		40 3 0.00 -1 0.332948 2.018681 -2.373515 1.79163
		41 3 0.00 1 0.332948 2.887596 2.006776 0.178976
		42 3 0.00 -1 0.332948 2.887596 2.006776 0.178976
		43 3 0.00 1 0.332948 0.98999 -1.251962 -2.705445
		44 3 0.00 -1 0.332948 0.98999 -1.251962 -2.705445
		45 3 0.00 1 0.332948 2.853997 -0.815965 -0.517029
		46 3 0.00 -1 0.332948 2.853997 -0.815965 -0.517029
		47 3 0.00 1 1.258000 -0.194028 2.057109 2.149677
		48 3 0.00 -1 1.258000 -0.194028 2.057109 2.149677
		49 3 0.00 1 1.258000 -0.628561 -0.13332 2.956089
		50 3 0.00 -1 1.258000 -0.628561 -0.13332 2.956089
		51 3 0.00 1 1.258000 -1.577458 -1.762557 1.513831
		52 3 0.00 -1 1.258000 -1.577458 -1.762557 1.513831
		53 3 0.00 1 1.258000 -2.091927 -1.201705 -0.735075
		54 3 0.00 -1 1.258000 -2.091927 -1.201705 -0.735075
		55 3 0.00 1 1.258000 -0.708477 2.617913 -0.098814
		56 3 0.00 -1 1.258000 -0.708477 2.617913 -0.098814
		57 3 0.00 1 1.258000 -1.657479 0.988336 -1.541308
		58 3 0.00 -1 1.258000 -1.657479 0.988336 -1.541308
		59 3 0.00 1 1.258000 0.686443 -1.959098 2.199962
		60 3 0.00 -1 1.258000 0.686443 -1.959098 2.199962
		61 3 0.00 1 1.258000 1.555434 2.421476 0.587223
		62 3 0.00 -1 1.258000 1.555434 2.421476 0.587223
		63 3 0.00 1 1.258000 -0.342371 -0.83747 -2.297482
		64 3 0.00 -1 1.258000 -0.342371 -0.83747 -2.297482
		65 3 0.00 1 1.258000 2.436339 -1.59474 0.637301
		66 3 0.00 -1 1.258000 2.436339 -1.59474 0.637301
		67 3 0.00 1 1.258000 2.870796 0.595405 -0.169027
		68 3 0.00 -1 1.258000 2.870796 0.595405 -0.169027
		69 3 0.00 1 1.258000 1.921993 -1.033964 -1.611237
		70 3 0.00 -1 1.258000 1.921993 -1.033964 -1.611237
		71 3 0.00 1 1.543000 -2.632724 -0.646884 -3.013913
		72 3 0.00 -1 1.543000 -2.632724 -0.646884 -3.013913
		73 3 0.00 1 1.543000 -3.885894 -1.587759 0.832324
		74 3 0.00 -1 1.543000 -3.885894 -1.587759 0.832324
		75 3 0.00 1 1.543000 -2.560118 -3.428028 0.069995
		76 3 0.00 -1 1.543000 -2.560118 -3.428028 0.069995
		77 3 0.00 1 1.543000 -1.075077 -2.344927 3.794588
		78 3 0.00 -1 1.543000 -1.075077 -2.344927 3.794588
		79 3 0.00 1 1.543000 -1.964103 1.711852 3.7533
		80 3 0.00 -1 1.543000 -1.964103 1.711852 3.7533
		81 3 0.00 1 1.543000 0.318181 1.513571 4.444458
		82 3 0.00 -1 1.543000 0.318181 1.513571 4.444458
		83 3 0.00 1 1.543000 0.240412 4.286604 1.353234
		84 3 0.00 -1 1.543000 0.240412 4.286604 1.353234
		85 3 0.00 1 1.543000 2.024586 -3.82604 1.459412
		86 3 0.00 -1 1.543000 2.024586 -3.82604 1.459412
		87 3 0.00 1 1.543000 2.980948 -2.183945 2.913367
		88 3 0.00 -1 1.543000 2.980948 -2.183945 2.913367
		89 3 0.00 1 1.543000 4.223287 -1.241907 -0.936157
		90 3 0.00 -1 1.543000 4.223287 -1.241907 -0.936157
		91 3 0.00 1 1.543000 -1.242407 3.214498 -2.375463
		92 3 0.00 -1 1.543000 -1.242407 3.214498 -2.375463
		93 3 0.00 1 1.543000 -3.006096 2.847556 -0.800517
		94 3 0.00 -1 1.543000 -3.006096 2.847556 -0.800517
		95 3 0.00 1 1.543000 1.420835 -0.48298 -3.906769
		96 3 0.00 -1 1.543000 1.420835 -0.48298 -3.906769
		97 3 0.00 1 1.543000 0.982976 -2.690326 -3.094098
		98 3 0.00 -1 1.543000 0.982976 -2.690326 -3.094098
		99 3 0.00 1 1.543000 3.860872 2.251751 1.280311
		100 3 0.00 -1 1.543000 3.860872 2.251751 1.280311
		101 3 0.00 1 1.543000 3.342182 2.816694 -0.986155
		102 3 0.00 -1 1.543000 3.342182 2.816694 -0.986155

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

0 → 100644

+118 −0

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 6.00 0 0.000000 0.224230 2.918607 1.015812
		2 1 6.00 0 0.000000 -0.634450 1.314460 3.390303
		3 1 6.00 0 0.000000 -0.670162 -1.590173 2.675707
		4 1 6.00 0 0.000000 -2.586695 -2.037708 0.422846
		5 1 6.00 0 0.000000 -1.729127 -0.435706 -1.953488
		6 1 6.00 0 0.000000 -1.692867 2.468206 -1.236000
		7 1 6.00 0 0.000000 2.071281 -2.442011 1.834504
		8 1 6.00 0 0.000000 2.965108 2.063979 0.175607
		9 1 6.00 0 0.000000 1.013015 -1.288254 -2.791737
		10 1 6.00 0 0.000000 2.931847 -0.840220 -0.540904
		11 2 1.00 0 0.000000 -3.237070 -0.788493 -3.724286
		12 2 1.00 0 0.000000 -4.691469 -1.429253 1.056080
		13 2 1.00 0 0.000000 -2.657034 -4.253233 -0.113602
		14 2 1.00 0 0.000000 -1.345725 -2.850372 4.543752
		15 2 1.00 0 0.000000 -2.707861 1.976434 4.071194
		16 2 1.00 0 0.000000 0.794230 1.672161 5.131751
		17 2 1.00 0 0.000000 0.251667 5.202465 1.579125
		18 2 1.00 0 0.000000 2.074796 -4.663951 1.320307
		19 2 1.00 0 0.000000 3.542471 -2.144066 3.551451
		20 2 1.00 0 0.000000 5.087753 -1.511020 -1.201338
		21 2 1.00 0 0.000000 -1.077021 3.711707 -3.045901
		22 2 1.00 0 0.000000 -3.783389 3.148492 -0.629227
		23 2 1.00 0 0.000000 1.671766 -0.104421 -4.626344
		24 2 1.00 0 0.000000 0.999815 -3.491890 -3.379184
		25 2 1.00 0 0.000000 4.450647 2.434018 1.865941
		26 2 1.00 0 0.000000 3.654660 3.300997 -1.612081
		27 3 0.00 -1 0.328405 -0.634804 1.315020 3.391634
		28 3 0.00 -1 0.328107 -0.670512 -1.590826 2.676675
		29 3 0.00 -1 0.328405 -2.587889 -2.038591 0.422899
		30 3 0.00 -1 0.328107 -1.729909 -0.435889 -1.954405
		31 3 0.00 -1 0.328405 -1.693676 2.469262 -1.236661
		32 3 0.00 -1 0.328405 2.072091 -2.443067 1.835165
		33 3 0.00 -1 0.328405 2.966303 2.064861 0.175553
		34 3 0.00 -1 0.328405 1.013370 -1.288814 -2.793067
		35 3 0.00 -1 0.328108 2.932965 -0.840567 -0.541247
		36 3 0.00 -1 1.326096 -0.210743 2.123398 2.223462
		37 3 0.00 -1 1.326096 -0.657351 -0.127988 3.052304
		38 3 0.00 -1 1.326093 -1.646634 -1.826737 1.548546
		39 3 0.00 -1 1.326095 -2.175416 -1.250260 -0.762988
		40 3 0.00 -1 1.326093 -0.747076 2.708081 -0.120938
		41 3 0.00 -1 1.326095 -1.722464 1.033139 -1.603613
		42 3 0.00 -1 1.326092 0.713852 -2.031645 2.263933
		43 3 0.00 -1 1.326092 1.613424 2.503259 0.594420
		44 3 0.00 -1 1.326098 -0.351222 -0.870483 -2.392027
		45 3 0.00 -1 1.326100 2.512477 -1.657113 0.657756
		46 3 0.00 -1 1.326099 2.965428 0.626295 -0.182887
		47 3 0.00 -1 1.326101 1.976186 -1.072464 -1.686660
		48 3 0.00 -1 1.603792 -2.952851 -0.722000 -3.390526
		49 3 0.00 -1 1.558563 -4.265445 -1.534526 0.932369
		50 3 0.00 -1 1.558562 -2.625986 -3.810249 -0.010226
		51 3 0.00 -1 1.603792 -1.218394 -2.612849 4.191661
		52 3 0.00 -1 1.558507 -2.300135 1.839753 3.919625
		53 3 0.00 -1 1.558620 0.522041 1.594565 4.774310
		54 3 0.00 -1 1.603792 0.246496 4.772002 1.472951
		55 3 0.00 -1 1.558582 2.062319 -4.217199 1.410516
		56 3 0.00 -1 1.558537 3.245048 -2.186529 3.208486
		57 3 0.00 -1 1.603791 4.681408 -1.384588 -1.076860
		58 3 0.00 -1 1.558565 -1.184793 3.454906 -2.684898
		59 3 0.00 -1 1.558559 -3.365733 3.001032 -0.737405
		60 3 0.00 -1 1.558551 1.538708 -0.326106 -4.250794
		61 3 0.00 -1 1.558563 0.997214 -3.055912 -3.245768
		62 3 0.00 -1 1.558524 4.144833 2.349324 1.538532
		63 3 0.00 -1 1.558594 3.503398 3.047996 -1.264247
		64 3 0.00 1 0.328107 0.224244 2.919790 1.016104
		65 3 0.00 1 0.328405 -0.634804 1.315020 3.391634
		66 3 0.00 1 0.328107 -0.670512 -1.590826 2.676675
		67 3 0.00 1 0.328405 -2.587889 -2.038591 0.422899
		68 3 0.00 1 0.328107 -1.729909 -0.435889 -1.954405
		69 3 0.00 1 0.328405 -1.693676 2.469262 -1.236661
		70 3 0.00 1 0.328405 2.072091 -2.443067 1.835165
		71 3 0.00 1 0.328405 2.966303 2.064861 0.175553
		72 3 0.00 1 0.328405 1.013370 -1.288814 -2.793067
		73 3 0.00 1 0.328108 2.932965 -0.840567 -0.541247
		74 3 0.00 1 1.326096 -0.210743 2.123398 2.223462
		75 3 0.00 1 1.326096 -0.657351 -0.127988 3.052304
		76 3 0.00 1 1.326093 -1.646634 -1.826737 1.548546
		77 3 0.00 1 1.326094 -2.175416 -1.250259 -0.762988
		78 3 0.00 1 1.326094 -0.747076 2.708081 -0.120938
		79 3 0.00 1 1.326096 -1.722464 1.033139 -1.603613
		80 3 0.00 1 1.326092 0.713852 -2.031645 2.263933
		81 3 0.00 1 1.326092 1.613424 2.503259 0.594420
		82 3 0.00 1 1.326098 -0.351222 -0.870483 -2.392027
		83 3 0.00 1 1.326100 2.512477 -1.657113 0.657756
		84 3 0.00 1 1.326099 2.965428 0.626295 -0.182887
		85 3 0.00 1 1.326101 1.976186 -1.072464 -1.686660
		86 3 0.00 1 1.603792 -2.952851 -0.722000 -3.390526
		87 3 0.00 1 1.558563 -4.265445 -1.534526 0.932369
		88 3 0.00 1 1.558562 -2.625986 -3.810249 -0.010226
		89 3 0.00 1 1.603792 -1.218394 -2.612849 4.191661
		90 3 0.00 1 1.558507 -2.300135 1.839753 3.919625
		91 3 0.00 1 1.558620 0.522041 1.594565 4.774310
		92 3 0.00 1 1.603792 0.246496 4.772002 1.472951
		93 3 0.00 1 1.558582 2.062319 -4.217199 1.410516
		94 3 0.00 1 1.558537 3.245048 -2.186529 3.208486
		95 3 0.00 1 1.603791 4.681408 -1.384588 -1.076860
		96 3 0.00 1 1.558565 -1.184793 3.454906 -2.684898
		97 3 0.00 1 1.558559 -3.365733 3.001032 -0.737405
		98 3 0.00 1 1.558551 1.538708 -0.326106 -4.250794
		99 3 0.00 1 1.558563 0.997214 -3.055912 -3.245768
		100 3 0.00 1 1.558524 4.144833 2.349324 1.538532
		101 3 0.00 1 1.558594 3.503398 3.047996 -1.264247

examples/USER/eff/Auger-Adamantane/in.adamantane_ionized.nve

0 → 100644

+51 −0

Original line number	Diff line number	Diff line
		variable sname index adamantane_ionized
		log ${sname}.nve.log

		units electron
		newton on
		boundary f f f

		atom_style electron

		read_data data.${sname}

		pair_style eff/cut 100.0 0 0
		pair_coeff * *

		communicate single vel yes

		compute effTemp all temp/eff

		thermo 1000
		thermo_style custom step pe temp press
		thermo_modify temp effTemp

		# Minimization
		min_style cg
		dump 1 all xyz 500 ${sname}.min.xyz
		dump 2 all custom 500 ${sname}.min.lammpstrj id type x y z spin eradius fx fy fz erforce
		min_modify line quadratic
		minimize 0.0 1.0e-5 10000 100000

		undump 1
		undump 2

		#restart timestep

		# set velocities for nve
		#velocity all create 300.0 4928459 dist uniform

		# NVE
		timestep 0.001

		fix 1 all nve/eff
		dump 1 all xyz 1000 ${sname}.nve.xyz
		dump 2 all custom 1000 ${sname}.nve.lammpstrj id type x y z spin eradius fx fy fz erforce
		#restart 1000 ${sname}.nve.restart1 ${sname}.nve.restart2

		run 200000

		unfix 1
		undump 1
		undump 2

examples/USER/eff/Be-solid/README

0 → 100644

+3 −0

Original line number	Diff line number	Diff line
		Be-solid.spe: beryllium bulk single point energy
		Beryllium in eFF and experiment exists as a hexagonal-close packed structure

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