diff --git a/doc/src/Packages_details.rst b/doc/src/Packages_details.rst index 74ddb066c6..70ebd90c97 100644 --- a/doc/src/Packages_details.rst +++ b/doc/src/Packages_details.rst @@ -2544,17 +2544,18 @@ REACTION package **Contents:** -This package allows for complex bond topology changes (reactions) -during a running MD simulation, when using classical force fields. -Topology changes are defined in pre- and post-reaction molecule -templates and can include creation and deletion of bonds, angles, -dihedrals, impropers, atom types, bond types, angle types, dihedral -types, improper types, and/or atomic charges. Other options currently -available include reaction constraints (e.g. angle and Arrhenius -constraints), deletion of reaction byproducts or other small -molecules, and chiral-sensitive reactions. +This package implements the REACTER protocol, which allows for complex +bond topology changes (reactions) during a running MD simulation when +using classical force fields. Topology changes are defined in pre- and +post-reaction molecule templates and can include creation and deletion +of bonds, angles, dihedrals, impropers, atom types, bond types, angle +types, dihedral types, improper types, and/or atomic charges. Other +options currently available include reaction constraints (e.g., angle +and Arrhenius constraints), deletion of reaction byproducts or other +small molecules, creation of new atoms or molecules bonded to existing +atoms, and using LAMMPS variables for input parameters. -**Author:** Jacob R. Gissinger (CU Boulder) while at NASA Langley Research Center. +**Author:** Jacob R. Gissinger (NASA Langley Research Center). **Supporting info:** @@ -2564,7 +2565,8 @@ molecules, and chiral-sensitive reactions. * examples/PACKAGES/reaction * `2017 LAMMPS Workshop `_ * `2019 LAMMPS Workshop `_ -* reacter.org +* `2021 LAMMPS Workshop `_ +* `REACTER website (reacter.org) `_ ---------- diff --git a/doc/src/fix_bond_react.rst b/doc/src/fix_bond_react.rst index 5385bec5b9..af3ee0fd48 100644 --- a/doc/src/fix_bond_react.rst +++ b/doc/src/fix_bond_react.rst @@ -123,6 +123,17 @@ using this fix is (4) create a map that relates the template-atom-IDs of each atom between pre- and post-reaction molecule templates (5) fill a simulation box with molecules and run a simulation with fix bond/react. +.. note:: + + .. versionadded:: 15Sep2022 + + :doc:`Type labels ` allow for molecule templates + and data files to use alphanumeric atom types that match those of + a force field. Input files that use type labels are inherently + compatible with each other and portable between different + simulations. Therefore, it is highly recommended to use type labels + to specify atom, bond, etc. types when using fix bond/react. + Only one 'fix bond/react' command can be used at a time. Multiple reactions can be simultaneously applied by specifying multiple *react* arguments to a single 'fix bond/react' command. This syntax is @@ -228,18 +239,18 @@ pairs are identified within the cutoff distance: initiator partners, these two atoms are identified as the initiator atom pair of the reaction site. -Note that it can be helpful to select -unique atom types for the initiator atoms: if an initiator atom pair -is identified, as described in the previous steps, but it does not -correspond to the same pair specified in the pre-reaction template, an -otherwise eligible reaction could be prevented from occurring. Once -this unique initiator atom pair is identified for each reaction, there -could be two or more reactions that involve the same atom on the same -time step. If this is the case, only one such reaction is permitted to -occur. This reaction is chosen randomly from all potential reactions -involving the overlapping atom. This capability allows, for example, -different reaction pathways to proceed from identical reaction sites -with user-specified probabilities. +Note that it can be helpful to select unique atom types for the +initiator atoms: if an initiator atom pair is identified, as described +in the previous steps, but it does not correspond to the same pair +specified in the pre-reaction template, an otherwise eligible reaction +could be prevented from occurring. Once this unique initiator atom +pair is identified for each reaction, there could be two or more +reactions that involve the same atom on the same time step. If this is +the case, only one such reaction is permitted to occur. This reaction +is chosen randomly from all potential reactions involving the +overlapping atom. This capability allows, for example, different +reaction pathways to proceed from identical reaction sites with +user-specified probabilities. The pre-reacted molecule template is specified by a molecule command. This molecule template file contains a sample reaction site and its @@ -280,7 +291,10 @@ for a given simulation. All atom types in the pre-reacted template must be the same as those of a potential reaction site in the simulation. A detailed discussion of matching molecule template atom types with the simulation is provided on the :doc:`molecule ` -command page. +command page. It is highly recommended to use :doc:`Type labels ` +(added in version 15Sep2022) in both molecule templates and data +files, which automates the process of syncing atom types between +different input files. The post-reacted molecule template contains a sample of the reaction site and its surrounding topology after the reaction has occurred. It 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 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 - -Coords - -1 24.130699 1.043900 -1.309300 -2 25.062700 1.582900 -1.309300 -3 22.900700 1.753900 -1.309300 -4 22.900700 3.253900 -1.309300 -5 21.670700 1.043900 -1.309300 -6 20.738701 1.582900 -1.309300 -7 21.670700 -0.376100 -1.309300 -8 20.738701 -0.915100 -1.309300 -9 22.900700 -1.086100 -1.309300 -10 22.900700 -2.163100 -1.309300 -11 24.130699 -0.376100 -1.309300 -12 25.062700 -0.915100 -1.309300 -13 23.766701 3.658900 -0.952300 -14 21.622700 3.802900 -1.871300 -15 21.672701 4.544900 -1.970300 -16 20.979700 2.979900 -2.165300 -17 13.465800 0.682500 -1.658900 -18 14.397800 1.221500 -1.658900 -19 12.235800 1.392500 -1.658900 -20 12.235800 2.892500 -1.658900 -21 11.005800 0.682500 -1.658900 -22 10.073800 1.221500 -1.658900 -23 11.005800 -0.737500 -1.658900 -24 10.073800 -1.276500 -1.658900 -25 12.235800 -1.447500 -1.658900 -26 12.235800 -2.524500 -1.658900 -27 13.465800 -0.737500 -1.658900 -28 14.397800 -1.276500 -1.658900 -29 13.101800 3.297500 -1.301900 -30 10.957800 3.441500 -2.220900 -31 18.663500 0.855500 -1.372100 -32 19.595501 1.394500 -1.372100 -33 17.433500 1.565500 -1.372100 -34 17.433500 3.065500 -1.372100 -35 16.203501 0.855500 -1.372100 -36 15.271500 1.394500 -1.372100 -37 16.203501 -0.564500 -1.372100 -38 15.271500 -1.103500 -1.372100 -39 17.433500 -1.274500 -1.372100 -40 17.433500 -2.351500 -1.372100 -41 18.663500 -0.564500 -1.372100 -42 19.595501 -1.103500 -1.372100 -43 18.299500 3.470500 -1.015100 -44 16.155500 3.614500 -1.934100 -45 16.205500 4.356500 -2.033100 -46 15.512500 2.791500 -2.228100 - -Bonds - -1 1 1 2 -2 2 1 3 -3 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11 9 12 -8 1 19 17 27 18 -9 5 17 19 21 20 -10 1 19 21 23 22 -11 1 21 23 25 24 -12 1 23 25 27 26 -13 1 17 27 25 28 -14 1 33 31 41 32 -15 5 31 33 35 34 -16 1 33 35 37 36 -17 1 35 37 39 38 -18 1 37 39 41 40 -19 1 31 41 39 42 -20 1 15 14 16 4 -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 diff --git a/examples/PACKAGES/reaction/create_atoms_polystyrene/grow_styrene_post.molecule_template b/examples/PACKAGES/reaction/create_atoms_polystyrene/grow_styrene_post.molecule_template new file mode 100644 index 0000000000..62b42afd3e --- /dev/null +++ b/examples/PACKAGES/reaction/create_atoms_polystyrene/grow_styrene_post.molecule_template @@ -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 + +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 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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 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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 5.9489073989392523e+01 8.0264057167571636e+01 6.1984002598976552e+01 -48 1276 2 3.5400000000000001e-02 5.9675170230342431e+01 8.0048052449390738e+01 6.0920159395372401e+01 -47 1276 2 1.2370000000000000e-01 5.9297455513100488e+01 8.3187777608476154e+01 5.9645157256520122e+01 -18 1 5 -1.8200000000000001e-02 6.2426251430535707e+01 8.2055473568260709e+01 6.2971661388612958e+01 -19 1 6 -6.9599999999999995e-02 6.1399255844467369e+01 8.1794665295860213e+01 6.1821819828185660e+01 -21 1 1 -1.2900000000000000e-01 6.4032918371445831e+01 8.0190179089286701e+01 6.3021564712316334e+01 -22 1 1 2.6599999999999999e-02 6.3672975135915053e+01 8.1418558650051665e+01 6.2448012627881994e+01 -23 1 2 3.5400000000000001e-02 6.1545198223694939e+01 8.0836309422842305e+01 6.1349823957467130e+01 -27 1276 2 5.1600000000000000e-02 5.9809503696580933e+01 8.1831265916389881e+01 6.3253745193271065e+01 -28 1276 5 -1.8200000000000001e-02 5.9900307947967441e+01 8.1677453781363639e+01 6.2190757403657820e+01 -31 1276 2 1.2370000000000000e-01 5.8050043823867973e+01 8.2698312265456622e+01 6.3667111329534436e+01 -38 1 2 1.2370000000000000e-01 6.3754126973935612e+01 7.9931147303963002e+01 6.4022259163067275e+01 -20 1 2 1.2370000000000000e-01 6.4070158368422781e+01 8.2950071388392274e+01 6.1042631212883315e+01 -24 1 1 -1.2900000000000000e-01 6.4337973861569580e+01 8.1916618276489871e+01 6.1387866780102470e+01 -37 1 2 1.4030000000000001e-01 6.5360115866618415e+01 7.8586112104863830e+01 6.3004997314380716e+01 -39 1 1 -1.7340000000000000e-01 6.5018338085325610e+01 7.9478260591306125e+01 6.2440745569712817e+01 -40 1 1 -1.1340000000000000e-01 6.5628759887796605e+01 7.9941156332165264e+01 6.1248476296558067e+01 -41 1 1 -1.7340000000000000e-01 6.5247995680260402e+01 8.1172439250598345e+01 6.0753045571239831e+01 -42 1 2 1.2880000000000000e-01 6.6569600059599281e+01 7.9514748976494360e+01 6.0810611807135601e+01 -43 1 2 1.4030000000000001e-01 6.5780165393063371e+01 8.1570974991007958e+01 5.9850915261812396e+01 -9 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8.3900077798460728e+01 6.4108991789590448e+01 -13 3822 6 -6.9599999999999995e-02 6.2604540882379787e+01 8.3491998603381077e+01 6.3249610918984622e+01 -14 3822 2 1.2370000000000000e-01 6.5739253131027880e+01 8.4813736128157771e+01 6.5351692111169555e+01 -15 3822 1 -1.2900000000000000e-01 6.5071144269009466e+01 8.5646783550482454e+01 6.5086813218945636e+01 -16 3822 1 2.6599999999999999e-02 6.3957099792282079e+01 8.5375816595044753e+01 6.4385073943729708e+01 -17 1 2 5.1600000000000000e-02 6.2256484483973310e+01 8.1576962161157596e+01 6.3963984654065122e+01 -26 3822 2 5.1600000000000000e-02 6.4196825763126355e+01 8.3291442832977836e+01 6.4907094488854057e+01 -29 1276 1 2.6599999999999999e-02 5.8784742332505303e+01 8.2766055380197670e+01 6.1667239692876961e+01 -32 1276 1 -1.2900000000000000e-01 5.7836199787435064e+01 8.3005060229118428e+01 6.2669788306756018e+01 -35 1276 1 -1.2900000000000000e-01 5.8572661840325132e+01 8.3404075689965083e+01 6.0443288532625175e+01 -36 1276 1 -1.7340000000000000e-01 5.7380616699226330e+01 8.4134680429976896e+01 6.0248710539932475e+01 -25 3822 2 3.5400000000000001e-02 6.2750675036816460e+01 8.3891633300878468e+01 6.2249429178485677e+01 -5 3822 2 1.4030000000000001e-01 6.2626160082050376e+01 8.8416565740835182e+01 6.4093918967496805e+01 -1 3822 2 1.2880000000000000e-01 6.4863557606529355e+01 8.9096029197548390e+01 6.5342927535537825e+01 -2 3822 1 -1.1340000000000000e-01 6.4627442641031166e+01 8.8047381925321190e+01 6.5138073202291650e+01 -3 3822 2 1.4030000000000001e-01 6.6470254992065406e+01 8.6991893750821745e+01 6.5857474890608984e+01 -4 3822 1 -1.7340000000000000e-01 6.5416488888088338e+01 8.6963894801200169e+01 6.5357641085394278e+01 - -Velocities - -44 -1.1274099342391698e-02 2.8614364731871914e-02 7.8116535486555949e-03 -45 2.3164382404151666e-03 3.9815732957733160e-03 -2.9971878581527899e-02 -46 -7.1653099619954563e-03 4.5491360587300133e-04 4.9898614093692017e-03 -48 9.8069086061434527e-03 4.0008139512159270e-03 6.2934259772882122e-03 -47 2.2646445306743783e-03 1.3029071608409702e-03 4.2232440120174040e-02 -18 7.0040064100195757e-03 3.2877451206009701e-03 -3.5376010407568422e-04 -19 -1.3998188760009689e-02 7.2238210565990146e-03 7.7956220633332383e-03 -21 3.1954292320462373e-03 -2.9717583309420764e-03 -3.1753395094325522e-03 -22 5.2997643939121201e-03 -2.9646963088534335e-03 -4.1351926198204894e-03 -23 7.6443400078766528e-03 4.0358953976530103e-02 -2.6684706183248367e-02 -27 1.9261652416455359e-03 -1.1632914130150688e-02 1.0061732021630769e-02 -28 -8.2251676802878315e-03 -1.5111873066969876e-04 1.3808893565582731e-02 -31 5.2475840572179860e-03 1.8266996572138715e-02 2.3453280610166885e-03 -38 -2.0343905130199073e-02 3.2815536859276281e-02 3.6511922534330152e-03 -20 2.2914549087537126e-02 1.4424503744223915e-02 2.1708279654645496e-03 -24 -2.4717233344142471e-03 1.2966123098719246e-02 8.1261459853411936e-03 -37 -2.4547379584186218e-02 -3.0213966592845171e-02 -3.1437442951939183e-02 -39 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1.0653751333175230e-02 -1 -1.7372868398038824e-02 -2.3625357536259349e-03 1.2220266128368908e-02 -2 3.7050246021929395e-03 -1.0236943515935205e-03 7.2206774682170580e-03 -3 2.3669435799326944e-02 2.7891427939155597e-02 -6.7091036888174346e-03 -4 3.4910623999263577e-03 2.6370880132825258e-03 -6.4694788112864129e-03 + 1 3 1 0.128800 64.863555908 89.096031189 65.342926025 0 0 0 # hc + 2 3 2 -0.113400 64.627441406 88.047378540 65.138076782 0 0 0 # cp + 3 3 1 0.140300 66.470252991 86.991889954 65.857475281 0 0 0 # hc + 4 3 2 -0.173400 65.416488647 86.963897705 65.357643127 0 0 0 # cp + 5 3 1 0.140300 62.626159668 88.416564941 64.093917847 0 0 0 # hc + 6 3 2 -0.173400 63.308101654 87.713508606 64.643081665 0 0 0 # cp + 7 3 2 -0.129000 63.010292053 86.423652649 64.252845764 0 0 0 # cp + 8 3 1 0.123700 62.089199066 86.309196472 63.711261749 0 0 0 # hc + 9 2 1 0.128800 55.651794434 85.074470520 61.094478607 0 0 0 # hc + 10 2 1 0.140300 57.266132355 84.599327087 59.281513214 0 0 0 # hc + 11 3 1 0.035400 61.694305420 83.823471069 63.778953552 0 0 0 # hc + 12 3 3 -0.018200 63.814926147 83.900077820 64.108993530 0 0 0 # c1 + 13 3 4 -0.069600 62.604541779 83.491996765 63.249610901 0 0 0 # c2 + 14 3 1 0.123700 65.739250183 84.813735962 65.351692200 0 0 0 # hc + 15 3 2 -0.129000 65.071144104 85.646781921 65.086814880 0 0 0 # cp + 16 3 2 0.026600 63.957099915 85.375816345 64.385070801 0 0 0 # cp + 17 1 1 0.051600 62.256484985 81.576965332 63.963985443 0 0 0 # hc + 18 1 3 -0.018200 62.426250458 82.055473328 62.971660614 0 0 0 # c1 + 19 1 4 -0.069600 61.399257660 81.794662476 61.821819305 0 0 0 # c2 + 20 1 1 0.123700 64.070159912 82.950073242 61.042633057 0 0 0 # hc + 21 1 2 -0.129000 64.032920837 80.190177917 63.021564484 0 0 0 # cp + 22 1 2 0.026600 63.672973633 81.418556213 62.448013306 0 0 0 # cp + 23 1 1 0.035400 61.545196533 80.836311340 61.349822998 0 0 0 # hc + 24 1 2 -0.129000 64.337974548 81.916618347 61.387866974 0 0 0 # cp + 25 3 1 0.035400 62.750675201 83.891632080 62.249427795 0 0 0 # hc + 26 3 1 0.051600 64.196823120 83.291442871 64.907096863 0 0 0 # hc + 27 2 1 0.051600 59.809505463 81.831268311 63.253746033 0 0 0 # hc + 28 2 3 -0.018200 59.900306702 81.677452087 62.190757751 0 0 0 # c1 + 29 2 2 0.026600 58.784740448 82.766052246 61.667240143 0 0 0 # cp + 30 2 1 0.140300 56.082981110 83.912864685 63.351890564 0 0 0 # hc + 31 2 1 0.123700 58.050045013 82.698310852 63.667110443 0 0 0 # hc + 32 2 2 -0.129000 57.836200714 83.005058289 62.669788361 0 0 0 # cp + 33 2 2 -0.173400 56.718132019 83.758476257 62.493293762 0 0 0 # cp + 34 2 2 -0.113400 56.498352051 84.426574707 61.290145874 0 0 0 # cp + 35 2 2 -0.129000 58.572662354 83.404075623 60.443286896 0 0 0 # cp + 36 2 2 -0.173400 57.380615234 84.134681702 60.248710632 0 0 0 # cp + 37 1 1 0.140300 65.360115051 78.586112976 63.004997253 0 0 0 # hc + 38 1 1 0.123700 63.754127502 79.931144714 64.022262573 0 0 0 # hc + 39 1 2 -0.173400 65.018341064 79.478263855 62.440746307 0 0 0 # cp + 40 1 2 -0.113400 65.628761292 79.941154480 61.248477936 0 0 0 # cp + 41 1 2 -0.173400 65.247993469 81.172439575 60.753044128 0 0 0 # cp + 42 1 1 0.128800 66.569602966 79.514747620 60.810611725 0 0 0 # hc + 43 1 1 0.140300 65.780166626 81.570976257 59.850914001 0 0 0 # hc + 44 1 1 0.035400 61.476398468 82.376487732 60.906940460 0 0 0 # hc + 45 2 1 0.035400 58.398689270 80.172950745 62.115535736 0 0 0 # hc + 46 2 4 -0.069600 59.489074707 80.264060974 61.984001160 0 0 0 # c2 + 47 2 1 0.123700 59.297454834 83.187774658 59.645156860 0 0 0 # hc + 48 2 1 0.035400 59.675170898 80.048049927 60.920158386 0 0 0 # hc Bonds -1 10 44 19 -2 10 45 46 -3 10 48 46 -4 9 19 18 -5 1 21 38 -6 2 21 22 -7 2 21 39 -8 7 22 18 -9 2 22 24 -10 10 23 19 -11 8 27 28 -12 9 28 46 -13 9 28 19 -14 1 24 20 -15 2 24 41 -16 1 39 37 -17 1 40 42 -18 2 40 39 -19 1 41 43 -20 2 41 40 -21 1 33 30 -22 1 34 9 -23 2 34 33 -24 1 6 5 -25 2 6 2 -26 1 7 8 -27 2 7 6 -28 10 11 13 -29 13 12 13 -30 9 13 18 -31 1 15 14 -32 2 15 16 -33 2 15 4 -34 11 16 12 -35 2 16 7 -36 8 17 18 -37 12 26 12 -38 7 29 28 -39 2 29 35 -40 1 32 31 -41 2 32 29 -42 2 32 33 -43 1 35 47 -44 2 35 36 -45 1 36 10 -46 2 36 34 -47 10 25 13 -48 1 2 1 -49 2 2 4 -50 1 4 3 + 1 1 1 2 + 2 2 2 6 + 3 2 2 4 + 4 1 3 4 + 5 2 4 15 + 6 1 5 6 + 7 2 6 7 + 8 1 8 7 + 9 2 7 16 + 10 1 9 34 + 11 1 10 36 + 12 3 11 13 + 13 4 12 13 + 14 5 16 12 + 15 6 26 12 + 16 4 18 13 + 17 3 25 13 + 18 1 14 15 + 19 2 15 16 + 20 6 17 18 + 21 4 18 19 + 22 5 22 18 + 23 3 44 19 + 24 3 23 19 + 25 4 28 19 + 26 1 20 24 + 27 1 38 21 + 28 2 21 22 + 29 2 21 39 + 30 2 22 24 + 31 2 24 41 + 32 6 27 28 + 33 4 28 46 + 34 5 29 28 + 35 2 29 35 + 36 2 29 32 + 37 1 30 33 + 38 1 31 32 + 39 2 32 33 + 40 2 33 34 + 41 2 34 36 + 42 1 47 35 + 43 2 35 36 + 44 1 37 39 + 45 2 39 40 + 46 1 42 40 + 47 2 40 41 + 48 1 43 41 + 49 3 45 46 + 50 3 48 46 Angles -1 14 45 46 28 -2 14 48 46 28 -3 15 45 46 48 -4 11 22 18 13 -5 12 17 18 13 -6 13 13 18 19 -7 10 22 18 17 -8 11 22 18 19 -9 12 17 18 19 -10 16 28 19 18 -11 14 44 19 28 -12 14 23 19 28 -13 14 44 19 18 -14 14 23 19 18 -15 15 44 19 23 -16 1 22 21 38 -17 1 39 21 38 -18 2 22 21 39 -19 9 21 22 18 -20 2 21 22 24 -21 9 24 22 18 -22 10 29 28 27 -23 11 29 28 46 -24 11 29 28 19 -25 12 27 28 46 -26 12 27 28 19 -27 13 46 28 19 -28 1 22 24 20 -29 2 22 24 41 -30 1 41 24 20 -31 2 21 39 40 -32 1 21 39 37 -33 1 40 39 37 -34 1 41 40 42 -35 2 41 40 39 -36 1 39 40 42 -37 1 24 41 43 -38 2 24 41 40 -39 1 40 41 43 -40 2 32 33 34 -41 1 32 33 30 -42 1 34 33 30 -43 1 36 34 9 -44 2 36 34 33 -45 1 33 34 9 -46 1 7 6 5 -47 2 7 6 2 -48 1 2 6 5 -49 1 16 7 8 -50 2 16 7 6 -51 1 6 7 8 -52 18 16 12 26 -53 19 16 12 13 -54 20 26 12 13 -55 21 25 13 12 -56 21 11 13 12 -57 22 12 13 18 -58 15 25 13 11 -59 14 25 13 18 -60 14 11 13 18 -61 1 16 15 14 -62 1 4 15 14 -63 2 16 15 4 -64 17 15 16 12 -65 2 15 16 7 -66 17 7 16 12 -67 9 32 29 28 -68 2 32 29 35 -69 9 35 29 28 -70 1 29 32 31 -71 1 33 32 31 -72 2 29 32 33 -73 1 29 35 47 -74 2 29 35 36 -75 1 36 35 47 -76 1 35 36 10 -77 2 35 36 34 -78 1 34 36 10 -79 1 6 2 1 -80 2 6 2 4 -81 1 4 2 1 -82 2 15 4 2 -83 1 15 4 3 -84 1 2 4 3 + 1 1 1 2 6 + 2 1 1 2 4 + 3 2 6 2 4 + 4 1 3 4 2 + 5 2 2 4 15 + 6 1 3 4 15 + 7 1 5 6 2 + 8 2 2 6 7 + 9 1 5 6 7 + 10 1 8 7 6 + 11 2 6 7 16 + 12 1 8 7 16 + 13 3 16 12 13 + 14 4 26 12 13 + 15 5 26 12 16 + 16 6 11 13 12 + 17 6 11 13 18 + 18 7 11 13 25 + 19 8 12 13 18 + 20 6 25 13 12 + 21 6 25 13 18 + 22 1 14 15 4 + 23 2 4 15 16 + 24 1 14 15 16 + 25 9 7 16 12 + 26 2 7 16 15 + 27 9 15 16 12 + 28 4 17 18 13 + 29 10 13 18 19 + 30 3 22 18 13 + 31 4 17 18 19 + 32 5 17 18 22 + 33 3 22 18 19 + 34 6 44 19 18 + 35 6 23 19 18 + 36 8 18 19 28 + 37 7 44 19 23 + 38 6 44 19 28 + 39 6 23 19 28 + 40 1 38 21 22 + 41 1 38 21 39 + 42 2 22 21 39 + 43 9 21 22 18 + 44 9 24 22 18 + 45 2 21 22 24 + 46 1 20 24 22 + 47 1 20 24 41 + 48 2 22 24 41 + 49 4 27 28 19 + 50 10 19 28 46 + 51 3 29 28 19 + 52 4 27 28 46 + 53 5 27 28 29 + 54 3 29 28 46 + 55 9 35 29 28 + 56 9 32 29 28 + 57 2 35 29 32 + 58 1 31 32 29 + 59 2 29 32 33 + 60 1 31 32 33 + 61 1 30 33 32 + 62 1 30 33 34 + 63 2 32 33 34 + 64 1 9 34 33 + 65 1 9 34 36 + 66 2 33 34 36 + 67 1 47 35 29 + 68 2 29 35 36 + 69 1 47 35 36 + 70 1 10 36 34 + 71 1 10 36 35 + 72 2 34 36 35 + 73 1 37 39 21 + 74 2 21 39 40 + 75 1 37 39 40 + 76 1 42 40 39 + 77 2 39 40 41 + 78 1 42 40 41 + 79 2 24 41 40 + 80 1 43 41 24 + 81 1 43 41 40 + 82 6 45 46 28 + 83 6 48 46 28 + 84 7 45 46 48 Dihedrals -1 34 18 19 28 29 -2 31 44 19 28 29 -3 31 23 19 28 29 -4 35 18 19 28 27 -5 32 44 19 28 27 -6 32 23 19 28 27 -7 36 18 19 28 46 -8 33 44 19 28 46 -9 33 23 19 28 46 -10 36 28 19 18 13 -11 33 44 19 18 13 -12 33 23 19 18 13 -13 34 28 19 18 22 -14 31 44 19 18 22 -15 31 23 19 18 22 -16 35 28 19 18 17 -17 32 44 19 18 17 -18 32 23 19 18 17 -19 10 38 21 22 18 -20 11 39 21 22 18 -21 4 39 21 22 24 -22 5 38 21 39 37 -23 4 22 21 39 40 -24 2 22 21 39 37 -25 2 24 22 21 38 -26 13 21 22 18 13 -27 12 21 22 18 17 -28 13 21 22 18 19 -29 13 24 22 18 13 -30 12 24 22 18 17 -31 13 24 22 18 19 -32 2 21 22 24 20 -33 4 21 22 24 41 -34 14 29 28 46 45 -35 14 29 28 46 48 -36 15 27 28 46 45 -37 15 27 28 46 48 -38 16 19 28 46 45 -39 16 19 28 46 48 -40 10 20 24 22 18 -41 11 41 24 22 18 -42 2 22 24 41 43 -43 4 22 24 41 40 -44 5 20 24 41 43 -45 2 40 39 21 38 -46 2 21 39 40 42 -47 2 39 40 41 43 -48 4 41 40 39 21 -49 2 41 40 39 37 -50 5 42 40 39 37 -51 2 40 41 24 20 -52 2 24 41 40 42 -53 4 24 41 40 39 -54 5 43 41 40 42 -55 2 34 33 32 31 -56 2 32 33 34 9 -57 2 33 34 36 10 -58 4 36 34 33 32 -59 2 36 34 33 30 -60 5 9 34 33 30 -61 2 2 6 7 8 -62 2 7 6 2 1 -63 4 7 6 2 4 -64 5 5 6 2 1 -65 20 8 7 16 12 -66 21 6 7 16 12 -67 2 16 7 6 5 -68 4 16 7 6 2 -69 5 8 7 6 5 -70 24 16 12 13 25 -71 24 16 12 13 11 -72 25 16 12 13 18 -73 26 26 12 13 25 -74 26 26 12 13 11 -75 27 26 12 13 18 -76 28 12 13 18 22 -77 29 12 13 18 17 -78 30 12 13 18 19 -79 31 25 13 18 22 -80 32 25 13 18 17 -81 33 25 13 18 19 -82 31 11 13 18 22 -83 32 11 13 18 17 -84 33 11 13 18 19 -85 20 14 15 16 12 -86 21 4 15 16 12 -87 4 4 15 16 7 -88 5 14 15 4 3 -89 4 16 15 4 2 -90 2 16 15 4 3 -91 2 7 16 15 14 -92 22 15 16 12 26 -93 23 15 16 12 13 -94 22 7 16 12 26 -95 23 7 16 12 13 -96 2 15 16 7 8 -97 4 15 16 7 6 -98 2 35 29 32 31 -99 12 32 29 28 27 -100 13 32 29 28 46 -101 13 32 29 28 19 -102 12 35 29 28 27 -103 13 35 29 28 46 -104 13 35 29 28 19 -105 2 32 29 35 47 -106 4 32 29 35 36 -107 10 31 32 29 28 -108 11 33 32 29 28 -109 4 33 32 29 35 -110 5 31 32 33 30 -111 4 29 32 33 34 -112 2 29 32 33 30 -113 10 47 35 29 28 -114 11 36 35 29 28 -115 2 29 35 36 10 -116 4 29 35 36 34 -117 5 47 35 36 10 -118 2 34 36 35 47 -119 2 35 36 34 9 -120 4 35 36 34 33 -121 5 10 36 34 9 -122 2 4 2 6 5 -123 4 6 2 4 15 -124 2 6 2 4 3 -125 5 1 2 4 3 -126 2 2 4 15 14 -127 2 15 4 2 1 + 1 1 1 2 6 5 + 2 2 1 2 6 7 + 3 2 5 6 2 4 + 4 3 4 2 6 7 + 5 1 1 2 4 3 + 6 2 1 2 4 15 + 7 2 3 4 2 6 + 8 3 6 2 4 15 + 9 2 14 15 4 2 + 10 3 2 4 15 16 + 11 1 3 4 15 14 + 12 2 3 4 15 16 + 13 2 8 7 6 2 + 14 3 2 6 7 16 + 15 1 5 6 7 8 + 16 2 5 6 7 16 + 17 4 6 7 16 12 + 18 3 6 7 16 15 + 19 5 8 7 16 12 + 20 2 8 7 16 15 + 21 6 16 12 13 11 + 22 7 16 12 13 18 + 23 6 16 12 13 25 + 24 8 26 12 13 11 + 25 9 26 12 13 18 + 26 8 26 12 13 25 + 27 10 7 16 12 13 + 28 10 15 16 12 13 + 29 11 7 16 12 26 + 30 11 15 16 12 26 + 31 8 17 18 13 11 + 32 12 19 18 13 11 + 33 6 22 18 13 11 + 34 9 17 18 13 12 + 35 13 19 18 13 12 + 36 7 22 18 13 12 + 37 8 17 18 13 25 + 38 12 19 18 13 25 + 39 6 22 18 13 25 + 40 3 4 15 16 7 + 41 4 4 15 16 12 + 42 2 14 15 16 7 + 43 5 14 15 16 12 + 44 12 13 18 19 44 + 45 12 13 18 19 23 + 46 13 13 18 19 28 + 47 8 17 18 19 44 + 48 8 17 18 19 23 + 49 9 17 18 19 28 + 50 6 22 18 19 44 + 51 6 22 18 19 23 + 52 7 22 18 19 28 + 53 10 21 22 18 13 + 54 10 24 22 18 13 + 55 11 21 22 18 17 + 56 11 24 22 18 17 + 57 10 21 22 18 19 + 58 10 24 22 18 19 + 59 9 27 28 19 18 + 60 13 46 28 19 18 + 61 7 29 28 19 18 + 62 8 27 28 19 44 + 63 12 46 28 19 44 + 64 6 29 28 19 44 + 65 8 27 28 19 23 + 66 12 46 28 19 23 + 67 6 29 28 19 23 + 68 5 38 21 22 18 + 69 2 38 21 22 24 + 70 4 39 21 22 18 + 71 3 39 21 22 24 + 72 1 38 21 39 37 + 73 2 38 21 39 40 + 74 2 37 39 21 22 + 75 3 22 21 39 40 + 76 5 20 24 22 18 + 77 4 41 24 22 18 + 78 2 20 24 22 21 + 79 3 21 22 24 41 + 80 2 20 24 41 40 + 81 1 20 24 41 43 + 82 3 22 24 41 40 + 83 2 43 41 24 22 + 84 12 19 28 46 45 + 85 12 19 28 46 48 + 86 8 27 28 46 45 + 87 8 27 28 46 48 + 88 6 29 28 46 45 + 89 6 29 28 46 48 + 90 10 35 29 28 19 + 91 10 32 29 28 19 + 92 11 35 29 28 27 + 93 11 32 29 28 27 + 94 10 35 29 28 46 + 95 10 32 29 28 46 + 96 5 47 35 29 28 + 97 4 36 35 29 28 + 98 2 47 35 29 32 + 99 3 32 29 35 36 + 100 5 31 32 29 28 + 101 4 33 32 29 28 + 102 2 31 32 29 35 + 103 3 35 29 32 33 + 104 2 30 33 32 29 + 105 3 29 32 33 34 + 106 1 31 32 33 30 + 107 2 31 32 33 34 + 108 1 30 33 34 9 + 109 2 30 33 34 36 + 110 2 9 34 33 32 + 111 3 32 33 34 36 + 112 1 9 34 36 10 + 113 2 9 34 36 35 + 114 2 10 36 34 33 + 115 3 33 34 36 35 + 116 2 10 36 35 29 + 117 3 29 35 36 34 + 118 1 47 35 36 10 + 119 2 47 35 36 34 + 120 2 42 40 39 21 + 121 3 21 39 40 41 + 122 1 37 39 40 42 + 123 2 37 39 40 41 + 124 3 39 40 41 24 + 125 2 43 41 40 39 + 126 2 42 40 41 24 + 127 1 42 40 41 43 Impropers -1 6 45 46 48 28 -2 1 22 18 17 13 -3 1 22 18 13 19 -4 1 17 18 13 19 -5 1 22 18 17 19 -6 1 44 19 18 28 -7 1 23 19 18 28 -8 1 44 19 23 28 -9 1 44 19 23 18 -10 1 22 21 39 38 -11 5 21 22 24 18 -12 1 29 28 27 46 -13 1 29 28 27 19 -14 1 29 28 46 19 -15 1 27 28 46 19 -16 1 22 24 41 20 -17 1 21 39 40 37 -18 1 41 40 39 42 -19 1 24 41 40 43 -20 1 32 33 34 30 -21 1 36 34 33 9 -22 1 7 6 2 5 -23 1 16 7 6 8 -24 9 16 12 26 13 -25 1 25 13 11 12 -26 1 25 13 12 18 -27 1 11 13 12 18 -28 1 25 13 11 18 -29 1 16 15 4 14 -30 8 15 16 7 12 -31 5 32 29 35 28 -32 1 29 32 33 31 -33 1 29 35 36 47 -34 1 35 36 34 10 -35 1 6 2 4 1 -36 1 15 4 2 3 + 1 1 1 2 6 4 + 2 1 3 4 2 15 + 3 1 5 6 2 7 + 4 1 8 7 6 16 + 5 2 26 12 16 13 + 6 1 14 15 4 16 + 7 3 7 16 15 12 + 8 1 38 21 22 39 + 9 3 21 22 24 18 + 10 1 20 24 22 41 + 11 3 35 29 32 28 + 12 1 31 32 29 33 + 13 1 30 33 32 34 + 14 1 9 34 33 36 + 15 1 47 35 29 36 + 16 1 10 36 34 35 + 17 1 37 39 21 40 + 18 1 42 40 39 41 + 19 1 43 41 40 24 + 20 4 45 46 48 28 diff --git a/examples/PACKAGES/reaction/nylon,6-6_melt/in.large_nylon_melt b/examples/PACKAGES/reaction/nylon,6-6_melt/in.large_nylon_melt index 3982da799d..6fbf46f844 100644 --- a/examples/PACKAGES/reaction/nylon,6-6_melt/in.large_nylon_melt +++ b/examples/PACKAGES/reaction/nylon,6-6_melt/in.large_nylon_melt @@ -18,14 +18,19 @@ dihedral_style class2 improper_style class2 -read_data large_nylon_melt.data.gz +read_data large_nylon_melt.data.gz & + 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 velocity all create 800.0 4928459 dist gaussian -molecule mol1 rxn1_stp1_unreacted.data_template -molecule mol2 rxn1_stp1_reacted.data_template -molecule mol3 rxn1_stp2_unreacted.data_template -molecule mol4 rxn1_stp2_reacted.data_template +molecule mol1 rxn1_stp1_unreacted.molecule_template +molecule mol2 rxn1_stp1_reacted.molecule_template +molecule mol3 rxn1_stp2_unreacted.molecule_template +molecule mol4 rxn1_stp2_reacted.molecule_template thermo 50 diff --git a/examples/PACKAGES/reaction/nylon,6-6_melt/large_nylon_melt.data.gz b/examples/PACKAGES/reaction/nylon,6-6_melt/large_nylon_melt.data.gz index c620b879a8..e1ec3079f7 100644 Binary files a/examples/PACKAGES/reaction/nylon,6-6_melt/large_nylon_melt.data.gz and b/examples/PACKAGES/reaction/nylon,6-6_melt/large_nylon_melt.data.gz differ diff --git a/examples/PACKAGES/reaction/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.1 b/examples/PACKAGES/reaction/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.1 deleted file mode 100644 index 653c7582f8..0000000000 --- a/examples/PACKAGES/reaction/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.1 +++ /dev/null @@ -1,175 +0,0 @@ -LAMMPS (20 Apr 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) - using 1 OpenMP thread(s) per MPI task -# 35,000 atom nylon melt example - -units real - -boundary p p p - -atom_style full - -kspace_style pppm 1.0e-4 - -pair_style lj/class2/coul/long 8.5 - -angle_style class2 - -bond_style class2 - -dihedral_style class2 - -improper_style class2 - -read_data large_nylon_melt.data.gz - orthogonal box = (-2.68344 -2.06791 -2.21988) to (73.4552 73.2448 73.4065) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 35200 atoms - reading velocities ... - 35200 velocities - scanning bonds ... - 9 = max bonds/atom - scanning angles ... - 21 = max angles/atom - scanning dihedrals ... - 31 = max dihedrals/atom - scanning impropers ... - 29 = max impropers/atom - reading bonds ... - 33600 bonds - reading angles ... - 59200 angles - reading dihedrals ... - 80000 dihedrals - reading impropers ... - 35200 impropers - 4 = max # of 1-2 neighbors - 6 = max # of 1-3 neighbors - 12 = max # of 1-4 neighbors - 41 = max # of special neighbors - -velocity all create 800.0 4928459 dist gaussian - -molecule mol1 rxn1_stp1_unreacted.data_template -Read molecule mol1: - 18 atoms with max type 8 - 16 bonds with max type 12 - 25 angles with max type 24 - 23 dihedrals with max type 33 - 14 impropers with max type 9 -molecule mol2 rxn1_stp1_reacted.data_template -Read molecule mol2: - 18 atoms with max type 9 - 17 bonds with max type 11 - 31 angles with max type 23 - 39 dihedrals with max type 30 - 20 impropers with max type 1 -molecule mol3 rxn1_stp2_unreacted.data_template -Read molecule mol3: - 15 atoms with max type 9 - 14 bonds with max type 11 - 25 angles with max type 23 - 30 dihedrals with max type 30 - 16 impropers with max type 1 -molecule mol4 rxn1_stp2_reacted.data_template -Read molecule mol4: - 15 atoms with max type 11 - 13 bonds with max type 13 - 19 angles with max type 25 - 16 dihedrals with max type 29 - 10 impropers with max type 11 - -thermo 50 - -# dump 1 all xyz 100 test_vis.xyz - -fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map -WARNING: An atom in 'react #1' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489) -WARNING: An atom in 'react #2' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489) -dynamic group bond_react_MASTER_group defined -dynamic group statted_grp defined -dynamic group bond_react_MASTER_group defined -dynamic group statted_grp defined - -# stable at 800K -fix 1 statted_grp nvt temp 800 800 100 - -# in order to customize behavior of reacting atoms, -# you can use the internally created 'bond_react_MASTER_group', like so: -# fix 2 bond_react_MASTER_group temp/rescale 1 800 800 10 1 - -thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] # cumulative reaction counts - -# restart 100 restart1 restart2 - -run 200 -PPPM initialization ... - using 12-bit tables for long-range coulomb (../kspace.cpp:321) - G vector (1/distance) = 0.20765 - grid = 18 18 18 - stencil order = 5 - estimated absolute RMS force accuracy = 0.0333156 - estimated relative force accuracy = 0.000100329 - using double precision FFTs - 3d grid and FFT values/proc = 12167 5832 -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 = 15 15 15 - 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 -Per MPI rank memory allocation (min/avg/max) = 209.1 | 209.1 | 209.1 Mbytes -Step Temp Press Density f_myrxns[1] f_myrxns[2] - 0 800 3666.3948 0.80366765 0 0 - 50 673.95238 -9670.9169 0.80366765 31 0 - 100 697.22819 -4624.0512 0.80366765 57 22 - 150 723.60507 -17175.571 0.80366765 76 48 - 200 736.71277 -12961.963 0.80366765 84 64 -Loop time of 102.825 on 1 procs for 200 steps with 35200 atoms - -Performance: 0.168 ns/day, 142.812 hours/ns, 1.945 timesteps/s -99.7% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 27.193 | 27.193 | 27.193 | 0.0 | 26.45 -Bond | 11.324 | 11.324 | 11.324 | 0.0 | 11.01 -Kspace | 4.1878 | 4.1878 | 4.1878 | 0.0 | 4.07 -Neigh | 54.724 | 54.724 | 54.724 | 0.0 | 53.22 -Comm | 0.40662 | 0.40662 | 0.40662 | 0.0 | 0.40 -Output | 0.0011101 | 0.0011101 | 0.0011101 | 0.0 | 0.00 -Modify | 4.9422 | 4.9422 | 4.9422 | 0.0 | 4.81 -Other | | 0.04545 | | | 0.04 - -Nlocal: 35200 ave 35200 max 35200 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 38403 ave 38403 max 38403 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 6.9281e+06 ave 6.9281e+06 max 6.9281e+06 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 6928101 -Ave neighs/atom = 196.821 -Ave special neighs/atom = 9.83727 -Neighbor list builds = 200 -Dangerous builds = 0 - -# write_restart restart_longrun -# write_data restart_longrun.data - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:01:43 diff --git a/examples/PACKAGES/reaction/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.4 b/examples/PACKAGES/reaction/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.4 deleted file mode 100644 index cc0dda60c7..0000000000 --- a/examples/PACKAGES/reaction/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.4 +++ /dev/null @@ -1,175 +0,0 @@ -LAMMPS (20 Apr 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) - using 1 OpenMP thread(s) per MPI task -# 35,000 atom nylon melt example - -units real - -boundary p p p - -atom_style full - -kspace_style pppm 1.0e-4 - -pair_style lj/class2/coul/long 8.5 - -angle_style class2 - -bond_style class2 - -dihedral_style class2 - -improper_style class2 - -read_data large_nylon_melt.data.gz - orthogonal box = (-2.68344 -2.06791 -2.21988) to (73.4552 73.2448 73.4065) - 2 by 1 by 2 MPI processor grid - reading atoms ... - 35200 atoms - reading velocities ... - 35200 velocities - scanning bonds ... - 9 = max bonds/atom - scanning angles ... - 21 = max angles/atom - scanning dihedrals ... - 31 = max dihedrals/atom - scanning impropers ... - 29 = max impropers/atom - reading bonds ... - 33600 bonds - reading angles ... - 59200 angles - reading dihedrals ... - 80000 dihedrals - reading impropers ... - 35200 impropers - 4 = max # of 1-2 neighbors - 6 = max # of 1-3 neighbors - 12 = max # of 1-4 neighbors - 41 = max # of special neighbors - -velocity all create 800.0 4928459 dist gaussian - -molecule mol1 rxn1_stp1_unreacted.data_template -Read molecule mol1: - 18 atoms with max type 8 - 16 bonds with max type 12 - 25 angles with max type 24 - 23 dihedrals with max type 33 - 14 impropers with max type 9 -molecule mol2 rxn1_stp1_reacted.data_template -Read molecule mol2: - 18 atoms with max type 9 - 17 bonds with max type 11 - 31 angles with max type 23 - 39 dihedrals with max type 30 - 20 impropers with max type 1 -molecule mol3 rxn1_stp2_unreacted.data_template -Read molecule mol3: - 15 atoms with max type 9 - 14 bonds with max type 11 - 25 angles with max type 23 - 30 dihedrals with max type 30 - 16 impropers with max type 1 -molecule mol4 rxn1_stp2_reacted.data_template -Read molecule mol4: - 15 atoms with max type 11 - 13 bonds with max type 13 - 19 angles with max type 25 - 16 dihedrals with max type 29 - 10 impropers with max type 11 - -thermo 50 - -# dump 1 all xyz 100 test_vis.xyz - -fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map -WARNING: An atom in 'react #1' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489) -WARNING: An atom in 'react #2' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489) -dynamic group bond_react_MASTER_group defined -dynamic group statted_grp defined -dynamic group bond_react_MASTER_group defined -dynamic group statted_grp defined - -# stable at 800K -fix 1 statted_grp nvt temp 800 800 100 - -# in order to customize behavior of reacting atoms, -# you can use the internally created 'bond_react_MASTER_group', like so: -# fix 2 bond_react_MASTER_group temp/rescale 1 800 800 10 1 - -thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] # cumulative reaction counts - -# restart 100 restart1 restart2 - -run 200 -PPPM initialization ... - using 12-bit tables for long-range coulomb (../kspace.cpp:321) - G vector (1/distance) = 0.20765 - grid = 18 18 18 - stencil order = 5 - estimated absolute RMS force accuracy = 0.0333156 - estimated relative force accuracy = 0.000100329 - using double precision FFTs - 3d grid and FFT values/proc = 4508 1620 -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 = 15 15 15 - 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 -Per MPI rank memory allocation (min/avg/max) = 81.11 | 81.13 | 81.15 Mbytes -Step Temp Press Density f_myrxns[1] f_myrxns[2] - 0 800 3666.3948 0.80366765 0 0 - 50 673.95238 -9670.9169 0.80366765 31 0 - 100 697.22819 -4624.0512 0.80366765 57 22 - 150 724.40407 -17166.729 0.80366765 76 49 - 200 737.28582 -12968.224 0.80366765 84 65 -Loop time of 51.171 on 4 procs for 200 steps with 35200 atoms - -Performance: 0.338 ns/day, 71.071 hours/ns, 3.908 timesteps/s -98.4% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 12.926 | 13.247 | 13.493 | 6.7 | 25.89 -Bond | 5.2132 | 5.2733 | 5.3367 | 1.9 | 10.31 -Kspace | 2.3601 | 2.6534 | 3.0067 | 16.0 | 5.19 -Neigh | 25.93 | 25.934 | 25.937 | 0.1 | 50.68 -Comm | 0.73273 | 0.75464 | 0.78505 | 2.3 | 1.47 -Output | 0.00045228 | 0.00067407 | 0.0013323 | 0.0 | 0.00 -Modify | 3.2682 | 3.2686 | 3.2692 | 0.0 | 6.39 -Other | | 0.03995 | | | 0.08 - -Nlocal: 8800 ave 8913 max 8652 min -Histogram: 1 0 0 0 1 0 0 0 1 1 -Nghost: 18366 ave 18461 max 18190 min -Histogram: 1 0 0 0 0 0 0 1 1 1 -Neighs: 1.73203e+06 ave 1.77261e+06 max 1.68165e+06 min -Histogram: 1 0 1 0 0 0 0 0 0 2 - -Total # of neighbors = 6928132 -Ave neighs/atom = 196.822 -Ave special neighs/atom = 9.83608 -Neighbor list builds = 200 -Dangerous builds = 0 - -# write_restart restart_longrun -# write_data restart_longrun.data - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:52 diff --git a/examples/PACKAGES/reaction/nylon,6-6_melt/log.4Nov2022.large_nylon_melt.g++.1 b/examples/PACKAGES/reaction/nylon,6-6_melt/log.4Nov2022.large_nylon_melt.g++.1 new file mode 100644 index 0000000000..440b2e5cf0 --- /dev/null +++ b/examples/PACKAGES/reaction/nylon,6-6_melt/log.4Nov2022.large_nylon_melt.g++.1 @@ -0,0 +1,215 @@ +LAMMPS (4 Nov 2022) +# 35,000 atom nylon melt example + +units real + +boundary p p p + +atom_style full + +kspace_style pppm 1.0e-4 + +pair_style lj/class2/coul/long 8.5 + +angle_style class2 + +bond_style class2 + +dihedral_style class2 + +improper_style class2 + +read_data large_nylon_melt.data.gz 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 = (-2.6834403 -2.0679138 -2.2198803) to (73.455228 73.244835 73.40648) + 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 ... + 35200 atoms + reading velocities ... + 35200 velocities + scanning bonds ... + 9 = max bonds/atom + scanning angles ... + 21 = max angles/atom + scanning dihedrals ... + 31 = max dihedrals/atom + scanning impropers ... + 29 = max impropers/atom + reading bonds ... + 33600 bonds + reading angles ... + 59200 angles + reading dihedrals ... + 80000 dihedrals + reading impropers ... + 35200 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 + 6 = max # of 1-3 neighbors + 12 = max # of 1-4 neighbors + 41 = max # of special neighbors + special bonds CPU = 0.026 seconds + read_data CPU = 0.937 seconds + +velocity all create 800.0 4928459 dist gaussian + +molecule mol1 rxn1_stp1_unreacted.molecule_template +Read molecule template mol1: + 1 molecules + 0 fragments + 18 atoms with max type 8 + 16 bonds with max type 12 + 25 angles with max type 24 + 23 dihedrals with max type 33 + 2 impropers with max type 9 +molecule mol2 rxn1_stp1_reacted.molecule_template +Read molecule template mol2: + 1 molecules + 0 fragments + 18 atoms with max type 9 + 17 bonds with max type 11 + 31 angles with max type 23 + 39 dihedrals with max type 30 + 0 impropers with max type 0 +molecule mol3 rxn1_stp2_unreacted.molecule_template +Read molecule template mol3: + 1 molecules + 0 fragments + 15 atoms with max type 9 + 14 bonds with max type 11 + 25 angles with max type 23 + 30 dihedrals with max type 30 + 0 impropers with max type 0 +molecule mol4 rxn1_stp2_reacted.molecule_template +Read molecule template mol4: + 1 molecules + 0 fragments + 15 atoms with max type 11 + 13 bonds with max type 13 + 19 angles with max type 25 + 16 dihedrals with max type 29 + 2 impropers with max type 11 + +thermo 50 + +# dump 1 all xyz 100 test_vis.xyz + +fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map +WARNING: Fix bond/react: Atom affected by reaction rxn2 is too close to template edge (../fix_bond_react.cpp:2624) +dynamic group bond_react_MASTER_group defined +dynamic group statted_grp_REACT defined + +# stable at 800K +fix 1 statted_grp_REACT nvt temp 800 800 100 + +# in order to customize behavior of reacting atoms, +# you can use the internally created 'bond_react_MASTER_group', like so: +# fix 2 bond_react_MASTER_group temp/rescale 1 800 800 10 1 + +thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] # cumulative reaction counts + +# restart 100 restart1 restart2 + +run 200 + +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 + +PPPM initialization ... + using 12-bit tables for long-range coulomb (../kspace.cpp:342) + G vector (1/distance) = 0.20765034 + grid = 18 18 18 + stencil order = 5 + estimated absolute RMS force accuracy = 0.033315619 + estimated relative force accuracy = 0.000100329 + using double precision KISS FFT + 3d grid and FFT values/proc = 12167 5832 +Generated 55 of 55 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 = 15 15 15 + 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 + 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) = 209.8 | 209.8 | 209.8 Mbytes + Step Temp Press Density f_myrxns[1] f_myrxns[2] + 0 800 3666.3948 0.80366765 0 0 + 50 673.94821 -9679.5038 0.80366765 31 0 + 100 694.45718 -2104.8514 0.80366765 57 22 + 150 716.53915 -12356.83 0.80366765 77 50 + 200 723.33218 -1319.9666 0.80366765 84 67 +Loop time of 87.9809 on 1 procs for 200 steps with 35200 atoms + +Performance: 0.196 ns/day, 122.196 hours/ns, 2.273 timesteps/s, 80.017 katom-step/s +100.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 25.691 | 25.691 | 25.691 | 0.0 | 29.20 +Bond | 15.772 | 15.772 | 15.772 | 0.0 | 17.93 +Kspace | 4.611 | 4.611 | 4.611 | 0.0 | 5.24 +Neigh | 35.616 | 35.616 | 35.616 | 0.0 | 40.48 +Comm | 0.24971 | 0.24971 | 0.24971 | 0.0 | 0.28 +Output | 0.00098602 | 0.00098602 | 0.00098602 | 0.0 | 0.00 +Modify | 5.9596 | 5.9596 | 5.9596 | 0.0 | 6.77 +Other | | 0.08051 | | | 0.09 + +Nlocal: 35200 ave 35200 max 35200 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 38403 ave 38403 max 38403 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 6.92764e+06 ave 6.92764e+06 max 6.92764e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 6927635 +Ave neighs/atom = 196.80781 +Ave special neighs/atom = 9.8480114 +Neighbor list builds = 128 +Dangerous builds = 0 + +# write_restart restart_longrun +# write_data restart_longrun.data +Total wall time: 0:01:29 diff --git a/examples/PACKAGES/reaction/nylon,6-6_melt/log.4Nov2022.large_nylon_melt.g++.4 b/examples/PACKAGES/reaction/nylon,6-6_melt/log.4Nov2022.large_nylon_melt.g++.4 new file mode 100644 index 0000000000..52b36325b8 --- /dev/null +++ b/examples/PACKAGES/reaction/nylon,6-6_melt/log.4Nov2022.large_nylon_melt.g++.4 @@ -0,0 +1,215 @@ +LAMMPS (4 Nov 2022) +# 35,000 atom nylon melt example + +units real + +boundary p p p + +atom_style full + +kspace_style pppm 1.0e-4 + +pair_style lj/class2/coul/long 8.5 + +angle_style class2 + +bond_style class2 + +dihedral_style class2 + +improper_style class2 + +read_data large_nylon_melt.data.gz 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 = (-2.6834403 -2.0679138 -2.2198803) to (73.455228 73.244835 73.40648) + 2 by 1 by 2 MPI processor grid + reading atom labelmap ... + reading bond labelmap ... + reading angle labelmap ... + reading dihedral labelmap ... + reading improper labelmap ... + reading atoms ... + 35200 atoms + reading velocities ... + 35200 velocities + scanning bonds ... + 9 = max bonds/atom + scanning angles ... + 21 = max angles/atom + scanning dihedrals ... + 31 = max dihedrals/atom + scanning impropers ... + 29 = max impropers/atom + reading bonds ... + 33600 bonds + reading angles ... + 59200 angles + reading dihedrals ... + 80000 dihedrals + reading impropers ... + 35200 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 + 6 = max # of 1-3 neighbors + 12 = max # of 1-4 neighbors + 41 = max # of special neighbors + special bonds CPU = 0.007 seconds + read_data CPU = 0.854 seconds + +velocity all create 800.0 4928459 dist gaussian + +molecule mol1 rxn1_stp1_unreacted.molecule_template +Read molecule template mol1: + 1 molecules + 0 fragments + 18 atoms with max type 8 + 16 bonds with max type 12 + 25 angles with max type 24 + 23 dihedrals with max type 33 + 2 impropers with max type 9 +molecule mol2 rxn1_stp1_reacted.molecule_template +Read molecule template mol2: + 1 molecules + 0 fragments + 18 atoms with max type 9 + 17 bonds with max type 11 + 31 angles with max type 23 + 39 dihedrals with max type 30 + 0 impropers with max type 0 +molecule mol3 rxn1_stp2_unreacted.molecule_template +Read molecule template mol3: + 1 molecules + 0 fragments + 15 atoms with max type 9 + 14 bonds with max type 11 + 25 angles with max type 23 + 30 dihedrals with max type 30 + 0 impropers with max type 0 +molecule mol4 rxn1_stp2_reacted.molecule_template +Read molecule template mol4: + 1 molecules + 0 fragments + 15 atoms with max type 11 + 13 bonds with max type 13 + 19 angles with max type 25 + 16 dihedrals with max type 29 + 2 impropers with max type 11 + +thermo 50 + +# dump 1 all xyz 100 test_vis.xyz + +fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map +WARNING: Fix bond/react: Atom affected by reaction rxn2 is too close to template edge (../fix_bond_react.cpp:2624) +dynamic group bond_react_MASTER_group defined +dynamic group statted_grp_REACT defined + +# stable at 800K +fix 1 statted_grp_REACT nvt temp 800 800 100 + +# in order to customize behavior of reacting atoms, +# you can use the internally created 'bond_react_MASTER_group', like so: +# fix 2 bond_react_MASTER_group temp/rescale 1 800 800 10 1 + +thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] # cumulative reaction counts + +# restart 100 restart1 restart2 + +run 200 + +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 + +PPPM initialization ... + using 12-bit tables for long-range coulomb (../kspace.cpp:342) + G vector (1/distance) = 0.20765034 + grid = 18 18 18 + stencil order = 5 + estimated absolute RMS force accuracy = 0.033315619 + estimated relative force accuracy = 0.000100329 + using double precision KISS FFT + 3d grid and FFT values/proc = 4508 1620 +Generated 55 of 55 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 = 15 15 15 + 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 + 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) = 81.39 | 81.41 | 81.43 Mbytes + Step Temp Press Density f_myrxns[1] f_myrxns[2] + 0 800 3666.3948 0.80366765 0 0 + 50 673.94821 -9679.5038 0.80366765 31 0 + 100 694.36354 -2108.4881 0.80366765 57 22 + 150 716.5075 -12356.04 0.80366765 77 50 + 200 722.97306 -1308.3439 0.80366765 84 67 +Loop time of 23.1041 on 4 procs for 200 steps with 35200 atoms + +Performance: 0.748 ns/day, 32.089 hours/ns, 8.656 timesteps/s, 304.708 katom-step/s +100.0% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 6.6935 | 6.8618 | 7.0049 | 5.1 | 29.70 +Bond | 3.8936 | 3.9807 | 4.0626 | 3.5 | 17.23 +Kspace | 1.1828 | 1.4033 | 1.6503 | 16.6 | 6.07 +Neigh | 8.7942 | 8.7945 | 8.7946 | 0.0 | 38.06 +Comm | 0.14682 | 0.15559 | 0.16441 | 1.8 | 0.67 +Output | 0.00035959 | 0.00037472 | 0.00041627 | 0.0 | 0.00 +Modify | 1.8787 | 1.8787 | 1.8788 | 0.0 | 8.13 +Other | | 0.02917 | | | 0.13 + +Nlocal: 8800 ave 8911 max 8662 min +Histogram: 1 0 0 1 0 0 0 0 1 1 +Nghost: 18358.5 ave 18438 max 18183 min +Histogram: 1 0 0 0 0 0 0 0 1 2 +Neighs: 1.73191e+06 ave 1.77313e+06 max 1.68375e+06 min +Histogram: 1 0 1 0 0 0 0 0 0 2 + +Total # of neighbors = 6927655 +Ave neighs/atom = 196.80838 +Ave special neighs/atom = 9.8480114 +Neighbor list builds = 128 +Dangerous builds = 0 + +# write_restart restart_longrun +# write_data restart_longrun.data +Total wall time: 0:00:24 diff --git a/examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp1_reacted.data_template b/examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp1_reacted.data_template deleted file mode 100644 index 61c0408ce3..0000000000 --- a/examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp1_reacted.data_template +++ /dev/null @@ -1,189 +0,0 @@ -this is a molecule template for: initial nylon crosslink, post-reacting - -18 atoms -17 bonds -31 angles -39 dihedrals -20 impropers - -Types - -1 9 -2 1 -3 1 -4 4 -5 4 -6 3 -7 3 -8 1 -9 1 -10 5 -11 8 -12 6 -13 3 -14 3 -15 7 -16 1 -17 3 -18 3 - -Charges - -1 -0.300000 -2 0.000000 -3 0.000000 -4 0.000000 -5 0.000000 -6 0.000000 -7 0.000000 -8 0.000000 -9 0.000000 -10 0.300000 -11 0.000000 -12 0.000000 -13 0.000000 -14 0.000000 -15 0.000000 -16 0.000000 -17 0.000000 -18 0.000000 - -Coords - -1 -5.522237 -0.752722 1.631158 -2 -5.170398 -0.545733 0.178130 -3 -6.469695 -0.553072 -0.648889 -4 -6.052076 -1.721152 1.744648 -5 -6.183059 0.071387 1.971497 -6 -4.489340 -1.389197 -0.173156 -7 -4.637591 0.453703 0.051252 -8 -5.618658 0.138919 4.386107 -9 -4.669492 -0.989819 3.943591 -10 -4.270194 -0.766405 2.474102 -11 -3.348470 -1.875393 2.024289 -12 -3.569794 0.564183 2.345995 -13 -5.201079 -1.993301 4.044219 -14 -3.736682 -0.984819 4.598305 -15 -4.255402 1.370923 2.679069 -16 -6.136394 -0.339866 -2.136775 -17 -6.996331 -1.555519 -0.517408 -18 -7.153308 0.284949 -0.289930 - -Bonds - -1 9 1 2 -2 10 1 4 -3 10 1 5 -4 11 1 10 -5 1 2 3 -6 2 2 6 -7 2 2 7 -8 1 3 16 -9 2 3 17 -10 2 3 18 -11 1 8 9 -12 6 9 10 -13 2 9 13 -14 2 9 14 -15 7 10 11 -16 5 10 12 -17 8 12 15 - -Angles - -1 14 2 1 4 -2 14 2 1 5 -3 15 2 1 10 -4 16 4 1 5 -5 17 4 1 10 -6 17 5 1 10 -7 18 1 2 3 -8 19 1 2 6 -9 19 1 2 7 -10 1 3 2 6 -11 1 3 2 7 -12 3 6 2 7 -13 2 2 3 16 -14 1 2 3 17 -15 1 2 3 18 -16 1 16 3 17 -17 1 16 3 18 -18 3 17 3 18 -19 12 8 9 10 -20 1 8 9 13 -21 1 8 9 14 -22 13 13 9 10 -23 13 14 9 10 -24 3 13 9 14 -25 10 9 10 11 -26 8 9 10 12 -27 20 1 10 9 -28 21 11 10 12 -29 22 1 10 11 -30 23 1 10 12 -31 11 10 12 15 - -Dihedrals - -1 16 4 1 2 3 -2 17 4 1 2 6 -3 17 4 1 2 7 -4 16 5 1 2 3 -5 17 5 1 2 6 -6 17 5 1 2 7 -7 18 10 1 2 3 -8 19 10 1 2 6 -9 19 10 1 2 7 -10 20 2 1 10 9 -11 21 2 1 10 11 -12 22 2 1 10 12 -13 23 4 1 10 9 -14 24 4 1 10 11 -15 25 4 1 10 12 -16 23 5 1 10 9 -17 24 5 1 10 11 -18 25 5 1 10 12 -19 26 1 2 3 16 -20 27 1 2 3 17 -21 27 1 2 3 18 -22 4 16 3 2 6 -23 2 6 2 3 17 -24 2 6 2 3 18 -25 4 16 3 2 7 -26 2 7 2 3 17 -27 2 7 2 3 18 -28 14 8 9 10 11 -29 12 8 9 10 12 -30 28 8 9 10 1 -31 15 13 9 10 11 -32 13 13 9 10 12 -33 29 13 9 10 1 -34 15 14 9 10 11 -35 13 14 9 10 12 -36 29 14 9 10 1 -37 10 9 10 12 15 -38 11 11 10 12 15 -39 30 1 10 12 15 - -Impropers - -1 1 2 1 4 5 -2 1 2 1 4 10 -3 1 2 1 5 10 -4 1 4 1 5 10 -5 1 1 2 3 6 -6 1 1 2 3 7 -7 1 1 2 6 7 -8 1 3 2 6 7 -9 1 2 3 16 17 -10 1 2 3 16 18 -11 1 2 3 17 18 -12 1 16 3 17 18 -13 1 8 9 13 10 -14 1 8 9 14 10 -15 1 8 9 13 14 -16 1 13 9 14 10 -17 1 9 10 11 12 -18 1 1 10 9 11 -19 1 1 10 9 12 -20 1 1 10 11 12 diff --git a/examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp1_reacted.molecule_template b/examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp1_reacted.molecule_template new file mode 100644 index 0000000000..40f3aa8276 --- /dev/null +++ b/examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp1_reacted.molecule_template @@ -0,0 +1,187 @@ +this is a molecule template for: initial nylon crosslink, post-reacting + + 18 atoms + 17 bonds + 31 angles + 39 dihedrals + 0 impropers + +Coords + + 1 -5.522237178 -0.752722499 1.631158408 + 2 -5.170398325 -0.545733378 0.178129978 + 3 -6.469694974 -0.553071841 -0.648889109 + 4 -6.052075697 -1.721152483 1.744647858 + 5 -6.183058842 0.071386755 1.971497329 + 6 -4.489339595 -1.389196844 -0.173156276 + 7 -4.637590712 0.453703382 0.051251954 + 8 -5.618657658 0.138918810 4.386106928 + 9 -4.669491736 -0.989818781 3.943591338 + 10 -4.270193542 -0.766405234 2.474102239 + 11 -3.348470373 -1.875393291 2.024289246 + 12 -3.569793683 0.564183226 2.345995471 + 13 -5.201078949 -1.993301389 4.044218837 + 14 -3.736681607 -0.984819193 4.598304847 + 15 -4.255401979 1.370923174 2.679069013 + 16 -6.136393628 -0.339866195 -2.136774990 + 17 -6.996331494 -1.555519161 -0.517408063 + 18 -7.153308038 0.284949373 -0.289930394 + +Types + + 1 n + 2 c2 + 3 c2 + 4 hn + 5 hn + 6 hc + 7 hc + 8 c2 + 9 c2 + 10 c_1 + 11 o_1 + 12 o + 13 hc + 14 hc + 15 ho + 16 c2 + 17 hc + 18 hc + +Charges + + 1 -0.300000 + 2 0.000000 + 3 0.000000 + 4 0.000000 + 5 0.000000 + 6 0.000000 + 7 0.000000 + 8 0.000000 + 9 0.000000 + 10 0.300000 + 11 0.000000 + 12 0.000000 + 13 0.000000 + 14 0.000000 + 15 0.000000 + 16 0.000000 + 17 0.000000 + 18 0.000000 + +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 + +Bonds + + 1 n-c2 1 2 + 2 n-hn 1 4 + 3 n-hn 1 5 + 4 n-c_1 1 10 + 5 c2-c2 2 3 + 6 c2-hc 2 6 + 7 c2-hc 2 7 + 8 c2-c2 3 16 + 9 c2-hc 3 17 + 10 c2-hc 3 18 + 11 c2-c2 8 9 + 12 c2-c_1 9 10 + 13 c2-hc 9 13 + 14 c2-hc 9 14 + 15 c_1-o_1 10 11 + 16 c_1-o 10 12 + 17 o-ho 12 15 + +Angles + + 1 c2-n-hn 2 1 4 + 2 c2-n-hn 2 1 5 + 3 c2-n-c_1 2 1 10 + 4 hn-n-hn 4 1 5 + 5 hn-n-c_1 4 1 10 + 6 hn-n-c_1 5 1 10 + 7 n-c2-c2 1 2 3 + 8 n-c2-hc 1 2 6 + 9 n-c2-hc 1 2 7 + 10 c2-c2-hc 3 2 6 + 11 c2-c2-hc 3 2 7 + 12 hc-c2-hc 6 2 7 + 13 c2-c2-c2 2 3 16 + 14 c2-c2-hc 2 3 17 + 15 c2-c2-hc 2 3 18 + 16 c2-c2-hc 16 3 17 + 17 c2-c2-hc 16 3 18 + 18 hc-c2-hc 17 3 18 + 19 c2-c2-c_1 8 9 10 + 20 c2-c2-hc 8 9 13 + 21 c2-c2-hc 8 9 14 + 22 hc-c2-c_1 13 9 10 + 23 hc-c2-c_1 14 9 10 + 24 hc-c2-hc 13 9 14 + 25 c2-c_1-o_1 9 10 11 + 26 c2-c_1-o 9 10 12 + 27 n-c_1-c2 1 10 9 + 28 o_1-c_1-o 11 10 12 + 29 n-c_1-o_1 1 10 11 + 30 n-c_1-o 1 10 12 + 31 c_1-o-ho 10 12 15 + +Dihedrals + + 1 hn-n-c2-c2 4 1 2 3 + 2 hn-n-c2-hc 4 1 2 6 + 3 hn-n-c2-hc 4 1 2 7 + 4 hn-n-c2-c2 5 1 2 3 + 5 hn-n-c2-hc 5 1 2 6 + 6 hn-n-c2-hc 5 1 2 7 + 7 c_1-n-c2-c2 10 1 2 3 + 8 c_1-n-c2-hc 10 1 2 6 + 9 c_1-n-c2-hc 10 1 2 7 + 10 c2-n-c_1-c2 2 1 10 9 + 11 c2-n-c_1-o_1 2 1 10 11 + 12 c2-n-c_1-o 2 1 10 12 + 13 hn-n-c_1-c2 4 1 10 9 + 14 hn-n-c_1-o_1 4 1 10 11 + 15 hn-n-c_1-o 4 1 10 12 + 16 hn-n-c_1-c2 5 1 10 9 + 17 hn-n-c_1-o_1 5 1 10 11 + 18 hn-n-c_1-o 5 1 10 12 + 19 n-c2-c2-c2 1 2 3 16 + 20 n-c2-c2-hc 1 2 3 17 + 21 n-c2-c2-hc 1 2 3 18 + 22 c2-c2-c2-hc 16 3 2 6 + 23 hc-c2-c2-hc 6 2 3 17 + 24 hc-c2-c2-hc 6 2 3 18 + 25 c2-c2-c2-hc 16 3 2 7 + 26 hc-c2-c2-hc 7 2 3 17 + 27 hc-c2-c2-hc 7 2 3 18 + 28 c2-c2-c_1-o_1 8 9 10 11 + 29 c2-c2-c_1-o 8 9 10 12 + 30 c2-c2-c_1-n 8 9 10 1 + 31 hc-c2-c_1-o_1 13 9 10 11 + 32 hc-c2-c_1-o 13 9 10 12 + 33 hc-c2-c_1-n 13 9 10 1 + 34 hc-c2-c_1-o_1 14 9 10 11 + 35 hc-c2-c_1-o 14 9 10 12 + 36 hc-c2-c_1-n 14 9 10 1 + 37 c2-c_1-o-ho 9 10 12 15 + 38 o_1-c_1-o-ho 11 10 12 15 + 39 n-c_1-o-ho 1 10 12 15 diff --git a/examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp1_unreacted.data_template b/examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp1_unreacted.data_template deleted file mode 100644 index 944d6918c5..0000000000 --- a/examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp1_unreacted.data_template +++ /dev/null @@ -1,160 +0,0 @@ -this is a molecule template for: initial nylon crosslink, pre-reacting - -18 atoms -16 bonds -25 angles -23 dihedrals -14 impropers - -Types - -1 2 -2 1 -3 1 -4 4 -5 4 -6 3 -7 3 -8 1 -9 1 -10 5 -11 8 -12 6 -13 3 -14 3 -15 7 -16 1 -17 3 -18 3 - -Charges - -1 -0.300000 -2 0.000000 -3 0.000000 -4 0.000000 -5 0.000000 -6 0.000000 -7 0.000000 -8 0.000000 -9 0.000000 -10 0.300000 -11 0.000000 -12 0.000000 -13 0.000000 -14 0.000000 -15 0.000000 -16 0.000000 -17 0.000000 -18 0.000000 - -Coords - -1 -4.922858 -0.946982 1.146055 -2 -5.047195 -0.935267 -0.358173 -3 -6.526281 -0.755366 -0.743523 -4 -5.282604 0.020447 1.552710 -5 -3.860697 -1.095850 1.428305 -6 -4.662382 -1.920900 -0.781524 -7 -4.433977 -0.072765 -0.784071 -8 -5.506279 0.202610 4.825816 -9 -4.449177 -0.844592 4.423366 -10 -4.103916 -0.749629 2.925195 -11 -3.376249 -1.886171 2.245643 -12 -4.493235 0.477214 2.137199 -13 -4.849053 -1.888877 4.663994 -14 -3.491823 -0.662913 5.018510 -15 -5.020777 1.189745 2.805427 -16 -3.964987 2.900602 -1.551341 -17 -4.460694 2.836102 0.668882 -18 -4.828494 3.219656 -0.122111 - -Bonds - -1 12 1 2 -2 4 1 4 -3 4 1 5 -4 1 2 3 -5 2 2 6 -6 2 2 7 -7 1 3 16 -8 2 3 17 -9 2 3 18 -10 1 8 9 -11 6 9 10 -12 2 9 13 -13 2 9 14 -14 7 10 11 -15 5 10 12 -16 8 12 15 - -Angles - -1 6 2 1 4 -2 6 2 1 5 -3 7 4 1 5 -4 24 1 2 3 -5 5 1 2 6 -6 5 1 2 7 -7 1 3 2 6 -8 1 3 2 7 -9 3 6 2 7 -10 2 2 3 16 -11 1 2 3 17 -12 1 2 3 18 -13 1 16 3 17 -14 1 16 3 18 -15 3 17 3 18 -16 12 8 9 10 -17 1 8 9 13 -18 1 8 9 14 -19 13 13 9 10 -20 13 14 9 10 -21 3 13 9 14 -22 10 9 10 11 -23 8 9 10 12 -24 21 11 10 12 -25 11 10 12 15 - -Dihedrals - -1 31 4 1 2 3 -2 32 4 1 2 6 -3 32 4 1 2 7 -4 31 5 1 2 3 -5 32 5 1 2 6 -6 32 5 1 2 7 -7 33 1 2 3 16 -8 1 1 2 3 17 -9 1 1 2 3 18 -10 4 16 3 2 6 -11 2 6 2 3 17 -12 2 6 2 3 18 -13 4 16 3 2 7 -14 2 7 2 3 17 -15 2 7 2 3 18 -16 14 8 9 10 11 -17 12 8 9 10 12 -18 15 13 9 10 11 -19 13 13 9 10 12 -20 15 14 9 10 11 -21 13 14 9 10 12 -22 10 9 10 12 15 -23 11 11 10 12 15 - -Impropers - -1 1 2 1 4 5 -2 9 9 10 11 12 -3 1 1 2 3 6 -4 1 1 2 3 7 -5 1 1 2 6 7 -6 1 3 2 6 7 -7 1 2 3 16 17 -8 1 2 3 16 18 -9 1 2 3 17 18 -10 1 16 3 17 18 -11 1 8 9 13 10 -12 1 8 9 14 10 -13 1 8 9 13 14 -14 1 13 9 14 10 diff --git a/examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp1_unreacted.molecule_template b/examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp1_unreacted.molecule_template new file mode 100644 index 0000000000..7de7512f1c --- /dev/null +++ b/examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp1_unreacted.molecule_template @@ -0,0 +1,169 @@ +this is a molecule template for: initial nylon crosslink, pre-reacting + + 18 atoms + 16 bonds + 25 angles + 23 dihedrals + 2 impropers + +Coords + + 1 -4.922858499 -0.946981747 1.146055346 + 2 -5.047194816 -0.935266843 -0.358172771 + 3 -6.526281447 -0.755365854 -0.743523227 + 4 -5.282604074 0.020446894 1.552710361 + 5 -3.860696509 -1.095850190 1.428304925 + 6 -4.662381862 -1.920899862 -0.781524026 + 7 -4.433976540 -0.072765142 -0.784070641 + 8 -5.506279186 0.202610302 4.825815562 + 9 -4.449176624 -0.844592213 4.423366146 + 10 -4.103915981 -0.749628655 2.925195217 + 11 -3.376248536 -1.886171498 2.245643443 + 12 -4.493235430 0.477213651 2.137199034 + 13 -4.849052953 -1.888876753 4.663993750 + 14 -3.491822950 -0.662913310 5.018510248 + 15 -5.020776528 1.189745133 2.805427194 + 16 -3.964987378 2.900602044 -1.551341170 + 17 -4.460693773 2.836101897 0.668881952 + 18 -4.828494000 3.219655862 -0.122111278 + +Types + + 1 na + 2 c2 + 3 c2 + 4 hn + 5 hn + 6 hc + 7 hc + 8 c2 + 9 c2 + 10 c_1 + 11 o_1 + 12 o + 13 hc + 14 hc + 15 ho + 16 c2 + 17 hc + 18 hc + +Charges + + 1 -0.300000 + 2 0.000000 + 3 0.000000 + 4 0.000000 + 5 0.000000 + 6 0.000000 + 7 0.000000 + 8 0.000000 + 9 0.000000 + 10 0.300000 + 11 0.000000 + 12 0.000000 + 13 0.000000 + 14 0.000000 + 15 0.000000 + 16 0.000000 + 17 0.000000 + 18 0.000000 + +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 + +Bonds + + 1 na-c2 1 2 + 2 na-hn 1 4 + 3 na-hn 1 5 + 4 c2-c2 2 3 + 5 c2-hc 2 6 + 6 c2-hc 2 7 + 7 c2-c2 3 16 + 8 c2-hc 3 17 + 9 c2-hc 3 18 + 10 c2-c2 8 9 + 11 c2-c_1 9 10 + 12 c2-hc 9 13 + 13 c2-hc 9 14 + 14 c_1-o_1 10 11 + 15 c_1-o 10 12 + 16 o-ho 12 15 + +Angles + + 1 c2-na-hn 2 1 4 + 2 c2-na-hn 2 1 5 + 3 hn-na-hn 4 1 5 + 4 na-c2-c2 1 2 3 + 5 na-c2-hc 1 2 6 + 6 na-c2-hc 1 2 7 + 7 c2-c2-hc 3 2 6 + 8 c2-c2-hc 3 2 7 + 9 hc-c2-hc 6 2 7 + 10 c2-c2-c2 2 3 16 + 11 c2-c2-hc 2 3 17 + 12 c2-c2-hc 2 3 18 + 13 c2-c2-hc 16 3 17 + 14 c2-c2-hc 16 3 18 + 15 hc-c2-hc 17 3 18 + 16 c2-c2-c_1 8 9 10 + 17 c2-c2-hc 8 9 13 + 18 c2-c2-hc 8 9 14 + 19 hc-c2-c_1 13 9 10 + 20 hc-c2-c_1 14 9 10 + 21 hc-c2-hc 13 9 14 + 22 c2-c_1-o_1 9 10 11 + 23 c2-c_1-o 9 10 12 + 24 o_1-c_1-o 11 10 12 + 25 c_1-o-ho 10 12 15 + +Dihedrals + + 1 hn-na-c2-c2 4 1 2 3 + 2 hn-na-c2-hc 4 1 2 6 + 3 hn-na-c2-hc 4 1 2 7 + 4 hn-na-c2-c2 5 1 2 3 + 5 hn-na-c2-hc 5 1 2 6 + 6 hn-na-c2-hc 5 1 2 7 + 7 na-c2-c2-c2 1 2 3 16 + 8 na-c2-c2-hc 1 2 3 17 + 9 na-c2-c2-hc 1 2 3 18 + 10 c2-c2-c2-hc 16 3 2 6 + 11 hc-c2-c2-hc 6 2 3 17 + 12 hc-c2-c2-hc 6 2 3 18 + 13 c2-c2-c2-hc 16 3 2 7 + 14 hc-c2-c2-hc 7 2 3 17 + 15 hc-c2-c2-hc 7 2 3 18 + 16 c2-c2-c_1-o_1 8 9 10 11 + 17 c2-c2-c_1-o 8 9 10 12 + 18 hc-c2-c_1-o_1 13 9 10 11 + 19 hc-c2-c_1-o 13 9 10 12 + 20 hc-c2-c_1-o_1 14 9 10 11 + 21 hc-c2-c_1-o 14 9 10 12 + 22 c2-c_1-o-ho 9 10 12 15 + 23 o_1-c_1-o-ho 11 10 12 15 + +Impropers + + 1 c2-na-hn-hn 2 1 4 5 + 2 c2-c_1-o_1-o 9 10 11 12 diff --git a/examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp2_reacted.data_template b/examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp2_reacted.data_template deleted file mode 100644 index ffd3ef733c..0000000000 --- a/examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp2_reacted.data_template +++ /dev/null @@ -1,131 +0,0 @@ -this is a molecule template for: water condensation, post-reacting - -15 atoms -13 bonds -19 angles -16 dihedrals -10 impropers - -Types - -1 9 -2 1 -3 1 -4 10 -5 4 -6 3 -7 3 -8 1 -9 1 -10 5 -11 8 -12 11 -13 3 -14 3 -15 10 - -Charges - -1 -0.300000 -2 0.000000 -3 0.000000 -4 0.410000 -5 0.000000 -6 0.000000 -7 0.000000 -8 0.000000 -9 0.000000 -10 0.300000 -11 0.000000 -12 -0.820000 -13 0.000000 -14 0.000000 -15 0.410000 - -Coords - -1 -4.856280 -1.050468 1.432625 -2 -5.047195 -0.935267 -0.358173 -3 -6.526281 -0.755366 -0.743523 -4 -5.282604 0.020447 1.552710 -5 -3.860697 -1.095850 1.428305 -6 -4.662382 -1.920900 -0.781524 -7 -4.433977 -0.072765 -0.784071 -8 -5.506279 0.202610 4.825816 -9 -4.449177 -0.844592 4.423366 -10 -4.103916 -0.749629 2.925195 -11 -3.376249 -1.886171 2.245643 -12 -4.493235 0.477214 2.137199 -13 -4.849053 -1.888877 4.663994 -14 -3.491823 -0.662913 5.018510 -15 -5.020777 1.189745 2.805427 - -Bonds - -1 9 1 2 -2 10 1 5 -3 11 1 10 -4 1 2 3 -5 2 2 6 -6 2 2 7 -7 13 4 12 -8 1 8 9 -9 6 9 10 -10 2 9 13 -11 2 9 14 -12 7 10 11 -13 13 15 12 - -Angles - -1 14 2 1 5 -2 15 2 1 10 -3 17 5 1 10 -4 18 1 2 3 -5 19 1 2 6 -6 19 1 2 7 -7 1 3 2 6 -8 1 3 2 7 -9 3 6 2 7 -10 12 8 9 10 -11 1 8 9 13 -12 1 8 9 14 -13 13 13 9 10 -14 13 14 9 10 -15 3 13 9 14 -16 10 9 10 11 -17 20 1 10 9 -18 22 1 10 11 -19 25 15 12 4 - -Dihedrals - -1 16 5 1 2 3 -2 17 5 1 2 6 -3 17 5 1 2 7 -4 18 10 1 2 3 -5 19 10 1 2 6 -6 19 10 1 2 7 -7 20 2 1 10 9 -8 21 2 1 10 11 -9 23 5 1 10 9 -10 24 5 1 10 11 -11 14 8 9 10 11 -12 28 8 9 10 1 -13 15 13 9 10 11 -14 29 13 9 10 1 -15 15 14 9 10 11 -16 29 14 9 10 1 - -Impropers - -1 10 2 1 5 10 -2 11 1 10 9 11 -3 1 1 2 3 6 -4 1 1 2 3 7 -5 1 1 2 6 7 -6 1 3 2 6 7 -7 1 8 9 13 10 -8 1 8 9 14 10 -9 1 8 9 13 14 -10 1 13 9 14 10 diff --git a/examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp2_reacted.molecule_template b/examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp2_reacted.molecule_template new file mode 100644 index 0000000000..2e91261468 --- /dev/null +++ b/examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp2_reacted.molecule_template @@ -0,0 +1,141 @@ +this is a molecule template for: water condensation, post-reacting + + 15 atoms + 13 bonds + 19 angles + 16 dihedrals + 2 impropers + +Coords + + 1 -4.856280281 -1.050467974 1.432625159 + 2 -5.047194816 -0.935266843 -0.358172771 + 3 -6.526281447 -0.755365854 -0.743523227 + 4 -5.282604074 0.020446894 1.552710361 + 5 -3.860696509 -1.095850190 1.428304925 + 6 -4.662381862 -1.920899862 -0.781524026 + 7 -4.433976540 -0.072765142 -0.784070641 + 8 -5.506279186 0.202610302 4.825815562 + 9 -4.449176624 -0.844592213 4.423366146 + 10 -4.103915981 -0.749628655 2.925195217 + 11 -3.376248536 -1.886171498 2.245643443 + 12 -4.493235430 0.477213651 2.137199034 + 13 -4.849052953 -1.888876753 4.663993750 + 14 -3.491822950 -0.662913310 5.018510248 + 15 -5.020776528 1.189745133 2.805427194 + +Types + + 1 n + 2 c2 + 3 c2 + 4 hw + 5 hn + 6 hc + 7 hc + 8 c2 + 9 c2 + 10 c_1 + 11 o_1 + 12 o* + 13 hc + 14 hc + 15 hw + +Charges + + 1 -0.300000 + 2 0.000000 + 3 0.000000 + 4 0.410000 + 5 0.000000 + 6 0.000000 + 7 0.000000 + 8 0.000000 + 9 0.000000 + 10 0.300000 + 11 0.000000 + 12 -0.820000 + 13 0.000000 + 14 0.000000 + 15 0.410000 + +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 + +Bonds + + 1 n-c2 1 2 + 2 n-hn 1 5 + 3 n-c_1 1 10 + 4 c2-c2 2 3 + 5 c2-hc 2 6 + 6 c2-hc 2 7 + 7 hw-o* 4 12 + 8 c2-c2 8 9 + 9 c2-c_1 9 10 + 10 c2-hc 9 13 + 11 c2-hc 9 14 + 12 c_1-o_1 10 11 + 13 hw-o* 15 12 + +Angles + + 1 c2-n-hn 2 1 5 + 2 c2-n-c_1 2 1 10 + 3 hn-n-c_1 5 1 10 + 4 n-c2-c2 1 2 3 + 5 n-c2-hc 1 2 6 + 6 n-c2-hc 1 2 7 + 7 c2-c2-hc 3 2 6 + 8 c2-c2-hc 3 2 7 + 9 hc-c2-hc 6 2 7 + 10 c2-c2-c_1 8 9 10 + 11 c2-c2-hc 8 9 13 + 12 c2-c2-hc 8 9 14 + 13 hc-c2-c_1 13 9 10 + 14 hc-c2-c_1 14 9 10 + 15 hc-c2-hc 13 9 14 + 16 c2-c_1-o_1 9 10 11 + 17 n-c_1-c2 1 10 9 + 18 n-c_1-o_1 1 10 11 + 19 hw-o*-hw 15 12 4 + +Dihedrals + + 1 hn-n-c2-c2 5 1 2 3 + 2 hn-n-c2-hc 5 1 2 6 + 3 hn-n-c2-hc 5 1 2 7 + 4 c_1-n-c2-c2 10 1 2 3 + 5 c_1-n-c2-hc 10 1 2 6 + 6 c_1-n-c2-hc 10 1 2 7 + 7 c2-n-c_1-c2 2 1 10 9 + 8 c2-n-c_1-o_1 2 1 10 11 + 9 hn-n-c_1-c2 5 1 10 9 + 10 hn-n-c_1-o_1 5 1 10 11 + 11 c2-c2-c_1-o_1 8 9 10 11 + 12 c2-c2-c_1-n 8 9 10 1 + 13 hc-c2-c_1-o_1 13 9 10 11 + 14 hc-c2-c_1-n 13 9 10 1 + 15 hc-c2-c_1-o_1 14 9 10 11 + 16 hc-c2-c_1-n 14 9 10 1 + +Impropers + + 1 c2-n-hn-c_1 2 1 5 10 + 2 n-c_1-c2-o_1 1 10 9 11 diff --git a/examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp2_unreacted.data_template b/examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp2_unreacted.data_template deleted file mode 100644 index 7abe15ada8..0000000000 --- a/examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp2_unreacted.data_template +++ /dev/null @@ -1,158 +0,0 @@ -this is a molecule template for: water condensation, pre-reacting - -15 atoms -14 bonds -25 angles -30 dihedrals -16 impropers - -Types - -1 9 -2 1 -3 1 -4 4 -5 4 -6 3 -7 3 -8 1 -9 1 -10 5 -11 8 -12 6 -13 3 -14 3 -15 7 - -Charges - -1 -0.300000 -2 0.000000 -3 0.000000 -4 0.000000 -5 0.000000 -6 0.000000 -7 0.000000 -8 0.000000 -9 0.000000 -10 0.300000 -11 0.000000 -12 0.000000 -13 0.000000 -14 0.000000 -15 0.000000 - -Coords - -1 -4.922858 -0.946982 1.146055 -2 -5.047195 -0.935267 -0.358173 -3 -6.526281 -0.755366 -0.743523 -4 -5.282604 0.020447 1.552710 -5 -3.860697 -1.095850 1.428305 -6 -4.662382 -1.920900 -0.781524 -7 -4.433977 -0.072765 -0.784071 -8 -5.506279 0.202610 4.825816 -9 -4.449177 -0.844592 4.423366 -10 -4.103916 -0.749629 2.925195 -11 -3.376249 -1.886171 2.245643 -12 -4.493235 0.477214 2.137199 -13 -4.849053 -1.888877 4.663994 -14 -3.491823 -0.662913 5.018510 -15 -5.020777 1.189745 2.805427 - -Bonds - -1 9 1 2 -2 10 1 4 -3 10 1 5 -4 11 1 10 -5 1 2 3 -6 2 2 6 -7 2 2 7 -8 1 8 9 -9 6 9 10 -10 2 9 13 -11 2 9 14 -12 7 10 11 -13 5 10 12 -14 8 12 15 - -Angles - -1 14 2 1 4 -2 14 2 1 5 -3 15 2 1 10 -4 16 4 1 5 -5 17 4 1 10 -6 17 5 1 10 -7 18 1 2 3 -8 19 1 2 6 -9 19 1 2 7 -10 1 3 2 6 -11 1 3 2 7 -12 3 6 2 7 -13 12 8 9 10 -14 1 8 9 13 -15 1 8 9 14 -16 13 13 9 10 -17 13 14 9 10 -18 3 13 9 14 -19 10 9 10 11 -20 8 9 10 12 -21 20 1 10 9 -22 21 11 10 12 -23 22 1 10 11 -24 23 1 10 12 -25 11 10 12 15 - -Dihedrals - -1 16 4 1 2 3 -2 17 4 1 2 6 -3 17 4 1 2 7 -4 16 5 1 2 3 -5 17 5 1 2 6 -6 17 5 1 2 7 -7 18 10 1 2 3 -8 19 10 1 2 6 -9 19 10 1 2 7 -10 20 2 1 10 9 -11 21 2 1 10 11 -12 22 2 1 10 12 -13 23 4 1 10 9 -14 24 4 1 10 11 -15 25 4 1 10 12 -16 23 5 1 10 9 -17 24 5 1 10 11 -18 25 5 1 10 12 -19 14 8 9 10 11 -20 12 8 9 10 12 -21 28 8 9 10 1 -22 15 13 9 10 11 -23 13 13 9 10 12 -24 29 13 9 10 1 -25 15 14 9 10 11 -26 13 14 9 10 12 -27 29 14 9 10 1 -28 10 9 10 12 15 -29 11 11 10 12 15 -30 30 1 10 12 15 - -Impropers - -1 1 2 1 4 5 -2 1 2 1 4 10 -3 1 2 1 5 10 -4 1 4 1 5 10 -5 1 1 2 3 6 -6 1 1 2 3 7 -7 1 1 2 6 7 -8 1 3 2 6 7 -9 1 8 9 13 10 -10 1 8 9 14 10 -11 1 8 9 13 14 -12 1 13 9 14 10 -13 1 9 10 11 12 -14 1 1 10 9 11 -15 1 1 10 9 12 -16 1 1 10 11 12 diff --git a/examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp2_unreacted.molecule_template b/examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp2_unreacted.molecule_template new file mode 100644 index 0000000000..86a772634d --- /dev/null +++ b/examples/PACKAGES/reaction/nylon,6-6_melt/rxn1_stp2_unreacted.molecule_template @@ -0,0 +1,157 @@ +this is a molecule template for: water condensation, pre-reacting + + 15 atoms + 14 bonds + 25 angles + 30 dihedrals + 0 impropers + +Coords + + 1 -4.922858499 -0.946981747 1.146055346 + 2 -5.047194816 -0.935266843 -0.358172771 + 3 -6.526281447 -0.755365854 -0.743523227 + 4 -5.282604074 0.020446894 1.552710361 + 5 -3.860696509 -1.095850190 1.428304925 + 6 -4.662381862 -1.920899862 -0.781524026 + 7 -4.433976540 -0.072765142 -0.784070641 + 8 -5.506279186 0.202610302 4.825815562 + 9 -4.449176624 -0.844592213 4.423366146 + 10 -4.103915981 -0.749628655 2.925195217 + 11 -3.376248536 -1.886171498 2.245643443 + 12 -4.493235430 0.477213651 2.137199034 + 13 -4.849052953 -1.888876753 4.663993750 + 14 -3.491822950 -0.662913310 5.018510248 + 15 -5.020776528 1.189745133 2.805427194 + +Types + + 1 n + 2 c2 + 3 c2 + 4 hn + 5 hn + 6 hc + 7 hc + 8 c2 + 9 c2 + 10 c_1 + 11 o_1 + 12 o + 13 hc + 14 hc + 15 ho + +Charges + + 1 -0.300000 + 2 0.000000 + 3 0.000000 + 4 0.000000 + 5 0.000000 + 6 0.000000 + 7 0.000000 + 8 0.000000 + 9 0.000000 + 10 0.300000 + 11 0.000000 + 12 0.000000 + 13 0.000000 + 14 0.000000 + 15 0.000000 + +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 + +Bonds + + 1 n-c2 1 2 + 2 n-hn 1 4 + 3 n-hn 1 5 + 4 n-c_1 1 10 + 5 c2-c2 2 3 + 6 c2-hc 2 6 + 7 c2-hc 2 7 + 8 c2-c2 8 9 + 9 c2-c_1 9 10 + 10 c2-hc 9 13 + 11 c2-hc 9 14 + 12 c_1-o_1 10 11 + 13 c_1-o 10 12 + 14 o-ho 12 15 + +Angles + + 1 c2-n-hn 2 1 4 + 2 c2-n-hn 2 1 5 + 3 c2-n-c_1 2 1 10 + 4 hn-n-hn 4 1 5 + 5 hn-n-c_1 4 1 10 + 6 hn-n-c_1 5 1 10 + 7 n-c2-c2 1 2 3 + 8 n-c2-hc 1 2 6 + 9 n-c2-hc 1 2 7 + 10 c2-c2-hc 3 2 6 + 11 c2-c2-hc 3 2 7 + 12 hc-c2-hc 6 2 7 + 13 c2-c2-c_1 8 9 10 + 14 c2-c2-hc 8 9 13 + 15 c2-c2-hc 8 9 14 + 16 hc-c2-c_1 13 9 10 + 17 hc-c2-c_1 14 9 10 + 18 hc-c2-hc 13 9 14 + 19 c2-c_1-o_1 9 10 11 + 20 c2-c_1-o 9 10 12 + 21 n-c_1-c2 1 10 9 + 22 o_1-c_1-o 11 10 12 + 23 n-c_1-o_1 1 10 11 + 24 n-c_1-o 1 10 12 + 25 c_1-o-ho 10 12 15 + +Dihedrals + + 1 hn-n-c2-c2 4 1 2 3 + 2 hn-n-c2-hc 4 1 2 6 + 3 hn-n-c2-hc 4 1 2 7 + 4 hn-n-c2-c2 5 1 2 3 + 5 hn-n-c2-hc 5 1 2 6 + 6 hn-n-c2-hc 5 1 2 7 + 7 c_1-n-c2-c2 10 1 2 3 + 8 c_1-n-c2-hc 10 1 2 6 + 9 c_1-n-c2-hc 10 1 2 7 + 10 c2-n-c_1-c2 2 1 10 9 + 11 c2-n-c_1-o_1 2 1 10 11 + 12 c2-n-c_1-o 2 1 10 12 + 13 hn-n-c_1-c2 4 1 10 9 + 14 hn-n-c_1-o_1 4 1 10 11 + 15 hn-n-c_1-o 4 1 10 12 + 16 hn-n-c_1-c2 5 1 10 9 + 17 hn-n-c_1-o_1 5 1 10 11 + 18 hn-n-c_1-o 5 1 10 12 + 19 c2-c2-c_1-o_1 8 9 10 11 + 20 c2-c2-c_1-o 8 9 10 12 + 21 c2-c2-c_1-n 8 9 10 1 + 22 hc-c2-c_1-o_1 13 9 10 11 + 23 hc-c2-c_1-o 13 9 10 12 + 24 hc-c2-c_1-n 13 9 10 1 + 25 hc-c2-c_1-o_1 14 9 10 11 + 26 hc-c2-c_1-o 14 9 10 12 + 27 hc-c2-c_1-n 14 9 10 1 + 28 c2-c_1-o-ho 9 10 12 15 + 29 o_1-c_1-o-ho 11 10 12 15 + 30 n-c_1-o-ho 1 10 12 15 diff --git a/examples/PACKAGES/reaction/tiny_epoxy/in.tiny_epoxy.stabilized b/examples/PACKAGES/reaction/tiny_epoxy/in.tiny_epoxy.stabilized index 0e6e97cd46..1309eff3a3 100644 --- a/examples/PACKAGES/reaction/tiny_epoxy/in.tiny_epoxy.stabilized +++ b/examples/PACKAGES/reaction/tiny_epoxy/in.tiny_epoxy.stabilized @@ -9,9 +9,9 @@ atom_style full pair_style lj/class2 8 -angle_style class2 +angle_style class2 -bond_style class2 +bond_style class2 dihedral_style class2 @@ -21,12 +21,12 @@ read_data tiny_epoxy.data velocity all create 300.0 4928459 dist gaussian -molecule mol1 rxn1_stp1_pre.data_template -molecule mol2 rxn1_stp1_post.data_template -molecule mol3 rxn1_stp2_post.data_template -molecule mol4 rxn2_stp1_pre.data_template -molecule mol5 rxn2_stp1_post.data_template -molecule mol6 rxn2_stp2_post.data_template +molecule mol1 rxn1_stp1_pre.molecule_template +molecule mol2 rxn1_stp1_post.molecule_template +molecule mol3 rxn1_stp2_post.molecule_template +molecule mol4 rxn2_stp1_pre.molecule_template +molecule mol5 rxn2_stp1_post.molecule_template +molecule mol6 rxn2_stp2_post.molecule_template thermo 50 diff --git a/examples/PACKAGES/reaction/tiny_epoxy/log.20Nov19.tiny_epoxy.stabilized.g++.1 b/examples/PACKAGES/reaction/tiny_epoxy/log.20Nov19.tiny_epoxy.stabilized.g++.1 deleted file mode 100644 index 6ca0361513..0000000000 --- a/examples/PACKAGES/reaction/tiny_epoxy/log.20Nov19.tiny_epoxy.stabilized.g++.1 +++ /dev/null @@ -1,172 +0,0 @@ -LAMMPS (20 Nov 2019) - -WARNING-WARNING-WARNING-WARNING-WARNING -This LAMMPS executable was compiled using C++98 compatibility. -Please report the compiler info below at https://github.com/lammps/lammps/issues/1659 -GNU C++ 4.8.5 -WARNING-WARNING-WARNING-WARNING-WARNING - -Reading data file ... - orthogonal box = (10 -10 -15) to (30 20 10) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 118 atoms - scanning bonds ... - 4 = max bonds/atom - scanning angles ... - 6 = max angles/atom - scanning dihedrals ... - 18 = max dihedrals/atom - scanning impropers ... - 4 = max impropers/atom - reading bonds ... - 123 bonds - reading angles ... - 221 angles - reading dihedrals ... - 302 dihedrals - reading impropers ... - 115 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 - 10 = max # of 1-3 neighbors - 19 = max # of 1-4 neighbors - 22 = max # of special neighbors - special bonds CPU = 0.000286808 secs - read_data CPU = 0.00724107 secs -Read molecule mol1: - 31 atoms with max type 10 - 30 bonds with max type 15 - 53 angles with max type 29 - 66 dihedrals with max type 39 - 31 impropers with max type 5 -Read molecule mol2: - 31 atoms with max type 10 - 30 bonds with max type 17 - 55 angles with max type 36 - 75 dihedrals with max type 51 - 34 impropers with max type 5 -Read molecule mol3: - 31 atoms with max type 11 - 30 bonds with max type 18 - 53 angles with max type 37 - 72 dihedrals with max type 53 - 31 impropers with max type 5 -Read molecule mol4: - 42 atoms with max type 11 - 41 bonds with max type 18 - 73 angles with max type 41 - 96 dihedrals with max type 54 - 43 impropers with max type 5 -Read molecule mol5: - 42 atoms with max type 11 - 41 bonds with max type 18 - 75 angles with max type 37 - 108 dihedrals with max type 53 - 46 impropers with max type 5 -Read molecule mol6: - 42 atoms with max type 11 - 41 bonds with max type 19 - 73 angles with max type 50 - 102 dihedrals with max type 66 - 43 impropers with max type 22 -dynamic group bond_react_MASTER_group defined -dynamic group statted_grp_REACT defined -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 10 - ghost atom cutoff = 10 - binsize = 5, bins = 4 6 5 - 2 neighbor lists, perpetual/occasional/extra = 1 1 0 - (1) pair lj/class2, 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) = 17.28 | 17.28 | 17.28 Mbytes -Step Temp f_rxns[1] f_rxns[2] f_rxns[3] f_rxns[4] - 0 300 0 0 0 0 - 50 391.52956 1 0 0 0 - 100 475.26826 1 1 0 0 - 150 605.26215 1 1 1 0 - 200 545.7485 1 1 1 0 - 250 461.64929 1 1 1 1 - 300 452.10611 1 1 1 1 - 350 379.61671 1 1 1 1 - 400 331.22444 1 1 1 1 - 450 275.63969 1 1 1 1 - 500 316.63407 1 1 1 1 - 550 261.39841 1 1 1 1 - 600 313.70928 1 1 1 1 - 650 294.24011 1 1 1 1 - 700 285.81736 1 1 1 1 - 750 340.37496 1 1 1 1 - 800 333.2496 1 1 1 1 - 850 307.40826 1 1 1 1 - 900 304.68718 1 1 1 1 - 950 328.0289 1 1 1 1 - 1000 290.22808 1 1 1 1 - 1050 272.78518 1 1 1 1 - 1100 291.30546 1 1 1 1 - 1150 320.33992 1 1 1 1 - 1200 330.57057 1 1 1 1 - 1250 300.51008 1 1 1 1 - 1300 293.6209 1 1 1 1 - 1350 324.36604 1 1 1 1 - 1400 331.15408 1 1 1 1 - 1450 302.23396 1 1 1 1 - 1500 297.55562 1 1 1 1 - 1550 277.3187 1 1 1 1 - 1600 289.66052 1 1 1 1 - 1650 281.85404 1 1 1 1 - 1700 293.4999 1 1 1 1 - 1750 306.21866 1 1 1 1 - 1800 283.22696 1 1 1 1 - 1850 295.10473 1 1 1 1 - 1900 317.3843 1 1 1 1 - 1950 305.14825 1 1 1 1 - 2000 289.00911 1 1 1 1 -Loop time of 1.87066 on 1 procs for 2000 steps with 118 atoms - -Performance: 92.374 ns/day, 0.260 hours/ns, 1069.141 timesteps/s -98.4% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.12832 | 0.12832 | 0.12832 | 0.0 | 6.86 -Bond | 0.77458 | 0.77458 | 0.77458 | 0.0 | 41.41 -Neigh | 0.45068 | 0.45068 | 0.45068 | 0.0 | 24.09 -Comm | 0.029785 | 0.029785 | 0.029785 | 0.0 | 1.59 -Output | 0.31635 | 0.31635 | 0.31635 | 0.0 | 16.91 -Modify | 0.16657 | 0.16657 | 0.16657 | 0.0 | 8.90 -Other | | 0.004368 | | | 0.23 - -Nlocal: 118 ave 118 max 118 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 332 ave 332 max 332 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 4338 ave 4338 max 4338 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 4338 -Ave neighs/atom = 36.7627 -Ave special neighs/atom = 10.5763 -Neighbor list builds = 2000 -Dangerous builds = 0 - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:02 diff --git a/examples/PACKAGES/reaction/tiny_epoxy/log.20Nov19.tiny_epoxy.stabilized.g++.4 b/examples/PACKAGES/reaction/tiny_epoxy/log.20Nov19.tiny_epoxy.stabilized.g++.4 deleted file mode 100644 index 4673ba3980..0000000000 --- a/examples/PACKAGES/reaction/tiny_epoxy/log.20Nov19.tiny_epoxy.stabilized.g++.4 +++ /dev/null @@ -1,172 +0,0 @@ -LAMMPS (20 Nov 2019) - -WARNING-WARNING-WARNING-WARNING-WARNING -This LAMMPS executable was compiled using C++98 compatibility. -Please report the compiler info below at https://github.com/lammps/lammps/issues/1659 -GNU C++ 4.8.5 -WARNING-WARNING-WARNING-WARNING-WARNING - -Reading data file ... - orthogonal box = (10 -10 -15) to (30 20 10) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 118 atoms - scanning bonds ... - 4 = max bonds/atom - scanning angles ... - 6 = max angles/atom - scanning dihedrals ... - 18 = max dihedrals/atom - scanning impropers ... - 4 = max impropers/atom - reading bonds ... - 123 bonds - reading angles ... - 221 angles - reading dihedrals ... - 302 dihedrals - reading impropers ... - 115 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 - 10 = max # of 1-3 neighbors - 19 = max # of 1-4 neighbors - 22 = max # of special neighbors - special bonds CPU = 0.000239905 secs - read_data CPU = 0.0080783 secs -Read molecule mol1: - 31 atoms with max type 10 - 30 bonds with max type 15 - 53 angles with max type 29 - 66 dihedrals with max type 39 - 31 impropers with max type 5 -Read molecule mol2: - 31 atoms with max type 10 - 30 bonds with max type 17 - 55 angles with max type 36 - 75 dihedrals with max type 51 - 34 impropers with max type 5 -Read molecule mol3: - 31 atoms with max type 11 - 30 bonds with max type 18 - 53 angles with max type 37 - 72 dihedrals with max type 53 - 31 impropers with max type 5 -Read molecule mol4: - 42 atoms with max type 11 - 41 bonds with max type 18 - 73 angles with max type 41 - 96 dihedrals with max type 54 - 43 impropers with max type 5 -Read molecule mol5: - 42 atoms with max type 11 - 41 bonds with max type 18 - 75 angles with max type 37 - 108 dihedrals with max type 53 - 46 impropers with max type 5 -Read molecule mol6: - 42 atoms with max type 11 - 41 bonds with max type 19 - 73 angles with max type 50 - 102 dihedrals with max type 66 - 43 impropers with max type 22 -dynamic group bond_react_MASTER_group defined -dynamic group statted_grp_REACT defined -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 10 - ghost atom cutoff = 10 - binsize = 5, bins = 4 6 5 - 2 neighbor lists, perpetual/occasional/extra = 1 1 0 - (1) pair lj/class2, 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) = 16.26 | 16.45 | 16.63 Mbytes -Step Temp f_rxns[1] f_rxns[2] f_rxns[3] f_rxns[4] - 0 300 0 0 0 0 - 50 391.52956 1 0 0 0 - 100 475.26826 1 1 0 0 - 150 605.26215 1 1 1 0 - 200 545.7485 1 1 1 0 - 250 461.64929 1 1 1 1 - 300 452.10611 1 1 1 1 - 350 379.61671 1 1 1 1 - 400 331.22444 1 1 1 1 - 450 275.63969 1 1 1 1 - 500 316.63407 1 1 1 1 - 550 261.39841 1 1 1 1 - 600 313.70928 1 1 1 1 - 650 294.24011 1 1 1 1 - 700 285.81736 1 1 1 1 - 750 340.37496 1 1 1 1 - 800 333.2496 1 1 1 1 - 850 307.40826 1 1 1 1 - 900 304.68718 1 1 1 1 - 950 328.0289 1 1 1 1 - 1000 290.22808 1 1 1 1 - 1050 272.78518 1 1 1 1 - 1100 291.30546 1 1 1 1 - 1150 320.33992 1 1 1 1 - 1200 330.57057 1 1 1 1 - 1250 300.51008 1 1 1 1 - 1300 293.6209 1 1 1 1 - 1350 324.36604 1 1 1 1 - 1400 331.15408 1 1 1 1 - 1450 302.23396 1 1 1 1 - 1500 297.55562 1 1 1 1 - 1550 277.3187 1 1 1 1 - 1600 289.66052 1 1 1 1 - 1650 281.85404 1 1 1 1 - 1700 293.4999 1 1 1 1 - 1750 306.21866 1 1 1 1 - 1800 283.22695 1 1 1 1 - 1850 295.10472 1 1 1 1 - 1900 317.38431 1 1 1 1 - 1950 305.14824 1 1 1 1 - 2000 289.00909 1 1 1 1 -Loop time of 0.689125 on 4 procs for 2000 steps with 118 atoms - -Performance: 250.753 ns/day, 0.096 hours/ns, 2902.231 timesteps/s -100.0% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.02002 | 0.030617 | 0.053133 | 7.7 | 4.44 -Bond | 0.10356 | 0.18908 | 0.22691 | 11.6 | 27.44 -Neigh | 0.16721 | 0.17002 | 0.17247 | 0.5 | 24.67 -Comm | 0.057286 | 0.12002 | 0.21612 | 17.0 | 17.42 -Output | 0.00028991 | 0.00034121 | 0.00049323 | 0.0 | 0.05 -Modify | 0.17626 | 0.17675 | 0.17721 | 0.1 | 25.65 -Other | | 0.002287 | | | 0.33 - -Nlocal: 29.5 ave 41 max 18 min -Histogram: 1 0 0 1 0 0 1 0 0 1 -Nghost: 306 ave 349 max 269 min -Histogram: 1 1 0 0 0 0 1 0 0 1 -Neighs: 1084.5 ave 2154 max 397 min -Histogram: 1 0 1 1 0 0 0 0 0 1 - -Total # of neighbors = 4338 -Ave neighs/atom = 36.7627 -Ave special neighs/atom = 10.5763 -Neighbor list builds = 2000 -Dangerous builds = 0 - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:01 diff --git a/examples/PACKAGES/reaction/tiny_epoxy/log.4Nov2022.tiny_epoxy.stabilized.g++.1 b/examples/PACKAGES/reaction/tiny_epoxy/log.4Nov2022.tiny_epoxy.stabilized.g++.1 new file mode 100644 index 0000000000..24b8fb0987 --- /dev/null +++ b/examples/PACKAGES/reaction/tiny_epoxy/log.4Nov2022.tiny_epoxy.stabilized.g++.1 @@ -0,0 +1,249 @@ +LAMMPS (4 Nov 2022) +# two molecules DGEBA (diepoxy) and one DETA (linker) +# two crosslinking reactions + +units real + +boundary p p p + +atom_style full + +pair_style lj/class2 8 + +angle_style class2 + +bond_style class2 + +dihedral_style class2 + +improper_style class2 + +read_data tiny_epoxy.data +Reading data file ... + orthogonal box = (10 -10 -15) to (30 20 10) + 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 ... + 118 atoms + scanning bonds ... + 4 = max bonds/atom + scanning angles ... + 6 = max angles/atom + scanning dihedrals ... + 18 = max dihedrals/atom + scanning impropers ... + 4 = max impropers/atom + reading bonds ... + 123 bonds + reading angles ... + 221 angles + reading dihedrals ... + 302 dihedrals + reading impropers ... + 115 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 + 10 = max # of 1-3 neighbors + 19 = max # of 1-4 neighbors + 22 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.015 seconds + +velocity all create 300.0 4928459 dist gaussian + +molecule mol1 rxn1_stp1_pre.molecule_template +Read molecule template mol1: + 1 molecules + 0 fragments + 31 atoms with max type 10 + 30 bonds with max type 15 + 53 angles with max type 29 + 66 dihedrals with max type 39 + 3 impropers with max type 5 +molecule mol2 rxn1_stp1_post.molecule_template +Read molecule template mol2: + 1 molecules + 0 fragments + 31 atoms with max type 10 + 30 bonds with max type 17 + 55 angles with max type 36 + 75 dihedrals with max type 51 + 2 impropers with max type 5 +molecule mol3 rxn1_stp2_post.molecule_template +Read molecule template mol3: + 1 molecules + 0 fragments + 31 atoms with max type 11 + 30 bonds with max type 18 + 53 angles with max type 37 + 72 dihedrals with max type 53 + 3 impropers with max type 5 +molecule mol4 rxn2_stp1_pre.molecule_template +Read molecule template mol4: + 1 molecules + 0 fragments + 42 atoms with max type 11 + 41 bonds with max type 18 + 73 angles with max type 41 + 96 dihedrals with max type 54 + 3 impropers with max type 5 +molecule mol5 rxn2_stp1_post.molecule_template +Read molecule template mol5: + 1 molecules + 0 fragments + 42 atoms with max type 11 + 41 bonds with max type 18 + 75 angles with max type 37 + 108 dihedrals with max type 53 + 2 impropers with max type 5 +molecule mol6 rxn2_stp2_post.molecule_template +Read molecule template mol6: + 1 molecules + 0 fragments + 42 atoms with max type 11 + 41 bonds with max type 19 + 73 angles with max type 50 + 102 dihedrals with max type 66 + 3 impropers with max type 22 + +thermo 50 + +# dump 1 all xyz 1 test_vis.xyz + +fix rxns all bond/react stabilization yes statted_grp .03 react rxn1_stp1 all 1 0.0 5 mol1 mol2 rxn1_stp1.map react rxn1_stp2 all 1 0.0 5 mol2 mol3 rxn1_stp2.map react rxn2_stp1 all 1 0.0 5 mol4 mol5 rxn2_stp1.map react rxn2_stp2 all 1 0.0 5 mol5 mol6 rxn2_stp2.map +dynamic group bond_react_MASTER_group defined +dynamic group statted_grp_REACT defined + + +fix 1 statted_grp_REACT nvt temp 300 300 100 + +thermo_style custom step temp f_rxns[1] f_rxns[2] f_rxns[3] f_rxns[4] + +run 2000 + +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 55 of 55 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 + ghost atom cutoff = 10 + binsize = 5, bins = 4 6 5 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) pair lj/class2, 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) = 16.64 | 16.64 | 16.64 Mbytes + Step Temp f_rxns[1] f_rxns[2] f_rxns[3] f_rxns[4] + 0 300 0 0 0 0 + 50 378.29345 1 0 0 0 + 100 471.04152 1 1 0 0 + 150 583.79755 1 1 1 0 + 200 526.00812 1 1 1 1 + 250 429.56812 1 1 1 1 + 300 512.54655 1 1 1 1 + 350 461.18357 1 1 1 1 + 400 379.38965 1 1 1 1 + 450 424.89528 1 1 1 1 + 500 324.72257 1 1 1 1 + 550 302.91042 1 1 1 1 + 600 253.80911 1 1 1 1 + 650 252.90262 1 1 1 1 + 700 270.62628 1 1 1 1 + 750 311.64391 1 1 1 1 + 800 318.9413 1 1 1 1 + 850 354.20196 1 1 1 1 + 900 302.19641 1 1 1 1 + 950 316.97905 1 1 1 1 + 1000 303.08194 1 1 1 1 + 1050 317.51619 1 1 1 1 + 1100 287.57204 1 1 1 1 + 1150 226.72101 1 1 1 1 + 1200 283.97519 1 1 1 1 + 1250 287.0607 1 1 1 1 + 1300 327.65278 1 1 1 1 + 1350 316.06809 1 1 1 1 + 1400 337.69947 1 1 1 1 + 1450 326.12278 1 1 1 1 + 1500 300.89265 1 1 1 1 + 1550 325.2415 1 1 1 1 + 1600 294.1844 1 1 1 1 + 1650 293.98596 1 1 1 1 + 1700 317.35477 1 1 1 1 + 1750 296.97768 1 1 1 1 + 1800 274.97297 1 1 1 1 + 1850 335.36697 1 1 1 1 + 1900 315.3756 1 1 1 1 + 1950 260.65335 1 1 1 1 + 2000 354.03612 1 1 1 1 +Loop time of 0.910097 on 1 procs for 2000 steps with 118 atoms + +Performance: 189.870 ns/day, 0.126 hours/ns, 2197.568 timesteps/s, 259.313 katom-step/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 | 0.10286 | 0.10286 | 0.10286 | 0.0 | 11.30 +Bond | 0.63714 | 0.63714 | 0.63714 | 0.0 | 70.01 +Neigh | 0.013949 | 0.013949 | 0.013949 | 0.0 | 1.53 +Comm | 0.0056606 | 0.0056606 | 0.0056606 | 0.0 | 0.62 +Output | 0.00055825 | 0.00055825 | 0.00055825 | 0.0 | 0.06 +Modify | 0.14629 | 0.14629 | 0.14629 | 0.0 | 16.07 +Other | | 0.003637 | | | 0.40 + +Nlocal: 118 ave 118 max 118 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 372 ave 372 max 372 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 3487 ave 3487 max 3487 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 3487 +Ave neighs/atom = 29.550847 +Ave special neighs/atom = 10.576271 +Neighbor list builds = 68 +Dangerous builds = 0 + +# write_restart restart_longrun +# write_data restart_longrun.data nofix +Total wall time: 0:00:01 diff --git a/examples/PACKAGES/reaction/tiny_epoxy/log.4Nov2022.tiny_epoxy.stabilized.g++.4 b/examples/PACKAGES/reaction/tiny_epoxy/log.4Nov2022.tiny_epoxy.stabilized.g++.4 new file mode 100644 index 0000000000..5d1a80405a --- /dev/null +++ b/examples/PACKAGES/reaction/tiny_epoxy/log.4Nov2022.tiny_epoxy.stabilized.g++.4 @@ -0,0 +1,249 @@ +LAMMPS (4 Nov 2022) +# two molecules DGEBA (diepoxy) and one DETA (linker) +# two crosslinking reactions + +units real + +boundary p p p + +atom_style full + +pair_style lj/class2 8 + +angle_style class2 + +bond_style class2 + +dihedral_style class2 + +improper_style class2 + +read_data tiny_epoxy.data +Reading data file ... + orthogonal box = (10 -10 -15) to (30 20 10) + 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 ... + 118 atoms + scanning bonds ... + 4 = max bonds/atom + scanning angles ... + 6 = max angles/atom + scanning dihedrals ... + 18 = max dihedrals/atom + scanning impropers ... + 4 = max impropers/atom + reading bonds ... + 123 bonds + reading angles ... + 221 angles + reading dihedrals ... + 302 dihedrals + reading impropers ... + 115 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 + 10 = max # of 1-3 neighbors + 19 = max # of 1-4 neighbors + 22 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.013 seconds + +velocity all create 300.0 4928459 dist gaussian + +molecule mol1 rxn1_stp1_pre.molecule_template +Read molecule template mol1: + 1 molecules + 0 fragments + 31 atoms with max type 10 + 30 bonds with max type 15 + 53 angles with max type 29 + 66 dihedrals with max type 39 + 3 impropers with max type 5 +molecule mol2 rxn1_stp1_post.molecule_template +Read molecule template mol2: + 1 molecules + 0 fragments + 31 atoms with max type 10 + 30 bonds with max type 17 + 55 angles with max type 36 + 75 dihedrals with max type 51 + 2 impropers with max type 5 +molecule mol3 rxn1_stp2_post.molecule_template +Read molecule template mol3: + 1 molecules + 0 fragments + 31 atoms with max type 11 + 30 bonds with max type 18 + 53 angles with max type 37 + 72 dihedrals with max type 53 + 3 impropers with max type 5 +molecule mol4 rxn2_stp1_pre.molecule_template +Read molecule template mol4: + 1 molecules + 0 fragments + 42 atoms with max type 11 + 41 bonds with max type 18 + 73 angles with max type 41 + 96 dihedrals with max type 54 + 3 impropers with max type 5 +molecule mol5 rxn2_stp1_post.molecule_template +Read molecule template mol5: + 1 molecules + 0 fragments + 42 atoms with max type 11 + 41 bonds with max type 18 + 75 angles with max type 37 + 108 dihedrals with max type 53 + 2 impropers with max type 5 +molecule mol6 rxn2_stp2_post.molecule_template +Read molecule template mol6: + 1 molecules + 0 fragments + 42 atoms with max type 11 + 41 bonds with max type 19 + 73 angles with max type 50 + 102 dihedrals with max type 66 + 3 impropers with max type 22 + +thermo 50 + +# dump 1 all xyz 1 test_vis.xyz + +fix rxns all bond/react stabilization yes statted_grp .03 react rxn1_stp1 all 1 0.0 5 mol1 mol2 rxn1_stp1.map react rxn1_stp2 all 1 0.0 5 mol2 mol3 rxn1_stp2.map react rxn2_stp1 all 1 0.0 5 mol4 mol5 rxn2_stp1.map react rxn2_stp2 all 1 0.0 5 mol5 mol6 rxn2_stp2.map +dynamic group bond_react_MASTER_group defined +dynamic group statted_grp_REACT defined + + +fix 1 statted_grp_REACT nvt temp 300 300 100 + +thermo_style custom step temp f_rxns[1] f_rxns[2] f_rxns[3] f_rxns[4] + +run 2000 + +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 55 of 55 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 + ghost atom cutoff = 10 + binsize = 5, bins = 4 6 5 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) pair lj/class2, 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) = 16.63 | 16.63 | 16.64 Mbytes + Step Temp f_rxns[1] f_rxns[2] f_rxns[3] f_rxns[4] + 0 300 0 0 0 0 + 50 378.29345 1 0 0 0 + 100 471.04152 1 1 0 0 + 150 583.79755 1 1 1 0 + 200 526.00812 1 1 1 1 + 250 429.56812 1 1 1 1 + 300 512.54655 1 1 1 1 + 350 461.18357 1 1 1 1 + 400 379.38965 1 1 1 1 + 450 424.89528 1 1 1 1 + 500 324.72257 1 1 1 1 + 550 302.91042 1 1 1 1 + 600 253.80911 1 1 1 1 + 650 252.90262 1 1 1 1 + 700 270.62628 1 1 1 1 + 750 311.64391 1 1 1 1 + 800 318.9413 1 1 1 1 + 850 354.20196 1 1 1 1 + 900 302.19641 1 1 1 1 + 950 316.97905 1 1 1 1 + 1000 303.08194 1 1 1 1 + 1050 317.51619 1 1 1 1 + 1100 287.57204 1 1 1 1 + 1150 226.72101 1 1 1 1 + 1200 283.97519 1 1 1 1 + 1250 287.0607 1 1 1 1 + 1300 327.65278 1 1 1 1 + 1350 316.06809 1 1 1 1 + 1400 337.69947 1 1 1 1 + 1450 326.12278 1 1 1 1 + 1500 300.89265 1 1 1 1 + 1550 325.2415 1 1 1 1 + 1600 294.1844 1 1 1 1 + 1650 293.98596 1 1 1 1 + 1700 317.35477 1 1 1 1 + 1750 296.97768 1 1 1 1 + 1800 274.97297 1 1 1 1 + 1850 335.36698 1 1 1 1 + 1900 315.3756 1 1 1 1 + 1950 260.65334 1 1 1 1 + 2000 354.03612 1 1 1 1 +Loop time of 0.47159 on 4 procs for 2000 steps with 118 atoms + +Performance: 366.420 ns/day, 0.065 hours/ns, 4240.970 timesteps/s, 500.434 katom-step/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 | 0.016546 | 0.024458 | 0.038858 | 5.5 | 5.19 +Bond | 0.072622 | 0.16458 | 0.21778 | 13.9 | 34.90 +Neigh | 0.0056307 | 0.0056812 | 0.0057292 | 0.1 | 1.20 +Comm | 0.028022 | 0.095922 | 0.19526 | 20.3 | 20.34 +Output | 0.00034591 | 0.00041633 | 0.00062378 | 0.0 | 0.09 +Modify | 0.17613 | 0.17649 | 0.17711 | 0.1 | 37.43 +Other | | 0.00404 | | | 0.86 + +Nlocal: 29.5 ave 45 max 7 min +Histogram: 1 0 0 0 0 0 1 1 0 1 +Nghost: 315 ave 343 max 287 min +Histogram: 1 1 0 0 0 0 0 0 1 1 +Neighs: 871.75 ave 1772 max 236 min +Histogram: 1 0 1 1 0 0 0 0 0 1 + +Total # of neighbors = 3487 +Ave neighs/atom = 29.550847 +Ave special neighs/atom = 10.576271 +Neighbor list builds = 68 +Dangerous builds = 0 + +# write_restart restart_longrun +# write_data restart_longrun.data nofix +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/reaction/tiny_epoxy/rxn1_stp1_post.data_template b/examples/PACKAGES/reaction/tiny_epoxy/rxn1_stp1_post.data_template deleted file mode 100644 index e510883432..0000000000 --- a/examples/PACKAGES/reaction/tiny_epoxy/rxn1_stp1_post.data_template +++ /dev/null @@ -1,315 +0,0 @@ -rxn1_stp1_post - -31 atoms -30 bonds -55 angles -75 dihedrals -34 impropers - -Types - -1 1 -2 6 -3 1 -4 7 -5 4 -6 7 -7 8 -8 8 -9 8 -10 8 -11 8 -12 9 -13 1 -14 1 -15 9 -16 9 -17 1 -18 1 -19 10 -20 8 -21 8 -22 8 -23 8 -24 10 -25 10 -26 10 -27 10 -28 8 -29 8 -30 8 -31 8 - -Charges - -1 0.000000 -2 0.000000 -3 0.000000 -4 0.100000 -5 0.000000 -6 0.000000 -7 0.000000 -8 0.000000 -9 0.000000 -10 0.000000 -11 0.000000 -12 0.000000 -13 0.000000 -14 0.000000 -15 -0.025000 -16 -0.025000 -17 0.000000 -18 0.000000 -19 0.000000 -20 0.000000 -21 0.000000 -22 0.000000 -23 0.000000 -24 0.000000 -25 0.000000 -26 0.000000 -27 0.000000 -28 0.000000 -29 0.000000 -30 0.000000 -31 0.000000 - -Coords - -1 22.582573 10.988183 -5.014054 -2 23.904713 10.750493 -4.202215 -3 23.989172 9.487042 -3.323374 -4 24.067001 11.723383 -4.037435 -5 24.627851 7.325302 -3.319944 -6 24.554632 8.418972 -4.080365 -7 22.667763 11.445703 -5.999605 -8 21.787441 10.247643 -4.916974 -9 24.964962 10.712683 -4.449374 -10 24.616703 9.689913 -2.456034 -11 22.989313 9.208153 -2.991455 -12 18.808882 13.758042 -3.958724 -13 19.293213 12.549683 -3.196594 -14 20.810543 12.417832 -3.417504 -15 21.090193 12.251203 -4.891234 -16 17.657042 16.437199 -3.985224 -17 19.126713 16.210239 -4.245154 -18 19.589151 14.957593 -3.479565 -19 19.000433 13.609432 -5.041715 -20 18.761223 11.614392 -3.573184 -21 19.082903 12.688992 -2.085145 -22 21.202852 11.511562 -2.848624 -23 21.328482 13.360252 -3.038924 -24 19.949852 12.199403 -5.680355 -25 21.477343 13.247442 -5.445915 -26 17.080341 15.555528 -4.334374 -27 17.319832 17.341927 -4.532204 -28 19.720472 17.115158 -3.887564 -29 19.298622 16.058659 -5.361685 -30 19.410772 15.105113 -2.363724 -31 20.700163 14.782252 -3.666344 - -Bonds - -1 1 1 8 -2 16 1 2 -3 1 1 7 -4 13 1 15 -5 16 3 2 -6 12 2 9 -7 17 2 4 -8 3 3 6 -9 1 3 10 -10 1 3 11 -11 8 6 5 -12 13 13 12 -13 13 18 12 -14 14 12 19 -15 15 13 14 -16 1 13 20 -17 1 13 21 -18 13 14 15 -19 1 14 22 -20 1 14 23 -21 14 15 24 -22 14 15 25 -23 13 17 16 -24 14 16 26 -25 14 16 27 -26 15 17 18 -27 1 17 28 -28 1 17 29 -29 1 18 30 -30 1 18 31 - -Angles - -1 30 2 1 8 -2 2 8 1 7 -3 26 8 1 15 -4 30 2 1 7 -5 31 2 1 15 -6 26 7 1 15 -7 32 1 2 3 -8 33 1 2 9 -9 34 1 2 4 -10 33 3 2 9 -11 34 3 2 4 -12 35 4 2 9 -13 36 2 3 6 -14 30 2 3 10 -15 30 2 3 11 -16 3 6 3 10 -17 3 6 3 11 -18 2 10 3 11 -19 22 3 6 5 -20 23 13 12 18 -21 24 13 12 19 -22 24 18 12 19 -23 25 14 13 12 -24 26 20 13 12 -25 26 21 13 12 -26 27 14 13 20 -27 27 14 13 21 -28 2 20 13 21 -29 25 13 14 15 -30 27 13 14 22 -31 27 13 14 23 -32 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3 6 + 9 c2-hc 3 10 + 10 c2-hc 3 11 + 11 oc-ho 4 25 + 12 cp-oc 6 5 + 13 c2-na 13 12 + 14 c2-na 18 12 + 15 na-hn 12 19 + 16 c2-c2 13 14 + 17 c2-hc 13 20 + 18 c2-hc 13 21 + 19 c2-na 14 15 + 20 c2-hc 14 22 + 21 c2-hc 14 23 + 22 c2-na 32 15 + 23 c2-na 17 16 + 24 na-hn 16 26 + 25 na-hn 16 27 + 26 c2-c2 17 18 + 27 c2-hc 17 28 + 28 c2-hc 17 29 + 29 c2-hc 18 30 + 30 c2-hc 18 31 + 31 oc-ho 35 24 + 32 c2-hc 32 39 + 33 c2-c3 32 33 + 34 c2-hc 32 38 + 35 c3-oc 35 33 + 36 c2-c3 34 33 + 37 c3-hc 40 33 + 38 c2-oc 34 37 + 39 c2-hc 34 41 + 40 c2-hc 34 42 + 41 cp-oc 37 36 + +Angles + + 1 c3m-c2-hc 2 1 8 + 2 hc-c2-hc 8 1 7 + 3 hc-c2-na 8 1 15 + 4 c3m-c2-hc 2 1 7 + 5 c3m-c2-na 2 1 15 + 6 hc-c2-na 7 1 15 + 7 c2-c3m-c2 1 2 3 + 8 c2-c3m-hc 1 2 9 + 9 c2-c3m-oc 1 2 4 + 10 c2-c3m-hc 3 2 9 + 11 c2-c3m-oc 3 2 4 + 12 oc-c3m-hc 4 2 9 + 13 c3m-c2-oc 2 3 6 + 14 c3m-c2-hc 2 3 10 + 15 c3m-c2-hc 2 3 11 + 16 oc-c2-hc 6 3 10 + 17 oc-c2-hc 6 3 11 + 18 hc-c2-hc 10 3 11 + 19 c3m-oc-ho 2 4 25 + 20 c2-oc-cp 3 6 5 + 21 c2-na-c2 13 12 18 + 22 c2-na-hn 13 12 19 + 23 c2-na-hn 18 12 19 + 24 c2-c2-na 14 13 12 + 25 hc-c2-na 20 13 12 + 26 hc-c2-na 21 13 12 + 27 c2-c2-hc 14 13 20 + 28 c2-c2-hc 14 13 21 + 29 hc-c2-hc 20 13 21 + 30 c2-c2-na 13 14 15 + 31 c2-c2-hc 13 14 22 + 32 c2-c2-hc 13 14 23 + 33 hc-c2-na 22 14 15 + 34 hc-c2-na 23 14 15 + 35 hc-c2-hc 22 14 23 + 36 c2-na-c2 1 15 14 + 37 c2-na-c2 1 15 32 + 38 c2-na-c2 14 15 32 + 39 c2-na-hn 17 16 26 + 40 c2-na-hn 17 16 27 + 41 hn-na-hn 26 16 27 + 42 c2-c2-na 18 17 16 + 43 hc-c2-na 28 17 16 + 44 hc-c2-na 29 17 16 + 45 c2-c2-hc 18 17 28 + 46 c2-c2-hc 18 17 29 + 47 hc-c2-hc 28 17 29 + 48 c2-c2-na 17 18 12 + 49 hc-c2-na 30 18 12 + 50 hc-c2-na 31 18 12 + 51 c2-c2-hc 17 18 30 + 52 c2-c2-hc 17 18 31 + 53 hc-c2-hc 30 18 31 + 54 hc-c2-na 39 32 15 + 55 na-c2-c3 15 32 33 + 56 hc-c2-na 38 32 15 + 57 hc-c2-c3 39 32 33 + 58 hc-c2-hc 39 32 38 + 59 hc-c2-c3 38 32 33 + 60 c2-c3-oc 32 33 35 + 61 c2-c3-c2 32 33 34 + 62 c2-c3-hc 32 33 40 + 63 c2-c3-oc 34 33 35 + 64 oc-c3-hc 35 33 40 + 65 c2-c3-hc 34 33 40 + 66 oc-c2-c3 37 34 33 + 67 hc-c2-c3 41 34 33 + 68 hc-c2-c3 42 34 33 + 69 oc-c2-hc 37 34 41 + 70 oc-c2-hc 37 34 42 + 71 hc-c2-hc 41 34 42 + 72 ho-oc-c3 24 35 33 + 73 c2-oc-cp 34 37 36 + +Dihedrals + + 1 hc-c2-c3m-c2 8 1 2 3 + 2 hc-c2-c3m-hc 8 1 2 9 + 3 hc-c2-c3m-oc 8 1 2 4 + 4 hc-c2-c3m-c2 7 1 2 3 + 5 hc-c2-c3m-hc 7 1 2 9 + 6 hc-c2-c3m-oc 7 1 2 4 + 7 na-c2-c3m-c2 15 1 2 3 + 8 na-c2-c3m-hc 15 1 2 9 + 9 na-c2-c3m-oc 15 1 2 4 + 10 hc-c2-na-c2 8 1 15 14 + 11 hc-c2-na-c2 8 1 15 32 + 12 c3m-c2-na-c2 2 1 15 14 + 13 c3m-c2-na-c2 2 1 15 32 + 14 hc-c2-na-c2 7 1 15 14 + 15 hc-c2-na-c2 7 1 15 32 + 16 oc-c2-c3m-c2 6 3 2 1 + 17 hc-c2-c3m-c2 10 3 2 1 + 18 hc-c2-c3m-c2 11 3 2 1 + 19 oc-c2-c3m-hc 6 3 2 9 + 20 hc-c2-c3m-hc 10 3 2 9 + 21 hc-c2-c3m-hc 11 3 2 9 + 22 oc-c2-c3m-oc 6 3 2 4 + 23 hc-c2-c3m-oc 10 3 2 4 + 24 hc-c2-c3m-oc 11 3 2 4 + 25 c2-c3m-oc-ho 1 2 4 25 + 26 c2-c3m-oc-ho 3 2 4 25 + 27 hc-c3m-oc-ho 9 2 4 25 + 28 c3m-c2-oc-cp 2 3 6 5 + 29 hc-c2-oc-cp 10 3 6 5 + 30 hc-c2-oc-cp 11 3 6 5 + 31 c2-c2-na-c2 14 13 12 18 + 32 hc-c2-na-c2 20 13 12 18 + 33 hc-c2-na-c2 21 13 12 18 + 34 c2-c2-na-hn 14 13 12 19 + 35 hc-c2-na-hn 20 13 12 19 + 36 hc-c2-na-hn 21 13 12 19 + 37 c2-c2-na-c2 17 18 12 13 + 38 hc-c2-na-c2 30 18 12 13 + 39 hc-c2-na-c2 31 18 12 13 + 40 c2-c2-na-hn 17 18 12 19 + 41 hc-c2-na-hn 30 18 12 19 + 42 hc-c2-na-hn 31 18 12 19 + 43 na-c2-c2-na 12 13 14 15 + 44 hc-c2-c2-na 22 14 13 12 + 45 hc-c2-c2-na 23 14 13 12 + 46 hc-c2-c2-na 20 13 14 15 + 47 hc-c2-c2-hc 20 13 14 22 + 48 hc-c2-c2-hc 20 13 14 23 + 49 hc-c2-c2-na 21 13 14 15 + 50 hc-c2-c2-hc 21 13 14 22 + 51 hc-c2-c2-hc 21 13 14 23 + 52 c2-c2-na-c2 13 14 15 1 + 53 c2-c2-na-c2 13 14 15 32 + 54 hc-c2-na-c2 22 14 15 1 + 55 hc-c2-na-c2 22 14 15 32 + 56 hc-c2-na-c2 23 14 15 1 + 57 hc-c2-na-c2 23 14 15 32 + 58 hc-c2-na-c2 39 32 15 1 + 59 c3-c2-na-c2 33 32 15 1 + 60 hc-c2-na-c2 38 32 15 1 + 61 hc-c2-na-c2 39 32 15 14 + 62 c3-c2-na-c2 33 32 15 14 + 63 hc-c2-na-c2 38 32 15 14 + 64 c2-c2-na-hn 18 17 16 26 + 65 hc-c2-na-hn 28 17 16 26 + 66 hc-c2-na-hn 29 17 16 26 + 67 c2-c2-na-hn 18 17 16 27 + 68 hc-c2-na-hn 28 17 16 27 + 69 hc-c2-na-hn 29 17 16 27 + 70 na-c2-c2-na 16 17 18 12 + 71 hc-c2-c2-na 30 18 17 16 + 72 hc-c2-c2-na 31 18 17 16 + 73 hc-c2-c2-na 28 17 18 12 + 74 hc-c2-c2-hc 28 17 18 30 + 75 hc-c2-c2-hc 28 17 18 31 + 76 hc-c2-c2-na 29 17 18 12 + 77 hc-c2-c2-hc 29 17 18 30 + 78 hc-c2-c2-hc 29 17 18 31 + 79 na-c2-c3-oc 15 32 33 35 + 80 na-c2-c3-c2 15 32 33 34 + 81 na-c2-c3-hc 15 32 33 40 + 82 hc-c2-c3-oc 39 32 33 35 + 83 hc-c2-c3-c2 39 32 33 34 + 84 hc-c2-c3-hc 39 32 33 40 + 85 hc-c2-c3-oc 38 32 33 35 + 86 hc-c2-c3-c2 38 32 33 34 + 87 hc-c2-c3-hc 38 32 33 40 + 88 ho-oc-c3-c2 24 35 33 32 + 89 ho-oc-c3-c2 24 35 33 34 + 90 ho-oc-c3-hc 24 35 33 40 + 91 oc-c2-c3-c2 37 34 33 32 + 92 hc-c2-c3-c2 41 34 33 32 + 93 hc-c2-c3-c2 42 34 33 32 + 94 oc-c2-c3-oc 37 34 33 35 + 95 hc-c2-c3-oc 41 34 33 35 + 96 hc-c2-c3-oc 42 34 33 35 + 97 oc-c2-c3-hc 37 34 33 40 + 98 hc-c2-c3-hc 41 34 33 40 + 99 hc-c2-c3-hc 42 34 33 40 + 100 c3-c2-oc-cp 33 34 37 36 + 101 hc-c2-oc-cp 41 34 37 36 + 102 hc-c2-oc-cp 42 34 37 36 + +Impropers + + 1 c2-na-c2-hn 13 12 18 19 + 2 c2-na-c2-c2 1 15 14 32 + 3 c2-na-hn-hn 17 16 26 27 diff --git a/examples/PACKAGES/reaction/tiny_epoxy/tiny_epoxy.data b/examples/PACKAGES/reaction/tiny_epoxy/tiny_epoxy.data index d98006b107..90c074fde0 100644 --- a/examples/PACKAGES/reaction/tiny_epoxy/tiny_epoxy.data +++ b/examples/PACKAGES/reaction/tiny_epoxy/tiny_epoxy.data @@ -1,1582 +1,1765 @@ # two molecules DGEBA (diepoxy) and one DETA (linker) -118 atoms -123 bonds -221 angles -302 dihedrals -115 impropers -11 atom types -19 bond types -50 angle types -66 dihedral types -22 improper types +118 atoms +123 bonds +221 angles +302 dihedrals +115 impropers +11 atom types +19 bond types +50 angle types +66 dihedral types +22 improper types 10 30 xlo xhi -10 20 ylo yhi -15 10 zlo zhi -Masses +Atom Type Labels -1 12.011150 # c2 -2 12.011150 # c3m -3 15.999400 # o3e -4 12.011150 # cp -5 12.011150 # c -6 12.011150 # c3 -7 15.999400 # oc -8 1.007970 # hc -9 14.006700 # na -10 1.007970 # hn -11 1.007970 # ho +1 c2 +2 c3m +3 o3e +4 cp +5 c +6 c3 +7 oc +8 hc +9 na +10 hn +11 ho -Pair Coeffs # lj/class2/coul/long +Bond Type Labels -1 0.0540000000 4.0100000000 # c2 -2 0.0540000000 4.0100000000 # c3m -3 0.2400000000 3.5350000000 # o3e -4 0.0640000000 4.0100000000 # cp -5 0.0540000000 4.0100000000 # c -6 0.0540000000 4.0100000000 # c3 -7 0.2400000000 3.5350000000 # oc -8 0.0200000000 2.7000000000 # hc -9 0.0650000000 4.0700000000 # na -10 0.0130000000 1.0980000000 # hn -11 0.0130000000 1.0980000000 # ho +1 c2-hc +2 c3m-c2 +3 c2-oc +4 c3m-o3e +5 c3m-c3m +6 c3m-hc +7 cp-cp +8 cp-oc +9 cp-hc +10 cp-c +11 c-c3 +12 c3-hc +13 c2-na +14 na-hn +15 c2-c2 +16 c2-c3 +17 c3-oc +18 oc-ho +19 c3m-oc -Bond Coeffs # class2 +Angle Type Labels -1 1.1010 345.0000 -691.8900 844.6000 # c2-hc -2 1.5300 299.6700 -501.7700 679.8100 # c2-c3m -3 1.4200 400.3954 -835.1951 1313.0142 # c2-oc -4 1.4200 400.3954 -835.1951 1313.0142 # c3m-o3e -5 1.5300 299.6700 -501.7700 679.8100 # c3m-c3m -6 1.1010 345.0000 -691.8900 844.6000 # c3m-hc -7 1.4170 470.8361 -627.6179 1327.6345 # cp-cp -8 1.3768 428.8798 -738.2351 1114.9655 # cp-oc -9 1.0982 372.8251 -803.4526 894.3173 # cp-hc -10 1.5010 321.9021 -521.8208 572.1628 # cp-c -11 1.5300 299.6700 -501.7700 679.8100 # c-c3 -12 1.1010 345.0000 -691.8900 844.6000 # c3-hc -13 1.4570 365.8052 -699.6368 998.4842 # c2-na -14 1.0060 466.7400 -1073.6018 1251.1056 # na-hn -15 1.5300 299.6700 -501.7700 679.8100 # c2-c2 -16 1.5300 299.6700 -501.7700 679.8100 # c2-c3 -17 1.4200 400.3954 -835.1951 1313.0142 # c3-oc -18 0.9650 532.5062 -1282.9050 2004.7658 # oc-ho -19 1.4200 400.3954 -835.1951 1313.0142 # c3m-oc +1 c3m-c2-hc +2 hc-c2-hc +3 oc-c2-hc +4 c3m-c2-oc +5 c2-c3m-o3e +6 c2-c3m-c3m +7 c2-c3m-hc +8 c3m-c3m-o3e +9 o3e-c3m-hc +10 c3m-c3m-hc +11 hc-c3m-hc +12 c3m-o3e-c3m +13 cp-cp-cp +14 cp-cp-oc +15 cp-cp-hc +16 cp-cp-c +17 cp-c-c3 +18 cp-c-cp +19 c3-c-c3 +20 c-c3-hc +21 hc-c3-hc +22 c2-oc-cp +23 c2-na-c2 +24 c2-na-hn +25 c2-c2-na +26 hc-c2-na +27 c2-c2-hc +28 hn-na-hn +29 c3m-c3m-c2 +30 c3-c2-hc +31 c3-c2-na +32 c2-c3-c2 +33 c2-c3-hc +34 c2-c3-oc +35 oc-c3-hc +36 c3-c2-oc +37 c3-oc-ho +38 hc-c3m-o3e +39 hc-c3m-c3m +40 oc-c2-c3m +41 hc-c2-c3m +42 c3m-c2-na +43 c2-c3m-c2 +44 c2-c3m-oc +45 oc-c3m-hc +46 c3m-oc-ho +47 na-c2-c3 +48 hc-c2-c3 +49 oc-c2-c3 +50 ho-oc-c3 -Angle Coeffs # class2 +Dihedral Type Labels -1 110.7700 41.4530 -10.6040 5.1290 # c3m-c2-hc -2 107.6600 39.6410 -12.9210 -2.4318 # hc-c2-hc -3 108.7280 58.5446 -10.8088 -12.4006 # oc-c2-hc -4 111.2700 54.5381 -8.3642 -13.0838 # c3m-c2-oc -5 111.2700 54.5381 -8.3642 -13.0838 # c2-c3m-o3e -6 112.6700 39.5160 -7.4430 -9.5583 # c2-c3m-c3m -7 110.7700 41.4530 -10.6040 5.1290 # c2-c3m-hc -8 111.2700 54.5381 -8.3642 -13.0838 # c3m-c3m-o3e -9 108.7280 58.5446 -10.8088 -12.4006 # o3e-c3m-hc -10 110.7700 41.4530 -10.6040 5.1290 # c3m-c3m-hc -11 107.6600 39.6410 -12.9210 -2.4318 # hc-c3m-hc -12 104.5000 35.7454 -10.0067 -6.2729 # c3m-o3e-c3m -13 118.9000 61.0226 -34.9931 0.0000 # cp-cp-cp -14 123.4200 73.6781 -21.6787 0.0000 # cp-cp-oc -15 117.9400 35.1558 -12.4682 0.0000 # cp-cp-hc -16 120.0500 44.7148 -22.7352 0.0000 # cp-cp-c -17 108.4000 43.9594 -8.3924 -9.3379 # cp-c-c3 -18 111.0000 44.3234 -9.4454 0.0000 # cp-c-cp -19 112.6700 39.5160 -7.4430 -9.5583 # c3-c-c3 -20 110.7700 41.4530 -10.6040 5.1290 # c-c3-hc -21 107.6600 39.6410 -12.9210 -2.4318 # hc-c3-hc -22 102.9695 38.9739 -6.2595 -8.1710 # c2-oc-cp -23 112.4436 47.2337 -10.6612 -10.2062 # c2-na-c2 -24 110.9538 50.8652 -4.4522 -10.0298 # c2-na-hn -25 111.9100 60.7147 -13.3366 -13.0785 # c2-c2-na -26 110.6204 51.3137 -6.7198 -2.6003 # hc-c2-na -27 110.7700 41.4530 -10.6040 5.1290 # c2-c2-hc -28 107.0671 45.2520 -7.5558 -9.5120 # hn-na-hn -29 112.6700 39.5160 -7.4430 -9.5583 # c3m-c3m-c2 -30 110.7700 41.4530 -10.6040 5.1290 # c3-c2-hc -31 111.9100 60.7147 -13.3366 -13.0785 # c3-c2-na -32 112.6700 39.5160 -7.4430 -9.5583 # c2-c3-c2 -33 110.7700 41.4530 -10.6040 5.1290 # c2-c3-hc -34 111.2700 54.5381 -8.3642 -13.0838 # c2-c3-oc -35 108.7280 58.5446 -10.8088 -12.4006 # oc-c3-hc -36 111.2700 54.5381 -8.3642 -13.0838 # c3-c2-oc -37 105.8000 52.7061 -12.1090 -9.8681 # c3-oc-ho -38 108.7280 58.5446 -10.8088 -12.4006 # hc-c3m-o3e -39 110.7700 41.4530 -10.6040 5.1290 # hc-c3m-c3m -40 111.2700 54.5381 -8.3642 -13.0838 # oc-c2-c3m -41 110.7700 41.4530 -10.6040 5.1290 # hc-c2-c3m -42 111.9100 60.7147 -13.3366 -13.0785 # c3m-c2-na -43 112.6700 39.5160 -7.4430 -9.5583 # c2-c3m-c2 -44 111.2700 54.5381 -8.3642 -13.0838 # c2-c3m-oc -45 108.7280 58.5446 -10.8088 -12.4006 # oc-c3m-hc -46 105.8000 52.7061 -12.1090 -9.8681 # c3m-oc-ho -47 111.9100 60.7147 -13.3366 -13.0785 # na-c2-c3 -48 110.7700 41.4530 -10.6040 5.1290 # hc-c2-c3 -49 111.2700 54.5381 -8.3642 -13.0838 # oc-c2-c3 -50 105.8000 52.7061 -12.1090 -9.8681 # ho-oc-c3 +1 hc-c2-c3m-o3e +2 hc-c2-c3m-c3m +3 hc-c2-c3m-hc +4 oc-c2-c3m-o3e +5 oc-c2-c3m-c3m +6 oc-c2-c3m-hc +7 hc-c2-oc-cp +8 c3m-c2-oc-cp +9 c2-c3m-o3e-c3m +10 hc-c3m-o3e-c3m +11 c2-c3m-c3m-o3e +12 c2-c3m-c3m-hc +13 o3e-c3m-c3m-hc +14 hc-c3m-c3m-hc +15 cp-cp-cp-cp +16 cp-cp-cp-hc +17 cp-cp-cp-oc +18 oc-cp-cp-hc +19 cp-cp-oc-c2 +20 hc-cp-cp-hc +21 cp-cp-cp-c +22 c-cp-cp-hc +23 cp-cp-c-c3 +24 cp-cp-c-cp +25 cp-c-c3-hc +26 c3-c-c3-hc +27 c2-c2-na-c2 +28 hc-c2-na-c2 +29 c2-c2-na-hn +30 hc-c2-na-hn +31 na-c2-c2-na +32 hc-c2-c2-na +33 hc-c2-c2-hc +34 c3m-c3m-c2-oc +35 c3m-c3m-c2-hc +36 o3e-c3m-c2-oc +37 o3e-c3m-c2-hc +38 hc-c3m-c2-oc +39 hc-c3m-c2-hc +40 hc-c2-c3-c2 +41 hc-c2-c3-hc +42 hc-c2-c3-oc +43 na-c2-c3-c2 +44 na-c2-c3-hc +45 na-c2-c3-oc +46 c3-c2-na-c2 +47 c3-c2-na-hn +48 oc-c2-c3-c2 +49 oc-c2-c3-hc +50 oc-c2-c3-oc +51 c3-c2-oc-cp +52 c2-c3-oc-ho +53 hc-c3-oc-ho +54 hc-c3m-c3m-o3e +55 hc-c2-c3m-c2 +56 hc-c2-c3m-oc +57 na-c2-c3m-c2 +58 na-c2-c3m-hc +59 na-c2-c3m-oc +60 c3m-c2-na-c2 +61 oc-c2-c3m-c2 +62 oc-c2-c3m-oc +63 c2-c3m-oc-ho +64 hc-c3m-oc-ho +65 ho-oc-c3-c2 +66 ho-oc-c3-hc -Dihedral Coeffs # class2 +Improper Type Labels -1 -0.1435 0.0000 0.2530 0.0000 -0.0905 0.0000# hc-c2-c3m-o3e -2 0.0000 0.0000 0.0316 0.0000 -0.1681 0.0000# hc-c2-c3m-c3m -3 -0.1432 0.0000 0.0617 0.0000 -0.1083 0.0000# hc-c2-c3m-hc -4 -0.1820 0.0000 -0.1084 0.0000 -0.7047 0.0000# oc-c2-c3m-o3e -5 0.7137 0.0000 0.2660 0.0000 -0.2545 0.0000# oc-c2-c3m-c3m -6 -0.1435 0.0000 0.2530 0.0000 -0.0905 0.0000# oc-c2-c3m-hc -7 0.9513 0.0000 0.1155 0.0000 0.0720 0.0000# hc-c2-oc-cp -8 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000# c3m-c2-oc-cp -9 -0.5203 0.0000 -0.3028 0.0000 -0.3450 0.0000# c2-c3m-o3e-c3m -10 0.5302 0.0000 0.0000 0.0000 -0.3966 0.0000# hc-c3m-o3e-c3m -11 0.7137 0.0000 0.2660 0.0000 -0.2545 0.0000# c2-c3m-c3m-o3e -12 0.0000 0.0000 0.0316 0.0000 -0.1681 0.0000# c2-c3m-c3m-hc -13 -0.1435 0.0000 0.2530 0.0000 -0.0905 0.0000# o3e-c3m-c3m-hc -14 -0.1432 0.0000 0.0617 0.0000 -0.1083 0.0000# hc-c3m-c3m-hc -15 8.3667 0.0000 1.1932 0.0000 0.0000 0.0000# cp-cp-cp-cp -16 0.0000 0.0000 3.9661 0.0000 0.0000 0.0000# cp-cp-cp-hc -17 0.0000 0.0000 4.8498 0.0000 0.0000 0.0000# cp-cp-cp-oc -18 0.0000 0.0000 1.7234 0.0000 0.0000 0.0000# oc-cp-cp-hc -19 0.0000 0.0000 1.5000 0.0000 0.0000 0.0000# cp-cp-oc-c2 -20 0.0000 0.0000 1.8769 0.0000 0.0000 0.0000# hc-cp-cp-hc -21 0.0000 0.0000 4.4072 0.0000 0.0000 0.0000# cp-cp-cp-c -22 0.0000 0.0000 1.5590 0.0000 0.0000 0.0000# c-cp-cp-hc -23 -0.2802 0.0000 -0.0678 0.0000 -0.0122 0.0000# cp-cp-c-c3 -24 -0.2802 0.0000 -0.0678 0.0000 -0.0122 0.0000# cp-cp-c-cp -25 -0.0228 0.0000 0.0280 0.0000 -0.1863 0.0000# cp-c-c3-hc -26 0.0000 0.0000 0.0316 0.0000 -0.1681 0.0000# c3-c-c3-hc -27 -0.1406 0.0000 0.4168 0.0000 0.0150 0.0000# c2-c2-na-c2 -28 0.1904 0.0000 -0.1342 0.0000 -0.2460 0.0000# hc-c2-na-c2 -29 -1.1506 0.0000 -0.6344 0.0000 -0.1845 0.0000# c2-c2-na-hn -30 -0.5187 0.0000 -0.4837 0.0000 -0.1692 0.0000# hc-c2-na-hn -31 0.3805 0.0000 0.3547 0.0000 -0.1102 0.0000# na-c2-c2-na -32 -0.2428 0.0000 0.4065 0.0000 -0.3079 0.0000# hc-c2-c2-na -33 -0.1432 0.0000 0.0617 0.0000 -0.1083 0.0000# hc-c2-c2-hc -34 0.7137 0.0000 0.2660 0.0000 -0.2545 0.0000# c3m-c3m-c2-oc -35 0.0000 0.0000 0.0316 0.0000 -0.1681 0.0000# c3m-c3m-c2-hc -36 -0.1820 0.0000 -0.1084 0.0000 -0.7047 0.0000# o3e-c3m-c2-oc -37 -0.1435 0.0000 0.2530 0.0000 -0.0905 0.0000# o3e-c3m-c2-hc -38 -0.1435 0.0000 0.2530 0.0000 -0.0905 0.0000# hc-c3m-c2-oc -39 -0.1432 0.0000 0.0617 0.0000 -0.1083 0.0000# hc-c3m-c2-hc -40 0.0000 0.0000 0.0316 0.0000 -0.1681 0.0000# hc-c2-c3-c2 -41 -0.1432 0.0000 0.0617 0.0000 -0.1083 0.0000# hc-c2-c3-hc -42 -0.1435 0.0000 0.2530 0.0000 -0.0905 0.0000# hc-c2-c3-oc -43 0.1764 0.0000 0.1766 0.0000 -0.5206 0.0000# na-c2-c3-c2 -44 -0.2428 0.0000 0.4065 0.0000 -0.3079 0.0000# na-c2-c3-hc -45 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000# na-c2-c3-oc -46 -0.1406 0.0000 0.4168 0.0000 0.0150 0.0000# c3-c2-na-c2 -47 -1.1506 0.0000 -0.6344 0.0000 -0.1845 0.0000# c3-c2-na-hn -48 0.7137 0.0000 0.2660 0.0000 -0.2545 0.0000# oc-c2-c3-c2 -49 -0.1435 0.0000 0.2530 0.0000 -0.0905 0.0000# oc-c2-c3-hc -50 -0.1820 0.0000 -0.1084 0.0000 -0.7047 0.0000# oc-c2-c3-oc -51 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000# c3-c2-oc-cp -52 -0.6732 0.0000 -0.4778 0.0000 -0.1670 0.0000# c2-c3-oc-ho -53 0.1863 0.0000 -0.4338 0.0000 -0.2121 0.0000# hc-c3-oc-ho -54 -0.1435 0.0000 0.2530 0.0000 -0.0905 0.0000# hc-c3m-c3m-o3e -55 0.0000 0.0000 0.0316 0.0000 -0.1681 0.0000# hc-c2-c3m-c2 -56 -0.1435 0.0000 0.2530 0.0000 -0.0905 0.0000# hc-c2-c3m-oc -57 0.1764 0.0000 0.1766 0.0000 -0.5206 0.0000# na-c2-c3m-c2 -58 -0.2428 0.0000 0.4065 0.0000 -0.3079 0.0000# na-c2-c3m-hc -59 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000# na-c2-c3m-oc -60 -0.1406 0.0000 0.4168 0.0000 0.0150 0.0000# c3m-c2-na-c2 -61 0.7137 0.0000 0.2660 0.0000 -0.2545 0.0000# oc-c2-c3m-c2 -62 -0.1820 0.0000 -0.1084 0.0000 -0.7047 0.0000# oc-c2-c3m-oc -63 -0.6732 0.0000 -0.4778 0.0000 -0.1670 0.0000# c2-c3m-oc-ho -64 0.1863 0.0000 -0.4338 0.0000 -0.2121 0.0000# hc-c3m-oc-ho -65 -0.6732 0.0000 -0.4778 0.0000 -0.1670 0.0000# ho-oc-c3-c2 -66 0.1863 0.0000 -0.4338 0.0000 -0.2121 0.0000# ho-oc-c3-hc +1 cp-cp-cp-oc +2 cp-cp-cp-hc +3 cp-cp-cp-c +4 c2-na-c2-hn +5 c2-na-hn-hn +6 zero6 +7 zero7 +8 zero8 +9 zero9 +10 zero10 +11 zero11 +12 zero12 +13 zero13 +14 zero14 +15 zero15 +16 zero16 +17 zero17 +18 zero18 +19 zero19 +20 zero20 +21 zero21 +22 c2-na-c2-c2 -Improper Coeffs # class2 +Masses -1 13.0421 0.0000 # cp-cp-cp-oc -2 4.8912 0.0000 # cp-cp-cp-hc -3 7.8153 0.0000 # cp-cp-cp-c -4 0.0000 0.0000 # c2-na-c2-hn -5 0.0000 0.0000 # c2-na-hn-hn -6 0.0000 0.0000 -7 0.0000 0.0000 -8 0.0000 0.0000 -9 0.0000 0.0000 -10 0.0000 0.0000 -11 0.0000 0.0000 -12 0.0000 0.0000 -13 0.0000 0.0000 -14 0.0000 0.0000 -15 0.0000 0.0000 -16 0.0000 0.0000 -17 0.0000 0.0000 -18 0.0000 0.0000 -19 0.0000 0.0000 -20 0.0000 0.0000 -21 0.0000 0.0000 -22 0.0000 0.0000 # c2-na-c2-c2 +1 12.011150 +2 12.011150 +3 15.999400 +4 12.011150 +5 12.011150 +6 12.011150 +7 15.999400 +8 1.007970 +9 14.006700 +10 1.007970 +11 1.007970 -BondBond Coeffs +Pair Coeffs # lj/class2/coul/long -1 3.3872 1.5300 1.1010 -2 5.3316 1.1010 1.1010 -3 23.1979 1.4200 1.1010 -4 11.4318 1.5300 1.4200 -5 11.4318 1.5300 1.4200 -6 0.0000 1.5300 1.5300 -7 3.3872 1.5300 1.1010 -8 11.4318 1.5300 1.4200 -9 23.1979 1.4200 1.1010 -10 3.3872 1.5300 1.1010 -11 5.3316 1.1010 1.1010 -12 -7.1131 1.4200 1.4200 -13 68.2856 1.4170 1.4170 -14 48.4754 1.4170 1.3768 -15 1.0795 1.4170 1.0982 -16 12.0676 1.4170 1.5010 -17 0.0000 1.5010 1.5300 -18 0.0000 1.5010 1.5010 -19 0.0000 1.5300 1.5300 -20 3.3872 1.5300 1.1010 -21 5.3316 1.1010 1.1010 -22 0.0000 1.4200 1.3768 -23 -2.1113 1.4570 1.4570 -24 -6.4168 1.4570 1.0060 -25 4.6217 1.5300 1.4570 -26 12.4260 1.1010 1.4570 -27 3.3872 1.5300 1.1010 -28 -1.8749 1.0060 1.0060 -29 0.0000 1.5300 1.5300 -30 3.3872 1.5300 1.1010 -31 4.6217 1.5300 1.4570 -32 0.0000 1.5300 1.5300 -33 3.3872 1.5300 1.1010 -34 11.4318 1.5300 1.4200 -35 23.1979 1.4200 1.1010 -36 11.4318 1.5300 1.4200 -37 -9.6879 1.4200 0.9650 -38 23.1979 1.1010 1.4200 -39 3.3872 1.1010 1.5300 -40 11.4318 1.4200 1.5300 -41 3.3872 1.1010 1.5300 -42 4.6217 1.5300 1.4570 -43 0.0000 1.5300 1.5300 -44 11.4318 1.5300 1.4200 -45 23.1979 1.4200 1.1010 -46 -9.6879 1.4200 0.9650 -47 4.6217 1.4570 1.5300 -48 3.3872 1.1010 1.5300 -49 11.4318 1.4200 1.5300 -50 -9.6879 0.9650 1.4200 +1 0.0540000000 4.0100000000 +2 0.0540000000 4.0100000000 +3 0.2400000000 3.5350000000 +4 0.0640000000 4.0100000000 +5 0.0540000000 4.0100000000 +6 0.0540000000 4.0100000000 +7 0.2400000000 3.5350000000 +8 0.0200000000 2.7000000000 +9 0.0650000000 4.0700000000 +10 0.0130000000 1.0980000000 +11 0.0130000000 1.0980000000 -BondAngle Coeffs +Bond Coeffs # class2 -1 20.7540 11.4210 1.5300 1.1010 -2 18.1030 18.1030 1.1010 1.1010 -3 55.3270 4.6189 1.4200 1.1010 -4 2.6868 20.4033 1.5300 1.4200 -5 2.6868 20.4033 1.5300 1.4200 -6 8.0160 8.0160 1.5300 1.5300 -7 20.7540 11.4210 1.5300 1.1010 -8 2.6868 20.4033 1.5300 1.4200 -9 55.3270 4.6189 1.4200 1.1010 -10 20.7540 11.4210 1.5300 1.1010 -11 18.1030 18.1030 1.1010 1.1010 -12 -2.8112 -2.8112 1.4200 1.4200 -13 28.8708 28.8708 1.4170 1.4170 -14 58.4790 107.6806 1.4170 1.3768 -15 20.0033 24.2183 1.4170 1.0982 -16 31.0771 47.0579 1.4170 1.5010 -17 0.0000 0.0000 1.5010 1.5300 -18 0.0000 0.0000 1.5010 1.5010 -19 8.0160 8.0160 1.5300 1.5300 -20 20.7540 11.4210 1.5300 1.1010 -21 18.1030 18.1030 1.1010 1.1010 -22 0.0000 0.0000 1.4200 1.3768 -23 -7.2229 -7.2229 1.4570 1.4570 -24 31.8096 20.5799 1.4570 1.0060 -25 6.0876 16.5702 1.5300 1.4570 -26 13.4582 42.4332 1.1010 1.4570 -27 20.7540 11.4210 1.5300 1.1010 -28 28.0322 28.0322 1.0060 1.0060 -29 8.0160 8.0160 1.5300 1.5300 -30 20.7540 11.4210 1.5300 1.1010 -31 6.0876 16.5702 1.5300 1.4570 -32 8.0160 8.0160 1.5300 1.5300 -33 20.7540 11.4210 1.5300 1.1010 -34 2.6868 20.4033 1.5300 1.4200 -35 55.3270 4.6189 1.4200 1.1010 -36 2.6868 20.4033 1.5300 1.4200 -37 28.5800 18.9277 1.4200 0.9650 -38 4.6189 55.3270 1.1010 1.4200 -39 11.4210 20.7540 1.1010 1.5300 -40 20.4033 2.6868 1.4200 1.5300 -41 11.4210 20.7540 1.1010 1.5300 -42 6.0876 16.5702 1.5300 1.4570 -43 8.0160 8.0160 1.5300 1.5300 -44 2.6868 20.4033 1.5300 1.4200 -45 55.3270 4.6189 1.4200 1.1010 -46 28.5800 18.9277 1.4200 0.9650 -47 16.5702 6.0876 1.4570 1.5300 -48 11.4210 20.7540 1.1010 1.5300 -49 20.4033 2.6868 1.4200 1.5300 -50 18.9277 28.5800 0.9650 1.4200 +1 1.1010 345.0000 -691.8900 844.6000 +2 1.5300 299.6700 -501.7700 679.8100 +3 1.4200 400.3954 -835.1951 1313.0142 +4 1.4200 400.3954 -835.1951 1313.0142 +5 1.5300 299.6700 -501.7700 679.8100 +6 1.1010 345.0000 -691.8900 844.6000 +7 1.4170 470.8361 -627.6179 1327.6345 +8 1.3768 428.8798 -738.2351 1114.9655 +9 1.0982 372.8251 -803.4526 894.3173 +10 1.5010 321.9021 -521.8208 572.1628 +11 1.5300 299.6700 -501.7700 679.8100 +12 1.1010 345.0000 -691.8900 844.6000 +13 1.4570 365.8052 -699.6368 998.4842 +14 1.0060 466.7400 -1073.6018 1251.1056 +15 1.5300 299.6700 -501.7700 679.8100 +16 1.5300 299.6700 -501.7700 679.8100 +17 1.4200 400.3954 -835.1951 1313.0142 +18 0.9650 532.5062 -1282.9050 2004.7658 +19 1.4200 400.3954 -835.1951 1313.0142 -AngleAngle Coeffs +Angle Coeffs # class2 -1 0.0000 0.0000 0.0000 118.9000 123.4200 123.4200 -2 0.0000 0.0000 0.0000 118.9000 117.9400 117.9400 -3 0.0000 0.0000 0.0000 118.9000 120.0500 120.0500 -4 0.0000 0.0000 0.0000 112.4436 110.9538 110.9538 -5 0.0000 0.0000 0.0000 110.9538 107.0671 110.9538 -6 0.2738 -0.4825 0.2738 110.7700 107.6600 110.7700 -7 0.1689 2.5926 3.9177 111.2700 108.7280 110.7700 -8 2.4259 2.1283 2.4259 108.7280 107.6600 108.7280 -9 -0.8330 -0.8330 -3.5744 112.6700 111.2700 111.2700 -10 0.1689 2.5926 3.9177 111.2700 108.7280 110.7700 -11 -1.3199 -1.3199 0.1184 112.6700 110.7700 110.7700 -12 0.1689 2.5926 3.9177 111.2700 108.7280 110.7700 -13 0.2738 -0.4825 0.2738 110.7700 107.6600 110.7700 -14 2.4259 2.1283 2.4259 108.7280 107.6600 108.7280 -15 0.0000 0.0000 0.0000 108.4000 112.6700 108.4000 -16 0.0000 0.0000 0.0000 111.0000 108.4000 108.4000 -17 0.2738 -0.4825 0.2738 110.7700 107.6600 110.7700 -18 -0.3157 -0.3157 -0.3157 107.6600 107.6600 107.6600 -19 2.4286 0.5381 -2.5301 110.7700 110.6204 111.9100 -20 2.4321 2.4321 -3.5496 107.6600 110.6204 110.6204 -21 0.2738 -0.4825 0.2738 110.7700 107.6600 110.7700 -22 0.0000 0.0000 0.0000 112.4436 112.4436 112.4436 +1 110.7700 41.4530 -10.6040 5.1290 +2 107.6600 39.6410 -12.9210 -2.4318 +3 108.7280 58.5446 -10.8088 -12.4006 +4 111.2700 54.5381 -8.3642 -13.0838 +5 111.2700 54.5381 -8.3642 -13.0838 +6 112.6700 39.5160 -7.4430 -9.5583 +7 110.7700 41.4530 -10.6040 5.1290 +8 111.2700 54.5381 -8.3642 -13.0838 +9 108.7280 58.5446 -10.8088 -12.4006 +10 110.7700 41.4530 -10.6040 5.1290 +11 107.6600 39.6410 -12.9210 -2.4318 +12 104.5000 35.7454 -10.0067 -6.2729 +13 118.9000 61.0226 -34.9931 0.0000 +14 123.4200 73.6781 -21.6787 0.0000 +15 117.9400 35.1558 -12.4682 0.0000 +16 120.0500 44.7148 -22.7352 0.0000 +17 108.4000 43.9594 -8.3924 -9.3379 +18 111.0000 44.3234 -9.4454 0.0000 +19 112.6700 39.5160 -7.4430 -9.5583 +20 110.7700 41.4530 -10.6040 5.1290 +21 107.6600 39.6410 -12.9210 -2.4318 +22 102.9695 38.9739 -6.2595 -8.1710 +23 112.4436 47.2337 -10.6612 -10.2062 +24 110.9538 50.8652 -4.4522 -10.0298 +25 111.9100 60.7147 -13.3366 -13.0785 +26 110.6204 51.3137 -6.7198 -2.6003 +27 110.7700 41.4530 -10.6040 5.1290 +28 107.0671 45.2520 -7.5558 -9.5120 +29 112.6700 39.5160 -7.4430 -9.5583 +30 110.7700 41.4530 -10.6040 5.1290 +31 111.9100 60.7147 -13.3366 -13.0785 +32 112.6700 39.5160 -7.4430 -9.5583 +33 110.7700 41.4530 -10.6040 5.1290 +34 111.2700 54.5381 -8.3642 -13.0838 +35 108.7280 58.5446 -10.8088 -12.4006 +36 111.2700 54.5381 -8.3642 -13.0838 +37 105.8000 52.7061 -12.1090 -9.8681 +38 108.7280 58.5446 -10.8088 -12.4006 +39 110.7700 41.4530 -10.6040 5.1290 +40 111.2700 54.5381 -8.3642 -13.0838 +41 110.7700 41.4530 -10.6040 5.1290 +42 111.9100 60.7147 -13.3366 -13.0785 +43 112.6700 39.5160 -7.4430 -9.5583 +44 111.2700 54.5381 -8.3642 -13.0838 +45 108.7280 58.5446 -10.8088 -12.4006 +46 105.8000 52.7061 -12.1090 -9.8681 +47 111.9100 60.7147 -13.3366 -13.0785 +48 110.7700 41.4530 -10.6040 5.1290 +49 111.2700 54.5381 -8.3642 -13.0838 +50 105.8000 52.7061 -12.1090 -9.8681 -AngleAngleTorsion Coeffs +Dihedral Coeffs # class2 -1 -20.2006 110.7700 111.2700 -2 -16.1640 110.7700 112.6700 -3 -12.5640 110.7700 110.7700 -4 -14.0484 111.2700 111.2700 -5 -29.0420 111.2700 112.6700 -6 -20.2006 111.2700 110.7700 -7 0.0000 108.7280 102.9695 -8 0.0000 111.2700 102.9695 -9 -19.0059 111.2700 104.5000 -10 -16.4438 108.7280 104.5000 -11 -29.0420 112.6700 111.2700 -12 -16.1640 112.6700 110.7700 -13 -20.2006 111.2700 110.7700 -14 -12.5640 110.7700 110.7700 -15 0.0000 118.9000 118.9000 -16 -4.8141 118.9000 117.9400 -17 -21.0247 118.9000 123.4200 -18 4.2296 123.4200 117.9400 -19 0.0000 123.4200 102.9695 -20 0.3598 117.9400 117.9400 -21 -14.4097 118.9000 120.0500 -22 4.4444 120.0500 117.9400 -23 0.0000 120.0500 108.4000 -24 0.0000 120.0500 111.0000 -25 0.0000 108.4000 110.7700 -26 -16.1640 112.6700 110.7700 -27 -24.3818 111.9100 112.4436 -28 -12.5567 110.6204 112.4436 -29 -7.5499 111.9100 110.9538 -30 -10.4258 110.6204 110.9538 -31 -11.2307 111.9100 111.9100 -32 -15.7572 110.7700 111.9100 -33 -12.5640 110.7700 110.7700 -34 -29.0420 112.6700 111.2700 -35 -16.1640 112.6700 110.7700 -36 -14.0484 111.2700 111.2700 -37 -20.2006 111.2700 110.7700 -38 -20.2006 110.7700 111.2700 -39 -12.5640 110.7700 110.7700 -40 -16.1640 110.7700 112.6700 -41 -12.5640 110.7700 110.7700 -42 -20.2006 110.7700 111.2700 -43 -27.3953 111.9100 112.6700 -44 -15.7572 111.9100 110.7700 -45 0.0000 111.9100 111.2700 -46 -24.3818 111.9100 112.4436 -47 -7.5499 111.9100 110.9538 -48 -29.0420 111.2700 112.6700 -49 -20.2006 111.2700 110.7700 -50 -14.0484 111.2700 111.2700 -51 0.0000 111.2700 102.9695 -52 -12.1038 111.2700 105.8000 -53 -10.5093 108.7280 105.8000 -54 -20.2006 110.7700 111.2700 -55 -16.1640 110.7700 112.6700 -56 -20.2006 110.7700 111.2700 -57 -27.3953 111.9100 112.6700 -58 -15.7572 111.9100 110.7700 -59 0.0000 111.9100 111.2700 -60 -24.3818 111.9100 112.4436 -61 -29.0420 111.2700 112.6700 -62 -14.0484 111.2700 111.2700 -63 -12.1038 111.2700 105.8000 -64 -10.5093 108.7280 105.8000 -65 -12.1038 105.8000 111.2700 -66 -10.5093 105.8000 108.7280 +1 -0.1435 0.0000 0.2530 0.0000 -0.0905 0.0000 +2 0.0000 0.0000 0.0316 0.0000 -0.1681 0.0000 +3 -0.1432 0.0000 0.0617 0.0000 -0.1083 0.0000 +4 -0.1820 0.0000 -0.1084 0.0000 -0.7047 0.0000 +5 0.7137 0.0000 0.2660 0.0000 -0.2545 0.0000 +6 -0.1435 0.0000 0.2530 0.0000 -0.0905 0.0000 +7 0.9513 0.0000 0.1155 0.0000 0.0720 0.0000 +8 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 +9 -0.5203 0.0000 -0.3028 0.0000 -0.3450 0.0000 +10 0.5302 0.0000 0.0000 0.0000 -0.3966 0.0000 +11 0.7137 0.0000 0.2660 0.0000 -0.2545 0.0000 +12 0.0000 0.0000 0.0316 0.0000 -0.1681 0.0000 +13 -0.1435 0.0000 0.2530 0.0000 -0.0905 0.0000 +14 -0.1432 0.0000 0.0617 0.0000 -0.1083 0.0000 +15 8.3667 0.0000 1.1932 0.0000 0.0000 0.0000 +16 0.0000 0.0000 3.9661 0.0000 0.0000 0.0000 +17 0.0000 0.0000 4.8498 0.0000 0.0000 0.0000 +18 0.0000 0.0000 1.7234 0.0000 0.0000 0.0000 +19 0.0000 0.0000 1.5000 0.0000 0.0000 0.0000 +20 0.0000 0.0000 1.8769 0.0000 0.0000 0.0000 +21 0.0000 0.0000 4.4072 0.0000 0.0000 0.0000 +22 0.0000 0.0000 1.5590 0.0000 0.0000 0.0000 +23 -0.2802 0.0000 -0.0678 0.0000 -0.0122 0.0000 +24 -0.2802 0.0000 -0.0678 0.0000 -0.0122 0.0000 +25 -0.0228 0.0000 0.0280 0.0000 -0.1863 0.0000 +26 0.0000 0.0000 0.0316 0.0000 -0.1681 0.0000 +27 -0.1406 0.0000 0.4168 0.0000 0.0150 0.0000 +28 0.1904 0.0000 -0.1342 0.0000 -0.2460 0.0000 +29 -1.1506 0.0000 -0.6344 0.0000 -0.1845 0.0000 +30 -0.5187 0.0000 -0.4837 0.0000 -0.1692 0.0000 +31 0.3805 0.0000 0.3547 0.0000 -0.1102 0.0000 +32 -0.2428 0.0000 0.4065 0.0000 -0.3079 0.0000 +33 -0.1432 0.0000 0.0617 0.0000 -0.1083 0.0000 +34 0.7137 0.0000 0.2660 0.0000 -0.2545 0.0000 +35 0.0000 0.0000 0.0316 0.0000 -0.1681 0.0000 +36 -0.1820 0.0000 -0.1084 0.0000 -0.7047 0.0000 +37 -0.1435 0.0000 0.2530 0.0000 -0.0905 0.0000 +38 -0.1435 0.0000 0.2530 0.0000 -0.0905 0.0000 +39 -0.1432 0.0000 0.0617 0.0000 -0.1083 0.0000 +40 0.0000 0.0000 0.0316 0.0000 -0.1681 0.0000 +41 -0.1432 0.0000 0.0617 0.0000 -0.1083 0.0000 +42 -0.1435 0.0000 0.2530 0.0000 -0.0905 0.0000 +43 0.1764 0.0000 0.1766 0.0000 -0.5206 0.0000 +44 -0.2428 0.0000 0.4065 0.0000 -0.3079 0.0000 +45 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 +46 -0.1406 0.0000 0.4168 0.0000 0.0150 0.0000 +47 -1.1506 0.0000 -0.6344 0.0000 -0.1845 0.0000 +48 0.7137 0.0000 0.2660 0.0000 -0.2545 0.0000 +49 -0.1435 0.0000 0.2530 0.0000 -0.0905 0.0000 +50 -0.1820 0.0000 -0.1084 0.0000 -0.7047 0.0000 +51 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 +52 -0.6732 0.0000 -0.4778 0.0000 -0.1670 0.0000 +53 0.1863 0.0000 -0.4338 0.0000 -0.2121 0.0000 +54 -0.1435 0.0000 0.2530 0.0000 -0.0905 0.0000 +55 0.0000 0.0000 0.0316 0.0000 -0.1681 0.0000 +56 -0.1435 0.0000 0.2530 0.0000 -0.0905 0.0000 +57 0.1764 0.0000 0.1766 0.0000 -0.5206 0.0000 +58 -0.2428 0.0000 0.4065 0.0000 -0.3079 0.0000 +59 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 +60 -0.1406 0.0000 0.4168 0.0000 0.0150 0.0000 +61 0.7137 0.0000 0.2660 0.0000 -0.2545 0.0000 +62 -0.1820 0.0000 -0.1084 0.0000 -0.7047 0.0000 +63 -0.6732 0.0000 -0.4778 0.0000 -0.1670 0.0000 +64 0.1863 0.0000 -0.4338 0.0000 -0.2121 0.0000 +65 -0.6732 0.0000 -0.4778 0.0000 -0.1670 0.0000 +66 0.1863 0.0000 -0.4338 0.0000 -0.2121 0.0000 -EndBondTorsion Coeffs +Improper Coeffs # class2 -1 0.9681 0.9551 0.0436 0.5903 0.6669 0.8584 1.1010 1.4200 -2 0.0814 0.0591 0.2219 0.2486 0.2422 -0.0925 1.1010 1.5300 -3 0.2130 0.3120 0.0777 0.2130 0.3120 0.0777 1.1010 1.1010 -4 1.0165 0.7553 -0.4609 1.0165 0.7553 -0.4609 1.4200 1.4200 -5 1.1538 0.8409 -0.9138 -0.3190 0.4411 -0.7174 1.4200 1.5300 -6 0.5903 0.6669 0.8584 0.9681 0.9551 0.0436 1.4200 1.1010 -7 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.1010 1.3768 -8 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.5300 1.3768 -9 -0.2456 1.0517 -0.7795 0.4741 1.2635 0.5576 1.5300 1.4200 -10 -0.6054 1.3339 0.9648 -0.1620 0.1564 -1.1408 1.1010 1.4200 -11 -0.3190 0.4411 -0.7174 1.1538 0.8409 -0.9138 1.5300 1.4200 -12 0.2486 0.2422 -0.0925 0.0814 0.0591 0.2219 1.5300 1.1010 -13 0.5903 0.6669 0.8584 0.9681 0.9551 0.0436 1.4200 1.1010 -14 0.2130 0.3120 0.0777 0.2130 0.3120 0.0777 1.1010 1.1010 -15 -0.1185 6.3204 0.0000 -0.1185 6.3204 0.0000 1.4170 1.4170 -16 0.0000 -6.8958 0.0000 0.0000 -0.4669 0.0000 1.4170 1.0982 -17 0.0000 0.2655 0.0000 0.0000 4.8905 0.0000 1.4170 1.3768 -18 0.0000 4.2641 0.0000 0.0000 -1.5867 0.0000 1.3768 1.0982 -19 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.4170 1.4200 -20 0.0000 -0.6890 0.0000 0.0000 -0.6890 0.0000 1.0982 1.0982 -21 0.0000 -0.6918 0.0000 0.0000 0.2421 0.0000 1.4170 1.5010 -22 0.0000 -1.7970 0.0000 0.0000 -0.4879 0.0000 1.5010 1.0982 -23 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.4170 1.5300 -24 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.4170 1.5010 -25 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.5010 1.1010 -26 0.2486 0.2422 -0.0925 0.0814 0.0591 0.2219 1.5300 1.1010 -27 0.0997 -0.0046 -0.2657 -0.0128 -0.0495 -0.1079 1.5300 1.4570 -28 -0.5892 0.7140 0.3505 0.0628 0.0873 -0.0882 1.1010 1.4570 -29 -0.9466 0.9356 -0.5542 0.0570 0.0625 0.4112 1.5300 1.0060 -30 -1.1685 0.9266 -0.0993 0.0850 0.3061 0.2104 1.1010 1.0060 -31 0.0286 0.0566 -0.0493 0.0286 0.0566 -0.0493 1.4570 1.4570 -32 0.1960 0.7056 0.1120 0.1022 0.2090 0.6433 1.1010 1.4570 -33 0.2130 0.3120 0.0777 0.2130 0.3120 0.0777 1.1010 1.1010 -34 -0.3190 0.4411 -0.7174 1.1538 0.8409 -0.9138 1.5300 1.4200 -35 0.2486 0.2422 -0.0925 0.0814 0.0591 0.2219 1.5300 1.1010 -36 1.0165 0.7553 -0.4609 1.0165 0.7553 -0.4609 1.4200 1.4200 -37 0.5903 0.6669 0.8584 0.9681 0.9551 0.0436 1.4200 1.1010 -38 0.9681 0.9551 0.0436 0.5903 0.6669 0.8584 1.1010 1.4200 -39 0.2130 0.3120 0.0777 0.2130 0.3120 0.0777 1.1010 1.1010 -40 0.0814 0.0591 0.2219 0.2486 0.2422 -0.0925 1.1010 1.5300 -41 0.2130 0.3120 0.0777 0.2130 0.3120 0.0777 1.1010 1.1010 -42 0.9681 0.9551 0.0436 0.5903 0.6669 0.8584 1.1010 1.4200 -43 0.0579 -0.0043 -0.1906 0.1032 0.5896 -0.4836 1.4570 1.5300 -44 0.1022 0.2090 0.6433 0.1960 0.7056 0.1120 1.4570 1.1010 -45 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.4570 1.4200 -46 0.0997 -0.0046 -0.2657 -0.0128 -0.0495 -0.1079 1.5300 1.4570 -47 -0.9466 0.9356 -0.5542 0.0570 0.0625 0.4112 1.5300 1.0060 -48 1.1538 0.8409 -0.9138 -0.3190 0.4411 -0.7174 1.4200 1.5300 -49 0.5903 0.6669 0.8584 0.9681 0.9551 0.0436 1.4200 1.1010 -50 1.0165 0.7553 -0.4609 1.0165 0.7553 -0.4609 1.4200 1.4200 -51 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.5300 1.3768 -52 -0.5800 0.9004 0.0000 0.0000 0.5343 0.9025 1.5300 0.9650 -53 -1.7554 1.3145 0.2263 0.2493 0.6803 0.0000 1.1010 0.9650 -54 0.9681 0.9551 0.0436 0.5903 0.6669 0.8584 1.1010 1.4200 -55 0.0814 0.0591 0.2219 0.2486 0.2422 -0.0925 1.1010 1.5300 -56 0.9681 0.9551 0.0436 0.5903 0.6669 0.8584 1.1010 1.4200 -57 0.0579 -0.0043 -0.1906 0.1032 0.5896 -0.4836 1.4570 1.5300 -58 0.1022 0.2090 0.6433 0.1960 0.7056 0.1120 1.4570 1.1010 -59 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.4570 1.4200 -60 0.0997 -0.0046 -0.2657 -0.0128 -0.0495 -0.1079 1.5300 1.4570 -61 1.1538 0.8409 -0.9138 -0.3190 0.4411 -0.7174 1.4200 1.5300 -62 1.0165 0.7553 -0.4609 1.0165 0.7553 -0.4609 1.4200 1.4200 -63 -0.5800 0.9004 0.0000 0.0000 0.5343 0.9025 1.5300 0.9650 -64 -1.7554 1.3145 0.2263 0.2493 0.6803 0.0000 1.1010 0.9650 -65 0.0000 0.5343 0.9025 -0.5800 0.9004 0.0000 0.9650 1.5300 -66 0.2493 0.6803 0.0000 -1.7554 1.3145 0.2263 0.9650 1.1010 +1 13.0421 0.0000 # cp-cp-cp-oc +2 4.8912 0.0000 # cp-cp-cp-hc +3 7.8153 0.0000 # cp-cp-cp-c +4 0.0000 0.0000 # c2-na-c2-hn +5 0.0000 0.0000 # c2-na-hn-hn +6 0.0000 0.0000 +7 0.0000 0.0000 +8 0.0000 0.0000 +9 0.0000 0.0000 +10 0.0000 0.0000 +11 0.0000 0.0000 +12 0.0000 0.0000 +13 0.0000 0.0000 +14 0.0000 0.0000 +15 0.0000 0.0000 +16 0.0000 0.0000 +17 0.0000 0.0000 +18 0.0000 0.0000 +19 0.0000 0.0000 +20 0.0000 0.0000 +21 0.0000 0.0000 +22 0.0000 0.0000 # c2-na-c2-c2 -MiddleBondTorsion Coeffs +BondBond Coeffs -1 -16.7975 -1.2296 -0.2750 1.5300 -2 -14.8790 -3.6581 -0.3138 1.5300 -3 -14.2610 -0.5322 -0.4864 1.5300 -4 -17.2585 -3.6157 -0.8364 1.5300 -5 -21.8842 -7.6764 -0.6868 1.5300 -6 -16.7975 -1.2296 -0.2750 1.5300 -7 0.0000 0.0000 0.0000 1.4200 -8 0.0000 0.0000 0.0000 1.4200 -9 -5.9288 -2.7007 -0.3175 1.4200 -10 -6.8007 -4.6546 -1.4101 1.4200 -11 -21.8842 -7.6764 -0.6868 1.5300 -12 -14.8790 -3.6581 -0.3138 1.5300 -13 -16.7975 -1.2296 -0.2750 1.5300 -14 -14.2610 -0.5322 -0.4864 1.5300 -15 27.5989 -2.3120 0.0000 1.4170 -16 0.0000 -1.1521 0.0000 1.4170 -17 0.0000 4.8255 0.0000 1.4170 -18 0.0000 5.5432 0.0000 1.4170 -19 0.0000 0.0000 0.0000 1.3768 -20 0.0000 4.8228 0.0000 1.4170 -21 0.0000 9.1792 0.0000 1.4170 -22 0.0000 3.9421 0.0000 1.4170 -23 0.0000 0.0000 0.0000 1.5010 -24 0.0000 0.0000 0.0000 1.5010 -25 0.0000 0.0000 0.0000 1.5300 -26 -14.8790 -3.6581 -0.3138 1.5300 -27 -8.0036 -7.7321 -3.0640 1.4570 -28 -6.4529 -6.8122 -1.1632 1.4570 -29 -2.2208 0.5479 -0.3527 1.4570 -30 -3.4611 1.6996 -0.6007 1.4570 -31 -3.3497 1.0143 -3.0062 1.5300 -32 -10.4959 -0.7647 -0.0545 1.5300 -33 -14.2610 -0.5322 -0.4864 1.5300 -34 -21.8842 -7.6764 -0.6868 1.5300 -35 -14.8790 -3.6581 -0.3138 1.5300 -36 -17.2585 -3.6157 -0.8364 1.5300 -37 -16.7975 -1.2296 -0.2750 1.5300 -38 -16.7975 -1.2296 -0.2750 1.5300 -39 -14.2610 -0.5322 -0.4864 1.5300 -40 -14.8790 -3.6581 -0.3138 1.5300 -41 -14.2610 -0.5322 -0.4864 1.5300 -42 -16.7975 -1.2296 -0.2750 1.5300 -43 -15.4174 -7.3055 -1.0749 1.5300 -44 -10.4959 -0.7647 -0.0545 1.5300 -45 0.0000 0.0000 0.0000 1.5300 -46 -8.0036 -7.7321 -3.0640 1.4570 -47 -2.2208 0.5479 -0.3527 1.4570 -48 -21.8842 -7.6764 -0.6868 1.5300 -49 -16.7975 -1.2296 -0.2750 1.5300 -50 -17.2585 -3.6157 -0.8364 1.5300 -51 0.0000 0.0000 0.0000 1.4200 -52 1.2472 0.0000 0.7485 1.4200 -53 0.0000 0.9241 -0.5889 1.4200 -54 -16.7975 -1.2296 -0.2750 1.5300 -55 -14.8790 -3.6581 -0.3138 1.5300 -56 -16.7975 -1.2296 -0.2750 1.5300 -57 -15.4174 -7.3055 -1.0749 1.5300 -58 -10.4959 -0.7647 -0.0545 1.5300 -59 0.0000 0.0000 0.0000 1.5300 -60 -8.0036 -7.7321 -3.0640 1.4570 -61 -21.8842 -7.6764 -0.6868 1.5300 -62 -17.2585 -3.6157 -0.8364 1.5300 -63 1.2472 0.0000 0.7485 1.4200 -64 0.0000 0.9241 -0.5889 1.4200 -65 1.2472 0.0000 0.7485 1.4200 -66 0.0000 0.9241 -0.5889 1.4200 +1 3.3872 1.5300 1.1010 +2 5.3316 1.1010 1.1010 +3 23.1979 1.4200 1.1010 +4 11.4318 1.5300 1.4200 +5 11.4318 1.5300 1.4200 +6 0.0000 1.5300 1.5300 +7 3.3872 1.5300 1.1010 +8 11.4318 1.5300 1.4200 +9 23.1979 1.4200 1.1010 +10 3.3872 1.5300 1.1010 +11 5.3316 1.1010 1.1010 +12 -7.1131 1.4200 1.4200 +13 68.2856 1.4170 1.4170 +14 48.4754 1.4170 1.3768 +15 1.0795 1.4170 1.0982 +16 12.0676 1.4170 1.5010 +17 0.0000 1.5010 1.5300 +18 0.0000 1.5010 1.5010 +19 0.0000 1.5300 1.5300 +20 3.3872 1.5300 1.1010 +21 5.3316 1.1010 1.1010 +22 0.0000 1.4200 1.3768 +23 -2.1113 1.4570 1.4570 +24 -6.4168 1.4570 1.0060 +25 4.6217 1.5300 1.4570 +26 12.4260 1.1010 1.4570 +27 3.3872 1.5300 1.1010 +28 -1.8749 1.0060 1.0060 +29 0.0000 1.5300 1.5300 +30 3.3872 1.5300 1.1010 +31 4.6217 1.5300 1.4570 +32 0.0000 1.5300 1.5300 +33 3.3872 1.5300 1.1010 +34 11.4318 1.5300 1.4200 +35 23.1979 1.4200 1.1010 +36 11.4318 1.5300 1.4200 +37 -9.6879 1.4200 0.9650 +38 23.1979 1.1010 1.4200 +39 3.3872 1.1010 1.5300 +40 11.4318 1.4200 1.5300 +41 3.3872 1.1010 1.5300 +42 4.6217 1.5300 1.4570 +43 0.0000 1.5300 1.5300 +44 11.4318 1.5300 1.4200 +45 23.1979 1.4200 1.1010 +46 -9.6879 1.4200 0.9650 +47 4.6217 1.4570 1.5300 +48 3.3872 1.1010 1.5300 +49 11.4318 1.4200 1.5300 +50 -9.6879 0.9650 1.4200 -BondBond13 Coeffs +BondAngle Coeffs -1 0.0000 1.1010 1.4200 -2 0.0000 1.1010 1.5300 -3 0.0000 1.1010 1.1010 -4 0.0000 1.4200 1.4200 -5 0.0000 1.4200 1.5300 -6 0.0000 1.4200 1.1010 -7 0.0000 1.1010 1.3768 -8 0.0000 1.5300 1.3768 -9 0.0000 1.5300 1.4200 -10 0.0000 1.1010 1.4200 -11 0.0000 1.5300 1.4200 -12 0.0000 1.5300 1.1010 -13 0.0000 1.4200 1.1010 -14 0.0000 1.1010 1.1010 -15 53.0000 1.4170 1.4170 -16 -6.2741 1.4170 1.0982 -17 -2.2436 1.4170 1.3768 -18 2.0517 1.3768 1.0982 -19 0.0000 1.4170 1.4200 -20 -1.7077 1.0982 1.0982 -21 2.5085 1.4170 1.5010 -22 0.8743 1.5010 1.0982 -23 0.0000 1.4170 1.5300 -24 0.0000 1.4170 1.5010 -25 0.0000 1.5010 1.1010 -26 0.0000 1.5300 1.1010 -27 0.0000 1.5300 1.4570 -28 0.0000 1.1010 1.4570 -29 0.0000 1.5300 1.0060 -30 0.0000 1.1010 1.0060 -31 0.0000 1.4570 1.4570 -32 0.0000 1.1010 1.4570 -33 0.0000 1.1010 1.1010 -34 0.0000 1.5300 1.4200 -35 0.0000 1.5300 1.1010 -36 0.0000 1.4200 1.4200 -37 0.0000 1.4200 1.1010 -38 0.0000 1.1010 1.4200 -39 0.0000 1.1010 1.1010 -40 0.0000 1.1010 1.5300 -41 0.0000 1.1010 1.1010 -42 0.0000 1.1010 1.4200 -43 0.0000 1.4570 1.5300 -44 0.0000 1.4570 1.1010 -45 0.0000 1.4570 1.4200 -46 0.0000 1.5300 1.4570 -47 0.0000 1.5300 1.0060 -48 0.0000 1.4200 1.5300 -49 0.0000 1.4200 1.1010 -50 0.0000 1.4200 1.4200 -51 0.0000 1.5300 1.3768 -52 0.0000 1.5300 0.9650 -53 0.0000 1.1010 0.9650 -54 0.0000 1.1010 1.4200 -55 0.0000 1.1010 1.5300 -56 0.0000 1.1010 1.4200 -57 0.0000 1.4570 1.5300 -58 0.0000 1.4570 1.1010 -59 0.0000 1.4570 1.4200 -60 0.0000 1.5300 1.4570 -61 0.0000 1.4200 1.5300 -62 0.0000 1.4200 1.4200 -63 0.0000 1.5300 0.9650 -64 0.0000 1.1010 0.9650 -65 0.0000 0.9650 1.5300 -66 0.0000 0.9650 1.1010 +1 20.7540 11.4210 1.5300 1.1010 +2 18.1030 18.1030 1.1010 1.1010 +3 55.3270 4.6189 1.4200 1.1010 +4 2.6868 20.4033 1.5300 1.4200 +5 2.6868 20.4033 1.5300 1.4200 +6 8.0160 8.0160 1.5300 1.5300 +7 20.7540 11.4210 1.5300 1.1010 +8 2.6868 20.4033 1.5300 1.4200 +9 55.3270 4.6189 1.4200 1.1010 +10 20.7540 11.4210 1.5300 1.1010 +11 18.1030 18.1030 1.1010 1.1010 +12 -2.8112 -2.8112 1.4200 1.4200 +13 28.8708 28.8708 1.4170 1.4170 +14 58.4790 107.6806 1.4170 1.3768 +15 20.0033 24.2183 1.4170 1.0982 +16 31.0771 47.0579 1.4170 1.5010 +17 0.0000 0.0000 1.5010 1.5300 +18 0.0000 0.0000 1.5010 1.5010 +19 8.0160 8.0160 1.5300 1.5300 +20 20.7540 11.4210 1.5300 1.1010 +21 18.1030 18.1030 1.1010 1.1010 +22 0.0000 0.0000 1.4200 1.3768 +23 -7.2229 -7.2229 1.4570 1.4570 +24 31.8096 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+115 21 104 105 117 118 diff --git a/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized b/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized index b152dec00a..81a12b4ccb 100644 --- a/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized +++ b/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized @@ -19,14 +19,19 @@ dihedral_style class2 improper_style class2 -read_data tiny_nylon.data +read_data tiny_nylon.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 velocity all create 300.0 4928459 dist gaussian -molecule mol1 rxn1_stp1_unreacted.data_template -molecule mol2 rxn1_stp1_reacted.data_template -molecule mol3 rxn1_stp2_unreacted.data_template -molecule mol4 rxn1_stp2_reacted.data_template +molecule mol1 rxn1_stp1_unreacted.molecule_template +molecule mol2 rxn1_stp1_reacted.molecule_template +molecule mol3 rxn1_stp2_unreacted.molecule_template +molecule mol4 rxn1_stp2_reacted.molecule_template thermo 50 diff --git a/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized_variable_probability b/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized_variable_probability index e81fedc34a..515d4cb2f8 100644 --- a/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized_variable_probability +++ b/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized_variable_probability @@ -19,7 +19,12 @@ dihedral_style class2 improper_style class2 -read_data tiny_nylon.data +read_data tiny_nylon.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 variable runsteps equal 1000 variable prob1 equal step/v_runsteps*2+0.1 @@ -27,10 +32,10 @@ variable prob2 equal (step/v_runsteps)>0.5 velocity all create 300.0 4928459 dist gaussian -molecule mol1 rxn1_stp1_unreacted.data_template -molecule mol2 rxn1_stp1_reacted.data_template -molecule mol3 rxn1_stp2_unreacted.data_template -molecule mol4 rxn1_stp2_reacted.data_template +molecule mol1 rxn1_stp1_unreacted.molecule_template +molecule mol2 rxn1_stp1_reacted.molecule_template +molecule mol3 rxn1_stp2_unreacted.molecule_template +molecule mol4 rxn1_stp2_reacted.molecule_template thermo 50 diff --git a/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.unstabilized b/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.unstabilized index 1e5a493821..4891e9ebff 100644 --- a/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.unstabilized +++ b/examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.unstabilized @@ -19,14 +19,20 @@ dihedral_style class2 improper_style class2 -read_data tiny_nylon.data +read_data tiny_nylon.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 + velocity all create 300.0 4928459 dist gaussian -molecule mol1 rxn1_stp1_unreacted.data_template -molecule mol2 rxn1_stp1_reacted.data_template -molecule mol3 rxn1_stp2_unreacted.data_template -molecule mol4 rxn1_stp2_reacted.data_template +molecule mol1 rxn1_stp1_unreacted.molecule_template +molecule mol2 rxn1_stp1_reacted.molecule_template +molecule mol3 rxn1_stp2_unreacted.molecule_template +molecule mol4 rxn1_stp2_reacted.molecule_template thermo 50 diff --git a/examples/PACKAGES/reaction/tiny_nylon/log.22Apr20.tiny_nylon.stabilized_variable_probability.g++.1 b/examples/PACKAGES/reaction/tiny_nylon/log.22Apr20.tiny_nylon.stabilized_variable_probability.g++.1 deleted file mode 100644 index 57455b04f4..0000000000 --- a/examples/PACKAGES/reaction/tiny_nylon/log.22Apr20.tiny_nylon.stabilized_variable_probability.g++.1 +++ /dev/null @@ -1,201 +0,0 @@ -LAMMPS (15 Apr 2020) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) - using 1 OpenMP thread(s) per MPI task -# two monomer nylon example -# reaction produces a condensed water molecule - -units real - -boundary p p p - -atom_style full - -kspace_style pppm 1.0e-4 - -pair_style lj/class2/coul/long 8.5 - -angle_style class2 - -bond_style class2 - -dihedral_style class2 - -improper_style class2 - -read_data tiny_nylon.data - orthogonal box = (-25 -25 -25) to (25 25 25) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 44 atoms - reading velocities ... - 44 velocities - scanning bonds ... - 9 = max bonds/atom - scanning angles ... - 21 = max angles/atom - scanning dihedrals ... - 29 = max dihedrals/atom - scanning impropers ... - 29 = max impropers/atom - reading bonds ... - 42 bonds - reading angles ... - 74 angles - reading dihedrals ... - 100 dihedrals - reading impropers ... - 44 impropers - 4 = max # of 1-2 neighbors - 6 = max # of 1-3 neighbors - 12 = max # of 1-4 neighbors - 41 = max # of special neighbors - special bonds CPU = 0.000385045 secs - read_data CPU = 0.013443 secs - -variable runsteps equal 1000 -variable prob1 equal step/v_runsteps*2 -variable prob2 equal (step/v_runsteps)>0.5 - -velocity all create 300.0 4928459 dist gaussian - -molecule mol1 rxn1_stp1_unreacted.data_template -Read molecule template mol1: - 1 molecules - 18 atoms with max type 8 - 16 bonds with max type 14 - 25 angles with max type 28 - 23 dihedrals with max type 36 - 14 impropers with max type 11 -molecule mol2 rxn1_stp1_reacted.data_template -Read molecule template mol2: - 1 molecules - 18 atoms with max type 9 - 17 bonds with max type 13 - 31 angles with max type 27 - 39 dihedrals with max type 33 - 20 impropers with max type 1 -molecule mol3 rxn1_stp2_unreacted.data_template -Read molecule template mol3: - 1 molecules - 15 atoms with max type 9 - 14 bonds with max type 13 - 25 angles with max type 27 - 30 dihedrals with max type 33 - 16 impropers with max type 1 -molecule mol4 rxn1_stp2_reacted.data_template -Read molecule template mol4: - 1 molecules - 15 atoms with max type 11 - 13 bonds with max type 15 - 19 angles with max type 29 - 16 dihedrals with max type 32 - 10 impropers with max type 13 - -thermo 50 - -# dump 1 all xyz 1 test_vis.xyz - -fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 5.0 mol1 mol2 rxn1_stp1_map prob v_prob1 1234 react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map prob v_prob2 1234 -WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (src/REACTION/fix_bond_react.cpp:2051) -WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (src/REACTION/fix_bond_react.cpp:2051) -dynamic group bond_react_MASTER_group defined -dynamic group statted_grp_REACT defined - -fix 1 statted_grp_REACT nvt temp 300 300 100 - -# optionally, you can customize behavior of reacting atoms, -# by using the internally-created 'bond_react_MASTER_group', like so: -fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1 - -thermo_style custom step temp press density v_prob1 v_prob2 f_myrxns[1] f_myrxns[2] - -# restart 100 restart1 restart2 - -run ${runsteps} -run 1000 -PPPM initialization ... - using 12-bit tables for long-range coulomb (src/kspace.cpp:332) - G vector (1/distance) = 0.0534597 - grid = 2 2 2 - stencil order = 5 - estimated absolute RMS force accuracy = 0.0402256 - estimated relative force accuracy = 0.000121138 - using double precision FFTW3 - 3d grid and FFT values/proc = 343 8 -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 = 10 10 10 - 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 -WARNING: Inconsistent image flags (src/domain.cpp:812) -Per MPI rank memory allocation (min/avg/max) = 33.78 | 33.78 | 33.78 Mbytes -Step Temp Press Density v_prob1 v_prob2 f_myrxns[1] f_myrxns[2] - 0 300 346.78165 0.0034851739 0 0 0 0 - 50 262.63913 -492.10749 0.0034851739 0.1 0 1 0 - 100 766.52962 -29.714349 0.0034851739 0.2 0 1 0 - 150 503.86837 50.220304 0.0034851739 0.3 0 1 0 - 200 456.51295 12.312892 0.0034851739 0.4 0 1 0 - 250 391.54928 9.2335844 0.0034851739 0.5 0 1 0 - 300 336.6988 -47.193937 0.0034851739 0.6 0 1 0 - 350 254.06985 -9.2867898 0.0034851739 0.7 0 1 0 - 400 259.41098 -25.657321 0.0034851739 0.8 0 1 0 - 450 258.10364 22.5086 0.0034851739 0.9 0 1 0 - 500 272.13412 -6.5391448 0.0034851739 1 0 1 0 - 550 202.75504 54.658731 0.0034851739 1.1 1 1 1 - 600 344.79887 23.798478 0.0034851739 1.2 1 1 1 - 650 328.44488 -29.908484 0.0034851739 1.3 1 1 1 - 700 280.13593 -8.3223255 0.0034851739 1.4 1 1 1 - 750 300.67624 1.0632669 0.0034851739 1.5 1 1 1 - 800 376.64234 12.488392 0.0034851739 1.6 1 1 1 - 850 321.07642 19.814074 0.0034851739 1.7 1 1 1 - 900 332.23751 30.814079 0.0034851739 1.8 1 1 1 - 950 311.14029 5.7853136 0.0034851739 1.9 1 1 1 - 1000 253.14634 -37.560642 0.0034851739 2 1 1 1 -Loop time of 0.379454 on 1 procs for 1000 steps with 44 atoms - -Performance: 227.696 ns/day, 0.105 hours/ns, 2635.368 timesteps/s -99.6% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.069723 | 0.069723 | 0.069723 | 0.0 | 18.37 -Bond | 0.14802 | 0.14802 | 0.14802 | 0.0 | 39.01 -Kspace | 0.044252 | 0.044252 | 0.044252 | 0.0 | 11.66 -Neigh | 0.072359 | 0.072359 | 0.072359 | 0.0 | 19.07 -Comm | 0.0044748 | 0.0044748 | 0.0044748 | 0.0 | 1.18 -Output | 0.0022775 | 0.0022775 | 0.0022775 | 0.0 | 0.60 -Modify | 0.036509 | 0.036509 | 0.036509 | 0.0 | 9.62 -Other | | 0.00184 | | | 0.48 - -Nlocal: 44 ave 44 max 44 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 3 ave 3 max 3 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 722 ave 722 max 722 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 722 -Ave neighs/atom = 16.4091 -Ave special neighs/atom = 9.77273 -Neighbor list builds = 1000 -Dangerous builds = 0 - -# write_restart restart_longrun -# write_data restart_longrun.data - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:00 diff --git a/examples/PACKAGES/reaction/tiny_nylon/log.22Apr20.tiny_nylon.stabilized_variable_probability.g++.4 b/examples/PACKAGES/reaction/tiny_nylon/log.22Apr20.tiny_nylon.stabilized_variable_probability.g++.4 deleted file mode 100644 index b6dcdafc54..0000000000 --- a/examples/PACKAGES/reaction/tiny_nylon/log.22Apr20.tiny_nylon.stabilized_variable_probability.g++.4 +++ /dev/null @@ -1,201 +0,0 @@ -LAMMPS (15 Apr 2020) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) - using 1 OpenMP thread(s) per MPI task -# two monomer nylon example -# reaction produces a condensed water molecule - -units real - -boundary p p p - -atom_style full - -kspace_style pppm 1.0e-4 - -pair_style lj/class2/coul/long 8.5 - -angle_style class2 - -bond_style class2 - -dihedral_style class2 - -improper_style class2 - -read_data tiny_nylon.data - orthogonal box = (-25 -25 -25) to (25 25 25) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 44 atoms - reading velocities ... - 44 velocities - scanning bonds ... - 9 = max bonds/atom - scanning angles ... - 21 = max angles/atom - scanning dihedrals ... - 29 = max dihedrals/atom - scanning impropers ... - 29 = max impropers/atom - reading bonds ... - 42 bonds - reading angles ... - 74 angles - reading dihedrals ... - 100 dihedrals - reading impropers ... - 44 impropers - 4 = max # of 1-2 neighbors - 6 = max # of 1-3 neighbors - 12 = max # of 1-4 neighbors - 41 = max # of special neighbors - special bonds CPU = 0.000431282 secs - read_data CPU = 0.0129571 secs - -variable runsteps equal 1000 -variable prob1 equal step/v_runsteps*2 -variable prob2 equal (step/v_runsteps)>0.5 - -velocity all create 300.0 4928459 dist gaussian - -molecule mol1 rxn1_stp1_unreacted.data_template -Read molecule template mol1: - 1 molecules - 18 atoms with max type 8 - 16 bonds with max type 14 - 25 angles with max type 28 - 23 dihedrals with max type 36 - 14 impropers with max type 11 -molecule mol2 rxn1_stp1_reacted.data_template -Read molecule template mol2: - 1 molecules - 18 atoms with max type 9 - 17 bonds with max type 13 - 31 angles with max type 27 - 39 dihedrals with max type 33 - 20 impropers with max type 1 -molecule mol3 rxn1_stp2_unreacted.data_template -Read molecule template mol3: - 1 molecules - 15 atoms with max type 9 - 14 bonds with max type 13 - 25 angles with max type 27 - 30 dihedrals with max type 33 - 16 impropers with max type 1 -molecule mol4 rxn1_stp2_reacted.data_template -Read molecule template mol4: - 1 molecules - 15 atoms with max type 11 - 13 bonds with max type 15 - 19 angles with max type 29 - 16 dihedrals with max type 32 - 10 impropers with max type 13 - -thermo 50 - -# dump 1 all xyz 1 test_vis.xyz - -fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 5.0 mol1 mol2 rxn1_stp1_map prob v_prob1 1234 react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map prob v_prob2 1234 -WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (src/REACTION/fix_bond_react.cpp:2051) -WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (src/REACTION/fix_bond_react.cpp:2051) -dynamic group bond_react_MASTER_group defined -dynamic group statted_grp_REACT defined - -fix 1 statted_grp_REACT nvt temp 300 300 100 - -# optionally, you can customize behavior of reacting atoms, -# by using the internally-created 'bond_react_MASTER_group', like so: -fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1 - -thermo_style custom step temp press density v_prob1 v_prob2 f_myrxns[1] f_myrxns[2] - -# restart 100 restart1 restart2 - -run ${runsteps} -run 1000 -PPPM initialization ... - using 12-bit tables for long-range coulomb (src/kspace.cpp:332) - G vector (1/distance) = 0.0534597 - grid = 2 2 2 - stencil order = 5 - estimated absolute RMS force accuracy = 0.0402256 - estimated relative force accuracy = 0.000121138 - using double precision FFTW3 - 3d grid and FFT values/proc = 252 2 -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 = 10 10 10 - 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 -WARNING: Inconsistent image flags (src/domain.cpp:812) -Per MPI rank memory allocation (min/avg/max) = 33.66 | 33.88 | 34.43 Mbytes -Step Temp Press Density v_prob1 v_prob2 f_myrxns[1] f_myrxns[2] - 0 300 346.78165 0.0034851739 0 0 0 0 - 50 266.5092 -90.813802 0.0034851739 0.1 0 1 0 - 100 559.41271 -53.23688 0.0034851739 0.2 0 1 0 - 150 489.90516 31.555817 0.0034851739 0.3 0 1 0 - 200 326.18391 7.7889992 0.0034851739 0.4 0 1 0 - 250 339.78203 2.3919541 0.0034851739 0.5 0 1 0 - 300 370.90263 -32.01673 0.0034851739 0.6 0 1 0 - 350 294.07547 -5.4019813 0.0034851739 0.7 0 1 0 - 400 287.76477 12.254133 0.0034851739 0.8 0 1 0 - 450 293.36482 66.372956 0.0034851739 0.9 0 1 0 - 500 246.84496 26.132317 0.0034851739 1 0 1 0 - 550 253.08778 -15.350262 0.0034851739 1.1 1 1 1 - 600 358.83641 25.007371 0.0034851739 1.2 1 1 1 - 650 320.51492 -32.34823 0.0034851739 1.3 1 1 1 - 700 310.87976 -8.2306669 0.0034851739 1.4 1 1 1 - 750 307.54142 12.025818 0.0034851739 1.5 1 1 1 - 800 272.51724 -22.92823 0.0034851739 1.6 1 1 1 - 850 268.66181 10.069534 0.0034851739 1.7 1 1 1 - 900 265.5531 -10.471377 0.0034851739 1.8 1 1 1 - 950 259.43086 9.4546712 0.0034851739 1.9 1 1 1 - 1000 247.14622 20.250308 0.0034851739 2 1 1 1 -Loop time of 0.357762 on 4 procs for 1000 steps with 44 atoms - -Performance: 241.502 ns/day, 0.099 hours/ns, 2795.157 timesteps/s -99.0% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0003917 | 0.015545 | 0.033317 | 11.9 | 4.35 -Bond | 0.0010131 | 0.030153 | 0.076975 | 18.2 | 8.43 -Kspace | 0.092857 | 0.1462 | 0.18688 | 10.7 | 40.87 -Neigh | 0.043786 | 0.044014 | 0.044189 | 0.1 | 12.30 -Comm | 0.03636 | 0.038345 | 0.040538 | 0.8 | 10.72 -Output | 0.00091578 | 0.0012541 | 0.0020923 | 1.4 | 0.35 -Modify | 0.075379 | 0.080791 | 0.086052 | 1.8 | 22.58 -Other | | 0.00146 | | | 0.41 - -Nlocal: 11 ave 32 max 0 min -Histogram: 2 0 1 0 0 0 0 0 0 1 -Nghost: 40 ave 51 max 19 min -Histogram: 1 0 0 0 0 0 0 1 0 2 -Neighs: 191 ave 529 max 0 min -Histogram: 2 0 0 0 1 0 0 0 0 1 - -Total # of neighbors = 764 -Ave neighs/atom = 17.3636 -Ave special neighs/atom = 9.77273 -Neighbor list builds = 1000 -Dangerous builds = 0 - -# write_restart restart_longrun -# write_data restart_longrun.data - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:00 diff --git a/examples/PACKAGES/reaction/tiny_nylon/log.4Nov2020.tiny_nylon.stabilized.g++.1 b/examples/PACKAGES/reaction/tiny_nylon/log.4Nov2020.tiny_nylon.stabilized.g++.1 new file mode 100644 index 0000000000..9a2d240ca4 --- /dev/null +++ b/examples/PACKAGES/reaction/tiny_nylon/log.4Nov2020.tiny_nylon.stabilized.g++.1 @@ -0,0 +1,412 @@ +LAMMPS (4 Nov 2022) +# two monomer nylon example +# reaction produces a condensed water molecule + +units real + +boundary p p p + +atom_style full + +kspace_style pppm 1.0e-4 + +pair_style lj/class2/coul/long 8.5 + +angle_style class2 + +bond_style class2 + +dihedral_style class2 + +improper_style class2 + +read_data tiny_nylon.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 = (-25 -25 -25) to (25 25 25) + 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 ... + 44 atoms + reading velocities ... + 44 velocities + scanning bonds ... + 9 = max bonds/atom + scanning angles ... + 21 = max angles/atom + scanning dihedrals ... + 29 = max dihedrals/atom + scanning impropers ... + 29 = max impropers/atom + reading bonds ... + 42 bonds + reading angles ... + 74 angles + reading dihedrals ... + 100 dihedrals + reading impropers ... + 44 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 + 6 = max # of 1-3 neighbors + 12 = max # of 1-4 neighbors + 41 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.007 seconds + +velocity all create 300.0 4928459 dist gaussian + +molecule mol1 rxn1_stp1_unreacted.molecule_template +Read molecule template mol1: + 1 molecules + 0 fragments + 18 atoms with max type 8 + 16 bonds with max type 10 + 25 angles with max type 28 + 23 dihedrals with max type 36 + 2 impropers with max type 3 +molecule mol2 rxn1_stp1_reacted.molecule_template +Read molecule template mol2: + 1 molecules + 0 fragments + 18 atoms with max type 9 + 17 bonds with max type 13 + 31 angles with max type 27 + 39 dihedrals with max type 33 + 0 impropers with max type 0 +molecule mol3 rxn1_stp2_unreacted.molecule_template +Read molecule template mol3: + 1 molecules + 0 fragments + 15 atoms with max type 9 + 14 bonds with max type 13 + 25 angles with max type 27 + 30 dihedrals with max type 33 + 0 impropers with max type 0 +molecule mol4 rxn1_stp2_reacted.molecule_template +Read molecule template mol4: + 1 molecules + 0 fragments + 15 atoms with max type 11 + 13 bonds with max type 15 + 19 angles with max type 29 + 16 dihedrals with max type 32 + 2 impropers with max type 13 + +thermo 50 + +# dump 1 all xyz 1 test_vis.xyz + +fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map +WARNING: Fix bond/react: Atom affected by reaction rxn2 is too close to template edge (../fix_bond_react.cpp:2624) +dynamic group bond_react_MASTER_group defined +dynamic group statted_grp_REACT defined + +fix 1 statted_grp_REACT nvt temp 300 300 100 + +# optionally, you can customize behavior of reacting atoms, +# by using the internally-created 'bond_react_MASTER_group', like so: +fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1 + +thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] + +# restart 100 restart1 restart2 + +run 10000 + +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 + +PPPM initialization ... + using 12-bit tables for long-range coulomb (../kspace.cpp:342) + G vector (1/distance) = 0.05345967 + grid = 2 2 2 + stencil order = 5 + estimated absolute RMS force accuracy = 0.040225597 + estimated relative force accuracy = 0.00012113819 + using double precision KISS FFT + 3d grid and FFT values/proc = 343 8 +Generated 55 of 55 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 = 10 10 10 + 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 + bin: standard + (2) fix bond/react, occasional, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +WARNING: Inconsistent image flags (../domain.cpp:819) +Per MPI rank memory allocation (min/avg/max) = 33.78 | 33.78 | 33.78 Mbytes + Step Temp Press Density f_myrxns[1] f_myrxns[2] + 0 300 346.78165 0.0034851739 0 0 + 50 283.51963 -47.16359 0.0034851739 1 0 + 100 256.04648 21.778898 0.0034851739 1 1 + 150 450.78138 -11.7887 0.0034851739 1 1 + 200 400.15754 49.489858 0.0034851739 1 1 + 250 347.06066 68.952063 0.0034851739 1 1 + 300 291.89228 -1.5986302 0.0034851739 1 1 + 350 290.25995 17.634558 0.0034851739 1 1 + 400 234.89168 26.36452 0.0034851739 1 1 + 450 305.80709 -28.923896 0.0034851739 1 1 + 500 375.19218 -37.024375 0.0034851739 1 1 + 550 321.86944 -4.6961825 0.0034851739 1 1 + 600 307.2639 -31.393161 0.0034851739 1 1 + 650 255.95833 8.4995589 0.0034851739 1 1 + 700 294.54665 -17.06105 0.0034851739 1 1 + 750 273.08231 -10.7175 0.0034851739 1 1 + 800 249.69175 9.9777683 0.0034851739 1 1 + 850 307.71806 -6.9950048 0.0034851739 1 1 + 900 367.39855 9.9874985 0.0034851739 1 1 + 950 327.57334 -4.7029779 0.0034851739 1 1 + 1000 348.85247 15.763492 0.0034851739 1 1 + 1050 328.94435 -35.031279 0.0034851739 1 1 + 1100 283.23971 -16.937443 0.0034851739 1 1 + 1150 266.69676 42.308482 0.0034851739 1 1 + 1200 244.61493 -8.291143 0.0034851739 1 1 + 1250 206.68495 6.6280168 0.0034851739 1 1 + 1300 257.83339 -7.0826267 0.0034851739 1 1 + 1350 358.0875 -7.6024741 0.0034851739 1 1 + 1400 353.66614 18.091914 0.0034851739 1 1 + 1450 302.27969 13.828755 0.0034851739 1 1 + 1500 262.57851 9.256794 0.0034851739 1 1 + 1550 252.39493 1.2438641 0.0034851739 1 1 + 1600 247.18352 10.008173 0.0034851739 1 1 + 1650 290.30112 -2.1829035 0.0034851739 1 1 + 1700 272.78999 -57.305766 0.0034851739 1 1 + 1750 253.35258 24.729795 0.0034851739 1 1 + 1800 278.67831 -0.95016566 0.0034851739 1 1 + 1850 302.04743 16.002867 0.0034851739 1 1 + 1900 330.67188 -22.034206 0.0034851739 1 1 + 1950 342.64206 8.0076017 0.0034851739 1 1 + 2000 348.74388 -12.159887 0.0034851739 1 1 + 2050 300.48093 36.01054 0.0034851739 1 1 + 2100 275.01699 8.7612261 0.0034851739 1 1 + 2150 303.92758 10.317056 0.0034851739 1 1 + 2200 308.89457 33.245018 0.0034851739 1 1 + 2250 265.74177 35.857118 0.0034851739 1 1 + 2300 273.40088 53.001593 0.0034851739 1 1 + 2350 287.74746 -0.14590128 0.0034851739 1 1 + 2400 278.76055 -8.2080851 0.0034851739 1 1 + 2450 331.88978 39.025208 0.0034851739 1 1 + 2500 280.04045 -21.423616 0.0034851739 1 1 + 2550 388.81531 -12.350023 0.0034851739 1 1 + 2600 311.13452 -13.287102 0.0034851739 1 1 + 2650 325.07681 88.710878 0.0034851739 1 1 + 2700 319.08502 14.118057 0.0034851739 1 1 + 2750 261.72066 26.051675 0.0034851739 1 1 + 2800 281.03508 -21.200833 0.0034851739 1 1 + 2850 312.27359 4.3892078 0.0034851739 1 1 + 2900 274.81147 -12.738114 0.0034851739 1 1 + 2950 281.76969 11.198451 0.0034851739 1 1 + 3000 291.83918 48.595884 0.0034851739 1 1 + 3050 297.40189 -24.91102 0.0034851739 1 1 + 3100 341.47331 13.82699 0.0034851739 1 1 + 3150 347.51825 -10.458257 0.0034851739 1 1 + 3200 301.24666 26.550464 0.0034851739 1 1 + 3250 281.3679 -23.02985 0.0034851739 1 1 + 3300 279.8332 -53.222264 0.0034851739 1 1 + 3350 289.41496 -8.793156 0.0034851739 1 1 + 3400 288.5722 -25.441134 0.0034851739 1 1 + 3450 259.59524 77.884773 0.0034851739 1 1 + 3500 296.00389 30.3654 0.0034851739 1 1 + 3550 302.14443 -5.1101538 0.0034851739 1 1 + 3600 288.98098 -12.688781 0.0034851739 1 1 + 3650 333.83238 -33.121195 0.0034851739 1 1 + 3700 347.7556 -24.693995 0.0034851739 1 1 + 3750 354.42689 6.7030374 0.0034851739 1 1 + 3800 341.24011 -18.775449 0.0034851739 1 1 + 3850 320.50998 35.492418 0.0034851739 1 1 + 3900 326.81918 -49.073015 0.0034851739 1 1 + 3950 299.55145 -19.487946 0.0034851739 1 1 + 4000 308.81019 30.579971 0.0034851739 1 1 + 4050 251.83279 -17.500379 0.0034851739 1 1 + 4100 242.0783 21.228088 0.0034851739 1 1 + 4150 265.59921 -3.9446469 0.0034851739 1 1 + 4200 369.32464 -14.626205 0.0034851739 1 1 + 4250 346.22904 -32.749662 0.0034851739 1 1 + 4300 369.43175 11.916047 0.0034851739 1 1 + 4350 321.17007 -9.3009147 0.0034851739 1 1 + 4400 312.41821 -31.360537 0.0034851739 1 1 + 4450 281.59211 40.338618 0.0034851739 1 1 + 4500 289.10806 -4.2135222 0.0034851739 1 1 + 4550 317.55705 -4.3727576 0.0034851739 1 1 + 4600 310.64469 -14.403478 0.0034851739 1 1 + 4650 284.43433 37.416848 0.0034851739 1 1 + 4700 353.88469 7.7633789 0.0034851739 1 1 + 4750 328.48834 -60.780145 0.0034851739 1 1 + 4800 390.23986 4.2691385 0.0034851739 1 1 + 4850 364.06188 40.18245 0.0034851739 1 1 + 4900 304.64696 6.3557092 0.0034851739 1 1 + 4950 309.12139 -16.598924 0.0034851739 1 1 + 5000 311.03552 14.748037 0.0034851739 1 1 + 5050 320.97847 -26.733755 0.0034851739 1 1 + 5100 275.1237 -29.734972 0.0034851739 1 1 + 5150 287.76954 -2.5726321 0.0034851739 1 1 + 5200 267.72493 -6.6677739 0.0034851739 1 1 + 5250 290.63862 29.209807 0.0034851739 1 1 + 5300 276.51052 -19.746615 0.0034851739 1 1 + 5350 255.69196 25.130356 0.0034851739 1 1 + 5400 313.43108 -18.556701 0.0034851739 1 1 + 5450 327.91785 -16.08265 0.0034851739 1 1 + 5500 342.03301 33.271603 0.0034851739 1 1 + 5550 272.96564 -5.0247163 0.0034851739 1 1 + 5600 315.93807 -16.793394 0.0034851739 1 1 + 5650 294.66353 19.720691 0.0034851739 1 1 + 5700 283.4631 -6.5193772 0.0034851739 1 1 + 5750 261.06436 12.755679 0.0034851739 1 1 + 5800 274.15767 -9.6693117 0.0034851739 1 1 + 5850 271.1371 18.441828 0.0034851739 1 1 + 5900 283.39277 -4.6324708 0.0034851739 1 1 + 5950 326.30497 12.106133 0.0034851739 1 1 + 6000 316.91847 -32.864812 0.0034851739 1 1 + 6050 344.86369 21.226768 0.0034851739 1 1 + 6100 295.85211 -7.3603837 0.0034851739 1 1 + 6150 256.72292 4.6010174 0.0034851739 1 1 + 6200 248.33379 -20.795929 0.0034851739 1 1 + 6250 259.4054 63.590928 0.0034851739 1 1 + 6300 264.16648 2.6570242 0.0034851739 1 1 + 6350 243.22677 -18.621317 0.0034851739 1 1 + 6400 269.96092 53.832036 0.0034851739 1 1 + 6450 252.06358 -26.231052 0.0034851739 1 1 + 6500 275.4825 25.577441 0.0034851739 1 1 + 6550 298.27441 11.17373 0.0034851739 1 1 + 6600 297.29358 -21.382334 0.0034851739 1 1 + 6650 334.78542 38.892678 0.0034851739 1 1 + 6700 299.48699 -20.336163 0.0034851739 1 1 + 6750 315.01936 21.000444 0.0034851739 1 1 + 6800 244.68344 -6.3625659 0.0034851739 1 1 + 6850 251.56543 27.857872 0.0034851739 1 1 + 6900 280.81518 -12.494398 0.0034851739 1 1 + 6950 273.87437 -34.211085 0.0034851739 1 1 + 7000 274.91068 33.483158 0.0034851739 1 1 + 7050 298.56432 -61.821668 0.0034851739 1 1 + 7100 299.08395 10.365875 0.0034851739 1 1 + 7150 317.38233 29.049831 0.0034851739 1 1 + 7200 317.24932 -27.515026 0.0034851739 1 1 + 7250 305.63931 12.732123 0.0034851739 1 1 + 7300 309.44007 -53.922033 0.0034851739 1 1 + 7350 280.35029 45.495031 0.0034851739 1 1 + 7400 228.60929 1.7072084 0.0034851739 1 1 + 7450 276.206 -19.170327 0.0034851739 1 1 + 7500 257.9851 77.105642 0.0034851739 1 1 + 7550 306.46848 -29.189265 0.0034851739 1 1 + 7600 296.84522 -20.83365 0.0034851739 1 1 + 7650 296.5965 -14.890206 0.0034851739 1 1 + 7700 322.80474 44.883023 0.0034851739 1 1 + 7750 293.7355 -48.487658 0.0034851739 1 1 + 7800 358.41838 13.156339 0.0034851739 1 1 + 7850 293.81457 -19.50566 0.0034851739 1 1 + 7900 309.49618 -28.562417 0.0034851739 1 1 + 7950 285.6339 -22.488886 0.0034851739 1 1 + 8000 262.85312 57.125049 0.0034851739 1 1 + 8050 243.28673 -28.082125 0.0034851739 1 1 + 8100 279.71604 10.011975 0.0034851739 1 1 + 8150 344.77027 -56.89744 0.0034851739 1 1 + 8200 366.36063 21.02453 0.0034851739 1 1 + 8250 347.07209 2.7752885 0.0034851739 1 1 + 8300 337.74753 -10.957676 0.0034851739 1 1 + 8350 300.41188 -22.840776 0.0034851739 1 1 + 8400 282.27447 0.32063982 0.0034851739 1 1 + 8450 285.40722 -3.7167264 0.0034851739 1 1 + 8500 321.32722 -21.308158 0.0034851739 1 1 + 8550 293.65903 15.681219 0.0034851739 1 1 + 8600 293.38929 37.727045 0.0034851739 1 1 + 8650 299.55185 -15.004573 0.0034851739 1 1 + 8700 270.7608 14.615287 0.0034851739 1 1 + 8750 306.46813 67.018302 0.0034851739 1 1 + 8800 308.35025 -91.212286 0.0034851739 1 1 + 8850 349.40419 31.906004 0.0034851739 1 1 + 8900 351.32706 -24.901778 0.0034851739 1 1 + 8950 320.84369 18.380221 0.0034851739 1 1 + 9000 289.2862 9.981138 0.0034851739 1 1 + 9050 270.53883 12.028672 0.0034851739 1 1 + 9100 270.63206 -0.87842772 0.0034851739 1 1 + 9150 274.30671 -4.1228725 0.0034851739 1 1 + 9200 343.78546 20.427647 0.0034851739 1 1 + 9250 348.1019 13.339075 0.0034851739 1 1 + 9300 345.11791 -32.515359 0.0034851739 1 1 + 9350 329.8365 12.644587 0.0034851739 1 1 + 9400 286.41337 -28.79111 0.0034851739 1 1 + 9450 321.92318 32.154255 0.0034851739 1 1 + 9500 302.68527 -42.576022 0.0034851739 1 1 + 9550 335.24034 26.675219 0.0034851739 1 1 + 9600 270.62012 17.230138 0.0034851739 1 1 + 9650 273.71088 35.651219 0.0034851739 1 1 + 9700 286.2141 -26.15835 0.0034851739 1 1 + 9750 262.25352 -4.1954047 0.0034851739 1 1 + 9800 314.29455 23.252049 0.0034851739 1 1 + 9850 273.71272 -29.586039 0.0034851739 1 1 + 9900 300.63743 42.595289 0.0034851739 1 1 + 9950 367.68979 -64.582508 0.0034851739 1 1 + 10000 357.17941 31.607766 0.0034851739 1 1 +Loop time of 1.82433 on 1 procs for 10000 steps with 44 atoms + +Performance: 473.599 ns/day, 0.051 hours/ns, 5481.467 timesteps/s, 241.185 katom-step/s +99.8% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.25039 | 0.25039 | 0.25039 | 0.0 | 13.72 +Bond | 1.0461 | 1.0461 | 1.0461 | 0.0 | 57.34 +Kspace | 0.34339 | 0.34339 | 0.34339 | 0.0 | 18.82 +Neigh | 0.0097352 | 0.0097352 | 0.0097352 | 0.0 | 0.53 +Comm | 0.0047764 | 0.0047764 | 0.0047764 | 0.0 | 0.26 +Output | 0.0030537 | 0.0030537 | 0.0030537 | 0.0 | 0.17 +Modify | 0.15534 | 0.15534 | 0.15534 | 0.0 | 8.51 +Other | | 0.01155 | | | 0.63 + +Nlocal: 44 ave 44 max 44 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 44 ave 44 max 44 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 823 ave 823 max 823 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 823 +Ave neighs/atom = 18.704545 +Ave special neighs/atom = 9.9090909 +Neighbor list builds = 221 +Dangerous builds = 0 + +# write_restart restart_longrun +# write_data restart_longrun.data +Total wall time: 0:00:01 diff --git a/examples/PACKAGES/reaction/tiny_nylon/log.4Nov2020.tiny_nylon.stabilized.g++.4 b/examples/PACKAGES/reaction/tiny_nylon/log.4Nov2020.tiny_nylon.stabilized.g++.4 new file mode 100644 index 0000000000..0a30cd6984 --- /dev/null +++ b/examples/PACKAGES/reaction/tiny_nylon/log.4Nov2020.tiny_nylon.stabilized.g++.4 @@ -0,0 +1,412 @@ +LAMMPS (4 Nov 2022) +# two monomer nylon example +# reaction produces a condensed water molecule + +units real + +boundary p p p + +atom_style full + +kspace_style pppm 1.0e-4 + +pair_style lj/class2/coul/long 8.5 + +angle_style class2 + +bond_style class2 + +dihedral_style class2 + +improper_style class2 + +read_data tiny_nylon.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 = (-25 -25 -25) to (25 25 25) + 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 ... + 44 atoms + reading velocities ... + 44 velocities + scanning bonds ... + 9 = max bonds/atom + scanning angles ... + 21 = max angles/atom + scanning dihedrals ... + 29 = max dihedrals/atom + scanning impropers ... + 29 = max impropers/atom + reading bonds ... + 42 bonds + reading angles ... + 74 angles + reading dihedrals ... + 100 dihedrals + reading impropers ... + 44 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 + 6 = max # of 1-3 neighbors + 12 = max # of 1-4 neighbors + 41 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.008 seconds + +velocity all create 300.0 4928459 dist gaussian + +molecule mol1 rxn1_stp1_unreacted.molecule_template +Read molecule template mol1: + 1 molecules + 0 fragments + 18 atoms with max type 8 + 16 bonds with max type 10 + 25 angles with max type 28 + 23 dihedrals with max type 36 + 2 impropers with max type 3 +molecule mol2 rxn1_stp1_reacted.molecule_template +Read molecule template mol2: + 1 molecules + 0 fragments + 18 atoms with max type 9 + 17 bonds with max type 13 + 31 angles with max type 27 + 39 dihedrals with max type 33 + 0 impropers with max type 0 +molecule mol3 rxn1_stp2_unreacted.molecule_template +Read molecule template mol3: + 1 molecules + 0 fragments + 15 atoms with max type 9 + 14 bonds with max type 13 + 25 angles with max type 27 + 30 dihedrals with max type 33 + 0 impropers with max type 0 +molecule mol4 rxn1_stp2_reacted.molecule_template +Read molecule template mol4: + 1 molecules + 0 fragments + 15 atoms with max type 11 + 13 bonds with max type 15 + 19 angles with max type 29 + 16 dihedrals with max type 32 + 2 impropers with max type 13 + +thermo 50 + +# dump 1 all xyz 1 test_vis.xyz + +fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map +WARNING: Fix bond/react: Atom affected by reaction rxn2 is too close to template edge (../fix_bond_react.cpp:2624) +dynamic group bond_react_MASTER_group defined +dynamic group statted_grp_REACT defined + +fix 1 statted_grp_REACT nvt temp 300 300 100 + +# optionally, you can customize behavior of reacting atoms, +# by using the internally-created 'bond_react_MASTER_group', like so: +fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1 + +thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] + +# restart 100 restart1 restart2 + +run 10000 + +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 + +PPPM initialization ... + using 12-bit tables for long-range coulomb (../kspace.cpp:342) + G vector (1/distance) = 0.05345967 + grid = 2 2 2 + stencil order = 5 + estimated absolute RMS force accuracy = 0.040225597 + estimated relative force accuracy = 0.00012113819 + using double precision KISS FFT + 3d grid and FFT values/proc = 252 2 +Generated 55 of 55 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 = 10 10 10 + 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 + bin: standard + (2) fix bond/react, occasional, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +WARNING: Inconsistent image flags (../domain.cpp:819) +Per MPI rank memory allocation (min/avg/max) = 33.66 | 33.88 | 34.43 Mbytes + Step Temp Press Density f_myrxns[1] f_myrxns[2] + 0 300 346.78165 0.0034851739 0 0 + 50 283.51963 -47.16359 0.0034851739 1 0 + 100 256.04648 21.778898 0.0034851739 1 1 + 150 450.78138 -11.7887 0.0034851739 1 1 + 200 400.15754 49.489858 0.0034851739 1 1 + 250 347.06066 68.952063 0.0034851739 1 1 + 300 291.89228 -1.5986302 0.0034851739 1 1 + 350 290.25995 17.634558 0.0034851739 1 1 + 400 234.89168 26.36452 0.0034851739 1 1 + 450 305.80709 -28.923896 0.0034851739 1 1 + 500 375.19218 -37.024375 0.0034851739 1 1 + 550 321.86944 -4.6961825 0.0034851739 1 1 + 600 307.2639 -31.393161 0.0034851739 1 1 + 650 255.95833 8.4995589 0.0034851739 1 1 + 700 294.54665 -17.06105 0.0034851739 1 1 + 750 273.08231 -10.7175 0.0034851739 1 1 + 800 249.69175 9.9777684 0.0034851739 1 1 + 850 307.71806 -6.9950047 0.0034851739 1 1 + 900 367.39855 9.9874984 0.0034851739 1 1 + 950 327.57334 -4.702978 0.0034851739 1 1 + 1000 348.85247 15.763492 0.0034851739 1 1 + 1050 328.94435 -35.031279 0.0034851739 1 1 + 1100 283.23971 -16.937443 0.0034851739 1 1 + 1150 266.69676 42.308482 0.0034851739 1 1 + 1200 244.61493 -8.2911432 0.0034851739 1 1 + 1250 206.68495 6.6280166 0.0034851739 1 1 + 1300 257.83339 -7.0826264 0.0034851739 1 1 + 1350 358.0875 -7.602474 0.0034851739 1 1 + 1400 353.66614 18.091914 0.0034851739 1 1 + 1450 302.27969 13.828755 0.0034851739 1 1 + 1500 262.57851 9.2567956 0.0034851739 1 1 + 1550 252.39492 1.2438631 0.0034851739 1 1 + 1600 247.18352 10.008173 0.0034851739 1 1 + 1650 290.30112 -2.1829055 0.0034851739 1 1 + 1700 272.78999 -57.305766 0.0034851739 1 1 + 1750 253.35258 24.729797 0.0034851739 1 1 + 1800 278.67832 -0.95017071 0.0034851739 1 1 + 1850 302.04743 16.002872 0.0034851739 1 1 + 1900 330.67188 -22.034206 0.0034851739 1 1 + 1950 342.64206 8.0075967 0.0034851739 1 1 + 2000 348.74388 -12.159899 0.0034851739 1 1 + 2050 300.48095 36.010534 0.0034851739 1 1 + 2100 275.017 8.7612294 0.0034851739 1 1 + 2150 303.92758 10.317032 0.0034851739 1 1 + 2200 308.89452 33.245012 0.0034851739 1 1 + 2250 265.74176 35.857111 0.0034851739 1 1 + 2300 273.40086 53.001626 0.0034851739 1 1 + 2350 287.74753 -0.14586562 0.0034851739 1 1 + 2400 278.7606 -8.20812 0.0034851739 1 1 + 2450 331.88979 39.02519 0.0034851739 1 1 + 2500 280.04041 -21.423589 0.0034851739 1 1 + 2550 388.81536 -12.350053 0.0034851739 1 1 + 2600 311.13468 -13.286785 0.0034851739 1 1 + 2650 325.07686 88.710881 0.0034851739 1 1 + 2700 319.08471 14.118288 0.0034851739 1 1 + 2750 261.72067 26.051439 0.0034851739 1 1 + 2800 281.03459 -21.201297 0.0034851739 1 1 + 2850 312.27342 4.3904047 0.0034851739 1 1 + 2900 274.81152 -12.739138 0.0034851739 1 1 + 2950 281.76873 11.199981 0.0034851739 1 1 + 3000 291.8377 48.595661 0.0034851739 1 1 + 3050 297.40212 -24.911752 0.0034851739 1 1 + 3100 341.48252 13.825136 0.0034851739 1 1 + 3150 347.5099 -10.452847 0.0034851739 1 1 + 3200 301.24901 26.553909 0.0034851739 1 1 + 3250 281.35392 -23.028031 0.0034851739 1 1 + 3300 279.82881 -53.225332 0.0034851739 1 1 + 3350 289.41016 -8.7866567 0.0034851739 1 1 + 3400 288.56923 -25.445059 0.0034851739 1 1 + 3450 259.59956 77.88466 0.0034851739 1 1 + 3500 295.99591 30.357393 0.0034851739 1 1 + 3550 302.1675 -5.103997 0.0034851739 1 1 + 3600 289.00244 -12.687621 0.0034851739 1 1 + 3650 333.89968 -33.124064 0.0034851739 1 1 + 3700 347.82328 -24.745583 0.0034851739 1 1 + 3750 354.51391 6.7131611 0.0034851739 1 1 + 3800 341.31124 -18.777474 0.0034851739 1 1 + 3850 320.48132 35.547595 0.0034851739 1 1 + 3900 326.8911 -49.153151 0.0034851739 1 1 + 3950 299.65543 -19.443322 0.0034851739 1 1 + 4000 308.97943 30.368402 0.0034851739 1 1 + 4050 251.46183 -17.518988 0.0034851739 1 1 + 4100 241.50223 22.103347 0.0034851739 1 1 + 4150 265.01178 -4.4952098 0.0034851739 1 1 + 4200 369.78569 -14.603579 0.0034851739 1 1 + 4250 348.20071 -33.060693 0.0034851739 1 1 + 4300 368.11836 11.897676 0.0034851739 1 1 + 4350 321.1145 -9.3124104 0.0034851739 1 1 + 4400 313.95395 -31.940883 0.0034851739 1 1 + 4450 280.50985 41.398853 0.0034851739 1 1 + 4500 289.36914 -2.3915112 0.0034851739 1 1 + 4550 318.52735 -5.0086703 0.0034851739 1 1 + 4600 308.68169 -13.642004 0.0034851739 1 1 + 4650 285.24153 35.314806 0.0034851739 1 1 + 4700 357.15021 8.8271927 0.0034851739 1 1 + 4750 359.11051 -59.672314 0.0034851739 1 1 + 4800 453.11584 0.54316266 0.0034851739 1 1 + 4850 392.52232 46.350736 0.0034851739 1 1 + 4900 310.42864 5.9002223 0.0034851739 1 1 + 4950 285.97355 -19.321724 0.0034851739 1 1 + 5000 309.41828 18.331381 0.0034851739 1 1 + 5050 324.96434 -27.143631 0.0034851739 1 1 + 5100 266.49422 -26.977074 0.0034851739 1 1 + 5150 295.35576 -14.271299 0.0034851739 1 1 + 5200 275.8961 14.057873 0.0034851739 1 1 + 5250 332.75955 26.04747 0.0034851739 1 1 + 5300 296.57102 -20.904181 0.0034851739 1 1 + 5350 264.68808 29.533914 0.0034851739 1 1 + 5400 293.373 -13.579532 0.0034851739 1 1 + 5450 290.55933 9.3458628 0.0034851739 1 1 + 5500 340.54834 8.8308229 0.0034851739 1 1 + 5550 336.08713 -6.9696582 0.0034851739 1 1 + 5600 331.77668 -7.9756709 0.0034851739 1 1 + 5650 307.8419 -10.263349 0.0034851739 1 1 + 5700 262.70119 78.855544 0.0034851739 1 1 + 5750 285.37985 -15.4042 0.0034851739 1 1 + 5800 267.44612 -30.053955 0.0034851739 1 1 + 5850 241.52125 3.2904907 0.0034851739 1 1 + 5900 265.13367 27.69901 0.0034851739 1 1 + 5950 277.95155 18.419031 0.0034851739 1 1 + 6000 309.62777 -20.054029 0.0034851739 1 1 + 6050 363.41588 16.435337 0.0034851739 1 1 + 6100 348.85793 -14.513241 0.0034851739 1 1 + 6150 323.73745 56.990265 0.0034851739 1 1 + 6200 338.66823 -19.93498 0.0034851739 1 1 + 6250 325.41329 -13.824943 0.0034851739 1 1 + 6300 279.82345 -9.0557197 0.0034851739 1 1 + 6350 285.90705 52.434161 0.0034851739 1 1 + 6400 260.34102 -15.766595 0.0034851739 1 1 + 6450 304.65686 7.5058044 0.0034851739 1 1 + 6500 265.02097 1.7203356 0.0034851739 1 1 + 6550 293.35057 1.8896974 0.0034851739 1 1 + 6600 284.06837 -9.3674953 0.0034851739 1 1 + 6650 307.29863 -2.3882614 0.0034851739 1 1 + 6700 336.20676 43.913926 0.0034851739 1 1 + 6750 291.53938 -16.749433 0.0034851739 1 1 + 6800 298.4418 -13.340335 0.0034851739 1 1 + 6850 264.13368 -11.219357 0.0034851739 1 1 + 6900 273.63109 -15.897238 0.0034851739 1 1 + 6950 282.64715 6.8275423 0.0034851739 1 1 + 7000 277.4091 -25.381099 0.0034851739 1 1 + 7050 278.07001 63.552969 0.0034851739 1 1 + 7100 293.33358 22.103462 0.0034851739 1 1 + 7150 308.36447 -27.212203 0.0034851739 1 1 + 7200 251.45077 -40.385347 0.0034851739 1 1 + 7250 317.57808 1.0302048 0.0034851739 1 1 + 7300 348.52627 48.392457 0.0034851739 1 1 + 7350 356.5821 27.933626 0.0034851739 1 1 + 7400 311.29835 -18.899768 0.0034851739 1 1 + 7450 274.24476 -19.41577 0.0034851739 1 1 + 7500 261.38075 1.2110527 0.0034851739 1 1 + 7550 299.78907 -17.64954 0.0034851739 1 1 + 7600 271.36191 25.99439 0.0034851739 1 1 + 7650 287.51241 1.532789 0.0034851739 1 1 + 7700 280.87778 -31.828432 0.0034851739 1 1 + 7750 312.22588 45.320976 0.0034851739 1 1 + 7800 312.73849 4.1022573 0.0034851739 1 1 + 7850 299.18742 50.272069 0.0034851739 1 1 + 7900 312.4916 -34.425195 0.0034851739 1 1 + 7950 284.5205 15.716375 0.0034851739 1 1 + 8000 248.39764 -7.1922339 0.0034851739 1 1 + 8050 242.65659 -32.701773 0.0034851739 1 1 + 8100 228.76112 54.351 0.0034851739 1 1 + 8150 308.67672 -15.835344 0.0034851739 1 1 + 8200 304.26746 -11.106867 0.0034851739 1 1 + 8250 338.67601 44.199636 0.0034851739 1 1 + 8300 308.59612 -9.6487546 0.0034851739 1 1 + 8350 287.08027 11.036122 0.0034851739 1 1 + 8400 319.79578 -78.918735 0.0034851739 1 1 + 8450 320.78978 57.275745 0.0034851739 1 1 + 8500 282.90803 33.716746 0.0034851739 1 1 + 8550 235.23686 -44.587941 0.0034851739 1 1 + 8600 265.62925 45.976855 0.0034851739 1 1 + 8650 260.35429 -9.3951434 0.0034851739 1 1 + 8700 236.16314 19.504695 0.0034851739 1 1 + 8750 291.51087 -13.996885 0.0034851739 1 1 + 8800 357.00246 -26.674845 0.0034851739 1 1 + 8850 327.72543 15.954838 0.0034851739 1 1 + 8900 321.17809 -14.794959 0.0034851739 1 1 + 8950 357.51102 39.861567 0.0034851739 1 1 + 9000 286.68385 -52.799636 0.0034851739 1 1 + 9050 283.96224 13.044025 0.0034851739 1 1 + 9100 304.04431 25.510777 0.0034851739 1 1 + 9150 261.33631 -18.611794 0.0034851739 1 1 + 9200 297.50501 25.733551 0.0034851739 1 1 + 9250 279.85018 -26.91045 0.0034851739 1 1 + 9300 336.07358 35.385228 0.0034851739 1 1 + 9350 326.27961 -36.941794 0.0034851739 1 1 + 9400 400.42857 7.5301492 0.0034851739 1 1 + 9450 296.80174 11.898673 0.0034851739 1 1 + 9500 275.98796 41.303486 0.0034851739 1 1 + 9550 278.56924 31.033397 0.0034851739 1 1 + 9600 260.24476 -11.416595 0.0034851739 1 1 + 9650 281.86065 12.60709 0.0034851739 1 1 + 9700 287.26789 -29.086626 0.0034851739 1 1 + 9750 290.82789 3.2830325 0.0034851739 1 1 + 9800 270.99421 -25.824595 0.0034851739 1 1 + 9850 385.1884 4.1048816 0.0034851739 1 1 + 9900 363.1711 18.815879 0.0034851739 1 1 + 9950 344.93572 17.375158 0.0034851739 1 1 + 10000 335.65852 -0.84087429 0.0034851739 1 1 +Loop time of 1.78856 on 4 procs for 10000 steps with 44 atoms + +Performance: 483.070 ns/day, 0.050 hours/ns, 5591.087 timesteps/s, 246.008 katom-step/s +100.0% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0021174 | 0.066025 | 0.20024 | 31.5 | 3.69 +Bond | 0.0035593 | 0.2715 | 0.74757 | 58.6 | 15.18 +Kspace | 0.50386 | 1.0492 | 1.3455 | 33.6 | 58.66 +Neigh | 0.0079056 | 0.0079463 | 0.0079766 | 0.0 | 0.44 +Comm | 0.044284 | 0.08173 | 0.10388 | 8.1 | 4.57 +Output | 0.0021661 | 0.0024497 | 0.0031314 | 0.8 | 0.14 +Modify | 0.2648 | 0.29459 | 0.33479 | 5.5 | 16.47 +Other | | 0.01514 | | | 0.85 + +Nlocal: 11 ave 41 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 1 +Nghost: 27.5 ave 41 max 0 min +Histogram: 1 0 0 0 0 0 0 0 2 1 +Neighs: 205.75 ave 820 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 823 +Ave neighs/atom = 18.704545 +Ave special neighs/atom = 9.9090909 +Neighbor list builds = 225 +Dangerous builds = 0 + +# write_restart restart_longrun +# write_data restart_longrun.data +Total wall time: 0:00:01 diff --git a/examples/PACKAGES/reaction/tiny_nylon/log.4Nov2020.tiny_nylon.stabilized_variable_probability.g++.1 b/examples/PACKAGES/reaction/tiny_nylon/log.4Nov2020.tiny_nylon.stabilized_variable_probability.g++.1 new file mode 100644 index 0000000000..ec822e8b3b --- /dev/null +++ b/examples/PACKAGES/reaction/tiny_nylon/log.4Nov2020.tiny_nylon.stabilized_variable_probability.g++.1 @@ -0,0 +1,237 @@ +LAMMPS (4 Nov 2022) +# two monomer nylon example +# reaction produces a condensed water molecule + +units real + +boundary p p p + +atom_style full + +kspace_style pppm 1.0e-4 + +pair_style lj/class2/coul/long 8.5 + +angle_style class2 + +bond_style class2 + +dihedral_style class2 + +improper_style class2 + +read_data tiny_nylon.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 = (-25 -25 -25) to (25 25 25) + 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 ... + 44 atoms + reading velocities ... + 44 velocities + scanning bonds ... + 9 = max bonds/atom + scanning angles ... + 21 = max angles/atom + scanning dihedrals ... + 29 = max dihedrals/atom + scanning impropers ... + 29 = max impropers/atom + reading bonds ... + 42 bonds + reading angles ... + 74 angles + reading dihedrals ... + 100 dihedrals + reading impropers ... + 44 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 + 6 = max # of 1-3 neighbors + 12 = max # of 1-4 neighbors + 41 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.007 seconds + +variable runsteps equal 1000 +variable prob1 equal step/v_runsteps*2+0.1 +variable prob2 equal (step/v_runsteps)>0.5 + +velocity all create 300.0 4928459 dist gaussian + +molecule mol1 rxn1_stp1_unreacted.molecule_template +Read molecule template mol1: + 1 molecules + 0 fragments + 18 atoms with max type 8 + 16 bonds with max type 10 + 25 angles with max type 28 + 23 dihedrals with max type 36 + 2 impropers with max type 3 +molecule mol2 rxn1_stp1_reacted.molecule_template +Read molecule template mol2: + 1 molecules + 0 fragments + 18 atoms with max type 9 + 17 bonds with max type 13 + 31 angles with max type 27 + 39 dihedrals with max type 33 + 0 impropers with max type 0 +molecule mol3 rxn1_stp2_unreacted.molecule_template +Read molecule template mol3: + 1 molecules + 0 fragments + 15 atoms with max type 9 + 14 bonds with max type 13 + 25 angles with max type 27 + 30 dihedrals with max type 33 + 0 impropers with max type 0 +molecule mol4 rxn1_stp2_reacted.molecule_template +Read molecule template mol4: + 1 molecules + 0 fragments + 15 atoms with max type 11 + 13 bonds with max type 15 + 19 angles with max type 29 + 16 dihedrals with max type 32 + 2 impropers with max type 13 + +thermo 50 + +# dump 1 all xyz 1 test_vis.xyz + +fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 5.0 mol1 mol2 rxn1_stp1_map prob v_prob1 1234 react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map prob v_prob2 1234 +WARNING: Fix bond/react: Atom affected by reaction rxn2 is too close to template edge (../fix_bond_react.cpp:2624) +dynamic group bond_react_MASTER_group defined +dynamic group statted_grp_REACT defined + +fix 1 statted_grp_REACT nvt temp 300 300 100 + +# optionally, you can customize behavior of reacting atoms, +# by using the internally-created 'bond_react_MASTER_group', like so: +fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1 + +thermo_style custom step temp press density v_prob1 v_prob2 f_myrxns[1] f_myrxns[2] + +# restart 100 restart1 restart2 + +run ${runsteps} +run 1000 + +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 + +PPPM initialization ... + using 12-bit tables for long-range coulomb (../kspace.cpp:342) + G vector (1/distance) = 0.05345967 + grid = 2 2 2 + stencil order = 5 + estimated absolute RMS force accuracy = 0.040225597 + estimated relative force accuracy = 0.00012113819 + using double precision KISS FFT + 3d grid and FFT values/proc = 343 8 +Generated 55 of 55 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 = 10 10 10 + 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 + bin: standard + (2) fix bond/react, occasional, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +WARNING: Inconsistent image flags (../domain.cpp:819) +Per MPI rank memory allocation (min/avg/max) = 33.78 | 33.78 | 33.78 Mbytes + Step Temp Press Density v_prob1 v_prob2 f_myrxns[1] f_myrxns[2] + 0 300 346.78165 0.0034851739 0.1 0 0 0 + 50 265.51039 -67.489756 0.0034851739 0.2 0 1 0 + 100 596.03388 -27.815189 0.0034851739 0.3 0 1 0 + 150 500.05269 2.9684972 0.0034851739 0.4 0 1 0 + 200 511.40295 56.791868 0.0034851739 0.5 0 1 0 + 250 375.95679 -4.0587677 0.0034851739 0.6 0 1 0 + 300 371.1629 -60.689059 0.0034851739 0.7 0 1 0 + 350 336.06545 8.6411023 0.0034851739 0.8 0 1 0 + 400 301.41962 50.628044 0.0034851739 0.9 0 1 0 + 450 281.08727 -15.590922 0.0034851739 1 0 1 0 + 500 297.35323 -9.5761786 0.0034851739 1.1 0 1 0 + 550 197.45298 3.6867353 0.0034851739 1.2 1 1 1 + 600 240.1748 -19.889198 0.0034851739 1.3 1 1 1 + 650 231.57018 -13.078808 0.0034851739 1.4 1 1 1 + 700 296.00816 -18.772183 0.0034851739 1.5 1 1 1 + 750 294.94016 15.43915 0.0034851739 1.6 1 1 1 + 800 316.51231 12.070563 0.0034851739 1.7 1 1 1 + 850 348.59373 9.0940092 0.0034851739 1.8 1 1 1 + 900 330.5264 -3.4868175 0.0034851739 1.9 1 1 1 + 950 307.02461 34.643373 0.0034851739 2 1 1 1 + 1000 250.06536 5.8440413 0.0034851739 2.1 1 1 1 +Loop time of 0.202863 on 1 procs for 1000 steps with 44 atoms + +Performance: 425.903 ns/day, 0.056 hours/ns, 4929.437 timesteps/s, 216.895 katom-step/s +100.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.025759 | 0.025759 | 0.025759 | 0.0 | 12.70 +Bond | 0.11024 | 0.11024 | 0.11024 | 0.0 | 54.34 +Kspace | 0.034344 | 0.034344 | 0.034344 | 0.0 | 16.93 +Neigh | 0.0015719 | 0.0015719 | 0.0015719 | 0.0 | 0.77 +Comm | 0.00045259 | 0.00045259 | 0.00045259 | 0.0 | 0.22 +Output | 0.0004759 | 0.0004759 | 0.0004759 | 0.0 | 0.23 +Modify | 0.028713 | 0.028713 | 0.028713 | 0.0 | 14.15 +Other | | 0.001307 | | | 0.64 + +Nlocal: 44 ave 44 max 44 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 3 ave 3 max 3 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 802 ave 802 max 802 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 802 +Ave neighs/atom = 18.227273 +Ave special neighs/atom = 9.9090909 +Neighbor list builds = 32 +Dangerous builds = 0 + +# write_restart restart_longrun +# write_data restart_longrun.data +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/reaction/tiny_nylon/log.4Nov2020.tiny_nylon.stabilized_variable_probability.g++.4 b/examples/PACKAGES/reaction/tiny_nylon/log.4Nov2020.tiny_nylon.stabilized_variable_probability.g++.4 new file mode 100644 index 0000000000..d85e7fb474 --- /dev/null +++ b/examples/PACKAGES/reaction/tiny_nylon/log.4Nov2020.tiny_nylon.stabilized_variable_probability.g++.4 @@ -0,0 +1,237 @@ +LAMMPS (4 Nov 2022) +# two monomer nylon example +# reaction produces a condensed water molecule + +units real + +boundary p p p + +atom_style full + +kspace_style pppm 1.0e-4 + +pair_style lj/class2/coul/long 8.5 + +angle_style class2 + +bond_style class2 + +dihedral_style class2 + +improper_style class2 + +read_data tiny_nylon.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 = (-25 -25 -25) to (25 25 25) + 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 ... + 44 atoms + reading velocities ... + 44 velocities + scanning bonds ... + 9 = max bonds/atom + scanning angles ... + 21 = max angles/atom + scanning dihedrals ... + 29 = max dihedrals/atom + scanning impropers ... + 29 = max impropers/atom + reading bonds ... + 42 bonds + reading angles ... + 74 angles + reading dihedrals ... + 100 dihedrals + reading impropers ... + 44 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 + 6 = max # of 1-3 neighbors + 12 = max # of 1-4 neighbors + 41 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.008 seconds + +variable runsteps equal 1000 +variable prob1 equal step/v_runsteps*2+0.1 +variable prob2 equal (step/v_runsteps)>0.5 + +velocity all create 300.0 4928459 dist gaussian + +molecule mol1 rxn1_stp1_unreacted.molecule_template +Read molecule template mol1: + 1 molecules + 0 fragments + 18 atoms with max type 8 + 16 bonds with max type 10 + 25 angles with max type 28 + 23 dihedrals with max type 36 + 2 impropers with max type 3 +molecule mol2 rxn1_stp1_reacted.molecule_template +Read molecule template mol2: + 1 molecules + 0 fragments + 18 atoms with max type 9 + 17 bonds with max type 13 + 31 angles with max type 27 + 39 dihedrals with max type 33 + 0 impropers with max type 0 +molecule mol3 rxn1_stp2_unreacted.molecule_template +Read molecule template mol3: + 1 molecules + 0 fragments + 15 atoms with max type 9 + 14 bonds with max type 13 + 25 angles with max type 27 + 30 dihedrals with max type 33 + 0 impropers with max type 0 +molecule mol4 rxn1_stp2_reacted.molecule_template +Read molecule template mol4: + 1 molecules + 0 fragments + 15 atoms with max type 11 + 13 bonds with max type 15 + 19 angles with max type 29 + 16 dihedrals with max type 32 + 2 impropers with max type 13 + +thermo 50 + +# dump 1 all xyz 1 test_vis.xyz + +fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 5.0 mol1 mol2 rxn1_stp1_map prob v_prob1 1234 react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map prob v_prob2 1234 +WARNING: Fix bond/react: Atom affected by reaction rxn2 is too close to template edge (../fix_bond_react.cpp:2624) +dynamic group bond_react_MASTER_group defined +dynamic group statted_grp_REACT defined + +fix 1 statted_grp_REACT nvt temp 300 300 100 + +# optionally, you can customize behavior of reacting atoms, +# by using the internally-created 'bond_react_MASTER_group', like so: +fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1 + +thermo_style custom step temp press density v_prob1 v_prob2 f_myrxns[1] f_myrxns[2] + +# restart 100 restart1 restart2 + +run ${runsteps} +run 1000 + +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 + +PPPM initialization ... + using 12-bit tables for long-range coulomb (../kspace.cpp:342) + G vector (1/distance) = 0.05345967 + grid = 2 2 2 + stencil order = 5 + estimated absolute RMS force accuracy = 0.040225597 + estimated relative force accuracy = 0.00012113819 + using double precision KISS FFT + 3d grid and FFT values/proc = 252 2 +Generated 55 of 55 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 = 10 10 10 + 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 + bin: standard + (2) fix bond/react, occasional, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +WARNING: Inconsistent image flags (../domain.cpp:819) +Per MPI rank memory allocation (min/avg/max) = 33.66 | 33.88 | 34.43 Mbytes + Step Temp Press Density v_prob1 v_prob2 f_myrxns[1] f_myrxns[2] + 0 300 346.78165 0.0034851739 0.1 0 0 0 + 50 275.80938 -29.158908 0.0034851739 0.2 0 1 0 + 100 751.80013 8.8967942 0.0034851739 0.3 0 1 0 + 150 412.82804 61.44542 0.0034851739 0.4 0 1 0 + 200 432.95275 81.052275 0.0034851739 0.5 0 1 0 + 250 338.65702 -39.770422 0.0034851739 0.6 0 1 0 + 300 326.15993 -46.690912 0.0034851739 0.7 0 1 0 + 350 286.66126 51.986782 0.0034851739 0.8 0 1 0 + 400 244.24575 25.460254 0.0034851739 0.9 0 1 0 + 450 294.06274 5.0448726 0.0034851739 1 0 1 0 + 500 280.71089 0.86710712 0.0034851739 1.1 0 1 0 + 550 241.94123 -5.7812057 0.0034851739 1.2 1 1 1 + 600 235.1535 61.669814 0.0034851739 1.3 1 1 1 + 650 359.33618 -22.053171 0.0034851739 1.4 1 1 1 + 700 329.37555 -4.7839581 0.0034851739 1.5 1 1 1 + 750 285.76974 11.553815 0.0034851739 1.6 1 1 1 + 800 303.29561 16.017529 0.0034851739 1.7 1 1 1 + 850 256.86479 8.7487305 0.0034851739 1.8 1 1 1 + 900 292.29316 -11.376211 0.0034851739 1.9 1 1 1 + 950 293.47531 -2.7153276 0.0034851739 2 1 1 1 + 1000 303.66454 -4.8603249 0.0034851739 2.1 1 1 1 +Loop time of 0.195512 on 4 procs for 1000 steps with 44 atoms + +Performance: 441.916 ns/day, 0.054 hours/ns, 5114.771 timesteps/s, 225.050 katom-step/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 | 0.000163 | 0.0068784 | 0.016583 | 8.5 | 3.52 +Bond | 0.00040383 | 0.028615 | 0.083462 | 20.0 | 14.64 +Kspace | 0.043566 | 0.10199 | 0.13314 | 11.4 | 52.16 +Neigh | 0.00096634 | 0.00097064 | 0.00097509 | 0.0 | 0.50 +Comm | 0.0052532 | 0.0093802 | 0.014076 | 3.2 | 4.80 +Output | 0.00039802 | 0.00043637 | 0.00050031 | 0.0 | 0.22 +Modify | 0.043549 | 0.045538 | 0.049781 | 1.2 | 23.29 +Other | | 0.001708 | | | 0.87 + +Nlocal: 11 ave 29 max 0 min +Histogram: 2 0 0 0 0 1 0 0 0 1 +Nghost: 32.5 ave 45 max 16 min +Histogram: 1 0 0 1 0 0 0 0 1 1 +Neighs: 196.25 ave 448 max 0 min +Histogram: 2 0 0 0 0 0 0 1 0 1 + +Total # of neighbors = 785 +Ave neighs/atom = 17.840909 +Ave special neighs/atom = 9.9090909 +Neighbor list builds = 27 +Dangerous builds = 0 + +# write_restart restart_longrun +# write_data restart_longrun.data +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/reaction/tiny_nylon/log.4Nov2020.tiny_nylon.unstabilized.g++.1 b/examples/PACKAGES/reaction/tiny_nylon/log.4Nov2020.tiny_nylon.unstabilized.g++.1 new file mode 100644 index 0000000000..5d696dae45 --- /dev/null +++ b/examples/PACKAGES/reaction/tiny_nylon/log.4Nov2020.tiny_nylon.unstabilized.g++.1 @@ -0,0 +1,228 @@ +LAMMPS (4 Nov 2022) +# two monomer nylon example +# reaction produces a condensed water molecule + +units real + +boundary p p p + +atom_style full + +kspace_style pppm 1.0e-4 + +pair_style lj/class2/coul/long 8.5 + +angle_style class2 + +bond_style class2 + +dihedral_style class2 + +improper_style class2 + +read_data tiny_nylon.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 = (-25 -25 -25) to (25 25 25) + 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 ... + 44 atoms + reading velocities ... + 44 velocities + scanning bonds ... + 9 = max bonds/atom + scanning angles ... + 21 = max angles/atom + scanning dihedrals ... + 29 = max dihedrals/atom + scanning impropers ... + 29 = max impropers/atom + reading bonds ... + 42 bonds + reading angles ... + 74 angles + reading dihedrals ... + 100 dihedrals + reading impropers ... + 44 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 + 6 = max # of 1-3 neighbors + 12 = max # of 1-4 neighbors + 41 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.008 seconds + + +velocity all create 300.0 4928459 dist gaussian + +molecule mol1 rxn1_stp1_unreacted.molecule_template +Read molecule template mol1: + 1 molecules + 0 fragments + 18 atoms with max type 8 + 16 bonds with max type 10 + 25 angles with max type 28 + 23 dihedrals with max type 36 + 2 impropers with max type 3 +molecule mol2 rxn1_stp1_reacted.molecule_template +Read molecule template mol2: + 1 molecules + 0 fragments + 18 atoms with max type 9 + 17 bonds with max type 13 + 31 angles with max type 27 + 39 dihedrals with max type 33 + 0 impropers with max type 0 +molecule mol3 rxn1_stp2_unreacted.molecule_template +Read molecule template mol3: + 1 molecules + 0 fragments + 15 atoms with max type 9 + 14 bonds with max type 13 + 25 angles with max type 27 + 30 dihedrals with max type 33 + 0 impropers with max type 0 +molecule mol4 rxn1_stp2_reacted.molecule_template +Read molecule template mol4: + 1 molecules + 0 fragments + 15 atoms with max type 11 + 13 bonds with max type 15 + 19 angles with max type 29 + 16 dihedrals with max type 32 + 2 impropers with max type 13 + +thermo 50 + +# dump 1 all xyz 1 test_vis.xyz + +fix myrxns all bond/react stabilization no react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map +WARNING: Fix bond/react: Atom affected by reaction rxn2 is too close to template edge (../fix_bond_react.cpp:2624) +dynamic group bond_react_MASTER_group defined + +fix 1 all nve/limit .03 + +thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] + +# restart 100 restart1 restart2 + +run 1000 + +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 + +PPPM initialization ... + using 12-bit tables for long-range coulomb (../kspace.cpp:342) + G vector (1/distance) = 0.05345967 + grid = 2 2 2 + stencil order = 5 + estimated absolute RMS force accuracy = 0.040225597 + estimated relative force accuracy = 0.00012113819 + using double precision KISS FFT + 3d grid and FFT values/proc = 343 8 +Generated 55 of 55 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 = 10 10 10 + 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 + bin: standard + (2) fix bond/react, occasional, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +WARNING: Inconsistent image flags (../domain.cpp:819) +Per MPI rank memory allocation (min/avg/max) = 33.72 | 33.72 | 33.72 Mbytes + Step Temp Press Density f_myrxns[1] f_myrxns[2] + 0 300 346.78165 0.0034851739 0 0 + 50 530.51001 -15.418012 0.0034851739 1 0 + 100 677.21327 16.545108 0.0034851739 1 1 + 150 386.79268 -28.445486 0.0034851739 1 1 + 200 380.29074 1.8065066 0.0034851739 1 1 + 250 353.27609 -7.3505628 0.0034851739 1 1 + 300 357.84405 -7.0569 0.0034851739 1 1 + 350 337.65224 54.441683 0.0034851739 1 1 + 400 322.54035 20.338902 0.0034851739 1 1 + 450 316.91217 44.76973 0.0034851739 1 1 + 500 345.40444 -8.2133383 0.0034851739 1 1 + 550 296.22085 -30.331582 0.0034851739 1 1 + 600 263.8024 -36.834323 0.0034851739 1 1 + 650 284.05699 1.2532577 0.0034851739 1 1 + 700 274.86269 4.6881357 0.0034851739 1 1 + 750 298.72284 -18.225831 0.0034851739 1 1 + 800 292.72143 -5.1622029 0.0034851739 1 1 + 850 279.30224 -10.72513 0.0034851739 1 1 + 900 284.97331 30.268801 0.0034851739 1 1 + 950 262.46089 16.98134 0.0034851739 1 1 + 1000 297.55359 28.583097 0.0034851739 1 1 +Loop time of 0.175951 on 1 procs for 1000 steps with 44 atoms + +Performance: 491.045 ns/day, 0.049 hours/ns, 5683.388 timesteps/s, 250.069 katom-step/s +99.6% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.022992 | 0.022992 | 0.022992 | 0.0 | 13.07 +Bond | 0.1045 | 0.1045 | 0.1045 | 0.0 | 59.39 +Kspace | 0.034057 | 0.034057 | 0.034057 | 0.0 | 19.36 +Neigh | 0.0013592 | 0.0013592 | 0.0013592 | 0.0 | 0.77 +Comm | 0.00040677 | 0.00040677 | 0.00040677 | 0.0 | 0.23 +Output | 0.00030929 | 0.00030929 | 0.00030929 | 0.0 | 0.18 +Modify | 0.01121 | 0.01121 | 0.01121 | 0.0 | 6.37 +Other | | 0.001118 | | | 0.64 + +Nlocal: 44 ave 44 max 44 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 8 ave 8 max 8 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 810 ave 810 max 810 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 810 +Ave neighs/atom = 18.409091 +Ave special neighs/atom = 9.9090909 +Neighbor list builds = 28 +Dangerous builds = 0 + +# write_restart restart_longrun +# write_data restart_longrun.data +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/reaction/tiny_nylon/log.4Nov2020.tiny_nylon.unstabilized.g++.4 b/examples/PACKAGES/reaction/tiny_nylon/log.4Nov2020.tiny_nylon.unstabilized.g++.4 new file mode 100644 index 0000000000..0b022918be --- /dev/null +++ b/examples/PACKAGES/reaction/tiny_nylon/log.4Nov2020.tiny_nylon.unstabilized.g++.4 @@ -0,0 +1,228 @@ +LAMMPS (4 Nov 2022) +# two monomer nylon example +# reaction produces a condensed water molecule + +units real + +boundary p p p + +atom_style full + +kspace_style pppm 1.0e-4 + +pair_style lj/class2/coul/long 8.5 + +angle_style class2 + +bond_style class2 + +dihedral_style class2 + +improper_style class2 + +read_data tiny_nylon.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 = (-25 -25 -25) to (25 25 25) + 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 ... + 44 atoms + reading velocities ... + 44 velocities + scanning bonds ... + 9 = max bonds/atom + scanning angles ... + 21 = max angles/atom + scanning dihedrals ... + 29 = max dihedrals/atom + scanning impropers ... + 29 = max impropers/atom + reading bonds ... + 42 bonds + reading angles ... + 74 angles + reading dihedrals ... + 100 dihedrals + reading impropers ... + 44 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 + 6 = max # of 1-3 neighbors + 12 = max # of 1-4 neighbors + 41 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.008 seconds + + +velocity all create 300.0 4928459 dist gaussian + +molecule mol1 rxn1_stp1_unreacted.molecule_template +Read molecule template mol1: + 1 molecules + 0 fragments + 18 atoms with max type 8 + 16 bonds with max type 10 + 25 angles with max type 28 + 23 dihedrals with max type 36 + 2 impropers with max type 3 +molecule mol2 rxn1_stp1_reacted.molecule_template +Read molecule template mol2: + 1 molecules + 0 fragments + 18 atoms with max type 9 + 17 bonds with max type 13 + 31 angles with max type 27 + 39 dihedrals with max type 33 + 0 impropers with max type 0 +molecule mol3 rxn1_stp2_unreacted.molecule_template +Read molecule template mol3: + 1 molecules + 0 fragments + 15 atoms with max type 9 + 14 bonds with max type 13 + 25 angles with max type 27 + 30 dihedrals with max type 33 + 0 impropers with max type 0 +molecule mol4 rxn1_stp2_reacted.molecule_template +Read molecule template mol4: + 1 molecules + 0 fragments + 15 atoms with max type 11 + 13 bonds with max type 15 + 19 angles with max type 29 + 16 dihedrals with max type 32 + 2 impropers with max type 13 + +thermo 50 + +# dump 1 all xyz 1 test_vis.xyz + +fix myrxns all bond/react stabilization no react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map +WARNING: Fix bond/react: Atom affected by reaction rxn2 is too close to template edge (../fix_bond_react.cpp:2624) +dynamic group bond_react_MASTER_group defined + +fix 1 all nve/limit .03 + +thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] + +# restart 100 restart1 restart2 + +run 1000 + +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 + +PPPM initialization ... + using 12-bit tables for long-range coulomb (../kspace.cpp:342) + G vector (1/distance) = 0.05345967 + grid = 2 2 2 + stencil order = 5 + estimated absolute RMS force accuracy = 0.040225597 + estimated relative force accuracy = 0.00012113819 + using double precision KISS FFT + 3d grid and FFT values/proc = 252 2 +Generated 55 of 55 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 = 10 10 10 + 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 + bin: standard + (2) fix bond/react, occasional, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +WARNING: Inconsistent image flags (../domain.cpp:819) +Per MPI rank memory allocation (min/avg/max) = 33.59 | 33.82 | 34.37 Mbytes + Step Temp Press Density f_myrxns[1] f_myrxns[2] + 0 300 346.78165 0.0034851739 0 0 + 50 530.51001 -15.418012 0.0034851739 1 0 + 100 677.21327 16.545108 0.0034851739 1 1 + 150 386.79268 -28.445486 0.0034851739 1 1 + 200 380.29074 1.8065066 0.0034851739 1 1 + 250 353.27609 -7.3505628 0.0034851739 1 1 + 300 357.84405 -7.0569 0.0034851739 1 1 + 350 337.65224 54.441683 0.0034851739 1 1 + 400 322.54035 20.338902 0.0034851739 1 1 + 450 316.91217 44.76973 0.0034851739 1 1 + 500 345.40444 -8.2133383 0.0034851739 1 1 + 550 296.22085 -30.331582 0.0034851739 1 1 + 600 263.8024 -36.834323 0.0034851739 1 1 + 650 284.05699 1.2532577 0.0034851739 1 1 + 700 274.86269 4.6881357 0.0034851739 1 1 + 750 298.72284 -18.225831 0.0034851739 1 1 + 800 292.72143 -5.1622029 0.0034851739 1 1 + 850 279.30224 -10.72513 0.0034851739 1 1 + 900 284.97331 30.268801 0.0034851739 1 1 + 950 262.46089 16.98134 0.0034851739 1 1 + 1000 297.55359 28.583097 0.0034851739 1 1 +Loop time of 0.179911 on 4 procs for 1000 steps with 44 atoms + +Performance: 480.238 ns/day, 0.050 hours/ns, 5558.315 timesteps/s, 244.566 katom-step/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 | 0.0001131 | 0.0060483 | 0.016546 | 8.7 | 3.36 +Bond | 0.00024262 | 0.027106 | 0.07455 | 18.6 | 15.07 +Kspace | 0.059795 | 0.11105 | 0.13995 | 9.9 | 61.72 +Neigh | 0.0012033 | 0.0012139 | 0.0012228 | 0.0 | 0.67 +Comm | 0.0056243 | 0.0098345 | 0.013482 | 2.9 | 5.47 +Output | 0.00025378 | 0.0002833 | 0.00034961 | 0.0 | 0.16 +Modify | 0.020145 | 0.02287 | 0.027899 | 2.1 | 12.71 +Other | | 0.001506 | | | 0.84 + +Nlocal: 11 ave 41 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 1 +Nghost: 34.5 ave 46 max 8 min +Histogram: 1 0 0 0 0 0 0 0 2 1 +Neighs: 202.5 ave 807 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 810 +Ave neighs/atom = 18.409091 +Ave special neighs/atom = 9.9090909 +Neighbor list builds = 28 +Dangerous builds = 0 + +# write_restart restart_longrun +# write_data restart_longrun.data +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/reaction/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.1 b/examples/PACKAGES/reaction/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.1 deleted file mode 100644 index de1167c652..0000000000 --- a/examples/PACKAGES/reaction/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.1 +++ /dev/null @@ -1,148 +0,0 @@ -LAMMPS (5 Jun 2019) -Reading data file ... - orthogonal box = (-25 -25 -25) to (25 25 25) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 44 atoms - reading velocities ... - 44 velocities - scanning bonds ... - 9 = max bonds/atom - scanning angles ... - 21 = max angles/atom - scanning dihedrals ... - 29 = max dihedrals/atom - scanning impropers ... - 29 = max impropers/atom - reading bonds ... - 42 bonds - reading angles ... - 74 angles - reading dihedrals ... - 100 dihedrals - reading impropers ... - 44 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 - 6 = max # of 1-3 neighbors - 12 = max # of 1-4 neighbors - 41 = max # of special neighbors - special bonds CPU = 0.000181113 secs - read_data CPU = 0.0251833 secs -Read molecule mol1: - 18 atoms with max type 8 - 16 bonds with max type 14 - 25 angles with max type 28 - 23 dihedrals with max type 36 - 14 impropers with max type 11 -Read molecule mol2: - 18 atoms with max type 9 - 17 bonds with max type 13 - 31 angles with max type 27 - 39 dihedrals with max type 33 - 20 impropers with max type 1 -Read molecule mol3: - 15 atoms with max type 9 - 14 bonds with max type 13 - 25 angles with max type 27 - 30 dihedrals with max type 33 - 16 impropers with max type 1 -Read molecule mol4: - 15 atoms with max type 11 - 13 bonds with max type 15 - 19 angles with max type 29 - 16 dihedrals with max type 32 - 10 impropers with max type 13 -WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (../fix_bond_react.cpp:1785) -WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (../fix_bond_react.cpp:1785) -dynamic group bond_react_MASTER_group defined -dynamic group statted_grp_REACT defined -PPPM initialization ... - using 12-bit tables for long-range coulomb (../kspace.cpp:319) - G vector (1/distance) = 0.0534597 - grid = 2 2 2 - stencil order = 5 - estimated absolute RMS force accuracy = 0.0402256 - estimated relative force accuracy = 0.000121138 - using double precision FFTs - 3d grid and FFT values/proc = 343 8 -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 = 10 10 10 - 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 -WARNING: Inconsistent image flags (../domain.cpp:784) -Per MPI rank memory allocation (min/avg/max) = 34.41 | 34.41 | 34.41 Mbytes -Step Temp Press Density f_myrxns[1] f_myrxns[2] - 0 300 346.78165 0.0034851739 0 0 - 50 293.70542 -52.547388 0.0034851739 1 0 - 100 276.36755 54.81826 0.0034851739 1 1 - 150 448.65869 16.874435 0.0034851739 1 1 - 200 379.84257 11.578545 0.0034851739 1 1 - 250 298.21983 90.656585 0.0034851739 1 1 - 300 333.3111 -30.139607 0.0034851739 1 1 - 350 266.57108 6.4505134 0.0034851739 1 1 - 400 264.05476 10.513204 0.0034851739 1 1 - 450 250.70418 -18.635379 0.0034851739 1 1 - 500 261.21632 10.231013 0.0034851739 1 1 - 550 309.89024 -8.8299506 0.0034851739 1 1 - 600 373.45851 30.368993 0.0034851739 1 1 - 650 338.26242 9.0362267 0.0034851739 1 1 - 700 295.67794 -5.6007538 0.0034851739 1 1 - 750 310.86563 -59.228181 0.0034851739 1 1 - 800 286.22678 -9.9022407 0.0034851739 1 1 - 850 218.42135 27.845352 0.0034851739 1 1 - 900 259.62551 24.216336 0.0034851739 1 1 - 950 250.21307 -14.560985 0.0034851739 1 1 - 1000 274.29245 -0.38768626 0.0034851739 1 1 -Loop time of 0.341061 on 1 procs for 1000 steps with 44 atoms - -Performance: 253.327 ns/day, 0.095 hours/ns, 2932.025 timesteps/s -87.9% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.031135 | 0.031135 | 0.031135 | 0.0 | 9.13 -Bond | 0.12623 | 0.12623 | 0.12623 | 0.0 | 37.01 -Kspace | 0.036491 | 0.036491 | 0.036491 | 0.0 | 10.70 -Neigh | 0.046395 | 0.046395 | 0.046395 | 0.0 | 13.60 -Comm | 0.0025396 | 0.0025396 | 0.0025396 | 0.0 | 0.74 -Output | 0.07775 | 0.07775 | 0.07775 | 0.0 | 22.80 -Modify | 0.019219 | 0.019219 | 0.019219 | 0.0 | 5.64 -Other | | 0.001306 | | | 0.38 - -Nlocal: 44 ave 44 max 44 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 2 ave 2 max 2 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 740 ave 740 max 740 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 740 -Ave neighs/atom = 16.8182 -Ave special neighs/atom = 9.77273 -Neighbor list builds = 1000 -Dangerous builds = 0 - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:00 diff --git a/examples/PACKAGES/reaction/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.4 b/examples/PACKAGES/reaction/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.4 deleted file mode 100644 index b9c7a3ba15..0000000000 --- a/examples/PACKAGES/reaction/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.4 +++ /dev/null @@ -1,148 +0,0 @@ -LAMMPS (5 Jun 2019) -Reading data file ... - orthogonal box = (-25 -25 -25) to (25 25 25) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 44 atoms - reading velocities ... - 44 velocities - scanning bonds ... - 9 = max bonds/atom - scanning angles ... - 21 = max angles/atom - scanning dihedrals ... - 29 = max dihedrals/atom - scanning impropers ... - 29 = max impropers/atom - reading bonds ... - 42 bonds - reading angles ... - 74 angles - reading dihedrals ... - 100 dihedrals - reading impropers ... - 44 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 - 6 = max # of 1-3 neighbors - 12 = max # of 1-4 neighbors - 41 = max # of special neighbors - special bonds CPU = 0.000178751 secs - read_data CPU = 0.0385782 secs -Read molecule mol1: - 18 atoms with max type 8 - 16 bonds with max type 14 - 25 angles with max type 28 - 23 dihedrals with max type 36 - 14 impropers with max type 11 -Read molecule mol2: - 18 atoms with max type 9 - 17 bonds with max type 13 - 31 angles with max type 27 - 39 dihedrals with max type 33 - 20 impropers with max type 1 -Read molecule mol3: - 15 atoms with max type 9 - 14 bonds with max type 13 - 25 angles with max type 27 - 30 dihedrals with max type 33 - 16 impropers with max type 1 -Read molecule mol4: - 15 atoms with max type 11 - 13 bonds with max type 15 - 19 angles with max type 29 - 16 dihedrals with max type 32 - 10 impropers with max type 13 -WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (../fix_bond_react.cpp:1785) -WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (../fix_bond_react.cpp:1785) -dynamic group bond_react_MASTER_group defined -dynamic group statted_grp_REACT defined -PPPM initialization ... - using 12-bit tables for long-range coulomb (../kspace.cpp:319) - G vector (1/distance) = 0.0534597 - grid = 2 2 2 - stencil order = 5 - estimated absolute RMS force accuracy = 0.0402256 - estimated relative force accuracy = 0.000121138 - using double precision FFTs - 3d grid and FFT values/proc = 252 2 -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 = 10 10 10 - 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 -WARNING: Inconsistent image flags (../domain.cpp:784) -Per MPI rank memory allocation (min/avg/max) = 34.42 | 34.77 | 35.45 Mbytes -Step Temp Press Density f_myrxns[1] f_myrxns[2] - 0 300 346.78165 0.0034851739 0 0 - 50 293.70542 -52.547388 0.0034851739 1 0 - 100 276.36755 54.81826 0.0034851739 1 1 - 150 448.65869 16.874435 0.0034851739 1 1 - 200 379.84257 11.578545 0.0034851739 1 1 - 250 298.21983 90.656585 0.0034851739 1 1 - 300 333.3111 -30.139607 0.0034851739 1 1 - 350 266.57108 6.4505134 0.0034851739 1 1 - 400 264.05476 10.513204 0.0034851739 1 1 - 450 250.70418 -18.635379 0.0034851739 1 1 - 500 261.21632 10.231013 0.0034851739 1 1 - 550 309.89024 -8.8299506 0.0034851739 1 1 - 600 373.45851 30.368993 0.0034851739 1 1 - 650 338.26242 9.0362267 0.0034851739 1 1 - 700 295.67794 -5.6007538 0.0034851739 1 1 - 750 310.86563 -59.228181 0.0034851739 1 1 - 800 286.22678 -9.9022407 0.0034851739 1 1 - 850 218.42135 27.845352 0.0034851739 1 1 - 900 259.62551 24.216336 0.0034851739 1 1 - 950 250.21307 -14.560985 0.0034851739 1 1 - 1000 274.29245 -0.38768626 0.0034851739 1 1 -Loop time of 0.271242 on 4 procs for 1000 steps with 44 atoms - -Performance: 318.535 ns/day, 0.075 hours/ns, 3686.747 timesteps/s -98.6% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.00023773 | 0.0077322 | 0.016042 | 8.4 | 2.85 -Bond | 0.00073385 | 0.032108 | 0.08446 | 19.4 | 11.84 -Kspace | 0.041659 | 0.098095 | 0.13373 | 12.3 | 36.16 -Neigh | 0.028894 | 0.029247 | 0.029558 | 0.1 | 10.78 -Comm | 0.012367 | 0.013642 | 0.01503 | 0.9 | 5.03 -Output | 0.032475 | 0.040504 | 0.061019 | 5.9 | 14.93 -Modify | 0.032934 | 0.049086 | 0.0577 | 4.3 | 18.10 -Other | | 0.0008281 | | | 0.31 - -Nlocal: 11 ave 21 max 0 min -Histogram: 1 1 0 0 0 0 0 0 0 2 -Nghost: 32.5 ave 43 max 23 min -Histogram: 2 0 0 0 0 0 0 0 0 2 -Neighs: 185 ave 376 max 0 min -Histogram: 2 0 0 0 0 0 0 0 0 2 - -Total # of neighbors = 740 -Ave neighs/atom = 16.8182 -Ave special neighs/atom = 9.77273 -Neighbor list builds = 1000 -Dangerous builds = 0 - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:00 diff --git a/examples/PACKAGES/reaction/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.1 b/examples/PACKAGES/reaction/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.1 deleted file mode 100644 index 14cac1dfad..0000000000 --- a/examples/PACKAGES/reaction/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.1 +++ /dev/null @@ -1,147 +0,0 @@ -LAMMPS (5 Jun 2019) -Reading data file ... - orthogonal box = (-25 -25 -25) to (25 25 25) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 44 atoms - reading velocities ... - 44 velocities - scanning bonds ... - 9 = max bonds/atom - scanning angles ... - 21 = max angles/atom - scanning dihedrals ... - 29 = max dihedrals/atom - scanning impropers ... - 29 = max impropers/atom - reading bonds ... - 42 bonds - reading angles ... - 74 angles - reading dihedrals ... - 100 dihedrals - reading impropers ... - 44 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 - 6 = max # of 1-3 neighbors - 12 = max # of 1-4 neighbors - 41 = max # of special neighbors - special bonds CPU = 0.000217102 secs - read_data CPU = 0.00630778 secs -Read molecule mol1: - 18 atoms with max type 8 - 16 bonds with max type 14 - 25 angles with max type 28 - 23 dihedrals with max type 36 - 14 impropers with max type 11 -Read molecule mol2: - 18 atoms with max type 9 - 17 bonds with max type 13 - 31 angles with max type 27 - 39 dihedrals with max type 33 - 20 impropers with max type 1 -Read molecule mol3: - 15 atoms with max type 9 - 14 bonds with max type 13 - 25 angles with max type 27 - 30 dihedrals with max type 33 - 16 impropers with max type 1 -Read molecule mol4: - 15 atoms with max type 11 - 13 bonds with max type 15 - 19 angles with max type 29 - 16 dihedrals with max type 32 - 10 impropers with max type 13 -WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (../fix_bond_react.cpp:1785) -WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (../fix_bond_react.cpp:1785) -dynamic group bond_react_MASTER_group defined -PPPM initialization ... - using 12-bit tables for long-range coulomb (../kspace.cpp:319) - G vector (1/distance) = 0.0534597 - grid = 2 2 2 - stencil order = 5 - estimated absolute RMS force accuracy = 0.0402256 - estimated relative force accuracy = 0.000121138 - using double precision FFTs - 3d grid and FFT values/proc = 343 8 -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 = 10 10 10 - 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 -WARNING: Inconsistent image flags (../domain.cpp:784) -Per MPI rank memory allocation (min/avg/max) = 34.35 | 34.35 | 34.35 Mbytes -Step Temp Press Density f_myrxns[1] f_myrxns[2] - 0 300 346.78165 0.0034851739 0 0 - 50 416.49412 -20.293038 0.0034851739 1 0 - 100 746.49323 91.912227 0.0034851739 1 1 - 150 515.15907 -1.4024709 0.0034851739 1 1 - 200 441.14572 -19.333087 0.0034851739 1 1 - 250 376.40996 30.717679 0.0034851739 1 1 - 300 326.15127 -3.0433799 0.0034851739 1 1 - 350 326.21116 6.235391 0.0034851739 1 1 - 400 366.48556 3.9807338 0.0034851739 1 1 - 450 313.79097 7.6674629 0.0034851739 1 1 - 500 278.89836 14.102052 0.0034851739 1 1 - 550 267.50214 18.241417 0.0034851739 1 1 - 600 276.28064 7.4649611 0.0034851739 1 1 - 650 255.26713 -8.5258573 0.0034851739 1 1 - 700 258.59752 -5.3341215 0.0034851739 1 1 - 750 263.71264 33.369869 0.0034851739 1 1 - 800 246.22976 -15.349137 0.0034851739 1 1 - 850 255.93887 16.331669 0.0034851739 1 1 - 900 239.72525 -0.20075789 0.0034851739 1 1 - 950 213.73064 12.17619 0.0034851739 1 1 - 1000 218.25094 -9.0955642 0.0034851739 1 1 -Loop time of 0.348252 on 1 procs for 1000 steps with 44 atoms - -Performance: 248.096 ns/day, 0.097 hours/ns, 2871.483 timesteps/s -91.8% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.031941 | 0.031941 | 0.031941 | 0.0 | 9.17 -Bond | 0.13031 | 0.13031 | 0.13031 | 0.0 | 37.42 -Kspace | 0.037554 | 0.037554 | 0.037554 | 0.0 | 10.78 -Neigh | 0.047397 | 0.047397 | 0.047397 | 0.0 | 13.61 -Comm | 0.0025814 | 0.0025814 | 0.0025814 | 0.0 | 0.74 -Output | 0.083526 | 0.083526 | 0.083526 | 0.0 | 23.98 -Modify | 0.013602 | 0.013602 | 0.013602 | 0.0 | 3.91 -Other | | 0.001336 | | | 0.38 - -Nlocal: 44 ave 44 max 44 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 3 ave 3 max 3 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 818 ave 818 max 818 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 818 -Ave neighs/atom = 18.5909 -Ave special neighs/atom = 9.77273 -Neighbor list builds = 1000 -Dangerous builds = 0 - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:00 diff --git a/examples/PACKAGES/reaction/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.4 b/examples/PACKAGES/reaction/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.4 deleted file mode 100644 index 6b13dd60d3..0000000000 --- a/examples/PACKAGES/reaction/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.4 +++ /dev/null @@ -1,147 +0,0 @@ -LAMMPS (5 Jun 2019) -Reading data file ... - orthogonal box = (-25 -25 -25) to (25 25 25) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 44 atoms - reading velocities ... - 44 velocities - scanning bonds ... - 9 = max bonds/atom - scanning angles ... - 21 = max angles/atom - scanning dihedrals ... - 29 = max dihedrals/atom - scanning impropers ... - 29 = max impropers/atom - reading bonds ... - 42 bonds - reading angles ... - 74 angles - reading dihedrals ... - 100 dihedrals - reading impropers ... - 44 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 - 6 = max # of 1-3 neighbors - 12 = max # of 1-4 neighbors - 41 = max # of special neighbors - special bonds CPU = 0.000163256 secs - read_data CPU = 0.0244579 secs -Read molecule mol1: - 18 atoms with max type 8 - 16 bonds with max type 14 - 25 angles with max type 28 - 23 dihedrals with max type 36 - 14 impropers with max type 11 -Read molecule mol2: - 18 atoms with max type 9 - 17 bonds with max type 13 - 31 angles with max type 27 - 39 dihedrals with max type 33 - 20 impropers with max type 1 -Read molecule mol3: - 15 atoms with max type 9 - 14 bonds with max type 13 - 25 angles with max type 27 - 30 dihedrals with max type 33 - 16 impropers with max type 1 -Read molecule mol4: - 15 atoms with max type 11 - 13 bonds with max type 15 - 19 angles with max type 29 - 16 dihedrals with max type 32 - 10 impropers with max type 13 -WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (../fix_bond_react.cpp:1785) -WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (../fix_bond_react.cpp:1785) -dynamic group bond_react_MASTER_group defined -PPPM initialization ... - using 12-bit tables for long-range coulomb (../kspace.cpp:319) - G vector (1/distance) = 0.0534597 - grid = 2 2 2 - stencil order = 5 - estimated absolute RMS force accuracy = 0.0402256 - estimated relative force accuracy = 0.000121138 - using double precision FFTs - 3d grid and FFT values/proc = 252 2 -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 = 10 10 10 - 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 -WARNING: Inconsistent image flags (../domain.cpp:784) -Per MPI rank memory allocation (min/avg/max) = 33.34 | 33.69 | 34.37 Mbytes -Step Temp Press Density f_myrxns[1] f_myrxns[2] - 0 300 346.78165 0.0034851739 0 0 - 50 416.49412 -20.293038 0.0034851739 1 0 - 100 746.49323 91.912227 0.0034851739 1 1 - 150 515.15907 -1.4024709 0.0034851739 1 1 - 200 441.14572 -19.333087 0.0034851739 1 1 - 250 376.40996 30.717679 0.0034851739 1 1 - 300 326.15127 -3.0433799 0.0034851739 1 1 - 350 326.21116 6.235391 0.0034851739 1 1 - 400 366.48556 3.9807338 0.0034851739 1 1 - 450 313.79097 7.6674629 0.0034851739 1 1 - 500 278.89836 14.102052 0.0034851739 1 1 - 550 267.50214 18.241417 0.0034851739 1 1 - 600 276.28064 7.4649611 0.0034851739 1 1 - 650 255.26713 -8.5258573 0.0034851739 1 1 - 700 258.59752 -5.3341215 0.0034851739 1 1 - 750 263.71264 33.369869 0.0034851739 1 1 - 800 246.22976 -15.349137 0.0034851739 1 1 - 850 255.93887 16.331669 0.0034851739 1 1 - 900 239.72525 -0.20075789 0.0034851739 1 1 - 950 213.73064 12.17619 0.0034851739 1 1 - 1000 218.25094 -9.0955642 0.0034851739 1 1 -Loop time of 0.254903 on 4 procs for 1000 steps with 44 atoms - -Performance: 338.952 ns/day, 0.071 hours/ns, 3923.053 timesteps/s -99.8% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.00014252 | 0.0090715 | 0.021332 | 9.6 | 3.56 -Bond | 0.00047028 | 0.037261 | 0.10789 | 22.7 | 14.62 -Kspace | 0.051006 | 0.12756 | 0.1693 | 13.6 | 50.04 -Neigh | 0.035644 | 0.036088 | 0.036523 | 0.2 | 14.16 -Comm | 0.013984 | 0.016074 | 0.018676 | 1.6 | 6.31 -Output | 0.0002816 | 0.00033726 | 0.00044251 | 0.0 | 0.13 -Modify | 0.023697 | 0.027803 | 0.033552 | 2.5 | 10.91 -Other | | 0.0007123 | | | 0.28 - -Nlocal: 11 ave 29 max 0 min -Histogram: 1 1 0 0 1 0 0 0 0 1 -Nghost: 25 ave 31 max 12 min -Histogram: 1 0 0 0 0 0 0 0 2 1 -Neighs: 204.5 ave 443 max 0 min -Histogram: 2 0 0 0 0 0 0 0 1 1 - -Total # of neighbors = 818 -Ave neighs/atom = 18.5909 -Ave special neighs/atom = 9.77273 -Neighbor list builds = 1000 -Dangerous builds = 0 - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:00 diff --git a/examples/PACKAGES/reaction/tiny_nylon/rxn1_stp1_reacted.data_template b/examples/PACKAGES/reaction/tiny_nylon/rxn1_stp1_reacted.data_template deleted file mode 100644 index d7256f43d2..0000000000 --- a/examples/PACKAGES/reaction/tiny_nylon/rxn1_stp1_reacted.data_template +++ /dev/null @@ -1,189 +0,0 @@ -this is a molecule template for: initial nylon crosslink, post-reacting - -18 atoms -17 bonds -31 angles -39 dihedrals -20 impropers - -Types - -1 9 -2 1 -3 1 -4 8 -5 8 -6 4 -7 4 -8 1 -9 1 -10 2 -11 6 -12 3 -13 4 -14 4 -15 5 -16 1 -17 4 -18 4 - -Charges - -1 -0.300000 -2 0.000000 -3 0.000000 -4 0.000000 -5 0.000000 -6 0.000000 -7 0.000000 -8 0.000000 -9 0.000000 -10 0.300000 -11 0.000000 -12 0.000000 -13 0.000000 -14 0.000000 -15 0.000000 -16 0.000000 -17 0.000000 -18 0.000000 - -Coords - -1 -5.522237 -0.752722 1.631158 -2 -5.170398 -0.545733 0.178130 -3 -6.469695 -0.553072 -0.648889 -4 -6.052076 -1.721152 1.744648 -5 -6.183059 0.071387 1.971497 -6 -4.489340 -1.389197 -0.173156 -7 -4.637591 0.453703 0.051252 -8 -5.618658 0.138919 4.386107 -9 -4.669492 -0.989819 3.943591 -10 -4.270194 -0.766405 2.474102 -11 -3.348470 -1.875393 2.024289 -12 -3.569794 0.564183 2.345995 -13 -5.201079 -1.993301 4.044219 -14 -3.736682 -0.984819 4.598305 -15 -4.255402 1.370923 2.679069 -16 -6.136394 -0.339866 -2.136775 -17 -6.996331 -1.555519 -0.517408 -18 -7.153308 0.284949 -0.289930 - -Bonds - -1 11 1 2 -2 12 1 4 -3 12 1 5 -4 13 1 10 -5 2 2 3 -6 1 2 6 -7 1 2 7 -8 2 3 16 -9 1 3 17 -10 1 3 18 -11 2 8 9 -12 4 9 10 -13 1 9 13 -14 1 9 14 -15 5 10 11 -16 3 10 12 -17 6 12 15 - -Angles - -1 17 2 1 4 -2 17 2 1 5 -3 18 2 1 10 -4 19 4 1 5 -5 20 4 1 10 -6 20 5 1 10 -7 21 1 2 3 -8 22 1 2 6 -9 22 1 2 7 -10 2 3 2 6 -11 2 3 2 7 -12 1 6 2 7 -13 3 2 3 16 -14 2 2 3 17 -15 2 2 3 18 -16 2 16 3 17 -17 2 16 3 18 -18 1 17 3 18 -19 8 8 9 10 -20 2 8 9 13 -21 2 8 9 14 -22 23 13 9 10 -23 23 14 9 10 -24 1 13 9 14 -25 6 9 10 11 -26 4 9 10 12 -27 24 1 10 9 -28 25 11 10 12 -29 26 1 10 11 -30 27 1 10 12 -31 7 10 12 15 - -Dihedrals - -1 19 4 1 2 3 -2 20 4 1 2 6 -3 20 4 1 2 7 -4 19 5 1 2 3 -5 20 5 1 2 6 -6 20 5 1 2 7 -7 21 10 1 2 3 -8 22 10 1 2 6 -9 22 10 1 2 7 -10 23 2 1 10 9 -11 24 2 1 10 11 -12 25 2 1 10 12 -13 26 4 1 10 9 -14 27 4 1 10 11 -15 28 4 1 10 12 -16 26 5 1 10 9 -17 27 5 1 10 11 -18 28 5 1 10 12 -19 29 1 2 3 16 -20 30 1 2 3 17 -21 30 1 2 3 18 -22 4 16 3 2 6 -23 2 6 2 3 17 -24 2 6 2 3 18 -25 4 16 3 2 7 -26 2 7 2 3 17 -27 2 7 2 3 18 -28 10 8 9 10 11 -29 8 8 9 10 12 -30 31 8 9 10 1 -31 11 13 9 10 11 -32 9 13 9 10 12 -33 32 13 9 10 1 -34 11 14 9 10 11 -35 9 14 9 10 12 -36 32 14 9 10 1 -37 6 9 10 12 15 -38 7 11 10 12 15 -39 33 1 10 12 15 - -Impropers - -1 1 2 1 4 5 -2 1 2 1 4 10 -3 1 2 1 5 10 -4 1 4 1 5 10 -5 1 1 2 3 6 -6 1 1 2 3 7 -7 1 1 2 6 7 -8 1 3 2 6 7 -9 1 2 3 16 17 -10 1 2 3 16 18 -11 1 2 3 17 18 -12 1 16 3 17 18 -13 1 8 9 13 10 -14 1 8 9 14 10 -15 1 8 9 13 14 -16 1 13 9 14 10 -17 1 9 10 11 12 -18 1 1 10 9 11 -19 1 1 10 9 12 -20 1 1 10 11 12 diff --git a/examples/PACKAGES/reaction/tiny_nylon/rxn1_stp1_reacted.molecule_template b/examples/PACKAGES/reaction/tiny_nylon/rxn1_stp1_reacted.molecule_template new file mode 100644 index 0000000000..40f3aa8276 --- /dev/null +++ b/examples/PACKAGES/reaction/tiny_nylon/rxn1_stp1_reacted.molecule_template @@ -0,0 +1,187 @@ +this is a molecule template for: initial nylon crosslink, post-reacting + + 18 atoms + 17 bonds + 31 angles + 39 dihedrals + 0 impropers + +Coords + + 1 -5.522237178 -0.752722499 1.631158408 + 2 -5.170398325 -0.545733378 0.178129978 + 3 -6.469694974 -0.553071841 -0.648889109 + 4 -6.052075697 -1.721152483 1.744647858 + 5 -6.183058842 0.071386755 1.971497329 + 6 -4.489339595 -1.389196844 -0.173156276 + 7 -4.637590712 0.453703382 0.051251954 + 8 -5.618657658 0.138918810 4.386106928 + 9 -4.669491736 -0.989818781 3.943591338 + 10 -4.270193542 -0.766405234 2.474102239 + 11 -3.348470373 -1.875393291 2.024289246 + 12 -3.569793683 0.564183226 2.345995471 + 13 -5.201078949 -1.993301389 4.044218837 + 14 -3.736681607 -0.984819193 4.598304847 + 15 -4.255401979 1.370923174 2.679069013 + 16 -6.136393628 -0.339866195 -2.136774990 + 17 -6.996331494 -1.555519161 -0.517408063 + 18 -7.153308038 0.284949373 -0.289930394 + +Types + + 1 n + 2 c2 + 3 c2 + 4 hn + 5 hn + 6 hc + 7 hc + 8 c2 + 9 c2 + 10 c_1 + 11 o_1 + 12 o + 13 hc + 14 hc + 15 ho + 16 c2 + 17 hc + 18 hc + +Charges + + 1 -0.300000 + 2 0.000000 + 3 0.000000 + 4 0.000000 + 5 0.000000 + 6 0.000000 + 7 0.000000 + 8 0.000000 + 9 0.000000 + 10 0.300000 + 11 0.000000 + 12 0.000000 + 13 0.000000 + 14 0.000000 + 15 0.000000 + 16 0.000000 + 17 0.000000 + 18 0.000000 + +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 + +Bonds + + 1 n-c2 1 2 + 2 n-hn 1 4 + 3 n-hn 1 5 + 4 n-c_1 1 10 + 5 c2-c2 2 3 + 6 c2-hc 2 6 + 7 c2-hc 2 7 + 8 c2-c2 3 16 + 9 c2-hc 3 17 + 10 c2-hc 3 18 + 11 c2-c2 8 9 + 12 c2-c_1 9 10 + 13 c2-hc 9 13 + 14 c2-hc 9 14 + 15 c_1-o_1 10 11 + 16 c_1-o 10 12 + 17 o-ho 12 15 + +Angles + + 1 c2-n-hn 2 1 4 + 2 c2-n-hn 2 1 5 + 3 c2-n-c_1 2 1 10 + 4 hn-n-hn 4 1 5 + 5 hn-n-c_1 4 1 10 + 6 hn-n-c_1 5 1 10 + 7 n-c2-c2 1 2 3 + 8 n-c2-hc 1 2 6 + 9 n-c2-hc 1 2 7 + 10 c2-c2-hc 3 2 6 + 11 c2-c2-hc 3 2 7 + 12 hc-c2-hc 6 2 7 + 13 c2-c2-c2 2 3 16 + 14 c2-c2-hc 2 3 17 + 15 c2-c2-hc 2 3 18 + 16 c2-c2-hc 16 3 17 + 17 c2-c2-hc 16 3 18 + 18 hc-c2-hc 17 3 18 + 19 c2-c2-c_1 8 9 10 + 20 c2-c2-hc 8 9 13 + 21 c2-c2-hc 8 9 14 + 22 hc-c2-c_1 13 9 10 + 23 hc-c2-c_1 14 9 10 + 24 hc-c2-hc 13 9 14 + 25 c2-c_1-o_1 9 10 11 + 26 c2-c_1-o 9 10 12 + 27 n-c_1-c2 1 10 9 + 28 o_1-c_1-o 11 10 12 + 29 n-c_1-o_1 1 10 11 + 30 n-c_1-o 1 10 12 + 31 c_1-o-ho 10 12 15 + +Dihedrals + + 1 hn-n-c2-c2 4 1 2 3 + 2 hn-n-c2-hc 4 1 2 6 + 3 hn-n-c2-hc 4 1 2 7 + 4 hn-n-c2-c2 5 1 2 3 + 5 hn-n-c2-hc 5 1 2 6 + 6 hn-n-c2-hc 5 1 2 7 + 7 c_1-n-c2-c2 10 1 2 3 + 8 c_1-n-c2-hc 10 1 2 6 + 9 c_1-n-c2-hc 10 1 2 7 + 10 c2-n-c_1-c2 2 1 10 9 + 11 c2-n-c_1-o_1 2 1 10 11 + 12 c2-n-c_1-o 2 1 10 12 + 13 hn-n-c_1-c2 4 1 10 9 + 14 hn-n-c_1-o_1 4 1 10 11 + 15 hn-n-c_1-o 4 1 10 12 + 16 hn-n-c_1-c2 5 1 10 9 + 17 hn-n-c_1-o_1 5 1 10 11 + 18 hn-n-c_1-o 5 1 10 12 + 19 n-c2-c2-c2 1 2 3 16 + 20 n-c2-c2-hc 1 2 3 17 + 21 n-c2-c2-hc 1 2 3 18 + 22 c2-c2-c2-hc 16 3 2 6 + 23 hc-c2-c2-hc 6 2 3 17 + 24 hc-c2-c2-hc 6 2 3 18 + 25 c2-c2-c2-hc 16 3 2 7 + 26 hc-c2-c2-hc 7 2 3 17 + 27 hc-c2-c2-hc 7 2 3 18 + 28 c2-c2-c_1-o_1 8 9 10 11 + 29 c2-c2-c_1-o 8 9 10 12 + 30 c2-c2-c_1-n 8 9 10 1 + 31 hc-c2-c_1-o_1 13 9 10 11 + 32 hc-c2-c_1-o 13 9 10 12 + 33 hc-c2-c_1-n 13 9 10 1 + 34 hc-c2-c_1-o_1 14 9 10 11 + 35 hc-c2-c_1-o 14 9 10 12 + 36 hc-c2-c_1-n 14 9 10 1 + 37 c2-c_1-o-ho 9 10 12 15 + 38 o_1-c_1-o-ho 11 10 12 15 + 39 n-c_1-o-ho 1 10 12 15 diff --git a/examples/PACKAGES/reaction/tiny_nylon/rxn1_stp1_unreacted.data_template b/examples/PACKAGES/reaction/tiny_nylon/rxn1_stp1_unreacted.data_template deleted file mode 100644 index ec3f109d7b..0000000000 --- a/examples/PACKAGES/reaction/tiny_nylon/rxn1_stp1_unreacted.data_template +++ /dev/null @@ -1,160 +0,0 @@ -this is a molecule template for: initial nylon crosslink, pre-reacting - -18 atoms -16 bonds -25 angles -23 dihedrals -14 impropers - -Types - -1 7 -2 1 -3 1 -4 8 -5 8 -6 4 -7 4 -8 1 -9 1 -10 2 -11 6 -12 3 -13 4 -14 4 -15 5 -16 1 -17 4 -18 4 - -Charges - -1 -0.300000 -2 0.000000 -3 0.000000 -4 0.000000 -5 0.000000 -6 0.000000 -7 0.000000 -8 0.000000 -9 0.000000 -10 0.300000 -11 0.000000 -12 0.000000 -13 0.000000 -14 0.000000 -15 0.000000 -16 0.000000 -17 0.000000 -18 0.000000 - -Coords - -1 -4.922858 -0.946982 1.146055 -2 -5.047195 -0.935267 -0.358173 -3 -6.526281 -0.755366 -0.743523 -4 -5.282604 0.020447 1.552710 -5 -3.860697 -1.095850 1.428305 -6 -4.662382 -1.920900 -0.781524 -7 -4.433977 -0.072765 -0.784071 -8 -5.506279 0.202610 4.825816 -9 -4.449177 -0.844592 4.423366 -10 -4.103916 -0.749629 2.925195 -11 -3.376249 -1.886171 2.245643 -12 -4.493235 0.477214 2.137199 -13 -4.849053 -1.888877 4.663994 -14 -3.491823 -0.662913 5.018510 -15 -5.020777 1.189745 2.805427 -16 -3.964987 2.900602 -1.551341 -17 -4.460694 2.836102 0.668882 -18 -4.828494 3.219656 -0.122111 - -Bonds - -1 14 1 2 -2 10 1 4 -3 10 1 5 -4 2 2 3 -5 1 2 6 -6 1 2 7 -7 2 3 16 -8 1 3 17 -9 1 3 18 -10 2 8 9 -11 4 9 10 -12 1 9 13 -13 1 9 14 -14 5 10 11 -15 3 10 12 -16 6 12 15 - -Angles - -1 15 2 1 4 -2 15 2 1 5 -3 16 4 1 5 -4 28 1 2 3 -5 14 1 2 6 -6 14 1 2 7 -7 2 3 2 6 -8 2 3 2 7 -9 1 6 2 7 -10 3 2 3 16 -11 2 2 3 17 -12 2 2 3 18 -13 2 16 3 17 -14 2 16 3 18 -15 1 17 3 18 -16 8 8 9 10 -17 2 8 9 13 -18 2 8 9 14 -19 23 13 9 10 -20 23 14 9 10 -21 1 13 9 14 -22 6 9 10 11 -23 4 9 10 12 -24 25 11 10 12 -25 7 10 12 15 - -Dihedrals - -1 34 4 1 2 3 -2 35 4 1 2 6 -3 35 4 1 2 7 -4 34 5 1 2 3 -5 35 5 1 2 6 -6 35 5 1 2 7 -7 36 1 2 3 16 -8 12 1 2 3 17 -9 12 1 2 3 18 -10 4 16 3 2 6 -11 2 6 2 3 17 -12 2 6 2 3 18 -13 4 16 3 2 7 -14 2 7 2 3 17 -15 2 7 2 3 18 -16 10 8 9 10 11 -17 8 8 9 10 12 -18 11 13 9 10 11 -19 9 13 9 10 12 -20 11 14 9 10 11 -21 9 14 9 10 12 -22 6 9 10 12 15 -23 7 11 10 12 15 - -Impropers - -1 6 2 1 4 5 -2 11 9 10 11 12 -3 1 1 2 3 6 -4 1 1 2 3 7 -5 1 1 2 6 7 -6 1 3 2 6 7 -7 1 2 3 16 17 -8 1 2 3 16 18 -9 1 2 3 17 18 -10 1 16 3 17 18 -11 1 8 9 13 10 -12 1 8 9 14 10 -13 1 8 9 13 14 -14 1 13 9 14 10 diff --git a/examples/PACKAGES/reaction/tiny_nylon/rxn1_stp1_unreacted.molecule_template b/examples/PACKAGES/reaction/tiny_nylon/rxn1_stp1_unreacted.molecule_template new file mode 100644 index 0000000000..7de7512f1c --- /dev/null +++ b/examples/PACKAGES/reaction/tiny_nylon/rxn1_stp1_unreacted.molecule_template @@ -0,0 +1,169 @@ +this is a molecule template for: initial nylon crosslink, pre-reacting + + 18 atoms + 16 bonds + 25 angles + 23 dihedrals + 2 impropers + +Coords + + 1 -4.922858499 -0.946981747 1.146055346 + 2 -5.047194816 -0.935266843 -0.358172771 + 3 -6.526281447 -0.755365854 -0.743523227 + 4 -5.282604074 0.020446894 1.552710361 + 5 -3.860696509 -1.095850190 1.428304925 + 6 -4.662381862 -1.920899862 -0.781524026 + 7 -4.433976540 -0.072765142 -0.784070641 + 8 -5.506279186 0.202610302 4.825815562 + 9 -4.449176624 -0.844592213 4.423366146 + 10 -4.103915981 -0.749628655 2.925195217 + 11 -3.376248536 -1.886171498 2.245643443 + 12 -4.493235430 0.477213651 2.137199034 + 13 -4.849052953 -1.888876753 4.663993750 + 14 -3.491822950 -0.662913310 5.018510248 + 15 -5.020776528 1.189745133 2.805427194 + 16 -3.964987378 2.900602044 -1.551341170 + 17 -4.460693773 2.836101897 0.668881952 + 18 -4.828494000 3.219655862 -0.122111278 + +Types + + 1 na + 2 c2 + 3 c2 + 4 hn + 5 hn + 6 hc + 7 hc + 8 c2 + 9 c2 + 10 c_1 + 11 o_1 + 12 o + 13 hc + 14 hc + 15 ho + 16 c2 + 17 hc + 18 hc + +Charges + + 1 -0.300000 + 2 0.000000 + 3 0.000000 + 4 0.000000 + 5 0.000000 + 6 0.000000 + 7 0.000000 + 8 0.000000 + 9 0.000000 + 10 0.300000 + 11 0.000000 + 12 0.000000 + 13 0.000000 + 14 0.000000 + 15 0.000000 + 16 0.000000 + 17 0.000000 + 18 0.000000 + +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 + +Bonds + + 1 na-c2 1 2 + 2 na-hn 1 4 + 3 na-hn 1 5 + 4 c2-c2 2 3 + 5 c2-hc 2 6 + 6 c2-hc 2 7 + 7 c2-c2 3 16 + 8 c2-hc 3 17 + 9 c2-hc 3 18 + 10 c2-c2 8 9 + 11 c2-c_1 9 10 + 12 c2-hc 9 13 + 13 c2-hc 9 14 + 14 c_1-o_1 10 11 + 15 c_1-o 10 12 + 16 o-ho 12 15 + +Angles + + 1 c2-na-hn 2 1 4 + 2 c2-na-hn 2 1 5 + 3 hn-na-hn 4 1 5 + 4 na-c2-c2 1 2 3 + 5 na-c2-hc 1 2 6 + 6 na-c2-hc 1 2 7 + 7 c2-c2-hc 3 2 6 + 8 c2-c2-hc 3 2 7 + 9 hc-c2-hc 6 2 7 + 10 c2-c2-c2 2 3 16 + 11 c2-c2-hc 2 3 17 + 12 c2-c2-hc 2 3 18 + 13 c2-c2-hc 16 3 17 + 14 c2-c2-hc 16 3 18 + 15 hc-c2-hc 17 3 18 + 16 c2-c2-c_1 8 9 10 + 17 c2-c2-hc 8 9 13 + 18 c2-c2-hc 8 9 14 + 19 hc-c2-c_1 13 9 10 + 20 hc-c2-c_1 14 9 10 + 21 hc-c2-hc 13 9 14 + 22 c2-c_1-o_1 9 10 11 + 23 c2-c_1-o 9 10 12 + 24 o_1-c_1-o 11 10 12 + 25 c_1-o-ho 10 12 15 + +Dihedrals + + 1 hn-na-c2-c2 4 1 2 3 + 2 hn-na-c2-hc 4 1 2 6 + 3 hn-na-c2-hc 4 1 2 7 + 4 hn-na-c2-c2 5 1 2 3 + 5 hn-na-c2-hc 5 1 2 6 + 6 hn-na-c2-hc 5 1 2 7 + 7 na-c2-c2-c2 1 2 3 16 + 8 na-c2-c2-hc 1 2 3 17 + 9 na-c2-c2-hc 1 2 3 18 + 10 c2-c2-c2-hc 16 3 2 6 + 11 hc-c2-c2-hc 6 2 3 17 + 12 hc-c2-c2-hc 6 2 3 18 + 13 c2-c2-c2-hc 16 3 2 7 + 14 hc-c2-c2-hc 7 2 3 17 + 15 hc-c2-c2-hc 7 2 3 18 + 16 c2-c2-c_1-o_1 8 9 10 11 + 17 c2-c2-c_1-o 8 9 10 12 + 18 hc-c2-c_1-o_1 13 9 10 11 + 19 hc-c2-c_1-o 13 9 10 12 + 20 hc-c2-c_1-o_1 14 9 10 11 + 21 hc-c2-c_1-o 14 9 10 12 + 22 c2-c_1-o-ho 9 10 12 15 + 23 o_1-c_1-o-ho 11 10 12 15 + +Impropers + + 1 c2-na-hn-hn 2 1 4 5 + 2 c2-c_1-o_1-o 9 10 11 12 diff --git a/examples/PACKAGES/reaction/tiny_nylon/rxn1_stp2_reacted.data_template b/examples/PACKAGES/reaction/tiny_nylon/rxn1_stp2_reacted.data_template deleted file mode 100644 index 7853634646..0000000000 --- a/examples/PACKAGES/reaction/tiny_nylon/rxn1_stp2_reacted.data_template +++ /dev/null @@ -1,131 +0,0 @@ -this is a molecule template for: water condensation, post-reacting - -15 atoms -13 bonds -19 angles -16 dihedrals -10 impropers - -Types - -1 9 -2 1 -3 1 -4 10 -5 8 -6 4 -7 4 -8 1 -9 1 -10 2 -11 6 -12 11 -13 4 -14 4 -15 10 - -Charges - -1 -0.300000 -2 0.000000 -3 0.000000 -4 0.410000 -5 0.000000 -6 0.000000 -7 0.000000 -8 0.000000 -9 0.000000 -10 0.300000 -11 0.000000 -12 -0.820000 -13 0.000000 -14 0.000000 -15 0.410000 - -Coords - -1 -4.856280 -1.050468 1.432625 -2 -5.047195 -0.935267 -0.358173 -3 -6.526281 -0.755366 -0.743523 -4 -5.282604 0.020447 1.552710 -5 -3.860697 -1.095850 1.428305 -6 -4.662382 -1.920900 -0.781524 -7 -4.433977 -0.072765 -0.784071 -8 -5.506279 0.202610 4.825816 -9 -4.449177 -0.844592 4.423366 -10 -4.103916 -0.749629 2.925195 -11 -3.376249 -1.886171 2.245643 -12 -4.493235 0.477214 2.137199 -13 -4.849053 -1.888877 4.663994 -14 -3.491823 -0.662913 5.018510 -15 -5.020777 1.189745 2.805427 - -Bonds - -1 11 1 2 -2 12 1 5 -3 13 1 10 -4 2 2 3 -5 1 2 6 -6 1 2 7 -7 15 4 12 -8 2 8 9 -9 4 9 10 -10 1 9 13 -11 1 9 14 -12 5 10 11 -13 15 15 12 - -Angles - -1 17 2 1 5 -2 18 2 1 10 -3 20 5 1 10 -4 21 1 2 3 -5 22 1 2 6 -6 22 1 2 7 -7 2 3 2 6 -8 2 3 2 7 -9 1 6 2 7 -10 8 8 9 10 -11 2 8 9 13 -12 2 8 9 14 -13 23 13 9 10 -14 23 14 9 10 -15 1 13 9 14 -16 6 9 10 11 -17 24 1 10 9 -18 26 1 10 11 -19 29 15 12 4 - -Dihedrals - -1 19 5 1 2 3 -2 20 5 1 2 6 -3 20 5 1 2 7 -4 21 10 1 2 3 -5 22 10 1 2 6 -6 22 10 1 2 7 -7 23 2 1 10 9 -8 24 2 1 10 11 -9 26 5 1 10 9 -10 27 5 1 10 11 -11 10 8 9 10 11 -12 31 8 9 10 1 -13 11 13 9 10 11 -14 32 13 9 10 1 -15 11 14 9 10 11 -16 32 14 9 10 1 - -Impropers - -1 12 2 1 5 10 -2 13 1 10 9 11 -3 1 1 2 3 6 -4 1 1 2 3 7 -5 1 1 2 6 7 -6 1 3 2 6 7 -7 1 8 9 13 10 -8 1 8 9 14 10 -9 1 8 9 13 14 -10 1 13 9 14 10 diff --git a/examples/PACKAGES/reaction/tiny_nylon/rxn1_stp2_reacted.molecule_template b/examples/PACKAGES/reaction/tiny_nylon/rxn1_stp2_reacted.molecule_template new file mode 100644 index 0000000000..2e91261468 --- /dev/null +++ b/examples/PACKAGES/reaction/tiny_nylon/rxn1_stp2_reacted.molecule_template @@ -0,0 +1,141 @@ +this is a molecule template for: water condensation, post-reacting + + 15 atoms + 13 bonds + 19 angles + 16 dihedrals + 2 impropers + +Coords + + 1 -4.856280281 -1.050467974 1.432625159 + 2 -5.047194816 -0.935266843 -0.358172771 + 3 -6.526281447 -0.755365854 -0.743523227 + 4 -5.282604074 0.020446894 1.552710361 + 5 -3.860696509 -1.095850190 1.428304925 + 6 -4.662381862 -1.920899862 -0.781524026 + 7 -4.433976540 -0.072765142 -0.784070641 + 8 -5.506279186 0.202610302 4.825815562 + 9 -4.449176624 -0.844592213 4.423366146 + 10 -4.103915981 -0.749628655 2.925195217 + 11 -3.376248536 -1.886171498 2.245643443 + 12 -4.493235430 0.477213651 2.137199034 + 13 -4.849052953 -1.888876753 4.663993750 + 14 -3.491822950 -0.662913310 5.018510248 + 15 -5.020776528 1.189745133 2.805427194 + +Types + + 1 n + 2 c2 + 3 c2 + 4 hw + 5 hn + 6 hc + 7 hc + 8 c2 + 9 c2 + 10 c_1 + 11 o_1 + 12 o* + 13 hc + 14 hc + 15 hw + +Charges + + 1 -0.300000 + 2 0.000000 + 3 0.000000 + 4 0.410000 + 5 0.000000 + 6 0.000000 + 7 0.000000 + 8 0.000000 + 9 0.000000 + 10 0.300000 + 11 0.000000 + 12 -0.820000 + 13 0.000000 + 14 0.000000 + 15 0.410000 + +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 + +Bonds + + 1 n-c2 1 2 + 2 n-hn 1 5 + 3 n-c_1 1 10 + 4 c2-c2 2 3 + 5 c2-hc 2 6 + 6 c2-hc 2 7 + 7 hw-o* 4 12 + 8 c2-c2 8 9 + 9 c2-c_1 9 10 + 10 c2-hc 9 13 + 11 c2-hc 9 14 + 12 c_1-o_1 10 11 + 13 hw-o* 15 12 + +Angles + + 1 c2-n-hn 2 1 5 + 2 c2-n-c_1 2 1 10 + 3 hn-n-c_1 5 1 10 + 4 n-c2-c2 1 2 3 + 5 n-c2-hc 1 2 6 + 6 n-c2-hc 1 2 7 + 7 c2-c2-hc 3 2 6 + 8 c2-c2-hc 3 2 7 + 9 hc-c2-hc 6 2 7 + 10 c2-c2-c_1 8 9 10 + 11 c2-c2-hc 8 9 13 + 12 c2-c2-hc 8 9 14 + 13 hc-c2-c_1 13 9 10 + 14 hc-c2-c_1 14 9 10 + 15 hc-c2-hc 13 9 14 + 16 c2-c_1-o_1 9 10 11 + 17 n-c_1-c2 1 10 9 + 18 n-c_1-o_1 1 10 11 + 19 hw-o*-hw 15 12 4 + +Dihedrals + + 1 hn-n-c2-c2 5 1 2 3 + 2 hn-n-c2-hc 5 1 2 6 + 3 hn-n-c2-hc 5 1 2 7 + 4 c_1-n-c2-c2 10 1 2 3 + 5 c_1-n-c2-hc 10 1 2 6 + 6 c_1-n-c2-hc 10 1 2 7 + 7 c2-n-c_1-c2 2 1 10 9 + 8 c2-n-c_1-o_1 2 1 10 11 + 9 hn-n-c_1-c2 5 1 10 9 + 10 hn-n-c_1-o_1 5 1 10 11 + 11 c2-c2-c_1-o_1 8 9 10 11 + 12 c2-c2-c_1-n 8 9 10 1 + 13 hc-c2-c_1-o_1 13 9 10 11 + 14 hc-c2-c_1-n 13 9 10 1 + 15 hc-c2-c_1-o_1 14 9 10 11 + 16 hc-c2-c_1-n 14 9 10 1 + +Impropers + + 1 c2-n-hn-c_1 2 1 5 10 + 2 n-c_1-c2-o_1 1 10 9 11 diff --git a/examples/PACKAGES/reaction/tiny_nylon/rxn1_stp2_unreacted.data_template b/examples/PACKAGES/reaction/tiny_nylon/rxn1_stp2_unreacted.data_template deleted file mode 100644 index 847f0622e5..0000000000 --- a/examples/PACKAGES/reaction/tiny_nylon/rxn1_stp2_unreacted.data_template +++ /dev/null @@ -1,158 +0,0 @@ -this is a molecule template for: water condensation, pre-reacting - -15 atoms -14 bonds -25 angles -30 dihedrals -16 impropers - -Types - -1 9 -2 1 -3 1 -4 8 -5 8 -6 4 -7 4 -8 1 -9 1 -10 2 -11 6 -12 3 -13 4 -14 4 -15 5 - -Charges - -1 -0.300000 -2 0.000000 -3 0.000000 -4 0.000000 -5 0.000000 -6 0.000000 -7 0.000000 -8 0.000000 -9 0.000000 -10 0.300000 -11 0.000000 -12 0.000000 -13 0.000000 -14 0.000000 -15 0.000000 - -Coords - -1 -4.922858 -0.946982 1.146055 -2 -5.047195 -0.935267 -0.358173 -3 -6.526281 -0.755366 -0.743523 -4 -5.282604 0.020447 1.552710 -5 -3.860697 -1.095850 1.428305 -6 -4.662382 -1.920900 -0.781524 -7 -4.433977 -0.072765 -0.784071 -8 -5.506279 0.202610 4.825816 -9 -4.449177 -0.844592 4.423366 -10 -4.103916 -0.749629 2.925195 -11 -3.376249 -1.886171 2.245643 -12 -4.493235 0.477214 2.137199 -13 -4.849053 -1.888877 4.663994 -14 -3.491823 -0.662913 5.018510 -15 -5.020777 1.189745 2.805427 - -Bonds - -1 11 1 2 -2 12 1 4 -3 12 1 5 -4 13 1 10 -5 2 2 3 -6 1 2 6 -7 1 2 7 -8 2 8 9 -9 4 9 10 -10 1 9 13 -11 1 9 14 -12 5 10 11 -13 3 10 12 -14 6 12 15 - -Angles - -1 17 2 1 4 -2 17 2 1 5 -3 18 2 1 10 -4 19 4 1 5 -5 20 4 1 10 -6 20 5 1 10 -7 21 1 2 3 -8 22 1 2 6 -9 22 1 2 7 -10 2 3 2 6 -11 2 3 2 7 -12 1 6 2 7 -13 8 8 9 10 -14 2 8 9 13 -15 2 8 9 14 -16 23 13 9 10 -17 23 14 9 10 -18 1 13 9 14 -19 6 9 10 11 -20 4 9 10 12 -21 24 1 10 9 -22 25 11 10 12 -23 26 1 10 11 -24 27 1 10 12 -25 7 10 12 15 - -Dihedrals - -1 19 4 1 2 3 -2 20 4 1 2 6 -3 20 4 1 2 7 -4 19 5 1 2 3 -5 20 5 1 2 6 -6 20 5 1 2 7 -7 21 10 1 2 3 -8 22 10 1 2 6 -9 22 10 1 2 7 -10 23 2 1 10 9 -11 24 2 1 10 11 -12 25 2 1 10 12 -13 26 4 1 10 9 -14 27 4 1 10 11 -15 28 4 1 10 12 -16 26 5 1 10 9 -17 27 5 1 10 11 -18 28 5 1 10 12 -19 10 8 9 10 11 -20 8 8 9 10 12 -21 31 8 9 10 1 -22 11 13 9 10 11 -23 9 13 9 10 12 -24 32 13 9 10 1 -25 11 14 9 10 11 -26 9 14 9 10 12 -27 32 14 9 10 1 -28 6 9 10 12 15 -29 7 11 10 12 15 -30 33 1 10 12 15 - -Impropers - -1 1 2 1 4 5 -2 1 2 1 4 10 -3 1 2 1 5 10 -4 1 4 1 5 10 -5 1 1 2 3 6 -6 1 1 2 3 7 -7 1 1 2 6 7 -8 1 3 2 6 7 -9 1 8 9 13 10 -10 1 8 9 14 10 -11 1 8 9 13 14 -12 1 13 9 14 10 -13 1 9 10 11 12 -14 1 1 10 9 11 -15 1 1 10 9 12 -16 1 1 10 11 12 diff --git a/examples/PACKAGES/reaction/tiny_nylon/rxn1_stp2_unreacted.molecule_template b/examples/PACKAGES/reaction/tiny_nylon/rxn1_stp2_unreacted.molecule_template new file mode 100644 index 0000000000..86a772634d --- /dev/null +++ b/examples/PACKAGES/reaction/tiny_nylon/rxn1_stp2_unreacted.molecule_template @@ -0,0 +1,157 @@ +this is a molecule template for: water condensation, pre-reacting + + 15 atoms + 14 bonds + 25 angles + 30 dihedrals + 0 impropers + +Coords + + 1 -4.922858499 -0.946981747 1.146055346 + 2 -5.047194816 -0.935266843 -0.358172771 + 3 -6.526281447 -0.755365854 -0.743523227 + 4 -5.282604074 0.020446894 1.552710361 + 5 -3.860696509 -1.095850190 1.428304925 + 6 -4.662381862 -1.920899862 -0.781524026 + 7 -4.433976540 -0.072765142 -0.784070641 + 8 -5.506279186 0.202610302 4.825815562 + 9 -4.449176624 -0.844592213 4.423366146 + 10 -4.103915981 -0.749628655 2.925195217 + 11 -3.376248536 -1.886171498 2.245643443 + 12 -4.493235430 0.477213651 2.137199034 + 13 -4.849052953 -1.888876753 4.663993750 + 14 -3.491822950 -0.662913310 5.018510248 + 15 -5.020776528 1.189745133 2.805427194 + +Types + + 1 n + 2 c2 + 3 c2 + 4 hn + 5 hn + 6 hc + 7 hc + 8 c2 + 9 c2 + 10 c_1 + 11 o_1 + 12 o + 13 hc + 14 hc + 15 ho + +Charges + + 1 -0.300000 + 2 0.000000 + 3 0.000000 + 4 0.000000 + 5 0.000000 + 6 0.000000 + 7 0.000000 + 8 0.000000 + 9 0.000000 + 10 0.300000 + 11 0.000000 + 12 0.000000 + 13 0.000000 + 14 0.000000 + 15 0.000000 + +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 + +Bonds + + 1 n-c2 1 2 + 2 n-hn 1 4 + 3 n-hn 1 5 + 4 n-c_1 1 10 + 5 c2-c2 2 3 + 6 c2-hc 2 6 + 7 c2-hc 2 7 + 8 c2-c2 8 9 + 9 c2-c_1 9 10 + 10 c2-hc 9 13 + 11 c2-hc 9 14 + 12 c_1-o_1 10 11 + 13 c_1-o 10 12 + 14 o-ho 12 15 + +Angles + + 1 c2-n-hn 2 1 4 + 2 c2-n-hn 2 1 5 + 3 c2-n-c_1 2 1 10 + 4 hn-n-hn 4 1 5 + 5 hn-n-c_1 4 1 10 + 6 hn-n-c_1 5 1 10 + 7 n-c2-c2 1 2 3 + 8 n-c2-hc 1 2 6 + 9 n-c2-hc 1 2 7 + 10 c2-c2-hc 3 2 6 + 11 c2-c2-hc 3 2 7 + 12 hc-c2-hc 6 2 7 + 13 c2-c2-c_1 8 9 10 + 14 c2-c2-hc 8 9 13 + 15 c2-c2-hc 8 9 14 + 16 hc-c2-c_1 13 9 10 + 17 hc-c2-c_1 14 9 10 + 18 hc-c2-hc 13 9 14 + 19 c2-c_1-o_1 9 10 11 + 20 c2-c_1-o 9 10 12 + 21 n-c_1-c2 1 10 9 + 22 o_1-c_1-o 11 10 12 + 23 n-c_1-o_1 1 10 11 + 24 n-c_1-o 1 10 12 + 25 c_1-o-ho 10 12 15 + +Dihedrals + + 1 hn-n-c2-c2 4 1 2 3 + 2 hn-n-c2-hc 4 1 2 6 + 3 hn-n-c2-hc 4 1 2 7 + 4 hn-n-c2-c2 5 1 2 3 + 5 hn-n-c2-hc 5 1 2 6 + 6 hn-n-c2-hc 5 1 2 7 + 7 c_1-n-c2-c2 10 1 2 3 + 8 c_1-n-c2-hc 10 1 2 6 + 9 c_1-n-c2-hc 10 1 2 7 + 10 c2-n-c_1-c2 2 1 10 9 + 11 c2-n-c_1-o_1 2 1 10 11 + 12 c2-n-c_1-o 2 1 10 12 + 13 hn-n-c_1-c2 4 1 10 9 + 14 hn-n-c_1-o_1 4 1 10 11 + 15 hn-n-c_1-o 4 1 10 12 + 16 hn-n-c_1-c2 5 1 10 9 + 17 hn-n-c_1-o_1 5 1 10 11 + 18 hn-n-c_1-o 5 1 10 12 + 19 c2-c2-c_1-o_1 8 9 10 11 + 20 c2-c2-c_1-o 8 9 10 12 + 21 c2-c2-c_1-n 8 9 10 1 + 22 hc-c2-c_1-o_1 13 9 10 11 + 23 hc-c2-c_1-o 13 9 10 12 + 24 hc-c2-c_1-n 13 9 10 1 + 25 hc-c2-c_1-o_1 14 9 10 11 + 26 hc-c2-c_1-o 14 9 10 12 + 27 hc-c2-c_1-n 14 9 10 1 + 28 c2-c_1-o-ho 9 10 12 15 + 29 o_1-c_1-o-ho 11 10 12 15 + 30 n-c_1-o-ho 1 10 12 15 diff --git a/examples/PACKAGES/reaction/tiny_nylon/tiny_nylon.data b/examples/PACKAGES/reaction/tiny_nylon/tiny_nylon.data index 8466e68ea5..ee8e397956 100644 --- a/examples/PACKAGES/reaction/tiny_nylon/tiny_nylon.data +++ b/examples/PACKAGES/reaction/tiny_nylon/tiny_nylon.data @@ -10,16 +10,130 @@ this is LAMMPS data file containing two nylon monomers 36 dihedral types 44 impropers 13 improper types -5 extra bond per atom -15 extra angle per atom -15 extra dihedral per atom -25 extra improper per atom -25 extra special per atom -25 25 xlo xhi -25 25 ylo yhi -25 25 zlo zhi +Atom Type Labels + +1 c2 +2 c_1 +3 o +4 hc +5 ho +6 o_1 +7 na +8 hn +9 n +10 hw +11 o* + +Bond Type Labels + +1 c2-hc +2 c2-c2 +3 c_1-o +4 c2-c_1 +5 c_1-o_1 +6 o-ho +7 c2-c2-repeat +8 c2-hc-repeat +9 na-c2 +10 na-hn +11 n-c2 +12 n-hn +13 n-c_1 +14 c2-na +15 hw-o* + +Angle Type Labels + +1 hc-c2-hc +2 c2-c2-hc +3 c2-c2-c2 +4 c2-c_1-o_1 +5 o-c_1-o_1 +6 c2-c_1-o +7 c_1-o-ho +8 c2-c2-c_1 +9 c_1-c2-hc +10 c2-c2-hc-repeat +11 c2-c2-c2-repeat +12 hc-c2-hc-repeat +13 c2-c2-na +14 na-c2-hc +15 c2-na-hn +16 hn-na-hn +17 c2-n-hn +18 c2-n-c_1 +19 hn-n-hn +20 hn-n-c_1 +21 n-c2-c2 +22 n-c2-hc +23 hc-c2-c_1 +24 n-c_1-c2 +25 o_1-c_1-o +26 n-c_1-o_1 +27 n-c_1-o +28 na-c2-c2 +29 hw-o*-hw + +Dihedral Type Labels + +1 c_1-c2-c2-hc +2 hc-c2-c2-hc +3 c2-c2-c2-c_1 +4 c2-c2-c2-hc +5 c2-c2-c2-c2 +6 c2-c_1-o-ho +7 o_1-c_1-o-ho +8 c2-c2-c_1-o +9 hc-c2-c_1-o +10 c2-c2-c_1-o_1 +11 hc-c2-c_1-o_1 +12 na-c2-c2-hc +13 hc-c2-c2-hc-repeat +14 c2-c2-c2-na +15 c2-c2-c2-hc-repeat +16 c2-c2-c2-c2-repeat +17 c2-c2-na-hn +18 hn-na-c2-hc +19 hn-n-c2-c2 +20 hn-n-c2-hc +21 c_1-n-c2-c2 +22 c_1-n-c2-hc +23 c2-n-c_1-c2 +24 c2-n-c_1-o_1 +25 c2-n-c_1-o +26 hn-n-c_1-c2 +27 hn-n-c_1-o_1 +28 hn-n-c_1-o +29 n-c2-c2-c2 +30 n-c2-c2-hc +31 c2-c2-c_1-n +32 hc-c2-c_1-n +33 n-c_1-o-ho +34 hn-na-c2-c2 +35 hc-c2-na-hn +36 na-c2-c2-c2 + +Improper Type Labels + +1 c2-c_1-o-o_1 +2 c2-na-hn-hn +3 c2-c_1-o_1-o +4 c2-n-hn-c_1 +5 zero5 +6 zero6 +7 zero7 +8 zero8 +9 zero9 +10 zero10 +11 zero11 +12 zero12 +13 n-c_1-c2-o_1 + Masses 1 12.0112 @@ -94,7 +208,7 @@ Angle Coeffs # class2 24 116.926 39.4193 -10.9945 -8.7733 25 118.986 98.6813 -22.2485 10.3673 26 125.542 92.572 -34.48 -11.1871 -27 0 0 0 0 +27 125.542 92.572 -34.48 -11.1871 28 111.91 60.7147 -13.3366 -13.0785 29 103.7 49.84 -11.6 -8 diff --git a/examples/PACKAGES/reaction/tiny_polystyrene/2styrene_reacted.data_template b/examples/PACKAGES/reaction/tiny_polystyrene/2styrene_reacted.data_template deleted file mode 100644 index c4fa646e9f..0000000000 --- a/examples/PACKAGES/reaction/tiny_polystyrene/2styrene_reacted.data_template +++ /dev/null @@ -1,312 +0,0 @@ -2styrene_reacted - -32 atoms -33 bonds -54 angles -79 dihedrals -22 impropers - -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 2 -32 2 - -Charges - -1 -0.129000 -2 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cp-cp-cp-hc 17 27 25 26 + 79 hc-cp-cp-hc 26 25 27 28 + +Impropers + + 1 cp-cp-cp-hc 3 1 11 2 + 2 cp-cp-cp-c1 1 3 5 4 + 3 cp-cp-cp-hc 3 5 7 6 + 4 cp-cp-cp-hc 5 7 9 8 + 5 cp-cp-cp-hc 7 9 11 10 + 6 cp-cp-cp-hc 1 11 9 12 + 7 hc-c2-hc-c1 15 14 16 4 + 8 cp-cp-cp-hc 19 17 27 18 + 9 cp-cp-cp-c1 17 19 21 20 + 10 cp-c1-hc-c2 19 20 29 30 + 11 cp-cp-cp-hc 19 21 23 22 + 12 cp-cp-cp-hc 21 23 25 24 + 13 cp-cp-cp-hc 23 25 27 26 + 14 cp-cp-cp-hc 17 27 25 28 diff --git a/examples/PACKAGES/reaction/tiny_polystyrene/2styrene_unreacted.data_template b/examples/PACKAGES/reaction/tiny_polystyrene/2styrene_unreacted.data_template deleted file mode 100644 index fc0a893191..0000000000 --- a/examples/PACKAGES/reaction/tiny_polystyrene/2styrene_unreacted.data_template +++ /dev/null @@ -1,284 +0,0 @@ -2styrene_unreacted - -32 atoms -32 bonds -48 angles -64 dihedrals -16 impropers - -Types - -1 1 -2 2 -3 1 -4 3 -5 1 -6 2 -7 1 -8 2 -9 1 -10 2 -11 1 -12 2 -13 2 -14 4 -15 2 -16 2 -17 1 -18 2 -19 1 -20 3 -21 1 -22 2 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20 + 51 cp-c1-c2-c1 19 20 44 34 + 52 cp-c1-c2-hc 19 20 44 45 + 53 cp-c1-c2-hc 19 20 44 46 + 54 hc-c1-c2-c1 29 20 44 34 + 55 hc-c1-c2-hc 29 20 44 45 + 56 hc-c1-c2-hc 29 20 44 46 + 57 c2-c1-c2-c1 30 20 44 34 + 58 c2-c1-c2-hc 30 20 44 45 + 59 c2-c1-c2-hc 30 20 44 46 + 60 cp-cp-cp-hc 19 21 23 24 + 61 cp-cp-cp-cp 19 21 23 25 + 62 hc-cp-cp-hc 22 21 23 24 + 63 cp-cp-cp-hc 25 23 21 22 + 64 cp-cp-cp-hc 21 23 25 26 + 65 cp-cp-cp-cp 21 23 25 27 + 66 hc-cp-cp-hc 24 23 25 26 + 67 cp-cp-cp-hc 27 25 23 24 + 68 cp-cp-cp-cp 23 25 27 17 + 69 cp-cp-cp-hc 23 25 27 28 + 70 cp-cp-cp-hc 17 27 25 26 + 71 hc-cp-cp-hc 26 25 27 28 + 72 hc-cp-cp-c1 32 31 33 34 + 73 cp-cp-cp-hc 35 33 31 32 + 74 cp-cp-cp-c1 41 31 33 34 + 75 cp-cp-cp-cp 41 31 33 35 + 76 cp-cp-cp-hc 39 41 31 32 + 77 hc-cp-cp-hc 32 31 41 42 + 78 cp-cp-cp-cp 33 31 41 39 + 79 cp-cp-cp-hc 33 31 41 42 + 80 cp-cp-c1-hc 31 33 34 43 + 81 cp-cp-c1-c2 31 33 34 44 + 82 cp-cp-c1-hc 35 33 34 43 + 83 cp-cp-c1-c2 35 33 34 44 + 84 cp-cp-cp-hc 31 33 35 36 + 85 cp-cp-cp-cp 31 33 35 37 + 86 hc-cp-cp-c1 36 35 33 34 + 87 cp-cp-cp-c1 37 35 33 34 + 88 cp-c1-c2-c1 33 34 44 20 + 89 cp-c1-c2-hc 33 34 44 45 + 90 cp-c1-c2-hc 33 34 44 46 + 91 hc-c1-c2-c1 43 34 44 20 + 92 hc-c1-c2-hc 43 34 44 45 + 93 hc-c1-c2-hc 43 34 44 46 + 94 cp-cp-cp-hc 33 35 37 38 + 95 cp-cp-cp-cp 33 35 37 39 + 96 hc-cp-cp-hc 36 35 37 38 + 97 cp-cp-cp-hc 39 37 35 36 + 98 cp-cp-cp-hc 35 37 39 40 + 99 cp-cp-cp-cp 35 37 39 41 + 100 hc-cp-cp-hc 38 37 39 40 + 101 cp-cp-cp-hc 41 39 37 38 + 102 cp-cp-cp-cp 37 39 41 31 + 103 cp-cp-cp-hc 37 39 41 42 + 104 cp-cp-cp-hc 31 41 39 40 + 105 hc-cp-cp-hc 40 39 41 42 + +Impropers + + 1 cp-cp-cp-hc 3 1 11 2 + 2 cp-cp-cp-c=1 1 3 5 4 + 3 cp-c=1-hc-c= 3 4 13 14 + 4 cp-cp-cp-hc 3 5 7 6 + 5 cp-cp-cp-hc 5 7 9 8 + 6 cp-cp-cp-hc 7 9 11 10 + 7 cp-cp-cp-hc 1 11 9 12 + 8 hc-c=-hc-c=1 15 14 16 4 + 9 cp-cp-cp-hc 19 17 27 18 + 10 cp-cp-cp-c1 17 19 21 20 + 11 cp-cp-cp-hc 19 21 23 22 + 12 cp-cp-cp-hc 21 23 25 24 + 13 cp-cp-cp-hc 23 25 27 26 + 14 cp-cp-cp-hc 17 27 25 28 + 15 cp-cp-cp-hc 33 31 41 32 + 16 cp-cp-cp-c1 31 33 35 34 + 17 cp-c1-hc-c2 33 34 43 44 + 18 cp-cp-cp-hc 33 35 37 36 + 19 cp-cp-cp-hc 35 37 39 38 + 20 cp-cp-cp-hc 37 39 41 40 + 21 cp-cp-cp-hc 31 41 39 42 diff --git a/examples/PACKAGES/reaction/tiny_polystyrene/in.tiny_polystyrene.stabilized b/examples/PACKAGES/reaction/tiny_polystyrene/in.tiny_polystyrene.stabilized index a711f3eaa9..ab9c012905 100644 --- a/examples/PACKAGES/reaction/tiny_polystyrene/in.tiny_polystyrene.stabilized +++ b/examples/PACKAGES/reaction/tiny_polystyrene/in.tiny_polystyrene.stabilized @@ -1,5 +1,5 @@ # 20 styrene molecules -# three reactions defined +# three reactions defined units real @@ -11,9 +11,9 @@ kspace_style pppm 1.0e-4 pair_style lj/class2/coul/long 8.5 -angle_style class2 +angle_style class2 -bond_style class2 +bond_style class2 dihedral_style class2 @@ -28,12 +28,12 @@ read_data tiny_polystyrene.data & extra/improper/per/atom 25 & extra/special/per/atom 25 -molecule mol1 2styrene_unreacted.data_template -molecule mol2 2styrene_reacted.data_template -molecule mol3 chain_plus_styrene_unreacted.data_template -molecule mol4 chain_plus_styrene_reacted.data_template -molecule mol5 chain_chain_unreacted.data_template -molecule mol6 chain_chain_reacted.data_template +molecule mol1 2styrene_unreacted.molecule_template +molecule mol2 2styrene_reacted.molecule_template +molecule mol3 chain_plus_styrene_unreacted.molecule_template +molecule mol4 chain_plus_styrene_reacted.molecule_template +molecule mol5 chain_chain_unreacted.molecule_template +molecule mol6 chain_chain_reacted.molecule_template thermo 100 @@ -53,4 +53,4 @@ thermo_style custom step temp press density f_rxn1[1] f_rxn1[2] f_rxn1[3] run 10000 # write_restart restart_longrun nofix -# write_data restart_longrun.data +# write_data restart_longrun.data diff --git a/examples/PACKAGES/reaction/tiny_polystyrene/log.20Nov19.tiny_polystyrene.stabilized.g++.1 b/examples/PACKAGES/reaction/tiny_polystyrene/log.20Nov19.tiny_polystyrene.stabilized.g++.1 deleted file mode 100644 index 274c72ece9..0000000000 --- a/examples/PACKAGES/reaction/tiny_polystyrene/log.20Nov19.tiny_polystyrene.stabilized.g++.1 +++ /dev/null @@ -1,245 +0,0 @@ -LAMMPS (20 Nov 2019) - -WARNING-WARNING-WARNING-WARNING-WARNING -This LAMMPS executable was compiled using C++98 compatibility. -Please report the compiler info below at https://github.com/lammps/lammps/issues/1659 -GNU C++ 4.8.5 -WARNING-WARNING-WARNING-WARNING-WARNING - -Reading data file ... - orthogonal box = (1.74267 1.74267 1.74267) to (18.2573 18.2573 18.2573) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 320 atoms - reading velocities ... - 320 velocities - scanning bonds ... - 8 = max bonds/atom - scanning angles ... - 18 = max angles/atom - scanning dihedrals ... - 22 = max dihedrals/atom - scanning impropers ... - 26 = max impropers/atom - reading bonds ... - 320 bonds - reading angles ... - 480 angles - reading dihedrals ... - 640 dihedrals - reading impropers ... - 160 impropers -Finding 1-2 1-3 1-4 neighbors ... - special bond factors lj: 0 0 0 - special bond factors coul: 0 0 0 - 3 = max # of 1-2 neighbors - 6 = max # of 1-3 neighbors - 12 = max # of 1-4 neighbors - 39 = max # of special neighbors - special bonds CPU = 0.000929056 secs - read_data CPU = 0.00930568 secs -Read molecule mol1: - 32 atoms with max type 4 - 32 bonds with max type 6 - 48 angles with max type 8 - 64 dihedrals with max type 9 - 16 impropers with max type 4 -Read molecule mol2: - 32 atoms with max type 6 - 33 bonds with max type 10 - 54 angles with max type 16 - 79 dihedrals with max type 19 - 22 impropers with max type 7 -Read molecule mol3: - 46 atoms with max type 6 - 47 bonds with max type 10 - 75 angles with max type 16 - 105 dihedrals with max type 19 - 29 impropers with max type 7 -Read molecule mol4: - 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 -Read molecule mol5: - 50 atoms with max type 6 - 51 bonds with max type 10 - 84 angles with max type 16 - 118 dihedrals with max type 19 - 36 impropers with max type 7 -Read molecule mol6: - 50 atoms with max type 6 - 52 bonds with max type 10 - 90 angles with max type 16 - 135 dihedrals with max type 19 - 42 impropers with max type 5 -dynamic group bond_react_MASTER_group defined -dynamic group statted_grp_REACT defined -PPPM initialization ... -WARNING: System is not charge neutral, net charge = -0.004 (../kspace.cpp:304) - using 12-bit tables for long-range coulomb (../kspace.cpp:323) - G vector (1/distance) = 0.255611 - grid = 6 6 6 - stencil order = 5 - estimated absolute RMS force accuracy = 0.00974692 - estimated relative force accuracy = 2.93525e-05 - using double precision FFTs - 3d grid and FFT values/proc = 1331 216 -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 = 4 4 4 - 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) = 31.14 | 31.14 | 31.14 Mbytes -Step Temp Press Density f_rxn1[1] f_rxn1[2] f_rxn1[3] - 0 320.13638 -376.0844 0.76796752 0 0 0 - 100 520.00782 3952.7008 0.76796752 8 0 0 - 200 499.9174 2360.8219 0.76796752 8 3 1 - 300 583.93895 2453.7374 0.76796752 8 3 2 - 400 560.65536 -2243.3464 0.76796752 8 3 3 - 500 556.27995 3598.7044 0.76796752 8 3 3 - 600 570.8397 -3340.1826 0.76796752 8 4 4 - 700 456.89894 -1087.8081 0.76796752 8 4 4 - 800 572.91817 -776.19188 0.76796752 8 4 4 - 900 530.13621 -246734.46 0.76796752 8 4 5 - 1000 542.34698 1044.0793 0.76796752 8 4 5 - 1100 562.86339 1207.1715 0.76796752 8 4 5 - 1200 520.1559 2725.6523 0.76796752 8 4 5 - 1300 534.01667 951.0972 0.76796752 8 4 5 - 1400 478.68681 1184.9224 0.76796752 8 4 5 - 1500 509.05445 2020.5224 0.76796752 8 4 5 - 1600 549.5382 810.17577 0.76796752 8 4 5 - 1700 549.46882 -6349.7751 0.76796752 8 4 5 - 1800 496.77334 3953.1043 0.76796752 8 4 5 - 1900 522.28719 -2271.7599 0.76796752 8 4 6 - 2000 569.95975 5633.4352 0.76796752 8 4 6 - 2100 590.8418 2355.8447 0.76796752 8 4 6 - 2200 537.64787 6459.6743 0.76796752 8 4 6 - 2300 548.38487 -1566.3528 0.76796752 8 4 6 - 2400 533.50353 6755.664 0.76796752 8 4 6 - 2500 512.57053 325.30968 0.76796752 8 4 6 - 2600 498.4597 -2468.1165 0.76796752 8 4 6 - 2700 559.03937 2428.3446 0.76796752 8 4 6 - 2800 585.85721 -2896.3607 0.76796752 8 4 6 - 2900 523.18635 1391.254 0.76796752 8 4 6 - 3000 524.62076 375.02973 0.76796752 8 4 6 - 3100 534.65688 -1522.7879 0.76796752 8 4 6 - 3200 499.42665 3725.5476 0.76796752 8 4 6 - 3300 514.36972 1725.8329 0.76796752 8 4 6 - 3400 482.52662 4648.5013 0.76796752 8 4 6 - 3500 495.36836 967.3482 0.76796752 8 4 6 - 3600 583.28736 745.21794 0.76796752 8 4 6 - 3700 531.99717 -804.39572 0.76796752 8 4 6 - 3800 555.08359 -2381.363 0.76796752 8 4 6 - 3900 520.1818 -547.34169 0.76796752 8 4 6 - 4000 444.38804 -2488.7881 0.76796752 8 4 6 - 4100 518.65622 -3135.9573 0.76796752 8 4 6 - 4200 484.15227 -1040.2447 0.76796752 8 4 6 - 4300 514.58006 550.14626 0.76796752 8 4 6 - 4400 579.81405 -849.81454 0.76796752 8 4 6 - 4500 522.8698 5222.654 0.76796752 8 4 6 - 4600 490.78275 3251.2892 0.76796752 8 4 6 - 4700 492.64299 3785.3482 0.76796752 8 4 6 - 4800 500.11059 4441.8978 0.76796752 8 4 6 - 4900 536.80009 965.33724 0.76796752 8 4 6 - 5000 516.98575 -3794.4213 0.76796752 8 4 6 - 5100 516.76648 -3593.9106 0.76796752 8 4 6 - 5200 521.6379 -6532.7773 0.76796752 8 4 6 - 5300 535.64798 2931.412 0.76796752 8 4 6 - 5400 559.83266 7628.1659 0.76796752 8 4 6 - 5500 538.91756 2841.6746 0.76796752 8 4 6 - 5600 539.13999 10445.173 0.76796752 8 4 6 - 5700 501.56603 -2106.3309 0.76796752 8 4 6 - 5800 496.72952 -4831.0565 0.76796752 8 4 6 - 5900 536.12979 -3916.8197 0.76796752 8 4 6 - 6000 553.10092 3142.6871 0.76796752 8 4 6 - 6100 558.09546 3154.584 0.76796752 8 4 6 - 6200 523.48472 9807.0034 0.76796752 8 4 6 - 6300 551.80343 -3608.2078 0.76796752 8 4 6 - 6400 484.28359 2255.4675 0.76796752 8 4 6 - 6500 560.68443 -4826.4868 0.76796752 8 4 6 - 6600 604.50797 402.32183 0.76796752 8 4 6 - 6700 538.84714 -7670.3312 0.76796752 8 4 6 - 6800 528.82853 -380.32058 0.76796752 8 4 6 - 6900 579.30919 4438.4574 0.76796752 8 4 6 - 7000 540.3406 3738.0524 0.76796752 8 4 6 - 7100 519.53645 -1825.5563 0.76796752 8 4 6 - 7200 474.136 1657.3863 0.76796752 8 4 6 - 7300 485.55159 -221.84939 0.76796752 8 4 6 - 7400 527.38494 1037.1777 0.76796752 8 4 6 - 7500 517.14767 -2313.5823 0.76796752 8 4 6 - 7600 517.95967 -4763.4709 0.76796752 8 4 6 - 7700 513.63507 4819.0253 0.76796752 8 4 6 - 7800 503.56828 1295.1212 0.76796752 8 4 6 - 7900 520.87804 1506.9417 0.76796752 8 4 6 - 8000 509.46453 -5800.0971 0.76796752 8 4 6 - 8100 566.67059 6065.4607 0.76796752 8 4 6 - 8200 592.53068 1097.2277 0.76796752 8 4 6 - 8300 529.55235 -580.81757 0.76796752 8 4 6 - 8400 518.22587 560.45589 0.76796752 8 4 6 - 8500 521.94561 5325.9459 0.76796752 8 4 6 - 8600 510.54416 -1929.1967 0.76796752 8 4 6 - 8700 562.71252 -629.90392 0.76796752 8 4 6 - 8800 540.23123 -3484.3893 0.76796752 8 4 6 - 8900 513.82411 -5227.152 0.76796752 8 4 6 - 9000 534.3307 -3299.088 0.76796752 8 4 6 - 9100 509.24467 -5676.2775 0.76796752 8 4 6 - 9200 506.3216 -7043.8493 0.76796752 8 4 7 - 9300 480.37682 2380.4696 0.76796752 8 4 7 - 9400 546.15532 1831.0103 0.76796752 8 4 7 - 9500 567.18341 3839.9843 0.76796752 8 4 7 - 9600 536.14883 4258.5304 0.76796752 8 4 7 - 9700 496.04153 3321.3561 0.76796752 8 4 7 - 9800 531.78927 3124.9156 0.76796752 8 4 7 - 9900 530.91395 38.987859 0.76796752 8 4 7 - 10000 551.22761 1027.5706 0.76796752 8 4 7 -Loop time of 57.7096 on 1 procs for 10000 steps with 320 atoms - -Performance: 14.972 ns/day, 1.603 hours/ns, 173.281 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 | 11.621 | 11.621 | 11.621 | 0.0 | 20.14 -Bond | 11.151 | 11.151 | 11.151 | 0.0 | 19.32 -Kspace | 2.2403 | 2.2403 | 2.2403 | 0.0 | 3.88 -Neigh | 25.467 | 25.467 | 25.467 | 0.0 | 44.13 -Comm | 0.90467 | 0.90467 | 0.90467 | 0.0 | 1.57 -Output | 0.0017984 | 0.0017984 | 0.0017984 | 0.0 | 0.00 -Modify | 6.2622 | 6.2622 | 6.2622 | 0.0 | 10.85 -Other | | 0.06192 | | | 0.11 - -Nlocal: 320 ave 320 max 320 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 3240 ave 3240 max 3240 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 54336 ave 54336 max 54336 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 54336 -Ave neighs/atom = 169.8 -Ave special neighs/atom = 11.3063 -Neighbor list builds = 10000 -Dangerous builds = 0 - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:58 diff --git a/examples/PACKAGES/reaction/tiny_polystyrene/log.20Nov19.tiny_polystyrene.stabilized.g++.4 b/examples/PACKAGES/reaction/tiny_polystyrene/log.20Nov19.tiny_polystyrene.stabilized.g++.4 deleted file mode 100644 index 29aae1cd0b..0000000000 --- a/examples/PACKAGES/reaction/tiny_polystyrene/log.20Nov19.tiny_polystyrene.stabilized.g++.4 +++ /dev/null @@ -1,255 +0,0 @@ -LAMMPS (20 Nov 2019) - -WARNING-WARNING-WARNING-WARNING-WARNING -This LAMMPS executable was compiled using C++98 compatibility. -Please report the compiler info below at https://github.com/lammps/lammps/issues/1659 -GNU C++ 4.8.5 -WARNING-WARNING-WARNING-WARNING-WARNING - -Reading data file ... - orthogonal box = (1.74267 1.74267 1.74267) to (18.2573 18.2573 18.2573) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 320 atoms - reading velocities ... - 320 velocities - scanning bonds ... - 8 = max bonds/atom - scanning angles ... - 18 = max angles/atom - scanning dihedrals ... - 22 = max dihedrals/atom - scanning impropers ... - 26 = max impropers/atom - reading bonds ... - 320 bonds - reading angles ... - 480 angles - reading dihedrals ... - 640 dihedrals - reading impropers ... - 160 impropers -Finding 1-2 1-3 1-4 neighbors ... - special bond factors lj: 0 0 0 - special bond factors coul: 0 0 0 - 3 = max # of 1-2 neighbors - 6 = max # of 1-3 neighbors - 12 = max # of 1-4 neighbors - 39 = max # of special neighbors - special bonds CPU = 0.000751222 secs - read_data CPU = 0.0268223 secs -Read molecule mol1: - 32 atoms with max type 4 - 32 bonds with max type 6 - 48 angles with max type 8 - 64 dihedrals with max type 9 - 16 impropers with max type 4 -Read molecule mol2: - 32 atoms with max type 6 - 33 bonds with max type 10 - 54 angles with max type 16 - 79 dihedrals with max type 19 - 22 impropers with max type 7 -Read molecule mol3: - 46 atoms with max type 6 - 47 bonds with max type 10 - 75 angles with max type 16 - 105 dihedrals with max type 19 - 29 impropers with max type 7 -Read molecule mol4: - 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 -Read molecule mol5: - 50 atoms with max type 6 - 51 bonds with max type 10 - 84 angles with max type 16 - 118 dihedrals with max type 19 - 36 impropers with max type 7 -Read molecule mol6: - 50 atoms with max type 6 - 52 bonds with max type 10 - 90 angles with max type 16 - 135 dihedrals with max type 19 - 42 impropers with max type 5 -dynamic group bond_react_MASTER_group defined -dynamic group statted_grp_REACT defined -PPPM initialization ... -WARNING: System is not charge neutral, net charge = -0.004 (../kspace.cpp:304) - using 12-bit tables for long-range coulomb (../kspace.cpp:323) - G vector (1/distance) = 0.255611 - grid = 6 6 6 - stencil order = 5 - estimated absolute RMS force accuracy = 0.00974692 - estimated relative force accuracy = 2.93525e-05 - using double precision FFTs - 3d grid and FFT values/proc = 704 72 -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 = 4 4 4 - 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) = 30.66 | 30.68 | 30.69 Mbytes -Step Temp Press Density f_rxn1[1] f_rxn1[2] f_rxn1[3] - 0 320.13638 -376.0844 0.76796752 0 0 0 - 100 522.71544 6623.0579 0.76796752 8 0 0 - 200 500.86716 -9439.5519 0.76796752 8 3 2 - 300 594.60588 6714.1323 0.76796752 8 3 3 - 400 598.68768 683.70457 0.76796752 8 3 3 - 500 563.1011 3576.6857 0.76796752 8 3 4 - 600 510.29713 -196148.37 0.76796752 8 3 5 - 700 494.14346 -118517.45 0.76796752 8 3 6 - 800 565.62849 7678.1235 0.76796752 8 3 6 - 900 515.74468 554.84571 0.76796752 8 3 6 - 1000 500.64636 450.15932 0.76796752 8 3 6 - 1100 463.34973 6023.8346 0.76796752 8 3 6 - 1200 529.88483 2748.185 0.76796752 8 3 6 - 1300 546.84049 1353.4891 0.76796752 8 3 6 - 1400 552.27356 1446.5807 0.76796752 8 3 6 - 1500 557.70874 -2745.1523 0.76796752 8 3 6 - 1600 572.0005 629.36722 0.76796752 8 3 6 - 1700 503.96569 5937.0231 0.76796752 8 3 6 - 1800 491.34262 -1175.8104 0.76796752 8 3 6 - 1900 538.24798 -81.197397 0.76796752 8 3 6 - 2000 523.89324 2857.2466 0.76796752 8 3 6 - 2100 515.1424 2288.2405 0.76796752 8 3 6 - 2200 546.80854 3807.1038 0.76796752 8 3 6 - 2300 500.31231 -135.33933 0.76796752 8 4 6 - 2400 497.16354 5516.857 0.76796752 8 4 6 - 2500 545.34187 3485.5645 0.76796752 8 4 6 - 2600 522.70122 3114.1284 0.76796752 8 4 6 - 2700 531.76604 6633.5518 0.76796752 8 4 6 - 2800 521.97643 -279.83682 0.76796752 8 4 6 - 2900 497.29575 7052.9409 0.76796752 8 4 6 - 3000 524.5942 2284.8918 0.76796752 8 4 6 - 3100 567.61329 -3667.4557 0.76796752 8 4 6 - 3200 506.82452 -2934.4936 0.76796752 8 4 6 - 3300 510.8521 313.36263 0.76796752 8 4 6 - 3400 516.70206 3671.1899 0.76796752 8 4 6 - 3500 535.12788 2645.2564 0.76796752 8 4 6 - 3600 580.14214 2604.3079 0.76796752 8 4 6 - 3700 529.77869 2684.0812 0.76796752 8 4 6 - 3800 502.93191 2838.6698 0.76796752 8 4 6 - 3900 585.91492 5308.0828 0.76796752 8 4 6 - 4000 548.89917 5262.5775 0.76796752 8 4 6 - 4100 550.7662 -1066.6807 0.76796752 8 4 6 - 4200 519.19198 2777.5276 0.76796752 8 4 6 - 4300 521.46332 -3429.7171 0.76796752 8 4 6 - 4400 532.64173 2301.3135 0.76796752 8 4 6 - 4500 528.96107 1369.0991 0.76796752 8 4 6 - 4600 564.66443 9687.2531 0.76796752 8 4 6 - 4700 558.49446 2322.6085 0.76796752 8 4 6 - 4800 497.78614 -442.45053 0.76796752 8 4 6 - 4900 511.09435 -10251.159 0.76796752 8 4 6 - 5000 525.6642 -1202.0584 0.76796752 8 4 6 - 5100 521.76974 1821.7811 0.76796752 8 4 6 - 5200 555.9859 7256.9632 0.76796752 8 4 6 - 5300 551.51971 -122893.16 0.76796752 8 4 7 - 5400 524.34705 2905.1033 0.76796752 8 4 7 - 5500 567.09396 2896.4824 0.76796752 8 4 7 - 5600 487.57746 1417.1715 0.76796752 8 4 7 - 5700 547.37304 3900.8734 0.76796752 8 4 7 - 5800 536.17647 -4048.7522 0.76796752 8 4 7 - 5900 536.85051 4497.9847 0.76796752 8 4 7 - 6000 548.58212 -4880.4979 0.76796752 8 4 7 - 6100 500.94692 6004.2105 0.76796752 8 4 7 - 6200 486.82494 402.5875 0.76796752 8 4 7 - 6300 478.09381 6600.767 0.76796752 8 4 7 - 6400 559.90398 2868.0805 0.76796752 8 4 7 - 6500 526.01866 -3398.4788 0.76796752 8 4 7 - 6600 539.68471 -1202.0012 0.76796752 8 4 7 - 6700 507.51217 -378.71164 0.76796752 8 4 7 - 6800 526.15958 -4536.9888 0.76796752 8 4 7 - 6900 511.37134 -2522.3553 0.76796752 8 4 7 - 7000 538.86918 -2028.0323 0.76796752 8 4 7 - 7100 523.25566 2911.9962 0.76796752 8 4 7 - 7200 513.28464 -1000.4758 0.76796752 8 4 7 - 7300 510.19826 5181.7976 0.76796752 8 4 7 - 7400 493.46528 -1166.3996 0.76796752 8 4 7 - 7500 491.51305 5669.2213 0.76796752 8 4 7 - 7600 506.72032 -2840.301 0.76796752 8 4 7 - 7700 513.4319 2802.1719 0.76796752 8 4 7 - 7800 543.7658 -7477.3623 0.76796752 8 4 7 - 7900 527.35619 -3182.3155 0.76796752 8 4 7 - 8000 533.50993 613.16561 0.76796752 8 4 7 - 8100 512.44958 -5037.3414 0.76796752 8 4 7 - 8200 494.88981 1799.3513 0.76796752 8 4 7 - 8300 554.81474 -2436.0507 0.76796752 8 4 7 - 8400 523.22917 364.30593 0.76796752 8 4 7 - 8500 515.12395 525.24581 0.76796752 8 4 7 - 8600 511.6321 -1679.8669 0.76796752 8 4 7 - 8700 531.6327 -1168.1215 0.76796752 8 4 7 - 8800 548.14438 -5222.7573 0.76796752 8 4 7 - 8900 517.72579 2073.9695 0.76796752 8 4 7 - 9000 543.11894 -5307.0759 0.76796752 8 4 7 - 9100 521.13747 -5546.8552 0.76796752 8 4 7 - 9200 509.66142 -1584.019 0.76796752 8 4 7 - 9300 488.73821 -277.85847 0.76796752 8 4 7 - 9400 513.67282 989.60653 0.76796752 8 4 7 - 9500 509.98833 -1754.8786 0.76796752 8 4 7 - 9600 558.72497 5616.6969 0.76796752 8 4 7 - 9700 533.74988 811.48871 0.76796752 8 4 7 - 9800 510.94641 -3136.5876 0.76796752 8 4 7 - 9900 517.80127 -1962.0837 0.76796752 8 4 7 - 10000 477.50428 -3768.1653 0.76796752 8 4 7 -Loop time of 20.9963 on 4 procs for 10000 steps with 320 atoms - -Performance: 41.150 ns/day, 0.583 hours/ns, 476.276 timesteps/s -100.0% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 2.4968 | 3.0329 | 3.3607 | 18.6 | 14.45 -Bond | 2.3164 | 2.8835 | 3.456 | 26.0 | 13.73 -Kspace | 1.3332 | 2.2082 | 3.285 | 48.0 | 10.52 -Neigh | 7.4831 | 7.4922 | 7.5012 | 0.3 | 35.68 -Comm | 1.2809 | 1.3121 | 1.3297 | 1.6 | 6.25 -Output | 0.0012138 | 0.0013506 | 0.0017552 | 0.6 | 0.01 -Modify | 4.0269 | 4.0301 | 4.0335 | 0.1 | 19.19 -Other | | 0.03583 | | | 0.17 - -Nlocal: 80 ave 94 max 66 min -Histogram: 2 0 0 0 0 0 0 0 0 2 -Nghost: 2243.75 ave 2260 max 2221 min -Histogram: 1 0 0 1 0 0 0 0 0 2 -Neighs: 13658.5 ave 17096 max 9421 min -Histogram: 1 0 0 0 0 1 1 0 0 1 - -Total # of neighbors = 54634 -Ave neighs/atom = 170.731 -Ave special neighs/atom = 11.3063 -Neighbor list builds = 10000 -Dangerous builds = 0 -System init for write_data ... -PPPM initialization ... - using 12-bit tables for long-range coulomb (../kspace.cpp:323) - G vector (1/distance) = 0.255611 - grid = 6 6 6 - stencil order = 5 - estimated absolute RMS force accuracy = 0.00974692 - estimated relative force accuracy = 2.93525e-05 - using double precision FFTs - 3d grid and FFT values/proc = 704 72 - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:21 diff --git a/examples/PACKAGES/reaction/tiny_polystyrene/log.4Nov19.tiny_polystyrene.stabilized.g++.4 b/examples/PACKAGES/reaction/tiny_polystyrene/log.4Nov19.tiny_polystyrene.stabilized.g++.4 new file mode 100644 index 0000000000..aaa8b2f190 --- /dev/null +++ b/examples/PACKAGES/reaction/tiny_polystyrene/log.4Nov19.tiny_polystyrene.stabilized.g++.4 @@ -0,0 +1,329 @@ +LAMMPS (4 Nov 2022) +# 20 styrene molecules +# three reactions defined + +units real + +boundary p p p + +atom_style full + +kspace_style pppm 1.0e-4 + +pair_style lj/class2/coul/long 8.5 + +angle_style class2 + +bond_style class2 + +dihedral_style class2 + +improper_style class2 + +variable T equal 530 + +read_data tiny_polystyrene.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 = (1.7426663 1.7426663 1.7426663) to (18.257334 18.257334 18.257334) + 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 ... + 320 atoms + reading velocities ... + 320 velocities + scanning bonds ... + 8 = max bonds/atom + scanning angles ... + 18 = max angles/atom + scanning dihedrals ... + 22 = max dihedrals/atom + scanning impropers ... + 26 = max impropers/atom + reading bonds ... + 320 bonds + reading angles ... + 480 angles + reading dihedrals ... + 640 dihedrals + reading impropers ... + 160 impropers +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 3 = max # of 1-2 neighbors + 6 = max # of 1-3 neighbors + 12 = max # of 1-4 neighbors + 39 = max # of special neighbors + special bonds CPU = 0.001 seconds + read_data CPU = 0.018 seconds + +molecule mol1 2styrene_unreacted.molecule_template +Read molecule template mol1: + 1 molecules + 0 fragments + 32 atoms with max type 4 + 32 bonds with max type 11 + 48 angles with max type 19 + 64 dihedrals with max type 21 + 16 impropers with max type 8 +molecule mol2 2styrene_reacted.molecule_template +Read molecule template mol2: + 1 molecules + 0 fragments + 32 atoms with max type 6 + 33 bonds with max type 13 + 54 angles with max type 22 + 79 dihedrals with max type 19 + 14 impropers with max type 7 +molecule mol3 chain_plus_styrene_unreacted.molecule_template +Read molecule template mol3: + 1 molecules + 0 fragments + 46 atoms with max type 6 + 47 bonds with max type 13 + 75 angles with max type 22 + 105 dihedrals with max type 21 + 21 impropers with max type 8 +molecule mol4 chain_plus_styrene_reacted.molecule_template +Read molecule template mol4: + 1 molecules + 0 fragments + 46 atoms with max type 6 + 48 bonds with max type 13 + 81 angles with max type 22 + 121 dihedrals with max type 19 + 19 impropers with max type 7 +molecule mol5 chain_chain_unreacted.molecule_template +Read molecule template mol5: + 1 molecules + 0 fragments + 50 atoms with max type 6 + 51 bonds with max type 13 + 84 angles with max type 22 + 118 dihedrals with max type 19 + 20 impropers with max type 7 +molecule mol6 chain_chain_reacted.molecule_template +Read molecule template mol6: + 1 molecules + 0 fragments + 50 atoms with max type 6 + 52 bonds with max type 13 + 90 angles with max type 22 + 135 dihedrals with max type 19 + 18 impropers with max type 2 + +thermo 100 + +# dump 1 all xyz 5 test_vis.xyz + +fix rxn1 all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0 3.0 mol1 mol2 2styrene_map stabilize_steps 100 react rxn2 all 1 0 3.0 mol3 mol4 chain_plus_styrene_map stabilize_steps 100 react rxn3 all 1 0 5.0 mol5 mol6 chain_chain_map stabilize_steps 100 +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_rxn1[1] f_rxn1[2] f_rxn1[3] + +run 10000 + +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 + +PPPM initialization ... +WARNING: System is not charge neutral, net charge = -0.004 (../kspace.cpp:327) + using 12-bit tables for long-range coulomb (../kspace.cpp:342) + G vector (1/distance) = 0.25561147 + grid = 6 6 6 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0097469157 + estimated relative force accuracy = 2.9352547e-05 + using double precision KISS FFT + 3d grid and FFT values/proc = 704 72 +Generated 21 of 21 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 = 4 4 4 + 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 + 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) = 31.03 | 31.05 | 31.06 Mbytes + Step Temp Press Density f_rxn1[1] f_rxn1[2] f_rxn1[3] + 0 320.13638 -376.0844 0.76796752 0 0 0 + 100 342.22237 -3489.4495 0.76796752 0 0 0 + 200 412.23828 -1367.104 0.76796752 0 0 0 + 300 467.98145 4841.002 0.76796752 0 0 0 + 400 505.39864 2213.0509 0.76796752 1 0 0 + 500 519.63371 -28223.513 0.76796752 2 0 0 + 600 526.40655 8701.2728 0.76796752 2 0 0 + 700 579.91953 2507.5868 0.76796752 2 0 0 + 800 517.29593 5558.2895 0.76796752 2 0 0 + 900 503.38392 -5027.1154 0.76796752 2 0 0 + 1000 509.30767 3979.0529 0.76796752 2 0 0 + 1100 551.34763 5119.0848 0.76796752 2 0 0 + 1200 562.5176 -2867.8688 0.76796752 2 0 0 + 1300 552.90918 2090.7508 0.76796752 2 0 0 + 1400 516.10716 3374.2169 0.76796752 2 0 0 + 1500 518.70418 471.99711 0.76796752 2 0 0 + 1600 559.49915 5450.8774 0.76796752 2 0 0 + 1700 531.50638 4525.5892 0.76796752 2 0 0 + 1800 529.18331 -3566.9245 0.76796752 2 0 0 + 1900 517.79846 -2364.8287 0.76796752 2 0 0 + 2000 495.0983 -488.99696 0.76796752 2 0 0 + 2100 567.80521 2050.9596 0.76796752 3 0 0 + 2200 553.24434 5665.0753 0.76796752 3 0 0 + 2300 561.08278 2879.1572 0.76796752 3 0 0 + 2400 461.3712 3185.6091 0.76796752 3 0 0 + 2500 500.95595 565.81792 0.76796752 4 0 0 + 2600 538.3865 463.58228 0.76796752 4 0 0 + 2700 525.95739 2011.1914 0.76796752 4 0 0 + 2800 533.4197 157.38106 0.76796752 4 0 0 + 2900 526.27036 1331.5115 0.76796752 5 1 0 + 3000 502.65015 -93.915921 0.76796752 5 1 0 + 3100 505.4224 -1314.224 0.76796752 5 1 0 + 3200 538.52692 10420.644 0.76796752 5 1 0 + 3300 518.32801 5933.553 0.76796752 5 2 0 + 3400 540.04815 741.54438 0.76796752 6 2 1 + 3500 554.07567 5778.8913 0.76796752 6 2 1 + 3600 546.90828 4751.5437 0.76796752 6 2 1 + 3700 529.75739 432.20829 0.76796752 6 2 1 + 3800 542.806 -380.00399 0.76796752 6 2 1 + 3900 521.55789 -1224.1912 0.76796752 6 2 2 + 4000 519.73935 2792.996 0.76796752 6 2 2 + 4100 535.06314 -1926.8692 0.76796752 6 2 2 + 4200 549.75482 2852.5521 0.76796752 6 2 2 + 4300 510.71949 6581.1729 0.76796752 7 2 2 + 4400 485.93403 -695.24007 0.76796752 7 2 2 + 4500 535.3677 2519.2711 0.76796752 7 2 2 + 4600 504.87216 533.16619 0.76796752 7 2 2 + 4700 495.68939 5502.1672 0.76796752 7 2 2 + 4800 534.13893 -1187.1228 0.76796752 7 2 2 + 4900 512.56394 1731.3856 0.76796752 7 2 2 + 5000 508.63054 2467.0387 0.76796752 7 2 2 + 5100 501.65027 3403.8111 0.76796752 7 2 2 + 5200 556.68281 4310.0492 0.76796752 7 2 2 + 5300 506.86652 -773630.77 0.76796752 7 2 3 + 5400 570.01783 11663.867 0.76796752 7 2 3 + 5500 538.08785 6391.6546 0.76796752 7 2 3 + 5600 502.48456 44.409604 0.76796752 7 2 3 + 5700 545.75445 1558.6373 0.76796752 7 2 3 + 5800 517.5076 -166.52488 0.76796752 7 2 3 + 5900 558.64383 1528.1198 0.76796752 7 2 3 + 6000 557.8358 442.21273 0.76796752 7 2 3 + 6100 483.13771 5201.4489 0.76796752 8 2 3 + 6200 533.42675 5112.0828 0.76796752 8 2 3 + 6300 576.32772 269.77058 0.76796752 8 2 3 + 6400 492.79331 565.35222 0.76796752 8 2 4 + 6500 514.5727 6233.7568 0.76796752 8 2 4 + 6600 509.86906 -943.58621 0.76796752 8 2 4 + 6700 546.62752 -323284.04 0.76796752 8 2 5 + 6800 541.19749 1306.3182 0.76796752 8 2 5 + 6900 497.72333 -1792.483 0.76796752 8 2 5 + 7000 516.02636 2028.3813 0.76796752 8 2 5 + 7100 486.54013 6153.9142 0.76796752 8 2 5 + 7200 553.33698 4352.3987 0.76796752 8 2 5 + 7300 519.23896 6536.766 0.76796752 8 2 5 + 7400 486.74787 -1744.8351 0.76796752 8 2 5 + 7500 516.71935 -315.43649 0.76796752 8 2 5 + 7600 513.62572 -1100.1363 0.76796752 8 2 5 + 7700 531.11296 1727.7113 0.76796752 8 2 5 + 7800 530.82809 9566.2386 0.76796752 8 2 5 + 7900 513.09884 8545.6728 0.76796752 8 2 5 + 8000 511.38714 2995.8438 0.76796752 8 2 5 + 8100 527.76731 709.63649 0.76796752 8 2 5 + 8200 514.09092 2103.8591 0.76796752 8 2 5 + 8300 534.90612 7707.3378 0.76796752 8 2 5 + 8400 547.40716 660.54641 0.76796752 8 2 5 + 8500 518.75522 -872.69754 0.76796752 8 2 5 + 8600 511.70922 6645.6264 0.76796752 8 2 5 + 8700 480.70739 -640.57939 0.76796752 8 2 5 + 8800 527.35475 6944.8472 0.76796752 8 2 5 + 8900 554.26477 -2311.6153 0.76796752 8 2 5 + 9000 520.48502 1469.4805 0.76796752 8 2 5 + 9100 522.0619 -4159.697 0.76796752 8 2 5 + 9200 501.34664 7486.8266 0.76796752 8 2 5 + 9300 524.96422 6158.2524 0.76796752 8 2 5 + 9400 564.30456 -2964.7187 0.76796752 8 2 6 + 9500 569.02736 5765.8856 0.76796752 8 2 6 + 9600 554.31532 2805.5671 0.76796752 8 2 6 + 9700 521.3957 -924.74562 0.76796752 8 2 6 + 9800 518.45356 -2440.5266 0.76796752 8 2 6 + 9900 512.03787 -834.07647 0.76796752 8 2 6 + 10000 573.10576 4372.5769 0.76796752 8 2 6 +Loop time of 11.2088 on 4 procs for 10000 steps with 320 atoms + +Performance: 77.082 ns/day, 0.311 hours/ns, 892.155 timesteps/s, 285.490 katom-step/s +100.0% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.6217 | 2.8126 | 3.0128 | 9.5 | 25.09 +Bond | 2.0439 | 2.1734 | 2.3326 | 7.0 | 19.39 +Kspace | 1.4277 | 1.7772 | 2.0148 | 17.9 | 15.86 +Neigh | 0.32002 | 0.3201 | 0.3202 | 0.0 | 2.86 +Comm | 0.42382 | 0.43347 | 0.4412 | 1.1 | 3.87 +Output | 0.0013461 | 0.0015202 | 0.0020328 | 0.8 | 0.01 +Modify | 3.6386 | 3.6396 | 3.6408 | 0.0 | 32.47 +Other | | 0.05092 | | | 0.45 + +Nlocal: 80 ave 93 max 71 min +Histogram: 1 1 0 0 1 0 0 0 0 1 +Nghost: 2184.75 ave 2276 max 2092 min +Histogram: 1 0 1 0 0 0 0 1 0 1 +Neighs: 13678.5 ave 15576 max 11682 min +Histogram: 1 0 0 1 0 0 0 1 0 1 + +Total # of neighbors = 54714 +Ave neighs/atom = 170.98125 +Ave special neighs/atom = 10.9125 +Neighbor list builds = 471 +Dangerous builds = 0 + +# write_restart restart_longrun nofix +# write_data restart_longrun.data +Total wall time: 0:00:11 diff --git a/examples/PACKAGES/reaction/tiny_polystyrene/log.4Nov2020.tiny_polystyrene.stabilized.g++.1 b/examples/PACKAGES/reaction/tiny_polystyrene/log.4Nov2020.tiny_polystyrene.stabilized.g++.1 new file mode 100644 index 0000000000..be40e6b0de --- /dev/null +++ b/examples/PACKAGES/reaction/tiny_polystyrene/log.4Nov2020.tiny_polystyrene.stabilized.g++.1 @@ -0,0 +1,329 @@ +LAMMPS (4 Nov 2022) +# 20 styrene molecules +# three reactions defined + +units real + +boundary p p p + +atom_style full + +kspace_style pppm 1.0e-4 + +pair_style lj/class2/coul/long 8.5 + +angle_style class2 + +bond_style class2 + +dihedral_style class2 + +improper_style class2 + +variable T equal 530 + +read_data tiny_polystyrene.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 = (1.7426663 1.7426663 1.7426663) to (18.257334 18.257334 18.257334) + 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 ... + 320 atoms + reading velocities ... + 320 velocities + scanning bonds ... + 8 = max bonds/atom + scanning angles ... + 18 = max angles/atom + scanning dihedrals ... + 22 = max dihedrals/atom + scanning impropers ... + 26 = max impropers/atom + reading bonds ... + 320 bonds + reading angles ... + 480 angles + reading dihedrals ... + 640 dihedrals + reading impropers ... + 160 impropers +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 3 = max # of 1-2 neighbors + 6 = max # of 1-3 neighbors + 12 = max # of 1-4 neighbors + 39 = max # of special neighbors + special bonds CPU = 0.001 seconds + read_data CPU = 0.015 seconds + +molecule mol1 2styrene_unreacted.molecule_template +Read molecule template mol1: + 1 molecules + 0 fragments + 32 atoms with max type 4 + 32 bonds with max type 11 + 48 angles with max type 19 + 64 dihedrals with max type 21 + 16 impropers with max type 8 +molecule mol2 2styrene_reacted.molecule_template +Read molecule template mol2: + 1 molecules + 0 fragments + 32 atoms with max type 6 + 33 bonds with max type 13 + 54 angles with max type 22 + 79 dihedrals with max type 19 + 14 impropers with max type 7 +molecule mol3 chain_plus_styrene_unreacted.molecule_template +Read molecule template mol3: + 1 molecules + 0 fragments + 46 atoms with max type 6 + 47 bonds with max type 13 + 75 angles with max type 22 + 105 dihedrals with max type 21 + 21 impropers with max type 8 +molecule mol4 chain_plus_styrene_reacted.molecule_template +Read molecule template mol4: + 1 molecules + 0 fragments + 46 atoms with max type 6 + 48 bonds with max type 13 + 81 angles with max type 22 + 121 dihedrals with max type 19 + 19 impropers with max type 7 +molecule mol5 chain_chain_unreacted.molecule_template +Read molecule template mol5: + 1 molecules + 0 fragments + 50 atoms with max type 6 + 51 bonds with max type 13 + 84 angles with max type 22 + 118 dihedrals with max type 19 + 20 impropers with max type 7 +molecule mol6 chain_chain_reacted.molecule_template +Read molecule template mol6: + 1 molecules + 0 fragments + 50 atoms with max type 6 + 52 bonds with max type 13 + 90 angles with max type 22 + 135 dihedrals with max type 19 + 18 impropers with max type 2 + +thermo 100 + +# dump 1 all xyz 5 test_vis.xyz + +fix rxn1 all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0 3.0 mol1 mol2 2styrene_map stabilize_steps 100 react rxn2 all 1 0 3.0 mol3 mol4 chain_plus_styrene_map stabilize_steps 100 react rxn3 all 1 0 5.0 mol5 mol6 chain_chain_map stabilize_steps 100 +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_rxn1[1] f_rxn1[2] f_rxn1[3] + +run 10000 + +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 + +PPPM initialization ... +WARNING: System is not charge neutral, net charge = -0.004 (../kspace.cpp:327) + using 12-bit tables for long-range coulomb (../kspace.cpp:342) + G vector (1/distance) = 0.25561147 + grid = 6 6 6 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0097469157 + estimated relative force accuracy = 2.9352547e-05 + using double precision KISS FFT + 3d grid and FFT values/proc = 1331 216 +Generated 21 of 21 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 = 4 4 4 + 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 + 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) = 31.51 | 31.51 | 31.51 Mbytes + Step Temp Press Density f_rxn1[1] f_rxn1[2] f_rxn1[3] + 0 320.13638 -376.0844 0.76796752 0 0 0 + 100 342.22237 -3489.4495 0.76796752 0 0 0 + 200 412.23828 -1367.104 0.76796752 0 0 0 + 300 467.98145 4841.002 0.76796752 0 0 0 + 400 505.39864 2213.0509 0.76796752 1 0 0 + 500 519.63371 -28223.513 0.76796752 2 0 0 + 600 526.40655 8701.2728 0.76796752 2 0 0 + 700 579.91953 2507.5868 0.76796752 2 0 0 + 800 517.29593 5558.2894 0.76796752 2 0 0 + 900 503.38392 -5027.1155 0.76796752 2 0 0 + 1000 509.30766 3979.0526 0.76796752 2 0 0 + 1100 551.34763 5119.0854 0.76796752 2 0 0 + 1200 562.51766 -2867.8721 0.76796752 2 0 0 + 1300 552.90947 2090.7196 0.76796752 2 0 0 + 1400 516.10667 3374.3471 0.76796752 2 0 0 + 1500 518.70363 472.0237 0.76796752 2 0 0 + 1600 559.50145 5451.1908 0.76796752 2 0 0 + 1700 531.49515 4526.9547 0.76796752 2 0 0 + 1800 529.18545 -3566.8838 0.76796752 2 0 0 + 1900 517.52577 -2390.6662 0.76796752 2 0 0 + 2000 495.24246 -485.62368 0.76796752 2 0 0 + 2100 567.90338 2009.3507 0.76796752 3 0 0 + 2200 553.05006 5694.0307 0.76796752 3 0 0 + 2300 561.22521 2944.2766 0.76796752 3 0 0 + 2400 460.05535 3058.3944 0.76796752 3 0 0 + 2500 501.01426 365.04418 0.76796752 4 0 0 + 2600 543.94728 267.33298 0.76796752 4 0 0 + 2700 539.40536 4258.9345 0.76796752 4 0 0 + 2800 557.67853 -2732.3135 0.76796752 4 0 0 + 2900 539.85456 3987.7331 0.76796752 4 1 0 + 3000 501.3125 3280.3821 0.76796752 4 1 0 + 3100 537.77092 -5290.371 0.76796752 4 1 0 + 3200 528.20744 11690.902 0.76796752 4 1 0 + 3300 548.56721 2464.6039 0.76796752 4 1 0 + 3400 542.73725 -27951.173 0.76796752 4 1 1 + 3500 547.63988 7925.1202 0.76796752 4 1 1 + 3600 502.69726 7875.8308 0.76796752 4 1 1 + 3700 495.26614 -1907.7215 0.76796752 4 1 1 + 3800 526.91826 -4267.1784 0.76796752 4 1 1 + 3900 538.8248 6811.7446 0.76796752 4 1 1 + 4000 531.42158 5031.2992 0.76796752 4 1 1 + 4100 539.69772 6278.9861 0.76796752 4 1 1 + 4200 519.11497 9206.6513 0.76796752 4 1 1 + 4300 518.08237 -63.769046 0.76796752 4 1 1 + 4400 582.43352 4189.0234 0.76796752 4 1 1 + 4500 541.87979 -2072.4133 0.76796752 4 1 1 + 4600 514.7508 7502.1057 0.76796752 4 1 1 + 4700 530.22173 51.50674 0.76796752 4 1 1 + 4800 507.14885 5148.7797 0.76796752 4 1 1 + 4900 516.05055 9110.3072 0.76796752 4 1 1 + 5000 552.55865 7310.0399 0.76796752 4 1 1 + 5100 581.79588 3282.8939 0.76796752 4 1 1 + 5200 523.07607 -1312.6111 0.76796752 4 1 1 + 5300 528.44235 -2242.0268 0.76796752 4 1 1 + 5400 537.63408 4599.5474 0.76796752 4 1 1 + 5500 526.75093 5551.7841 0.76796752 4 1 1 + 5600 562.74766 2764.4556 0.76796752 4 1 1 + 5700 545.12259 -3139.3468 0.76796752 4 1 1 + 5800 563.77404 4261.7786 0.76796752 4 1 1 + 5900 514.07804 4057.43 0.76796752 4 1 1 + 6000 548.42605 -2814.3308 0.76796752 4 1 1 + 6100 525.16391 -2902.5409 0.76796752 4 1 1 + 6200 504.92542 -706.19923 0.76796752 4 1 2 + 6300 531.55271 1217.7795 0.76796752 4 1 2 + 6400 537.29797 264.24006 0.76796752 4 1 2 + 6500 581.8752 2228.1037 0.76796752 4 1 2 + 6600 536.95487 -10318.365 0.76796752 4 2 2 + 6700 498.26961 5005.4587 0.76796752 5 2 2 + 6800 526.00873 -2678.0327 0.76796752 5 2 2 + 6900 542.74619 -1567.8558 0.76796752 5 2 2 + 7000 549.02037 8321.4935 0.76796752 5 2 2 + 7100 542.28295 -1513.6114 0.76796752 5 2 2 + 7200 474.70347 2120.9699 0.76796752 5 2 2 + 7300 506.58637 2588.8837 0.76796752 5 2 2 + 7400 512.45393 -2101371.7 0.76796752 5 2 3 + 7500 546.20285 -2458.3002 0.76796752 5 2 3 + 7600 551.57132 3148.9131 0.76796752 5 2 3 + 7700 544.3684 -775.59686 0.76796752 5 2 3 + 7800 511.32529 2353.0343 0.76796752 5 2 3 + 7900 520.30502 10726.007 0.76796752 5 2 3 + 8000 561.81009 12476.296 0.76796752 5 2 3 + 8100 588.85859 5905.4979 0.76796752 5 2 3 + 8200 490.1071 1132.5027 0.76796752 5 2 3 + 8300 537.65085 -1445.0979 0.76796752 5 2 3 + 8400 523.60343 -589.18012 0.76796752 5 2 3 + 8500 538.90848 -300.32152 0.76796752 5 2 3 + 8600 573.63835 5912.9027 0.76796752 5 2 3 + 8700 557.82593 2585.6634 0.76796752 5 2 3 + 8800 562.5277 -1843272.8 0.76796752 5 2 4 + 8900 564.26894 -1396.8521 0.76796752 5 2 4 + 9000 576.4382 5029.6995 0.76796752 5 2 4 + 9100 514.83258 -935.9015 0.76796752 5 2 4 + 9200 536.33755 -1671.9254 0.76796752 5 2 4 + 9300 494.49553 582.08687 0.76796752 5 2 4 + 9400 532.12156 -6991.3223 0.76796752 6 2 4 + 9500 528.87489 4587.7048 0.76796752 6 2 4 + 9600 555.92299 -3688.5966 0.76796752 6 2 4 + 9700 510.09341 1545.1276 0.76796752 6 2 4 + 9800 505.94984 -4677.2879 0.76796752 6 2 4 + 9900 531.38104 4891.0352 0.76796752 6 2 4 + 10000 517.59995 4299.0553 0.76796752 6 2 4 +Loop time of 29.4182 on 1 procs for 10000 steps with 320 atoms + +Performance: 29.370 ns/day, 0.817 hours/ns, 339.926 timesteps/s, 108.776 katom-step/s +100.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 10.883 | 10.883 | 10.883 | 0.0 | 36.99 +Bond | 8.0953 | 8.0953 | 8.0953 | 0.0 | 27.52 +Kspace | 2.6136 | 2.6136 | 2.6136 | 0.0 | 8.88 +Neigh | 1.0863 | 1.0863 | 1.0863 | 0.0 | 3.69 +Comm | 0.2095 | 0.2095 | 0.2095 | 0.0 | 0.71 +Output | 0.0019263 | 0.0019263 | 0.0019263 | 0.0 | 0.01 +Modify | 6.4695 | 6.4695 | 6.4695 | 0.0 | 21.99 +Other | | 0.05924 | | | 0.20 + +Nlocal: 320 ave 320 max 320 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 3425 ave 3425 max 3425 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 54783 ave 54783 max 54783 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 54783 +Ave neighs/atom = 171.19688 +Ave special neighs/atom = 10.3375 +Neighbor list builds = 460 +Dangerous builds = 0 + +# write_restart restart_longrun nofix +# write_data restart_longrun.data +Total wall time: 0:00:29 diff --git a/examples/PACKAGES/reaction/tiny_polystyrene/tiny_polystyrene.data b/examples/PACKAGES/reaction/tiny_polystyrene/tiny_polystyrene.data index 5f0ed4cfa6..ab12e8d4b1 100644 --- a/examples/PACKAGES/reaction/tiny_polystyrene/tiny_polystyrene.data +++ b/examples/PACKAGES/reaction/tiny_polystyrene/tiny_polystyrene.data @@ -15,6 +15,108 @@ LAMMPS data file via write_data, version 20 Nov 2019, timestep = 25000 1.7426663385337786e+00 1.8257333661465619e+01 ylo yhi 1.7426663385337786e+00 1.8257333661465619e+01 zlo zhi +Atom Type Labels + +1 cp +2 hc +3 c=1 +4 c= +5 c1 +6 c2 +7 c3 + +Bond Type Labels + +1 cp-hc +2 cp-cp +3 cp-c1 +4 hc-c=1 +5 c=1-c= +6 hc-c= +7 cp-c3 +8 hc-c3 +9 c3-c2 +10 hc-c2 +11 cp-c=1 +12 hc-c1 +13 c1-c2 + +Angle Type Labels + +1 cp-cp-hc +2 cp-cp-cp +3 cp-cp-c1 +4 cp-c1-hc +5 cp-c1-c2 +6 hc-c=1-c= +7 hc-c=-c=1 +8 hc-c=-hc +9 cp-cp-c3 +10 cp-c3-hc +11 cp-c3-c2 +12 hc-c3-c2 +13 c3-c2-c1 +14 hc-c2-c3 +15 hc-c2-hc +16 c1-c2-c1 +17 cp-cp-c=1 +18 cp-c=1-hc +19 cp-c=1-c= +20 hc-c2-c1 +21 hc-c1-c2 +22 c2-c1-c2 + +Dihedral Type Labels + +1 hc-cp-cp-c1 +2 cp-cp-cp-hc +3 cp-cp-cp-c1 +4 cp-cp-cp-cp +5 hc-cp-cp-hc +6 cp-cp-c=1-hc +7 cp-cp-c=1-c= +8 cp-c=1-c=-hc +9 hc-c=1-c=-hc +10 hc-cp-cp-c3 +11 cp-cp-cp-c3 +12 cp-cp-c1-hc +13 cp-cp-c1-c2 +14 cp-c1-c2-hc +15 hc-c1-c2-hc +16 c2-c1-c2-hc +17 cp-c1-c2-c1 +18 hc-c1-c2-c1 +19 c2-c1-c2-c1 +20 hc-cp-cp-c=1 +21 cp-cp-cp-c=1 +22 cp-cp-c3-hc +23 cp-cp-c3-c2 +24 cp-c3-c2-hc +25 cp-c3-c2-c1 +26 hc-c3-c2-hc +27 hc-c3-c2-c1 +28 c3-c2-c1-cp +29 c3-c2-c1-hc +30 c3-c2-c1-c2 +31 hc-c2-c1-cp +32 hc-c2-c1-hc +33 hc-c2-c1-c2 +34 c1-c2-c1-cp +35 c1-c2-c1-hc +36 c1-c2-c1-c2 + +Improper Type Labels + +1 cp-cp-cp-hc +2 cp-cp-cp-c1 +3 cp-c=1-hc-c= +4 hc-c=-hc-c=1 +5 cp-cp-cp-c3 +6 hc-c2-hc-c1 +7 cp-c1-hc-c2 +8 cp-cp-cp-c=1 +9 cp-c3-hc-c2 + Masses 1 12.0112 diff --git a/src/REACTION/README b/src/REACTION/README index f5fc929c9d..99a5d604ec 100644 --- a/src/REACTION/README +++ b/src/REACTION/README @@ -13,12 +13,16 @@ crosslinked materials. Any number of competing or reversible reaction pathways can be specified, and reacting sites can be stabilized. Other advanced options currently available include reaction constraints (e.g. angle and Arrhenius constraints), deletion of reaction -byproducts or other small molecules, and chiral-sensitive reactions. +byproducts or other small molecules, creation of new atoms or +molecules bonded to existing atoms, and using LAMMPS variables for +input parameters. The REACTER methodology is detailed in: Gissinger et al., Polymer 128, 211-217 (2017) https://doi.org/10.1016/j.polymer.2017.09.038 + Gissinger et al., Macromolecules 53, 22, 9953-9961 (2020). + https://doi.org/10.1021/acs.macromol.0c02012 + This package was created by Jacob Gissinger -(jacob.r.gissinger@gmail.com), while at the NASA Langley Research -Center. +(jacob.r.gissinger@gmail.com) at the NASA Langley Research Center. diff --git a/src/REACTION/fix_bond_react.cpp b/src/REACTION/fix_bond_react.cpp index 87d83da1ae..edddac1cb8 100644 --- a/src/REACTION/fix_bond_react.cpp +++ b/src/REACTION/fix_bond_react.cpp @@ -1476,9 +1476,6 @@ void FixBondReact::superimpose_algorithm() // this updates topology next step next_reneighbor = update->ntimestep; - // call limit_bond in 'global_mega_glove mode.' oh, and local mode - limit_bond(LOCAL); // add reacting atoms to nve/limit - limit_bond(GLOBAL); update_everything(); // change topology } @@ -2779,80 +2776,6 @@ void FixBondReact::dedup_mega_gloves(int dedup_mode) delete [] dup_list; } -/* ---------------------------------------------------------------------- -let's limit movement of newly bonded atoms -and exclude them from other thermostats via exclude_group -------------------------------------------------------------------------- */ - -void FixBondReact::limit_bond(int limit_bond_mode) -{ - //two types of passes: 1) while superimpose algorithm is iterating (only local atoms) - // 2) once more for global_mega_glove [after de-duplicating rxn instances] - //in second case, only add local atoms to group - //as with update_everything, we can pre-prepare these arrays, then run generic limit_bond code - - //create local, generic variables for onemol->natoms and glove - //to be filled differently on respective passes - - int nlocal = atom->nlocal; - int temp_limit_num = 0; - tagint *temp_limit_glove; - if (limit_bond_mode == LOCAL) { - int max_temp = local_num_mega * (max_natoms + 1); - temp_limit_glove = new tagint[max_temp]; - for (int j = 0; j < local_num_mega; j++) { - rxnID = local_mega_glove[0][j]; - onemol = atom->molecules[unreacted_mol[rxnID]]; - for (int i = 0; i < onemol->natoms; i++) { - temp_limit_glove[temp_limit_num++] = local_mega_glove[i+1][j]; - } - } - - } else if (limit_bond_mode == GLOBAL) { - int max_temp = global_megasize * (max_natoms + 1); - temp_limit_glove = new tagint[max_temp]; - for (int j = 0; j < global_megasize; j++) { - rxnID = global_mega_glove[0][j]; - onemol = atom->molecules[unreacted_mol[rxnID]]; - for (int i = 0; i < onemol->natoms; i++) { - if (atom->map(global_mega_glove[i+1][j]) >= 0 && - atom->map(global_mega_glove[i+1][j]) < nlocal) - temp_limit_glove[temp_limit_num++] = global_mega_glove[i+1][j]; - } - } - } - - if (temp_limit_num == 0) { - delete [] temp_limit_glove; - return; - } - - // we must keep our own list of limited atoms - // this will be a new per-atom property! - - int flag,cols; - int index1 = atom->find_custom("limit_tags",flag,cols); - int *i_limit_tags = atom->ivector[index1]; - - int *i_statted_tags; - if (stabilization_flag == 1) { - int index2 = atom->find_custom(statted_id,flag,cols); - i_statted_tags = atom->ivector[index2]; - } - - int index3 = atom->find_custom("react_tags",flag,cols); - int *i_react_tags = atom->ivector[index3]; - - for (int i = 0; i < temp_limit_num; i++) { - // update->ntimestep could be 0. so add 1 throughout - i_limit_tags[atom->map(temp_limit_glove[i])] = update->ntimestep + 1; - if (stabilization_flag == 1) i_statted_tags[atom->map(temp_limit_glove[i])] = 0; - i_react_tags[atom->map(temp_limit_glove[i])] = rxnID; - } - - delete [] temp_limit_glove; -} - /* ---------------------------------------------------------------------- let's unlimit movement of newly bonded atoms after n timesteps. we give them back to the system thermostat @@ -3055,6 +2978,21 @@ void FixBondReact::update_everything() int delta_dihed = 0; int delta_imprp = 0; + // use the following per-atom arrays to keep track of reacting atoms + + int flag,cols; + int index1 = atom->find_custom("limit_tags",flag,cols); + int *i_limit_tags = atom->ivector[index1]; + + int *i_statted_tags; + if (stabilization_flag == 1) { + int index2 = atom->find_custom(statted_id,flag,cols); + i_statted_tags = atom->ivector[index2]; + } + + int index3 = atom->find_custom("react_tags",flag,cols); + int *i_react_tags = atom->ivector[index3]; + // pass through twice // redefining 'update_num_mega' and 'update_mega_glove' each time // first pass: when glove is all local atoms @@ -3175,18 +3113,25 @@ void FixBondReact::update_everything() } // update charges and types of landlocked atoms + // also keep track of 'stabilization' groups here for (int i = 0; i < update_num_mega; i++) { rxnID = update_mega_glove[0][i]; twomol = atom->molecules[reacted_mol[rxnID]]; for (int j = 0; j < twomol->natoms; j++) { int jj = equivalences[j][1][rxnID]-1; - if (atom->map(update_mega_glove[jj+1][i]) >= 0 && - atom->map(update_mega_glove[jj+1][i]) < nlocal) { + int ilocal = atom->map(update_mega_glove[jj+1][i]); + if (ilocal >= 0 && ilocal < nlocal) { + + // update->ntimestep could be 0. so add 1 throughout + i_limit_tags[ilocal] = update->ntimestep + 1; + if (stabilization_flag == 1) i_statted_tags[ilocal] = 0; + i_react_tags[ilocal] = rxnID; + if (landlocked_atoms[j][rxnID] == 1) - type[atom->map(update_mega_glove[jj+1][i])] = twomol->type[j]; + type[ilocal] = twomol->type[j]; if (twomol->qflag && atom->q_flag && custom_charges[jj][rxnID] == 1) { double *q = atom->q; - q[atom->map(update_mega_glove[jj+1][i])] = twomol->q[j]+charge_rescale_addend; + q[ilocal] = twomol->q[j]+charge_rescale_addend; } } } @@ -3913,25 +3858,6 @@ int FixBondReact::insert_atoms(tagint **my_mega_glove, int iupdate) v[n][1] = v[n][1]/vnorm*vtnorm; v[n][2] = v[n][2]/vnorm*vtnorm; modify->create_attribute(n); - - // initialize group statuses - // why aren't these more global... - int flag,cols; - int index1 = atom->find_custom("limit_tags",flag,cols); - int *i_limit_tags = atom->ivector[index1]; - - int *i_statted_tags; - if (stabilization_flag == 1) { - int index2 = atom->find_custom(statted_id,flag,cols); - i_statted_tags = atom->ivector[index2]; - } - - int index3 = atom->find_custom("react_tags",flag,cols); - int *i_react_tags = atom->ivector[index3]; - - i_limit_tags[n] = update->ntimestep + 1; - if (stabilization_flag == 1) i_statted_tags[n] = 0; - i_react_tags[n] = rxnID; } // globally update mega_glove and equivalences MPI_Allreduce(MPI_IN_PLACE,&root,1,MPI_INT,MPI_SUM,world); diff --git a/src/REACTION/fix_bond_react.h b/src/REACTION/fix_bond_react.h index 4751bc4eef..b434699ec7 100644 --- a/src/REACTION/fix_bond_react.h +++ b/src/REACTION/fix_bond_react.h @@ -209,7 +209,6 @@ class FixBondReact : public Fix { void update_everything(); int insert_atoms(tagint **, int); void unlimit_bond(); // removes atoms from stabilization, and other post-reaction every-step operations - void limit_bond(int); void dedup_mega_gloves(int); //dedup global mega_glove void write_restart(FILE *) override; void restart(char *buf) override;