type labels for create_atoms_polystyrene example
This commit is contained in:
Jacob Gissinger
@ -1,456 +0,0 @@
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molecule template: end of chain plus polymerized styrene
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46 atoms
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48 bonds
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81 angles
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121 dihedrals
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35 impropers
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1 fragments
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Fragments
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create_fit 34 44
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Types
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1 1
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2 2
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3 1
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4 5
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5 1
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6 2
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7 1
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8 2
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9 1
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10 2
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11 1
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12 2
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13 2
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14 6
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15 2
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16 2
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17 1
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18 2
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19 1
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20 5
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21 1
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22 2
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23 1
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24 2
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25 1
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26 2
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27 1
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28 2
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29 2
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30 6
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31 1
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32 2
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33 1
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34 5
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35 1
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36 2
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37 1
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38 2
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39 1
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40 2
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41 1
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42 2
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43 2
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44 6
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45 2
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46 2
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Charges
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1 -0.129000
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2 0.123700
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3 0.026600
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4 -0.018200
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5 -0.129000
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6 0.123700
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7 -0.173400
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8 0.140300
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9 -0.113400
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10 0.128800
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11 -0.173400
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12 0.140300
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13 0.051600
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14 -0.069600
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15 0.035400
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16 0.035400
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17 -0.129000
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18 0.123700
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19 0.026600
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20 -0.018200
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21 -0.129000
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22 0.123700
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23 -0.173400
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24 0.140300
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25 -0.113400
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26 0.128800
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27 -0.173400
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28 0.140300
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29 0.051600
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30 -0.069600
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31 -0.129000
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32 0.123700
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33 0.026600
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34 -0.018200
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35 -0.129000
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36 0.123700
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37 -0.173400
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38 0.140300
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39 -0.113400
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40 0.128800
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41 -0.173400
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42 0.140300
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43 0.051600
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44 -0.069600
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45 0.035400
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46 0.035400
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Coords
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1 24.130699 1.043900 -1.309300
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2 25.062700 1.582900 -1.309300
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3 22.900700 1.753900 -1.309300
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4 22.900700 3.253900 -1.309300
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5 21.670700 1.043900 -1.309300
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6 20.738701 1.582900 -1.309300
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7 21.670700 -0.376100 -1.309300
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8 20.738701 -0.915100 -1.309300
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9 22.900700 -1.086100 -1.309300
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10 22.900700 -2.163100 -1.309300
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11 24.130699 -0.376100 -1.309300
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12 25.062700 -0.915100 -1.309300
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13 23.766701 3.658900 -0.952300
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14 21.622700 3.802900 -1.871300
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15 21.672701 4.544900 -1.970300
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16 20.979700 2.979900 -2.165300
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17 13.465800 0.682500 -1.658900
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18 14.397800 1.221500 -1.658900
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19 12.235800 1.392500 -1.658900
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20 12.235800 2.892500 -1.658900
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21 11.005800 0.682500 -1.658900
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22 10.073800 1.221500 -1.658900
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23 11.005800 -0.737500 -1.658900
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24 10.073800 -1.276500 -1.658900
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25 12.235800 -1.447500 -1.658900
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26 12.235800 -2.524500 -1.658900
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27 13.465800 -0.737500 -1.658900
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28 14.397800 -1.276500 -1.658900
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29 13.101800 3.297500 -1.301900
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30 10.957800 3.441500 -2.220900
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31 18.663500 0.855500 -1.372100
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32 19.595501 1.394500 -1.372100
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33 17.433500 1.565500 -1.372100
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34 17.433500 3.065500 -1.372100
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35 16.203501 0.855500 -1.372100
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36 15.271500 1.394500 -1.372100
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37 16.203501 -0.564500 -1.372100
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38 15.271500 -1.103500 -1.372100
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39 17.433500 -1.274500 -1.372100
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40 17.433500 -2.351500 -1.372100
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41 18.663500 -0.564500 -1.372100
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42 19.595501 -1.103500 -1.372100
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43 18.299500 3.470500 -1.015100
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44 16.155500 3.614500 -1.934100
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45 16.205500 4.356500 -2.033100
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46 15.512500 2.791500 -2.228100
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Bonds
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1 1 1 2
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2 2 1 3
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3 2 1 11
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4 11 3 4
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5 2 3 5
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6 12 13 4
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7 13 4 14
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8 1 5 6
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9 2 5 7
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10 1 7 8
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11 2 7 9
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12 1 9 10
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13 2 9 11
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14 1 11 12
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15 10 15 14
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16 10 16 14
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17 9 14 34
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18 1 17 18
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19 2 17 19
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20 2 17 27
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21 7 19 20
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22 2 19 21
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23 8 29 20
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24 9 30 20
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25 9 44 20
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26 1 21 22
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27 2 21 23
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28 1 23 24
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29 2 23 25
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30 1 25 26
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31 2 25 27
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32 1 27 28
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33 1 31 32
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34 2 31 33
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35 2 31 41
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36 7 33 34
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37 2 33 35
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38 8 43 34
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39 9 44 34
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40 1 35 36
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41 2 35 37
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42 1 37 38
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43 2 37 39
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44 1 39 40
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45 2 39 41
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46 1 41 42
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47 10 45 44
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48 10 46 44
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Angles
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1 1 3 1 2
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2 1 11 1 2
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3 2 3 1 11
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4 17 1 3 4
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5 2 1 3 5
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6 17 5 3 4
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7 18 3 4 13
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8 19 3 4 14
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9 20 13 4 14
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10 1 3 5 6
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11 2 3 5 7
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12 1 7 5 6
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13 1 5 7 8
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14 2 5 7 9
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15 1 9 7 8
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16 1 7 9 10
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17 2 7 9 11
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18 1 11 9 10
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19 2 1 11 9
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20 1 1 11 12
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21 1 9 11 12
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22 21 15 14 4
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23 21 16 14 4
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24 22 4 14 34
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25 15 15 14 16
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26 14 15 14 34
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27 14 16 14 34
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28 1 19 17 18
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29 1 27 17 18
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30 2 19 17 27
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31 9 17 19 20
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32 2 17 19 21
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33 9 21 19 20
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34 10 19 20 29
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35 11 19 20 30
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36 11 19 20 44
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37 12 29 20 30
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38 12 29 20 44
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39 13 30 20 44
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40 1 19 21 22
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41 2 19 21 23
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42 1 23 21 22
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43 1 21 23 24
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44 2 21 23 25
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45 1 25 23 24
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46 1 23 25 26
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47 2 23 25 27
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48 1 27 25 26
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49 2 17 27 25
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50 1 17 27 28
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51 1 25 27 28
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52 1 33 31 32
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53 1 41 31 32
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54 2 33 31 41
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55 9 31 33 34
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56 2 31 33 35
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57 9 35 33 34
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58 11 33 34 14
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59 12 43 34 14
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60 13 14 34 44
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61 10 33 34 43
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62 11 33 34 44
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63 12 43 34 44
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64 1 33 35 36
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65 2 33 35 37
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66 1 37 35 36
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67 1 35 37 38
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68 2 35 37 39
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69 1 39 37 38
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70 1 37 39 40
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71 2 37 39 41
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72 1 41 39 40
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73 2 31 41 39
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74 1 31 41 42
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75 1 39 41 42
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76 16 20 44 34
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77 14 45 44 20
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78 14 46 44 20
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79 14 45 44 34
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80 14 46 44 34
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81 15 45 44 46
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Dihedrals
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1 20 2 1 3 4
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2 2 5 3 1 2
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3 21 11 1 3 4
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4 4 11 1 3 5
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5 2 9 11 1 2
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6 5 2 1 11 12
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7 4 3 1 11 9
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8 2 3 1 11 12
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9 22 1 3 4 13
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10 23 1 3 4 14
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11 22 5 3 4 13
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12 23 5 3 4 14
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13 2 1 3 5 6
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14 4 1 3 5 7
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15 20 6 5 3 4
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16 21 7 5 3 4
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17 24 3 4 14 15
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18 24 3 4 14 16
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19 25 3 4 14 34
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20 26 13 4 14 15
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21 26 13 4 14 16
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22 27 13 4 14 34
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23 2 3 5 7 8
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24 4 3 5 7 9
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25 5 6 5 7 8
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26 2 9 7 5 6
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27 2 5 7 9 10
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28 4 5 7 9 11
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29 5 8 7 9 10
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30 2 11 9 7 8
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31 4 7 9 11 1
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32 2 7 9 11 12
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33 2 1 11 9 10
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34 5 10 9 11 12
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35 28 4 14 34 33
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36 29 4 14 34 43
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37 30 4 14 34 44
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38 31 15 14 34 33
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39 32 15 14 34 43
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40 33 15 14 34 44
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41 31 16 14 34 33
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42 32 16 14 34 43
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43 33 16 14 34 44
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44 10 18 17 19 20
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45 2 21 19 17 18
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46 11 27 17 19 20
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47 4 27 17 19 21
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48 2 25 27 17 18
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49 5 18 17 27 28
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50 4 19 17 27 25
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51 2 19 17 27 28
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52 12 17 19 20 29
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53 13 17 19 20 30
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54 13 17 19 20 44
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55 12 21 19 20 29
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56 13 21 19 20 30
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57 13 21 19 20 44
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58 2 17 19 21 22
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59 4 17 19 21 23
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60 10 22 21 19 20
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61 11 23 21 19 20
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62 34 34 44 20 19
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63 31 45 44 20 19
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64 31 46 44 20 19
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65 35 34 44 20 29
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66 32 45 44 20 29
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67 32 46 44 20 29
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68 36 34 44 20 30
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69 33 45 44 20 30
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70 33 46 44 20 30
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71 2 19 21 23 24
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72 4 19 21 23 25
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73 5 22 21 23 24
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74 2 25 23 21 22
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75 2 21 23 25 26
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76 4 21 23 25 27
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77 5 24 23 25 26
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78 2 27 25 23 24
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79 4 23 25 27 17
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80 2 23 25 27 28
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81 2 17 27 25 26
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82 5 26 25 27 28
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83 10 32 31 33 34
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84 2 35 33 31 32
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85 11 41 31 33 34
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86 4 41 31 33 35
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87 2 39 41 31 32
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88 5 32 31 41 42
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89 4 33 31 41 39
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90 2 33 31 41 42
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91 13 31 33 34 14
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92 12 31 33 34 43
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93 13 31 33 34 44
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94 13 35 33 34 14
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95 12 35 33 34 43
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96 13 35 33 34 44
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97 2 31 33 35 36
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98 4 31 33 35 37
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99 10 36 35 33 34
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100 11 37 35 33 34
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101 36 20 44 34 14
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102 33 45 44 34 14
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103 33 46 44 34 14
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104 34 20 44 34 33
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105 31 45 44 34 33
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106 31 46 44 34 33
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107 35 20 44 34 43
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108 32 45 44 34 43
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109 32 46 44 34 43
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110 2 33 35 37 38
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111 4 33 35 37 39
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112 5 36 35 37 38
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113 2 39 37 35 36
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114 2 35 37 39 40
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115 4 35 37 39 41
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116 5 38 37 39 40
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117 2 41 39 37 38
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118 4 37 39 41 31
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119 2 37 39 41 42
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120 2 31 41 39 40
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121 5 40 39 41 42
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|
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Impropers
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1 1 3 1 11 2
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2 8 1 3 5 4
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3 9 3 4 13 14
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4 1 3 5 7 6
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5 1 5 7 9 8
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6 1 7 9 11 10
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7 1 1 11 9 12
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8 1 19 17 27 18
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9 5 17 19 21 20
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10 1 19 21 23 22
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11 1 21 23 25 24
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12 1 23 25 27 26
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13 1 17 27 25 28
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14 1 33 31 41 32
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15 5 31 33 35 34
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16 1 33 35 37 36
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17 1 35 37 39 38
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18 1 37 39 41 40
|
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19 1 31 41 39 42
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||||
20 1 15 14 16 4
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21 1 15 14 4 34
|
||||
22 1 16 14 4 34
|
||||
23 1 15 14 16 34
|
||||
24 1 19 20 29 30
|
||||
25 1 19 20 29 44
|
||||
26 1 19 20 30 44
|
||||
27 1 29 20 30 44
|
||||
28 1 33 34 43 14
|
||||
29 1 33 34 14 44
|
||||
30 1 43 34 14 44
|
||||
31 1 33 34 43 44
|
||||
32 1 45 44 34 20
|
||||
33 1 46 44 34 20
|
||||
34 1 45 44 46 20
|
||||
35 1 45 44 46 34
|
||||
@ -0,0 +1,489 @@
|
||||
molecule template: end of chain plus polymerized styrene
|
||||
|
||||
46 atoms
|
||||
48 bonds
|
||||
81 angles
|
||||
121 dihedrals
|
||||
19 impropers
|
||||
1 fragments
|
||||
|
||||
Fragments
|
||||
|
||||
create_fit 34 44
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||||
|
||||
Coords
|
||||
|
||||
1 24.130699158 1.043900013 -1.309299946
|
||||
2 25.062700272 1.582900047 -1.309299946
|
||||
3 22.900699615 1.753900051 -1.309299946
|
||||
4 22.900699615 3.253900051 -1.309299946
|
||||
5 21.670700073 1.043900013 -1.309299946
|
||||
6 20.738700867 1.582900047 -1.309299946
|
||||
7 21.670700073 -0.376100004 -1.309299946
|
||||
8 20.738700867 -0.915099978 -1.309299946
|
||||
9 22.900699615 -1.086099982 -1.309299946
|
||||
10 22.900699615 -2.163100004 -1.309299946
|
||||
11 24.130699158 -0.376100004 -1.309299946
|
||||
12 25.062700272 -0.915099978 -1.309299946
|
||||
13 23.766700745 3.658900023 -0.952300012
|
||||
14 21.622699738 3.802900076 -1.871299982
|
||||
15 21.672700882 4.544899940 -1.970299959
|
||||
16 20.979700089 2.979899883 -2.165299892
|
||||
17 13.465800285 0.682500005 -1.658900023
|
||||
18 14.397800446 1.221500039 -1.658900023
|
||||
19 12.235799789 1.392500043 -1.658900023
|
||||
20 12.235799789 2.892499924 -1.658900023
|
||||
21 11.005800247 0.682500005 -1.658900023
|
||||
22 10.073800087 1.221500039 -1.658900023
|
||||
23 11.005800247 -0.737500012 -1.658900023
|
||||
24 10.073800087 -1.276499987 -1.658900023
|
||||
25 12.235799789 -1.447499990 -1.658900023
|
||||
26 12.235799789 -2.524499893 -1.658900023
|
||||
27 13.465800285 -0.737500012 -1.658900023
|
||||
28 14.397800446 -1.276499987 -1.658900023
|
||||
29 13.101799965 3.297499895 -1.301900029
|
||||
30 10.957799911 3.441499949 -2.220900059
|
||||
31 18.663499832 0.855499983 -1.372099996
|
||||
32 19.595500946 1.394500017 -1.372099996
|
||||
33 17.433500290 1.565500021 -1.372099996
|
||||
34 17.433500290 3.065500021 -1.372099996
|
||||
35 16.203500748 0.855499983 -1.372099996
|
||||
36 15.271499634 1.394500017 -1.372099996
|
||||
37 16.203500748 -0.564499974 -1.372099996
|
||||
38 15.271499634 -1.103500009 -1.372099996
|
||||
39 17.433500290 -1.274500012 -1.372099996
|
||||
40 17.433500290 -2.351500034 -1.372099996
|
||||
41 18.663499832 -0.564499974 -1.372099996
|
||||
42 19.595500946 -1.103500009 -1.372099996
|
||||
43 18.299499512 3.470499992 -1.015100002
|
||||
44 16.155500412 3.614500046 -1.934100032
|
||||
45 16.205499649 4.356500149 -2.033099890
|
||||
46 15.512499809 2.791500092 -2.228100061
|
||||
|
||||
Types
|
||||
|
||||
1 cp
|
||||
2 hc
|
||||
3 cp
|
||||
4 c1
|
||||
5 cp
|
||||
6 hc
|
||||
7 cp
|
||||
8 hc
|
||||
9 cp
|
||||
10 hc
|
||||
11 cp
|
||||
12 hc
|
||||
13 hc
|
||||
14 c2
|
||||
15 hc
|
||||
16 hc
|
||||
17 cp
|
||||
18 hc
|
||||
19 cp
|
||||
20 c1
|
||||
21 cp
|
||||
22 hc
|
||||
23 cp
|
||||
24 hc
|
||||
25 cp
|
||||
26 hc
|
||||
27 cp
|
||||
28 hc
|
||||
29 hc
|
||||
30 c2
|
||||
31 cp
|
||||
32 hc
|
||||
33 cp
|
||||
34 c1
|
||||
35 cp
|
||||
36 hc
|
||||
37 cp
|
||||
38 hc
|
||||
39 cp
|
||||
40 hc
|
||||
41 cp
|
||||
42 hc
|
||||
43 hc
|
||||
44 c2
|
||||
45 hc
|
||||
46 hc
|
||||
|
||||
Charges
|
||||
|
||||
1 -0.129000
|
||||
2 0.123700
|
||||
3 0.026600
|
||||
4 -0.018200
|
||||
5 -0.129000
|
||||
6 0.123700
|
||||
7 -0.173400
|
||||
8 0.140300
|
||||
9 -0.113400
|
||||
10 0.128800
|
||||
11 -0.173400
|
||||
12 0.140300
|
||||
13 0.051600
|
||||
14 -0.069600
|
||||
15 0.035400
|
||||
16 0.035400
|
||||
17 -0.129000
|
||||
18 0.123700
|
||||
19 0.026600
|
||||
20 -0.018200
|
||||
21 -0.129000
|
||||
22 0.123700
|
||||
23 -0.173400
|
||||
24 0.140300
|
||||
25 -0.113400
|
||||
26 0.128800
|
||||
27 -0.173400
|
||||
28 0.140300
|
||||
29 0.051600
|
||||
30 -0.069600
|
||||
31 -0.129000
|
||||
32 0.123700
|
||||
33 0.026600
|
||||
34 -0.018200
|
||||
35 -0.129000
|
||||
36 0.123700
|
||||
37 -0.173400
|
||||
38 0.140300
|
||||
39 -0.113400
|
||||
40 0.128800
|
||||
41 -0.173400
|
||||
42 0.140300
|
||||
43 0.051600
|
||||
44 -0.069600
|
||||
45 0.035400
|
||||
46 0.035400
|
||||
|
||||
Molecules
|
||||
|
||||
1 1
|
||||
2 1
|
||||
3 1
|
||||
4 1
|
||||
5 1
|
||||
6 1
|
||||
7 1
|
||||
8 1
|
||||
9 1
|
||||
10 1
|
||||
11 1
|
||||
12 1
|
||||
13 1
|
||||
14 1
|
||||
15 1
|
||||
16 1
|
||||
17 1
|
||||
18 1
|
||||
19 1
|
||||
20 1
|
||||
21 1
|
||||
22 1
|
||||
23 1
|
||||
24 1
|
||||
25 1
|
||||
26 1
|
||||
27 1
|
||||
28 1
|
||||
29 1
|
||||
30 1
|
||||
31 1
|
||||
32 1
|
||||
33 1
|
||||
34 1
|
||||
35 1
|
||||
36 1
|
||||
37 1
|
||||
38 1
|
||||
39 1
|
||||
40 1
|
||||
41 1
|
||||
42 1
|
||||
43 1
|
||||
44 1
|
||||
45 1
|
||||
46 1
|
||||
|
||||
Bonds
|
||||
|
||||
1 hc-cp 1 2
|
||||
2 cp-cp 1 3
|
||||
3 cp-cp 1 11
|
||||
4 cp-c1 3 4
|
||||
5 cp-cp 3 5
|
||||
6 hc-c1 13 4
|
||||
7 c1-c2 4 14
|
||||
8 hc-cp 5 6
|
||||
9 cp-cp 5 7
|
||||
10 hc-cp 7 8
|
||||
11 cp-cp 7 9
|
||||
12 hc-cp 9 10
|
||||
13 cp-cp 9 11
|
||||
14 hc-cp 11 12
|
||||
15 hc-c2 15 14
|
||||
16 hc-c2 16 14
|
||||
17 c1-c2 34 14
|
||||
18 hc-cp 17 18
|
||||
19 cp-cp 17 19
|
||||
20 cp-cp 17 27
|
||||
21 cp-c1 19 20
|
||||
22 cp-cp 19 21
|
||||
23 hc-c1 29 20
|
||||
24 c1-c2 20 30
|
||||
25 c1-c2 20 44
|
||||
26 hc-cp 21 22
|
||||
27 cp-cp 21 23
|
||||
28 hc-cp 23 24
|
||||
29 cp-cp 23 25
|
||||
30 hc-cp 25 26
|
||||
31 cp-cp 25 27
|
||||
32 hc-cp 27 28
|
||||
33 hc-cp 31 32
|
||||
34 cp-cp 31 33
|
||||
35 cp-cp 31 41
|
||||
36 cp-c1 33 34
|
||||
37 cp-cp 33 35
|
||||
38 hc-c1 43 34
|
||||
39 c1-c2 34 44
|
||||
40 hc-cp 35 36
|
||||
41 cp-cp 35 37
|
||||
42 hc-cp 37 38
|
||||
43 cp-cp 37 39
|
||||
44 hc-cp 39 40
|
||||
45 cp-cp 39 41
|
||||
46 hc-cp 41 42
|
||||
47 hc-c2 45 44
|
||||
48 hc-c2 46 44
|
||||
|
||||
Angles
|
||||
|
||||
1 hc-cp-cp 3 1 2
|
||||
2 hc-cp-cp 11 1 2
|
||||
3 cp-cp-cp 3 1 11
|
||||
4 cp-cp-c1 1 3 4
|
||||
5 cp-cp-cp 1 3 5
|
||||
6 cp-cp-c1 5 3 4
|
||||
7 hc-c1-cp 3 4 13
|
||||
8 cp-c1-c2 3 4 14
|
||||
9 hc-c1-c2 13 4 14
|
||||
10 hc-cp-cp 3 5 6
|
||||
11 cp-cp-cp 3 5 7
|
||||
12 hc-cp-cp 7 5 6
|
||||
13 hc-cp-cp 5 7 8
|
||||
14 cp-cp-cp 5 7 9
|
||||
15 hc-cp-cp 9 7 8
|
||||
16 hc-cp-cp 7 9 10
|
||||
17 cp-cp-cp 7 9 11
|
||||
18 hc-cp-cp 11 9 10
|
||||
19 cp-cp-cp 1 11 9
|
||||
20 hc-cp-cp 1 11 12
|
||||
21 hc-cp-cp 9 11 12
|
||||
22 hc-c2-c1 15 14 4
|
||||
23 hc-c2-c1 16 14 4
|
||||
24 c1-c2-c1 4 14 34
|
||||
25 hc-c2-hc 15 14 16
|
||||
26 hc-c2-c1 15 14 34
|
||||
27 hc-c2-c1 16 14 34
|
||||
28 hc-cp-cp 19 17 18
|
||||
29 hc-cp-cp 27 17 18
|
||||
30 cp-cp-cp 19 17 27
|
||||
31 cp-cp-c1 17 19 20
|
||||
32 cp-cp-cp 17 19 21
|
||||
33 cp-cp-c1 21 19 20
|
||||
34 hc-c1-cp 19 20 29
|
||||
35 cp-c1-c2 19 20 30
|
||||
36 cp-c1-c2 19 20 44
|
||||
37 hc-c1-c2 29 20 30
|
||||
38 hc-c1-c2 29 20 44
|
||||
39 c2-c1-c2 30 20 44
|
||||
40 hc-cp-cp 19 21 22
|
||||
41 cp-cp-cp 19 21 23
|
||||
42 hc-cp-cp 23 21 22
|
||||
43 hc-cp-cp 21 23 24
|
||||
44 cp-cp-cp 21 23 25
|
||||
45 hc-cp-cp 25 23 24
|
||||
46 hc-cp-cp 23 25 26
|
||||
47 cp-cp-cp 23 25 27
|
||||
48 hc-cp-cp 27 25 26
|
||||
49 cp-cp-cp 17 27 25
|
||||
50 hc-cp-cp 17 27 28
|
||||
51 hc-cp-cp 25 27 28
|
||||
52 hc-cp-cp 33 31 32
|
||||
53 hc-cp-cp 41 31 32
|
||||
54 cp-cp-cp 33 31 41
|
||||
55 cp-cp-c1 31 33 34
|
||||
56 cp-cp-cp 31 33 35
|
||||
57 cp-cp-c1 35 33 34
|
||||
58 cp-c1-c2 33 34 14
|
||||
59 hc-c1-c2 43 34 14
|
||||
60 c2-c1-c2 14 34 44
|
||||
61 hc-c1-cp 33 34 43
|
||||
62 cp-c1-c2 33 34 44
|
||||
63 hc-c1-c2 43 34 44
|
||||
64 hc-cp-cp 33 35 36
|
||||
65 cp-cp-cp 33 35 37
|
||||
66 hc-cp-cp 37 35 36
|
||||
67 hc-cp-cp 35 37 38
|
||||
68 cp-cp-cp 35 37 39
|
||||
69 hc-cp-cp 39 37 38
|
||||
70 hc-cp-cp 37 39 40
|
||||
71 cp-cp-cp 37 39 41
|
||||
72 hc-cp-cp 41 39 40
|
||||
73 cp-cp-cp 31 41 39
|
||||
74 hc-cp-cp 31 41 42
|
||||
75 hc-cp-cp 39 41 42
|
||||
76 c1-c2-c1 20 44 34
|
||||
77 hc-c2-c1 45 44 20
|
||||
78 hc-c2-c1 46 44 20
|
||||
79 hc-c2-c1 45 44 34
|
||||
80 hc-c2-c1 46 44 34
|
||||
81 hc-c2-hc 45 44 46
|
||||
|
||||
Dihedrals
|
||||
|
||||
1 hc-cp-cp-c1 2 1 3 4
|
||||
2 hc-cp-cp-cp 5 3 1 2
|
||||
3 cp-cp-cp-c1 11 1 3 4
|
||||
4 cp-cp-cp-cp 11 1 3 5
|
||||
5 hc-cp-cp-cp 9 11 1 2
|
||||
6 hc-cp-cp-hc 2 1 11 12
|
||||
7 cp-cp-cp-cp 3 1 11 9
|
||||
8 hc-cp-cp-cp 3 1 11 12
|
||||
9 cp-cp-c1-hc 1 3 4 13
|
||||
10 cp-cp-c1-c2 1 3 4 14
|
||||
11 cp-cp-c1-hc 5 3 4 13
|
||||
12 cp-cp-c1-c2 5 3 4 14
|
||||
13 hc-cp-cp-cp 1 3 5 6
|
||||
14 cp-cp-cp-cp 1 3 5 7
|
||||
15 hc-cp-cp-c1 6 5 3 4
|
||||
16 cp-cp-cp-c1 7 5 3 4
|
||||
17 cp-c1-c2-hc 3 4 14 15
|
||||
18 cp-c1-c2-hc 3 4 14 16
|
||||
19 cp-c1-c2-c1 3 4 14 34
|
||||
20 hc-c1-c2-hc 13 4 14 15
|
||||
21 hc-c1-c2-hc 13 4 14 16
|
||||
22 hc-c1-c2-c1 13 4 14 34
|
||||
23 hc-cp-cp-cp 3 5 7 8
|
||||
24 cp-cp-cp-cp 3 5 7 9
|
||||
25 hc-cp-cp-hc 6 5 7 8
|
||||
26 hc-cp-cp-cp 9 7 5 6
|
||||
27 hc-cp-cp-cp 5 7 9 10
|
||||
28 cp-cp-cp-cp 5 7 9 11
|
||||
29 hc-cp-cp-hc 8 7 9 10
|
||||
30 hc-cp-cp-cp 11 9 7 8
|
||||
31 cp-cp-cp-cp 7 9 11 1
|
||||
32 hc-cp-cp-cp 7 9 11 12
|
||||
33 hc-cp-cp-cp 1 11 9 10
|
||||
34 hc-cp-cp-hc 10 9 11 12
|
||||
35 cp-c1-c2-c1 33 34 14 4
|
||||
36 hc-c1-c2-c1 43 34 14 4
|
||||
37 c2-c1-c2-c1 44 34 14 4
|
||||
38 cp-c1-c2-hc 33 34 14 15
|
||||
39 hc-c1-c2-hc 43 34 14 15
|
||||
40 c2-c1-c2-hc 44 34 14 15
|
||||
41 cp-c1-c2-hc 33 34 14 16
|
||||
42 hc-c1-c2-hc 43 34 14 16
|
||||
43 c2-c1-c2-hc 44 34 14 16
|
||||
44 hc-cp-cp-c1 18 17 19 20
|
||||
45 hc-cp-cp-cp 21 19 17 18
|
||||
46 cp-cp-cp-c1 27 17 19 20
|
||||
47 cp-cp-cp-cp 27 17 19 21
|
||||
48 hc-cp-cp-cp 25 27 17 18
|
||||
49 hc-cp-cp-hc 18 17 27 28
|
||||
50 cp-cp-cp-cp 19 17 27 25
|
||||
51 hc-cp-cp-cp 19 17 27 28
|
||||
52 cp-cp-c1-hc 17 19 20 29
|
||||
53 cp-cp-c1-c2 17 19 20 30
|
||||
54 cp-cp-c1-c2 17 19 20 44
|
||||
55 cp-cp-c1-hc 21 19 20 29
|
||||
56 cp-cp-c1-c2 21 19 20 30
|
||||
57 cp-cp-c1-c2 21 19 20 44
|
||||
58 hc-cp-cp-cp 17 19 21 22
|
||||
59 cp-cp-cp-cp 17 19 21 23
|
||||
60 hc-cp-cp-c1 22 21 19 20
|
||||
61 cp-cp-cp-c1 23 21 19 20
|
||||
62 cp-c1-c2-c1 19 20 44 34
|
||||
63 cp-c1-c2-hc 19 20 44 45
|
||||
64 cp-c1-c2-hc 19 20 44 46
|
||||
65 hc-c1-c2-c1 29 20 44 34
|
||||
66 hc-c1-c2-hc 29 20 44 45
|
||||
67 hc-c1-c2-hc 29 20 44 46
|
||||
68 c2-c1-c2-c1 30 20 44 34
|
||||
69 c2-c1-c2-hc 30 20 44 45
|
||||
70 c2-c1-c2-hc 30 20 44 46
|
||||
71 hc-cp-cp-cp 19 21 23 24
|
||||
72 cp-cp-cp-cp 19 21 23 25
|
||||
73 hc-cp-cp-hc 22 21 23 24
|
||||
74 hc-cp-cp-cp 25 23 21 22
|
||||
75 hc-cp-cp-cp 21 23 25 26
|
||||
76 cp-cp-cp-cp 21 23 25 27
|
||||
77 hc-cp-cp-hc 24 23 25 26
|
||||
78 hc-cp-cp-cp 27 25 23 24
|
||||
79 cp-cp-cp-cp 23 25 27 17
|
||||
80 hc-cp-cp-cp 23 25 27 28
|
||||
81 hc-cp-cp-cp 17 27 25 26
|
||||
82 hc-cp-cp-hc 26 25 27 28
|
||||
83 hc-cp-cp-c1 32 31 33 34
|
||||
84 hc-cp-cp-cp 35 33 31 32
|
||||
85 cp-cp-cp-c1 41 31 33 34
|
||||
86 cp-cp-cp-cp 41 31 33 35
|
||||
87 hc-cp-cp-cp 39 41 31 32
|
||||
88 hc-cp-cp-hc 32 31 41 42
|
||||
89 cp-cp-cp-cp 33 31 41 39
|
||||
90 hc-cp-cp-cp 33 31 41 42
|
||||
91 cp-cp-c1-c2 31 33 34 14
|
||||
92 cp-cp-c1-hc 31 33 34 43
|
||||
93 cp-cp-c1-c2 31 33 34 44
|
||||
94 cp-cp-c1-c2 35 33 34 14
|
||||
95 cp-cp-c1-hc 35 33 34 43
|
||||
96 cp-cp-c1-c2 35 33 34 44
|
||||
97 hc-cp-cp-cp 31 33 35 36
|
||||
98 cp-cp-cp-cp 31 33 35 37
|
||||
99 hc-cp-cp-c1 36 35 33 34
|
||||
100 cp-cp-cp-c1 37 35 33 34
|
||||
101 c2-c1-c2-c1 14 34 44 20
|
||||
102 c2-c1-c2-hc 14 34 44 45
|
||||
103 c2-c1-c2-hc 14 34 44 46
|
||||
104 cp-c1-c2-c1 33 34 44 20
|
||||
105 cp-c1-c2-hc 33 34 44 45
|
||||
106 cp-c1-c2-hc 33 34 44 46
|
||||
107 hc-c1-c2-c1 43 34 44 20
|
||||
108 hc-c1-c2-hc 43 34 44 45
|
||||
109 hc-c1-c2-hc 43 34 44 46
|
||||
110 hc-cp-cp-cp 33 35 37 38
|
||||
111 cp-cp-cp-cp 33 35 37 39
|
||||
112 hc-cp-cp-hc 36 35 37 38
|
||||
113 hc-cp-cp-cp 39 37 35 36
|
||||
114 hc-cp-cp-cp 35 37 39 40
|
||||
115 cp-cp-cp-cp 35 37 39 41
|
||||
116 hc-cp-cp-hc 38 37 39 40
|
||||
117 hc-cp-cp-cp 41 39 37 38
|
||||
118 cp-cp-cp-cp 37 39 41 31
|
||||
119 hc-cp-cp-cp 37 39 41 42
|
||||
120 hc-cp-cp-cp 31 41 39 40
|
||||
121 hc-cp-cp-hc 40 39 41 42
|
||||
|
||||
Impropers
|
||||
|
||||
1 hc-cp-cp-cp 3 1 11 2
|
||||
2 cp-cp-cp-c1 1 3 5 4
|
||||
3 hc-c1-cp-c2 3 4 13 14
|
||||
4 hc-cp-cp-cp 3 5 7 6
|
||||
5 hc-cp-cp-cp 5 7 9 8
|
||||
6 hc-cp-cp-cp 7 9 11 10
|
||||
7 hc-cp-cp-cp 1 11 9 12
|
||||
8 hc-cp-cp-cp 19 17 27 18
|
||||
9 cp-cp-cp-c1 17 19 21 20
|
||||
10 hc-cp-cp-cp 19 21 23 22
|
||||
11 hc-cp-cp-cp 21 23 25 24
|
||||
12 hc-cp-cp-cp 23 25 27 26
|
||||
13 hc-cp-cp-cp 17 27 25 28
|
||||
14 hc-cp-cp-cp 33 31 41 32
|
||||
15 cp-cp-cp-c1 31 33 35 34
|
||||
16 hc-cp-cp-cp 33 35 37 36
|
||||
17 hc-cp-cp-cp 35 37 39 38
|
||||
18 hc-cp-cp-cp 37 39 41 40
|
||||
19 hc-cp-cp-cp 31 41 39 42
|
||||
@ -1,294 +0,0 @@
|
||||
molecule template: end of styrene chain
|
||||
|
||||
30 atoms
|
||||
31 bonds
|
||||
51 angles
|
||||
73 dihedrals
|
||||
21 impropers
|
||||
|
||||
Types
|
||||
|
||||
1 2
|
||||
2 2
|
||||
3 6
|
||||
4 2
|
||||
5 2
|
||||
6 1
|
||||
7 2
|
||||
8 1
|
||||
9 2
|
||||
10 1
|
||||
11 2
|
||||
12 1
|
||||
13 5
|
||||
14 1
|
||||
15 2
|
||||
16 1
|
||||
17 1
|
||||
18 2
|
||||
19 1
|
||||
20 5
|
||||
21 1
|
||||
22 2
|
||||
23 1
|
||||
24 2
|
||||
25 1
|
||||
26 2
|
||||
27 1
|
||||
28 2
|
||||
29 2
|
||||
30 6
|
||||
|
||||
Coords
|
||||
|
||||
1 59.89981112372972 62.733697275315585 59.09884284578856
|
||||
2 61.41970248324232 63.42116581894993 59.52874545893742
|
||||
3 60.864754970096406 62.91724243011892 59.559720865992695
|
||||
4 62.139819000186826 61.41011937002877 60.81065044071466
|
||||
5 60.036455711425084 57.160029629288026 60.31958663310848
|
||||
6 59.734195751174056 58.18706337912225 60.20562410798949
|
||||
7 57.64574781117771 57.712432799329 59.860109977091554
|
||||
8 58.37408644866664 58.50134169314242 59.94422053768215
|
||||
9 56.94300092269842 60.093170109004795 59.5955638127831
|
||||
10 57.974275786582744 59.85577775892068 59.793714995577716
|
||||
11 58.63231375134033 61.922969938852454 59.79065033121885
|
||||
12 58.934573711591355 60.89593618901822 59.904612856337835
|
||||
13 61.30908151524225 61.68041745837013 60.28316188676589
|
||||
14 60.29468229868386 60.58165855333751 60.16601625920239
|
||||
15 61.725768540066994 58.98982945913568 60.51467315154424
|
||||
16 60.69449367618267 59.2272218092198 60.31652196874961
|
||||
17 56.90935800040509 62.609851248143706 59.150831390216375
|
||||
18 57.940632148874506 62.37245957639904 59.3489824055682
|
||||
19 56.509546622906285 63.96428799226142 59.00032568066915
|
||||
20 57.52394583946467 65.06304689729403 59.11747130823266
|
||||
21 55.14943732039887 64.27856630628159 58.738922110361806
|
||||
22 54.84717807556275 65.30559937777636 58.62495975268562
|
||||
23 54.18913939539026 63.23840787618404 58.62802424960169
|
||||
24 53.15786524692084 63.4757995479287 58.42987323424986
|
||||
25 54.58895077288906 61.88397113206633 58.77852995914891
|
||||
26 53.86061213540014 61.09506223825291 58.69441939855832
|
||||
27 55.94906007539648 61.56969281804616 59.039933529456256
|
||||
28 56.2513193202326 60.54265974655139 59.15389588713244
|
||||
29 58.35468332440925 64.79274880895268 59.64495986218142
|
||||
30 57.07961929431883 66.29987186904283 58.394030287459465
|
||||
|
||||
Charges
|
||||
|
||||
1 0.0354
|
||||
2 0.0354
|
||||
3 -0.0696
|
||||
4 0.0516
|
||||
5 0.1403
|
||||
6 -0.1734
|
||||
7 0.1288
|
||||
8 -0.1134
|
||||
9 0.1403
|
||||
10 -0.1734
|
||||
11 0.1237
|
||||
12 -0.129
|
||||
13 -0.0182
|
||||
14 0.0266
|
||||
15 0.1237
|
||||
16 -0.129
|
||||
17 -0.129
|
||||
18 0.1237
|
||||
19 0.0266
|
||||
20 -0.0182
|
||||
21 -0.129
|
||||
22 0.1237
|
||||
23 -0.1734
|
||||
24 0.1403
|
||||
25 -0.1134
|
||||
26 0.1288
|
||||
27 -0.1734
|
||||
28 0.1403
|
||||
29 0.0516
|
||||
30 -0.0696
|
||||
|
||||
Bonds
|
||||
|
||||
1 10 1 3
|
||||
2 10 2 3
|
||||
3 8 4 13
|
||||
4 1 6 5
|
||||
5 1 8 7
|
||||
6 2 8 6
|
||||
7 1 10 9
|
||||
8 2 10 8
|
||||
9 1 12 11
|
||||
10 2 12 10
|
||||
11 9 13 3
|
||||
12 7 14 13
|
||||
13 2 14 12
|
||||
14 1 16 15
|
||||
15 2 16 14
|
||||
16 2 16 6
|
||||
17 1 17 18
|
||||
18 2 17 19
|
||||
19 2 17 27
|
||||
20 7 19 20
|
||||
21 2 19 21
|
||||
22 9 20 30
|
||||
23 9 20 3
|
||||
24 1 21 22
|
||||
25 2 21 23
|
||||
26 1 23 24
|
||||
27 2 23 25
|
||||
28 1 25 26
|
||||
29 2 25 27
|
||||
30 1 27 28
|
||||
31 8 29 20
|
||||
|
||||
Angles
|
||||
|
||||
1 16 20 3 13
|
||||
2 14 2 3 20
|
||||
3 14 1 3 20
|
||||
4 14 2 3 13
|
||||
5 14 1 3 13
|
||||
6 15 2 3 1
|
||||
7 2 16 6 8
|
||||
8 1 16 6 5
|
||||
9 1 8 6 5
|
||||
10 1 10 8 7
|
||||
11 2 10 8 6
|
||||
12 1 6 8 7
|
||||
13 1 12 10 9
|
||||
14 2 12 10 8
|
||||
15 1 8 10 9
|
||||
16 1 14 12 11
|
||||
17 2 14 12 10
|
||||
18 1 10 12 11
|
||||
19 10 14 13 4
|
||||
20 11 14 13 3
|
||||
21 12 4 13 3
|
||||
22 9 16 14 13
|
||||
23 2 16 14 12
|
||||
24 9 12 14 13
|
||||
25 1 14 16 15
|
||||
26 1 6 16 15
|
||||
27 2 14 16 6
|
||||
28 1 19 17 18
|
||||
29 1 27 17 18
|
||||
30 2 19 17 27
|
||||
31 9 17 19 20
|
||||
32 2 17 19 21
|
||||
33 9 21 19 20
|
||||
34 10 19 20 29
|
||||
35 11 19 20 30
|
||||
36 11 19 20 3
|
||||
37 12 29 20 30
|
||||
38 12 29 20 3
|
||||
39 13 30 20 3
|
||||
40 1 19 21 22
|
||||
41 2 19 21 23
|
||||
42 1 23 21 22
|
||||
43 1 21 23 24
|
||||
44 2 21 23 25
|
||||
45 1 25 23 24
|
||||
46 1 23 25 26
|
||||
47 2 23 25 27
|
||||
48 1 27 25 26
|
||||
49 2 17 27 25
|
||||
50 1 17 27 28
|
||||
51 1 25 27 28
|
||||
|
||||
Dihedrals
|
||||
|
||||
1 2 8 6 16 15
|
||||
2 2 16 6 8 7
|
||||
3 2 6 8 10 9
|
||||
4 4 10 8 6 16
|
||||
5 2 10 8 6 5
|
||||
6 5 7 8 6 5
|
||||
7 2 8 10 12 11
|
||||
8 2 12 10 8 7
|
||||
9 4 12 10 8 6
|
||||
10 5 9 10 8 7
|
||||
11 10 11 12 14 13
|
||||
12 11 10 12 14 13
|
||||
13 2 14 12 10 9
|
||||
14 4 14 12 10 8
|
||||
15 5 11 12 10 9
|
||||
16 17 14 13 3 20
|
||||
17 14 14 13 3 2
|
||||
18 14 14 13 3 1
|
||||
19 18 4 13 3 20
|
||||
20 15 4 13 3 2
|
||||
21 15 4 13 3 1
|
||||
22 2 12 14 16 15
|
||||
23 12 16 14 13 4
|
||||
24 13 16 14 13 3
|
||||
25 12 12 14 13 4
|
||||
26 13 12 14 13 3
|
||||
27 2 16 14 12 11
|
||||
28 4 16 14 12 10
|
||||
29 10 15 16 14 13
|
||||
30 11 6 16 14 13
|
||||
31 4 6 16 14 12
|
||||
32 5 15 16 6 5
|
||||
33 4 14 16 6 8
|
||||
34 2 14 16 6 5
|
||||
35 10 18 17 19 20
|
||||
36 11 27 17 19 20
|
||||
37 4 27 17 19 21
|
||||
38 5 18 17 27 28
|
||||
39 4 19 17 27 25
|
||||
40 2 19 17 27 28
|
||||
41 2 21 19 17 18
|
||||
42 12 17 19 20 29
|
||||
43 13 17 19 20 30
|
||||
44 13 17 19 20 3
|
||||
45 12 21 19 20 29
|
||||
46 13 21 19 20 30
|
||||
47 13 21 19 20 3
|
||||
48 2 17 19 21 22
|
||||
49 4 17 19 21 23
|
||||
50 17 19 20 3 13
|
||||
51 14 19 20 3 2
|
||||
52 14 19 20 3 1
|
||||
53 18 29 20 3 13
|
||||
54 15 29 20 3 2
|
||||
55 15 29 20 3 1
|
||||
56 19 30 20 3 13
|
||||
57 16 30 20 3 2
|
||||
58 16 30 20 3 1
|
||||
59 10 22 21 19 20
|
||||
60 11 23 21 19 20
|
||||
61 2 19 21 23 24
|
||||
62 4 19 21 23 25
|
||||
63 5 22 21 23 24
|
||||
64 2 25 23 21 22
|
||||
65 2 21 23 25 26
|
||||
66 4 21 23 25 27
|
||||
67 5 24 23 25 26
|
||||
68 2 27 25 23 24
|
||||
69 4 23 25 27 17
|
||||
70 2 23 25 27 28
|
||||
71 5 26 25 27 28
|
||||
72 2 25 27 17 18
|
||||
73 2 17 27 25 26
|
||||
|
||||
Impropers
|
||||
|
||||
1 1 2 3 13 20
|
||||
2 1 1 3 13 20
|
||||
3 1 2 3 1 20
|
||||
4 1 2 3 1 13
|
||||
5 1 16 6 8 5
|
||||
6 1 10 8 6 7
|
||||
7 1 12 10 8 9
|
||||
8 1 14 12 10 11
|
||||
9 7 14 13 4 3
|
||||
10 5 16 14 12 13
|
||||
11 1 14 16 6 15
|
||||
12 1 19 17 27 18
|
||||
13 5 17 19 21 20
|
||||
14 1 19 20 29 30
|
||||
15 1 19 20 29 3
|
||||
16 1 19 20 30 3
|
||||
17 1 29 20 30 3
|
||||
18 1 19 21 23 22
|
||||
19 1 21 23 25 24
|
||||
20 1 23 25 27 26
|
||||
21 1 17 27 25 28
|
||||
@ -0,0 +1,319 @@
|
||||
molecule template: end of styrene chain
|
||||
|
||||
30 atoms
|
||||
31 bonds
|
||||
51 angles
|
||||
73 dihedrals
|
||||
13 impropers
|
||||
|
||||
Coords
|
||||
|
||||
1 59.899810791 62.733695984 59.098842621
|
||||
2 61.419700623 63.421165466 59.528743744
|
||||
3 60.864753723 62.917243958 59.559719086
|
||||
4 62.139820099 61.410118103 60.810649872
|
||||
5 60.036457062 57.160030365 60.319587708
|
||||
6 59.734195709 58.187065125 60.205623627
|
||||
7 57.645748138 57.712432861 59.860111237
|
||||
8 58.374088287 58.501342773 59.944221497
|
||||
9 56.943000793 60.093170166 59.595561981
|
||||
10 57.974277496 59.855777740 59.793716431
|
||||
11 58.632312775 61.922969818 59.790649414
|
||||
12 58.934574127 60.895935059 59.904613495
|
||||
13 61.309082031 61.680416107 60.283161163
|
||||
14 60.294681549 60.581657410 60.166015625
|
||||
15 61.725769043 58.989830017 60.514671326
|
||||
16 60.694492340 59.227222443 60.316520691
|
||||
17 56.909358978 62.609851837 59.150833130
|
||||
18 57.940631866 62.372459412 59.348983765
|
||||
19 56.509548187 63.964286804 59.000324249
|
||||
20 57.523944855 65.063049316 59.117469788
|
||||
21 55.149436951 64.278564453 58.738922119
|
||||
22 54.847179413 65.305603027 58.624958038
|
||||
23 54.189140320 63.238407135 58.628025055
|
||||
24 53.157863617 63.475799561 58.429874420
|
||||
25 54.588951111 61.883972168 58.778530121
|
||||
26 53.860610962 61.095062256 58.694419861
|
||||
27 55.949058533 61.569694519 59.039932251
|
||||
28 56.251319885 60.542659760 59.153896332
|
||||
29 58.354682922 64.792747498 59.644958496
|
||||
30 57.079620361 66.299873352 58.394031525
|
||||
|
||||
Types
|
||||
|
||||
1 hc
|
||||
2 hc
|
||||
3 c2
|
||||
4 hc
|
||||
5 hc
|
||||
6 cp
|
||||
7 hc
|
||||
8 cp
|
||||
9 hc
|
||||
10 cp
|
||||
11 hc
|
||||
12 cp
|
||||
13 c1
|
||||
14 cp
|
||||
15 hc
|
||||
16 cp
|
||||
17 cp
|
||||
18 hc
|
||||
19 cp
|
||||
20 c1
|
||||
21 cp
|
||||
22 hc
|
||||
23 cp
|
||||
24 hc
|
||||
25 cp
|
||||
26 hc
|
||||
27 cp
|
||||
28 hc
|
||||
29 hc
|
||||
30 c2
|
||||
|
||||
Charges
|
||||
|
||||
1 0.035400
|
||||
2 0.035400
|
||||
3 -0.069600
|
||||
4 0.051600
|
||||
5 0.140300
|
||||
6 -0.173400
|
||||
7 0.128800
|
||||
8 -0.113400
|
||||
9 0.140300
|
||||
10 -0.173400
|
||||
11 0.123700
|
||||
12 -0.129000
|
||||
13 -0.018200
|
||||
14 0.026600
|
||||
15 0.123700
|
||||
16 -0.129000
|
||||
17 -0.129000
|
||||
18 0.123700
|
||||
19 0.026600
|
||||
20 -0.018200
|
||||
21 -0.129000
|
||||
22 0.123700
|
||||
23 -0.173400
|
||||
24 0.140300
|
||||
25 -0.113400
|
||||
26 0.128800
|
||||
27 -0.173400
|
||||
28 0.140300
|
||||
29 0.051600
|
||||
30 -0.069600
|
||||
|
||||
Molecules
|
||||
|
||||
1 1
|
||||
2 1
|
||||
3 1
|
||||
4 1
|
||||
5 1
|
||||
6 1
|
||||
7 1
|
||||
8 1
|
||||
9 1
|
||||
10 1
|
||||
11 1
|
||||
12 1
|
||||
13 1
|
||||
14 1
|
||||
15 1
|
||||
16 1
|
||||
17 1
|
||||
18 1
|
||||
19 1
|
||||
20 1
|
||||
21 1
|
||||
22 1
|
||||
23 1
|
||||
24 1
|
||||
25 1
|
||||
26 1
|
||||
27 1
|
||||
28 1
|
||||
29 1
|
||||
30 1
|
||||
|
||||
Bonds
|
||||
|
||||
1 hc-c2 1 3
|
||||
2 hc-c2 2 3
|
||||
3 c1-c2 3 13
|
||||
4 c1-c2 3 20
|
||||
5 hc-c1 4 13
|
||||
6 hc-cp 5 6
|
||||
7 cp-cp 6 8
|
||||
8 cp-cp 6 16
|
||||
9 hc-cp 7 8
|
||||
10 cp-cp 8 10
|
||||
11 hc-cp 9 10
|
||||
12 cp-cp 10 12
|
||||
13 hc-cp 11 12
|
||||
14 cp-cp 12 14
|
||||
15 cp-c1 14 13
|
||||
16 cp-cp 14 16
|
||||
17 hc-cp 15 16
|
||||
18 hc-cp 18 17
|
||||
19 cp-cp 17 19
|
||||
20 cp-cp 17 27
|
||||
21 cp-c1 19 20
|
||||
22 cp-cp 19 21
|
||||
23 c1-c2 30 20
|
||||
24 hc-c1 29 20
|
||||
25 hc-cp 22 21
|
||||
26 cp-cp 21 23
|
||||
27 hc-cp 24 23
|
||||
28 cp-cp 23 25
|
||||
29 hc-cp 26 25
|
||||
30 cp-cp 25 27
|
||||
31 hc-cp 28 27
|
||||
|
||||
Angles
|
||||
|
||||
1 hc-c2-hc 1 3 2
|
||||
2 hc-c2-c1 1 3 13
|
||||
3 hc-c2-c1 1 3 20
|
||||
4 hc-c2-c1 2 3 13
|
||||
5 hc-c2-c1 2 3 20
|
||||
6 c1-c2-c1 13 3 20
|
||||
7 hc-cp-cp 5 6 8
|
||||
8 hc-cp-cp 5 6 16
|
||||
9 cp-cp-cp 8 6 16
|
||||
10 hc-cp-cp 7 8 6
|
||||
11 cp-cp-cp 6 8 10
|
||||
12 hc-cp-cp 7 8 10
|
||||
13 hc-cp-cp 9 10 8
|
||||
14 cp-cp-cp 8 10 12
|
||||
15 hc-cp-cp 9 10 12
|
||||
16 hc-cp-cp 11 12 10
|
||||
17 cp-cp-cp 10 12 14
|
||||
18 hc-cp-cp 11 12 14
|
||||
19 hc-c1-c2 4 13 3
|
||||
20 cp-c1-c2 3 13 14
|
||||
21 hc-c1-cp 4 13 14
|
||||
22 cp-cp-c1 12 14 13
|
||||
23 cp-cp-cp 12 14 16
|
||||
24 cp-cp-c1 16 14 13
|
||||
25 cp-cp-cp 6 16 14
|
||||
26 hc-cp-cp 15 16 6
|
||||
27 hc-cp-cp 15 16 14
|
||||
28 hc-cp-cp 18 17 19
|
||||
29 hc-cp-cp 18 17 27
|
||||
30 cp-cp-cp 19 17 27
|
||||
31 cp-cp-c1 17 19 20
|
||||
32 cp-cp-cp 17 19 21
|
||||
33 cp-cp-c1 21 19 20
|
||||
34 cp-c1-c2 3 20 19
|
||||
35 c2-c1-c2 3 20 30
|
||||
36 hc-c1-c2 29 20 3
|
||||
37 cp-c1-c2 30 20 19
|
||||
38 hc-c1-cp 29 20 19
|
||||
39 hc-c1-c2 29 20 30
|
||||
40 hc-cp-cp 22 21 19
|
||||
41 cp-cp-cp 19 21 23
|
||||
42 hc-cp-cp 22 21 23
|
||||
43 hc-cp-cp 24 23 21
|
||||
44 cp-cp-cp 21 23 25
|
||||
45 hc-cp-cp 24 23 25
|
||||
46 hc-cp-cp 26 25 23
|
||||
47 cp-cp-cp 23 25 27
|
||||
48 hc-cp-cp 26 25 27
|
||||
49 cp-cp-cp 17 27 25
|
||||
50 hc-cp-cp 28 27 17
|
||||
51 hc-cp-cp 28 27 25
|
||||
|
||||
Dihedrals
|
||||
|
||||
1 hc-c1-c2-hc 1 3 13 4
|
||||
2 cp-c1-c2-hc 1 3 13 14
|
||||
3 hc-c1-c2-hc 2 3 13 4
|
||||
4 cp-c1-c2-hc 2 3 13 14
|
||||
5 hc-c1-c2-c1 20 3 13 4
|
||||
6 cp-c1-c2-c1 20 3 13 14
|
||||
7 cp-c1-c2-hc 1 3 20 19
|
||||
8 c2-c1-c2-hc 1 3 20 30
|
||||
9 hc-c1-c2-hc 1 3 20 29
|
||||
10 cp-c1-c2-hc 2 3 20 19
|
||||
11 c2-c1-c2-hc 2 3 20 30
|
||||
12 hc-c1-c2-hc 2 3 20 29
|
||||
13 cp-c1-c2-c1 13 3 20 19
|
||||
14 c2-c1-c2-c1 13 3 20 30
|
||||
15 hc-c1-c2-c1 13 3 20 29
|
||||
16 hc-cp-cp-hc 5 6 8 7
|
||||
17 hc-cp-cp-cp 5 6 8 10
|
||||
18 hc-cp-cp-cp 7 8 6 16
|
||||
19 cp-cp-cp-cp 16 6 8 10
|
||||
20 hc-cp-cp-cp 5 6 16 14
|
||||
21 hc-cp-cp-hc 5 6 16 15
|
||||
22 cp-cp-cp-cp 8 6 16 14
|
||||
23 hc-cp-cp-cp 15 16 6 8
|
||||
24 hc-cp-cp-cp 9 10 8 6
|
||||
25 cp-cp-cp-cp 6 8 10 12
|
||||
26 hc-cp-cp-hc 7 8 10 9
|
||||
27 hc-cp-cp-cp 7 8 10 12
|
||||
28 hc-cp-cp-cp 11 12 10 8
|
||||
29 cp-cp-cp-cp 8 10 12 14
|
||||
30 hc-cp-cp-hc 9 10 12 11
|
||||
31 hc-cp-cp-cp 9 10 12 14
|
||||
32 cp-cp-cp-c1 10 12 14 13
|
||||
33 cp-cp-cp-cp 10 12 14 16
|
||||
34 hc-cp-cp-c1 11 12 14 13
|
||||
35 hc-cp-cp-cp 11 12 14 16
|
||||
36 cp-cp-c1-c2 12 14 13 3
|
||||
37 cp-cp-c1-c2 16 14 13 3
|
||||
38 cp-cp-c1-hc 12 14 13 4
|
||||
39 cp-cp-c1-hc 16 14 13 4
|
||||
40 cp-cp-cp-cp 12 14 16 6
|
||||
41 hc-cp-cp-cp 15 16 14 12
|
||||
42 cp-cp-cp-c1 6 16 14 13
|
||||
43 hc-cp-cp-c1 15 16 14 13
|
||||
44 hc-cp-cp-c1 18 17 19 20
|
||||
45 hc-cp-cp-cp 18 17 19 21
|
||||
46 cp-cp-cp-c1 27 17 19 20
|
||||
47 cp-cp-cp-cp 27 17 19 21
|
||||
48 hc-cp-cp-cp 18 17 27 25
|
||||
49 hc-cp-cp-hc 18 17 27 28
|
||||
50 cp-cp-cp-cp 19 17 27 25
|
||||
51 hc-cp-cp-cp 28 27 17 19
|
||||
52 cp-cp-c1-c2 17 19 20 3
|
||||
53 cp-cp-c1-c2 17 19 20 30
|
||||
54 cp-cp-c1-hc 17 19 20 29
|
||||
55 cp-cp-c1-c2 21 19 20 3
|
||||
56 cp-cp-c1-c2 21 19 20 30
|
||||
57 cp-cp-c1-hc 21 19 20 29
|
||||
58 hc-cp-cp-cp 22 21 19 17
|
||||
59 cp-cp-cp-cp 17 19 21 23
|
||||
60 hc-cp-cp-c1 22 21 19 20
|
||||
61 cp-cp-cp-c1 23 21 19 20
|
||||
62 hc-cp-cp-cp 24 23 21 19
|
||||
63 cp-cp-cp-cp 19 21 23 25
|
||||
64 hc-cp-cp-hc 22 21 23 24
|
||||
65 hc-cp-cp-cp 22 21 23 25
|
||||
66 hc-cp-cp-cp 26 25 23 21
|
||||
67 cp-cp-cp-cp 21 23 25 27
|
||||
68 hc-cp-cp-hc 24 23 25 26
|
||||
69 hc-cp-cp-cp 24 23 25 27
|
||||
70 cp-cp-cp-cp 23 25 27 17
|
||||
71 hc-cp-cp-cp 28 27 25 23
|
||||
72 hc-cp-cp-cp 26 25 27 17
|
||||
73 hc-cp-cp-hc 26 25 27 28
|
||||
|
||||
Impropers
|
||||
|
||||
1 hc-cp-cp-cp 5 6 8 16
|
||||
2 hc-cp-cp-cp 7 8 6 10
|
||||
3 hc-cp-cp-cp 9 10 8 12
|
||||
4 hc-cp-cp-cp 11 12 10 14
|
||||
5 hc-c1-cp-c2 4 13 3 14
|
||||
6 cp-cp-cp-c1 12 14 16 13
|
||||
7 hc-cp-cp-cp 15 16 14 6
|
||||
8 hc-cp-cp-cp 18 17 19 27
|
||||
9 cp-cp-cp-c1 17 19 21 20
|
||||
10 hc-cp-cp-cp 22 21 19 23
|
||||
11 hc-cp-cp-cp 24 23 21 25
|
||||
12 hc-cp-cp-cp 26 25 23 27
|
||||
13 hc-cp-cp-cp 28 27 25 17
|
||||
@ -6,9 +6,7 @@ boundary p p p
|
||||
|
||||
atom_style full
|
||||
|
||||
kspace_style pppm 1.0e-4
|
||||
|
||||
pair_style lj/class2/coul/long 8.5
|
||||
pair_style lj/class2/coul/cut 8.5
|
||||
|
||||
angle_style class2
|
||||
|
||||
@ -27,13 +25,13 @@ read_data trimer.data &
|
||||
extra/improper/per/atom 25 &
|
||||
extra/special/per/atom 25
|
||||
|
||||
molecule mol1 grow_styrene_pre.data_template
|
||||
molecule mol2 grow_styrene_post.data_template
|
||||
molecule mol1 grow_styrene_pre.molecule_template
|
||||
molecule mol2 grow_styrene_post.molecule_template
|
||||
|
||||
fix myrxns all bond/react stabilization yes statted_grp .03 &
|
||||
react rxn1 all 1 0 3.0 mol1 mol2 grow_styrene.map &
|
||||
modify_create fit create_fit overlap 2.0 &
|
||||
stabilize_steps 100 max_rxn 30
|
||||
stabilize_steps 200 max_rxn 30
|
||||
|
||||
fix 1 statted_grp_REACT nvt temp $T $T 100
|
||||
|
||||
|
||||
@ -1,196 +0,0 @@
|
||||
LAMMPS (24 Dec 2020)
|
||||
Reading data file ...
|
||||
orthogonal box = (50.000000 50.000000 50.000000) to (250.00000 250.00000 250.00000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
48 atoms
|
||||
reading velocities ...
|
||||
48 velocities
|
||||
scanning bonds ...
|
||||
8 = max bonds/atom
|
||||
scanning angles ...
|
||||
21 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
33 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
29 = max impropers/atom
|
||||
reading bonds ...
|
||||
50 bonds
|
||||
reading angles ...
|
||||
84 angles
|
||||
reading dihedrals ...
|
||||
127 dihedrals
|
||||
reading impropers ...
|
||||
36 impropers
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
4 = max # of 1-2 neighbors
|
||||
8 = max # of 1-3 neighbors
|
||||
17 = max # of 1-4 neighbors
|
||||
46 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.077 seconds
|
||||
Read molecule template mol1:
|
||||
1 molecules
|
||||
30 atoms with max type 6
|
||||
31 bonds with max type 10
|
||||
51 angles with max type 16
|
||||
73 dihedrals with max type 19
|
||||
21 impropers with max type 7
|
||||
Read molecule template mol2:
|
||||
1 molecules
|
||||
46 atoms with max type 6
|
||||
48 bonds with max type 13
|
||||
81 angles with max type 22
|
||||
121 dihedrals with max type 36
|
||||
35 impropers with max type 9
|
||||
dynamic group bond_react_MASTER_group defined
|
||||
dynamic group statted_grp_REACT defined
|
||||
PPPM initialization ...
|
||||
WARNING: System is not charge neutral, net charge = -0.00060000000 (../kspace.cpp:324)
|
||||
using 12-bit tables for long-range coulomb (../kspace.cpp:339)
|
||||
G vector (1/distance) = 0.20144813
|
||||
grid = 45 45 45
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.00053712952
|
||||
estimated relative force accuracy = 1.6175496e-06
|
||||
using double precision KISS FFT
|
||||
3d grid and FFT values/proc = 125000 91125
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 10.5
|
||||
ghost atom cutoff = 10.5
|
||||
binsize = 5.25, bins = 39 39 39
|
||||
2 neighbor lists, perpetual/occasional/extra = 1 1 0
|
||||
(1) pair lj/class2/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
(2) fix bond/react, occasional, copy from (1)
|
||||
attributes: half, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Setting up Verlet run ...
|
||||
Unit style : real
|
||||
Current step : 0
|
||||
Time step : 1
|
||||
Per MPI rank memory allocation (min/avg/max) = 48.02 | 48.02 | 48.02 Mbytes
|
||||
Step Temp Press Density f_myrxns[1]
|
||||
0 496.23742 0.9983211 6.4856516e-05 0
|
||||
100 534.05394 -0.76952227 6.4856516e-05 0
|
||||
200 552.2225 -0.55375493 6.4856516e-05 0
|
||||
300 857.52834 -0.4272061 8.6475354e-05 1
|
||||
400 714.10681 1.5004615 8.6475354e-05 1
|
||||
500 678.19171 0.21965471 8.6475354e-05 1
|
||||
600 572.3234 0.87879933 8.6475354e-05 1
|
||||
700 996.17398 -0.24269717 0.00010809419 2
|
||||
800 904.50395 1.3662054 0.00010809419 2
|
||||
900 1097.1568 -2.2909907 0.00012971303 3
|
||||
1000 954.08892 1.7705672 0.00012971303 3
|
||||
1100 1102.0377 -1.7018446 0.00015133187 4
|
||||
1200 1239.785 -0.30442903 0.00015133187 4
|
||||
1300 1388.4127 1.3301175 0.00017295071 5
|
||||
1400 1559.3853 1.6709729 0.00017295071 5
|
||||
1500 1471.8623 0.8268427 0.00017295071 5
|
||||
1600 1543.6793 2.1987908 0.00019456955 6
|
||||
1700 1694.5595 0.48852817 0.00019456955 6
|
||||
1800 1632.7737 -1.4617692 0.00021618839 7
|
||||
1900 1922.6502 1.1664257 0.00021618839 7
|
||||
2000 2223.503 -0.95799878 0.00023780722 8
|
||||
2100 2142.6035 0.88444463 0.00025942606 9
|
||||
2200 2298.8636 3.4239313 0.00025942606 9
|
||||
2300 2252.4355 0.82167302 0.00025942606 9
|
||||
2400 2321.0788 1.7499714 0.00025942606 9
|
||||
2500 2095.6715 0.55288444 0.00025942606 9
|
||||
2600 2136.0316 -3.833114 0.00025942606 9
|
||||
2700 2466.3134 -2.2519511 0.00025942606 9
|
||||
2800 2294.3454 1.0637304 0.00025942606 9
|
||||
2900 2340.3891 1.3997049 0.0002810449 10
|
||||
3000 2272.0013 -0.27591886 0.0002810449 10
|
||||
3100 2333.9696 -0.11772138 0.0002810449 10
|
||||
3200 2409.0946 -1.025473 0.0002810449 10
|
||||
3300 2148.023 1.6752329 0.0002810449 10
|
||||
3400 2267.636 -0.45297583 0.0002810449 10
|
||||
3500 2457.622 0.35627297 0.0002810449 10
|
||||
3600 2288.008 -15.516626 0.00030266374 11
|
||||
3700 2458.2681 1.4571773 0.00030266374 11
|
||||
3800 2566.7623 -29.140553 0.00032428258 12
|
||||
3900 2839.4062 0.64583638 0.00032428258 12
|
||||
4000 2893.9852 -52.954497 0.00034590142 13
|
||||
4100 3021.3611 -65.03731 0.00036752025 14
|
||||
4200 3002.7136 1.5750081 0.00036752025 14
|
||||
4300 3218.6248 -120.74039 0.00038913909 15
|
||||
4400 3345.1482 -0.96545269 0.00038913909 15
|
||||
4500 3603.2429 1.2438833 0.00038913909 15
|
||||
4600 3129.8814 -249.91806 0.00041075793 16
|
||||
4700 3769.052 -289.24351 0.00043237677 17
|
||||
4800 3560.4714 -3.1655406 0.00043237677 17
|
||||
4900 3452.2717 -2.1270765 0.00043237677 17
|
||||
5000 3594.3247 -523.48506 0.00045399561 18
|
||||
5100 3578.4199 1.0009097 0.00045399561 18
|
||||
5200 3822.1566 1.0526914 0.00047561445 19
|
||||
5300 3901.8883 -0.14607602 0.00047561445 19
|
||||
5400 4059.3644 -1.7789927 0.00049723329 20
|
||||
5500 4163.6847 1.0240127 0.00049723329 20
|
||||
5600 4109.1649 0.80199787 0.00049723329 20
|
||||
5700 4391.2091 2.8730036 0.00049723329 20
|
||||
5800 4279.6579 -0.36499822 0.00051885212 21
|
||||
5900 4296.2695 -1.3064528 0.00051885212 21
|
||||
6000 4065.3758 -2.0483224 0.00051885212 21
|
||||
6100 4772.5362 -2.6814694 0.00054047096 22
|
||||
6200 4627.029 2.999215 0.0005620898 23
|
||||
6300 5120.7881 0.65372968 0.00058370864 24
|
||||
6400 4588.9559 3.7570705 0.00058370864 24
|
||||
6500 5008.7814 2.3595833 0.00060532748 25
|
||||
6600 5195.0053 1.4641612 0.00060532748 25
|
||||
6700 5622.293 -0.33396047 0.00062694632 26
|
||||
6800 5515.1957 -4.234874 0.00062694632 26
|
||||
6900 5156.7455 0.40171954 0.00064856516 27
|
||||
7000 5120.1639 -1.6065245 0.00064856516 27
|
||||
7100 5650.0327 0.94436323 0.00067018399 28
|
||||
7200 5985.1115 -3.8940347 0.00069180283 29
|
||||
7300 5983.197 0.5293568 0.00069180283 29
|
||||
7400 6001.1559 -0.13712834 0.00071342167 30
|
||||
7500 5889.2134 0.17230892 0.00071342167 30
|
||||
7600 5797.31 2.0920058 0.00071342167 30
|
||||
7700 5865.2783 -0.18556395 0.00071342167 30
|
||||
7800 6207.0659 -5.6237083 0.00071342167 30
|
||||
7900 5627.5108 -2.3718942 0.00071342167 30
|
||||
8000 5823.9502 -0.85418578 0.00071342167 30
|
||||
Loop time of 184.87 on 1 procs for 8000 steps with 528 atoms
|
||||
|
||||
Performance: 3.739 ns/day, 6.419 hours/ns, 43.274 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 3.3043 | 3.3043 | 3.3043 | 0.0 | 1.79
|
||||
Bond | 8.0003 | 8.0003 | 8.0003 | 0.0 | 4.33
|
||||
Kspace | 168.33 | 168.33 | 168.33 | 0.0 | 91.05
|
||||
Neigh | 4.6322 | 4.6322 | 4.6322 | 0.0 | 2.51
|
||||
Comm | 0.077927 | 0.077927 | 0.077927 | 0.0 | 0.04
|
||||
Output | 0.0020548 | 0.0020548 | 0.0020548 | 0.0 | 0.00
|
||||
Modify | 0.5005 | 0.5005 | 0.5005 | 0.0 | 0.27
|
||||
Other | | 0.02483 | | | 0.01
|
||||
|
||||
Nlocal: 528.000 ave 528 max 528 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 341.000 ave 341 max 341 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 35111.0 ave 35111 max 35111 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 35111
|
||||
Ave neighs/atom = 66.498106
|
||||
Ave special neighs/atom = 11.409091
|
||||
Neighbor list builds = 8000
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:03:05
|
||||
@ -1,196 +0,0 @@
|
||||
LAMMPS (24 Dec 2020)
|
||||
Reading data file ...
|
||||
orthogonal box = (50.000000 50.000000 50.000000) to (250.00000 250.00000 250.00000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
48 atoms
|
||||
reading velocities ...
|
||||
48 velocities
|
||||
scanning bonds ...
|
||||
8 = max bonds/atom
|
||||
scanning angles ...
|
||||
21 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
33 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
29 = max impropers/atom
|
||||
reading bonds ...
|
||||
50 bonds
|
||||
reading angles ...
|
||||
84 angles
|
||||
reading dihedrals ...
|
||||
127 dihedrals
|
||||
reading impropers ...
|
||||
36 impropers
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
4 = max # of 1-2 neighbors
|
||||
8 = max # of 1-3 neighbors
|
||||
17 = max # of 1-4 neighbors
|
||||
46 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.007 seconds
|
||||
Read molecule template mol1:
|
||||
1 molecules
|
||||
30 atoms with max type 6
|
||||
31 bonds with max type 10
|
||||
51 angles with max type 16
|
||||
73 dihedrals with max type 19
|
||||
21 impropers with max type 7
|
||||
Read molecule template mol2:
|
||||
1 molecules
|
||||
46 atoms with max type 6
|
||||
48 bonds with max type 13
|
||||
81 angles with max type 22
|
||||
121 dihedrals with max type 36
|
||||
35 impropers with max type 9
|
||||
dynamic group bond_react_MASTER_group defined
|
||||
dynamic group statted_grp_REACT defined
|
||||
PPPM initialization ...
|
||||
WARNING: System is not charge neutral, net charge = -0.00060000000 (../kspace.cpp:324)
|
||||
using 12-bit tables for long-range coulomb (../kspace.cpp:339)
|
||||
G vector (1/distance) = 0.20144813
|
||||
grid = 45 45 45
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.00053712952
|
||||
estimated relative force accuracy = 1.6175496e-06
|
||||
using double precision KISS FFT
|
||||
3d grid and FFT values/proc = 39200 24300
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 10.5
|
||||
ghost atom cutoff = 10.5
|
||||
binsize = 5.25, bins = 39 39 39
|
||||
2 neighbor lists, perpetual/occasional/extra = 1 1 0
|
||||
(1) pair lj/class2/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
(2) fix bond/react, occasional, copy from (1)
|
||||
attributes: half, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Setting up Verlet run ...
|
||||
Unit style : real
|
||||
Current step : 0
|
||||
Time step : 1
|
||||
Per MPI rank memory allocation (min/avg/max) = 38.70 | 38.92 | 39.43 Mbytes
|
||||
Step Temp Press Density f_myrxns[1]
|
||||
0 496.23742 0.9983211 6.4856516e-05 0
|
||||
100 534.05394 -0.76952227 6.4856516e-05 0
|
||||
200 552.2225 -0.55375493 6.4856516e-05 0
|
||||
300 857.52834 -0.4272061 8.6475354e-05 1
|
||||
400 714.10681 1.5004615 8.6475354e-05 1
|
||||
500 678.19171 0.21965471 8.6475354e-05 1
|
||||
600 572.3234 0.87879933 8.6475354e-05 1
|
||||
700 996.17398 -0.24269717 0.00010809419 2
|
||||
800 904.50395 1.3662054 0.00010809419 2
|
||||
900 1097.1568 -2.2909907 0.00012971303 3
|
||||
1000 954.08892 1.7705672 0.00012971303 3
|
||||
1100 1102.0377 -1.7018446 0.00015133187 4
|
||||
1200 1239.785 -0.30442903 0.00015133187 4
|
||||
1300 1388.4127 1.3301175 0.00017295071 5
|
||||
1400 1559.3853 1.6709729 0.00017295071 5
|
||||
1500 1471.8623 0.8268427 0.00017295071 5
|
||||
1600 1543.6793 2.1987908 0.00019456955 6
|
||||
1700 1694.5595 0.48852817 0.00019456955 6
|
||||
1800 1632.7737 -1.4617692 0.00021618839 7
|
||||
1900 1922.6502 1.1664257 0.00021618839 7
|
||||
2000 2223.503 -0.95799878 0.00023780722 8
|
||||
2100 2142.6035 0.88444463 0.00025942606 9
|
||||
2200 2298.8636 3.4239313 0.00025942606 9
|
||||
2300 2252.4355 0.82167302 0.00025942606 9
|
||||
2400 2321.0788 1.7499714 0.00025942606 9
|
||||
2500 2095.6715 0.55288444 0.00025942606 9
|
||||
2600 2136.0316 -3.833114 0.00025942606 9
|
||||
2700 2466.3134 -2.2519511 0.00025942606 9
|
||||
2800 2294.3454 1.0637304 0.00025942606 9
|
||||
2900 2340.3891 1.3997049 0.0002810449 10
|
||||
3000 2272.0013 -0.27591886 0.0002810449 10
|
||||
3100 2333.9696 -0.11772138 0.0002810449 10
|
||||
3200 2409.0946 -1.025473 0.0002810449 10
|
||||
3300 2148.023 1.6752329 0.0002810449 10
|
||||
3400 2267.636 -0.45297583 0.0002810449 10
|
||||
3500 2457.622 0.35627297 0.0002810449 10
|
||||
3600 2288.008 -15.516626 0.00030266374 11
|
||||
3700 2458.2681 1.4571773 0.00030266374 11
|
||||
3800 2566.7623 -29.140553 0.00032428258 12
|
||||
3900 2839.4062 0.64583638 0.00032428258 12
|
||||
4000 2893.2204 -53.187892 0.00034590142 13
|
||||
4100 3024.6375 -65.068146 0.00036752025 14
|
||||
4200 3004.6784 1.4155214 0.00036752025 14
|
||||
4300 3033.1895 1.8572273 0.00036752025 14
|
||||
4400 3157.2542 -0.92462977 0.00036752025 14
|
||||
4500 3557.7137 -194.46498 0.00038913909 15
|
||||
4600 3096.485 -1.830492 0.00038913909 15
|
||||
4700 3488.088 -286.81055 0.00041075793 16
|
||||
4800 3390.5493 -372.77818 0.00043237677 17
|
||||
4900 3773.7226 -446.58574 0.00045399561 18
|
||||
5000 3703.0159 -0.81188551 0.00045399561 18
|
||||
5100 4051.3067 1.2567439 0.00045399561 18
|
||||
5200 3813.3682 0.92945737 0.00047561445 19
|
||||
5300 4036.0078 -2.5336258 0.00049723329 20
|
||||
5400 4219.803 -0.96928261 0.00049723329 20
|
||||
5500 4433.7447 -0.026762463 0.00051885212 21
|
||||
5600 4477.4505 -1.417316 0.00054047096 22
|
||||
5700 4500.0306 -1.0551443 0.00054047096 22
|
||||
5800 4600.3507 -4.9580056 0.00054047096 22
|
||||
5900 4765.4978 -2.2546941 0.0005620898 23
|
||||
6000 5442.6193 0.91161284 0.00058370864 24
|
||||
6100 5086.8047 -0.9875332 0.00060532748 25
|
||||
6200 5485.3437 -2.8296626 0.00062694632 26
|
||||
6300 4988.0396 -0.15179023 0.00064856516 27
|
||||
6400 5597.3703 4.2941885 0.00067018399 28
|
||||
6500 5677.0263 -2.8611595 0.00069180283 29
|
||||
6600 6058.0009 1.4111778 0.00071342167 30
|
||||
6700 5859.0817 -2.5782466 0.00071342167 30
|
||||
6800 5879.3941 -4.5681807 0.00071342167 30
|
||||
6900 6398.288 2.5259412 0.00071342167 30
|
||||
7000 6250.1096 -2.6049627 0.00071342167 30
|
||||
7100 5849.651 -0.44062578 0.00071342167 30
|
||||
7200 5778.6532 -0.27299118 0.00071342167 30
|
||||
7300 5977.6661 4.2483639 0.00071342167 30
|
||||
7400 5862.4231 1.0289519 0.00071342167 30
|
||||
7500 6482.376 7.5412373 0.00071342167 30
|
||||
7600 5810.4325 1.0343075 0.00071342167 30
|
||||
7700 5916.7304 2.304302 0.00071342167 30
|
||||
7800 5869.9504 -0.5946555 0.00071342167 30
|
||||
7900 5804.0522 -4.1207689 0.00071342167 30
|
||||
8000 6077.1704 0.52211243 0.00071342167 30
|
||||
Loop time of 60.5603 on 4 procs for 8000 steps with 528 atoms
|
||||
|
||||
Performance: 11.413 ns/day, 2.103 hours/ns, 132.100 timesteps/s
|
||||
99.9% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0041695 | 0.90113 | 2.3423 | 102.8 | 1.49
|
||||
Bond | 0.011606 | 2.1188 | 5.8107 | 163.9 | 3.50
|
||||
Kspace | 47.987 | 52.817 | 55.679 | 43.7 | 87.21
|
||||
Neigh | 3.5961 | 3.6262 | 3.6496 | 1.2 | 5.99
|
||||
Comm | 0.11097 | 0.16569 | 0.26369 | 15.3 | 0.27
|
||||
Output | 0.0020366 | 0.0023427 | 0.0032469 | 1.1 | 0.00
|
||||
Modify | 0.62302 | 0.91659 | 1.1227 | 21.5 | 1.51
|
||||
Other | | 0.0126 | | | 0.02
|
||||
|
||||
Nlocal: 132.000 ave 295 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||
Nghost: 133.000 ave 349 max 0 min
|
||||
Histogram: 2 0 0 0 0 1 0 0 0 1
|
||||
Neighs: 8383.50 ave 20143 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 33534
|
||||
Ave neighs/atom = 63.511364
|
||||
Ave special neighs/atom = 11.409091
|
||||
Neighbor list builds = 8000
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:01:00
|
||||
@ -0,0 +1,256 @@
|
||||
LAMMPS (4 Nov 2022)
|
||||
# use bond/react 'create atoms' feature to add 30 new styrene monomers to chain
|
||||
|
||||
units real
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
|
||||
pair_style lj/class2/coul/cut 8.5
|
||||
|
||||
angle_style class2
|
||||
|
||||
bond_style class2
|
||||
|
||||
dihedral_style class2
|
||||
|
||||
improper_style class2
|
||||
|
||||
variable T equal 530
|
||||
|
||||
read_data trimer.data extra/bond/per/atom 5 extra/angle/per/atom 15 extra/dihedral/per/atom 15 extra/improper/per/atom 25 extra/special/per/atom 25
|
||||
Reading data file ...
|
||||
orthogonal box = (-200 -200 -200) to (200 200 200)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atom labelmap ...
|
||||
reading bond labelmap ...
|
||||
reading angle labelmap ...
|
||||
reading dihedral labelmap ...
|
||||
reading improper labelmap ...
|
||||
reading atoms ...
|
||||
48 atoms
|
||||
scanning bonds ...
|
||||
8 = max bonds/atom
|
||||
scanning angles ...
|
||||
21 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
33 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
26 = max impropers/atom
|
||||
reading bonds ...
|
||||
50 bonds
|
||||
reading angles ...
|
||||
84 angles
|
||||
reading dihedrals ...
|
||||
127 dihedrals
|
||||
reading impropers ...
|
||||
20 impropers
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
4 = max # of 1-2 neighbors
|
||||
8 = max # of 1-3 neighbors
|
||||
17 = max # of 1-4 neighbors
|
||||
46 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.011 seconds
|
||||
|
||||
molecule mol1 grow_styrene_pre.molecule_template
|
||||
Read molecule template mol1:
|
||||
1 molecules
|
||||
0 fragments
|
||||
30 atoms with max type 4
|
||||
31 bonds with max type 6
|
||||
51 angles with max type 10
|
||||
73 dihedrals with max type 13
|
||||
13 impropers with max type 3
|
||||
molecule mol2 grow_styrene_post.molecule_template
|
||||
Read molecule template mol2:
|
||||
1 molecules
|
||||
1 fragments
|
||||
46 atoms with max type 4
|
||||
48 bonds with max type 6
|
||||
81 angles with max type 10
|
||||
121 dihedrals with max type 13
|
||||
19 impropers with max type 3
|
||||
|
||||
fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0 3.0 mol1 mol2 grow_styrene.map modify_create fit create_fit overlap 2.0 stabilize_steps 200 max_rxn 30
|
||||
dynamic group bond_react_MASTER_group defined
|
||||
dynamic group statted_grp_REACT defined
|
||||
|
||||
fix 1 statted_grp_REACT nvt temp $T $T 100
|
||||
fix 1 statted_grp_REACT nvt temp 530 $T 100
|
||||
fix 1 statted_grp_REACT nvt temp 530 530 100
|
||||
|
||||
fix 4 bond_react_MASTER_group temp/rescale 1 $T $T 1 1
|
||||
fix 4 bond_react_MASTER_group temp/rescale 1 530 $T 1 1
|
||||
fix 4 bond_react_MASTER_group temp/rescale 1 530 530 1 1
|
||||
|
||||
thermo_style custom step temp press density f_myrxns[1]
|
||||
|
||||
thermo 100
|
||||
|
||||
dump 1 all xyz 1 test_vis.xyz
|
||||
|
||||
run 8000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- fix bond/react: reacter.org doi:10.1016/j.polymer.2017.09.038, doi:10.1021/acs.macromol.0c02012
|
||||
|
||||
@Article{Gissinger17,
|
||||
author = {J. R. Gissinger and B. D. Jensen and K. E. Wise},
|
||||
title = {Modeling Chemical Reactions in Classical Molecular Dynamics Simulations},
|
||||
journal = {Polymer},
|
||||
year = 2017,
|
||||
volume = 128,
|
||||
pages = {211--217}
|
||||
}
|
||||
|
||||
@Article{Gissinger20,
|
||||
author = {J. R. Gissinger, B. D. Jensen, K. E. Wise},
|
||||
title = {{REACTER}: A Heuristic Method for Reactive Molecular Dynamics},
|
||||
journal = {Macromolecules},
|
||||
year = 2020,
|
||||
volume = 53,
|
||||
number = 22,
|
||||
pages = {9953--9961}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 6 of 6 mixed pair_coeff terms from sixthpower/geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 10.5
|
||||
ghost atom cutoff = 10.5
|
||||
binsize = 5.25, bins = 77 77 77
|
||||
2 neighbor lists, perpetual/occasional/extra = 1 1 0
|
||||
(1) pair lj/class2/coul/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
(2) fix bond/react, occasional, copy from (1)
|
||||
attributes: half, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 36.99 | 36.99 | 36.99 Mbytes
|
||||
Step Temp Press Density f_myrxns[1]
|
||||
0 0 0.076588866 8.1070333e-06 0
|
||||
100 598.41967 -0.1670029 1.0809378e-05 1
|
||||
200 696.77845 0.11857422 1.0809378e-05 1
|
||||
300 932.97222 -0.058615676 1.3511722e-05 2
|
||||
400 1016.3732 0.062233715 1.3511722e-05 2
|
||||
500 1006.451 -0.17987841 1.6214067e-05 3
|
||||
600 1143.8859 0.33297898 1.6214067e-05 3
|
||||
700 1209.6144 -0.22743773 1.8916411e-05 4
|
||||
800 1429.1639 0.14048255 1.8916411e-05 4
|
||||
900 1375.0968 -0.04016551 2.1618755e-05 5
|
||||
1000 1583.6696 -0.23364852 2.1618755e-05 5
|
||||
1100 1811.0697 -0.054436797 2.43211e-05 6
|
||||
1200 1928.4658 0.012242837 2.43211e-05 6
|
||||
1300 1666.6176 0.057157656 2.43211e-05 6
|
||||
1400 1686.18 -28.442814 2.7023444e-05 7
|
||||
1500 1704.6248 -0.16861218 2.7023444e-05 7
|
||||
1600 2171.7628 -33.6156 2.9725789e-05 8
|
||||
1700 1991.2922 -0.11813381 2.9725789e-05 8
|
||||
1800 2037.4991 -40.015612 3.2428133e-05 9
|
||||
1900 2143.9447 -0.090964375 3.2428133e-05 9
|
||||
2000 1927.9564 0.29856007 3.2428133e-05 9
|
||||
2100 2255.5877 -4.9166327 3.5130478e-05 10
|
||||
2200 2512.5193 0.00044804842 3.5130478e-05 10
|
||||
2300 2336.1503 -45.094726 3.7832822e-05 11
|
||||
2400 2508.9655 -0.1024684 3.7832822e-05 11
|
||||
2500 2747.7344 -53.939212 4.0535167e-05 12
|
||||
2600 2790.5736 0.07042181 4.0535167e-05 12
|
||||
2700 3014.7092 -0.0025387793 4.0535167e-05 12
|
||||
2800 2745.0295 -0.099361314 4.3237511e-05 13
|
||||
2900 2952.1281 -0.13667582 4.3237511e-05 13
|
||||
3000 3032.5298 0.28882784 4.5939855e-05 14
|
||||
3100 3149.992 0.55269076 4.5939855e-05 14
|
||||
3200 3422.5233 -0.11794908 4.86422e-05 15
|
||||
3300 3040.2691 -0.067532834 4.86422e-05 15
|
||||
3400 3323.3263 0.049969149 5.1344544e-05 16
|
||||
3500 3539.0877 -0.065546641 5.1344544e-05 16
|
||||
3600 3894.6897 -0.24222461 5.4046889e-05 17
|
||||
3700 3689.3513 0.21366533 5.4046889e-05 17
|
||||
3800 3924.799 -0.60817646 5.6749233e-05 18
|
||||
3900 3713.1947 -0.024834682 5.6749233e-05 18
|
||||
4000 3887.6151 0.052787631 5.9451578e-05 19
|
||||
4100 3868.2877 0.42532898 5.9451578e-05 19
|
||||
4200 3784.9874 -0.12018512 5.9451578e-05 19
|
||||
4300 4169.9997 0.19652089 6.2153922e-05 20
|
||||
4400 4112.291 -0.084839982 6.2153922e-05 20
|
||||
4500 3974.2226 -0.13641761 6.2153922e-05 20
|
||||
4600 4064.3852 0.16435039 6.2153922e-05 20
|
||||
4700 3880.0044 -0.42874552 6.2153922e-05 20
|
||||
4800 4508.2324 0.20208091 6.2153922e-05 20
|
||||
4900 4364.033 -0.56300441 6.2153922e-05 20
|
||||
5000 4030.4642 -0.29006515 6.2153922e-05 20
|
||||
5100 4010.9518 0.32060145 6.2153922e-05 20
|
||||
5200 4058.5072 0.088924924 6.2153922e-05 20
|
||||
5300 4529.9866 -0.38882748 6.4856266e-05 21
|
||||
5400 4305.9161 0.24046553 6.4856266e-05 21
|
||||
5500 4556.8628 -0.014044879 6.4856266e-05 21
|
||||
5600 4730.2206 0.1526293 6.4856266e-05 21
|
||||
5700 4810.9968 -17.600253 6.7558611e-05 22
|
||||
5800 4655.651 -0.25941928 6.7558611e-05 22
|
||||
5900 4507.1045 -0.084691005 6.7558611e-05 22
|
||||
6000 4516.0965 0.092662842 7.0260955e-05 23
|
||||
6100 4592.4068 0.10403004 7.0260955e-05 23
|
||||
6200 4583.9491 0.1692786 7.29633e-05 24
|
||||
6300 4512.226 0.32590723 7.29633e-05 24
|
||||
6400 4885.9205 -0.24208842 7.5665644e-05 25
|
||||
6500 5250.5008 0.4135064 7.5665644e-05 25
|
||||
6600 5216.9452 0.00059199905 7.8367989e-05 26
|
||||
6700 5302.2925 0.50452368 7.8367989e-05 26
|
||||
6800 4931.7328 -0.064719953 8.1070333e-05 27
|
||||
6900 5549.8746 0.55101191 8.1070333e-05 27
|
||||
7000 5472.9107 0.31358281 8.3772677e-05 28
|
||||
7100 5559.9339 0.14034743 8.3772677e-05 28
|
||||
7200 5726.4492 -0.39732059 8.6475022e-05 29
|
||||
7300 5869.324 0.18989804 8.6475022e-05 29
|
||||
7400 6109.5519 0.11206572 8.9177366e-05 30
|
||||
7500 5966.7085 0.2059557 8.9177366e-05 30
|
||||
7600 6051.2064 0.025316679 8.9177366e-05 30
|
||||
7700 5719.6669 0.16548544 8.9177366e-05 30
|
||||
7800 6118.8183 -0.20036999 8.9177366e-05 30
|
||||
7900 6477.1901 0.10308473 8.9177366e-05 30
|
||||
8000 6241.9498 0.090165102 8.9177366e-05 30
|
||||
Loop time of 17.4848 on 1 procs for 8000 steps with 528 atoms
|
||||
|
||||
Performance: 39.531 ns/day, 0.607 hours/ns, 457.540 timesteps/s, 241.581 katom-step/s
|
||||
97.6% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 3.0991 | 3.0991 | 3.0991 | 0.0 | 17.72
|
||||
Bond | 7.6807 | 7.6807 | 7.6807 | 0.0 | 43.93
|
||||
Neigh | 1.6906 | 1.6906 | 1.6906 | 0.0 | 9.67
|
||||
Comm | 0.019091 | 0.019091 | 0.019091 | 0.0 | 0.11
|
||||
Output | 4.5095 | 4.5095 | 4.5095 | 0.0 | 25.79
|
||||
Modify | 0.46277 | 0.46277 | 0.46277 | 0.0 | 2.65
|
||||
Other | | 0.02296 | | | 0.13
|
||||
|
||||
Nlocal: 528 ave 528 max 528 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 35904 ave 35904 max 35904 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 35904
|
||||
Ave neighs/atom = 68
|
||||
Ave special neighs/atom = 11.409091
|
||||
Neighbor list builds = 1836
|
||||
Dangerous builds = 0
|
||||
|
||||
# write_data final.data nofix
|
||||
Total wall time: 0:00:17
|
||||
@ -0,0 +1,256 @@
|
||||
LAMMPS (4 Nov 2022)
|
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# use bond/react 'create atoms' feature to add 30 new styrene monomers to chain
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units real
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boundary p p p
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||||
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||||
atom_style full
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||||
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||||
pair_style lj/class2/coul/cut 8.5
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||||
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||||
angle_style class2
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||||
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||||
bond_style class2
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||||
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||||
dihedral_style class2
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||||
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||||
improper_style class2
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||||
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||||
variable T equal 530
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||||
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||||
read_data trimer.data extra/bond/per/atom 5 extra/angle/per/atom 15 extra/dihedral/per/atom 15 extra/improper/per/atom 25 extra/special/per/atom 25
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Reading data file ...
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orthogonal box = (-200 -200 -200) to (200 200 200)
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1 by 2 by 2 MPI processor grid
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||||
reading atom labelmap ...
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reading bond labelmap ...
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||||
reading angle labelmap ...
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||||
reading dihedral labelmap ...
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||||
reading improper labelmap ...
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||||
reading atoms ...
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||||
48 atoms
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||||
scanning bonds ...
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||||
8 = max bonds/atom
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scanning angles ...
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||||
21 = max angles/atom
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||||
scanning dihedrals ...
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||||
33 = max dihedrals/atom
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||||
scanning impropers ...
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||||
26 = max impropers/atom
|
||||
reading bonds ...
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||||
50 bonds
|
||||
reading angles ...
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||||
84 angles
|
||||
reading dihedrals ...
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||||
127 dihedrals
|
||||
reading impropers ...
|
||||
20 impropers
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
4 = max # of 1-2 neighbors
|
||||
8 = max # of 1-3 neighbors
|
||||
17 = max # of 1-4 neighbors
|
||||
46 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
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||||
read_data CPU = 0.007 seconds
|
||||
|
||||
molecule mol1 grow_styrene_pre.molecule_template
|
||||
Read molecule template mol1:
|
||||
1 molecules
|
||||
0 fragments
|
||||
30 atoms with max type 4
|
||||
31 bonds with max type 6
|
||||
51 angles with max type 10
|
||||
73 dihedrals with max type 13
|
||||
13 impropers with max type 3
|
||||
molecule mol2 grow_styrene_post.molecule_template
|
||||
Read molecule template mol2:
|
||||
1 molecules
|
||||
1 fragments
|
||||
46 atoms with max type 4
|
||||
48 bonds with max type 6
|
||||
81 angles with max type 10
|
||||
121 dihedrals with max type 13
|
||||
19 impropers with max type 3
|
||||
|
||||
fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0 3.0 mol1 mol2 grow_styrene.map modify_create fit create_fit overlap 2.0 stabilize_steps 200 max_rxn 30
|
||||
dynamic group bond_react_MASTER_group defined
|
||||
dynamic group statted_grp_REACT defined
|
||||
|
||||
fix 1 statted_grp_REACT nvt temp $T $T 100
|
||||
fix 1 statted_grp_REACT nvt temp 530 $T 100
|
||||
fix 1 statted_grp_REACT nvt temp 530 530 100
|
||||
|
||||
fix 4 bond_react_MASTER_group temp/rescale 1 $T $T 1 1
|
||||
fix 4 bond_react_MASTER_group temp/rescale 1 530 $T 1 1
|
||||
fix 4 bond_react_MASTER_group temp/rescale 1 530 530 1 1
|
||||
|
||||
thermo_style custom step temp press density f_myrxns[1]
|
||||
|
||||
thermo 100
|
||||
|
||||
dump 1 all xyz 1 test_vis.xyz
|
||||
|
||||
run 8000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- fix bond/react: reacter.org doi:10.1016/j.polymer.2017.09.038, doi:10.1021/acs.macromol.0c02012
|
||||
|
||||
@Article{Gissinger17,
|
||||
author = {J. R. Gissinger and B. D. Jensen and K. E. Wise},
|
||||
title = {Modeling Chemical Reactions in Classical Molecular Dynamics Simulations},
|
||||
journal = {Polymer},
|
||||
year = 2017,
|
||||
volume = 128,
|
||||
pages = {211--217}
|
||||
}
|
||||
|
||||
@Article{Gissinger20,
|
||||
author = {J. R. Gissinger, B. D. Jensen, K. E. Wise},
|
||||
title = {{REACTER}: A Heuristic Method for Reactive Molecular Dynamics},
|
||||
journal = {Macromolecules},
|
||||
year = 2020,
|
||||
volume = 53,
|
||||
number = 22,
|
||||
pages = {9953--9961}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 6 of 6 mixed pair_coeff terms from sixthpower/geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 10.5
|
||||
ghost atom cutoff = 10.5
|
||||
binsize = 5.25, bins = 77 77 77
|
||||
2 neighbor lists, perpetual/occasional/extra = 1 1 0
|
||||
(1) pair lj/class2/coul/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
(2) fix bond/react, occasional, copy from (1)
|
||||
attributes: half, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 35.37 | 35.56 | 36.15 Mbytes
|
||||
Step Temp Press Density f_myrxns[1]
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||||
0 0 0.076588866 8.1070333e-06 0
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||||
100 598.29879 -0.17888669 1.0809378e-05 1
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||||
200 699.08337 0.11172183 1.0809378e-05 1
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||||
300 931.85797 -0.13923465 1.3511722e-05 2
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||||
400 893.78126 0.14680427 1.3511722e-05 2
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||||
500 1001.0848 -0.021703999 1.6214067e-05 3
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||||
600 989.24943 0.04641672 1.6214067e-05 3
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||||
700 1244.794 -0.19464667 1.8916411e-05 4
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||||
800 1210.997 -0.06710628 1.8916411e-05 4
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||||
900 1310.0005 0.099408095 2.1618755e-05 5
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||||
1000 1640.5956 -0.05975911 2.1618755e-05 5
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||||
1100 1380.7273 -0.025206389 2.1618755e-05 5
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||||
1200 1637.6542 0.057149266 2.43211e-05 6
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||||
1300 1757.3409 0.3232123 2.43211e-05 6
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||||
1400 1664.5048 -0.29656858 2.7023444e-05 7
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||||
1500 1578.9691 0.21997047 2.7023444e-05 7
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||||
1600 1848.9227 -0.11783672 2.9725789e-05 8
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||||
1700 1981.1695 0.28374154 2.9725789e-05 8
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||||
1800 2330.8852 -0.082109894 3.2428133e-05 9
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||||
1900 2177.4096 0.23853778 3.2428133e-05 9
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||||
2000 2095.1618 -1.5405667 3.5130478e-05 10
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||||
2100 2272.2653 0.05572226 3.5130478e-05 10
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||||
2200 2599.5994 -2.2307507 3.7832822e-05 11
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||||
2300 2457.7904 0.40228312 3.7832822e-05 11
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||||
2400 2372.9736 -3.3415973 4.0535167e-05 12
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||||
2500 2427.4613 -0.16211888 4.0535167e-05 12
|
||||
2600 3022.2608 -4.3278098 4.3237511e-05 13
|
||||
2700 3115.6526 0.013828954 4.3237511e-05 13
|
||||
2800 2841.7091 -6.4163443 4.5939855e-05 14
|
||||
2900 3047.8436 0.16052429 4.5939855e-05 14
|
||||
3000 3373.7997 -7.7904706 4.86422e-05 15
|
||||
3100 3381.6653 0.35152687 4.86422e-05 15
|
||||
3200 3589.5561 -10.754027 5.1344544e-05 16
|
||||
3300 3473.4415 -0.13274479 5.1344544e-05 16
|
||||
3400 3696.3283 -13.75504 5.4046889e-05 17
|
||||
3500 3486.5442 -0.31091832 5.4046889e-05 17
|
||||
3600 3647.0818 0.34662993 5.4046889e-05 17
|
||||
3700 3636.7138 -0.041981737 5.4046889e-05 17
|
||||
3800 3427.6532 0.42008936 5.6749233e-05 18
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||||
3900 3574.0094 -0.05475272 5.6749233e-05 18
|
||||
4000 4158.9339 0.14426361 5.9451578e-05 19
|
||||
4100 3862.5026 0.094232438 5.9451578e-05 19
|
||||
4200 3969.4378 -0.10602108 6.2153922e-05 20
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||||
4300 3840.0126 0.29190336 6.2153922e-05 20
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||||
4400 4365.9912 -36.954812 6.4856266e-05 21
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||||
4500 4565.3708 0.061879092 6.4856266e-05 21
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||||
4600 4565.491 -70.588435 6.7558611e-05 22
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||||
4700 4570.2702 -0.56661378 6.7558611e-05 22
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||||
4800 4445.786 0.20534323 6.7558611e-05 22
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||||
4900 4782.6436 0.012783481 7.0260955e-05 23
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||||
5000 4777.2132 0.092416308 7.0260955e-05 23
|
||||
5100 4944.0402 0.11614993 7.29633e-05 24
|
||||
5200 5139.165 -0.23180938 7.29633e-05 24
|
||||
5300 4647.2328 0.13570142 7.5665644e-05 25
|
||||
5400 4982.7355 -0.25477884 7.5665644e-05 25
|
||||
5500 5400.5924 0.19902824 7.8367989e-05 26
|
||||
5600 5761.3552 0.083102065 7.8367989e-05 26
|
||||
5700 5723.8581 0.039332796 8.1070333e-05 27
|
||||
5800 5548.0789 -0.14511631 8.1070333e-05 27
|
||||
5900 5358.5431 -0.099694264 8.3772677e-05 28
|
||||
6000 5591.2678 9.9924655e-05 8.3772677e-05 28
|
||||
6100 6101.8008 0.26538732 8.6475022e-05 29
|
||||
6200 5848.9979 0.091137862 8.6475022e-05 29
|
||||
6300 5582.1828 -0.039900602 8.9177366e-05 30
|
||||
6400 6077.0548 0.3191104 8.9177366e-05 30
|
||||
6500 5794.6827 0.69322336 8.9177366e-05 30
|
||||
6600 5610.4331 0.080420058 8.9177366e-05 30
|
||||
6700 5615.3492 0.12810868 8.9177366e-05 30
|
||||
6800 5900.9749 -0.31704866 8.9177366e-05 30
|
||||
6900 6233.9524 0.010288514 8.9177366e-05 30
|
||||
7000 5972.7488 -1.0442089 8.9177366e-05 30
|
||||
7100 6258.1332 0.56270399 8.9177366e-05 30
|
||||
7200 6172.5919 -0.19595153 8.9177366e-05 30
|
||||
7300 5898.7547 0.020862491 8.9177366e-05 30
|
||||
7400 5815.1659 -0.0020680171 8.9177366e-05 30
|
||||
7500 6003.867 -0.12288131 8.9177366e-05 30
|
||||
7600 5966.0609 -0.1504333 8.9177366e-05 30
|
||||
7700 6274.3331 -0.62752757 8.9177366e-05 30
|
||||
7800 6051.0914 0.22821201 8.9177366e-05 30
|
||||
7900 5981.5209 -0.19623554 8.9177366e-05 30
|
||||
8000 5835.4657 0.3602475 8.9177366e-05 30
|
||||
Loop time of 13.936 on 4 procs for 8000 steps with 528 atoms
|
||||
|
||||
Performance: 49.598 ns/day, 0.484 hours/ns, 574.051 timesteps/s, 303.099 katom-step/s
|
||||
99.4% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.001058 | 0.78388 | 3.1317 | 153.1 | 5.62
|
||||
Bond | 0.0031874 | 2.0525 | 8.1984 | 247.7 | 14.73
|
||||
Neigh | 0.53495 | 0.53527 | 0.53551 | 0.0 | 3.84
|
||||
Comm | 0.01177 | 0.012451 | 0.013306 | 0.5 | 0.09
|
||||
Output | 1.3336 | 1.4735 | 1.7322 | 13.2 | 10.57
|
||||
Modify | 0.55142 | 9.0568 | 12.031 | 163.3 | 64.99
|
||||
Other | | 0.02159 | | | 0.15
|
||||
|
||||
Nlocal: 132 ave 528 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 9115.75 ave 36463 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 36463
|
||||
Ave neighs/atom = 69.058712
|
||||
Ave special neighs/atom = 11.409091
|
||||
Neighbor list builds = 771
|
||||
Dangerous builds = 0
|
||||
|
||||
# write_data final.data nofix
|
||||
Total wall time: 0:00:13
|
||||
File diff suppressed because it is too large
Load Diff
Reference in New Issue
Block a user