git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4648 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2010-09-01 18:55:48 +00:00
parent 7d832b4db1
commit 6ce7d46695
31 changed files with 40376 additions and 0 deletions

View File

@ -0,0 +1,9 @@
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.

View File

@ -0,0 +1,119 @@
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

View File

@ -0,0 +1,118 @@
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

View File

@ -0,0 +1,51 @@
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

View File

@ -0,0 +1,3 @@
Be-solid.spe: beryllium bulk single point energy
Beryllium in eFF and experiment exists as a hexagonal-close packed structure

File diff suppressed because it is too large Load Diff

View File

@ -0,0 +1,30 @@
variable sname index Be-solid
log ${sname}.spe.log
units electron
newton on
boundary p p p
atom_style electron
read_data data.${sname}
pair_style eff/cut 31.6125 0 0
pair_coeff * *
communicate single vel yes
neigh_modify one 10000 page 100000
compute effTemp all temp/eff
thermo 10
thermo_style custom step etotal pe ke temp press
thermo_modify temp effTemp
dump 1 all custom 1 ${sname}.spe.lammpstrj id type x y z spin eradius
fix 1 all nve/eff
run 0

View File

@ -0,0 +1,2 @@
Methane, valence electron ionization and full molecule tests (spe, min, dynamics).
Note: electron mass set to 1

View File

@ -0,0 +1,32 @@
Created by AJB
15 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 mass
2 1.000794 # H nuclei mass
3 1.000000 # electron mass
Atoms
#id|type|q|spin|eradius|x|y|z|
1 1 6.0 0 0.0 0.0 0.0 0.0
2 2 1.0 0 0.0 1.0 1.0 1.0
3 2 1.0 0 0.0 -1.0 -1.0 1.0
4 2 1.0 0 0.0 1.0 -1.0 -1.0
5 2 1.0 0 0.0 -1.0 1.0 -1.0
6 3 0.0 -1 0.5 0.0 0.0 0.0
7 3 0.0 -1 1.0 1.0 1.0 1.0
8 3 0.0 -1 1.0 -1.0 -1.0 1.0
9 3 0.0 -1 1.0 1.0 -1.0 -1.0
10 3 0.0 -1 1.0 -1.0 1.0 -1.0
11 3 0.0 1 0.5 0.0 0.0 0.0
12 3 0.0 1 1.0 1.0 1.0 1.0
13 3 0.0 1 1.0 -1.0 -1.0 1.0
14 3 0.0 1 1.0 1.0 -1.0 -1.0
15 3 0.0 1 1.0 -1.0 1.0 -1.0

View File

@ -0,0 +1,31 @@
Created by AJB
14 atoms
3 atom types
-5000.0 5000.0 xlo xhi
-5000.0 5000.0 ylo yhi
-5000.0 5000.0 zlo zhi
Masses
1 12.01070 # C nuclei mass
2 1.000794 # H nuclei mass
3 1.000000 # electron mass
Atoms
1 1 6.000000 0 0.0 0.000000 -0.000000 0.000000
2 2 1.000000 0 0.0 1.247211 1.247211 1.247211
3 2 1.000000 0 0.0 -1.247211 -1.247211 1.247211
4 2 1.000000 0 0.0 1.247211 -1.247211 -1.247211
5 2 1.000000 0 0.0 -1.247211 1.247211 -1.247211
6 3 0.000000 -1 0.329128 -0.000000 0.000000 -0.000000
7 3 0.000000 -1 1.486181 0.979221 0.979221 0.979221
8 3 0.000000 -1 1.486181 -0.979221 -0.979221 0.979221
9 3 0.000000 -1 1.486181 0.979221 -0.979221 -0.979221
10 3 0.000000 -1 1.486181 -0.979221 0.979221 -0.979221
11 3 0.000000 1 0.329128 -0.000000 0.000000 0.000000
12 3 0.000000 1 1.486181 -0.979221 -0.979221 0.979221
13 3 0.000000 1 1.486181 0.979221 -0.979221 -0.979221
14 3 0.000000 1 1.486181 -0.979221 0.979221 -0.979221

View File

@ -0,0 +1,40 @@
variable sname index ch4
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
pair_coeff * *
communicate single vel yes
# Minimize
min_style cg
dump 1 all custom 1 ${sname}.min.lammpstrj id type q spin eradius x y z
min_modify line quadratic dmax 0.1
minimize 0 1.0e-6 1000 10000
# Dynamics
compute effTemp all temp/eff
thermo 1000
thermo_style custom step pe temp press
thermo_modify temp effTemp
velocity all create 300.0 4928459 dist gaussian rot yes mom yes
timestep 0.005
fix 1 all nve/eff
# the custom dump includes the radii
dump 2 all custom 1000 ${sname}.nve.lammpstrj id type q spin eradius x y z
dump 3 all xyz 1000 ${sname}.nve.xyz
run 100000

View File

@ -0,0 +1,41 @@
variable sname index ch4_ionized
log ${sname}.nvt.log
units electron
newton on
boundary f f f
atom_style electron
read_data data.${sname}
pair_style eff/cut 5000.0 0 0
pair_coeff * *
communicate single vel yes
# minimize
min_style cg
min_modify line quadratic
minimize 0 1.0e-6 10000 100000
# dynamics
compute effTemp all temp/eff
thermo 100
thermo_style custom step etotal pe ke temp press
thermo_modify temp effTemp
# equilibrate
timestep 0.001
fix 1 all nvt/eff temp 300.0 300.0 0.1
# the custom dump includes the radii
dump 1 all custom 100 ${sname}.nvt.lammpstrj id type x y z spin eradius
dump 2 all xyz 100 ${sname}.nvt.xyz
run 1000000
fix 2 all nve/eff
run 1000000

View File

@ -0,0 +1 @@
Simple Hydrogen atom example (finite)

View File

@ -0,0 +1,19 @@
Created by AJB
2 atoms
2 atom types
-10.0 10.0 xlo xhi
-10.0 10.0 ylo yhi
-10.0 10.0 zlo zhi
Masses
1 1.000794 # H nuclei mass
2 1.000000 # electron mass
Atoms
#id|type|q|spin|r|x|y|z|
1 1 1.0 0 0.0 0.0 0.0 0.0
2 2 0.0 1 1.0 0.0 0.0 0.0

View File

@ -0,0 +1,30 @@
variable sname index h_atom
log ${sname}.min.log
units electron
newton on
boundary f f f
atom_style electron
read_data data.${sname}
pair_style eff/cut 10.0 0 0
pair_coeff * *
communicate single vel yes
compute effTemp all temp/eff
thermo 1
thermo_style multi
thermo_modify temp effTemp
dump 1 all xyz 1 ${sname}.min.xyz
dump 2 all custom 1 ${sname}.min.lammpstrj id type x y z eradius
dump 3 all custom 1 ${sname}.min.forces id type fx fy fz erforce
min_style cg
min_modify line quadratic dmax 2.0
minimize 1.0e-4 1.0e-4 1000 100000

View File

@ -0,0 +1,23 @@
variable sname index h_atom
log ${sname}.spe.log
units electron
newton on
boundary f f f
atom_style electron
read_data data.${sname}
pair_style eff/cut 500.0 0 0
pair_coeff * *
communicate single vel yes
compute effTemp all temp/eff
thermo 1
thermo_style multi
thermo_modify temp effTemp
run 0

View File

@ -0,0 +1 @@
This example demonstrates the use of several eff-related commands. No particular physics is explored.

View File

@ -0,0 +1,144 @@
Created with h2.pl
128 atoms
2 atom types
0.000000 12.895936 xlo xhi
0.000000 12.895936 ylo yhi
0.000000 12.895936 zlo zhi
Masses
1 1.007940
2 1.000000
Atoms
1 1 1.000000 0 0.000000 1.611992 1.611992 2.111992
2 1 1.000000 0 0.000000 1.611992 1.611992 4.335976
3 1 1.000000 0 0.000000 1.611992 1.611992 8.559960
4 1 1.000000 0 0.000000 1.611992 1.611992 10.783944
5 1 1.000000 0 0.000000 1.611992 4.835976 2.111992
6 1 1.000000 0 0.000000 1.611992 4.835976 4.335976
7 1 1.000000 0 0.000000 1.611992 4.835976 8.559960
8 1 1.000000 0 0.000000 1.611992 4.835976 10.783944
9 1 1.000000 0 0.000000 1.611992 8.059960 2.111992
10 1 1.000000 0 0.000000 1.611992 8.059960 4.335976
11 1 1.000000 0 0.000000 1.611992 8.059960 8.559960
12 1 1.000000 0 0.000000 1.611992 8.059960 10.783944
13 1 1.000000 0 0.000000 1.611992 11.283944 2.111992
14 1 1.000000 0 0.000000 1.611992 11.283944 4.335976
15 1 1.000000 0 0.000000 1.611992 11.283944 8.559960
16 1 1.000000 0 0.000000 1.611992 11.283944 10.783944
17 1 1.000000 0 0.000000 4.835976 1.611992 2.111992
18 1 1.000000 0 0.000000 4.835976 1.611992 4.335976
19 1 1.000000 0 0.000000 4.835976 1.611992 8.559960
20 1 1.000000 0 0.000000 4.835976 1.611992 10.783944
21 1 1.000000 0 0.000000 4.835976 4.835976 2.111992
22 1 1.000000 0 0.000000 4.835976 4.835976 4.335976
23 1 1.000000 0 0.000000 4.835976 4.835976 8.559960
24 1 1.000000 0 0.000000 4.835976 4.835976 10.783944
25 1 1.000000 0 0.000000 4.835976 8.059960 2.111992
26 1 1.000000 0 0.000000 4.835976 8.059960 4.335976
27 1 1.000000 0 0.000000 4.835976 8.059960 8.559960
28 1 1.000000 0 0.000000 4.835976 8.059960 10.783944
29 1 1.000000 0 0.000000 4.835976 11.283944 2.111992
30 1 1.000000 0 0.000000 4.835976 11.283944 4.335976
31 1 1.000000 0 0.000000 4.835976 11.283944 8.559960
32 1 1.000000 0 0.000000 4.835976 11.283944 10.783944
33 1 1.000000 0 0.000000 8.059960 1.611992 2.111992
34 1 1.000000 0 0.000000 8.059960 1.611992 4.335976
35 1 1.000000 0 0.000000 8.059960 1.611992 8.559960
36 1 1.000000 0 0.000000 8.059960 1.611992 10.783944
37 1 1.000000 0 0.000000 8.059960 4.835976 2.111992
38 1 1.000000 0 0.000000 8.059960 4.835976 4.335976
39 1 1.000000 0 0.000000 8.059960 4.835976 8.559960
40 1 1.000000 0 0.000000 8.059960 4.835976 10.783944
41 1 1.000000 0 0.000000 8.059960 8.059960 2.111992
42 1 1.000000 0 0.000000 8.059960 8.059960 4.335976
43 1 1.000000 0 0.000000 8.059960 8.059960 8.559960
44 1 1.000000 0 0.000000 8.059960 8.059960 10.783944
45 1 1.000000 0 0.000000 8.059960 11.283944 2.111992
46 1 1.000000 0 0.000000 8.059960 11.283944 4.335976
47 1 1.000000 0 0.000000 8.059960 11.283944 8.559960
48 1 1.000000 0 0.000000 8.059960 11.283944 10.783944
49 1 1.000000 0 0.000000 11.283944 1.611992 2.111992
50 1 1.000000 0 0.000000 11.283944 1.611992 4.335976
51 1 1.000000 0 0.000000 11.283944 1.611992 8.559960
52 1 1.000000 0 0.000000 11.283944 1.611992 10.783944
53 1 1.000000 0 0.000000 11.283944 4.835976 2.111992
54 1 1.000000 0 0.000000 11.283944 4.835976 4.335976
55 1 1.000000 0 0.000000 11.283944 4.835976 8.559960
56 1 1.000000 0 0.000000 11.283944 4.835976 10.783944
57 1 1.000000 0 0.000000 11.283944 8.059960 2.111992
58 1 1.000000 0 0.000000 11.283944 8.059960 4.335976
59 1 1.000000 0 0.000000 11.283944 8.059960 8.559960
60 1 1.000000 0 0.000000 11.283944 8.059960 10.783944
61 1 1.000000 0 0.000000 11.283944 11.283944 2.111992
62 1 1.000000 0 0.000000 11.283944 11.283944 4.335976
63 1 1.000000 0 0.000000 11.283944 11.283944 8.559960
64 1 1.000000 0 0.000000 11.283944 11.283944 10.783944
65 2 0.000000 -1 1.823572 1.611992 1.611992 2.111992
66 2 0.000000 1 1.823572 1.611992 1.611992 4.335976
67 2 0.000000 -1 1.823572 1.611992 1.611992 8.559960
68 2 0.000000 1 1.823572 1.611992 1.611992 10.783944
69 2 0.000000 -1 1.823572 1.611992 4.835976 2.111992
70 2 0.000000 1 1.823572 1.611992 4.835976 4.335976
71 2 0.000000 -1 1.823572 1.611992 4.835976 8.559960
72 2 0.000000 1 1.823572 1.611992 4.835976 10.783944
73 2 0.000000 -1 1.823572 1.611992 8.059960 2.111992
74 2 0.000000 1 1.823572 1.611992 8.059960 4.335976
75 2 0.000000 -1 1.823572 1.611992 8.059960 8.559960
76 2 0.000000 1 1.823572 1.611992 8.059960 10.783944
77 2 0.000000 -1 1.823572 1.611992 11.283944 2.111992
78 2 0.000000 1 1.823572 1.611992 11.283944 4.335976
79 2 0.000000 -1 1.823572 1.611992 11.283944 8.559960
80 2 0.000000 1 1.823572 1.611992 11.283944 10.783944
81 2 0.000000 -1 1.823572 4.835976 1.611992 2.111992
82 2 0.000000 1 1.823572 4.835976 1.611992 4.335976
83 2 0.000000 -1 1.823572 4.835976 1.611992 8.559960
84 2 0.000000 1 1.823572 4.835976 1.611992 10.783944
85 2 0.000000 -1 1.823572 4.835976 4.835976 2.111992
86 2 0.000000 1 1.823572 4.835976 4.835976 4.335976
87 2 0.000000 -1 1.823572 4.835976 4.835976 8.559960
88 2 0.000000 1 1.823572 4.835976 4.835976 10.783944
89 2 0.000000 -1 1.823572 4.835976 8.059960 2.111992
90 2 0.000000 1 1.823572 4.835976 8.059960 4.335976
91 2 0.000000 -1 1.823572 4.835976 8.059960 8.559960
92 2 0.000000 1 1.823572 4.835976 8.059960 10.783944
93 2 0.000000 -1 1.823572 4.835976 11.283944 2.111992
94 2 0.000000 1 1.823572 4.835976 11.283944 4.335976
95 2 0.000000 -1 1.823572 4.835976 11.283944 8.559960
96 2 0.000000 1 1.823572 4.835976 11.283944 10.783944
97 2 0.000000 -1 1.823572 8.059960 1.611992 2.111992
98 2 0.000000 1 1.823572 8.059960 1.611992 4.335976
99 2 0.000000 -1 1.823572 8.059960 1.611992 8.559960
100 2 0.000000 1 1.823572 8.059960 1.611992 10.783944
101 2 0.000000 -1 1.823572 8.059960 4.835976 2.111992
102 2 0.000000 1 1.823572 8.059960 4.835976 4.335976
103 2 0.000000 -1 1.823572 8.059960 4.835976 8.559960
104 2 0.000000 1 1.823572 8.059960 4.835976 10.783944
105 2 0.000000 -1 1.823572 8.059960 8.059960 2.111992
106 2 0.000000 1 1.823572 8.059960 8.059960 4.335976
107 2 0.000000 -1 1.823572 8.059960 8.059960 8.559960
108 2 0.000000 1 1.823572 8.059960 8.059960 10.783944
109 2 0.000000 -1 1.823572 8.059960 11.283944 2.111992
110 2 0.000000 1 1.823572 8.059960 11.283944 4.335976
111 2 0.000000 -1 1.823572 8.059960 11.283944 8.559960
112 2 0.000000 1 1.823572 8.059960 11.283944 10.783944
113 2 0.000000 -1 1.823572 11.283944 1.611992 2.111992
114 2 0.000000 1 1.823572 11.283944 1.611992 4.335976
115 2 0.000000 -1 1.823572 11.283944 1.611992 8.559960
116 2 0.000000 1 1.823572 11.283944 1.611992 10.783944
117 2 0.000000 -1 1.823572 11.283944 4.835976 2.111992
118 2 0.000000 1 1.823572 11.283944 4.835976 4.335976
119 2 0.000000 -1 1.823572 11.283944 4.835976 8.559960
120 2 0.000000 1 1.823572 11.283944 4.835976 10.783944
121 2 0.000000 -1 1.823572 11.283944 8.059960 2.111992
122 2 0.000000 1 1.823572 11.283944 8.059960 4.335976
123 2 0.000000 -1 1.823572 11.283944 8.059960 8.559960
124 2 0.000000 1 1.823572 11.283944 8.059960 10.783944
125 2 0.000000 -1 1.823572 11.283944 11.283944 2.111992
126 2 0.000000 1 1.823572 11.283944 11.283944 4.335976
127 2 0.000000 -1 1.823572 11.283944 11.283944 8.559960
128 2 0.000000 1 1.823572 11.283944 11.283944 10.783944

View File

@ -0,0 +1,49 @@
variable sname index h2
log ${sname}.spe.log
units electron
newton on
boundary p p p
atom_style electron
read_data data.${sname}
pair_style eff/cut 6.447968 0 1
pair_coeff * *
communicate single vel yes
min_style cg
min_modify line quadratic
minimize 0 1.0e-6 1000 2000
region part block INF 2.0 INF 2.0 INF 5.0 units box
group sub id < 32
compute effTemp all temp/eff
compute effPress all pressure effTemp
compute regionT sub temp/region/eff part
compute peratom all stress/atom
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
thermo 100
thermo_style custom step etotal pe ke temp press v_press c_regionT
thermo_modify temp effTemp press effPress
#velocity all create 300.0 4928459 rot yes dist gaussian
fix 3 all temp/rescale/eff 10 0.0 300.0 0.02 1.0
fix 1 all nve/eff
run 10000
unfix 3
#fix 1 all npt/eff temp 3000.0 3000.0 0.1 iso 1e7 1e7 1.0 drag 0.5
#dump 1 all custom 100 dump.file id type q spin eradius x y z
#fix 1 all nve/eff
run 100000

View File

@ -0,0 +1,2 @@
Example of a hydrogen plasma, using pre-set velocities for a temperature of 20000K (nve), setting the velocities to 50000K (nvt), and an isobaric-isothermic case (npt) to show volume and density convergence at specified temperature (20000K) and pressure (1GPa).

File diff suppressed because it is too large Load Diff

View File

@ -0,0 +1,47 @@
variable sname index h2bulk
log ${sname}.npt.log
units electron
newton on
boundary p p p
atom_style electron
read_data data.${sname}
pair_style eff/cut 30.627847 0 0
pair_coeff * *
neigh_modify one 20000 page 200000
communicate single vel yes
compute effTemp all temp/eff
thermo 100
thermo_style custom step pe temp press vol
thermo_modify temp effTemp
# structure minimization
dump 1 all xyz 1 ${sname}.min.xyz
min_style cg
minimize 0 1.0e-4 1 10000
undump 1
# create initial velocities according to temp, w/out e radial dof
velocity all create 20000.0 4928459 rot yes dist gaussian
# npt
fix 1 all npt/eff temp 20000.0 20000.0 1.0 iso 1e9 1e9 1.0
variable density equal 11.2058851*mass(all)
thermo_style custom step pe temp press vol v_density
thermo_modify temp effTemp
dump 2 all xyz 10000 ${sname}.npt.xyz
dump 3 all custom 10000 ${sname}.npt.lammpstrj id type x y z spin eradius
run 10000000
unfix 1
undump 2
undump 3

View File

@ -0,0 +1,48 @@
variable sname index h2bulk
log ${sname}.nve.log
units electron
newton on
boundary p p p
atom_style electron
read_data data.${sname}
pair_style eff/cut 30.627847 0 0
pair_coeff * *
neigh_modify one 10000 page 100000
communicate single vel yes
compute effTemp all temp/eff
thermo 1000
thermo_style custom step pe temp press
thermo_modify temp effTemp
# structure minimization
min_style cg
minimize 0 1.0e-4 1000 10000
timestep 0.001
velocity all create 20000.0 4928459 rot yes mom yes dist gaussian
# nve
fix 1 all nve/eff
#fix 2 all imd 8888 trate 1 unwrap on nowait on
compute peatom all pe/atom
compute keatom all ke/atom/eff
dump 2 all xyz 1000 ${sname}.nve.xyz
dump 3 all custom 1000 ${sname}.nve.lammpstrj id type x y z spin eradius c_peatom c_keatom
run 100000
unfix 1
#unfix 2
undump 2
undump 3

View File

@ -0,0 +1,2 @@
Shows the formation of lithium dendrites during the minimization of a volume expanded lithium cell with particle positions remaped to fit the cell.
This depicts the process of electrode replating in lithium batteries, which leads to failure (short-circuit).

File diff suppressed because it is too large Load Diff

View File

@ -0,0 +1,37 @@
variable sname index Li-dendritic
log ${sname}.min.log
units electron
newton on
boundary p p p
atom_style electron
#read_data data.${sname}
read_restart ${sname}.min.restart2
pair_style eff/cut 50.112 0 0
pair_coeff * *
communicate single vel yes
compute effTemp all temp/eff
thermo 10
thermo_style custom step etotal pe ke temp press
thermo_modify temp effTemp
dump 1 all custom 10 ${sname}.min.lammpstrj id type q spin eradius x y z
dump 2 all xyz 10 ${sname}.min.xyz
restart 10 ${sname}.nve.restart1 ${sname}.nve.restart2
#min_style cg
#min_modify line quadratic dmax 2.0
#minimize 0.0 1.0e-5 10000 100000
velocity all create 300.0 4928459 rot yes dist gaussian
fix 1 all nve/eff
run 100

View File

@ -0,0 +1,51 @@
variable sname index Li-dendritic
log ${sname}.min.log
units electron
newton on
boundary p p p
atom_style electron
read_data data.${sname}
#read_restart ${sname}.min.restart
pair_style eff/cut 50.112 0 0
pair_coeff * *
communicate single vel yes
compute effTemp all temp/eff
compute effPress all pressure effTemp
thermo 10
thermo_style custom step pe temp press
thermo_modify temp effTemp press effPress
print "Starting minimizer"
min_style cg
#dump 1 all custom 100 ${sname}.min.lammpstrj id type x y z q spin eradius
#dump 2 all xyz 100 ${sname}.min.xyz
min_modify line quadratic dmax 0.05
minimize 0 1.0e-7 1000 2000
write_restart ${sname}.min.restart
#undump 1
#undump 2
# NVT
reset_timestep 0
timestep 0.005
print "Starting nvt"
fix 1 all nvt/eff temp 300.0 300.0 0.1
dump 1 all custom 100 ${sname}.nvt.lammpstrj id type x y z spin eradius
dump 2 all xyz 100 ${sname}.nvt.xyz
restart 100 ${sname}.nvt.restart1 ${sname}.nvt.restart2
run 10000
undump 1
undump 2

View File

@ -0,0 +1,3 @@
Lithium fcc example, verifies global pressure, computed through the total virials and kinetics,
is equal to the sum of atomic virials and kinetics.

File diff suppressed because it is too large Load Diff

View File

@ -0,0 +1,34 @@
variable sname index Li
log ${sname}.spe.log
units electron
newton off
boundary p p p
atom_style electron
read_data data.${sname}
pair_style eff/cut 20.88 1 1
pair_coeff * *
communicate single vel yes
neigh_modify one 2000 page 20000
compute effTemp all temp/eff
compute effPress all pressure effTemp
compute peratom all stress/atom
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
thermo 1
thermo_style custom step etotal pe ke temp press v_press
thermo_modify temp effTemp press effPress
fix 1 all npt/eff temp 3000.0 3000.0 0.1 iso 1e7 1e7 1.0
dump 1 all custom 1 ${sname}.spe.lammpstrj id type x y z spin eradius
run 100000

11
examples/USER/eff/README Normal file
View File

@ -0,0 +1,11 @@
NOTE: most of these examples are provided to demonstrate the
functionality of pEFF, i.e. as illustrative examples, and should not
be used w/out including the proper equilibration procedures, or data
files with unit cell sizes appropriate for minimum image calculations.
Also, most of the electron masses are set to 1, instead of the true
electron mass in amu. If the electron mass is set to the true value,
the recommended integration time step should be 0.0001 (i.e. need to
change it with the "timestep 0.0001" command)
For more details, please contact the author at
Andres Jaramillo-Botero, ajaramil@wag.caltech.edu