diff --git a/examples/PACKAGES/reaction/create_atoms_polystyrene/grow_styrene_post.data_template b/examples/PACKAGES/reaction/create_atoms_polystyrene/grow_styrene_post.data_template deleted file mode 100644 index 7269e3a269..0000000000 --- a/examples/PACKAGES/reaction/create_atoms_polystyrene/grow_styrene_post.data_template +++ /dev/null @@ -1,456 +0,0 @@ -molecule template: end of chain plus polymerized styrene - -46 atoms -48 bonds -81 angles -121 dihedrals -35 impropers -1 fragments - -Fragments - -create_fit 34 44 - -Types - -1 1 -2 2 -3 1 -4 5 -5 1 -6 2 -7 1 -8 2 -9 1 -10 2 -11 1 -12 2 -13 2 -14 6 -15 2 -16 2 -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 -31 1 -32 2 -33 1 -34 5 -35 1 -36 2 -37 1 -38 2 -39 1 -40 2 -41 1 -42 2 -43 2 -44 6 -45 2 -46 2 - -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 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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 diff --git a/examples/PACKAGES/reaction/create_atoms_polystyrene/grow_styrene_pre.data_template b/examples/PACKAGES/reaction/create_atoms_polystyrene/grow_styrene_pre.data_template deleted file mode 100644 index d04fefccf5..0000000000 --- a/examples/PACKAGES/reaction/create_atoms_polystyrene/grow_styrene_pre.data_template +++ /dev/null @@ -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 diff --git a/examples/PACKAGES/reaction/create_atoms_polystyrene/grow_styrene_pre.molecule_template b/examples/PACKAGES/reaction/create_atoms_polystyrene/grow_styrene_pre.molecule_template new file mode 100644 index 0000000000..2ef1453d72 --- /dev/null +++ b/examples/PACKAGES/reaction/create_atoms_polystyrene/grow_styrene_pre.molecule_template @@ -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 diff --git a/examples/PACKAGES/reaction/create_atoms_polystyrene/in.grow_styrene b/examples/PACKAGES/reaction/create_atoms_polystyrene/in.grow_styrene index 6e34fd2a67..b17b321fe5 100644 --- a/examples/PACKAGES/reaction/create_atoms_polystyrene/in.grow_styrene +++ b/examples/PACKAGES/reaction/create_atoms_polystyrene/in.grow_styrene @@ -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 diff --git a/examples/PACKAGES/reaction/create_atoms_polystyrene/log.24Dec20.grow_styrene.g++.1 b/examples/PACKAGES/reaction/create_atoms_polystyrene/log.24Dec20.grow_styrene.g++.1 deleted file mode 100644 index 5f1f2c6698..0000000000 --- a/examples/PACKAGES/reaction/create_atoms_polystyrene/log.24Dec20.grow_styrene.g++.1 +++ /dev/null @@ -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 diff --git a/examples/PACKAGES/reaction/create_atoms_polystyrene/log.24Dec20.grow_styrene.g++.4 b/examples/PACKAGES/reaction/create_atoms_polystyrene/log.24Dec20.grow_styrene.g++.4 deleted file mode 100644 index 8daa6d8161..0000000000 --- a/examples/PACKAGES/reaction/create_atoms_polystyrene/log.24Dec20.grow_styrene.g++.4 +++ /dev/null @@ -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 diff --git a/examples/PACKAGES/reaction/create_atoms_polystyrene/log.4Nov2022.grow_styrene.g++.1 b/examples/PACKAGES/reaction/create_atoms_polystyrene/log.4Nov2022.grow_styrene.g++.1 new file mode 100644 index 0000000000..fb9b22d134 --- /dev/null +++ b/examples/PACKAGES/reaction/create_atoms_polystyrene/log.4Nov2022.grow_styrene.g++.1 @@ -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 diff --git a/examples/PACKAGES/reaction/create_atoms_polystyrene/log.4Nov2022.grow_styrene.g++.4 b/examples/PACKAGES/reaction/create_atoms_polystyrene/log.4Nov2022.grow_styrene.g++.4 new file mode 100644 index 0000000000..b14ff6c8d0 --- /dev/null +++ b/examples/PACKAGES/reaction/create_atoms_polystyrene/log.4Nov2022.grow_styrene.g++.4 @@ -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 2 by 2 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 = 0.007 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] + 0 0 0.076588866 8.1070333e-06 0 + 100 598.29879 -0.17888669 1.0809378e-05 1 + 200 699.08337 0.11172183 1.0809378e-05 1 + 300 931.85797 -0.13923465 1.3511722e-05 2 + 400 893.78126 0.14680427 1.3511722e-05 2 + 500 1001.0848 -0.021703999 1.6214067e-05 3 + 600 989.24943 0.04641672 1.6214067e-05 3 + 700 1244.794 -0.19464667 1.8916411e-05 4 + 800 1210.997 -0.06710628 1.8916411e-05 4 + 900 1310.0005 0.099408095 2.1618755e-05 5 + 1000 1640.5956 -0.05975911 2.1618755e-05 5 + 1100 1380.7273 -0.025206389 2.1618755e-05 5 + 1200 1637.6542 0.057149266 2.43211e-05 6 + 1300 1757.3409 0.3232123 2.43211e-05 6 + 1400 1664.5048 -0.29656858 2.7023444e-05 7 + 1500 1578.9691 0.21997047 2.7023444e-05 7 + 1600 1848.9227 -0.11783672 2.9725789e-05 8 + 1700 1981.1695 0.28374154 2.9725789e-05 8 + 1800 2330.8852 -0.082109894 3.2428133e-05 9 + 1900 2177.4096 0.23853778 3.2428133e-05 9 + 2000 2095.1618 -1.5405667 3.5130478e-05 10 + 2100 2272.2653 0.05572226 3.5130478e-05 10 + 2200 2599.5994 -2.2307507 3.7832822e-05 11 + 2300 2457.7904 0.40228312 3.7832822e-05 11 + 2400 2372.9736 -3.3415973 4.0535167e-05 12 + 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 + 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 + 4300 3840.0126 0.29190336 6.2153922e-05 20 + 4400 4365.9912 -36.954812 6.4856266e-05 21 + 4500 4565.3708 0.061879092 6.4856266e-05 21 + 4600 4565.491 -70.588435 6.7558611e-05 22 + 4700 4570.2702 -0.56661378 6.7558611e-05 22 + 4800 4445.786 0.20534323 6.7558611e-05 22 + 4900 4782.6436 0.012783481 7.0260955e-05 23 + 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 diff --git a/examples/PACKAGES/reaction/create_atoms_polystyrene/trimer.data b/examples/PACKAGES/reaction/create_atoms_polystyrene/trimer.data index b3ad132f03..2608a0ed10 100644 --- a/examples/PACKAGES/reaction/create_atoms_polystyrene/trimer.data +++ b/examples/PACKAGES/reaction/create_atoms_polystyrene/trimer.data @@ -1,796 +1,585 @@ polystyrene trimer -48 atoms -7 atom types -50 bonds -13 bond types -84 angles -22 angle types -127 dihedrals -36 dihedral types -36 impropers -9 improper types + 48 atoms + 50 bonds + 84 angles + 127 dihedrals + 20 impropers -50 250 xlo xhi -50 250 ylo yhi -50 250 zlo zhi + 4 atom types + 6 bond types + 10 angle types + 13 dihedral types + 4 improper types + + -200 200 xlo xhi + -200 200 ylo yhi + -200 200 zlo zhi + +Atom Type Labels + + 1 hc + 2 cp + 3 c1 + 4 c2 + +Bond Type Labels + + 1 hc-cp + 2 cp-cp + 3 hc-c2 + 4 c1-c2 + 5 cp-c1 + 6 hc-c1 + +Angle Type Labels + + 1 hc-cp-cp + 2 cp-cp-cp + 3 cp-c1-c2 + 4 hc-c1-c2 + 5 hc-c1-cp + 6 hc-c2-c1 + 7 hc-c2-hc + 8 c1-c2-c1 + 9 cp-cp-c1 + 10 c2-c1-c2 + +Dihedral Type Labels + + 1 hc-cp-cp-hc + 2 hc-cp-cp-cp + 3 cp-cp-cp-cp + 4 cp-cp-cp-c1 + 5 hc-cp-cp-c1 + 6 cp-c1-c2-hc + 7 cp-c1-c2-c1 + 8 hc-c1-c2-hc + 9 hc-c1-c2-c1 + 10 cp-cp-c1-c2 + 11 cp-cp-c1-hc + 12 c2-c1-c2-hc + 13 c2-c1-c2-c1 + +Improper Type Labels + + 1 hc-cp-cp-cp + 2 hc-c1-cp-c2 + 3 cp-cp-cp-c1 + 4 hc-c2-hc-c1 Masses -1 12.0112 -2 1.00797 -3 12.0112 -4 12.0112 -5 12.0112 -6 12.0112 -7 12.0112 + 1 1.007970 # hc + 2 12.011150 # cp + 3 12.011150 # c1 + 4 12.011150 # c2 Pair Coeffs # lj/class2/coul/long -1 0.064 4.01 -2 0.02 2.7 -3 0.064 4.01 -4 0.064 3.9 -5 0.054 4.01 -6 0.054 4.01 -7 0.054 4.01 + 1 0.0200000000 2.7000000000 + 2 0.0640000000 4.0100000000 + 3 0.0540000000 4.0100000000 + 4 0.0540000000 4.0100000000 Bond Coeffs # class2 -1 1.0982 372.825 -803.453 894.317 -2 1.417 470.836 -627.618 1327.63 -3 1.501 321.902 -521.821 572.163 -4 1.0883 365.768 -725.54 781.662 -5 1.34 543.99 -1238.2 1644.03 -6 1.0883 365.768 -725.54 781.662 -7 1.501 321.902 -521.821 572.163 -8 1.101 345 -691.89 844.6 -9 1.53 299.67 -501.77 679.81 -10 1.101 345 -691.89 844.6 -11 1.501 321.902 -521.821 572.163 -12 1.101 345 -691.89 844.6 -13 1.53 299.67 -501.77 679.81 + 1 1.0982 372.8251 -803.4526 894.3173 + 2 1.4170 470.8361 -627.6179 1327.6345 + 3 1.1010 345.0000 -691.8900 844.6000 + 4 1.5300 299.6700 -501.7700 679.8100 + 5 1.5010 321.9021 -521.8208 572.1628 + 6 1.1010 345.0000 -691.8900 844.6000 Angle Coeffs # class2 -1 117.94 35.1558 -12.4682 0 -2 118.9 61.0226 -34.9931 0 -3 120.05 44.7148 -22.7352 0 -4 111 44.3234 -9.4454 0 -5 108.4 43.9594 -8.3924 -9.3379 -6 124.88 35.2766 -17.774 -1.6215 -7 124.88 35.2766 -17.774 -1.6215 -8 115.49 29.6363 -12.4853 -6.2218 -9 120.05 44.7148 -22.7352 0 -10 111 44.3234 -9.4454 0 -11 108.4 43.9594 -8.3924 -9.3379 -12 110.77 41.453 -10.604 5.129 -13 112.67 39.516 -7.443 -9.5583 -14 110.77 41.453 -10.604 5.129 -15 107.66 39.641 -12.921 -2.4318 -16 112.67 39.516 -7.443 -9.5583 -17 120.05 44.7148 -22.7352 0 -18 111 44.3234 -9.4454 0 -19 108.4 43.9594 -8.3924 -9.3379 -20 110.77 41.453 -10.604 5.129 -21 110.77 41.453 -10.604 5.129 -22 112.67 39.516 -7.443 -9.5583 - -BondBond Coeffs - -1 1.0795 1.417 1.0982 -2 68.2856 1.417 1.417 -3 12.0676 1.417 1.501 -4 2.9168 1.501 1.0883 -5 0 1.501 1.34 -6 10.1047 1.0883 1.34 -7 10.1047 1.0883 1.34 -8 4.8506 1.0883 1.0883 -9 12.0676 1.417 1.501 -10 2.9168 1.501 1.101 -11 0 1.501 1.53 -12 3.3872 1.101 1.53 -13 0 1.53 1.53 -14 3.3872 1.101 1.53 -15 5.3316 1.101 1.101 -16 0 1.53 1.53 -17 12.0676 1.417 1.501 -18 2.9168 1.501 1.101 -19 0 1.501 1.53 -20 3.3872 1.101 1.53 -21 3.3872 1.101 1.53 -22 0 1.53 1.53 - -BondAngle Coeffs - -1 20.0033 24.2183 1.417 1.0982 -2 28.8708 28.8708 1.417 1.417 -3 31.0771 47.0579 1.417 1.501 -4 26.4608 11.7717 1.501 1.0883 -5 0 0 1.501 1.34 -6 19.0592 23.3588 1.0883 1.34 -7 19.0592 23.3588 1.0883 1.34 -8 17.9795 17.9795 1.0883 1.0883 -9 31.0771 47.0579 1.417 1.501 -10 26.4608 11.7717 1.501 1.101 -11 0 0 1.501 1.53 -12 11.421 20.754 1.101 1.53 -13 8.016 8.016 1.53 1.53 -14 11.421 20.754 1.101 1.53 -15 18.103 18.103 1.101 1.101 -16 8.016 8.016 1.53 1.53 -17 31.0771 47.0579 1.417 1.501 -18 26.4608 11.7717 1.501 1.101 -19 0 0 1.501 1.53 -20 11.421 20.754 1.101 1.53 -21 11.421 20.754 1.101 1.53 -22 8.016 8.016 1.53 1.53 + 1 117.9400 35.1558 -12.4682 0.0000 + 2 118.9000 61.0226 -34.9931 0.0000 + 3 108.4000 43.9594 -8.3924 -9.3379 + 4 110.7700 41.4530 -10.6040 5.1290 + 5 111.0000 44.3234 -9.4454 0.0000 + 6 110.7700 41.4530 -10.6040 5.1290 + 7 107.6600 39.6410 -12.9210 -2.4318 + 8 112.6700 39.5160 -7.4430 -9.5583 + 9 120.0500 44.7148 -22.7352 0.0000 + 10 112.6700 39.5160 -7.4430 -9.5583 Dihedral Coeffs # class2 -1 0 0 1.559 0 0 0 -2 0 0 3.9661 0 0 0 -3 0 0 4.4072 0 0 0 -4 8.3667 0 1.1932 0 0 0 -5 0 0 1.8769 0 0 0 -6 0 0 0 0 0 0 -7 0 0 0 0 0 0 -8 0 0 0 0 0 0 -9 0 0 4.8974 0 0 0 -10 0 0 1.559 0 0 0 -11 0 0 4.4072 0 0 0 -12 -0.2801 0 -0.0678 0 -0.0122 0 -13 -0.2802 0 -0.0678 0 -0.0122 0 -14 -0.0228 0 0.028 0 -0.1863 0 -15 -0.1432 0 0.0617 0 -0.1083 0 -16 0 0 0.0316 0 -0.1681 0 -17 0 0 0 0 0 0 -18 0 0 0.0316 0 -0.1681 0 -19 0 0 0.0514 0 -0.143 0 -20 0 0 1.559 0 0 0 -21 0 0 4.4072 0 0 0 -22 -0.2801 0 -0.0678 0 -0.0122 0 -23 -0.2802 0 -0.0678 0 -0.0122 0 -24 -0.0228 0 0.028 0 -0.1863 0 -25 0 0 0 0 0 0 -26 -0.1432 0 0.0617 0 -0.1083 0 -27 0 0 0.0316 0 -0.1681 0 -28 0 0 0 0 0 0 -29 0 0 0.0316 0 -0.1681 0 -30 0 0 0.0514 0 -0.143 0 -31 -0.0228 0 0.028 0 -0.1863 0 -32 -0.1432 0 0.0617 0 -0.1083 0 -33 0 0 0.0316 0 -0.1681 0 -34 0 0 0 0 0 0 -35 0 0 0.0316 0 -0.1681 0 -36 0 0 0.0514 0 -0.143 0 - -AngleAngleTorsion Coeffs - -1 4.4444 117.94 120.05 -2 -4.8141 118.9 117.94 -3 -14.4097 118.9 120.05 -4 0 118.9 118.9 -5 0.3598 117.94 117.94 -6 0 120.05 111 -7 0 120.05 108.4 -8 0 108.4 124.88 -9 -7.0058 124.88 124.88 -10 4.4444 117.94 120.05 -11 -14.4097 118.9 120.05 -12 -5.8888 120.05 111 -13 0 120.05 108.4 -14 0 108.4 110.77 -15 -12.564 110.77 110.77 -16 -16.164 112.67 110.77 -17 0 108.4 112.67 -18 -16.164 110.77 112.67 -19 -22.045 112.67 112.67 -20 4.4444 117.94 120.05 -21 -14.4097 118.9 120.05 -22 -5.8888 120.05 111 -23 0 120.05 108.4 -24 0 108.4 110.77 -25 0 108.4 112.67 -26 -12.564 110.77 110.77 -27 -16.164 110.77 112.67 -28 0 112.67 108.4 -29 -16.164 112.67 110.77 -30 -22.045 112.67 112.67 -31 0 110.77 108.4 -32 -12.564 110.77 110.77 -33 -16.164 110.77 112.67 -34 0 112.67 108.4 -35 -16.164 112.67 110.77 -36 -22.045 112.67 112.67 - -EndBondTorsion Coeffs - -1 0 -0.4879 0 0 -1.797 0 1.0982 1.501 -2 0 -6.8958 0 0 -0.4669 0 1.417 1.0982 -3 0 -0.6918 0 0 0.2421 0 1.417 1.501 -4 -0.1185 6.3204 0 -0.1185 6.3204 0 1.417 1.417 -5 0 -0.689 0 0 -0.689 0 1.0982 1.0982 -6 0 0 0 0 0 0 1.417 1.0883 -7 0 0 0 0 0 0 1.417 1.34 -8 0 0 0 0 0 0 1.501 1.0883 -9 0.7129 0.5161 0 0.7129 0.5161 0 1.0883 1.0883 -10 0 -0.4879 0 0 -1.797 0 1.0982 1.501 -11 0 -0.6918 0 0 0.2421 0 1.417 1.501 -12 -0.5835 1.122 0.3978 1.3997 0.7756 0 1.417 1.101 -13 0 0 0 0 0 0 1.417 1.53 -14 0 0 0 0 0 0 1.501 1.101 -15 0.213 0.312 0.0777 0.213 0.312 0.0777 1.101 1.101 -16 0.2486 0.2422 -0.0925 0.0814 0.0591 0.2219 1.53 1.101 -17 0 0 0 0 0 0 1.501 1.53 -18 0.0814 0.0591 0.2219 0.2486 0.2422 -0.0925 1.101 1.53 -19 -0.0732 0 0 -0.0732 0 0 1.53 1.53 -20 0 -0.4879 0 0 -1.797 0 1.0982 1.501 -21 0 -0.6918 0 0 0.2421 0 1.417 1.501 -22 -0.5835 1.122 0.3978 1.3997 0.7756 0 1.417 1.101 -23 0 0 0 0 0 0 1.417 1.53 -24 0 0 0 0 0 0 1.501 1.101 -25 0 0 0 0 0 0 1.501 1.53 -26 0.213 0.312 0.0777 0.213 0.312 0.0777 1.101 1.101 -27 0.0814 0.0591 0.2219 0.2486 0.2422 -0.0925 1.101 1.53 -28 0 0 0 0 0 0 1.53 1.501 -29 0.2486 0.2422 -0.0925 0.0814 0.0591 0.2219 1.53 1.101 -30 -0.0732 0 0 -0.0732 0 0 1.53 1.53 -31 0 0 0 0 0 0 1.101 1.501 -32 0.213 0.312 0.0777 0.213 0.312 0.0777 1.101 1.101 -33 0.0814 0.0591 0.2219 0.2486 0.2422 -0.0925 1.101 1.53 -34 0 0 0 0 0 0 1.53 1.501 -35 0.2486 0.2422 -0.0925 0.0814 0.0591 0.2219 1.53 1.101 -36 -0.0732 0 0 -0.0732 0 0 1.53 1.53 - -MiddleBondTorsion Coeffs - -1 0 3.9421 0 1.417 -2 0 -1.1521 0 1.417 -3 0 9.1792 0 1.417 -4 27.5989 -2.312 0 1.417 -5 0 4.8228 0 1.417 -6 0 0 0 1.501 -7 0 0 0 1.501 -8 0 0 0 1.34 -9 0.8558 6.3911 0 1.34 -10 0 3.9421 0 1.417 -11 0 9.1792 0 1.417 -12 -5.5679 1.4083 0.301 1.501 -13 0 0 0 1.501 -14 0 0 0 1.53 -15 -14.261 -0.5322 -0.4864 1.53 -16 -14.879 -3.6581 -0.3138 1.53 -17 0 0 0 1.53 -18 -14.879 -3.6581 -0.3138 1.53 -19 -17.787 -7.1877 0 1.53 -20 0 3.9421 0 1.417 -21 0 9.1792 0 1.417 -22 -5.5679 1.4083 0.301 1.501 -23 0 0 0 1.501 -24 0 0 0 1.53 -25 0 0 0 1.53 -26 -14.261 -0.5322 -0.4864 1.53 -27 -14.879 -3.6581 -0.3138 1.53 -28 0 0 0 1.53 -29 -14.879 -3.6581 -0.3138 1.53 -30 -17.787 -7.1877 0 1.53 -31 0 0 0 1.53 -32 -14.261 -0.5322 -0.4864 1.53 -33 -14.879 -3.6581 -0.3138 1.53 -34 0 0 0 1.53 -35 -14.879 -3.6581 -0.3138 1.53 -36 -17.787 -7.1877 0 1.53 - -BondBond13 Coeffs - -1 0.8743 1.0982 1.501 -2 -6.2741 1.417 1.0982 -3 2.5085 1.417 1.501 -4 53 1.417 1.417 -5 -1.7077 1.0982 1.0982 -6 0 1.417 1.0883 -7 0 1.417 1.34 -8 0 1.501 1.0883 -9 0 1.0883 1.0883 -10 0.8743 1.0982 1.501 -11 2.5085 1.417 1.501 -12 -3.4826 1.417 1.101 -13 0 1.417 1.53 -14 0 1.501 1.101 -15 0 1.101 1.101 -16 0 1.53 1.101 -17 0 1.501 1.53 -18 0 1.101 1.53 -19 0 1.53 1.53 -20 0.8743 1.0982 1.501 -21 2.5085 1.417 1.501 -22 -3.4826 1.417 1.101 -23 0 1.417 1.53 -24 0 1.501 1.101 -25 0 1.501 1.53 -26 0 1.101 1.101 -27 0 1.101 1.53 -28 0 1.53 1.501 -29 0 1.53 1.101 -30 0 1.53 1.53 -31 0 1.101 1.501 -32 0 1.101 1.101 -33 0 1.101 1.53 -34 0 1.53 1.501 -35 0 1.53 1.101 -36 0 1.53 1.53 - -AngleTorsion Coeffs - -1 0 3.4601 0 0 -0.1242 0 117.94 120.05 -2 0 2.5014 0 0 2.7147 0 118.9 117.94 -3 0 3.8987 0 0 -4.4683 0 118.9 120.05 -4 1.9767 1.0239 0 1.9767 1.0239 0 118.9 118.9 -5 0 2.4501 0 0 2.4501 0 117.94 117.94 -6 0 0 0 0 0 0 120.05 111 -7 0 0 0 0 0 0 120.05 108.4 -8 0 0 0 0 0 0 108.4 124.88 -9 -1.8911 3.254 0 -1.8911 3.254 0 124.88 124.88 -10 0 3.4601 0 0 -0.1242 0 117.94 120.05 -11 0 3.8987 0 0 -4.4683 0 118.9 120.05 -12 0.2251 0.6548 0.1237 4.6266 0.1632 0.0461 120.05 111 -13 0 0 0 0 0 0 120.05 108.4 -14 0 0 0 0 0 0 108.4 110.77 -15 -0.8085 0.5569 -0.2466 -0.8085 0.5569 -0.2466 110.77 110.77 -16 -0.2454 0 -0.1136 0.3113 0.4516 -0.1988 112.67 110.77 -17 0 0 0 0 0 0 108.4 112.67 -18 0.3113 0.4516 -0.1988 -0.2454 0 -0.1136 110.77 112.67 -19 0.3886 -0.3139 0.1389 0.3886 -0.3139 0.1389 112.67 112.67 -20 0 3.4601 0 0 -0.1242 0 117.94 120.05 -21 0 3.8987 0 0 -4.4683 0 118.9 120.05 -22 0.2251 0.6548 0.1237 4.6266 0.1632 0.0461 120.05 111 -23 0 0 0 0 0 0 120.05 108.4 -24 0 0 0 0 0 0 108.4 110.77 -25 0 0 0 0 0 0 108.4 112.67 -26 -0.8085 0.5569 -0.2466 -0.8085 0.5569 -0.2466 110.77 110.77 -27 0.3113 0.4516 -0.1988 -0.2454 0 -0.1136 110.77 112.67 -28 0 0 0 0 0 0 112.67 108.4 -29 -0.2454 0 -0.1136 0.3113 0.4516 -0.1988 112.67 110.77 -30 0.3886 -0.3139 0.1389 0.3886 -0.3139 0.1389 112.67 112.67 -31 0 0 0 0 0 0 110.77 108.4 -32 -0.8085 0.5569 -0.2466 -0.8085 0.5569 -0.2466 110.77 110.77 -33 0.3113 0.4516 -0.1988 -0.2454 0 -0.1136 110.77 112.67 -34 0 0 0 0 0 0 112.67 108.4 -35 -0.2454 0 -0.1136 0.3113 0.4516 -0.1988 112.67 110.77 -36 0.3886 -0.3139 0.1389 0.3886 -0.3139 0.1389 112.67 112.67 + 1 0.0000 0.0000 1.8769 0.0000 0.0000 0.0000 + 2 0.0000 0.0000 3.9661 0.0000 0.0000 0.0000 + 3 8.3667 0.0000 1.1932 0.0000 0.0000 0.0000 + 4 0.0000 0.0000 4.4072 0.0000 0.0000 0.0000 + 5 0.0000 0.0000 1.5590 0.0000 0.0000 0.0000 + 6 -0.0228 0.0000 0.0280 0.0000 -0.1863 0.0000 + 7 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 + 8 -0.1432 0.0000 0.0617 0.0000 -0.1083 0.0000 + 9 0.0000 0.0000 0.0316 0.0000 -0.1681 0.0000 + 10 -0.2802 0.0000 -0.0678 0.0000 -0.0122 0.0000 + 11 -0.2801 0.0000 -0.0678 0.0000 -0.0122 0.0000 + 12 0.0000 0.0000 0.0316 0.0000 -0.1681 0.0000 + 13 0.0000 0.0000 0.0514 0.0000 -0.1430 0.0000 Improper Coeffs # class2 -1 4.8912 0 -2 7.8153 0 -3 0 0 -4 2.8561 0 -5 7.8153 0 -6 0 0 -7 0 0 -8 7.8153 0 -9 0 0 + 1 4.8912 0.0000 + 2 0.0000 0.0000 + 3 7.8153 0.0000 + 4 0.0000 0.0000 + +BondBond Coeffs + + 1 1.0795 1.0982 1.4170 + 2 68.2856 1.4170 1.4170 + 3 0.0000 1.5010 1.5300 + 4 3.3872 1.1010 1.5300 + 5 2.9168 1.1010 1.5010 + 6 3.3872 1.1010 1.5300 + 7 5.3316 1.1010 1.1010 + 8 0.0000 1.5300 1.5300 + 9 12.0676 1.4170 1.5010 + 10 0.0000 1.5300 1.5300 + +BondAngle Coeffs + + 1 24.2183 20.0033 1.0982 1.4170 + 2 28.8708 28.8708 1.4170 1.4170 + 3 0.0000 0.0000 1.5010 1.5300 + 4 11.4210 20.7540 1.1010 1.5300 + 5 11.7717 26.4608 1.1010 1.5010 + 6 11.4210 20.7540 1.1010 1.5300 + 7 18.1030 18.1030 1.1010 1.1010 + 8 8.0160 8.0160 1.5300 1.5300 + 9 31.0771 47.0579 1.4170 1.5010 + 10 8.0160 8.0160 1.5300 1.5300 AngleAngle Coeffs -1 0 0 0 118.9 117.94 117.94 -2 0 0 0 118.9 120.05 120.05 -3 0 0 0 111 124.88 108.4 -4 0 0 0 115.49 124.88 124.88 -5 0 0 0 118.9 120.05 120.05 -6 0 0 0 107.66 110.77 110.77 -7 0 0 0 111 110.77 108.4 -8 0 0 0 118.9 120.05 120.05 -9 0 0 0 111 110.77 108.4 + 1 0.0000 0.0000 0.0000 117.9400 118.9000 117.9400 + 2 0.0000 0.0000 0.0000 111.0000 108.4000 110.7700 + 3 0.0000 0.0000 0.0000 118.9000 120.0500 120.0500 + 4 0.0000 0.0000 0.0000 107.6600 110.7700 110.7700 + +AngleAngleTorsion Coeffs + + 1 0.3598 117.9400 117.9400 + 2 -4.8141 117.9400 118.9000 + 3 0.0000 118.9000 118.9000 + 4 -14.4097 118.9000 120.0500 + 5 4.4444 117.9400 120.0500 + 6 0.0000 108.4000 110.7700 + 7 0.0000 108.4000 112.6700 + 8 -12.5640 110.7700 110.7700 + 9 -16.1640 110.7700 112.6700 + 10 0.0000 120.0500 108.4000 + 11 -5.8888 120.0500 111.0000 + 12 -16.1640 112.6700 110.7700 + 13 -22.0450 112.6700 112.6700 + +EndBondTorsion Coeffs + +1 0.0000 -0.6890 0.0000 0.0000 -0.6890 0.0000 1.0982 1.0982 +2 0.0000 -0.4669 0.0000 0.0000 -6.8958 0.0000 1.0982 1.4170 +3 -0.1185 6.3204 0.0000 -0.1185 6.3204 0.0000 1.4170 1.4170 +4 0.0000 -0.6918 0.0000 0.0000 0.2421 0.0000 1.4170 1.5010 +5 0.0000 -0.4879 0.0000 0.0000 -1.7970 0.0000 1.0982 1.5010 +6 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.5010 1.1010 +7 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.5010 1.5300 +8 0.2130 0.3120 0.0777 0.2130 0.3120 0.0777 1.1010 1.1010 +9 0.0814 0.0591 0.2219 0.2486 0.2422 -0.0925 1.1010 1.5300 +10 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.4170 1.5300 +11 -0.5835 1.1220 0.3978 1.3997 0.7756 0.0000 1.4170 1.1010 +12 0.2486 0.2422 -0.0925 0.0814 0.0591 0.2219 1.5300 1.1010 +13 -0.0732 0.0000 0.0000 -0.0732 0.0000 0.0000 1.5300 1.5300 + +MiddleBondTorsion Coeffs + + 1 0.0000 4.8228 0.0000 1.4170 + 2 0.0000 -1.1521 0.0000 1.4170 + 3 27.5989 -2.3120 0.0000 1.4170 + 4 0.0000 9.1792 0.0000 1.4170 + 5 0.0000 3.9421 0.0000 1.4170 + 6 0.0000 0.0000 0.0000 1.5300 + 7 0.0000 0.0000 0.0000 1.5300 + 8 -14.2610 -0.5322 -0.4864 1.5300 + 9 -14.8790 -3.6581 -0.3138 1.5300 + 10 0.0000 0.0000 0.0000 1.5010 + 11 -5.5679 1.4083 0.3010 1.5010 + 12 -14.8790 -3.6581 -0.3138 1.5300 + 13 -17.7870 -7.1877 0.0000 1.5300 + +BondBond13 Coeffs + + 1 -1.7077 1.0982 1.0982 + 2 -6.2741 1.0982 1.4170 + 3 53.0000 1.4170 1.4170 + 4 2.5085 1.4170 1.5010 + 5 0.8743 1.0982 1.5010 + 6 0.0000 1.5010 1.1010 + 7 0.0000 1.5010 1.5300 + 8 0.0000 1.1010 1.1010 + 9 0.0000 1.1010 1.5300 + 10 0.0000 1.4170 1.5300 + 11 -3.4826 1.4170 1.1010 + 12 0.0000 1.5300 1.1010 + 13 0.0000 1.5300 1.5300 + +AngleTorsion Coeffs + + 1 0.0000 2.4501 0.0000 0.0000 2.4501 0.0000 117.9400 117.9400 + 2 0.0000 2.7147 0.0000 0.0000 2.5014 0.0000 117.9400 118.9000 + 3 1.9767 1.0239 0.0000 1.9767 1.0239 0.0000 118.9000 118.9000 + 4 0.0000 3.8987 0.0000 0.0000 -4.4683 0.0000 118.9000 120.0500 + 5 0.0000 3.4601 0.0000 0.0000 -0.1242 0.0000 117.9400 120.0500 + 6 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 108.4000 110.7700 + 7 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 108.4000 112.6700 + 8 -0.8085 0.5569 -0.2466 -0.8085 0.5569 -0.2466 110.7700 110.7700 + 9 0.3113 0.4516 -0.1988 -0.2454 0.0000 -0.1136 110.7700 112.6700 + 10 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 120.0500 108.4000 + 11 0.2251 0.6548 0.1237 4.6266 0.1632 0.0461 120.0500 111.0000 + 12 -0.2454 0.0000 -0.1136 0.3113 0.4516 -0.1988 112.6700 110.7700 + 13 0.3886 -0.3139 0.1389 0.3886 -0.3139 0.1389 112.6700 112.6700 Atoms # full -44 1 2 3.5400000000000001e-02 6.1476397222913839e+01 8.2376490601205234e+01 6.0906939115836181e+01 -45 1276 2 3.5400000000000001e-02 5.8398688202244472e+01 8.0172948526664996e+01 6.2115536813582672e+01 -46 1276 6 -6.9599999999999995e-02 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