merging stable and exaalt branches into exaaltstable
This commit is contained in:
Richard Zamora
36
examples/latte/TBparam/bondints.nonortho
Normal file
36
examples/latte/TBparam/bondints.nonortho
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@ -0,0 +1,36 @@
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||||
Noints= 34
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Element1 Element2 Kind H0 B1 B2 B3 B4 B5 R1 Rcut H0 B1 B2 B3 B4 B5 R1 Rcut
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N O sss -11.430028 -2.257346 -1.152844 0.000000 0.000000 1.200000 3.500000 4.000000 0.340064 -1.703613 -0.622348 0.036738 -0.040158 1.200000 3.500000 4.000000
|
||||
N O sps 11.597479 -1.382001 -0.765170 0.000000 0.000000 1.200000 3.500000 4.000000 -0.370946 -1.040947 -0.931097 0.252441 -0.115450 1.200000 3.500000 4.000000
|
||||
O N sps 12.143744 -0.822913 -0.676127 0.000000 0.000000 1.200000 3.500000 4.000000 -0.420014 -1.107918 -0.905594 0.188424 -0.088365 1.200000 3.500000 4.000000
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||||
N O pps 9.465191 -1.082032 -0.769214 0.000000 0.000000 1.200000 3.500000 4.000000 -0.314073 0.499050 -2.914288 2.067657 -0.738439 1.200000 3.500000 4.000000
|
||||
N O ppp -4.676789 -2.171480 -0.288002 0.000000 0.000000 1.200000 3.500000 4.000000 0.223937 -1.991867 -0.537630 -0.081270 -0.004130 1.200000 3.500000 4.000000
|
||||
C O sss -14.369472 -2.077439 -0.875471 0.000000 0.000000 1.200000 3.500000 4.000000 0.375339 -1.547372 -0.642492 0.020614 -0.026699 1.200000 3.500000 4.000000
|
||||
C O sps 9.576296 -1.156217 -0.494803 0.000000 0.000000 1.200000 3.500000 4.000000 -0.373027 -0.776043 -1.019920 0.257539 -0.102838 1.200000 3.500000 4.000000
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||||
O C sps 14.037374 -1.192632 -0.654572 0.000000 0.000000 1.200000 3.500000 4.000000 -0.458068 -1.035067 -0.937868 0.190562 -0.077841 1.200000 3.500000 4.000000
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||||
C O pps 9.331152 -0.718120 -0.822100 0.000000 0.000000 1.200000 3.500000 4.000000 -0.322293 0.795473 -3.476601 2.589965 -0.897800 1.200000 3.500000 4.000000
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||||
C O ppp -5.334367 -2.263939 -0.204910 0.000000 0.000000 1.200000 3.500000 4.000000 0.244570 -1.922717 -0.573671 -0.057280 -0.004108 1.200000 3.500000 4.000000
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||||
C N sss -7.010061 -1.730597 -0.575559 0.000000 0.000000 1.500000 3.500000 4.000000 0.263438 -1.754525 -0.584215 -0.007801 -0.021729 1.500000 3.500000 4.000000
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||||
C N sps 7.543283 -1.293768 -0.624363 0.000000 0.000000 1.500000 3.500000 4.000000 -0.326609 -1.197485 -0.807786 0.134891 -0.084373 1.500000 3.500000 4.000000
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N C sps 9.090970 -1.494255 -0.616711 0.000000 0.000000 1.500000 3.500000 4.000000 -0.337943 -1.335442 -0.769693 0.119373 -0.079493 1.500000 3.500000 4.000000
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C N pps 6.892240 -0.931920 -0.769164 0.000000 0.000000 1.500000 3.500000 4.000000 -0.350240 -0.467439 -1.849316 1.854403 -0.988471 1.500000 3.500000 4.000000
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C N ppp -2.903346 -2.149349 -0.253006 0.000000 0.000000 1.500000 3.500000 4.000000 0.158424 -2.114409 -0.582346 -0.051076 -0.006183 1.500000 3.500000 4.000000
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C C sss -9.404207 -1.363297 -0.507128 0.000000 0.000000 1.400000 3.500000 4.000000 0.346977 -1.519820 -0.570812 -0.013518 -0.015829 1.400000 3.500000 4.000000
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C C sps 8.662429 -1.047410 -0.661999 0.000000 0.000000 1.400000 3.500000 4.000000 -0.400467 -0.984048 -0.853949 0.157178 -0.073381 1.400000 3.500000 4.000000
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C C pps 6.811512 -0.552299 -0.776890 0.000000 0.000000 1.400000 3.500000 4.000000 -0.382417 0.102889 -2.786680 2.646356 -1.134320 1.400000 3.500000 4.000000
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C C ppp -3.550127 -1.925572 -0.132715 0.000000 0.000000 1.400000 3.500000 4.000000 0.214357 -1.948923 -0.578323 -0.034356 -0.007257 1.400000 3.500000 4.000000
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H C sss -9.072577 -1.393093 -0.430611 0.000000 0.000000 1.100000 3.500000 4.000000 0.416003 -1.459596 -0.654874 0.009140 -0.012658 1.100000 3.500000 4.000000
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H C sps 8.176008 -0.985177 -0.427403 0.000000 0.000000 1.100000 3.500000 4.000000 -0.495695 -0.901626 -1.007214 0.189808 -0.057087 1.100000 3.500000 4.000000
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H H sss -9.340000 -1.145903 -0.391777 0.000000 0.000000 0.750000 3.500000 4.000000 0.575007 -1.391261 -0.778831 0.080209 -0.017759 0.750000 3.500000 4.000000
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O O sss -12.737687 -1.851608 -0.666621 0.000000 0.000000 1.200000 3.500000 4.000000 0.296445 -1.911896 -0.663451 0.038054 -0.046608 1.200000 3.500000 4.000000
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O O sps 13.683050 -1.684554 -0.468349 0.000000 0.000000 1.200000 3.500000 4.000000 -0.362143 -1.285274 -0.939591 0.204641 -0.106438 1.200000 3.500000 4.000000
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O O pps 9.460772 -1.211748 -0.581016 0.000000 0.000000 1.200000 3.500000 4.000000 -0.312044 0.121814 -2.519352 1.681266 -0.644566 1.200000 3.500000 4.000000
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||||
O O ppp -4.494595 -2.709223 -0.284124 0.000000 0.000000 1.200000 3.500000 4.000000 0.193010 -2.168462 -0.580629 -0.105104 0.004891 1.200000 3.500000 4.000000
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H O sss -12.230931 -1.808632 -0.421164 0.000000 0.000000 1.000000 3.500000 4.000000 0.404725 -1.702546 -0.707938 0.074904 -0.039922 1.000000 3.500000 4.000000
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H O sps 9.466088 -1.321262 -0.386336 0.000000 0.000000 1.000000 3.500000 4.000000 -0.447660 -0.952979 -1.163537 0.400616 -0.156965 1.000000 3.500000 4.000000
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||||
N N sss -7.710330 -2.365312 -0.525527 0.000000 0.000000 1.500000 3.500000 4.000000 0.231654 -1.879002 -0.572765 -0.004579 -0.031106 1.500000 3.500000 4.000000
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N N sps 8.222314 -1.612118 -0.690081 0.000000 0.000000 1.500000 3.500000 4.000000 -0.305271 -1.385158 -0.751032 0.114531 -0.090839 1.500000 3.500000 4.000000
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||||
N N pps 7.178570 -1.176467 -0.571049 0.000000 0.000000 1.500000 3.500000 4.000000 -0.324668 -0.547805 -1.638658 1.495168 -0.827868 1.500000 3.500000 4.000000
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N N ppp -2.829344 -2.408049 -0.387709 0.000000 0.000000 1.500000 3.500000 4.000000 0.142909 -2.162036 -0.571942 -0.071640 -0.004682 1.500000 3.500000 4.000000
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H N sss -12.095890 -1.519057 -0.277247 0.000000 0.000000 1.000000 3.500000 4.000000 0.446693 -1.500463 -0.657448 0.065741 -0.037004 1.000000 3.500000 4.000000
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H N sps 9.851338 -1.231616 -0.370836 0.000000 0.000000 1.000000 3.500000 4.000000 -0.501530 -0.785734 -1.123232 0.394878 -0.148501 1.000000 3.500000 4.000000
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7
examples/latte/TBparam/electrons.dat
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7
examples/latte/TBparam/electrons.dat
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@ -0,0 +1,7 @@
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Noelem= 5
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Element basis Numel Es Ep Ed Ef Mass HubbardU Wss Wpp Wdd Wff
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N sp 5.0 -18.58 -7.09 0.0 0.0 14.0067 15.93 0.0 -0.6950 0.0 0.0
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O sp 6.0 -23.96 -9.02 0.0 0.0 15.9994 12.15 0.0 -0.7577 0.0 0.0
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H s 1.0 -6.35 0.0 0.0 0.0 1.0079 12.85 -1.7937 0.0 0.0 0.0
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C sp 4.0 -13.75 -5.28 0.0 0.0 12.01 10.0 0.0 -0.621 0.0 0.0
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Ti sd 4.0 -5.5 0.0 -3.0 0.0 47.867 10.0 0.0 0.0 0.0 0.0
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12
examples/latte/TBparam/ppots.nonortho
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12
examples/latte/TBparam/ppots.nonortho
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@ -0,0 +1,12 @@
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Nopps= 10
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Ele1 Ele2 A0 A1 A2 A3 A4 A5 A6 C R1 Rcut
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N O 13.182426 20.050322 -46.806321 38.206953 -12.319656 0.000000 0.000000 0.000000 1.600000 1.700000
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C N 88.953762 10.294988 -27.706877 22.101434 -6.836438 0.000000 0.000000 0.000000 1.600000 1.700000
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C O 0.944093 30.116337 -59.608215 45.107654 -13.178839 0.000000 0.000000 0.000000 1.600000 1.700000
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C H 104.889589 3.971095 -23.823043 26.408093 -11.317522 0.000000 0.000000 0.000000 1.200000 1.300000
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C C 3.962931 24.467772 -51.156024 39.031644 -11.342979 0.000000 0.000000 0.000000 1.600000 1.700000
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H H 38.512100 3.887860 -37.769100 57.083500 -34.512200 0.000000 0.000000 0.000000 0.900000 1.000000
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N N 43.228899 15.004605 -36.621777 29.234888 -8.912743 0.000000 0.000000 0.000000 1.600000 1.700000
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||||
N H 0.625470 28.081241 -63.414297 53.286361 -17.352234 0.000000 0.000000 0.000000 1.300000 1.400000
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O O 10.999870 19.303033 -45.747853 37.946431 -11.935755 0.000000 0.000000 0.000000 1.500000 1.600000
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O H 0.481176 33.175383 -81.158683 74.935408 -26.792315 0.000000 0.000000 0.000000 1.200000 1.300000
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63
examples/latte/data.sucrose_non_opt.lmp
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63
examples/latte/data.sucrose_non_opt.lmp
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@ -0,0 +1,63 @@
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LAMMPS Description
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||||
45 atoms
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3 atom types
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||||
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||||
0.0000000000000000 18.917000000000002 xlo xhi
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||||
0.0000000000000000 17.350999999999999 ylo yhi
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0.0000000000000000 15.472000000000000 zlo zhi
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Masses
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||||
|
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1 15.994915008544922
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||||
2 12.000000000000000
|
||||
3 1.0078250169754028
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||||
|
||||
Atoms
|
||||
|
||||
1 1 1 0.0 11.47359 7.39174 7.26456
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||||
2 1 2 0.0 12.66159 8.24474 7.53356
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||||
3 1 3 0.0 13.49759 7.72474 7.00656
|
||||
4 1 2 0.0 12.92859 8.18374 9.02956
|
||||
5 1 1 0.0 13.69659 9.10274 10.46556
|
||||
6 1 2 0.0 12.83959 10.10474 6.64056
|
||||
7 1 3 0.0 13.24359 10.33074 7.58456
|
||||
8 1 1 0.0 13.17359 9.67874 5.60956
|
||||
9 1 2 0.0 11.20559 10.26374 6.86456
|
||||
10 1 3 0.0 11.22159 11.15674 6.18156
|
||||
11 1 1 0.0 10.78559 10.69674 8.19156
|
||||
12 1 2 0.0 10.23459 9.20474 6.34356
|
||||
13 1 3 0.0 9.23359 9.62574 6.11656
|
||||
14 1 1 0.0 10.73959 8.65074 5.08856
|
||||
15 1 2 0.0 10.18759 8.08774 7.38056
|
||||
16 1 3 0.0 10.03259 8.49174 8.42656
|
||||
17 1 1 0.0 9.22959 7.03374 7.08156
|
||||
18 1 2 0.0 7.79359 7.27874 7.34356
|
||||
19 1 1 0.0 7.44259 8.64274 6.96956
|
||||
20 1 2 0.0 7.01059 9.43674 8.13856
|
||||
21 1 3 0.0 5.95059 9.74974 7.96256
|
||||
22 1 2 0.0 7.08359 8.51474 9.35656
|
||||
23 1 3 0.0 8.19359 8.08474 9.80956
|
||||
24 1 1 0.0 5.86059 8.56174 10.14056
|
||||
25 1 2 0.0 7.34259 7.10674 8.80356
|
||||
26 1 3 0.0 6.37259 6.54074 8.80556
|
||||
27 1 1 0.0 8.32159 6.38474 9.58156
|
||||
28 1 2 0.0 7.89859 10.67174 8.17156
|
||||
29 1 1 0.0 6.06859 12.11474 7.59256
|
||||
30 1 2 0.0 7.47359 7.05174 5.99256
|
||||
31 1 1 0.0 5.66359 6.54374 6.50656
|
||||
32 1 3 0.0 12.00659 8.11374 9.61556
|
||||
33 1 3 0.0 13.35859 7.21774 9.30856
|
||||
34 1 3 0.0 13.67759 8.46774 11.22956
|
||||
35 1 3 0.0 12.44459 9.34474 5.00556
|
||||
36 1 3 0.0 11.54859 11.18274 8.59756
|
||||
37 1 3 0.0 11.00959 7.71574 5.30056
|
||||
38 1 3 0.0 5.09459 8.45474 9.52056
|
||||
39 1 3 0.0 7.92859 6.23074 10.47756
|
||||
40 1 3 0.0 8.53259 10.62974 7.23156
|
||||
41 1 3 0.0 8.58159 10.63874 9.05856
|
||||
42 1 3 0.0 6.42359 13.37374 7.86056
|
||||
43 1 3 0.0 7.58559 6.90074 4.62256
|
||||
44 1 3 0.0 7.35159 5.27974 6.61456
|
||||
45 1 3 0.0 5.22759 6.18974 5.69256
|
||||
41
examples/latte/data.water
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41
examples/latte/data.water
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@ -0,0 +1,41 @@
|
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LAMMPS Description
|
||||
|
||||
24 atoms
|
||||
|
||||
2 atom types
|
||||
|
||||
0.0000000000000000 6.2670000000000003 xlo xhi
|
||||
0.0000000000000000 6.2670000000000003 ylo yhi
|
||||
0.0000000000000000 6.2670000000000003 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 15.994915008544922
|
||||
2 1.0078250169754028
|
||||
|
||||
Atoms
|
||||
|
||||
1 1 1 0.0 3.08800 3.70000 3.12400
|
||||
2 1 2 0.0 4.05800 3.70000 3.12400
|
||||
3 1 2 0.0 2.76400 3.13200 3.84100
|
||||
4 1 1 0.0 2.47000 0.39000 1.36000
|
||||
5 1 2 0.0 1.54000 0.37000 1.73000
|
||||
6 1 2 0.0 2.48000 0.00000 0.44000
|
||||
7 1 1 0.0 1.99300 0.41700 5.25000
|
||||
8 1 2 0.0 2.39300 1.32700 5.16000
|
||||
9 1 2 0.0 0.99300 0.49700 5.31000
|
||||
10 1 1 0.0 2.05300 6.09700 3.48000
|
||||
11 1 2 0.0 2.12300 5.20700 3.02000
|
||||
12 1 2 0.0 1.11300 0.17000 3.40000
|
||||
13 1 1 0.0 4.90000 5.37700 2.14000
|
||||
14 1 2 0.0 5.51000 6.17700 2.18000
|
||||
15 1 2 0.0 3.95000 5.68700 2.21000
|
||||
16 1 1 0.0 0.92000 3.82700 0.56000
|
||||
17 1 2 0.0 0.00000 3.54700 0.27000
|
||||
18 1 2 0.0 1.23000 4.59700 0.00000
|
||||
19 1 1 0.0 0.89000 2.03700 3.41000
|
||||
20 1 2 0.0 0.72000 2.86700 2.87000
|
||||
21 1 2 0.0 1.79000 1.66700 3.19000
|
||||
22 1 1 0.0 4.45000 4.61700 5.43000
|
||||
23 1 2 0.0 4.75000 3.89700 4.81000
|
||||
24 1 2 0.0 4.06000 4.21700 6.26000
|
||||
43
examples/latte/in.latte.sucrose.min
Normal file
43
examples/latte/in.latte.sucrose.min
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@ -0,0 +1,43 @@
|
||||
# simple water model with LATTE
|
||||
|
||||
units metal
|
||||
atom_style full
|
||||
atom_modify sort 0 0.0 # turn off sorting of the coordinates
|
||||
|
||||
read_data data.sucrose_non_opt.lmp
|
||||
|
||||
# replicate system if requested
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable nrep equal v_x*v_y*v_z
|
||||
if "${nrep} > 1" then "replicate $x $y $z"
|
||||
|
||||
# initialize system
|
||||
|
||||
velocity all create 0.0 87287 loop geom
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
timestep 0.00025
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
fix 2 all latte NULL
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo_style custom step temp pe etotal
|
||||
|
||||
# minimization
|
||||
|
||||
thermo 1
|
||||
min_style cg
|
||||
min_modify dmax 0.1
|
||||
min_modify line quadratic
|
||||
minimize 1.0e-6 1.0e-6 10000 10000
|
||||
40
examples/latte/in.latte.water
Normal file
40
examples/latte/in.latte.water
Normal file
@ -0,0 +1,40 @@
|
||||
# simple water model with LATTE
|
||||
|
||||
units metal
|
||||
atom_style full
|
||||
atom_modify sort 0 0.0 # turn off sorting of the coordinates
|
||||
|
||||
read_data data.water
|
||||
|
||||
# replicate system if requested
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable nrep equal v_x*v_y*v_z
|
||||
if "${nrep} > 1" then "replicate $x $y $z"
|
||||
|
||||
# initialize system
|
||||
|
||||
velocity all create 0.0 87287 loop geom
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
timestep 0.00025
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
fix 2 all latte NULL
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo_style custom step temp pe etotal
|
||||
|
||||
# dynamics
|
||||
|
||||
thermo 10
|
||||
run 100
|
||||
41
examples/latte/in.latte.water.min
Normal file
41
examples/latte/in.latte.water.min
Normal file
@ -0,0 +1,41 @@
|
||||
# simple water model with LATTE
|
||||
|
||||
units metal
|
||||
atom_style full
|
||||
atom_modify sort 0 0.0 # turn off sorting of the coordinates
|
||||
|
||||
read_data data.water
|
||||
|
||||
# replicate system if requested
|
||||
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable nrep equal v_x*v_y*v_z
|
||||
if "${nrep} > 1" then "replicate $x $y $z"
|
||||
|
||||
# initialize system
|
||||
|
||||
velocity all create 0.0 87287 loop geom
|
||||
|
||||
pair_style zero 1.0
|
||||
pair_coeff * *
|
||||
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
timestep 0.00025
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
fix 2 all latte NULL
|
||||
fix_modify 2 energy yes
|
||||
|
||||
thermo_style custom step temp pe etotal
|
||||
|
||||
# minimization
|
||||
|
||||
thermo 1
|
||||
min_style fire
|
||||
minimize 1.0e-9 1.0e-9 1000 1000
|
||||
39
examples/latte/latte.in
Normal file
39
examples/latte/latte.in
Normal file
@ -0,0 +1,39 @@
|
||||
LATTE INPUT FILE
|
||||
================
|
||||
#This input file resumes the content of MDcontroller and TBparam/control.in
|
||||
#The parser will only read it if it's present inside the running folder.
|
||||
#In case this file is not present Latte will read the two files as original.
|
||||
#The order of the kewords is not important in this file.
|
||||
#To get a full description of these keywords please see:
|
||||
## https://github.com/lanl/LATTE/blob/master/Manual/LATTE_manual.pdf
|
||||
|
||||
#General controls
|
||||
CONTROL{
|
||||
xControl= 1
|
||||
BASISTYPE= NONORTHO
|
||||
COORDSFILE= "./coords.dat"
|
||||
KBT= 0.0
|
||||
ENTROPYKIND= 1
|
||||
PPOTON= 1
|
||||
SPINON= 0 SPINTOL= 1.0e-4
|
||||
ELECTRO= 1 ELECMETH= 0 ELEC_QTOL= 1.0e-8
|
||||
MAXSCF= 450
|
||||
BREAKTOL= 1.0E-6 MINSP2ITER= 22 SP2CONV= REL
|
||||
FULLQCONV= 1 QITER= 3
|
||||
QMIX= 0.25 SPINMIX= 0.25 MDMIX= 0.25
|
||||
SPARSEON= 1 THRESHOLDON= 1 NUMTHRESH= 1.0e-6 FILLINSTOP= 100 BLKSZ= 4
|
||||
MSPARSE= 1500
|
||||
RELAX= 0 RELAXTYPE= SD MAXITER= 100000 RLXFTOL= 0.0000001
|
||||
SKIN= 1.0
|
||||
CHARGE= 0
|
||||
XBO= 1
|
||||
XBODISON= 1
|
||||
XBODISORDER= 5
|
||||
KON= 0
|
||||
}
|
||||
|
||||
#Controls for QMD (if using lammps MAXITER must be set to -1)
|
||||
MDCONTROL{
|
||||
MAXITER= -1
|
||||
}
|
||||
|
||||
Reference in New Issue
Block a user