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simongravellesimongravelle
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improved inputs
1 parent 83dba28 commit f979c1e

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‎.gitignore‎

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# To be remove when final version is published
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# To be removed when final version is published
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lammps-tutorials.pdf
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# LaTex files for the manuscript
@@ -32,3 +32,4 @@ _region_.*
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# LAMMPS output files
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dump.*.jpg
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dump.*.ppn
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dump.*.ppm

‎files/tutorial8/cnt-nylon-mix.data‎

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‎files/tutorial8/mixing.lmp‎

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@@ -23,34 +23,40 @@ read_data nylon.data &
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replicate 3 4 4
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molecule CNT cnt.molecule
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create_atoms 0 random 5 8305 NULL overlap 3 maxtry 500 mol CNT 7687
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create_atoms 0 random 5 8305 NULL overlap 3 &
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maxtry 500 mol CNT 7687
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minimize 1.0e-4 1.0e-6 100 1000
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reset_timestep 0
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dump mydmp all image 1000 dump.mixing.*.ppm type &
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type shiny 0.1 box no 0.01 &
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view 0 0 zoom 1.8 fsaa yes bond atom 0.5
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dump mydmp all image 1000 dump.mixing.*.ppm &
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type type shiny 0.1 box no 0.01 &
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view 0 0 zoom 1.8 fsaa yes bond atom 0.5
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dump_modify mydmp backcolor white &
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acolor c2 gray acolor c_1 lightslategray &
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acolor o dimgray acolor o_1 dimgray &
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acolor hc lightslategray acolor ho lightslategray &
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acolor hn lightslategray acolor hw white &
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acolor o* red acolor n darkslategray &
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acolor na darkslategray acolor cp lightpink &
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adiam c2 0.3 adiam c_1 0.3 adiam cp 0.3 &
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adiam o 0.28 adiam o_1 0.28 adiam o* 2.8 &
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adiam hc 0.15 adiam ho 0.15 adiam hn 0.15 &
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adiam hw 1.5 adiam n 0.3 adiam na 0.3
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fix mynpt all npt temp 300 300 100 iso 1000 1000 1000
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acolor c2 gray acolor c_1 lightslategray &
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acolor o dimgray acolor o_1 dimgray &
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acolor hc lightslategray &
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acolor ho lightslategray &
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acolor hn lightslategray acolor hw white &
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acolor o* red acolor n darkslategray &
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acolor na darkslategray &
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acolor cp lightpink &
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adiam c2 0.3 adiam c_1 0.3 &
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adiam cp 0.3 adiam o 0.28 &
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adiam o_1 0.28 adiam o* 2.8 &
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adiam hc 0.15 adiam ho 0.15 &
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adiam hn 0.15 adiam hw 1.5 &
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adiam n 0.3 adiam na 0.3
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velocity all create 300 1829 dist gaussian &
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mom yes rot yes
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fix mynpt all npt temp 300 300 100 &
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iso 1000 1000 1000
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thermo 1000
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thermo_style custom step temp pe etotal press density vol
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thermo_style custom step temp pe etotal &
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press density
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run 10000
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unfix mynpt
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velocity all create 300 1829 dist gaussian mom yes rot yes
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fix mynpt all npt temp 300 300 100 iso 1 1 1000
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run 20000

‎files/tutorial8/mixing.log‎

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LAMMPS (27 Jun 2024 - Development - patch_27Jun2024-709-g67dccdc52f)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
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using 1 OpenMP thread(s) per MPI task
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# LAMMPS input file
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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-5
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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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pair_modify tail yes mix sixthpower
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special_bonds lj/coul 0 0 1
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read_data 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
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Reading data file ...
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orthogonal box = (-12 -9 -9) to (12 9 9)
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1 by 1 by 1 MPI processor grid
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reading atom labelmap ...
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reading bond labelmap ...
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reading angle labelmap ...
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reading dihedral labelmap ...
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reading improper labelmap ...
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reading atoms ...
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44 atoms
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reading velocities ...
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44 velocities
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scanning bonds ...
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9 = max bonds/atom
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scanning angles ...
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21 = max angles/atom
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scanning dihedrals ...
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29 = max dihedrals/atom
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scanning impropers ...
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29 = max impropers/atom
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orthogonal box = (-12 -9 -9) to (12 9 9)
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1 by 1 by 1 MPI processor grid
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reading bonds ...
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42 bonds
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reading angles ...
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74 angles
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reading dihedrals ...
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100 dihedrals
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reading impropers ...
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16 impropers
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 0 1
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special bond factors coul: 0 0 1
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4 = max # of 1-2 neighbors
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6 = max # of 1-3 neighbors
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35 = max # of special neighbors
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special bonds CPU = 0.000 seconds
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read_data CPU = 0.012 seconds
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replicate 3 4 4
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Replication is creating a 3x4x4 = 48 times larger system...
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orthogonal box = (-12 -9 -9) to (60 63 63)
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1 by 1 by 1 MPI processor grid
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2112 atoms
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2016 bonds
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3552 angles
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4800 dihedrals
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768 impropers
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 0 1
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special bond factors coul: 0 0 1
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4 = max # of 1-2 neighbors
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6 = max # of 1-3 neighbors
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35 = max # of special neighbors
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special bonds CPU = 0.001 seconds
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replicate CPU = 0.008 seconds
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molecule CNT cnt.molecule
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Read molecule template CNT:
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(no title)
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1 molecules
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0 fragments
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250 atoms with max type 12
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360 bonds with max type 14
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690 angles with max type 27
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1330 dihedrals with max type 34
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220 impropers with max type 6
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create_atoms 0 random 5 8305 NULL overlap 3 maxtry 500 mol CNT 7687
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Created 1250 atoms
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using lattice units in orthogonal box = (-12 -9 -9) to (60 63 63)
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create_atoms CPU = 4.942 seconds
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minimize 1.0e-4 1.0e-6 100 1000
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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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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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PPPM initialization ...
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using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
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G vector (1/distance) = 0.31302569
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grid = 45 45 45
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stencil order = 5
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estimated absolute RMS force accuracy = 0.0026080771
118+
estimated relative force accuracy = 7.8541466e-06
119+
using double precision KISS FFT
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3d grid and FFT values/proc = 140608 91125
121+
Generated 66 of 66 mixed pair_coeff terms from sixthpower/sixthpower mixing rule
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Neighbor list info ...
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update: every = 1 steps, delay = 0 steps, check = yes
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max neighbors/atom: 2000, page size: 100000
125+
master list distance cutoff = 10.5
126+
ghost atom cutoff = 10.5
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binsize = 5.25, bins = 14 14 14
128+
1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/class2/coul/long, perpetual
130+
attributes: half, newton on
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pair build: half/bin/newton
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stencil: half/bin/3d
133+
bin: standard
134+
Per MPI rank memory allocation (min/avg/max) = 48.33 | 48.33 | 48.33 Mbytes
135+
Step Temp E_pair E_mol TotEng Press
136+
0 205.77271 7757.7183 55840.905 65660.158 5198.2641
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38 205.77271 -3130.3511 52955.781 51886.965 376.38883
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Loop time of 3.0283 on 1 procs for 38 steps with 3362 atoms
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99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
141+
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Minimization stats:
143+
Stopping criterion = energy tolerance
144+
Energy initial, next-to-last, final =
145+
63598.6234264749 49830.0476791473 49825.4301878258
146+
Force two-norm initial, final = 7809.4255 105.34236
147+
Force max component initial, final = 805.7253 4.0623845
148+
Final line search alpha, max atom move = 0.0053414896 0.021699184
149+
Iterations, force evaluations = 38 70
150+
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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 | 0.39009 | 0.39009 | 0.39009 | 0.0 | 12.88
155+
Bond | 0.73857 | 0.73857 | 0.73857 | 0.0 | 24.39
156+
Kspace | 1.8785 | 1.8785 | 1.8785 | 0.0 | 62.03
157+
Neigh | 0.01096 | 0.01096 | 0.01096 | 0.0 | 0.36
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Comm | 0.0031208 | 0.0031208 | 0.0031208 | 0.0 | 0.10
159+
Output | 0 | 0 | 0 | 0.0 | 0.00
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Modify | 0 | 0 | 0 | 0.0 | 0.00
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Other | | 0.007021 | | | 0.23
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Nlocal: 3362 ave 3362 max 3362 min
164+
Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 4400 ave 4400 max 4400 min
166+
Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 160131 ave 160131 max 160131 min
168+
Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 160131
171+
Ave neighs/atom = 47.629685
172+
Ave special neighs/atom = 9.4098751
173+
Neighbor list builds = 1
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Dangerous builds = 0
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reset_timestep 0
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dump mydmp all image 1000 dump.mixing.*.ppm type type shiny 0.1 box no 0.01 view 0 0 zoom 1.8 fsaa yes bond atom 0.5
178+
dump_modify mydmp backcolor white acolor c2 gray acolor c_1 lightslategray acolor o dimgray acolor o_1 dimgray acolor hc lightslategray acolor ho lightslategray acolor hn lightslategray acolor hw white acolor o* red acolor n darkslategray acolor na darkslategray acolor cp lightpink adiam c2 0.3 adiam c_1 0.3 adiam cp 0.3 adiam o 0.28 adiam o_1 0.28 adiam o* 2.8 adiam hc 0.15 adiam ho 0.15 adiam hn 0.15 adiam hw 1.5 adiam n 0.3 adiam na 0.3
179+
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velocity all create 300 1829 dist gaussian mom yes rot yes
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fix mynpt all npt temp 300 300 100 iso 1000 1000 1000
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thermo 1000
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thermo_style custom step temp pe etotal press density
184+
run 10000
185+
PPPM initialization ...
186+
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
187+
G vector (1/distance) = 0.31302569
188+
grid = 45 45 45
189+
stencil order = 5
190+
estimated absolute RMS force accuracy = 0.0026080771
191+
estimated relative force accuracy = 7.8541466e-06
192+
using double precision KISS FFT
193+
3d grid and FFT values/proc = 140608 91125
194+
Generated 66 of 66 mixed pair_coeff terms from sixthpower/sixthpower mixing rule
195+
Per MPI rank memory allocation (min/avg/max) = 47.2 | 47.2 | 47.2 Mbytes
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Step Temp PotEng TotEng Press Density
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0 300 49825.43 52830.981 492.00401 0.12282015
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1000 289.56875 51879.291 54780.337 -184.87884 0.17640177
199+
2000 301.09839 51720.39 54736.945 180.68637 0.23065719
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3000 301.41884 51396.628 54416.393 62.548961 0.28926653
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4000 303.06565 51180.094 54216.358 344.84963 0.35305844
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5000 298.10772 50948.894 53935.487 103.03276 0.42466898
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6000 298.27976 50678.346 53666.663 -124.60965 0.5012718
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7000 292.11554 50542.512 53469.072 471.56439 0.58215591
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8000 305.74366 50369.556 53432.65 -606.96113 0.67409645
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9000 301.50442 50238.269 53258.892 -1243.4097 0.78209883
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10000 306.85765 50057.974 53132.228 -2078.3289 0.89289932
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Loop time of 650.463 on 1 procs for 10000 steps with 3362 atoms
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Performance: 1.328 ns/day, 18.068 hours/ns, 15.374 timesteps/s, 51.686 katom-step/s
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99.8% CPU use with 1 MPI tasks x 1 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 | 80.667 | 80.667 | 80.667 | 0.0 | 12.40
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Bond | 109.63 | 109.63 | 109.63 | 0.0 | 16.85
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Kspace | 282.11 | 282.11 | 282.11 | 0.0 | 43.37
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Neigh | 11.527 | 11.527 | 11.527 | 0.0 | 1.77
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Comm | 0.76443 | 0.76443 | 0.76443 | 0.0 | 0.12
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Output | 1.2289 | 1.2289 | 1.2289 | 0.0 | 0.19
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Modify | 164.07 | 164.07 | 164.07 | 0.0 | 25.22
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Other | | 0.4643 | | | 0.07
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Nlocal: 3362 ave 3362 max 3362 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 9276 ave 9276 max 9276 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 563418 ave 563418 max 563418 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 563418
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Ave neighs/atom = 167.58418
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Ave special neighs/atom = 9.4098751
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Neighbor list builds = 467
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Dangerous builds = 0
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fix mynpt all npt temp 300 300 100 iso 1 1 1000
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run 20000
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PPPM initialization ...
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using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
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G vector (1/distance) = 0.32771495
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grid = 27 27 27
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stencil order = 5
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estimated absolute RMS force accuracy = 0.0035678524
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estimated relative force accuracy = 1.0744482e-05
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using double precision KISS FFT
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3d grid and FFT values/proc = 39304 19683
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Generated 66 of 66 mixed pair_coeff terms from sixthpower/sixthpower mixing rule
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Per MPI rank memory allocation (min/avg/max) = 39.3 | 39.3 | 39.3 Mbytes
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Step Temp PotEng TotEng Press Density
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10000 306.85765 50057.988 53132.242 -2078.6519 0.89289932
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11000 304.2996 49809.174 52857.8 -1306.0614 0.99794835
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12000 298.43734 49668.912 52658.807 532.11108 1.0897847
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13000 310.63279 49522.706 52634.782 -1650.2223 1.1386107
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14000 294.00406 49510.269 52455.75 -786.16441 1.1695291
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15000 299.39774 49467.329 52466.846 -1375.0438 1.1805836
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16000 294.76646 49319.037 52272.155 -1527.7711 1.1871495
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17000 306.6779 49354.403 52426.856 1109.0844 1.2112368
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18000 304.07183 49269.869 52316.214 349.38334 1.2243133
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19000 299.83807 49278.384 52282.313 -1846.2243 1.2510185
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20000 305.96045 49336.121 52401.387 -117.36068 1.2434974
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21000 300.05216 49249.822 52255.895 983.09187 1.2586523
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22000 299.82171 49180.228 52183.992 -2460.8622 1.2571288
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23000 294.86426 49037.444 51991.542 -115.27629 1.2704513
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24000 300.23958 49078.834 52086.785 977.76683 1.2567804
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25000 294.0766 49003.112 51949.319 -2508.0723 1.2819973
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26000 302.11786 49095.233 52122.002 -18.733823 1.2835335
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27000 298.76282 48968 51961.156 63.053507 1.2866769
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28000 291.75618 49082.231 52005.191 1211.5975 1.2910412
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29000 300.85158 49061.618 52075.701 -1394.1089 1.2843408
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30000 300.62623 49000.37 52012.195 615.05694 1.2787748
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Loop time of 828.155 on 1 procs for 20000 steps with 3362 atoms
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Performance: 2.087 ns/day, 11.502 hours/ns, 24.150 timesteps/s, 81.193 katom-step/s
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99.8% CPU use with 1 MPI tasks x 1 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 | 341.53 | 341.53 | 341.53 | 0.0 | 41.24
283+
Bond | 218.37 | 218.37 | 218.37 | 0.0 | 26.37
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Kspace | 150.37 | 150.37 | 150.37 | 0.0 | 18.16
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Neigh | 38.346 | 38.346 | 38.346 | 0.0 | 4.63
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Comm | 2.1935 | 2.1935 | 2.1935 | 0.0 | 0.26
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Output | 2.6451 | 2.6451 | 2.6451 | 0.0 | 0.32
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Modify | 73.748 | 73.748 | 73.748 | 0.0 | 8.91
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Other | | 0.9582 | | | 0.12
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Nlocal: 3362 ave 3362 max 3362 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 11461 ave 11461 max 11461 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 769031 ave 769031 max 769031 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 769031
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Ave neighs/atom = 228.74212
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Ave special neighs/atom = 9.4098751
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Neighbor list builds = 762
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Dangerous builds = 0
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write_data cnt-nylon-mix.data
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System init for write_data ...
305+
PPPM initialization ...
306+
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
307+
G vector (1/distance) = 0.33176765
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grid = 25 25 25
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stencil order = 5
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estimated absolute RMS force accuracy = 0.0035198929
311+
estimated relative force accuracy = 1.0600053e-05
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using double precision KISS FFT
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3d grid and FFT values/proc = 32768 15625
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Generated 66 of 66 mixed pair_coeff terms from sixthpower/sixthpower mixing rule
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Total wall time: 0:24:47

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