add examples for demonstrating the use of atom style template
This commit is contained in:
Axel Kohlmeyer
@ -111,6 +111,7 @@ srd: stochastic rotation dynamics (SRD) particles as solvent
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steinhardt: Steinhardt-Nelson Q_l and W_l parameters usng orientorder/atom
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streitz: Streitz-Mintmire potential for Al2O3
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tad: temperature-accelerated dynamics of vacancy diffusion in bulk Si
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template: examples for using atom_style template and comparing to atom style molecular
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threebody: regression test input for a variety of manybody potentials
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vashishta: models using the Vashishta potential
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voronoi: Voronoi tesselation via compute voronoi/atom command
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63
examples/template/co2.mol
Normal file
63
examples/template/co2.mol
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@ -0,0 +1,63 @@
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# CO2 molecule file. TraPPE model.
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3 atoms
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2 bonds
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1 angles
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Coords
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1 0.0 0.0 0.0
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2 -1.16 0.0 0.0
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3 1.16 0.0 0.0
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Types
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1 1
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2 2
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3 2
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Charges
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1 0.7
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2 -0.35
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3 -0.35
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Bonds
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1 1 1 2
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2 1 1 3
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Angles
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1 1 2 1 3
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Special Bond Counts
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1 2 0 0
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2 1 1 0
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3 1 1 0
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Special Bonds
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1 2 3
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2 1 3
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3 1 2
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Shake Flags
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1 0
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2 0
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3 0
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Shake Atoms
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1
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2
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3
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Shake Bond Types
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1
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2
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3
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68
examples/template/cyclohexane.mol
Normal file
68
examples/template/cyclohexane.mol
Normal file
@ -0,0 +1,68 @@
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LAMMPS molecule file. Cyclohexane(UA)
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6 atoms
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6 bonds
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6 angles
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6 dihedrals
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Coords
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1 0.000000 0.000000 0.000000
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2 0.000000 0.000000 1.536000
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3 1.431000 0.000000 2.094000
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4 2.247000 1.176000 1.536000
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5 2.247000 1.176000 0.000000
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6 0.815000 1.176000 -0.557000
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Types
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1 1
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2 1
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3 1
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4 1
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5 1
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6 1
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Bonds
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1 1 1 6
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2 1 1 2
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3 1 2 3
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4 1 3 4
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5 1 4 5
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6 1 5 6
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Angles
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1 1 2 1 6
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2 1 1 2 3
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3 1 2 3 4
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4 1 3 4 5
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5 1 4 5 6
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6 1 1 6 5
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Dihedrals
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1 1 2 1 6 5
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2 1 6 1 2 3
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3 1 1 2 3 4
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4 1 2 3 4 5
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5 1 3 4 5 6
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6 1 4 5 6 1
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Special Bond Counts
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1 2 2 1
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2 2 2 1
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3 2 2 1
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4 2 2 1
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5 2 2 1
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6 2 2 1
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Special Bonds
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1 2 6 3 5 4
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2 3 1 4 6 5
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3 4 2 5 1 6
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4 5 3 6 2 1
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5 6 4 1 3 2
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6 1 5 2 4 3
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428
examples/template/h2o-co2.data
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428
examples/template/h2o-co2.data
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@ -0,0 +1,428 @@
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LAMMPS data file via write_data, version 22 Oct 2020, timestep = 0
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384 atoms
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4 atom types
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2 bond types
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2 angle types
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-10.0 10.0 xlo xhi
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-10.0 10.0 ylo yhi
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-10.0 10.0 zlo zhi
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Masses
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1 15.9994
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2 1
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3 12.0107
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4 15.9994
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PairIJ Coeffs # lj/cut/coul/cut
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1 1 0.15535 3.166 14
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1 2 0 0 14
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1 3 0.0912928 2.983 14
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1 4 0.156159 3.108 14
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2 2 0 0 14
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2 3 0 1.4 14
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2 4 0 1.525 14
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3 3 0.053649 2.8 14
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3 4 0.0917684 2.925 14
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4 4 0.156973 3.05 14
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Bond Coeffs # harmonic
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1 1000 1
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2 1000 1.16
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Angle Coeffs # harmonic
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1 100 109.47
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2 100 180
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Atoms # hybrid
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1 1 -9.915603425183674 9.642074614047225 9.886373806057632 1 1 1 -0.8472 0 -1 -1
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2 2 -9.955077256991814 9.952071397945474 -9.163725932085827 1 1 2 0.4236 0 -1 0
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3 2 9.870680682175488 -9.594146011992699 9.277352126028195 1 1 3 0.4236 -1 0 -1
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4 1 -5.377413308169694 -9.975845367284359 9.928445655374531 2 1 1 -0.8472 0 0 -1
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5 2 -4.868089392205772 9.173804835517629 -9.939414010387674 2 1 2 0.4236 0 -1 0
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6 2 -4.754497299624534 -9.19795946823327 -9.989031644986857 2 1 3 0.4236 0 0 0
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7 1 0.2862645369165933 -9.834750023705109 9.802796207089045 3 1 1 -0.8472 0 0 -1
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8 2 -0.20506315473823142 -9.416615546409432 -9.433183272761259 3 1 2 0.4236 0 0 0
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9 2 -0.08120138217836187 9.25136557011454 9.630387065672213 3 1 3 0.4236 0 -1 -1
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10 1 4.954244542709665 9.733846444128554 9.725750116636055 4 1 1 -0.8472 0 -1 -1
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11 2 5.314186858355006 9.562011307112279 -9.357254293410282 4 1 2 0.4236 0 -1 0
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12 2 4.731568598935329 -9.295857751240833 9.631504176774227 4 1 3 0.4236 0 0 -1
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13 1 -9.885042196263848 -5.366646729833796 -9.977658232783796 5 1 1 -0.8472 0 0 0
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14 2 -9.499988310087788 -4.607821917003056 -9.452410572081622 5 1 2 0.4236 0 0 0
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15 2 9.385030506351637 -5.025531353163147 9.430068804865417 5 1 3 0.4236 -1 0 -1
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16 1 -5.3381930384891545 -4.817187821023332 -9.98130637447481 6 1 1 -0.8472 0 0 0
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17 2 -4.814226078866727 -5.143876565241305 -9.194731656774504 6 1 2 0.4236 0 0 0
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18 2 -4.8475808826441185 -5.038935613735363 9.176038031249314 6 1 3 0.4236 0 0 -1
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19 1 -0.17437585816420464 -5.00267209015634 -9.656881659301497 7 1 1 -0.8472 0 0 0
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20 2 0.5142734508723548 -5.661488493390246 -9.959684850984493 7 1 2 0.4236 0 0 0
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21 2 -0.3398975927081498 -4.335839416453415 9.61656651028599 7 1 3 0.4236 0 0 -1
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22 1 5.027007160081784 -5.376778433628809 -9.926156239555816 8 1 1 -0.8472 0 0 0
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23 2 5.040872603784614 -4.651165711374701 -9.238216835484566 8 1 2 0.4236 0 0 0
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24 2 4.932120236133603 -4.97205585499649 9.164373075040384 8 1 3 0.4236 0 0 -1
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25 1 -9.774983021942727 -0.11627625671956153 9.710187185567547 9 1 1 -0.8472 0 0 -1
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26 2 -9.547719336441409 -0.18624762678535645 -9.31851372479864 9 1 2 0.4236 0 0 0
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27 2 9.322702358384136 0.30252388350491777 9.608326539231093 9 1 3 0.4236 -1 0 -1
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28 1 -4.839301125374413 -0.3224292196811998 9.864502598955395 10 1 1 -0.8472 0 0 -1
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29 2 -4.437095111731628 0.2761002399087885 -9.442706303026958 10 1 2 0.4236 0 0 0
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30 2 -5.723603762893959 0.04632897977241136 9.578203704071562 10 1 3 0.4236 0 0 -1
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31 1 0.3575211513985558 0.13924369294039318 -9.96943701619651 11 1 1 -0.8472 0 0 0
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32 2 -0.15738037709944985 -0.29662855771206287 -9.231291709389254 11 1 2 0.4236 0 0 0
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33 2 -0.20014077429910587 0.1573848647716694 9.200728725585764 11 1 3 0.4236 0 0 -1
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34 1 4.945607877161568 0.17822976107332558 -9.663221252242849 12 1 1 -0.8472 0 0 0
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35 2 5.686261102802035 -0.4628832126235319 -9.864153208899683 12 1 2 0.4236 0 0 0
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36 2 4.368131020036397 0.284653451550206 9.527374461142534 12 1 3 0.4236 0 0 -1
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37 1 9.834131265901467 5.002816508870191 -9.652690475186276 13 1 1 -0.8472 -1 0 0
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38 2 -9.523525531039581 4.309893511844079 -9.980134556788492 13 1 2 0.4236 0 0 0
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39 2 9.689394265138116 5.68728997928573 9.63282503197477 13 1 3 0.4236 -1 0 -1
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40 1 -4.896522832471423 4.844697230053857 -9.6633729049121 14 1 1 -0.8472 0 0 0
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41 2 -5.719481843054487 5.391203391339132 -9.818408963548082 14 1 2 0.4236 0 0 0
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42 2 -4.383995324474091 4.764099378607011 9.481781868460182 14 1 3 0.4236 0 0 -1
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43 1 0.08644475731548724 4.625177647828908 -9.986591646424854 15 1 1 -0.8472 0 0 0
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44 2 0.483199632298402 5.33056133050579 -9.399236450405876 15 1 2 0.4236 0 0 0
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45 2 -0.5696443896138887 5.044261021665302 9.38582809683073 15 1 3 0.4236 0 0 -1
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46 1 5.279904505775219 4.8738580855036995 9.767866502301072 16 1 1 -0.8472 0 0 -1
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47 2 5.051646557564443 5.834165665231483 9.928098703484146 16 1 2 0.4236 0 0 -1
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48 2 4.6684489366603374 4.291976249264819 -9.695965205785217 16 1 3 0.4236 0 0 0
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49 1 9.908445669769623 9.636632008310487 -4.912103567014368 17 1 1 -0.8472 -1 -1 0
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50 2 -9.305514433129819 -9.862297561377305 -4.550114063115585 17 1 2 0.4236 0 0 0
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51 2 9.397068763360195 -9.774334446933182 -5.537782369870047 17 1 3 0.4236 -1 0 0
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52 1 -5.201907594124834 -9.68877920222961 -5.102563220356437 18 1 1 -0.8472 0 0 0
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53 2 -4.940302726022812 9.565133612451614 -5.714840528272083 18 1 2 0.4236 0 -1 0
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54 2 -4.857789679852353 -9.876354410222005 -4.182596251371481 18 1 3 0.4236 0 0 0
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55 1 0.37327634941779875 -9.91440084751388 -4.961505484040201 19 1 1 -0.8472 0 0 0
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56 2 -0.024482580199505652 9.563262486125167 -5.715772636834634 19 1 2 0.4236 0 -1 0
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57 2 -0.34879376921829297 -9.648861638611287 -4.322721879125167 19 1 3 0.4236 0 0 0
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58 1 5.099017423466195 9.70150361815792 -4.778099717040957 20 1 1 -0.8472 0 -1 0
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59 2 5.136067712418359 9.715462771782358 -5.77729895393951 20 1 2 0.4236 0 -1 0
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60 2 4.764914864115446 -9.416966389940278 -4.444601329019534 20 1 3 0.4236 0 0 0
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61 1 9.67209962879851 -5.197853819118096 -5.0384641199861475 21 1 1 -0.8472 -1 0 0
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62 2 9.738936599885 -4.205377815142725 -4.936039036490629 21 1 2 0.4236 -1 0 0
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63 2 -9.41103622868351 -5.5967683657391785 -5.025496843523223 21 1 3 0.4236 0 0 0
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64 1 -4.689795490189235 -5.165487837213749 -4.843375565356555 22 1 1 -0.8472 0 0 0
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65 2 -4.832160266019467 -5.015491947934958 -5.82174165261749 22 1 2 0.4236 0 0 0
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66 2 -5.478044243791298 -4.819020214851294 -4.334882782025955 22 1 3 0.4236 0 0 0
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67 1 -0.0615634035841769 -4.677472055633765 -5.200823176306976 23 1 1 -0.8472 0 0 0
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68 2 -0.6036354578743581 -5.514703146142694 -5.272716750031286 23 1 2 0.4236 0 0 0
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69 2 0.6651988614585344 -4.807824798223541 -4.526460073661738 23 1 3 0.4236 0 0 0
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70 1 4.802754604301762 -5.1046044449424395 -5.313522630242427 24 1 1 -0.8472 0 0 0
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71 2 4.674742935683063 -5.484552334539641 -4.397433491136363 24 1 2 0.4236 0 0 0
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72 2 5.522502460015175 -4.410843220517918 -5.28904387862121 24 1 3 0.4236 0 0 0
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73 1 -9.83451039343324 -0.34326467353508094 -4.9458998177338245 25 1 1 -0.8472 0 0 0
|
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74 2 -9.500257580872022 0.5235593797386398 -4.5759568290706625 25 1 2 0.4236 0 0 0
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75 2 9.334767974305263 -0.18029470620355853 -5.478143353195513 25 1 3 0.4236 -1 0 0
|
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76 1 -5.307686388170551 -0.09393136703842697 -4.788693917454198 26 1 1 -0.8472 0 0 0
|
||||
77 2 -5.322666676950796 0.48158209129479823 -5.606328644655405 26 1 2 0.4236 0 0 0
|
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78 2 -4.369646934878654 -0.38765072425637087 -4.604977437890398 26 1 3 0.4236 0 0 0
|
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79 1 0.25915920502631956 0.1183661006970869 -5.258786105415057 27 1 1 -0.8472 0 0 0
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80 2 0.4129987454382328 0.060712811699061064 -4.2723905503898125 27 1 2 0.4236 0 0 0
|
||||
81 2 -0.6721579504645518 -0.17907891239614798 -5.46882334419513 27 1 3 0.4236 0 0 0
|
||||
82 1 4.645093317547853 -0.032892978577141976 -5.145270693572841 28 1 1 -0.8472 0 0 0
|
||||
83 2 5.384532151641317 -0.6939822880761514 -5.272384156276919 28 1 2 0.4236 0 0 0
|
||||
84 2 4.9703745308108305 0.7268752666532926 -4.58234515015024 28 1 3 0.4236 0 0 0
|
||||
85 1 -9.935887941471492 4.620929536576184 -4.981574381668706 29 1 1 -0.8472 0 0 0
|
||||
86 2 -9.510577225229298 5.307736013867678 -4.392189656467925 29 1 2 0.4236 0 0 0
|
||||
87 2 9.44646516670079 5.071334449556138 -5.626235961863369 29 1 3 0.4236 -1 0 0
|
||||
88 1 -5.008590477951656 4.617494616944972 -5.041953680678674 30 1 1 -0.8472 0 0 0
|
||||
89 2 -4.783022517847073 5.100600801092718 -4.195966560733896 30 1 2 0.4236 0 0 0
|
||||
90 2 -5.2083870042012705 5.281904581962309 -5.762079758587429 30 1 3 0.4236 0 0 0
|
||||
91 1 -0.10236681102215972 4.670575674519795 -5.170718849231903 31 1 1 -0.8472 0 0 0
|
||||
92 2 0.6714005117953412 5.244086072416178 -5.439673586212998 31 1 2 0.4236 0 0 0
|
||||
93 2 -0.569033700773181 5.085338253064027 -4.389607564555099 31 1 3 0.4236 0 0 0
|
||||
94 1 4.793442916655695 4.895053625339889 -4.692648888946219 32 1 1 -0.8472 0 0 0
|
||||
95 2 5.78790922296981 4.82542619694358 -4.771105779790033 32 1 2 0.4236 0 0 0
|
||||
96 2 4.418647860374495 5.279520177716531 -5.536245331263747 32 1 3 0.4236 0 0 0
|
||||
97 1 -9.972346516877309 9.813426641245107 0.3355144443598525 33 1 1 -0.8472 0 -1 0
|
||||
98 2 9.902394946876838 9.380578255545881 -0.5571889055807204 33 1 2 0.4236 -1 -1 0
|
||||
99 2 -9.930048429999529 -9.194004896790988 0.22167446122086756 33 1 3 0.4236 0 0 0
|
||||
100 1 -5.055092848610487 9.62043108608943 -0.032194616393628146 34 1 1 -0.8472 0 -1 0
|
||||
101 2 -4.242564100118214 -9.944998495531546 0.35627968294091067 34 1 2 0.4236 0 0 0
|
||||
102 2 -5.702343051271298 -9.675432590557886 -0.3240850665472822 34 1 3 0.4236 0 0 0
|
||||
103 1 -0.16422105747150104 -9.658585046539034 0.06790839076424156 35 1 1 -0.8472 0 0 0
|
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104 2 0.24178705531724526 9.747651563696497 0.7625803609956086 35 1 2 0.4236 0 -1 0
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||||
105 2 -0.07756599784574403 9.910933482842538 -0.8304887517598495 35 1 3 0.4236 0 -1 0
|
||||
106 1 5.252774480020046 -9.731538918744256 0.11035391158265477 36 1 1 -0.8472 0 0 0
|
||||
107 2 4.897417222941987 -9.843232415673553 -0.8176614328409508 36 1 2 0.4236 0 0 0
|
||||
108 2 4.849808297037967 9.57477133441781 0.7073075212582953 36 1 3 0.4236 0 -1 0
|
||||
109 1 -9.974235357986496 -5.3824393899672485 -0.03493668449344743 37 1 1 -0.8472 0 0 0
|
||||
110 2 -9.424638978370009 -4.718082489267676 -0.5414348828173003 37 1 2 0.4236 0 0 0
|
||||
111 2 9.398874336356506 -4.8994781207650755 0.5763715673107472 37 1 3 0.4236 -1 0 0
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112 1 -4.9279099757557 -5.3611565776237216 -0.11186255201619967 38 1 1 -0.8472 0 0 0
|
||||
113 2 -4.312252322613385 -4.791643655121096 0.43273581570979314 38 1 2 0.4236 0 0 0
|
||||
114 2 -5.759837701630914 -4.847199767255183 -0.3208732636935932 38 1 3 0.4236 0 0 0
|
||||
115 1 -0.1760601646477313 -4.705054107276162 0.17364911312630318 39 1 1 -0.8472 0 0 0
|
||||
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|
||||
297 4 3.645815970643011 -7.67004417492298 2.5615689856516917 99 2 3 -0.35 0 0 0
|
||||
298 3 7.5 -7.5 2.5 100 2 1 0.7 0 0 0
|
||||
299 4 6.890528994434403 -6.53074739493991 2.6862645456309138 100 2 2 -0.35 0 0 0
|
||||
300 4 8.109471005565597 -8.46925260506009 2.3137354543690862 100 2 3 -0.35 0 0 0
|
||||
301 3 -7.5 -2.5 2.5 101 2 1 0.7 0 0 0
|
||||
302 4 -8.402413809003143 -1.9960963670464098 1.9733782704667298 101 2 2 -0.35 0 0 0
|
||||
303 4 -6.597586190996857 -3.00390363295359 3.0266217295332702 101 2 3 -0.35 0 0 0
|
||||
304 3 -2.5 -2.5 2.5 102 2 1 0.7 0 0 0
|
||||
305 4 -3.1146628699497816 -3.0155291909493633 1.6621341338948146 102 2 2 -0.35 0 0 0
|
||||
306 4 -1.8853371300502184 -1.9844708090506367 3.3378658661051857 102 2 3 -0.35 0 0 0
|
||||
307 3 2.5 -2.5 2.5 103 2 1 0.7 0 0 0
|
||||
308 4 1.7091896213819626 -3.348636804240857 2.505875334702054 103 2 2 -0.35 0 0 0
|
||||
309 4 3.2908103786180374 -1.651363195759143 2.494124665297946 103 2 3 -0.35 0 0 0
|
||||
310 3 7.5 -2.5 2.5 104 2 1 0.7 0 0 0
|
||||
311 4 7.846121450678692 -1.863352310559478 1.5941966764743452 104 2 2 -0.35 0 0 0
|
||||
312 4 7.153878549321308 -3.136647689440522 3.405803323525655 104 2 3 -0.35 0 0 0
|
||||
313 3 -7.5 2.5 2.5 105 2 1 0.7 0 0 0
|
||||
314 4 -7.415505185247761 1.3693275996894718 2.2549682684711767 105 2 2 -0.35 0 0 0
|
||||
315 4 -7.584494814752239 3.6306724003105284 2.7450317315288233 105 2 3 -0.35 0 0 0
|
||||
316 3 -2.5 2.5 2.5 106 2 1 0.7 0 0 0
|
||||
317 4 -1.6566227058869707 3.061399569140947 3.0649294323567706 106 2 2 -0.35 0 0 0
|
||||
318 4 -3.3433772941130293 1.938600430859053 1.9350705676432294 106 2 3 -0.35 0 0 0
|
||||
319 3 2.5 2.5 2.5 107 2 1 0.7 0 0 0
|
||||
320 4 1.8018606440593001 1.6504313913225857 2.1306294288432994 107 2 2 -0.35 0 0 0
|
||||
321 4 3.1981393559407 3.3495686086774143 2.8693705711567006 107 2 3 -0.35 0 0 0
|
||||
322 3 7.5 2.5 2.5 108 2 1 0.7 0 0 0
|
||||
323 4 7.454398927291544 1.350628262336051 2.3501162089244056 108 2 2 -0.35 0 0 0
|
||||
324 4 7.545601072708456 3.649371737663949 2.6498837910755944 108 2 3 -0.35 0 0 0
|
||||
325 3 -7.5 7.5 2.5 109 2 1 0.7 0 0 0
|
||||
326 4 -7.639487922633921 8.47694083419964 1.8903035788914426 109 2 2 -0.35 0 0 0
|
||||
327 4 -7.360512077366079 6.523059165800359 3.1096964211085574 109 2 3 -0.35 0 0 0
|
||||
328 3 -2.5 7.5 2.5 110 2 1 0.7 0 0 0
|
||||
329 4 -3.653132322293053 7.551646962835361 2.385028531744119 110 2 2 -0.35 0 0 0
|
||||
330 4 -1.3468676777069468 7.448353037164639 2.614971468255881 110 2 3 -0.35 0 0 0
|
||||
331 3 2.5 7.5 2.5 111 2 1 0.7 0 0 0
|
||||
332 4 2.8364898316331035 7.678145325449636 3.595736663723528 111 2 2 -0.35 0 0 0
|
||||
333 4 2.1635101683668965 7.321854674550364 1.4042633362764718 111 2 3 -0.35 0 0 0
|
||||
334 3 7.5 7.5 2.5 112 2 1 0.7 0 0 0
|
||||
335 4 6.479552888446932 7.807048742079671 2.958267130078399 112 2 2 -0.35 0 0 0
|
||||
336 4 8.520447111553068 7.192951257920329 2.041732869921601 112 2 3 -0.35 0 0 0
|
||||
337 3 -7.5 -7.5 7.5 113 2 1 0.7 0 0 0
|
||||
338 4 -7.6197834102650095 -6.871306065029082 8.46746879575316 113 2 2 -0.35 0 0 0
|
||||
339 4 -7.3802165897349905 -8.128693934970917 6.53253120424684 113 2 3 -0.35 0 0 0
|
||||
340 3 -2.5 -7.5 7.5 114 2 1 0.7 0 0 0
|
||||
341 4 -3.6462582687736766 -7.5580642653980155 7.6682870237177 114 2 2 -0.35 0 0 0
|
||||
342 4 -1.3537417312263231 -7.4419357346019845 7.3317129762823 114 2 3 -0.35 0 0 0
|
||||
343 3 2.5 -7.5 7.5 115 2 1 0.7 0 0 0
|
||||
344 4 1.3734554259918312 -7.525081897193473 7.224558134616524 115 2 2 -0.35 0 0 0
|
||||
345 4 3.626544574008169 -7.474918102806527 7.775441865383476 115 2 3 -0.35 0 0 0
|
||||
346 3 7.5 -7.5 7.5 116 2 1 0.7 0 0 0
|
||||
347 4 8.414658305507071 -7.215850731078148 8.154415294089395 116 2 2 -0.35 0 0 0
|
||||
348 4 6.585341694492928 -7.784149268921852 6.845584705910605 116 2 3 -0.35 0 0 0
|
||||
349 3 -7.5 -2.5 7.5 117 2 1 0.7 0 0 0
|
||||
350 4 -8.645413670915179 -2.6453055222059496 7.611865221123771 117 2 2 -0.35 0 0 0
|
||||
351 4 -6.354586329084821 -2.3546944777940504 7.388134778876229 117 2 3 -0.35 0 0 0
|
||||
352 3 -2.5 -2.5 7.5 118 2 1 0.7 0 0 0
|
||||
353 4 -2.601509341816184 -1.9084001398846042 8.492625538174135 118 2 2 -0.35 0 0 0
|
||||
354 4 -2.398490658183816 -3.091599860115396 6.507374461825866 118 2 3 -0.35 0 0 0
|
||||
355 3 2.5 -2.5 7.5 119 2 1 0.7 0 0 0
|
||||
356 4 2.2485924178438 -2.364925227008703 8.624343823452472 119 2 2 -0.35 0 0 0
|
||||
357 4 2.7514075821562 -2.635074772991297 6.375656176547529 119 2 3 -0.35 0 0 0
|
||||
358 3 7.5 -2.5 7.5 120 2 1 0.7 0 0 0
|
||||
359 4 6.784038999809617 -1.8413110953985297 8.13176639128819 120 2 2 -0.35 0 0 0
|
||||
360 4 8.215961000190383 -3.1586889046014703 6.86823360871181 120 2 3 -0.35 0 0 0
|
||||
361 3 -7.5 2.5 7.5 121 2 1 0.7 0 0 0
|
||||
362 4 -7.537548740040521 3.6593910439642627 7.49841908354891 121 2 2 -0.35 0 0 0
|
||||
363 4 -7.462451259959479 1.340608956035737 7.50158091645109 121 2 3 -0.35 0 0 0
|
||||
364 3 -2.5 2.5 7.5 122 2 1 0.7 0 0 0
|
||||
365 4 -1.649121019955475 1.7301813803117607 7.3297523741731405 122 2 2 -0.35 0 0 0
|
||||
366 4 -3.350878980044525 3.2698186196882393 7.6702476258268595 122 2 3 -0.35 0 0 0
|
||||
367 3 2.5 2.5 7.5 123 2 1 0.7 0 0 0
|
||||
368 4 3.2379752354871414 1.771831388509018 6.979651054534562 123 2 2 -0.35 0 0 0
|
||||
369 4 1.7620247645128586 3.228168611490982 8.020348945465438 123 2 3 -0.35 0 0 0
|
||||
370 3 7.5 2.5 7.5 124 2 1 0.7 0 0 0
|
||||
371 4 7.334452984137467 1.3548227605993108 7.582239138478142 124 2 2 -0.35 0 0 0
|
||||
372 4 7.665547015862533 3.645177239400689 7.417760861521858 124 2 3 -0.35 0 0 0
|
||||
373 3 -7.5 7.5 7.5 125 2 1 0.7 0 0 0
|
||||
374 4 -8.324913544328572 8.31456508779972 7.459982977108372 125 2 2 -0.35 0 0 0
|
||||
375 4 -6.675086455671429 6.6854349122002805 7.540017022891628 125 2 3 -0.35 0 0 0
|
||||
376 3 -2.5 7.5 7.5 126 2 1 0.7 0 0 0
|
||||
377 4 -2.8359455597090397 6.421926623286971 7.76551530150699 126 2 2 -0.35 0 0 0
|
||||
378 4 -2.1640544402909603 8.578073376713029 7.23448469849301 126 2 3 -0.35 0 0 0
|
||||
379 3 2.5 7.5 7.5 127 2 1 0.7 0 0 0
|
||||
380 4 1.4186788873677927 7.288670506833647 7.862883585594468 127 2 2 -0.35 0 0 0
|
||||
381 4 3.5813211126322075 7.711329493166353 7.137116414405532 127 2 3 -0.35 0 0 0
|
||||
382 3 7.5 7.5 7.5 128 2 1 0.7 0 0 0
|
||||
383 4 6.9664096100856385 6.501410755376355 7.247609793547735 128 2 2 -0.35 0 0 0
|
||||
384 4 8.03359038991436 8.498589244623645 7.752390206452265 128 2 3 -0.35 0 0 0
|
||||
|
||||
62
examples/template/h2o.mol
Normal file
62
examples/template/h2o.mol
Normal file
@ -0,0 +1,62 @@
|
||||
# Water molecule. SPC/E model.
|
||||
|
||||
3 atoms
|
||||
2 bonds
|
||||
1 angles
|
||||
|
||||
Coords
|
||||
|
||||
1 1.12456 0.09298 1.27452
|
||||
2 1.53683 0.75606 1.89928
|
||||
3 0.49482 0.56390 0.65678
|
||||
|
||||
Types
|
||||
|
||||
1 1
|
||||
2 2
|
||||
3 2
|
||||
|
||||
Charges
|
||||
|
||||
1 -0.8472
|
||||
2 0.4236
|
||||
3 0.4236
|
||||
|
||||
Bonds
|
||||
|
||||
1 1 1 2
|
||||
2 1 1 3
|
||||
|
||||
Angles
|
||||
|
||||
1 1 2 1 3
|
||||
|
||||
Shake Flags
|
||||
|
||||
1 1
|
||||
2 1
|
||||
3 1
|
||||
|
||||
Shake Atoms
|
||||
|
||||
1 1 2 3
|
||||
2 1 2 3
|
||||
3 1 2 3
|
||||
|
||||
Shake Bond Types
|
||||
|
||||
1 1 1 1
|
||||
2 1 1 1
|
||||
3 1 1 1
|
||||
|
||||
Special Bond Counts
|
||||
|
||||
1 2 0 0
|
||||
2 1 1 0
|
||||
3 1 1 0
|
||||
|
||||
Special Bonds
|
||||
|
||||
1 2 3
|
||||
2 1 3
|
||||
3 1 2
|
||||
29
examples/template/in.hybrid
Normal file
29
examples/template/in.hybrid
Normal file
@ -0,0 +1,29 @@
|
||||
# demo using atom style hybrid template charge to simulate a h2o/co2 mixture
|
||||
|
||||
units real
|
||||
molecule twomols h2o.mol co2.mol offset 2 1 1 0 0
|
||||
atom_style hybrid template twomols charge
|
||||
boundary p p p
|
||||
pair_style lj/cut/coul/long 12
|
||||
pair_modify mix arithmetic tail yes
|
||||
kspace_style pppm 0.0001
|
||||
pair_style lj/cut/coul/long 12
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
|
||||
read_data h2o-co2.data
|
||||
|
||||
group h2o type 1 2
|
||||
group co2 type 3 4
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 1 check yes
|
||||
timestep 1.0
|
||||
|
||||
velocity all create 300.0 34672
|
||||
thermo 100
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all shake 1.0e-4 1000 500 b 1 a 1 mol twomols
|
||||
#dump 1 all custom 100 h2o-co2.lammpstrj id mol xu yu zu
|
||||
|
||||
run 2500
|
||||
21
examples/template/in.mol-data-mix
Normal file
21
examples/template/in.mol-data-mix
Normal file
@ -0,0 +1,21 @@
|
||||
# demo for atom style template simulating a cyclohexane methane mixture
|
||||
# part 2: continuing from data file
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
molecule cychex cyclohexane.mol
|
||||
atom_style molecular
|
||||
|
||||
pair_style lj/cut 12.0
|
||||
pair_modify mix geometric tail yes
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style harmonic
|
||||
|
||||
read_data molecular-mix.data
|
||||
|
||||
thermo 100
|
||||
|
||||
fix 1 all nvt temp 300.0 300.0 1.0
|
||||
# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu
|
||||
run 2000
|
||||
41
examples/template/in.molecular-mix
Normal file
41
examples/template/in.molecular-mix
Normal file
@ -0,0 +1,41 @@
|
||||
# demo for atom style template simulating a cyclohexane methane mixture
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
molecule cychex cyclohexane.mol
|
||||
atom_style molecular
|
||||
|
||||
pair_style lj/cut 12.0
|
||||
pair_modify mix geometric tail yes
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style harmonic
|
||||
|
||||
lattice sc 6.0
|
||||
variable boxlen index 4.0
|
||||
region box block -${boxlen} ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
|
||||
create_box 2 box bond/types 1 angle/types 1 dihedral/types 1 extra/special/per/atom 6 &
|
||||
extra/bond/per/atom 2 extra/angle/per/atom 2 extra/dihedral/per/atom 2
|
||||
|
||||
create_atoms 0 box mol cychex 734594
|
||||
create_atoms 2 random 800 495437 box
|
||||
|
||||
mass 1 14.027
|
||||
mass 2 16.043
|
||||
|
||||
pair_coeff 1 1 0.1180 3.905
|
||||
pair_coeff 2 2 0.2940 3.730
|
||||
|
||||
bond_coeff 1 260.00 1.5260
|
||||
angle_coeff 1 63.0 112.40
|
||||
dihedral_coeff 1 2.0 1 3
|
||||
|
||||
thermo 100
|
||||
minimize 0.001 0.001 500 1000
|
||||
reset_timestep 0
|
||||
|
||||
velocity all create 100.0 6234235
|
||||
fix 1 all nvt temp 100.0 300.0 1.0
|
||||
# dump 1 all custom 100 cychex-methane.lammpstrj id xu yu zu
|
||||
run 2500
|
||||
write_data molecular-mix.data
|
||||
41
examples/template/in.template-mix
Normal file
41
examples/template/in.template-mix
Normal file
@ -0,0 +1,41 @@
|
||||
# demo for atom style template simulating a cyclohexane methane mixture
|
||||
# part 1: creating system with create_atoms
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
molecule cychex cyclohexane.mol
|
||||
atom_style template cychex
|
||||
|
||||
pair_style lj/cut 12.0
|
||||
pair_modify mix geometric tail yes
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style harmonic
|
||||
|
||||
lattice sc 6.0
|
||||
variable boxlen index 4.0
|
||||
region box block -${boxlen} ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
|
||||
create_box 2 box bond/types 1 angle/types 1 dihedral/types 1
|
||||
|
||||
create_atoms 0 box mol cychex 734594
|
||||
create_atoms 2 random 800 495437 box
|
||||
|
||||
mass 1 14.027
|
||||
mass 2 16.043
|
||||
|
||||
pair_coeff 1 1 0.1180 3.905
|
||||
pair_coeff 2 2 0.2940 3.730
|
||||
|
||||
bond_coeff 1 260.00 1.5260
|
||||
angle_coeff 1 63.0 112.40
|
||||
dihedral_coeff 1 2.0 1 3
|
||||
|
||||
thermo 100
|
||||
minimize 0.001 0.001 500 1000
|
||||
reset_timestep 0
|
||||
|
||||
velocity all create 100.0 6234235
|
||||
fix 1 all nvt temp 100.0 300.0 1.0
|
||||
# dump 1 all custom 100 cychex-methane.lammpstrj id xu yu zu
|
||||
run 2500
|
||||
write_data template-mix.data
|
||||
21
examples/template/in.tmpl-data-mix
Normal file
21
examples/template/in.tmpl-data-mix
Normal file
@ -0,0 +1,21 @@
|
||||
# demo for atom style template simulating a cyclohexane methane mixture
|
||||
# part 2: continuing from data file
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
molecule cychex cyclohexane.mol
|
||||
atom_style template cychex
|
||||
|
||||
pair_style lj/cut 12.0
|
||||
pair_modify mix geometric tail yes
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style harmonic
|
||||
|
||||
read_data template-mix.data
|
||||
|
||||
thermo 100
|
||||
|
||||
fix 1 all nvt temp 300.0 300.0 1.0
|
||||
# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu
|
||||
run 2000
|
||||
158
examples/template/log.22Oct20.hybrid.g++.1
Normal file
158
examples/template/log.22Oct20.hybrid.g++.1
Normal file
@ -0,0 +1,158 @@
|
||||
LAMMPS (22 Oct 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# demo using atom style hybrid template charge to simulate a h2o/co2 mixture
|
||||
|
||||
units real
|
||||
molecule twomols h2o.mol co2.mol offset 2 1 1 0 0
|
||||
Read molecule template twomols:
|
||||
1 molecules
|
||||
3 atoms with max type 2
|
||||
2 bonds with max type 1
|
||||
1 angles with max type 1
|
||||
0 dihedrals with max type 0
|
||||
0 impropers with max type 0
|
||||
Read molecule template twomols:
|
||||
1 molecules
|
||||
3 atoms with max type 4
|
||||
2 bonds with max type 2
|
||||
1 angles with max type 2
|
||||
0 dihedrals with max type 0
|
||||
0 impropers with max type 0
|
||||
atom_style hybrid template twomols charge
|
||||
boundary p p p
|
||||
pair_style lj/cut/coul/long 12
|
||||
pair_modify mix arithmetic tail yes
|
||||
kspace_style pppm 0.0001
|
||||
pair_style lj/cut/coul/long 12
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
|
||||
read_data h2o-co2.data
|
||||
Reading data file ...
|
||||
orthogonal box = (-10.000000 -10.000000 -10.000000) to (10.000000 10.000000 10.000000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
384 atoms
|
||||
256 template bonds
|
||||
128 template angles
|
||||
read_data CPU = 0.003 seconds
|
||||
|
||||
group h2o type 1 2
|
||||
192 atoms in group h2o
|
||||
group co2 type 3 4
|
||||
192 atoms in group co2
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 1 check yes
|
||||
timestep 1.0
|
||||
|
||||
velocity all create 300.0 34672
|
||||
thermo 100
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all shake 1.0e-4 1000 500 b 1 a 1 mol twomols
|
||||
WARNING: Molecule template for fix shake has multiple molecules (src/RIGID/fix_shake.cpp:174)
|
||||
0 = # of size 2 clusters
|
||||
0 = # of size 3 clusters
|
||||
0 = # of size 4 clusters
|
||||
64 = # of frozen angles
|
||||
find clusters CPU = 0.000 seconds
|
||||
#dump 1 all custom 100 h2o-co2.lammpstrj id mol xu yu zu
|
||||
|
||||
run 2500
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:328)
|
||||
G vector (1/distance) = 0.21452218
|
||||
grid = 8 8 8
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0237525
|
||||
estimated relative force accuracy = 7.1529949e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 2197 512
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 1 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 15
|
||||
ghost atom cutoff = 15
|
||||
binsize = 7.5, bins = 3 3 3
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
SHAKE stats (type/ave/delta/count) on step 0
|
||||
1 1.99995 1.29379e-05 192
|
||||
1 328.411 6.25278e-13 64
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.625 | 5.625 | 5.625 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 360.18809 -173.24472 3.5527137e-13 169.25036 2429.6019
|
||||
100 363.1919 -274.40147 44.351072 115.30094 -883.3694
|
||||
200 427.79493 -329.78833 38.354106 115.34674 1523.3792
|
||||
300 465.88637 -350.56147 22.604289 115.04411 385.4719
|
||||
400 436.9596 -357.24661 57.161471 115.41032 2307.0158
|
||||
SHAKE stats (type/ave/delta/count) on step 500
|
||||
1 2.00000 4.02911e-07 192
|
||||
1 328.410 5.78944e-05 64
|
||||
500 480.93508 -378.08914 36.26854 115.49018 2822.245
|
||||
600 457.38119 -381.9922 62.73272 115.65441 -387.65281
|
||||
700 488.20843 -393.89334 45.144546 115.47805 3086.293
|
||||
800 463.52123 -384.28537 59.827245 116.2942 3310.9672
|
||||
900 500.42748 -424.29715 64.614956 116.16348 -612.56056
|
||||
SHAKE stats (type/ave/delta/count) on step 1000
|
||||
1 2.00000 8.23271e-07 192
|
||||
1 328.410 5.98754e-05 64
|
||||
1000 522.46734 -424.93564 44.24152 116.1088 3948.9908
|
||||
1100 470.79532 -398.30875 66.721422 116.08177 2480.4521
|
||||
1200 515.87076 -433.25982 58.802584 116.07313 1913.2295
|
||||
1300 517.25521 -425.5203 49.308433 115.63494 3343.755
|
||||
1400 515.28471 -427.75141 53.078285 115.29997 2755.9048
|
||||
SHAKE stats (type/ave/delta/count) on step 1500
|
||||
1 2.00000 8.95165e-07 192
|
||||
1 328.410 7.19288e-05 64
|
||||
1500 514.22181 -421.99736 48.624007 115.58906 2400.1515
|
||||
1600 533.9392 -430.89564 38.263047 115.07866 4331.2167
|
||||
1700 529.29154 -424.02106 35.673551 114.94439 2973.3181
|
||||
1800 535.52166 -438.41572 43.952454 114.75272 1799.8588
|
||||
1900 519.40791 -413.30717 34.399008 114.9856 4270.415
|
||||
SHAKE stats (type/ave/delta/count) on step 2000
|
||||
1 2.00000 8.04353e-07 192
|
||||
1 328.410 7.97925e-05 64
|
||||
2000 553.26572 -446.67936 35.423618 114.83268 1729.4708
|
||||
2100 546.58793 -448.39367 43.475288 114.82028 1266.9778
|
||||
2200 536.17021 -442.03485 46.968579 114.76641 2419.0965
|
||||
2300 556.29724 -457.19766 43.217115 114.99049 1122.5796
|
||||
2400 529.02178 -437.66639 49.530498 114.89949 1714.4747
|
||||
SHAKE stats (type/ave/delta/count) on step 2500
|
||||
1 2.00000 6.70601e-07 192
|
||||
1 328.410 6.39002e-05 64
|
||||
2500 500.56024 -423.00108 62.368402 115.33925 3750.7564
|
||||
Loop time of 6.4485 on 1 procs for 2500 steps with 384 atoms
|
||||
|
||||
Performance: 33.496 ns/day, 0.717 hours/ns, 387.687 timesteps/s
|
||||
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 4.9332 | 4.9332 | 4.9332 | 0.0 | 76.50
|
||||
Bond | 0.013685 | 0.013685 | 0.013685 | 0.0 | 0.21
|
||||
Kspace | 0.33226 | 0.33226 | 0.33226 | 0.0 | 5.15
|
||||
Neigh | 1.0663 | 1.0663 | 1.0663 | 0.0 | 16.54
|
||||
Comm | 0.062471 | 0.062471 | 0.062471 | 0.0 | 0.97
|
||||
Output | 0.00048861 | 0.00048861 | 0.00048861 | 0.0 | 0.01
|
||||
Modify | 0.030447 | 0.030447 | 0.030447 | 0.0 | 0.47
|
||||
Other | | 0.009605 | | | 0.15
|
||||
|
||||
Nlocal: 384.000 ave 384 max 384 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 5594.00 ave 5594 max 5594 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 129739.0 ave 129739 max 129739 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 129739
|
||||
Ave neighs/atom = 337.86198
|
||||
Ave special neighs/atom = 2.0000000
|
||||
Neighbor list builds = 320
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:06
|
||||
158
examples/template/log.22Oct20.hybrid.g++.4
Normal file
158
examples/template/log.22Oct20.hybrid.g++.4
Normal file
@ -0,0 +1,158 @@
|
||||
LAMMPS (22 Oct 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# demo using atom style hybrid template charge to simulate a h2o/co2 mixture
|
||||
|
||||
units real
|
||||
molecule twomols h2o.mol co2.mol offset 2 1 1 0 0
|
||||
Read molecule template twomols:
|
||||
1 molecules
|
||||
3 atoms with max type 2
|
||||
2 bonds with max type 1
|
||||
1 angles with max type 1
|
||||
0 dihedrals with max type 0
|
||||
0 impropers with max type 0
|
||||
Read molecule template twomols:
|
||||
1 molecules
|
||||
3 atoms with max type 4
|
||||
2 bonds with max type 2
|
||||
1 angles with max type 2
|
||||
0 dihedrals with max type 0
|
||||
0 impropers with max type 0
|
||||
atom_style hybrid template twomols charge
|
||||
boundary p p p
|
||||
pair_style lj/cut/coul/long 12
|
||||
pair_modify mix arithmetic tail yes
|
||||
kspace_style pppm 0.0001
|
||||
pair_style lj/cut/coul/long 12
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
|
||||
read_data h2o-co2.data
|
||||
Reading data file ...
|
||||
orthogonal box = (-10.000000 -10.000000 -10.000000) to (10.000000 10.000000 10.000000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
384 atoms
|
||||
256 template bonds
|
||||
128 template angles
|
||||
read_data CPU = 0.002 seconds
|
||||
|
||||
group h2o type 1 2
|
||||
192 atoms in group h2o
|
||||
group co2 type 3 4
|
||||
192 atoms in group co2
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 1 check yes
|
||||
timestep 1.0
|
||||
|
||||
velocity all create 300.0 34672
|
||||
thermo 100
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all shake 1.0e-4 1000 500 b 1 a 1 mol twomols
|
||||
WARNING: Molecule template for fix shake has multiple molecules (src/RIGID/fix_shake.cpp:174)
|
||||
0 = # of size 2 clusters
|
||||
0 = # of size 3 clusters
|
||||
0 = # of size 4 clusters
|
||||
64 = # of frozen angles
|
||||
find clusters CPU = 0.000 seconds
|
||||
#dump 1 all custom 100 h2o-co2.lammpstrj id mol xu yu zu
|
||||
|
||||
run 2500
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:328)
|
||||
G vector (1/distance) = 0.21452218
|
||||
grid = 8 8 8
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0237525
|
||||
estimated relative force accuracy = 7.1529949e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 1053 128
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 1 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 15
|
||||
ghost atom cutoff = 15
|
||||
binsize = 7.5, bins = 3 3 3
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
SHAKE stats (type/ave/delta/count) on step 0
|
||||
1 1.99995 1.29379e-05 192
|
||||
1 328.411 6.25278e-13 64
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.952 | 4.952 | 4.952 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 360.18809 -173.24472 3.5527137e-13 169.25036 2429.6019
|
||||
100 363.1919 -274.40147 44.351072 115.30094 -883.3694
|
||||
200 427.79493 -329.78833 38.354106 115.34674 1523.3792
|
||||
300 465.88637 -350.56147 22.60429 115.0441 385.47189
|
||||
400 436.9596 -357.24661 57.161471 115.41032 2307.0158
|
||||
SHAKE stats (type/ave/delta/count) on step 500
|
||||
1 2.00000 4.02911e-07 192
|
||||
1 328.410 5.78945e-05 64
|
||||
500 480.93505 -378.08914 36.268541 115.49016 2822.245
|
||||
600 457.38144 -381.99241 62.732739 115.65446 -387.65505
|
||||
700 488.20801 -393.89265 45.144482 115.47829 3086.2987
|
||||
800 463.5234 -384.28682 59.826927 116.2945 3310.9691
|
||||
900 500.48024 -424.35693 64.621298 116.16022 -612.4406
|
||||
SHAKE stats (type/ave/delta/count) on step 1000
|
||||
1 2.00000 8.21157e-07 192
|
||||
1 328.410 5.79572e-05 64
|
||||
1000 522.3905 -424.85292 44.232122 116.10905 3948.1535
|
||||
1100 466.7856 -395.03916 67.204265 116.02145 2555.2069
|
||||
1200 505.58079 -424.30563 59.681049 116.12127 1919.2701
|
||||
1300 510.78441 -418.28838 48.398524 115.804 3476.7443
|
||||
1400 494.39282 -407.60176 52.9665 115.47219 2343.5129
|
||||
SHAKE stats (type/ave/delta/count) on step 1500
|
||||
1 2.00000 7.21617e-07 192
|
||||
1 328.410 8.01168e-05 64
|
||||
1500 533.48096 -444.9571 53.263393 115.58182 1055.8053
|
||||
1600 548.84084 -449.81134 43.134527 115.20409 3084.0678
|
||||
1700 522.65205 -419.10648 37.279839 115.1519 1813.2589
|
||||
1800 497.72839 -403.88156 45.774501 115.17212 1822.8113
|
||||
1900 535.04509 -434.52042 40.685094 114.9275 4216.4353
|
||||
SHAKE stats (type/ave/delta/count) on step 2000
|
||||
1 2.00000 1.03652e-06 192
|
||||
1 328.410 5.49305e-05 64
|
||||
2000 540.42903 -436.41996 37.284032 114.74637 1422.0078
|
||||
2100 534.80707 -439.51681 46.068646 115.08833 1460.2864
|
||||
2200 507.8413 -419.62464 51.912776 115.18345 3790.8003
|
||||
2300 553.37305 -456.23124 45.592723 115.55197 515.72888
|
||||
2400 538.60716 -447.65657 51.130476 115.62382 2087.6217
|
||||
SHAKE stats (type/ave/delta/count) on step 2500
|
||||
1 2.00000 6.38759e-07 192
|
||||
1 328.410 5.54712e-05 64
|
||||
2500 507.38323 -436.58125 69.949293 115.8278 3313.9095
|
||||
Loop time of 2.62759 on 4 procs for 2500 steps with 384 atoms
|
||||
|
||||
Performance: 82.205 ns/day, 0.292 hours/ns, 951.443 timesteps/s
|
||||
93.7% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.1769 | 1.3595 | 1.5961 | 13.1 | 51.74
|
||||
Bond | 0.0040634 | 0.0042451 | 0.0044163 | 0.2 | 0.16
|
||||
Kspace | 0.37643 | 0.62177 | 0.8124 | 20.0 | 23.66
|
||||
Neigh | 0.35517 | 0.35603 | 0.35688 | 0.1 | 13.55
|
||||
Comm | 0.15521 | 0.16781 | 0.18101 | 2.8 | 6.39
|
||||
Output | 0.00039921 | 0.00083364 | 0.0018058 | 0.0 | 0.03
|
||||
Modify | 0.081231 | 0.095032 | 0.10957 | 3.5 | 3.62
|
||||
Other | | 0.02238 | | | 0.85
|
||||
|
||||
Nlocal: 96.0000 ave 105 max 84 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 1 1
|
||||
Nghost: 3764.00 ave 3776 max 3755 min
|
||||
Histogram: 1 1 0 0 0 1 0 0 0 1
|
||||
Neighs: 32527.2 ave 34260 max 29030 min
|
||||
Histogram: 1 0 0 0 0 0 0 1 1 1
|
||||
|
||||
Total # of neighbors = 130109
|
||||
Ave neighs/atom = 338.82552
|
||||
Ave special neighs/atom = 2.0000000
|
||||
Neighbor list builds = 321
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:02
|
||||
122
examples/template/log.22Oct20.mol-data-mix.g++.1
Normal file
122
examples/template/log.22Oct20.mol-data-mix.g++.1
Normal file
@ -0,0 +1,122 @@
|
||||
LAMMPS (22 Oct 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# demo for atom style template simulating a cyclohexane methane mixture
|
||||
# part 2: continuing from data file
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
molecule cychex cyclohexane.mol
|
||||
Read molecule template cychex:
|
||||
1 molecules
|
||||
6 atoms with max type 1
|
||||
6 bonds with max type 1
|
||||
6 angles with max type 1
|
||||
6 dihedrals with max type 1
|
||||
0 impropers with max type 0
|
||||
atom_style molecular
|
||||
|
||||
pair_style lj/cut 12.0
|
||||
pair_modify mix geometric tail yes
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style harmonic
|
||||
|
||||
read_data molecular-mix.data
|
||||
Reading data file ...
|
||||
orthogonal box = (-24.000000 -24.000000 -24.000000) to (24.000000 24.000000 24.000000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
3872 atoms
|
||||
reading velocities ...
|
||||
3872 velocities
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
scanning angles ...
|
||||
1 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
2 = max dihedrals/atom
|
||||
reading bonds ...
|
||||
3072 bonds
|
||||
reading angles ...
|
||||
3072 angles
|
||||
reading dihedrals ...
|
||||
3072 dihedrals
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0.0 0.0 0.0
|
||||
special bond factors coul: 0.0 0.0 0.0
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
4 = max # of 1-4 neighbors
|
||||
5 = max # of special neighbors
|
||||
special bonds CPU = 0.001 seconds
|
||||
read_data CPU = 0.028 seconds
|
||||
|
||||
thermo 100
|
||||
|
||||
fix 1 all nvt temp 300.0 300.0 1.0
|
||||
# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu
|
||||
run 2000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 14
|
||||
ghost atom cutoff = 14
|
||||
binsize = 7, bins = 7 7 7
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 10.75 | 10.75 | 10.75 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 302.37248 -4957.687 1700.6563 231.95939 10617.134
|
||||
100 305.85975 -4885.1313 1589.9657 234.06312 9178.0262
|
||||
200 296.72843 -4951.5636 1681.209 153.51039 10767.695
|
||||
300 308.16536 -4956.3355 1604.2261 203.72314 9266.9134
|
||||
400 297.43236 -4959.7758 1596.8717 69.083277 10221.765
|
||||
500 304.09059 -5004.7041 1531.3818 35.492587 9778.2126
|
||||
600 301.19423 -4974.2139 1694.3778 195.55858 9597.0895
|
||||
700 297.83153 -4993.867 1671.6871 114.41347 10360.771
|
||||
800 301.50873 -5038.4606 1671.0584 111.62133 8730.9918
|
||||
900 298.13466 -5056.328 1719.8923 103.65538 10561.792
|
||||
1000 297.16177 -4951.3098 1655.784 133.33949 8784.2239
|
||||
1100 303.33432 -4972.3579 1696.3014 224.03195 10764.88
|
||||
1200 307.51509 -4909.5175 1773.9263 412.73795 9220.984
|
||||
1300 305.02405 -4974.013 1714.5967 260.16943 10357.602
|
||||
1400 293.6948 -4998.3679 1683.6803 74.173172 9499.7569
|
||||
1500 300.79313 -4978.7126 1719.2548 211.30869 9602.7975
|
||||
1600 302.62922 -4924.5134 1709.726 277.16506 10649.017
|
||||
1700 301.27221 -4935.4932 1744.1182 284.9194 9169.4275
|
||||
1800 296.72398 -5019.7387 1712.9372 117.0122 10540.894
|
||||
1900 301.63962 -4971.0508 1757.1132 266.59621 8983.2539
|
||||
2000 304.05902 -5013.5663 1752.1581 247.04237 10422.56
|
||||
Loop time of 15.6283 on 1 procs for 2000 steps with 3872 atoms
|
||||
|
||||
Performance: 11.057 ns/day, 2.171 hours/ns, 127.973 timesteps/s
|
||||
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 14.126 | 14.126 | 14.126 | 0.0 | 90.39
|
||||
Bond | 0.60335 | 0.60335 | 0.60335 | 0.0 | 3.86
|
||||
Neigh | 0.69884 | 0.69884 | 0.69884 | 0.0 | 4.47
|
||||
Comm | 0.083166 | 0.083166 | 0.083166 | 0.0 | 0.53
|
||||
Output | 0.00054701 | 0.00054701 | 0.00054701 | 0.0 | 0.00
|
||||
Modify | 0.079684 | 0.079684 | 0.079684 | 0.0 | 0.51
|
||||
Other | | 0.03683 | | | 0.24
|
||||
|
||||
Nlocal: 3872.00 ave 3872 max 3872 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11716.0 ave 11716 max 11716 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 769907.0 ave 769907 max 769907 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 769907
|
||||
Ave neighs/atom = 198.83962
|
||||
Ave special neighs/atom = 3.9669421
|
||||
Neighbor list builds = 35
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:15
|
||||
122
examples/template/log.22Oct20.mol-data-mix.g++.4
Normal file
122
examples/template/log.22Oct20.mol-data-mix.g++.4
Normal file
@ -0,0 +1,122 @@
|
||||
LAMMPS (22 Oct 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# demo for atom style template simulating a cyclohexane methane mixture
|
||||
# part 2: continuing from data file
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
molecule cychex cyclohexane.mol
|
||||
Read molecule template cychex:
|
||||
1 molecules
|
||||
6 atoms with max type 1
|
||||
6 bonds with max type 1
|
||||
6 angles with max type 1
|
||||
6 dihedrals with max type 1
|
||||
0 impropers with max type 0
|
||||
atom_style molecular
|
||||
|
||||
pair_style lj/cut 12.0
|
||||
pair_modify mix geometric tail yes
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style harmonic
|
||||
|
||||
read_data molecular-mix.data
|
||||
Reading data file ...
|
||||
orthogonal box = (-24.000000 -24.000000 -24.000000) to (24.000000 24.000000 24.000000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
3872 atoms
|
||||
reading velocities ...
|
||||
3872 velocities
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
scanning angles ...
|
||||
1 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
2 = max dihedrals/atom
|
||||
reading bonds ...
|
||||
3072 bonds
|
||||
reading angles ...
|
||||
3072 angles
|
||||
reading dihedrals ...
|
||||
3072 dihedrals
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0.0 0.0 0.0
|
||||
special bond factors coul: 0.0 0.0 0.0
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
4 = max # of 1-4 neighbors
|
||||
5 = max # of special neighbors
|
||||
special bonds CPU = 0.010 seconds
|
||||
read_data CPU = 0.041 seconds
|
||||
|
||||
thermo 100
|
||||
|
||||
fix 1 all nvt temp 300.0 300.0 1.0
|
||||
# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu
|
||||
run 2000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 14
|
||||
ghost atom cutoff = 14
|
||||
binsize = 7, bins = 7 7 7
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 8.101 | 8.197 | 8.483 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 297.79426 -4928.7403 1686.5107 193.93377 11481.089
|
||||
100 298.75001 -4870.5672 1619.1613 195.78563 8813.1303
|
||||
200 301.9265 -4884.8594 1745.0359 344.02042 11561.79
|
||||
300 298.78957 -4854.0769 1638.3567 231.92774 9180.5245
|
||||
400 302 -4951.4895 1664.5419 197.74463 10784.638
|
||||
500 299.17946 -4983.7996 1615.0068 83.354011 9578.745
|
||||
600 294.32777 -5000.7554 1591.1992 -13.391775 9181.3926
|
||||
700 300.90925 -4959.9309 1653.6347 165.81003 11121.514
|
||||
800 293.14833 -4895.5912 1707.8754 194.83943 8397.927
|
||||
900 299.0508 -5032.8395 1726.0885 143.91128 11478.847
|
||||
1000 295.15206 -4888.4533 1777.4719 294.69437 8388.738
|
||||
1100 301.13534 -5004.2113 1761.645 232.14877 11246.198
|
||||
1200 296.93159 -4944.3223 1703.1744 185.06123 8808.4178
|
||||
1300 300.79377 -5011.7826 1642.093 101.08422 10390.705
|
||||
1400 295.85952 -4987.9927 1708.8415 134.68768 9680.88
|
||||
1500 296.37146 -5009.887 1637.2239 47.082942 9235.3487
|
||||
1600 298.68972 -4962.1273 1747.402 231.77054 10941.114
|
||||
1700 299.03141 -5022.0046 1755.8881 184.32195 8248.312
|
||||
1800 297.26645 -5023.9459 1740.9512 147.07837 11357.02
|
||||
1900 293.16007 -5023.8887 1754.1333 112.93534 7969.1102
|
||||
2000 307.66497 -5046.5928 1803.9999 307.46576 11249.704
|
||||
Loop time of 4.64055 on 4 procs for 2000 steps with 3872 atoms
|
||||
|
||||
Performance: 37.237 ns/day, 0.645 hours/ns, 430.983 timesteps/s
|
||||
96.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 3.5991 | 3.7143 | 4.0014 | 8.7 | 80.04
|
||||
Bond | 0.14736 | 0.15557 | 0.16949 | 2.1 | 3.35
|
||||
Neigh | 0.19097 | 0.191 | 0.19101 | 0.0 | 4.12
|
||||
Comm | 0.22193 | 0.52405 | 0.64844 | 24.3 | 11.29
|
||||
Output | 0.00034875 | 0.00062747 | 0.001461 | 0.0 | 0.01
|
||||
Modify | 0.024692 | 0.026943 | 0.028768 | 1.0 | 0.58
|
||||
Other | | 0.02802 | | | 0.60
|
||||
|
||||
Nlocal: 968.000 ave 979 max 948 min
|
||||
Histogram: 1 0 0 0 0 0 0 1 1 1
|
||||
Nghost: 6321.25 ave 6336 max 6309 min
|
||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||
Neighs: 192540.0 ave 195406 max 187182 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
||||
|
||||
Total # of neighbors = 770161
|
||||
Ave neighs/atom = 198.90522
|
||||
Ave special neighs/atom = 3.9669421
|
||||
Neighbor list builds = 35
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:04
|
||||
174
examples/template/log.22Oct20.molecular-mix.g++.1
Normal file
174
examples/template/log.22Oct20.molecular-mix.g++.1
Normal file
@ -0,0 +1,174 @@
|
||||
LAMMPS (22 Oct 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# demo for atom style template simulating a cyclohexane methane mixture
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
molecule cychex cyclohexane.mol
|
||||
Read molecule template cychex:
|
||||
1 molecules
|
||||
6 atoms with max type 1
|
||||
6 bonds with max type 1
|
||||
6 angles with max type 1
|
||||
6 dihedrals with max type 1
|
||||
0 impropers with max type 0
|
||||
atom_style molecular
|
||||
|
||||
pair_style lj/cut 12.0
|
||||
pair_modify mix geometric tail yes
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style harmonic
|
||||
|
||||
lattice sc 6.0
|
||||
Lattice spacing in x,y,z = 6.0000000 6.0000000 6.0000000
|
||||
variable boxlen index 4.0
|
||||
region box block -${boxlen} ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
|
||||
region box block -4.0 ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
|
||||
region box block -4.0 4.0 -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
|
||||
region box block -4.0 4.0 -4.0 ${boxlen} -${boxlen} ${boxlen} units lattice
|
||||
region box block -4.0 4.0 -4.0 4.0 -${boxlen} ${boxlen} units lattice
|
||||
region box block -4.0 4.0 -4.0 4.0 -4.0 ${boxlen} units lattice
|
||||
region box block -4.0 4.0 -4.0 4.0 -4.0 4.0 units lattice
|
||||
create_box 2 box bond/types 1 angle/types 1 dihedral/types 1 extra/special/per/atom 6 extra/bond/per/atom 2 extra/angle/per/atom 2 extra/dihedral/per/atom 2
|
||||
Created orthogonal box = (-24.000000 -24.000000 -24.000000) to (24.000000 24.000000 24.000000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
|
||||
create_atoms 0 box mol cychex 734594
|
||||
Created 3072 atoms
|
||||
create_atoms CPU = 0.003 seconds
|
||||
create_atoms 2 random 800 495437 box
|
||||
Created 800 atoms
|
||||
create_atoms CPU = 0.000 seconds
|
||||
|
||||
mass 1 14.027
|
||||
mass 2 16.043
|
||||
|
||||
pair_coeff 1 1 0.1180 3.905
|
||||
pair_coeff 2 2 0.2940 3.730
|
||||
|
||||
bond_coeff 1 260.00 1.5260
|
||||
angle_coeff 1 63.0 112.40
|
||||
dihedral_coeff 1 2.0 1 3
|
||||
|
||||
thermo 100
|
||||
minimize 0.001 0.001 500 1000
|
||||
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:187)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 14
|
||||
ghost atom cutoff = 14
|
||||
binsize = 7, bins = 7 7 7
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 12.28 | 12.28 | 12.28 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 4.3897851e+13 341.92144 4.3897851e+13 1.0886888e+14
|
||||
100 0 -4351.8383 516.49891 -3835.3394 11635.037
|
||||
190 0 -6191.8175 457.61209 -5734.2054 4365.373
|
||||
Loop time of 3.46057 on 1 procs for 190 steps with 3872 atoms
|
||||
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = energy tolerance
|
||||
Energy initial, next-to-last, final =
|
||||
43897850768892.8 -5729.17187196146 -5734.20542785978
|
||||
Force two-norm initial, final = 1.1080994e+15 72.746805
|
||||
Force max component initial, final = 4.6607099e+14 17.394645
|
||||
Final line search alpha, max atom move = 0.0041634525 0.072421779
|
||||
Iterations, force evaluations = 190 297
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 3.0573 | 3.0573 | 3.0573 | 0.0 | 88.35
|
||||
Bond | 0.10271 | 0.10271 | 0.10271 | 0.0 | 2.97
|
||||
Neigh | 0.26654 | 0.26654 | 0.26654 | 0.0 | 7.70
|
||||
Comm | 0.013532 | 0.013532 | 0.013532 | 0.0 | 0.39
|
||||
Output | 3.3796e-05 | 3.3796e-05 | 3.3796e-05 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 0.02041 | | | 0.59
|
||||
|
||||
Nlocal: 3872.00 ave 3872 max 3872 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 12122.0 ave 12122 max 12122 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 774375.0 ave 774375 max 774375 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 774375
|
||||
Ave neighs/atom = 199.99354
|
||||
Ave special neighs/atom = 3.9669421
|
||||
Neighbor list builds = 14
|
||||
Dangerous builds = 0
|
||||
reset_timestep 0
|
||||
|
||||
velocity all create 100.0 6234235
|
||||
fix 1 all nvt temp 100.0 300.0 1.0
|
||||
# dump 1 all custom 100 cychex-methane.lammpstrj id xu yu zu
|
||||
run 2500
|
||||
Per MPI rank memory allocation (min/avg/max) = 11.16 | 11.16 | 11.16 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 100 -6191.8175 457.61209 -4580.3339 4842.3161
|
||||
100 106.81295 -5670.2783 921.20332 -3516.5907 5959.5039
|
||||
200 119.22024 -5701.0103 1040.0336 -3285.3283 6755.0994
|
||||
300 127.23574 -5706.7587 1023.9882 -3214.6335 6081.4162
|
||||
400 133.7471 -5734.1781 1113.1696 -3077.7387 6569.8751
|
||||
500 138.72092 -5756.3282 1191.5668 -2964.1003 6433.1441
|
||||
600 149.02612 -5731.7291 1205.3124 -2806.8466 6366.853
|
||||
700 153.5469 -5670.5879 925.61956 -2973.2344 7677.5226
|
||||
800 163.38118 -5629.0757 1180.6507 -2563.216 5865.8079
|
||||
900 173.27279 -5639.6903 1160.2138 -2480.131 8168.7364
|
||||
1000 178.05354 -5579.0492 913.19337 -2611.3466 6220.8001
|
||||
1100 188.99752 -5551.4873 1178.9541 -2191.7446 7734.6527
|
||||
1200 196.9019 -5511.951 1121.4617 -2118.4942 7602.4591
|
||||
1300 202.98293 -5433.6794 1194.3592 -1897.1579 7067.1876
|
||||
1400 212.86876 -5411.3798 1276.3809 -1678.7668 8867.2713
|
||||
1500 221.26247 -5359.7405 1390.3889 -1416.2668 6939.8559
|
||||
1600 228.1783 -5288.5782 1375.3053 -1280.3883 9387.8277
|
||||
1700 234.74001 -5255.1136 1192.2292 -1354.2862 7400.1124
|
||||
1800 244.1285 -5282.2876 1386.5554 -1078.8029 9473.6491
|
||||
1900 253.62148 -5158.5569 1242.3041 -989.78669 8596.2722
|
||||
2000 260.24011 -5157.2005 1477.2039 -677.16002 9136.1769
|
||||
2100 263.80129 -5096.4397 1403.9977 -648.51387 9640.0807
|
||||
2200 278.10721 -5098.89 1545.7716 -344.11827 8509.7183
|
||||
2300 278.05084 -5053.818 1495.944 -349.52438 10299.97
|
||||
2400 287.92949 -5011.3524 1527.0261 -161.98978 8854.8877
|
||||
2500 302.37248 -4957.687 1700.6563 231.95939 10617.134
|
||||
Loop time of 18.6761 on 1 procs for 2500 steps with 3872 atoms
|
||||
|
||||
Performance: 11.566 ns/day, 2.075 hours/ns, 133.861 timesteps/s
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 17.06 | 17.06 | 17.06 | 0.0 | 91.35
|
||||
Bond | 0.73068 | 0.73068 | 0.73068 | 0.0 | 3.91
|
||||
Neigh | 0.63671 | 0.63671 | 0.63671 | 0.0 | 3.41
|
||||
Comm | 0.10272 | 0.10272 | 0.10272 | 0.0 | 0.55
|
||||
Output | 0.00064976 | 0.00064976 | 0.00064976 | 0.0 | 0.00
|
||||
Modify | 0.098028 | 0.098028 | 0.098028 | 0.0 | 0.52
|
||||
Other | | 0.04742 | | | 0.25
|
||||
|
||||
Nlocal: 3872.00 ave 3872 max 3872 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11793.0 ave 11793 max 11793 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 770411.0 ave 770411 max 770411 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 770411
|
||||
Ave neighs/atom = 198.96978
|
||||
Ave special neighs/atom = 3.9669421
|
||||
Neighbor list builds = 33
|
||||
Dangerous builds = 0
|
||||
write_data molecular-mix.data
|
||||
System init for write_data ...
|
||||
Total wall time: 0:00:22
|
||||
175
examples/template/log.22Oct20.molecular-mix.g++.4
Normal file
175
examples/template/log.22Oct20.molecular-mix.g++.4
Normal file
@ -0,0 +1,175 @@
|
||||
LAMMPS (22 Oct 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# demo for atom style template simulating a cyclohexane methane mixture
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
molecule cychex cyclohexane.mol
|
||||
Read molecule template cychex:
|
||||
1 molecules
|
||||
6 atoms with max type 1
|
||||
6 bonds with max type 1
|
||||
6 angles with max type 1
|
||||
6 dihedrals with max type 1
|
||||
0 impropers with max type 0
|
||||
atom_style molecular
|
||||
|
||||
pair_style lj/cut 12.0
|
||||
pair_modify mix geometric tail yes
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style harmonic
|
||||
|
||||
lattice sc 6.0
|
||||
Lattice spacing in x,y,z = 6.0000000 6.0000000 6.0000000
|
||||
variable boxlen index 4.0
|
||||
region box block -${boxlen} ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
|
||||
region box block -4.0 ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
|
||||
region box block -4.0 4.0 -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
|
||||
region box block -4.0 4.0 -4.0 ${boxlen} -${boxlen} ${boxlen} units lattice
|
||||
region box block -4.0 4.0 -4.0 4.0 -${boxlen} ${boxlen} units lattice
|
||||
region box block -4.0 4.0 -4.0 4.0 -4.0 ${boxlen} units lattice
|
||||
region box block -4.0 4.0 -4.0 4.0 -4.0 4.0 units lattice
|
||||
create_box 2 box bond/types 1 angle/types 1 dihedral/types 1 extra/special/per/atom 6 extra/bond/per/atom 2 extra/angle/per/atom 2 extra/dihedral/per/atom 2
|
||||
Created orthogonal box = (-24.000000 -24.000000 -24.000000) to (24.000000 24.000000 24.000000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
|
||||
create_atoms 0 box mol cychex 734594
|
||||
Created 3072 atoms
|
||||
create_atoms CPU = 0.011 seconds
|
||||
create_atoms 2 random 800 495437 box
|
||||
Created 800 atoms
|
||||
create_atoms CPU = 0.000 seconds
|
||||
|
||||
mass 1 14.027
|
||||
mass 2 16.043
|
||||
|
||||
pair_coeff 1 1 0.1180 3.905
|
||||
pair_coeff 2 2 0.2940 3.730
|
||||
|
||||
bond_coeff 1 260.00 1.5260
|
||||
angle_coeff 1 63.0 112.40
|
||||
dihedral_coeff 1 2.0 1 3
|
||||
|
||||
thermo 100
|
||||
minimize 0.001 0.001 500 1000
|
||||
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:187)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 14
|
||||
ghost atom cutoff = 14
|
||||
binsize = 7, bins = 7 7 7
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 9.623 | 9.719 | 10.01 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 7.5430044e+16 341.92144 7.5430044e+16 1.8707026e+17
|
||||
100 0 -3410.6986 572.28283 -2838.4158 14603.831
|
||||
200 0 -6109.2306 483.67771 -5625.5529 5069.1821
|
||||
204 0 -6137.0238 483.14639 -5653.8774 4952.4081
|
||||
Loop time of 1.10481 on 4 procs for 204 steps with 3872 atoms
|
||||
|
||||
98.2% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = energy tolerance
|
||||
Energy initial, next-to-last, final =
|
||||
7.54300441078755e+16 -5648.75822692028 -5653.87742448419
|
||||
Force two-norm initial, final = 8.7430661e+18 74.636845
|
||||
Force max component initial, final = 4.1468626e+18 8.6800755
|
||||
Final line search alpha, max atom move = 0.0032186736 0.02793833
|
||||
Iterations, force evaluations = 204 328
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.89902 | 0.90561 | 0.90821 | 0.4 | 81.97
|
||||
Bond | 0.029749 | 0.030411 | 0.031345 | 0.4 | 2.75
|
||||
Neigh | 0.088655 | 0.088662 | 0.088666 | 0.0 | 8.03
|
||||
Comm | 0.063187 | 0.068096 | 0.070678 | 1.1 | 6.16
|
||||
Output | 4.8304e-05 | 0.00011426 | 0.00031124 | 0.0 | 0.01
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 0.01191 | | | 1.08
|
||||
|
||||
Nlocal: 968.000 ave 980 max 954 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||
Nghost: 6630.00 ave 6644 max 6616 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
Neighs: 193550.0 ave 195957 max 191376 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 774200
|
||||
Ave neighs/atom = 199.94835
|
||||
Ave special neighs/atom = 3.9669421
|
||||
Neighbor list builds = 14
|
||||
Dangerous builds = 0
|
||||
reset_timestep 0
|
||||
|
||||
velocity all create 100.0 6234235
|
||||
fix 1 all nvt temp 100.0 300.0 1.0
|
||||
# dump 1 all custom 100 cychex-methane.lammpstrj id xu yu zu
|
||||
run 2500
|
||||
Per MPI rank memory allocation (min/avg/max) = 8.498 | 8.785 | 8.881 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 100 -6137.0238 483.14639 -4500.0059 5429.3513
|
||||
100 107.18608 -5623.5468 925.13786 -3461.6193 5640.5924
|
||||
200 119.37927 -5671.054 1050.9079 -3242.6626 7494.8637
|
||||
300 127.21276 -5646.2809 1053.2662 -3125.143 5661.4525
|
||||
400 133.89893 -5674.1417 1139.7 -2989.42 7206.4877
|
||||
500 138.74889 -5679.3757 1234.644 -2843.7477 6741.4965
|
||||
600 150.20403 -5665.0258 1211.9245 -2719.9398 6299.2406
|
||||
700 156.0507 -5681.5445 978.62091 -2902.2989 8429.7188
|
||||
800 160.67293 -5579.9146 1214.6749 -2511.2805 5217.5425
|
||||
900 172.06808 -5627.6903 1118.4786 -2523.767 8995.6018
|
||||
1000 179.82813 -5508.1617 925.22393 -2507.9521 5760.9688
|
||||
1100 190.36338 -5536.6687 1176.6794 -2163.4405 8079.5754
|
||||
1200 195.57864 -5508.64 1163.8098 -2088.1038 7738.58
|
||||
1300 204.05249 -5401.8527 1219.9794 -1827.3697 6562.2311
|
||||
1400 211.74944 -5365.2571 1326.2667 -1595.6738 9772.2773
|
||||
1500 222.08023 -5265.4213 1418.3572 -1284.5435 6395.1161
|
||||
1600 225.86408 -5316.5874 1288.1407 -1422.2653 10163.26
|
||||
1700 232.35057 -5192.56 1254.0031 -1257.5297 7437.3606
|
||||
1800 238.16652 -5199.008 1457.8824 -992.98993 9783.4089
|
||||
1900 250.86418 -5166.917 1256.4887 -1015.7777 8635.027
|
||||
2000 262.41293 -5088.5573 1494.6069 -566.04218 9100.8833
|
||||
2100 268.55207 -5057.9273 1459.8499 -499.33144 10002.961
|
||||
2200 279.96891 -4963.9376 1526.8577 -206.59825 8943.2443
|
||||
2300 286.55635 -5047.2961 1538.5334 -202.27038 10711.176
|
||||
2400 292.56468 -4910.7083 1625.6283 90.740663 8482.6522
|
||||
2500 297.79426 -4928.7403 1686.5107 193.93377 11481.089
|
||||
Loop time of 5.954 on 4 procs for 2500 steps with 3872 atoms
|
||||
|
||||
Performance: 36.278 ns/day, 0.662 hours/ns, 419.886 timesteps/s
|
||||
95.5% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 4.4642 | 4.6298 | 4.8946 | 7.5 | 77.76
|
||||
Bond | 0.18992 | 0.19849 | 0.20566 | 1.3 | 3.33
|
||||
Neigh | 0.18926 | 0.18928 | 0.18929 | 0.0 | 3.18
|
||||
Comm | 0.56456 | 0.82727 | 1.0096 | 17.9 | 13.89
|
||||
Output | 0.00044023 | 0.00092791 | 0.0020343 | 0.0 | 0.02
|
||||
Modify | 0.077974 | 0.080378 | 0.082874 | 0.8 | 1.35
|
||||
Other | | 0.02782 | | | 0.47
|
||||
|
||||
Nlocal: 968.000 ave 989 max 944 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 0 2
|
||||
Nghost: 6381.50 ave 6416 max 6351 min
|
||||
Histogram: 1 0 0 1 0 1 0 0 0 1
|
||||
Neighs: 192557.0 ave 197456 max 188754 min
|
||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 770229
|
||||
Ave neighs/atom = 198.92278
|
||||
Ave special neighs/atom = 3.9669421
|
||||
Neighbor list builds = 34
|
||||
Dangerous builds = 0
|
||||
write_data molecular-mix.data
|
||||
System init for write_data ...
|
||||
Total wall time: 0:00:07
|
||||
175
examples/template/log.22Oct20.template-mix.g++.1
Normal file
175
examples/template/log.22Oct20.template-mix.g++.1
Normal file
@ -0,0 +1,175 @@
|
||||
LAMMPS (22 Oct 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# demo for atom style template simulating a cyclohexane methane mixture
|
||||
# part 1: creating system with create_atoms
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
molecule cychex cyclohexane.mol
|
||||
Read molecule template cychex:
|
||||
1 molecules
|
||||
6 atoms with max type 1
|
||||
6 bonds with max type 1
|
||||
6 angles with max type 1
|
||||
6 dihedrals with max type 1
|
||||
0 impropers with max type 0
|
||||
atom_style template cychex
|
||||
|
||||
pair_style lj/cut 12.0
|
||||
pair_modify mix geometric tail yes
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style harmonic
|
||||
|
||||
lattice sc 6.0
|
||||
Lattice spacing in x,y,z = 6.0000000 6.0000000 6.0000000
|
||||
variable boxlen index 4.0
|
||||
region box block -${boxlen} ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
|
||||
region box block -4.0 ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
|
||||
region box block -4.0 4.0 -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
|
||||
region box block -4.0 4.0 -4.0 ${boxlen} -${boxlen} ${boxlen} units lattice
|
||||
region box block -4.0 4.0 -4.0 4.0 -${boxlen} ${boxlen} units lattice
|
||||
region box block -4.0 4.0 -4.0 4.0 -4.0 ${boxlen} units lattice
|
||||
region box block -4.0 4.0 -4.0 4.0 -4.0 4.0 units lattice
|
||||
create_box 2 box bond/types 1 angle/types 1 dihedral/types 1
|
||||
Created orthogonal box = (-24.000000 -24.000000 -24.000000) to (24.000000 24.000000 24.000000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
|
||||
create_atoms 0 box mol cychex 734594
|
||||
Created 3072 atoms
|
||||
create_atoms CPU = 0.001 seconds
|
||||
create_atoms 2 random 800 495437 box
|
||||
Created 800 atoms
|
||||
create_atoms CPU = 0.000 seconds
|
||||
|
||||
mass 1 14.027
|
||||
mass 2 16.043
|
||||
|
||||
pair_coeff 1 1 0.1180 3.905
|
||||
pair_coeff 2 2 0.2940 3.730
|
||||
|
||||
bond_coeff 1 260.00 1.5260
|
||||
angle_coeff 1 63.0 112.40
|
||||
dihedral_coeff 1 2.0 1 3
|
||||
|
||||
thermo 100
|
||||
minimize 0.001 0.001 500 1000
|
||||
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:187)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 14
|
||||
ghost atom cutoff = 14
|
||||
binsize = 7, bins = 7 7 7
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 8.050 | 8.050 | 8.050 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 4.3897851e+13 341.92144 4.3897851e+13 1.0886888e+14
|
||||
100 0 -4351.8383 516.49891 -3835.3394 11635.037
|
||||
190 0 -6191.8175 457.61209 -5734.2054 4365.373
|
||||
Loop time of 3.4619 on 1 procs for 190 steps with 3872 atoms
|
||||
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = energy tolerance
|
||||
Energy initial, next-to-last, final =
|
||||
43897850768892.8 -5729.17187196146 -5734.20542785978
|
||||
Force two-norm initial, final = 1.1080994e+15 72.746805
|
||||
Force max component initial, final = 4.6607099e+14 17.394645
|
||||
Final line search alpha, max atom move = 0.0041634525 0.072421779
|
||||
Iterations, force evaluations = 190 297
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 3.0549 | 3.0549 | 3.0549 | 0.0 | 88.24
|
||||
Bond | 0.10344 | 0.10344 | 0.10344 | 0.0 | 2.99
|
||||
Neigh | 0.2695 | 0.2695 | 0.2695 | 0.0 | 7.78
|
||||
Comm | 0.013772 | 0.013772 | 0.013772 | 0.0 | 0.40
|
||||
Output | 3.3707e-05 | 3.3707e-05 | 3.3707e-05 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 0.02027 | | | 0.59
|
||||
|
||||
Nlocal: 3872.00 ave 3872 max 3872 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 12122.0 ave 12122 max 12122 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 774375.0 ave 774375 max 774375 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 774375
|
||||
Ave neighs/atom = 199.99354
|
||||
Ave special neighs/atom = 3.9669421
|
||||
Neighbor list builds = 14
|
||||
Dangerous builds = 0
|
||||
reset_timestep 0
|
||||
|
||||
velocity all create 100.0 6234235
|
||||
fix 1 all nvt temp 100.0 300.0 1.0
|
||||
# dump 1 all custom 100 cychex-methane.lammpstrj id xu yu zu
|
||||
run 2500
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.925 | 6.925 | 6.925 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 100 -6191.8175 457.61209 -4580.3339 4842.3161
|
||||
100 106.81295 -5670.2783 921.20332 -3516.5907 5959.5039
|
||||
200 119.22024 -5701.0103 1040.0336 -3285.3283 6755.0994
|
||||
300 127.23574 -5706.7587 1023.9882 -3214.6335 6081.4162
|
||||
400 133.7471 -5734.1781 1113.1696 -3077.7387 6569.8751
|
||||
500 138.72092 -5756.3282 1191.5668 -2964.1003 6433.1441
|
||||
600 149.02612 -5731.7291 1205.3124 -2806.8466 6366.853
|
||||
700 153.5469 -5670.5879 925.61956 -2973.2344 7677.5226
|
||||
800 163.38118 -5629.0757 1180.6507 -2563.216 5865.8079
|
||||
900 173.27279 -5639.6903 1160.2138 -2480.131 8168.7364
|
||||
1000 178.05354 -5579.0492 913.19337 -2611.3466 6220.8001
|
||||
1100 188.99752 -5551.4873 1178.9541 -2191.7446 7734.6527
|
||||
1200 196.9019 -5511.951 1121.4617 -2118.4942 7602.4591
|
||||
1300 202.98293 -5433.6794 1194.3592 -1897.1579 7067.1876
|
||||
1400 212.86876 -5411.3798 1276.3809 -1678.7668 8867.2713
|
||||
1500 221.26247 -5359.7405 1390.3889 -1416.2668 6939.8559
|
||||
1600 228.1783 -5288.5782 1375.3053 -1280.3883 9387.8277
|
||||
1700 234.74001 -5255.1136 1192.2292 -1354.2862 7400.1124
|
||||
1800 244.1285 -5282.2876 1386.5554 -1078.8029 9473.6491
|
||||
1900 253.62148 -5158.5569 1242.3041 -989.78669 8596.2722
|
||||
2000 260.24011 -5157.2005 1477.2039 -677.16002 9136.1769
|
||||
2100 263.80129 -5096.4397 1403.9977 -648.51387 9640.0807
|
||||
2200 278.10721 -5098.89 1545.7716 -344.11827 8509.7183
|
||||
2300 278.05084 -5053.818 1495.944 -349.52438 10299.97
|
||||
2400 287.92949 -5011.3524 1527.0261 -161.98978 8854.8877
|
||||
2500 302.37248 -4957.687 1700.6563 231.95939 10617.134
|
||||
Loop time of 18.7845 on 1 procs for 2500 steps with 3872 atoms
|
||||
|
||||
Performance: 11.499 ns/day, 2.087 hours/ns, 133.089 timesteps/s
|
||||
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 17.14 | 17.14 | 17.14 | 0.0 | 91.25
|
||||
Bond | 0.74217 | 0.74217 | 0.74217 | 0.0 | 3.95
|
||||
Neigh | 0.65005 | 0.65005 | 0.65005 | 0.0 | 3.46
|
||||
Comm | 0.10364 | 0.10364 | 0.10364 | 0.0 | 0.55
|
||||
Output | 0.0006739 | 0.0006739 | 0.0006739 | 0.0 | 0.00
|
||||
Modify | 0.099647 | 0.099647 | 0.099647 | 0.0 | 0.53
|
||||
Other | | 0.04816 | | | 0.26
|
||||
|
||||
Nlocal: 3872.00 ave 3872 max 3872 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11793.0 ave 11793 max 11793 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 770411.0 ave 770411 max 770411 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 770411
|
||||
Ave neighs/atom = 198.96978
|
||||
Ave special neighs/atom = 3.9669421
|
||||
Neighbor list builds = 33
|
||||
Dangerous builds = 0
|
||||
write_data template-mix.data
|
||||
System init for write_data ...
|
||||
Total wall time: 0:00:22
|
||||
176
examples/template/log.22Oct20.template-mix.g++.4
Normal file
176
examples/template/log.22Oct20.template-mix.g++.4
Normal file
@ -0,0 +1,176 @@
|
||||
LAMMPS (22 Oct 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# demo for atom style template simulating a cyclohexane methane mixture
|
||||
# part 1: creating system with create_atoms
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
molecule cychex cyclohexane.mol
|
||||
Read molecule template cychex:
|
||||
1 molecules
|
||||
6 atoms with max type 1
|
||||
6 bonds with max type 1
|
||||
6 angles with max type 1
|
||||
6 dihedrals with max type 1
|
||||
0 impropers with max type 0
|
||||
atom_style template cychex
|
||||
|
||||
pair_style lj/cut 12.0
|
||||
pair_modify mix geometric tail yes
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style harmonic
|
||||
|
||||
lattice sc 6.0
|
||||
Lattice spacing in x,y,z = 6.0000000 6.0000000 6.0000000
|
||||
variable boxlen index 4.0
|
||||
region box block -${boxlen} ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
|
||||
region box block -4.0 ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
|
||||
region box block -4.0 4.0 -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
|
||||
region box block -4.0 4.0 -4.0 ${boxlen} -${boxlen} ${boxlen} units lattice
|
||||
region box block -4.0 4.0 -4.0 4.0 -${boxlen} ${boxlen} units lattice
|
||||
region box block -4.0 4.0 -4.0 4.0 -4.0 ${boxlen} units lattice
|
||||
region box block -4.0 4.0 -4.0 4.0 -4.0 4.0 units lattice
|
||||
create_box 2 box bond/types 1 angle/types 1 dihedral/types 1
|
||||
Created orthogonal box = (-24.000000 -24.000000 -24.000000) to (24.000000 24.000000 24.000000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
|
||||
create_atoms 0 box mol cychex 734594
|
||||
Created 3072 atoms
|
||||
create_atoms CPU = 0.001 seconds
|
||||
create_atoms 2 random 800 495437 box
|
||||
Created 800 atoms
|
||||
create_atoms CPU = 0.000 seconds
|
||||
|
||||
mass 1 14.027
|
||||
mass 2 16.043
|
||||
|
||||
pair_coeff 1 1 0.1180 3.905
|
||||
pair_coeff 2 2 0.2940 3.730
|
||||
|
||||
bond_coeff 1 260.00 1.5260
|
||||
angle_coeff 1 63.0 112.40
|
||||
dihedral_coeff 1 2.0 1 3
|
||||
|
||||
thermo 100
|
||||
minimize 0.001 0.001 500 1000
|
||||
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:187)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 14
|
||||
ghost atom cutoff = 14
|
||||
binsize = 7, bins = 7 7 7
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.345 | 5.441 | 5.728 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 7.5430044e+16 341.92144 7.5430044e+16 1.8707026e+17
|
||||
100 0 -3410.6986 572.28283 -2838.4158 14603.831
|
||||
200 0 -6109.2306 483.67771 -5625.5529 5069.1821
|
||||
204 0 -6137.0238 483.14639 -5653.8774 4952.4081
|
||||
Loop time of 1.08919 on 4 procs for 204 steps with 3872 atoms
|
||||
|
||||
97.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = energy tolerance
|
||||
Energy initial, next-to-last, final =
|
||||
7.54300441078755e+16 -5648.75822692028 -5653.87742448419
|
||||
Force two-norm initial, final = 8.7430661e+18 74.636845
|
||||
Force max component initial, final = 4.1468626e+18 8.6800755
|
||||
Final line search alpha, max atom move = 0.0032186736 0.02793833
|
||||
Iterations, force evaluations = 204 328
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.8748 | 0.88765 | 0.9004 | 1.2 | 81.50
|
||||
Bond | 0.029354 | 0.029865 | 0.030434 | 0.2 | 2.74
|
||||
Neigh | 0.07699 | 0.077483 | 0.077966 | 0.2 | 7.11
|
||||
Comm | 0.072926 | 0.084481 | 0.097433 | 3.8 | 7.76
|
||||
Output | 4.7316e-05 | 0.00010999 | 0.00029778 | 0.0 | 0.01
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 0.009602 | | | 0.88
|
||||
|
||||
Nlocal: 968.000 ave 980 max 954 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||
Nghost: 6630.00 ave 6644 max 6616 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
Neighs: 193550.0 ave 195957 max 191376 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 774200
|
||||
Ave neighs/atom = 199.94835
|
||||
Ave special neighs/atom = 3.9669421
|
||||
Neighbor list builds = 14
|
||||
Dangerous builds = 0
|
||||
reset_timestep 0
|
||||
|
||||
velocity all create 100.0 6234235
|
||||
fix 1 all nvt temp 100.0 300.0 1.0
|
||||
# dump 1 all custom 100 cychex-methane.lammpstrj id xu yu zu
|
||||
run 2500
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.220 | 4.507 | 4.603 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 100 -6137.0238 483.14639 -4500.0059 5429.3513
|
||||
100 107.18608 -5623.5468 925.13786 -3461.6193 5640.5924
|
||||
200 119.37927 -5671.054 1050.9079 -3242.6626 7494.8637
|
||||
300 127.21276 -5646.2809 1053.2662 -3125.143 5661.4525
|
||||
400 133.89893 -5674.1417 1139.7 -2989.42 7206.4877
|
||||
500 138.74889 -5679.3757 1234.644 -2843.7477 6741.4965
|
||||
600 150.20403 -5665.0258 1211.9245 -2719.9398 6299.2406
|
||||
700 156.0507 -5681.5445 978.62091 -2902.2989 8429.7188
|
||||
800 160.67293 -5579.9146 1214.6749 -2511.2805 5217.5425
|
||||
900 172.06808 -5627.6903 1118.4786 -2523.767 8995.6018
|
||||
1000 179.82813 -5508.1617 925.22393 -2507.9521 5760.9688
|
||||
1100 190.36338 -5536.6687 1176.6794 -2163.4405 8079.5754
|
||||
1200 195.57864 -5508.64 1163.8098 -2088.1038 7738.58
|
||||
1300 204.05249 -5401.8527 1219.9794 -1827.3697 6562.2311
|
||||
1400 211.74944 -5365.2571 1326.2667 -1595.6738 9772.2773
|
||||
1500 222.08023 -5265.4213 1418.3572 -1284.5435 6395.1161
|
||||
1600 225.86408 -5316.5874 1288.1407 -1422.2653 10163.26
|
||||
1700 232.35057 -5192.56 1254.0031 -1257.5297 7437.3606
|
||||
1800 238.16652 -5199.008 1457.8824 -992.98993 9783.4089
|
||||
1900 250.86418 -5166.917 1256.4887 -1015.7777 8635.027
|
||||
2000 262.41293 -5088.5573 1494.6069 -566.04218 9100.8833
|
||||
2100 268.55207 -5057.9273 1459.8499 -499.33144 10002.961
|
||||
2200 279.96891 -4963.9376 1526.8577 -206.59825 8943.2443
|
||||
2300 286.55635 -5047.2961 1538.5334 -202.27038 10711.176
|
||||
2400 292.56468 -4910.7083 1625.6283 90.740663 8482.6522
|
||||
2500 297.79426 -4928.7403 1686.5107 193.93377 11481.089
|
||||
Loop time of 5.70106 on 4 procs for 2500 steps with 3872 atoms
|
||||
|
||||
Performance: 37.888 ns/day, 0.633 hours/ns, 438.515 timesteps/s
|
||||
96.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 4.4476 | 4.5874 | 4.9593 | 10.1 | 80.47
|
||||
Bond | 0.18485 | 0.19038 | 0.19543 | 0.9 | 3.34
|
||||
Neigh | 0.18057 | 0.18059 | 0.18062 | 0.0 | 3.17
|
||||
Comm | 0.30256 | 0.67081 | 0.81456 | 26.1 | 11.77
|
||||
Output | 0.00042399 | 0.00053327 | 0.00085633 | 0.0 | 0.01
|
||||
Modify | 0.035251 | 0.043755 | 0.052209 | 4.0 | 0.77
|
||||
Other | | 0.02758 | | | 0.48
|
||||
|
||||
Nlocal: 968.000 ave 989 max 944 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 0 2
|
||||
Nghost: 6381.50 ave 6416 max 6351 min
|
||||
Histogram: 1 0 0 1 0 1 0 0 0 1
|
||||
Neighs: 192557.0 ave 197456 max 188754 min
|
||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 770229
|
||||
Ave neighs/atom = 198.92278
|
||||
Ave special neighs/atom = 3.9669421
|
||||
Neighbor list builds = 34
|
||||
Dangerous builds = 0
|
||||
write_data template-mix.data
|
||||
System init for write_data ...
|
||||
Total wall time: 0:00:06
|
||||
105
examples/template/log.22Oct20.tmpl-data-mix.g++.1
Normal file
105
examples/template/log.22Oct20.tmpl-data-mix.g++.1
Normal file
@ -0,0 +1,105 @@
|
||||
LAMMPS (22 Oct 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# demo for atom style template simulating a cyclohexane methane mixture
|
||||
# part 2: continuing from data file
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
molecule cychex cyclohexane.mol
|
||||
Read molecule template cychex:
|
||||
1 molecules
|
||||
6 atoms with max type 1
|
||||
6 bonds with max type 1
|
||||
6 angles with max type 1
|
||||
6 dihedrals with max type 1
|
||||
0 impropers with max type 0
|
||||
atom_style template cychex
|
||||
|
||||
pair_style lj/cut 12.0
|
||||
pair_modify mix geometric tail yes
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style harmonic
|
||||
|
||||
read_data template-mix.data
|
||||
Reading data file ...
|
||||
orthogonal box = (-24.000000 -24.000000 -24.000000) to (24.000000 24.000000 24.000000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
3872 atoms
|
||||
reading velocities ...
|
||||
3872 velocities
|
||||
3072 template bonds
|
||||
3072 template angles
|
||||
3072 template dihedrals
|
||||
read_data CPU = 0.016 seconds
|
||||
|
||||
thermo 100
|
||||
|
||||
fix 1 all nvt temp 300.0 300.0 1.0
|
||||
# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu
|
||||
run 2000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 14
|
||||
ghost atom cutoff = 14
|
||||
binsize = 7, bins = 7 7 7
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.879 | 6.879 | 6.879 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 302.37248 -4957.687 1700.6563 231.95939 10617.134
|
||||
100 305.85975 -4885.1313 1589.9657 234.06312 9178.0262
|
||||
200 296.72843 -4951.5636 1681.209 153.51039 10767.695
|
||||
300 308.16536 -4956.3355 1604.2261 203.72314 9266.9134
|
||||
400 297.43236 -4959.7758 1596.8717 69.083277 10221.765
|
||||
500 304.09059 -5004.7041 1531.3818 35.492587 9778.2126
|
||||
600 301.19423 -4974.2139 1694.3778 195.55858 9597.0895
|
||||
700 297.83153 -4993.867 1671.6871 114.41347 10360.771
|
||||
800 301.50873 -5038.4606 1671.0584 111.62133 8730.9918
|
||||
900 298.13466 -5056.328 1719.8923 103.65538 10561.792
|
||||
1000 297.16177 -4951.3098 1655.784 133.33949 8784.2239
|
||||
1100 303.33432 -4972.3579 1696.3014 224.03195 10764.88
|
||||
1200 307.51509 -4909.5175 1773.9263 412.73795 9220.984
|
||||
1300 305.02405 -4974.013 1714.5967 260.16943 10357.602
|
||||
1400 293.6948 -4998.3679 1683.6803 74.173172 9499.7569
|
||||
1500 300.79313 -4978.7126 1719.2548 211.30869 9602.7975
|
||||
1600 302.62922 -4924.5134 1709.726 277.16506 10649.017
|
||||
1700 301.27221 -4935.4932 1744.1182 284.9194 9169.4275
|
||||
1800 296.72398 -5019.7387 1712.9372 117.0122 10540.894
|
||||
1900 301.63962 -4971.0508 1757.1132 266.59621 8983.2539
|
||||
2000 304.05902 -5013.5663 1752.1581 247.04237 10422.56
|
||||
Loop time of 15.3127 on 1 procs for 2000 steps with 3872 atoms
|
||||
|
||||
Performance: 11.285 ns/day, 2.127 hours/ns, 130.610 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 13.831 | 13.831 | 13.831 | 0.0 | 90.32
|
||||
Bond | 0.58974 | 0.58974 | 0.58974 | 0.0 | 3.85
|
||||
Neigh | 0.69463 | 0.69463 | 0.69463 | 0.0 | 4.54
|
||||
Comm | 0.082146 | 0.082146 | 0.082146 | 0.0 | 0.54
|
||||
Output | 0.00053225 | 0.00053225 | 0.00053225 | 0.0 | 0.00
|
||||
Modify | 0.077863 | 0.077863 | 0.077863 | 0.0 | 0.51
|
||||
Other | | 0.03663 | | | 0.24
|
||||
|
||||
Nlocal: 3872.00 ave 3872 max 3872 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11716.0 ave 11716 max 11716 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 769907.0 ave 769907 max 769907 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 769907
|
||||
Ave neighs/atom = 198.83962
|
||||
Ave special neighs/atom = 3.9669421
|
||||
Neighbor list builds = 35
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:15
|
||||
105
examples/template/log.22Oct20.tmpl-data-mix.g++.4
Normal file
105
examples/template/log.22Oct20.tmpl-data-mix.g++.4
Normal file
@ -0,0 +1,105 @@
|
||||
LAMMPS (22 Oct 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# demo for atom style template simulating a cyclohexane methane mixture
|
||||
# part 2: continuing from data file
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
molecule cychex cyclohexane.mol
|
||||
Read molecule template cychex:
|
||||
1 molecules
|
||||
6 atoms with max type 1
|
||||
6 bonds with max type 1
|
||||
6 angles with max type 1
|
||||
6 dihedrals with max type 1
|
||||
0 impropers with max type 0
|
||||
atom_style template cychex
|
||||
|
||||
pair_style lj/cut 12.0
|
||||
pair_modify mix geometric tail yes
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style harmonic
|
||||
|
||||
read_data template-mix.data
|
||||
Reading data file ...
|
||||
orthogonal box = (-24.000000 -24.000000 -24.000000) to (24.000000 24.000000 24.000000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
3872 atoms
|
||||
reading velocities ...
|
||||
3872 velocities
|
||||
3072 template bonds
|
||||
3072 template angles
|
||||
3072 template dihedrals
|
||||
read_data CPU = 0.016 seconds
|
||||
|
||||
thermo 100
|
||||
|
||||
fix 1 all nvt temp 300.0 300.0 1.0
|
||||
# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu
|
||||
run 2000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 14
|
||||
ghost atom cutoff = 14
|
||||
binsize = 7, bins = 7 7 7
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.193 | 4.289 | 4.575 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 297.79426 -4928.7403 1686.5107 193.93377 11481.089
|
||||
100 298.75001 -4870.5672 1619.1613 195.78563 8813.1303
|
||||
200 301.9265 -4884.8594 1745.0359 344.02042 11561.79
|
||||
300 298.78957 -4854.0769 1638.3567 231.92774 9180.5245
|
||||
400 302 -4951.4895 1664.5419 197.74463 10784.638
|
||||
500 299.17946 -4983.7996 1615.0068 83.354011 9578.745
|
||||
600 294.32777 -5000.7554 1591.1992 -13.391775 9181.3926
|
||||
700 300.90925 -4959.9309 1653.6347 165.81003 11121.514
|
||||
800 293.14833 -4895.5912 1707.8754 194.83943 8397.927
|
||||
900 299.0508 -5032.8395 1726.0885 143.91128 11478.847
|
||||
1000 295.15206 -4888.4533 1777.4719 294.69437 8388.738
|
||||
1100 301.13534 -5004.2113 1761.645 232.14877 11246.198
|
||||
1200 296.93159 -4944.3223 1703.1744 185.06123 8808.4178
|
||||
1300 300.79377 -5011.7826 1642.093 101.08422 10390.705
|
||||
1400 295.85952 -4987.9927 1708.8415 134.68768 9680.88
|
||||
1500 296.37146 -5009.887 1637.2239 47.082942 9235.3487
|
||||
1600 298.68972 -4962.1273 1747.402 231.77054 10941.114
|
||||
1700 299.03141 -5022.0046 1755.8881 184.32195 8248.312
|
||||
1800 297.26645 -5023.9459 1740.9512 147.07837 11357.02
|
||||
1900 293.16007 -5023.8887 1754.1333 112.93534 7969.1102
|
||||
2000 307.66497 -5046.5928 1803.9999 307.46576 11249.704
|
||||
Loop time of 4.72996 on 4 procs for 2000 steps with 3872 atoms
|
||||
|
||||
Performance: 36.533 ns/day, 0.657 hours/ns, 422.837 timesteps/s
|
||||
96.8% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 3.6012 | 3.7424 | 4.0388 | 9.0 | 79.12
|
||||
Bond | 0.14459 | 0.15175 | 0.15709 | 1.3 | 3.21
|
||||
Neigh | 0.19337 | 0.19339 | 0.19341 | 0.0 | 4.09
|
||||
Comm | 0.29583 | 0.58602 | 0.72455 | 22.6 | 12.39
|
||||
Output | 0.00034471 | 0.00061632 | 0.0014299 | 0.0 | 0.01
|
||||
Modify | 0.02601 | 0.038184 | 0.05025 | 6.1 | 0.81
|
||||
Other | | 0.01759 | | | 0.37
|
||||
|
||||
Nlocal: 968.000 ave 979 max 948 min
|
||||
Histogram: 1 0 0 0 0 0 0 1 1 1
|
||||
Nghost: 6321.25 ave 6336 max 6309 min
|
||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||
Neighs: 192540.0 ave 195406 max 187182 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
||||
|
||||
Total # of neighbors = 770161
|
||||
Ave neighs/atom = 198.90522
|
||||
Ave special neighs/atom = 3.9669421
|
||||
Neighbor list builds = 35
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:04
|
||||
17011
examples/template/molecular-mix.data
Normal file
17011
examples/template/molecular-mix.data
Normal file
File diff suppressed because it is too large
Load Diff
7783
examples/template/template-mix.data
Normal file
7783
examples/template/template-mix.data
Normal file
File diff suppressed because it is too large
Load Diff
Reference in New Issue
Block a user