mirror of https://github.com/lammps/lammps.git
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5715 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
f50885fd46
commit
1d4a6440d1
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@ -0,0 +1,9 @@
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In the Auger process, a valence electron falls in to a core hole, which
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releases enough energy to eject another valence electron. Thus a state with
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two valence holes is created. Using eFF it is possible to track, for the first
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time, the continuous evolution of a core-hole state into a two-valence hole state,
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with full electron and nuclear dynamics included (Adamantane case).
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To simulate the dissociation dynamics of core-ionized adamantane, we proceed
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by deleting a core electron from the data.adamantane structure.
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An complete Adamantane molecule is also provided.
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Finite system.
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@ -0,0 +1,119 @@
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Created by AJB
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102 atoms
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3 atom types
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-500.0 500.0 xlo xhi
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-500.0 500.0 ylo yhi
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-500.0 500.0 zlo zhi
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Masses
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1 12.01070 # C nuclei
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2 1.000794 # H nuclei
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3 1.000000 # electron
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Atoms
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1 1 6.00 0 0.000000 0.223271 2.836177 0.99547
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2 1 6.00 0 0.000000 -0.611326 1.278041 3.303884
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3 1 6.00 0 0.000000 -0.645795 -1.544681 2.608294
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||||
4 1 6.00 0 0.000000 -2.509122 -1.980433 0.419368
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||||
5 1 6.00 0 0.000000 -1.674732 -0.422977 -1.889518
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||||
6 1 6.00 0 0.000000 -1.640226 2.39965 -1.193097
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7 1 6.00 0 0.000000 2.018681 -2.373515 1.79163
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||||
8 1 6.00 0 0.000000 2.887596 2.006776 0.178976
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||||
9 1 6.00 0 0.000000 0.98999 -1.251962 -2.705445
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||||
10 1 6.00 0 0.000000 2.853997 -0.815965 -0.517029
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||||
11 2 1.00 0 0.000000 -3.029741 -0.739677 -3.479893
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||||
12 2 1.00 0 0.000000 -4.456466 -1.425024 1.003463
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||||
13 2 1.00 0 0.000000 -2.581253 -4.027951 -0.074795
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||||
14 2 1.00 0 0.000000 -1.252983 -2.67657 4.28622
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||||
15 2 1.00 0 0.000000 -2.524731 1.891635 3.93955
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||||
16 2 1.00 0 0.000000 0.703394 1.61118 4.917143
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||||
17 2 1.00 0 0.000000 0.247516 4.887701 1.501501
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||||
18 2 1.00 0 0.000000 2.027034 -4.428006 1.321731
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||||
19 2 1.00 0 0.000000 3.379737 -2.105382 3.378244
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||||
20 2 1.00 0 0.000000 4.790758 -1.418428 -1.109855
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||||
21 2 1.00 0 0.000000 -1.077541 3.552194 -2.865467
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||||
22 2 1.00 0 0.000000 -3.572149 3.033181 -0.63782
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23 2 1.00 0 0.000000 1.599389 -0.164293 -4.40463
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||||
24 2 1.00 0 0.000000 0.980069 -3.286423 -3.255167
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25 2 1.00 0 0.000000 4.264224 2.353276 1.736734
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||||
26 2 1.00 0 0.000000 3.530575 3.152347 -1.469016
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27 3 0.00 1 0.332948 0.223271 2.836177 0.99547
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28 3 0.00 -1 0.332948 0.223271 2.836177 0.99547
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29 3 0.00 1 0.332948 -0.611326 1.278041 3.303884
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30 3 0.00 -1 0.332948 -0.611326 1.278041 3.303884
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||||
31 3 0.00 1 0.332948 -0.645795 -1.544681 2.608294
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32 3 0.00 -1 0.332948 -0.645795 -1.544681 2.608294
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33 3 0.00 1 0.332948 -2.509122 -1.980433 0.419368
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34 3 0.00 -1 0.332948 -2.509122 -1.980433 0.419368
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||||
35 3 0.00 1 0.332948 -1.674732 -0.422977 -1.889518
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||||
36 3 0.00 -1 0.332948 -1.674732 -0.422977 -1.889518
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37 3 0.00 1 0.332948 -1.640226 2.39965 -1.193097
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38 3 0.00 -1 0.332948 -1.640226 2.39965 -1.193097
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39 3 0.00 1 0.332948 2.018681 -2.373515 1.79163
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40 3 0.00 -1 0.332948 2.018681 -2.373515 1.79163
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41 3 0.00 1 0.332948 2.887596 2.006776 0.178976
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42 3 0.00 -1 0.332948 2.887596 2.006776 0.178976
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43 3 0.00 1 0.332948 0.98999 -1.251962 -2.705445
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44 3 0.00 -1 0.332948 0.98999 -1.251962 -2.705445
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45 3 0.00 1 0.332948 2.853997 -0.815965 -0.517029
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46 3 0.00 -1 0.332948 2.853997 -0.815965 -0.517029
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47 3 0.00 1 1.258000 -0.194028 2.057109 2.149677
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48 3 0.00 -1 1.258000 -0.194028 2.057109 2.149677
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49 3 0.00 1 1.258000 -0.628561 -0.13332 2.956089
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50 3 0.00 -1 1.258000 -0.628561 -0.13332 2.956089
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51 3 0.00 1 1.258000 -1.577458 -1.762557 1.513831
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52 3 0.00 -1 1.258000 -1.577458 -1.762557 1.513831
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53 3 0.00 1 1.258000 -2.091927 -1.201705 -0.735075
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54 3 0.00 -1 1.258000 -2.091927 -1.201705 -0.735075
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55 3 0.00 1 1.258000 -0.708477 2.617913 -0.098814
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56 3 0.00 -1 1.258000 -0.708477 2.617913 -0.098814
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57 3 0.00 1 1.258000 -1.657479 0.988336 -1.541308
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58 3 0.00 -1 1.258000 -1.657479 0.988336 -1.541308
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59 3 0.00 1 1.258000 0.686443 -1.959098 2.199962
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60 3 0.00 -1 1.258000 0.686443 -1.959098 2.199962
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61 3 0.00 1 1.258000 1.555434 2.421476 0.587223
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62 3 0.00 -1 1.258000 1.555434 2.421476 0.587223
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63 3 0.00 1 1.258000 -0.342371 -0.83747 -2.297482
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64 3 0.00 -1 1.258000 -0.342371 -0.83747 -2.297482
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65 3 0.00 1 1.258000 2.436339 -1.59474 0.637301
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66 3 0.00 -1 1.258000 2.436339 -1.59474 0.637301
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67 3 0.00 1 1.258000 2.870796 0.595405 -0.169027
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68 3 0.00 -1 1.258000 2.870796 0.595405 -0.169027
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69 3 0.00 1 1.258000 1.921993 -1.033964 -1.611237
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70 3 0.00 -1 1.258000 1.921993 -1.033964 -1.611237
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71 3 0.00 1 1.543000 -2.632724 -0.646884 -3.013913
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72 3 0.00 -1 1.543000 -2.632724 -0.646884 -3.013913
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73 3 0.00 1 1.543000 -3.885894 -1.587759 0.832324
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74 3 0.00 -1 1.543000 -3.885894 -1.587759 0.832324
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75 3 0.00 1 1.543000 -2.560118 -3.428028 0.069995
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76 3 0.00 -1 1.543000 -2.560118 -3.428028 0.069995
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77 3 0.00 1 1.543000 -1.075077 -2.344927 3.794588
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78 3 0.00 -1 1.543000 -1.075077 -2.344927 3.794588
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79 3 0.00 1 1.543000 -1.964103 1.711852 3.7533
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80 3 0.00 -1 1.543000 -1.964103 1.711852 3.7533
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81 3 0.00 1 1.543000 0.318181 1.513571 4.444458
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82 3 0.00 -1 1.543000 0.318181 1.513571 4.444458
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83 3 0.00 1 1.543000 0.240412 4.286604 1.353234
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84 3 0.00 -1 1.543000 0.240412 4.286604 1.353234
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85 3 0.00 1 1.543000 2.024586 -3.82604 1.459412
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86 3 0.00 -1 1.543000 2.024586 -3.82604 1.459412
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87 3 0.00 1 1.543000 2.980948 -2.183945 2.913367
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88 3 0.00 -1 1.543000 2.980948 -2.183945 2.913367
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89 3 0.00 1 1.543000 4.223287 -1.241907 -0.936157
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90 3 0.00 -1 1.543000 4.223287 -1.241907 -0.936157
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91 3 0.00 1 1.543000 -1.242407 3.214498 -2.375463
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92 3 0.00 -1 1.543000 -1.242407 3.214498 -2.375463
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93 3 0.00 1 1.543000 -3.006096 2.847556 -0.800517
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94 3 0.00 -1 1.543000 -3.006096 2.847556 -0.800517
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95 3 0.00 1 1.543000 1.420835 -0.48298 -3.906769
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96 3 0.00 -1 1.543000 1.420835 -0.48298 -3.906769
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97 3 0.00 1 1.543000 0.982976 -2.690326 -3.094098
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98 3 0.00 -1 1.543000 0.982976 -2.690326 -3.094098
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99 3 0.00 1 1.543000 3.860872 2.251751 1.280311
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100 3 0.00 -1 1.543000 3.860872 2.251751 1.280311
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101 3 0.00 1 1.543000 3.342182 2.816694 -0.986155
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102 3 0.00 -1 1.543000 3.342182 2.816694 -0.986155
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@ -0,0 +1,118 @@
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Created by AJB
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101 atoms
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3 atom types
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-50.0 50.0 xlo xhi
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-50.0 50.0 ylo yhi
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-50.0 50.0 zlo zhi
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Masses
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1 12.01070 # C nuclei
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2 1.000794 # H nuclei
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3 1.000000 # electron
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Atoms
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1 1 6.00 0 0.000000 0.224230 2.918607 1.015812
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2 1 6.00 0 0.000000 -0.634450 1.314460 3.390303
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3 1 6.00 0 0.000000 -0.670162 -1.590173 2.675707
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4 1 6.00 0 0.000000 -2.586695 -2.037708 0.422846
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5 1 6.00 0 0.000000 -1.729127 -0.435706 -1.953488
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6 1 6.00 0 0.000000 -1.692867 2.468206 -1.236000
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7 1 6.00 0 0.000000 2.071281 -2.442011 1.834504
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8 1 6.00 0 0.000000 2.965108 2.063979 0.175607
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9 1 6.00 0 0.000000 1.013015 -1.288254 -2.791737
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10 1 6.00 0 0.000000 2.931847 -0.840220 -0.540904
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11 2 1.00 0 0.000000 -3.237070 -0.788493 -3.724286
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12 2 1.00 0 0.000000 -4.691469 -1.429253 1.056080
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13 2 1.00 0 0.000000 -2.657034 -4.253233 -0.113602
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14 2 1.00 0 0.000000 -1.345725 -2.850372 4.543752
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15 2 1.00 0 0.000000 -2.707861 1.976434 4.071194
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16 2 1.00 0 0.000000 0.794230 1.672161 5.131751
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17 2 1.00 0 0.000000 0.251667 5.202465 1.579125
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18 2 1.00 0 0.000000 2.074796 -4.663951 1.320307
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19 2 1.00 0 0.000000 3.542471 -2.144066 3.551451
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20 2 1.00 0 0.000000 5.087753 -1.511020 -1.201338
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21 2 1.00 0 0.000000 -1.077021 3.711707 -3.045901
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22 2 1.00 0 0.000000 -3.783389 3.148492 -0.629227
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23 2 1.00 0 0.000000 1.671766 -0.104421 -4.626344
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24 2 1.00 0 0.000000 0.999815 -3.491890 -3.379184
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25 2 1.00 0 0.000000 4.450647 2.434018 1.865941
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26 2 1.00 0 0.000000 3.654660 3.300997 -1.612081
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27 3 0.00 -1 0.328405 -0.634804 1.315020 3.391634
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28 3 0.00 -1 0.328107 -0.670512 -1.590826 2.676675
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29 3 0.00 -1 0.328405 -2.587889 -2.038591 0.422899
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30 3 0.00 -1 0.328107 -1.729909 -0.435889 -1.954405
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31 3 0.00 -1 0.328405 -1.693676 2.469262 -1.236661
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32 3 0.00 -1 0.328405 2.072091 -2.443067 1.835165
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33 3 0.00 -1 0.328405 2.966303 2.064861 0.175553
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34 3 0.00 -1 0.328405 1.013370 -1.288814 -2.793067
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35 3 0.00 -1 0.328108 2.932965 -0.840567 -0.541247
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36 3 0.00 -1 1.326096 -0.210743 2.123398 2.223462
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37 3 0.00 -1 1.326096 -0.657351 -0.127988 3.052304
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38 3 0.00 -1 1.326093 -1.646634 -1.826737 1.548546
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39 3 0.00 -1 1.326095 -2.175416 -1.250260 -0.762988
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40 3 0.00 -1 1.326093 -0.747076 2.708081 -0.120938
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41 3 0.00 -1 1.326095 -1.722464 1.033139 -1.603613
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42 3 0.00 -1 1.326092 0.713852 -2.031645 2.263933
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43 3 0.00 -1 1.326092 1.613424 2.503259 0.594420
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44 3 0.00 -1 1.326098 -0.351222 -0.870483 -2.392027
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45 3 0.00 -1 1.326100 2.512477 -1.657113 0.657756
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46 3 0.00 -1 1.326099 2.965428 0.626295 -0.182887
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47 3 0.00 -1 1.326101 1.976186 -1.072464 -1.686660
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48 3 0.00 -1 1.603792 -2.952851 -0.722000 -3.390526
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49 3 0.00 -1 1.558563 -4.265445 -1.534526 0.932369
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50 3 0.00 -1 1.558562 -2.625986 -3.810249 -0.010226
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51 3 0.00 -1 1.603792 -1.218394 -2.612849 4.191661
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52 3 0.00 -1 1.558507 -2.300135 1.839753 3.919625
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53 3 0.00 -1 1.558620 0.522041 1.594565 4.774310
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54 3 0.00 -1 1.603792 0.246496 4.772002 1.472951
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55 3 0.00 -1 1.558582 2.062319 -4.217199 1.410516
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56 3 0.00 -1 1.558537 3.245048 -2.186529 3.208486
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57 3 0.00 -1 1.603791 4.681408 -1.384588 -1.076860
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58 3 0.00 -1 1.558565 -1.184793 3.454906 -2.684898
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59 3 0.00 -1 1.558559 -3.365733 3.001032 -0.737405
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60 3 0.00 -1 1.558551 1.538708 -0.326106 -4.250794
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61 3 0.00 -1 1.558563 0.997214 -3.055912 -3.245768
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62 3 0.00 -1 1.558524 4.144833 2.349324 1.538532
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63 3 0.00 -1 1.558594 3.503398 3.047996 -1.264247
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64 3 0.00 1 0.328107 0.224244 2.919790 1.016104
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65 3 0.00 1 0.328405 -0.634804 1.315020 3.391634
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66 3 0.00 1 0.328107 -0.670512 -1.590826 2.676675
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67 3 0.00 1 0.328405 -2.587889 -2.038591 0.422899
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68 3 0.00 1 0.328107 -1.729909 -0.435889 -1.954405
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||||
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
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||||
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
|
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101 3 0.00 1 1.558594 3.503398 3.047996 -1.264247
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@ -0,0 +1,51 @@
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variable sname index adamantane_ionized
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log ${sname}.nve.log
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units electron
|
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newton on
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boundary f f f
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atom_style electron
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read_data data.${sname}
|
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|
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pair_style eff/cut 100.0 0 0
|
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pair_coeff * *
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communicate single vel yes
|
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|
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compute effTemp all temp/eff
|
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|
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thermo 1000
|
||||
thermo_style custom step pe temp press
|
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thermo_modify temp effTemp
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|
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# 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
|
||||
|
||||
|
|
@ -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
|
|
@ -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
|
||||
|
||||
|
|
@ -0,0 +1,2 @@
|
|||
Methane, valence electron ionization and full molecule tests (spe, min, dynamics).
|
||||
Note: electron mass set to 1
|
||||
|
|
@ -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
|
||||
|
|
@ -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
|
||||
|
|
@ -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
|
||||
|
|
@ -0,0 +1,31 @@
|
|||
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
|
||||
|
||||
compute effTemp all temp/eff
|
||||
|
||||
compute energies all pair eff/cut
|
||||
variable eke equal c_energies[1]
|
||||
variable epauli equal c_energies[2]
|
||||
variable ecoul equal c_energies[3]
|
||||
variable erres equal c_energies[4]
|
||||
|
||||
thermo 1
|
||||
thermo_style custom step etotal pe ke v_eke v_epauli v_ecoul v_erres
|
||||
|
||||
min_style cg
|
||||
dump 2 all custom 10 ${sname}.min.lammpstrj id type q spin eradius x y z fx fy fz erforce
|
||||
minimize 0 1e-6 2000 4000
|
||||
|
||||
|
|
@ -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
|
||||
|
|
@ -0,0 +1,3 @@
|
|||
Provides an example using effective core pseudopotentials for Si
|
||||
|
||||
Structure files provided by Patrick Theofanis (Caltech)
|
||||
|
|
@ -0,0 +1,40 @@
|
|||
Created using cfg2lammps (c) AJB-2009
|
||||
|
||||
22 atoms
|
||||
3 atom types
|
||||
|
||||
-1000.000 1000.0 xlo xhi
|
||||
-1000.000 1000.0 ylo yhi
|
||||
-1000.000 1000.0 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 9.012182
|
||||
2 1.007940
|
||||
3 1.000000
|
||||
|
||||
Atoms
|
||||
|
||||
1 1 4.00 3 1.691398 0.000000 0.000000 -1.176371
|
||||
2 1 4.00 3 1.691398 0.000000 0.000000 1.176371
|
||||
3 2 1.00 0 0.0 -2.280293 1.316528 -3.203870
|
||||
4 2 1.00 0 0.0 2.280293 1.316528 -3.203870
|
||||
5 2 1.00 0 0.0 0.000000 -2.633055 -3.203870
|
||||
6 2 1.00 0 0.0 2.280293 -1.316528 3.203870
|
||||
7 2 1.00 0 0.0 0.000000 2.633055 3.203870
|
||||
8 2 1.00 0 0.0 -2.280293 -1.316528 3.203870
|
||||
9 3 0.0 1 1.984000 -1.612167 0.930785 -2.916481
|
||||
10 3 0.0 -1 1.984000 -1.612167 0.930785 -2.916481
|
||||
11 3 0.0 1 1.984000 1.612167 0.930785 -2.916481
|
||||
12 3 0.0 -1 1.984000 1.612167 0.930785 -2.916481
|
||||
13 3 0.0 1 1.984000 0.000000 -1.861570 -2.916481
|
||||
14 3 0.0 -1 1.984000 0.000000 -1.861570 -2.916481
|
||||
15 3 0.0 1 1.810000 0.000000 0.000000 0.000000
|
||||
16 3 0.0 -1 1.810000 0.000000 0.000000 0.000000
|
||||
17 3 0.0 1 1.984000 1.612167 -0.930785 2.916481
|
||||
18 3 0.0 -1 1.984000 1.612167 -0.930785 2.916481
|
||||
19 3 0.0 1 1.984000 0.000000 1.861570 2.916481
|
||||
20 3 0.0 -1 1.984000 0.000000 1.861570 2.916481
|
||||
21 3 0.0 1 1.984000 -1.612167 -0.930785 2.916481
|
||||
22 3 0.0 -1 1.984000 -1.612167 -0.930785 2.916481
|
||||
|
||||
|
|
@ -0,0 +1,40 @@
|
|||
Created using cfg2lammps (c) AJB-2009
|
||||
|
||||
22 atoms
|
||||
3 atom types
|
||||
|
||||
-529.177249 529.177249 xlo xhi
|
||||
-529.177249 529.177249 ylo yhi
|
||||
-529.177249 529.177249 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 28.086589324618736
|
||||
2 1.007940
|
||||
3 0.0005446623093682
|
||||
|
||||
Atoms
|
||||
|
||||
1 1 4.00 3 0.895049 0.000000 0.000000 -0.622509
|
||||
2 1 4.00 3 0.895049 0.000000 0.000000 0.622509
|
||||
3 2 1.00 0 0.000000 -1.206679 0.696677 -1.695415
|
||||
4 2 1.00 0 0.000000 1.206679 0.696677 -1.695415
|
||||
5 2 1.00 0 0.000000 0.000000 -1.393353 -1.695415
|
||||
6 2 1.00 0 0.000000 1.206679 -0.696677 1.695415
|
||||
7 2 1.00 0 0.000000 0.000000 1.393353 1.695415
|
||||
8 2 1.00 0 0.000000 -1.206679 -0.696677 1.695415
|
||||
9 3 0.0 1 1.049888 -0.853122 0.492550 -1.543335
|
||||
10 3 0.0 -1 1.049888 -0.853122 0.492550 -1.543335
|
||||
11 3 0.0 1 1.049888 0.853122 0.492550 -1.543335
|
||||
12 3 0.0 -1 1.049888 0.853122 0.492550 -1.543335
|
||||
13 3 0.0 1 1.049888 0.000000 -0.985100 -1.543335
|
||||
14 3 0.0 -1 1.049888 0.000000 -0.985100 -1.543335
|
||||
15 3 0.0 1 0.957811 0.000000 0.000000 0.000000
|
||||
16 3 0.0 -1 0.957811 0.000000 0.000000 0.000000
|
||||
17 3 0.0 1 1.049888 0.853122 -0.492550 1.543335
|
||||
18 3 0.0 -1 1.049888 0.853122 -0.492550 1.543335
|
||||
19 3 0.0 1 1.049888 0.000000 0.985100 1.543335
|
||||
20 3 0.0 -1 1.049888 0.000000 0.985100 1.543335
|
||||
21 3 0.0 1 1.049888 -0.853122 -0.492550 1.543335
|
||||
22 3 0.0 -1 1.049888 -0.853122 -0.492550 1.543335
|
||||
|
||||
|
|
@ -0,0 +1,49 @@
|
|||
|
||||
# Created 2011-01-07
|
||||
|
||||
# General parameters
|
||||
|
||||
variable sname index Si2H6
|
||||
log ${sname}.log
|
||||
|
||||
units electron
|
||||
newton on
|
||||
boundary f f f
|
||||
|
||||
atom_style electron
|
||||
|
||||
read_data data.${sname}
|
||||
|
||||
pair_style eff/cut 1000.0
|
||||
pair_coeff * *
|
||||
|
||||
compute energies all pair eff/cut
|
||||
variable eke equal c_energies[1]
|
||||
variable epauli equal c_energies[2]
|
||||
variable estatics equal c_energies[3]
|
||||
variable errestrain equal c_energies[4]
|
||||
|
||||
communicate single vel yes
|
||||
|
||||
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)
|
||||
|
||||
compute effTemp all temp/eff
|
||||
compute effPress all pressure effTemp
|
||||
|
||||
thermo 2
|
||||
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
|
||||
thermo_modify temp effTemp press effPress
|
||||
|
||||
# Minimization
|
||||
|
||||
min_style cg
|
||||
dump 1 all xyz 2 ${sname}.min.xyz
|
||||
dump 2 all custom 2 ${sname}.min.lammpstrj id type q spin eradius x y z fx fy fz erforce
|
||||
min_modify line quadratic
|
||||
minimize 0 1.0e-5 1000 10000
|
||||
|
||||
undump 1
|
||||
undump 2
|
||||
|
||||
|
|
@ -0,0 +1,61 @@
|
|||
|
||||
# Created 2011-01-07
|
||||
|
||||
# General parameters
|
||||
|
||||
variable sname index Si2H6.ang
|
||||
log ${sname}.log
|
||||
|
||||
units real
|
||||
newton on
|
||||
boundary f f f
|
||||
|
||||
atom_style electron
|
||||
|
||||
read_data data.${sname}
|
||||
|
||||
pair_style eff/cut 529.177249
|
||||
pair_coeff * *
|
||||
|
||||
compute energies all pair eff/cut
|
||||
variable eke equal c_energies[1]
|
||||
variable epauli equal c_energies[2]
|
||||
variable estatics equal c_energies[3]
|
||||
variable errestrain equal c_energies[4]
|
||||
|
||||
communicate single vel yes
|
||||
|
||||
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)
|
||||
|
||||
compute effTemp all temp/eff
|
||||
compute effPress all pressure effTemp
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
|
||||
thermo_modify temp effTemp press effPress
|
||||
|
||||
# Minimization
|
||||
|
||||
min_style cg
|
||||
dump 1 all xyz 10 ${sname}.min.xyz
|
||||
dump 2 all custom 10 ${sname}.min.lammpstrj id type q spin eradius x y z fx fy fz erforce
|
||||
min_modify line quadratic
|
||||
minimize 0 1.0e-6 2000 10000
|
||||
|
||||
undump 1
|
||||
undump 2
|
||||
|
||||
# Equilibrate at 300K
|
||||
velocity all create 300.0 4928459 rot yes mom yes dist gaussian
|
||||
|
||||
timestep 0.001
|
||||
|
||||
dump 1 all custom 1000 ${sname}.nvt.lammpstrj id type q spin eradius x y z fx fy fz erforce
|
||||
#fix 0 all langevin/eff 300.0 300.0 0.1
|
||||
fix 1 all nvt/eff temp 300.0 300.0 0.1
|
||||
|
||||
run 200000
|
||||
|
||||
|
||||
|
|
@ -0,0 +1,31 @@
|
|||
Created using cfg2lammps (c) AJB-2009
|
||||
|
||||
13 atoms
|
||||
3 atom types
|
||||
|
||||
-1000.000 1000.0 xlo xhi
|
||||
-1000.000 1000.0 ylo yhi
|
||||
-1000.000 1000.0 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 9.012182
|
||||
2 1.007940
|
||||
3 1.000000
|
||||
|
||||
Atoms
|
||||
|
||||
1 1 4.00 3 1.691398 0.000000 0.000000 0.000000
|
||||
2 2 1.00 0 0.0 -1.619843 1.619843 1.619843
|
||||
3 2 1.00 0 0.0 -1.619843 -1.619843 -1.619843
|
||||
4 2 1.00 0 0.0 1.619843 1.619843 -1.619843
|
||||
5 2 1.00 0 0.0 1.619843 -1.619843 1.619843
|
||||
6 3 0.0 1 1.984000 -1.145229 1.145229 1.145229
|
||||
7 3 0.0 -1 1.984000 -1.145229 1.145229 1.145229
|
||||
8 3 0.0 1 1.984000 -1.145229 -1.145229 -1.145229
|
||||
9 3 0.0 -1 1.984000 -1.145229 -1.145229 -1.145229
|
||||
10 3 0.0 1 1.984000 1.145229 1.145229 -1.145229
|
||||
11 3 0.0 -1 1.984000 1.145229 1.145229 -1.145229
|
||||
12 3 0.0 1 1.984000 1.145229 -1.145229 1.145229
|
||||
13 3 0.0 -1 1.984000 1.145229 -1.145229 1.145229
|
||||
|
||||
|
|
@ -0,0 +1,31 @@
|
|||
Created using cfg2lammps (c) AJB-2009
|
||||
|
||||
13 atoms
|
||||
3 atom types
|
||||
|
||||
-529.177249 529.177249 xlo xhi
|
||||
-529.177249 529.177249 ylo yhi
|
||||
-529.177249 529.177249 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 9.012182
|
||||
2 1.007940
|
||||
3 1.000000
|
||||
|
||||
Atoms
|
||||
|
||||
1 1 4.00 3 0.895049 0.000000 0.000000 0.000000
|
||||
2 2 1.00 0 0.000000 -0.857184 0.857184 0.857184
|
||||
3 2 1.00 0 0.000000 -0.857184 -0.857184 -0.857184
|
||||
4 2 1.00 0 0.000000 0.857184 0.857184 -0.857184
|
||||
5 2 1.00 0 0.000000 0.857184 -0.857184 0.857184
|
||||
6 3 0.0 1 1.049888 -0.606029 0.606029 0.606029
|
||||
7 3 0.0 -1 1.049888 -0.606029 0.606029 0.606029
|
||||
8 3 0.0 1 1.049888 -0.606029 -0.606029 -0.606029
|
||||
9 3 0.0 -1 1.049888 -0.606029 -0.606029 -0.606029
|
||||
10 3 0.0 1 1.049888 0.606029 0.606029 -0.606029
|
||||
11 3 0.0 -1 1.049888 0.606029 0.606029 -0.606029
|
||||
12 3 0.0 1 1.049888 0.606029 -0.606029 0.606029
|
||||
13 3 0.0 -1 1.049888 0.606029 -0.606029 0.606029
|
||||
|
||||
|
|
@ -0,0 +1,50 @@
|
|||
|
||||
# Created 2011-01-07
|
||||
|
||||
# General parameters
|
||||
|
||||
variable sname index SiH4
|
||||
log ${sname}.log
|
||||
|
||||
units electron
|
||||
newton on
|
||||
boundary f f f
|
||||
special_bonds coul 1 0 0
|
||||
|
||||
atom_style electron
|
||||
|
||||
read_data data.${sname}
|
||||
|
||||
pair_style eff/cut 1000.0
|
||||
pair_coeff * *
|
||||
|
||||
compute energies all pair eff/cut
|
||||
variable eke equal c_energies[1]
|
||||
variable epauli equal c_energies[2]
|
||||
variable estatics equal c_energies[3]
|
||||
variable errestrain equal c_energies[4]
|
||||
|
||||
communicate single vel yes
|
||||
|
||||
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)
|
||||
|
||||
compute effTemp all temp/eff
|
||||
compute effPress all pressure effTemp
|
||||
|
||||
thermo 1
|
||||
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
|
||||
thermo_modify temp effTemp press effPress
|
||||
|
||||
# Minimization
|
||||
|
||||
min_style cg
|
||||
dump 1 all xyz 1 ${sname}.min.xyz
|
||||
dump 2 all custom 1 ${sname}.min.lammpstrj id type q spin eradius x y z fx fy fz erforce
|
||||
min_modify line quadratic
|
||||
minimize 0 1.0e-5 1000 10000
|
||||
|
||||
undump 1
|
||||
undump 2
|
||||
|
||||
|
|
@ -0,0 +1,49 @@
|
|||
|
||||
# Created 2011-01-07
|
||||
|
||||
# General parameters
|
||||
|
||||
variable sname index SiH4.ang
|
||||
log ${sname}.log
|
||||
|
||||
units real
|
||||
newton on
|
||||
boundary f f f
|
||||
|
||||
atom_style electron
|
||||
|
||||
read_data data.${sname}
|
||||
|
||||
pair_style eff/cut 529.177249
|
||||
pair_coeff * *
|
||||
|
||||
compute energies all pair eff/cut
|
||||
variable eke equal c_energies[1]
|
||||
variable epauli equal c_energies[2]
|
||||
variable estatics equal c_energies[3]
|
||||
variable errestrain equal c_energies[4]
|
||||
|
||||
communicate single vel yes
|
||||
|
||||
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)
|
||||
|
||||
compute effTemp all temp/eff
|
||||
compute effPress all pressure effTemp
|
||||
|
||||
thermo 1
|
||||
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
|
||||
thermo_modify temp effTemp press effPress
|
||||
|
||||
# Minimization
|
||||
|
||||
min_style cg
|
||||
dump 1 all xyz 1 ${sname}.min.xyz
|
||||
dump 2 all custom 1 ${sname}.min.lammpstrj id type q spin eradius x y z fx fy fz erforce
|
||||
min_modify line quadratic
|
||||
minimize 0 1.0e-5 1000 10000
|
||||
|
||||
undump 1
|
||||
undump 2
|
||||
|
||||
|
|
@ -0,0 +1 @@
|
|||
Simple Hydrogen atom example (finite)
|
||||
|
|
@ -0,0 +1,21 @@
|
|||
Created by AJB
|
||||
|
||||
4 atoms
|
||||
2 atom types
|
||||
|
||||
-0.529177 0.529177 xlo xhi
|
||||
-0.529177 0.529177 ylo yhi
|
||||
-0.529177 0.529177 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 1.000794 # H nuclei mass
|
||||
2 1.000000 # electron mass
|
||||
|
||||
Atoms
|
||||
|
||||
1 1 1.0 0 0.000000 0.000000 0.000000 0.000000
|
||||
2 2 0.0 1 0.529177 0.000000 0.000000 0.000000
|
||||
3 1 1.0 0 0.000000 0.264589 0.000000 0.000000
|
||||
4 2 0.0 1 0.529177 0.264589 0.000000 0.000000
|
||||
|
||||
|
|
@ -0,0 +1,19 @@
|
|||
Created by AJB
|
||||
|
||||
2 atoms
|
||||
2 atom types
|
||||
|
||||
-1.0 1.0 xlo xhi
|
||||
-1.0 1.0 ylo yhi
|
||||
-1.0 1.0 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 1.000794 # H nuclei mass
|
||||
2 1.000000 # electron mass
|
||||
|
||||
Atoms
|
||||
|
||||
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
|
||||
|
||||
|
|
@ -0,0 +1,34 @@
|
|||
variable sname index h_atom.ang
|
||||
log ${sname}.spe.log
|
||||
|
||||
units real
|
||||
newton on
|
||||
boundary p p p
|
||||
|
||||
atom_style electron
|
||||
|
||||
read_data data.${sname}
|
||||
|
||||
pair_style eff/cut 0.529177249 0 0
|
||||
pair_coeff * *
|
||||
|
||||
communicate single vel yes
|
||||
|
||||
compute energies all pair eff/cut
|
||||
variable eke equal c_energies[1]
|
||||
variable epauli equal c_energies[2]
|
||||
variable estatics equal c_energies[3]
|
||||
variable errestrain equal c_energies[4]
|
||||
|
||||
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)
|
||||
|
||||
compute effTemp all temp/eff
|
||||
compute effPress all pressure effTemp
|
||||
|
||||
thermo 1
|
||||
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
|
||||
thermo_modify temp effTemp press effPress
|
||||
|
||||
run 0
|
||||
|
|
@ -0,0 +1,34 @@
|
|||
variable sname index h_atom.bohr
|
||||
log ${sname}.spe.log
|
||||
|
||||
units electron
|
||||
newton on
|
||||
boundary p p p
|
||||
|
||||
atom_style electron
|
||||
|
||||
read_data data.${sname}
|
||||
|
||||
pair_style eff/cut 1.0 0 0
|
||||
pair_coeff * *
|
||||
|
||||
communicate single vel yes
|
||||
|
||||
compute energies all pair eff/cut
|
||||
variable eke equal c_energies[1]
|
||||
variable epauli equal c_energies[2]
|
||||
variable estatics equal c_energies[3]
|
||||
variable errestrain equal c_energies[4]
|
||||
|
||||
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)
|
||||
|
||||
compute effTemp all temp/eff
|
||||
compute effPress all pressure effTemp
|
||||
|
||||
thermo 1
|
||||
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
|
||||
thermo_modify temp effTemp press effPress
|
||||
|
||||
run 0
|
||||
|
|
@ -0,0 +1 @@
|
|||
This example demonstrates the use of several eff-related commands. No particular physics is explored.
|
||||
|
|
@ -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
|
||||
|
|
@ -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
|
||||
|
|
@ -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
File diff suppressed because it is too large
Load Diff
|
|
@ -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
|
||||
|
|
@ -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
|
||||
|
|
@ -0,0 +1,59 @@
|
|||
variable sname index h2bulk.ang
|
||||
log ${sname}.nve.log
|
||||
|
||||
units real
|
||||
newton on
|
||||
boundary p p p
|
||||
|
||||
atom_style electron
|
||||
|
||||
read_data data.${sname}
|
||||
|
||||
pair_style eff/cut 16.207559818252903 1 1
|
||||
pair_coeff * *
|
||||
|
||||
neigh_modify one 10000 page 100000
|
||||
|
||||
communicate single vel yes
|
||||
|
||||
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)
|
||||
|
||||
compute effTemp all temp/eff
|
||||
compute effPress all pressure effTemp
|
||||
|
||||
compute energies all pair eff/cut
|
||||
variable eke equal c_energies[1]
|
||||
variable epauli equal c_energies[2]
|
||||
variable ecoul equal c_energies[3]
|
||||
variable erres equal c_energies[4]
|
||||
|
||||
thermo 100
|
||||
thermo_style custom step etotal pe ke v_eke v_epauli v_ecoul v_erres press v_press temp
|
||||
thermo_modify temp effTemp press effPress flush yes
|
||||
|
||||
# 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
|
||||
|
|
@ -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
|
|
@ -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
|
||||
|
|
@ -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
|
||||
|
||||
|
|
@ -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
File diff suppressed because it is too large
Load Diff
|
|
@ -0,0 +1,57 @@
|
|||
variable sname index Li.ang
|
||||
log ${sname}.spe.log
|
||||
|
||||
units real
|
||||
newton on
|
||||
boundary p p p
|
||||
dielectric 1.0
|
||||
|
||||
atom_style electron
|
||||
|
||||
#read_data data.${sname}
|
||||
read_restart ${sname}.min.restart
|
||||
|
||||
pair_style eff/cut 11.049221 1 1
|
||||
pair_coeff * *
|
||||
|
||||
communicate single vel yes
|
||||
|
||||
neigh_modify one 2000 page 20000
|
||||
|
||||
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)
|
||||
|
||||
compute effTemp all temp/eff
|
||||
compute effPress all pressure effTemp
|
||||
|
||||
compute energies all pair eff/cut
|
||||
variable eke equal c_energies[1]
|
||||
variable epauli equal c_energies[2]
|
||||
variable ecoul equal c_energies[3]
|
||||
variable erres equal c_energies[4]
|
||||
|
||||
thermo 100
|
||||
thermo_style custom step etotal pe ke v_eke v_epauli v_ecoul v_erres press v_press temp
|
||||
thermo_modify temp effTemp press effPress flush yes
|
||||
|
||||
#min_style cg
|
||||
#minimize 0 1e-6 100 1000
|
||||
#write_restart ${sname}.min.restart
|
||||
|
||||
timestep 0.005
|
||||
|
||||
velocity all create 10.0 4928459 rot yes mom yes dist gaussian
|
||||
fix 0 all temp/rescale/eff 1 10.0 3000.0 0.05 1.0
|
||||
#fix 0 all langevin/eff 3000.0 3000.0 10.0 699483
|
||||
fix 1 all nve/eff
|
||||
|
||||
run 1000
|
||||
unfix 0
|
||||
unfix 1
|
||||
|
||||
fix 1 all nvt/eff temp 3000.0 3000.0 100.0
|
||||
dump 1 all custom 1000 ${sname}.nvt.lammpstrj id type q spin eradius x y z vx vy vz ervel
|
||||
|
||||
run 100000
|
||||
|
||||
|
|
@ -0,0 +1,46 @@
|
|||
variable sname index Li.bohr
|
||||
log ${sname}.spe.log
|
||||
|
||||
units electron
|
||||
newton off
|
||||
boundary p p p
|
||||
dielectric 1.0
|
||||
|
||||
atom_style electron
|
||||
|
||||
read_data data.${sname}
|
||||
|
||||
pair_style eff/cut 20.88 1 1
|
||||
pair_coeff * *
|
||||
|
||||
communicate single vel yes
|
||||
|
||||
neigh_modify one 2000 page 20000
|
||||
|
||||
compute 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)
|
||||
|
||||
compute effTemp all temp/eff
|
||||
compute effPress all pressure effTemp
|
||||
|
||||
compute energies all pair eff/cut
|
||||
variable eke equal c_energies[1]
|
||||
variable epauli equal c_energies[2]
|
||||
variable estatics equal c_energies[3]
|
||||
variable errestrain equal c_energies[4]
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain press v_press temp
|
||||
thermo_modify temp effTemp press effPress
|
||||
|
||||
min_style cg
|
||||
minimize 0 1e-6 100 2000
|
||||
|
||||
fix 0 all temp/rescale/eff 1 0.0 3000.0 0.02 0.5
|
||||
|
||||
fix 1 all npt/eff temp 3000.0 3000.0 0.1 iso 1e7 1e7 1.0
|
||||
dump 1 all custom 100 ${sname}.spe.lammpstrj id type q spin eradius x y z
|
||||
|
||||
run 1000
|
||||
|
||||
|
|
@ -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
|
||||
|
|
@ -0,0 +1,40 @@
|
|||
Created using cfg2lammps (c) AJB-2009
|
||||
|
||||
22 atoms
|
||||
3 atom types
|
||||
|
||||
-529.177249 529.177249 xlo xhi
|
||||
-529.177249 529.177249 ylo yhi
|
||||
-529.177249 529.177249 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 12.011789324618736
|
||||
2 1.007940
|
||||
3 0.0005446623093682
|
||||
|
||||
Atoms
|
||||
|
||||
1 1 6 2 0.173923 -0.000000 -0.000000 0.750495
|
||||
2 1 6 2 0.173923 0.000000 0.000000 -0.750495
|
||||
3 2 1 0 0.000000 -1.096376 0.000000 1.167561
|
||||
4 2 1 0 0.000000 0.548185 0.949487 1.167561
|
||||
5 2 1 0 0.000000 0.548185 -0.949487 1.167561
|
||||
6 2 1 0 0.000000 1.096376 -0.000000 -1.167561
|
||||
7 2 1 0 0.000000 -0.548185 -0.949487 -1.167561
|
||||
8 2 1 0 0.000000 -0.548185 0.949487 -1.167561
|
||||
9 3 0 1 0.672944 0.000000 0.000000 -0.000000
|
||||
10 3 0 -1 0.672944 -0.000000 -0.000000 0.000000
|
||||
11 3 0 1 0.804498 -0.871444 -0.000000 1.075706
|
||||
12 3 0 -1 0.804498 -0.871444 0.000000 1.075706
|
||||
13 3 0 1 0.804498 0.435722 0.754691 1.075706
|
||||
14 3 0 -1 0.804498 0.435722 0.754691 1.075706
|
||||
15 3 0 1 0.804498 0.435722 -0.754691 1.075706
|
||||
16 3 0 -1 0.804498 0.435722 -0.754691 1.075706
|
||||
17 3 0 1 0.804498 0.871444 0.000000 -1.075706
|
||||
18 3 0 -1 0.804498 0.871444 -0.000000 -1.075706
|
||||
19 3 0 1 0.804498 -0.435722 -0.754691 -1.075706
|
||||
20 3 0 -1 0.804498 -0.435722 -0.754691 -1.075706
|
||||
21 3 0 1 0.804498 -0.435722 0.754691 -1.075706
|
||||
22 3 0 -1 0.804498 -0.435722 0.754691 -1.075706
|
||||
|
||||
|
|
@ -0,0 +1,40 @@
|
|||
Created using cfg2lammps (c) AJB-2009
|
||||
|
||||
22 atoms
|
||||
3 atom types
|
||||
|
||||
-1000.000 1000.0 xlo xhi
|
||||
-1000.000 1000.0 ylo yhi
|
||||
-1000.000 1000.0 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 12.010700
|
||||
2 1.007940
|
||||
3 1.000000
|
||||
|
||||
Atoms
|
||||
|
||||
1 1 6 2 0.328666 -2.01891e-07 -2.24196e-11 1.41823
|
||||
2 1 6 2 0.328666 2.02074e-07 2.13734e-12 -1.41823
|
||||
3 2 1 0 0 -2.07185 1.73981e-11 2.20637
|
||||
4 2 1 0 0 1.03592 1.79427 2.20637
|
||||
5 2 1 0 0 1.03592 -1.79427 2.20637
|
||||
6 2 1 0 0 2.07185 -4.74225e-12 -2.20637
|
||||
7 2 1 0 0 -1.03592 -1.79427 -2.20637
|
||||
8 2 1 0 0 -1.03592 1.79427 -2.20637
|
||||
9 3 0 1 1.27168 8.92203e-10 2.31772e-09 -1.56875e-07
|
||||
10 3 0 -1 1.27168 -2.00948e-10 -2.36629e-09 1.21337e-07
|
||||
11 3 0 1 1.52028 -1.64679 -3.01708e-10 2.03279
|
||||
12 3 0 -1 1.52028 -1.64679 3.02717e-10 2.03279
|
||||
13 3 0 1 1.52028 0.823395 1.42616 2.03279
|
||||
14 3 0 -1 1.52028 0.823395 1.42616 2.03279
|
||||
15 3 0 1 1.52028 0.823395 -1.42616 2.03279
|
||||
16 3 0 -1 1.52028 0.823395 -1.42616 2.03279
|
||||
17 3 0 1 1.52028 1.64679 5.18964e-10 -2.03279
|
||||
18 3 0 -1 1.52028 1.64679 -5.17001e-10 -2.03279
|
||||
19 3 0 1 1.52028 -0.823395 -1.42616 -2.03279
|
||||
20 3 0 -1 1.52028 -0.823395 -1.42616 -2.03279
|
||||
21 3 0 1 1.52028 -0.823395 1.42616 -2.03279
|
||||
22 3 0 -1 1.52028 -0.823395 1.42616 -2.03279
|
||||
|
||||
|
|
@ -0,0 +1,60 @@
|
|||
|
||||
# Created 2010-12-13
|
||||
|
||||
# General parameters
|
||||
|
||||
variable sname index C2H6fc.ang
|
||||
|
||||
units real
|
||||
newton on
|
||||
boundary f f f
|
||||
|
||||
atom_style electron
|
||||
|
||||
read_data data.${sname}
|
||||
|
||||
pair_style eff/cut 529.177249
|
||||
pair_coeff * *
|
||||
|
||||
compute energies all pair eff/cut
|
||||
variable eke equal c_energies[1]
|
||||
variable epauli equal c_energies[2]
|
||||
variable estatics equal c_energies[3]
|
||||
variable errestrain equal c_energies[4]
|
||||
|
||||
communicate single vel yes
|
||||
|
||||
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)
|
||||
|
||||
compute effTemp all temp/eff
|
||||
compute effPress all pressure effTemp
|
||||
|
||||
thermo 100
|
||||
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
|
||||
thermo_modify temp effTemp press effPress
|
||||
|
||||
# Minimization
|
||||
|
||||
min_style cg
|
||||
dump 1 all xyz 100 ${sname}.min.xyz
|
||||
dump 2 all custom 100 ${sname}.min.lammpstrj id type q spin eradius x y z fx fy fz erforce
|
||||
dump 3 all custom 100 data.${sname}.restart id type q spin eradius x y z
|
||||
min_modify line quadratic
|
||||
minimize 0 1e-6 1000 2000
|
||||
|
||||
undump 1
|
||||
undump 2
|
||||
undump 3
|
||||
|
||||
# Equilibrate at 5000K
|
||||
velocity all create 1.0 4928459 rot yes mom yes dist gaussian
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 all nvt/eff temp 1.0 10000.0 1.0
|
||||
dump 2 all custom 100 ${sname}.nvt.lammpstrj id type q spin eradius x y z fx fy fz erforce
|
||||
|
||||
run 100000
|
||||
|
||||
|
|
@ -0,0 +1,53 @@
|
|||
|
||||
# Created 2010-12-13
|
||||
|
||||
# General parameters
|
||||
|
||||
variable sname index C2H6fc.bohr
|
||||
|
||||
units electron
|
||||
newton on
|
||||
boundary f f f
|
||||
|
||||
atom_style electron
|
||||
|
||||
read_data data.${sname}
|
||||
|
||||
pair_style eff/cut 1000.0
|
||||
pair_coeff * *
|
||||
|
||||
compute energies all pair eff/cut
|
||||
variable eke equal c_energies[1]
|
||||
variable epauli equal c_energies[2]
|
||||
variable estatics equal c_energies[3]
|
||||
variable errestrain equal c_energies[4]
|
||||
|
||||
communicate single vel yes
|
||||
|
||||
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)
|
||||
|
||||
compute effTemp all temp/eff
|
||||
compute effPress all pressure effTemp
|
||||
|
||||
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
|
||||
thermo_modify temp effTemp press effPress
|
||||
|
||||
# Minimization
|
||||
|
||||
min_style cg
|
||||
dump 1 all xyz 10 ${sname}.min.xyz
|
||||
dump 2 all custom 10 ${sname}.min.lammpstrj id type q spin eradius x y z fx fy fz erforce
|
||||
dump 3 all custom 10 data.${sname}.restart id type q spin eradius x y z
|
||||
min_modify line quadratic
|
||||
minimize 0 1e-6 1000 2000
|
||||
|
||||
undump 1
|
||||
undump 2
|
||||
undump 3
|
||||
|
||||
fix 1 all nvt/eff 1 2000 1.0
|
||||
dump 2 all custom 10 ${sname}.nvt.lammpstrj id type q spin eradius x y z fx fy fz erforce
|
||||
|
||||
run 10000
|
||||
|
|
@ -0,0 +1,31 @@
|
|||
Created using cfg2lammps (c) AJB-2009
|
||||
|
||||
13 atoms
|
||||
3 atom types
|
||||
|
||||
-529.177249 529.177249 xlo xhi
|
||||
-529.177249 529.177249 ylo yhi
|
||||
-529.177249 529.177249 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 12.011789324618736
|
||||
2 1.007940
|
||||
3 0.0005446623093682
|
||||
|
||||
Atoms
|
||||
|
||||
1 1 6.000000 2 0.174166 0.000000 0.000000 0.000000
|
||||
2 2 1.000000 0 0.000000 0.627600 0.627600 0.627600
|
||||
3 2 1.000000 0 0.000000 0.627600 -0.627600 -0.627600
|
||||
4 2 1.000000 0 0.000000 -0.627600 0.627600 -0.627600
|
||||
5 2 1.000000 0 0.000000 -0.627600 -0.627600 0.627600
|
||||
6 3 0.0 1 0.799655 0.313800 0.313800 0.313800
|
||||
7 3 0.0 -1 0.799655 0.313800 0.313800 0.313800
|
||||
8 3 0.0 1 0.799655 0.313800 -0.313800 -0.313800
|
||||
9 3 0.0 -1 0.799655 0.313800 -0.313800 -0.313800
|
||||
10 3 0.0 1 0.799655 -0.313800 0.313800 -0.313800
|
||||
11 3 0.0 -1 0.799655 -0.313800 0.313800 -0.313800
|
||||
12 3 0.0 1 0.799655 -0.313800 -0.313800 0.313800
|
||||
13 3 0.0 -1 0.799655 -0.313800 -0.313800 0.313800
|
||||
|
||||
|
|
@ -0,0 +1,31 @@
|
|||
Created using cfg2lammps (c) AJB-2009
|
||||
|
||||
13 atoms
|
||||
3 atom types
|
||||
|
||||
-1000.000 1000.0 xlo xhi
|
||||
-1000.000 1000.0 ylo yhi
|
||||
-1000.000 1000.0 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 12.011789324618736
|
||||
2 1.007940
|
||||
3 0.0005446623093682
|
||||
|
||||
Atoms
|
||||
|
||||
1 1 6.000000 2 0.329126 0.000000 0.000000 0.000000
|
||||
2 2 1.000000 0 0.0 1.185992 1.185992 1.185992
|
||||
3 2 1.000000 0 0.0 1.185992 -1.185992 -1.185992
|
||||
4 2 1.000000 0 0.0 -1.185992 1.185992 -1.185992
|
||||
5 2 1.000000 0 0.0 -1.185992 -1.185992 1.185992
|
||||
6 3 0.0 1 1.511128 0.592996 0.592996 0.592996
|
||||
7 3 0.0 -1 1.511128 0.592996 0.592996 0.592996
|
||||
8 3 0.0 1 1.511128 0.592996 -0.592996 -0.592996
|
||||
9 3 0.0 -1 1.511128 0.592996 -0.592996 -0.592996
|
||||
10 3 0.0 1 1.511128 -0.592996 0.592996 -0.592996
|
||||
11 3 0.0 -1 1.511128 -0.592996 0.592996 -0.592996
|
||||
12 3 0.0 1 1.511128 -0.592996 -0.592996 0.592996
|
||||
13 3 0.0 -1 1.511128 -0.592996 -0.592996 0.592996
|
||||
|
||||
|
|
@ -0,0 +1,58 @@
|
|||
# Created 2010-11-28
|
||||
|
||||
# General parameters
|
||||
|
||||
variable sname index CH4fc.ang
|
||||
|
||||
units real
|
||||
newton on
|
||||
boundary f f f
|
||||
|
||||
atom_style electron
|
||||
|
||||
read_data data.${sname}
|
||||
|
||||
pair_style eff/cut 529.177249 0 0
|
||||
pair_coeff * *
|
||||
|
||||
compute energies all pair eff/cut
|
||||
variable eke equal c_energies[1]
|
||||
variable epauli equal c_energies[2]
|
||||
variable estatics equal c_energies[3]
|
||||
variable errestrain equal c_energies[4]
|
||||
|
||||
communicate single vel yes
|
||||
|
||||
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)
|
||||
|
||||
compute effTemp all temp/eff
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
|
||||
thermo_modify temp effTemp
|
||||
|
||||
# Minimization
|
||||
|
||||
min_style cg
|
||||
dump 1 all xyz 10 ${sname}.min.xyz
|
||||
dump 2 all custom 10 ${sname}.min.lammpstrj id type q spin eradius x y z fx fy fz erforce
|
||||
#min_modify line quadratic
|
||||
minimize 0 1.0e-6 1000 10000
|
||||
|
||||
undump 1
|
||||
undump 2
|
||||
|
||||
# Equilibrate at 300K
|
||||
velocity all create 10.0 4928459 rot yes mom yes dist gaussian
|
||||
|
||||
timestep 0.0005
|
||||
|
||||
dump 1 all custom 1000 ${sname}.nvt.lammpstrj id type q spin eradius x y z fx fy fz erforce
|
||||
#fix 0 all langevin/eff 300.0 300.0 0.1
|
||||
fix 1 all nvt/eff temp 10.0 10000.0 0.1
|
||||
|
||||
run 400000
|
||||
|
||||
|
||||
|
|
@ -0,0 +1,59 @@
|
|||
# Created 2010-11-28
|
||||
|
||||
# General parameters
|
||||
|
||||
variable sname index CH4fc.bohr
|
||||
|
||||
units electron
|
||||
newton on
|
||||
boundary f f f
|
||||
|
||||
atom_style electron
|
||||
|
||||
read_data data.${sname}
|
||||
|
||||
pair_style eff/cut 1000.0 0 0
|
||||
pair_coeff * *
|
||||
|
||||
compute energies all pair eff/cut
|
||||
variable eke equal c_energies[1]
|
||||
variable epauli equal c_energies[2]
|
||||
variable estatics equal c_energies[3]
|
||||
variable errestrain equal c_energies[4]
|
||||
|
||||
communicate single vel yes
|
||||
|
||||
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)
|
||||
|
||||
compute effTemp all temp/eff
|
||||
compute effPress all pressure effTemp
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
|
||||
thermo_modify temp effTemp press effPress
|
||||
|
||||
# Minimization
|
||||
|
||||
min_style cg
|
||||
dump 1 all xyz 10 ${sname}.min.xyz
|
||||
dump 2 all custom 10 ${sname}.min.lammpstrj id type q spin eradius x y z fx fy fz erforce
|
||||
min_modify line quadratic
|
||||
minimize 0 1.0e-6 1000 10000
|
||||
|
||||
undump 1
|
||||
undump 2
|
||||
|
||||
# Equilibrate at 300K
|
||||
velocity all create 10000.0 4928459 rot yes mom yes dist gaussian
|
||||
|
||||
timestep 0.001
|
||||
|
||||
dump 1 all custom 1000 ${sname}.nvt.lammpstrj id type q spin eradius x y z fx fy fz erforce
|
||||
#fix 0 all langevin/eff 300.0 300.0 0.1
|
||||
fix 1 all nvt/eff temp 10000.0 10000.0 0.1
|
||||
|
||||
run 40000
|
||||
|
||||
|
||||
|
|
@ -0,0 +1,39 @@
|
|||
# Created 2010-11-28
|
||||
|
||||
# General parameters
|
||||
|
||||
variable sname index CH4fc.ang
|
||||
|
||||
units real
|
||||
newton on
|
||||
boundary p p p
|
||||
|
||||
atom_style electron
|
||||
|
||||
read_data data.${sname}
|
||||
|
||||
pair_style eff/cut 1000.0 1 1
|
||||
pair_coeff * *
|
||||
|
||||
compute energies all pair eff/cut
|
||||
variable eke equal c_energies[1]
|
||||
variable epauli equal c_energies[2]
|
||||
variable estatics equal c_energies[3]
|
||||
variable errestrain equal c_energies[4]
|
||||
|
||||
communicate single vel yes
|
||||
|
||||
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)
|
||||
|
||||
compute effTemp all temp/eff
|
||||
compute effPress all pressure effTemp
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
|
||||
thermo_modify temp effTemp press effPress
|
||||
|
||||
run 0
|
||||
|
||||
|
||||
|
|
@ -0,0 +1,39 @@
|
|||
# Created 2010-11-28
|
||||
|
||||
# General parameters
|
||||
|
||||
variable sname index CH4fc.bohr
|
||||
|
||||
units electron
|
||||
newton on
|
||||
boundary p p p
|
||||
|
||||
atom_style electron
|
||||
|
||||
read_data data.${sname}
|
||||
|
||||
pair_style eff/cut 1000.0 1 1
|
||||
pair_coeff * *
|
||||
|
||||
compute energies all pair eff/cut
|
||||
variable eke equal c_energies[1]
|
||||
variable epauli equal c_energies[2]
|
||||
variable estatics equal c_energies[3]
|
||||
variable errestrain equal c_energies[4]
|
||||
|
||||
communicate single vel yes
|
||||
|
||||
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)
|
||||
|
||||
compute effTemp all temp/eff
|
||||
compute effPress all pressure effTemp
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
|
||||
thermo_modify temp effTemp press effPress
|
||||
|
||||
run 0
|
||||
|
||||
|
||||
|
|
@ -0,0 +1,5 @@
|
|||
Examples of using the fixed-core option in pEFF.
|
||||
This fixes the two s electrons in an atom to be nuclei-centered
|
||||
and with fixed radii
|
||||
|
||||
Structure files provided by Hai Xiao (Caltech)
|
||||
Loading…
Reference in New Issue