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‎files/tutorial8/reacting.lmp‎

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@@ -37,8 +37,6 @@ fix rxn all bond/react stabilization yes statted_grp 0.03 &
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fix 1 statted_grp_REACT nvt temp 530 530 100
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fix 4 bond_react_MASTER_group temp/rescale 1 530 530 1 1
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thermo_style custom step temp press density f_rxn[*]
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dump mydmp all image 1000 dump.mixing.*.ppm &

‎files/tutorial8/reacting.log‎

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@@ -1,4 +1,21 @@
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LAMMPS (29 Aug 2024 - Development - patch_29Aug2024-1065-gcf05700897)
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# polymerization of PS-CNT composite using REACTER
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units real
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boundary p p p
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atom_style full
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kspace_style pppm 1.0e-4
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pair_style lj/class2/coul/long 8.5
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angle_style class2
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bond_style class2
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dihedral_style class2
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improper_style class2
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special_bonds lj/coul 0 0 1
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pair_modify tail yes mix sixthpower
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read_data CNT-PS-mix.data extra/bond/per/atom 5 extra/angle/per/atom 15 extra/dihedral/per/atom 15 extra/improper/per/atom 25 extra/special/per/atom 25
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Reading data file ...
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orthogonal box = (-2.3164529 -26.16 -26.16) to (13.21044 26.16 26.16)
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1 by 1 by 1 MPI processor grid
@@ -37,6 +54,8 @@ Finding 1-2 1-3 1-4 neighbors ...
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34 = max # of special neighbors
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special bonds CPU = 0.001 seconds
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read_data CPU = 0.091 seconds
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molecule mol1 M-M_pre.lmpmol
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Read molecule template mol1:
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2styrene_unreacted
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1 molecules
@@ -46,6 +65,7 @@ Read molecule template mol1:
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48 angles with max type 19
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64 dihedrals with max type 21
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16 impropers with max type 9
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molecule mol2 M-M_post.lmpmol
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Read molecule template mol2:
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2styrene_reacted
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1 molecules
@@ -55,6 +75,7 @@ Read molecule template mol2:
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54 angles with max type 22
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79 dihedrals with max type 19
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14 impropers with max type 8
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molecule mol3 M-P_pre.lmpmol
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Read molecule template mol3:
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chain_plus_styrene_unreacted
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1 molecules
@@ -64,6 +85,7 @@ chain_plus_styrene_unreacted
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75 angles with max type 22
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105 dihedrals with max type 21
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21 impropers with max type 9
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molecule mol4 M-P_post.lmpmol
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Read molecule template mol4:
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chain_plus_styrene_reacted
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1 molecules
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81 angles with max type 22
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121 dihedrals with max type 19
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19 impropers with max type 8
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molecule mol5 P-P_pre.lmpmol
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Read molecule template mol5:
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chain_chain_unreacted
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1 molecules
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84 angles with max type 22
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118 dihedrals with max type 19
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20 impropers with max type 8
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molecule mol6 P-P_post.lmpmol
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Read molecule template mol6:
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chain_chain_reacted
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1 molecules
@@ -91,15 +115,69 @@ chain_chain_reacted
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90 angles with max type 22
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135 dihedrals with max type 19
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18 impropers with max type 3
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thermo 250
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fix rxn1 all bond/react stabilization yes statted_grp 0.03 react R1 all 1 0 3.0 mol1 mol2 M-M.rxnmap stabilize_steps 100 react R2 all 1 0 3.0 mol3 mol4 M-P.rxnmap stabilize_steps 100 react R3 all 1 0 5.0 mol5 mol6 P-P.rxnmap stabilize_steps 100
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dynamic group bond_react_MASTER_group defined
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dynamic group statted_grp_REACT defined
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fix 1 statted_grp_REACT nvt temp 530 530 100
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#fix 4 bond_react_MASTER_group temp/rescale 1 530 530 1 1
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thermo_style custom step temp press density f_rxn1[*]
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dump mydmp all image 1000 dump.mixing.*.ppm type type shiny 0.1 box no 0.01 view 90 0 zoom 1.5 fsaa yes bond atom 0.5
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dump_modify mydmp backcolor white acolor cp gray acolor c=1 gray acolor c= gray acolor c1 gray acolor c2 gray acolor c3 gray adiam cp 0.3 adiam c=1 0.3 adiam c= 0.3 adiam c1 0.3 adiam c2 0.3 adiam c3 0.3 acolor hc white adiam hc 0.15
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run 10000
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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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Your simulation uses code contributions which should be cited:
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- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
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@Article{Gissinger24,
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author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
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title = {Type Label Framework for Bonded Force Fields in LAMMPS},
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journal = {J. Phys. Chem. B},
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year = 2024,
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volume = 128,
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number = 13,
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pages = {3282--3297}
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}
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- fix bond/react: reacter.org doi:10.1016/j.polymer.2017.09.038, doi:10.1021/acs.macromol.0c02012, doi:10.1016/j.cpc.2024.109287
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The log file lists these citations in BibTeX format.
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@Article{Gissinger17,
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author = {J. R. Gissinger and B. D. Jensen and K. E. Wise},
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title = {Modeling Chemical Reactions in Classical Molecular Dynamics Simulations},
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journal = {Polymer},
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year = 2017,
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volume = 128,
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pages = {211--217}
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}
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@Article{Gissinger20,
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author = {J. R. Gissinger, B. D. Jensen, K. E. Wise},
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title = {{REACTER}: A Heuristic Method for Reactive Molecular Dynamics},
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journal = {Macromolecules},
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year = 2020,
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volume = 53,
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number = 22,
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pages = {9953--9961}
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}
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@Article{Gissinger24,
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author = {J. R. Gissinger, B. D. Jensen, K. E. Wise},
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title = {Molecular Modeling of Reactive Systems with REACTER},
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journal = {Computer Physics Communications},
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year = 2024,
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volume = 304,
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number = 109287
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}
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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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@@ -131,83 +209,81 @@ Neighbor list info ...
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pair build: copy
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stencil: none
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bin: none
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Setting up Verlet run ...
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Unit style : real
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Current step : 0
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Time step : 1
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WARNING: Inconsistent image flags (../domain.cpp:1051)
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Per MPI rank memory allocation (min/avg/max) = 35.86 | 35.86 | 35.86 Mbytes
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Step Temp Press Density f_rxn1[1] f_rxn1[2] f_rxn1[3]
141215
0 302.27771 -9596.9435 0.90392574 0 0 0
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250 389.53088 -13850.265 0.90392574 3 0 0
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500 485.68521 -9007.2658 0.90392574 8 0 0
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750 542.3226 -23248.667 0.90392574 16 0 1
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1000 534.7719 -12762.21 0.90392574 19 1 1
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1250 516.99898 -11075.439 0.90392574 24 1 3
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1500 543.76181 -7868.2943 0.90392574 30 1 4
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1750 513.87518 -25520.029 0.90392574 37 1 8
149-
2000 535.3342 -12037.406 0.90392574 41 3 12
150-
2250 531.66857 -8743.6113 0.90392574 43 4 13
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2500 527.99965 -12390.768 0.90392574 45 4 17
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2750 530.87307 -62829.341 0.90392574 47 5 20
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3000 521.16815 -15127.611 0.90392574 50 5 22
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3250 523.34123 -10305.497 0.90392574 54 5 23
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3500 531.02862 -8035.5586 0.90392574 56 5 23
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3750 537.03195 -7481.4729 0.90392574 57 7 26
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4000 529.24999 -131818.3 0.90392574 57 7 28
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4250 535.47954 -15352.285 0.90392574 62 7 31
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4500 530.34472 -9252.827 0.90392574 63 8 32
160-
4750 534.81427 -51105.955 0.90392574 67 8 35
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5000 522.77673 -58794.632 0.90392574 68 8 38
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5250 534.0386 -11023.165 0.90392574 69 9 38
163-
5500 533.83622 -179338.2 0.90392574 70 9 41
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5750 533.65206 -9994.6046 0.90392574 71 9 45
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6000 529.82185 -8416.1706 0.90392574 72 9 46
166-
6250 531.81262 -71335.905 0.90392574 74 9 50
167-
6500 542.45727 -208291.06 0.90392574 75 9 51
168-
6750 519.63414 -8612.4281 0.90392574 75 9 51
169-
7000 530.64062 -10287.366 0.90392574 75 9 51
170-
7250 520.41821 -8764.4035 0.90392574 75 9 52
171-
7500 531.01859 -7844.5152 0.90392574 77 11 53
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7750 527.27692 -9686.8375 0.90392574 77 12 54
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8000 536.78229 -10465.507 0.90392574 78 12 54
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8250 517.53142 -18790.931 0.90392574 78 12 55
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8500 547.23107 -11464.695 0.90392574 78 12 57
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8750 529.14376 -9877.1628 0.90392574 78 12 57
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9000 526.70037 -12063.703 0.90392574 78 12 58
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9250 541.9196 -8608.9846 0.90392574 79 12 59
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9500 516.09736 -8818.5419 0.90392574 79 13 59
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9750 548.34487 -26718.708 0.90392574 79 13 62
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10000 530.89214 -11239.132 0.90392574 79 13 62
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Loop time of 230.245 on 1 procs for 10000 steps with 3392 atoms
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Performance: 3.753 ns/day, 6.396 hours/ns, 43.432 timesteps/s, 147.322 katom-step/s
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99.4% CPU use with 1 MPI tasks x no OpenMP threads
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250 389.62661 -13771.24 0.90392574 3 0 0
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500 496.13936 -8387.4543 0.90392574 8 0 0
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750 563.07162 -7466.3885 0.90392574 17 0 0
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1000 532.39002 -237215.55 0.90392574 25 0 1
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1250 519.59296 -9014.2788 0.90392574 28 2 2
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1500 528.67689 -6693.843 0.90392574 34 2 4
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1750 546.01113 -7038.0434 0.90392574 36 4 8
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2000 526.58304 -6909.547 0.90392574 42 4 11
224+
2250 551.46275 -7135.5723 0.90392574 45 4 15
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2500 531.51382 -6816.0616 0.90392574 49 4 15
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2750 527.79367 -8993.9614 0.90392574 50 4 17
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3000 535.77409 -8200.5447 0.90392574 51 5 17
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3250 531.26987 -11768.345 0.90392574 52 6 19
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3500 543.42131 -8565.5964 0.90392574 52 6 22
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3750 538.99985 -94280.857 0.90392574 54 7 25
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4000 535.75775 -7002.1693 0.90392574 61 7 29
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4250 539.03236 -6676.7884 0.90392574 63 8 31
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4500 524.03635 -29603.541 0.90392574 63 8 32
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4750 536.66093 -219467.93 0.90392574 63 8 36
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5000 534.64995 -7777.0902 0.90392574 64 8 38
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5250 530.73662 -8320.2412 0.90392574 66 9 39
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5500 522.46297 -7760.4153 0.90392574 66 9 40
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5750 530.41956 -7919.3994 0.90392574 67 9 42
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6000 548.51896 -4949.9725 0.90392574 67 9 42
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6250 514.90331 -8398.5823 0.90392574 68 10 42
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6500 532.59521 -8099.478 0.90392574 70 10 43
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6750 528.09969 -9745.5438 0.90392574 70 11 45
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7000 536.15819 -16114.684 0.90392574 72 11 46
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7250 538.63772 -110866.47 0.90392574 73 11 48
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7500 540.49827 -6574.2117 0.90392574 74 11 49
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7750 537.27053 -10202.909 0.90392574 75 11 50
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8000 530.75755 -10371.958 0.90392574 75 12 51
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8250 528.48172 -8879.1006 0.90392574 75 12 53
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8500 537.78827 -7153.8509 0.90392574 75 12 54
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8750 533.06702 -6964.6352 0.90392574 75 12 55
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9000 540.99978 -6204.6325 0.90392574 75 12 55
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9250 537.23535 -8742.3545 0.90392574 75 13 55
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9500 535.42716 -10138.52 0.90392574 75 13 56
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9750 532.41898 -10556.994 0.90392574 75 13 56
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10000 527.68125 -7598.2347 0.90392574 75 14 56
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Loop time of 228.008 on 1 procs for 10000 steps with 3392 atoms
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Performance: 3.789 ns/day, 6.334 hours/ns, 43.858 timesteps/s, 148.767 katom-step/s
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99.7% CPU use with 1 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 92.741 | 92.741 | 92.741 | 0.0 | 40.28
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Bond | 51.39 | 51.39 | 51.39 | 0.0 | 22.32
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Kspace | 11.155 | 11.155 | 11.155 | 0.0 | 4.85
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Neigh | 19.65 | 19.65 | 19.65 | 0.0 | 8.53
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Comm | 0.625 | 0.625 | 0.625 | 0.0 | 0.27
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Output | 2.331 | 2.331 | 2.331 | 0.0 | 1.01
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Modify | 52.174 | 52.174 | 52.174 | 0.0 | 22.66
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Other | | 0.1784 | | | 0.08
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Pair | 92.944 | 92.944 | 92.944 | 0.0 | 40.76
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Bond | 51.204 | 51.204 | 51.204 | 0.0 | 22.46
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Kspace | 11.353 | 11.353 | 11.353 | 0.0 | 4.98
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Neigh | 18.861 | 18.861 | 18.861 | 0.0 | 8.27
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Comm | 0.60999 | 0.60999 | 0.60999 | 0.0 | 0.27
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Output | 1.0048 | 1.0048 | 1.0048 | 0.0 | 0.44
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Modify | 51.868 | 51.868 | 51.868 | 0.0 | 22.75
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Other | | 0.163 | | | 0.07
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Nlocal: 3392 ave 3392 max 3392 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 12379 ave 12379 max 12379 min
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Nghost: 12415 ave 12415 max 12415 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 654516 ave 654516 max 654516 min
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Neighs: 656042 ave 656042 max 656042 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 654516
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Ave neighs/atom = 192.95873
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Ave special neighs/atom = 10.228774
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Neighbor list builds = 822
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Total # of neighbors = 656042
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Ave neighs/atom = 193.40861
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Ave special neighs/atom = 9.9858491
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Neighbor list builds = 793
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Dangerous builds = 0
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write_restart restart_longrun
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System init for write_restart ...
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PPPM initialization ...
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using 12-bit tables for long-range coulomb (../kspace.cpp:342)
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219295
using double precision KISS FFT
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3d grid and FFT values/proc = 4400 1350
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Generated 21 of 21 mixed pair_coeff terms from sixthpower/sixthpower mixing rule
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write_data restart_longrun.data nofix
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System init for write_data ...
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PPPM initialization ...
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using 12-bit tables for long-range coulomb (../kspace.cpp:342)
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using double precision KISS FFT
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3d grid and FFT values/proc = 4400 1350
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Generated 21 of 21 mixed pair_coeff terms from sixthpower/sixthpower mixing rule
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Total wall time: 0:03:50
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Total wall time: 0:03:48

‎lammps-tutorials.tex‎

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Original file line numberDiff line numberDiff line change
@@ -4160,7 +4160,7 @@ \subsubsection{Simulating the reaction}
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\begin{verbatim}
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dump mydmp all image 1000 dump.mix.*.ppm &
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type type shiny 0.1 box no 0.01 &
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view 90 0 zoom 3 fsaa yes bond atom 0.5
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view 90 0 zoom 1.5 fsaa yes bond atom 0.5
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dump_modify mydmp backcolor white &
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acolor cp gray acolor c=1 gray &
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acolor c= gray acolor c1 gray &
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\label{fig:evolution-reacting}
42184218
\end{figure}
42194219

4220-
\begin{figure}
4221-
\centering
4222-
\includegraphics[width=\linewidth]{REACTED_VMD}
4223-
\caption{Polymer composite model of polystyrene and a CNT created in
4224-
\hyperref[bond-react-label]{Tutorial 8} by in-situ polymerization of
4225-
styrene using REACTER. The polymer chains are shown unwrapped from
4226-
the simulation box and the CNT (red) is also shifted along its axis
4227-
for visibility. Image rendered using VMD.}
4228-
\label{fig:REACTED_VMD}
4229-
\end{figure}
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\section*{Author Contributions}
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% S.G. to update
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S.G. conceived and wrote all the online tutorials and underlying Sphinx documentation

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