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simongravellesimongravelle
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created files for tutorial 4
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‎files/tutorial4/create.lmp‎

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boundary p p f
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units real
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atom_style full
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bond_style harmonic
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angle_style harmonic
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pair_style lj/cut/tip4p/long O H O−H H−O−H 0.1546 12.0
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kspace_style pppm/tip4p 1.0e−4
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kspace_modify slab 3.0
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‎files/tutorial4/groups.inc‎

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group H2O type O H
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group Na type Na+
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group Cl type Cl−
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group ions union Na Cl
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group fluid union H2O ions
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group wall type WALL
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region rtop block INF INF INF INF 0 INF
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region rbot block INF INF INF INF INF 0
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group top region rtop
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group bot region rbot
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group walltop intersect wall top
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group wallbot intersect wall bot

‎files/tutorial4/minimize.lmp‎

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boundary p p f
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units real
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atom_style full
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bond_style harmonic
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angle_style harmonic
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pair_style lj/cut/tip4p/long O H O−H H−O−H 0.1546 12.0
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kspace_style pppm/tip4p 1.0e−4
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kspace_modify slab 3.0
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read_data create.data
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include parameters.inc
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include groups.inc

‎files/tutorial4/parameters.inc‎

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mass O 15.9994
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mass H 1.008
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mass Na+ 22.990
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mass Cl− 35.453
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mass WALL 26.9815
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pair_coeff O O 0.185199 3.1589
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pair_coeff H H 0.0 1.0
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pair_coeff Na+ Na+ 0.04690 2.4299
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pair_coeff Cl− Cl− 0.1500 4.04470
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pair_coeff WALL WALL 11.697 2.574
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pair_coeff O WALL 0.4 2.86645
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bond_coeff O−H 0 0.9572
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angle_coeff H−O−H 0 104.52

‎files/tutorial4/solution/create.data‎

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‎files/tutorial4/solution/create.lmp‎

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boundary p p f
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units real
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atom_style full
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bond_style harmonic
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angle_style harmonic
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pair_style lj/cut/tip4p/long O H O−H H−O−H 0.1546 12.0
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kspace_style pppm/tip4p 1.0e−5
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kspace_modify slab 3.0
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lattice fcc 4.04
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region box block −3 3 −3 3 −5 5
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create_box 5 box &
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bond/types 1 &
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angle/types 1 &
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extra/bond/per/atom 2 &
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extra/angle/per/atom 1 &
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extra/special/per/atom 2
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labelmap atom 1 O 2 H 3 Na+ 4 Cl− 5 WALL
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labelmap bond 1 O−H
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labelmap angle 1 H−O−H
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region rbotwall block −3 3 −3 3 −4 −3
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region rtopwall block −3 3 −3 3 3 4
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region rwall union 2 rbotwall rtopwall
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create_atoms WALL region rwall
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region rliquid block INF INF INF INF −2 2
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molecule h2omol water.mol
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create_atoms 0 region rliquid mol h2omol 482793
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create_atoms Na+ random 15 52802 rliquid overlap 0.3 maxtry 500
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create_atoms Cl− random 15 90182 rliquid overlap 0.3 maxtry 500
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set type Na+ charge 1
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set type Cl− charge −1
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include parameters.inc
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include groups.inc
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delete_atoms random fraction 0.15 yes H2O NULL 482793 mol yes
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dump mydmp all image 200 myimage-*.ppm type type &
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shiny 0.1 box no 0.01 view 90 0 zoom 1.8
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dump_modify mydmp backcolor white &
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acolor O red adiam O 2 &
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acolor H white adiam H 1 &
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acolor Na+ blue adiam Na+ 2.5 &
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acolor Cl− cyan adiam Cl− 3 &
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acolor WALL gray adiam WALL 3
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run 0
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write_data create.data nocoeff

‎files/tutorial4/solution/create.log‎

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using 8 OpenMP thread(s) per MPI task
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using multi-threaded neighbor list subroutines
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Lattice spacing in x,y,z = 4.04 4.04 4.04
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Created orthogonal box = (-12.12 -12.12 -20.2) to (12.12 12.12 20.2)
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1 by 1 by 1 MPI processor grid
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Created 432 atoms
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using lattice units in orthogonal box = (-12.12 -12.12 -20.2) to (12.12 12.12 20.2)
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create_atoms CPU = 0.003 seconds
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Read molecule template h2omol:
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# Water molecule.
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1 molecules
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0 fragments
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3 atoms with max type 2
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2 bonds with max type 1
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1 angles with max type 1
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0 dihedrals with max type 0
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0 impropers with max type 0
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Created 1944 atoms
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using lattice units in orthogonal box = (-12.12 -12.12 -20.2) to (12.12 12.12 20.2)
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create_atoms CPU = 0.001 seconds
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Created 15 atoms
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using lattice units in orthogonal box = (-12.12 -12.12 -20.2) to (12.12 12.12 20.2)
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create_atoms CPU = 0.004 seconds
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Created 15 atoms
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using lattice units in orthogonal box = (-12.12 -12.12 -20.2) to (12.12 12.12 20.2)
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create_atoms CPU = 0.004 seconds
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Setting atom values ...
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15 settings made for charge
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Setting atom values ...
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15 settings made for charge
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1944 atoms in group H2O
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15 atoms in group Na
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15 atoms in group Cl
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30 atoms in group ions
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1974 atoms in group fluid
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432 atoms in group wall
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1198 atoms in group top
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1208 atoms in group bot
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216 atoms in group walltop
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216 atoms in group wallbot
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WARNING: Ignoring 'compress yes' for molecular system (src/delete_atoms.cpp:141)
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Deleted 726 atoms, new total = 1680
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Deleted 484 bonds, new total = 812
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Deleted 242 angles, new total = 406
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WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
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PPPM initialization ...
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extracting TIP4P info from pair style
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using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
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G vector (1/distance) = 0.22477066
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grid = 12 12 40
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stencil order = 5
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estimated absolute RMS force accuracy = 0.023314918
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estimated relative force accuracy = 7.0212184e-05
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using double precision KISS FFT
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3d grid and FFT values/proc = 15162 5760
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WARNING: Communication cutoff 0 is shorter than a bond length based estimate of 3.4358. This may lead to errors. (src/comm.cpp:731)
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WARNING: Increasing communication cutoff to 15.1118 for TIP4P pair style (src/KSPACE/pair_lj_cut_tip4p_long.cpp:497)
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Generated 9 of 10 mixed pair_coeff terms from geometric mixing rule
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Last active /omp style is kspace_style pppm/tip4p/omp
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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
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master list distance cutoff = 14.3092
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ghost atom cutoff = 15.1118
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binsize = 7.1546, bins = 4 4 6
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cut/tip4p/long/omp, perpetual
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attributes: half, newton on, omp
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pair build: half/bin/newton/omp
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stencil: half/bin/3d
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bin: standard
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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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Per MPI rank memory allocation (min/avg/max) = 17.03 | 17.03 | 17.03 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 0 665588.16 0 665588.16 8064451.7
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Loop time of 3.863e-06 on 8 procs for 0 steps with 1680 atoms
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181.2% CPU use with 1 MPI tasks x 8 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 | 0 | 0 | 0 | 0.0 | 0.00
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Bond | 0 | 0 | 0 | 0.0 | 0.00
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Kspace | 0 | 0 | 0 | 0.0 | 0.00
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0 | 0 | 0 | 0.0 | 0.00
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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 | | 3.863e-06 | | |100.00
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Nlocal: 1680 ave 1680 max 1680 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 6818 ave 6818 max 6818 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 829498 ave 829498 max 829498 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 829498
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Ave neighs/atom = 493.74881
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Ave special neighs/atom = 1.45
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Neighbor list builds = 0
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Dangerous builds = 0
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System init for write_data ...
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PPPM initialization ...
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extracting TIP4P info from pair style
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using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
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G vector (1/distance) = 0.22477066
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grid = 12 12 40
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stencil order = 5
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estimated absolute RMS force accuracy = 0.023314918
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estimated relative force accuracy = 7.0212184e-05
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using double precision KISS FFT
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3d grid and FFT values/proc = 15162 5760
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Generated 9 of 10 mixed pair_coeff terms from geometric mixing rule
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Last active /omp style is kspace_style pppm/tip4p/omp

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