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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13150 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2015-02-24 16:28:56 +00:00
parent 471fa5e969
commit cb912c1954
7 changed files with 26399 additions and 0 deletions
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78
examples/USER/quip/data_gap Normal file
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Position data for Silicon system
64 atoms
1 atom types
0.00 10.968476161 xlo xhi
0.00 10.968476161 ylo yhi
0.00 10.968476161 zlo zhi
Masses
1 28.0000
Atoms
1 1 4.1342 7.7779 2.6819
2 1 3.8227 4.8354 8.5466
3 1 3.3367 5.6117 3.2337
4 1 7.3383 4.1429 7.1334
5 1 5.2910 3.1335 7.8493
6 1 8.1878 7.7574 7.8028
7 1 6.1818 0.4249 10.5615
8 1 9.1403 2.7125 0.5025
9 1 6.1226 5.5502 5.6825
10 1 6.5245 10.6025 3.3104
11 1 8.2568 5.6311 8.7584
12 1 6.4173 8.2115 2.8958
13 1 3.2696 9.4267 6.1683
14 1 8.8185 10.6128 2.8109
15 1 9.1383 7.7201 5.6200
16 1 2.9562 9.4480 3.8264
17 1 4.9564 4.1652 4.2213
18 1 4.5523 2.4166 5.6766
19 1 7.5887 6.6794 4.2710
20 1 3.0825 0.6677 2.9952
21 1 3.8820 7.8988 0.3445
22 1 3.7083 4.3355 1.2749
23 1 1.6428 8.4303 10.8359
24 1 10.0218 1.5852 2.3550
25 1 9.9128 10.3677 10.2253
26 1 6.9276 5.7429 10.7359
27 1 0.7388 8.7933 3.7372
28 1 8.3962 1.1772 9.8375
29 1 6.3129 0.8043 5.3560
30 1 1.1391 5.3208 3.9628
31 1 0.1480 7.9404 1.6436
32 1 8.1491 2.2614 5.8950
33 1 2.3851 1.7006 5.0877
34 1 0.7199 3.3948 5.2624
35 1 5.2010 0.8339 1.7756
36 1 2.0562 3.2183 8.9577
37 1 0.5238 7.0741 5.3607
38 1 0.8347 7.3680 8.8659
39 1 5.9322 8.3676 8.0954
40 1 9.5288 1.6806 7.7323
41 1 9.2224 9.1364 1.0783
42 1 2.5214 0.9185 8.8916
43 1 1.2933 1.1758 1.5612
44 1 10.5698 5.3114 9.0911
45 1 10.1242 8.9562 8.4044
46 1 5.5419 3.1240 2.1335
47 1 5.7385 9.0604 10.3366
48 1 4.5726 6.6481 7.1382
49 1 7.4725 4.1120 1.3191
50 1 7.2648 7.8923 0.7153
51 1 4.8518 0.9400 8.6860
52 1 1.8862 3.1393 0.3805
53 1 1.8559 0.1787 6.7949
54 1 9.8477 9.8585 4.7997
55 1 2.2623 7.4090 6.9539
56 1 10.5601 10.6960 6.8908
57 1 0.1288 3.5134 7.5873
58 1 4.5534 5.7282 10.5966
59 1 10.8612 4.3183 0.2217
60 1 10.6960 5.6883 2.1032
61 1 5.3321 10.3488 6.9890
62 1 1.2772 10.7874 10.6074
63 1 8.7088 4.9646 3.1069
64 1 9.6083 3.0215 4.1879

22
examples/USER/quip/data_sw Normal file
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Position data for Silicon SW test system
8 atoms
1 atom types
0.00 5.431 xlo xhi
0.00 5.431 ylo yhi
0.00 5.431 zlo zhi
Masses
1 28.0000
Atoms
1 1 0.00000000 0.00000000 0.00000000
2 1 1.35775000 1.35775000 1.35775000
3 1 2.71550000 2.71550000 0.00000000
4 1 4.07325000 4.07325000 1.35775000
5 1 2.71550000 0.00000000 2.71550000
6 1 4.07325000 1.35775000 4.07325000
7 1 0.00000000 2.71550000 2.71550000
8 1 1.35775000 4.07325000 4.07325000

707
examples/USER/quip/gap_example.xml Normal file
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<GAP_2015_2_20_0_10_54_35_765>
<Potential label="GAP_2015_2_20_0_10_54_35_765" init_args="Sum init_args_pot1={IP Glue} init_args_pot2={IP GAP label=GAP_2015_2_20_0_10_54_35_765}"/>
<Glue_params n_types="2">
<per_type_data atomic_num="14" type="1">
<!-- Si -->
<density num_points="14" density_y1="-0.4144" density_yn="0.0">
<point a="0.821917808219178" rho="0.258391"/>
<point a="1.027397260273973" rho="0.173248"/>
<point a="1.232876712328767" rho="0.097399"/>
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<point a="2.054794520547945" rho="0.006107"/>
<point a="2.260273972602740" rho="0.003182"/>
<point a="2.465753424657535" rho="0.001524"/>
<point a="2.671232876712329" rho="0.000913"/>
<point a="2.876712328767124" rho="0.000383"/>
<point a="3.082191780821919" rho="0.000295"/>
<point a="3.287671232876713" rho="0.000080"/>
<point a="3.493150684931507" rho="0.000000"/>
</density>
<potential_density num_points="12">
<point rho="0.0000000000000" E="0.0"/>
<point rho="0.0572259106295" E="0.0"/>
<point rho="0.0633096739107" E="0.0"/>
<point rho="0.0689221129285" E="0.0"/>
<point rho="0.0741074612625" E="0.0"/>
<point rho="0.0789857895134" E="0.0"/>
<point rho="0.0835293161324" E="0.0"/>
<point rho="0.1529969346048" E="0.0"/>
<point rho="0.2168736082455" E="0.0"/>
<point rho="0.2697341539351" E="0.0"/>
<point rho="0.3158337343334" E="0.0"/>
<point rho="0.3570433660014" E="0.0"/>
</potential_density>
</per_type_data>
<per_type_data atomic_num="8" type="2">
<!-- O -->
<density num_points="13" density_y1="-12.096333" density_yn="0.0">
<point a="0.275229" rho="5.207325"/>
<point a="0.412844" rho="3.542692"/>
<point a="0.550458" rho="1.841125"/>
<point a="0.688073" rho="0.878272"/>
<point a="0.825688" rho="0.407461"/>
<point a="0.963302" rho="0.201061"/>
<point a="1.100917" rho="0.096121"/>
<point a="1.238532" rho="0.047733"/>
<point a="1.376146" rho="0.021994"/>
<point a="1.513761" rho="0.013445"/>
<point a="1.651376" rho="0.005751"/>
<point a="1.788990" rho="0.004175"/>
<point a="2.000000" rho="0.000000"/>
</density>
<potential_density num_points="6">
<point rho="0.000000000000" E="-162.5696"/>
<point rho="0.007455445248" E="-162.6855"/>
<point rho="0.017732566824" E="-162.2040"/>
<point rho="0.030441208637" E="-160.5319"/>
<point rho="0.056284772194" E="-156.7397"/>
<point rho="0.074786922252" E="-153.6122"/>
</potential_density>
</per_type_data>
<per_pair_data type1="1" type2="1">
<!-- Si -->
<potential_pair num_points="11" density_y1="0.0" density_yn="0.0">
<point r=" 1.2" E=" 13.4896897268455"/>
<point r="1.33" E=" 6.35102226195354"/>
<point r="1.46" E=" 2.85261290997884"/>
<point r="1.59" E=" 1.17069139864555"/>
<point r="1.72" E=" 0.410915649591501"/>
<point r="1.85" E=" 0.11009036654669"/>
<point r="1.98" E=" 0.0180148277318245"/>
<point r="2.11" E=" 0.00107543820001212"/>
<point r="2.24" E=" 5.0184779157859e-06"/>
<point r="2.37" E=" 8.33906077334409e-13"/>
<point r=" 2.5" E="0.00000000000000000"/>
</potential_pair>
</per_pair_data>
</Glue_params>
<GAP_params label="GAP_2015_2_20_0_10_54_35_765" gap_version="1423607965">
<GAP_data do_core="T">
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<gpSparse label="GAP_2015_2_20_0_10_54_35_765" n_coordinate="1">
<gpCoordinates label="GAP_2015_2_20_0_10_54_35_7651" dimensions="51" signal_variance="1.00000000000000000" signal_mean="0.00000000000000000" sparsified="T" n_permutations="1" covariance_type="2" n_sparseX="500" sparseX_filename="gap_example_sparse.dat">
<theta> 0.40000000000000000E+01 </theta>
<descriptor>soap l_max=4 n_max=4 atom_sigma=0.5 zeta=4 cutoff=4.0 cutoff_transition_width=0.5 central_weight=0.2 n_sparseX=500 delta=1.0 f0=0.0 covariance_type=dot_product sparse_method=kmeans</descriptor>
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</GAP_params>
</GAP_2015_2_20_0_10_54_35_765>

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examples/USER/quip/gap_example_sparse.dat Normal file
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examples/USER/quip/in.gap Normal file
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# Test of GAP potential for Si system
units metal
boundary p p p
atom_style atomic
read_data data_gap
pair_style quip
pair_coeff * * gap_example.xml "Potential xml_label=GAP_2015_2_20_0_10_54_35_765" 14
neighbor 0.3 bin
neigh_modify delay 10
fix 1 all nve
thermo 10
timestep 0.001
dump 1 all custom 10 dump.gap id fx fy fz
dump_modify 1 format "%d %20.15g %20.15g %20.15g"
run 40

23
examples/USER/quip/in.sw Normal file
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# Test of SW potential for Si system
units metal
boundary p p p
atom_style atomic
read_data data_sw
pair_style quip
pair_coeff * * sw_example.xml "IP SW" 14
neighbor 0.3 bin
neigh_modify delay 10
fix 1 all nve
thermo 10
timestep 0.001
dump 1 all custom 10 dump.sw id fx fy fz
dump_modify 1 format "%d %20.15g %20.15g %20.15g"
run 1

46
examples/USER/quip/sw_example.xml Normal file
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<SW_params n_types="3" label="PRB_31_plus_H_Ge">
<comment> Stillinger and Weber, Phys. Rev. B 31 p 5262 (1984), extended for other elements. Ge and Si-Ge from Ethier and Lewis '92 </comment>
<per_type_data type="1" atomic_num="1" />
<per_type_data type="2" atomic_num="14" />
<per_type_data type="3" atomic_num="32" />
<per_pair_data atnum_i="1" atnum_j="1" AA="0.0" BB="0.0"
p="0" q="0" a="1.0" sigma="1.0" eps="0.0" />
<per_pair_data atnum_i="1" atnum_j="14" AA="8.581214" BB="0.0327827"
p="4" q="0" a="1.25" sigma="2.537884" eps="2.1672" />
<per_pair_data atnum_i="14" atnum_j="14" AA="7.049556277" BB="0.6022245584"
p="4" q="0" a="1.80" sigma="2.0951" eps="2.1675" />
<!-- pair data for Ge and Si-Ge -->
<per_pair_data atnum_i="32" atnum_j="32" AA="7.049556277" BB="0.6022245584"
p="4" q="0" a="1.80" sigma="2.181" eps="1.92590365783410138248" />
<per_pair_data atnum_i="14" atnum_j="32" AA="7.049556277" BB="0.6022245584"
p="4" q="0" a="1.80" sigma="2.138" eps="2.04313391101890694121" />
<!-- triplet terms: atnum_c is the center atom, neighbours j and k -->
<per_triplet_data atnum_c="1" atnum_j="1" atnum_k="1"
lambda="21.0" gamma="1.20" eps="2.1675" />
<per_triplet_data atnum_c="1" atnum_j="1" atnum_k="14"
lambda="21.0" gamma="1.20" eps="2.1675" />
<per_triplet_data atnum_c="1" atnum_j="14" atnum_k="14"
lambda="21.0" gamma="1.20" eps="2.1675" />
<per_triplet_data atnum_c="14" atnum_j="1" atnum_k="1"
lambda="21.0" gamma="1.20" eps="2.1675" />
<per_triplet_data atnum_c="14" atnum_j="1" atnum_k="14"
lambda="21.0" gamma="1.20" eps="2.1675" />
<per_triplet_data atnum_c="14" atnum_j="14" atnum_k="14"
lambda="21.0" gamma="1.20" eps="2.1675" />
<!-- triplet data for Ge and Si-Ge -->
<per_triplet_data atnum_c="14" atnum_j="14" atnum_k="32"
lambda="23.1" gamma="1.20" eps="2.10444772465437788017" />
<per_triplet_data atnum_c="14" atnum_j="32" atnum_k="32"
lambda="25.5" gamma="1.20" eps="2.04326828917050691242" />
<per_triplet_data atnum_c="32" atnum_j="14" atnum_k="14"
lambda="25.5" gamma="1.20" eps="2.04326828917050691242" />
<per_triplet_data atnum_c="32" atnum_j="14" atnum_k="32"
lambda="28.1" gamma="1.20" eps="1.98396169354838709676" />
<per_triplet_data atnum_c="32" atnum_j="32" atnum_k="32"
lambda="31.0" gamma="1.20" eps="1.92590365783410138247" />
</SW_params>