finished cleaning tutorial 4

Author: simongravelle

files/tutorial4/equilibrate.lmp

@@ -0,0 +1,15 @@
+
+boundary p p f
+units real
+atom_style full
+bond_style harmonic
+angle_style harmonic
+pair_style lj/cut/tip4p/long O H O−H H−O−H 0.1546 12.0
+kspace_style pppm/tip4p 1.0e−5
+kspace_modify slab 3.0
+
+read_data minimize.data
+
+include parameters.inc
+include groups.inc
+

files/tutorial4/shearing.lmp

@@ -0,0 +1,15 @@
+
+boundary p p f
+units real
+atom_style full
+bond_style harmonic
+angle_style harmonic
+pair_style lj/cut/tip4p/long O H O−H H−O−H 0.1546 12.0
+kspace_style pppm/tip4p 1.0e−5
+kspace_modify slab 3.0
+
+read_data equilibrate.data
+
+include parameters.inc
+include groups.inc
+

files/tutorial4/solution/equilibrate.data

@@ -18,20 +18,21 @@ fix myshk H2O shake 1.0e−5 200 0 b O−H a H−O−H
 fix myrct all recenter NULL NULL 0
 timestep 1.0
 
-dump mydmp all image 200 myimage-*.ppm type type &
+dump mydmp all image 250 myimage-*.ppm type type &
   shiny 0.1 box no 0.01 view 90 0 zoom 1.8
 dump_modify mydmp backcolor white &
   acolor O red adiam O 2 &
   acolor H white adiam H 1 &
   acolor Na+ blue adiam Na+ 2.5 &
   acolor Cl− cyan adiam Cl− 3 &
   acolor WALL gray adiam WALL 3
-thermo 500
 
 variable walltopz equal xcm(walltop,z)
 variable wallbotz equal xcm(wallbot,z)
 variable deltaz equal v_walltopz−v_wallbotz
-fix myat1 all ave/time 100 1 100 v_deltaz file interwall_distance.dat
+
+thermo 250
+thermo_style custom step temp etotal press v_deltaz
 
 run 30000
 

files/tutorial4/solution/equilibrate.lmp

@@ -0,0 +1,242 @@
+  using 8 OpenMP thread(s) per MPI task
+using multi-threaded neighbor list subroutines
+Reading data file ...
+  orthogonal box = (-12.12 -12.12 -20.2) to (12.12 12.12 20.2)
+  1 by 1 by 1 MPI processor grid
+  reading atom labelmap ...
+  reading bond labelmap ...
+  reading angle labelmap ...
+  reading atoms ...
+  1680 atoms
+  reading velocities ...
+  1680 velocities
+  scanning bonds ...
+  2 = max bonds/atom
+  scanning angles ...
+  1 = max angles/atom
+  orthogonal box = (-12.12 -12.12 -20.2) to (12.12 12.12 20.2)
+  1 by 1 by 1 MPI processor grid
+  reading bonds ...
+  812 bonds
+  reading angles ...
+  406 angles
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0        0        0       
+  special bond factors coul:  0        0        0       
+     2 = max # of 1-2 neighbors
+     1 = max # of 1-3 neighbors
+     1 = max # of 1-4 neighbors
+     2 = max # of special neighbors
+  special bonds CPU = 0.001 seconds
+  read_data CPU = 0.042 seconds
+1218 atoms in group H2O
+15 atoms in group Na
+15 atoms in group Cl
+30 atoms in group ions
+1248 atoms in group fluid
+432 atoms in group wall
+852 atoms in group top
+828 atoms in group bot
+216 atoms in group walltop
+216 atoms in group wallbot
+Finding SHAKE clusters ...
+       0 = # of size 2 clusters
+       0 = # of size 3 clusters
+       0 = # of size 4 clusters
+     406 = # of frozen angles
+  find clusters CPU = 0.001 seconds
+PPPM initialization ...
+  extracting TIP4P info from pair style
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
+  G vector (1/distance) = 0.25237451
+  grid = 18 18 60
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0034985124
+  estimated relative force accuracy = 1.0535666e-05
+  using double precision KISS FFT
+  3d grid and FFT values/proc = 39375 19440
+WARNING: Communication cutoff 0 is shorter than a bond length based estimate of 3.4358. This may lead to errors. (src/comm.cpp:731)
+WARNING: Increasing communication cutoff to 15.1118 for TIP4P pair style (src/KSPACE/pair_lj_cut_tip4p_long.cpp:497)
+Generated 9 of 10 mixed pair_coeff terms from geometric mixing rule
+Last active /omp style is kspace_style pppm/tip4p/omp
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 14.3092
+  ghost atom cutoff = 15.1118
+  binsize = 7.1546, bins = 4 4 6
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut/tip4p/long/omp, perpetual
+      attributes: half, newton on, omp
+      pair build: half/bin/newton/omp
+      stencil: half/bin/3d
+      bin: standard
+Setting up Verlet run ...
+  Unit style    : real
+  Current step  : 0
+  Time step     : 1
+Per MPI rank memory allocation (min/avg/max) = 19.96 | 19.96 | 19.96 Mbytes
+   Step          Temp          TotEng         Press         v_deltaz   
+         0   195.26511     -37795.526     -20887.597      28.28        
+       250   232.27823     -37436.953     -13859.156      28.224131    
+       500   289.71547     -36997.694     -18733.784      28.213748    
+       750   291.51658     -36752.986     -12759.68       28.328293    
+      1000   297.97401     -36707.271     -18403.708      28.483078    
+      1250   289.47179     -36730.103     -15694.087      28.688668    
+      1500   303.28306     -36664.834     -16608.648      28.967119    
+      1750   294.98678     -36710.3       -17064.448      29.322353    
+      2000   300.14536     -36623.92      -17289.549      29.660241    
+      2250   308.32131     -36612.464     -17311.766      30.025099    
+      2500   300.2547      -36642.101     -15850.768      30.337654    
+      2750   304.09099     -36563.928     -18967.245      30.644654    
+      3000   297.80502     -36598.736     -16633.14       30.934611    
+      3250   295.44758     -36518.415     -18657.304      31.096237    
+      3500   288.46243     -36589.598     -16198.531      31.237927    
+      3750   294.05745     -36549.131     -17609.755      31.338167    
+      4000   303.90312     -36532.629     -16843.768      31.351265    
+      4250   295.93646     -36532.516     -17280.201      31.297871    
+      4500   306.4059      -36544.084     -18244.31       31.177856    
+      4750   312.01639     -36507.157     -16426.913      31.035481    
+      5000   307.29778     -36570.29      -18249.507      30.803341    
+      5250   297.01732     -36615.761     -16498.598      30.483898    
+      5500   281.56765     -36708.988     -16897.581      30.198443    
+      5750   305.87057     -36636.778     -16622.415      29.969421    
+      6000   302.51018     -36672.061     -17138.142      29.667817    
+      6250   297.39648     -36601.905     -15524.3        29.356708    
+      6500   297.21136     -36748.479     -15223.489      29.141286    
+      6750   294.44548     -36798.889     -16588.259      29.006534    
+      7000   309.15698     -36703.184     -15499.214      28.838859    
+      7250   295.49969     -36785.618     -16496.846      28.746626    
+      7500   309.14217     -36750.967     -16384.561      28.667253    
+      7750   304.88662     -36672.637     -16266.985      28.565564    
+      8000   299.30197     -36746.816     -14988.715      28.481843    
+      8250   315.87161     -36694.905     -17070.05       28.483576    
+      8500   298.15169     -36786.688     -15417.079      28.466934    
+      8750   291.1702      -36847.007     -16277.272      28.536366    
+      9000   303.66364     -36765.338     -15349.339      28.620093    
+      9250   303.54607     -36751.535     -15742.63       28.714115    
+      9500   304.71282     -36665.132     -17932.517      28.805149    
+      9750   293.93516     -36747.021     -15616.272      28.825629    
+     10000   297.50483     -36746.717     -15628.795      28.79897     
+     10250   295.83392     -36823.61      -16458.109      28.779699    
+     10500   311.78216     -36748.274     -17558.384      28.765269    
+     10750   301.01847     -36733.893     -15559.865      28.646696    
+     11000   307.47095     -36734.922     -16735.635      28.551303    
+     11250   291.57328     -36821.668     -16207.85       28.458455    
+     11500   313.87763     -36770.642     -16377.887      28.363781    
+     11750   302.69333     -36851.592     -15949.515      28.340738    
+     12000   307.22569     -36758.367     -16844.056      28.298383    
+     12250   296.01918     -36804.895     -16067.9        28.207218    
+     12500   298.01113     -36828.93      -16299.135      28.165025    
+     12750   297.94507     -36836.593     -15721.749      28.172412    
+     13000   316.948       -36789.252     -16646.288      28.204538    
+     13250   293.63566     -36842.032     -15624.255      28.289008    
+     13500   310.5345      -36757.278     -15790.753      28.321949    
+     13750   301.00951     -36770.515     -15254.694      28.417951    
+     14000   291.82107     -36838.788     -16409.696      28.552703    
+     14250   306.03961     -36751.848     -14850.42       28.559422    
+     14500   291.13322     -36841.462     -15702.619      28.579752    
+     14750   300.82882     -36788.809     -15472.009      28.614837    
+     15000   305.09861     -36801.509     -16090.026      28.658203    
+     15250   303.28965     -36843.091     -16246.215      28.630459    
+     15500   295.42715     -36918.226     -15839.213      28.572414    
+     15750   304.29863     -36835.68      -17016.14       28.538192    
+     16000   292.78191     -36885.377     -15436.873      28.485205    
+     16250   286.3344      -36974.478     -15764.088      28.372474    
+     16500   306.47139     -36883.187     -16397.852      28.287448    
+     16750   293.60715     -36916.544     -15026.719      28.241182    
+     17000   312.66807     -36838.022     -15561.737      28.197392    
+     17250   295.68257     -36908.815     -15980.842      28.233347    
+     17500   299.68448     -36874.043     -16209.851      28.199537    
+     17750   307.22711     -36805.123     -14556.366      28.137894    
+     18000   292.99391     -36879.878     -16759.836      28.150913    
+     18250   311.03378     -36822.505     -15672.263      28.170514    
+     18500   302.26081     -36854.251     -14639.495      28.222761    
+     18750   291.2757      -36894.901     -16655.637      28.29753     
+     19000   311.76207     -36828.821     -14765.978      28.309174    
+     19250   304.08573     -36921.78      -16174.531      28.397196    
+     19500   294.4363      -36886.812     -15614.509      28.479546    
+     19750   314.84002     -36791.314     -15805.311      28.571846    
+     20000   310.98039     -36891.139     -16475.706      28.63118     
+     20250   295.96939     -36924.108     -14884.407      28.663669    
+     20500   290.34475     -36855.33      -16684.759      28.645933    
+     20750   305.47907     -36814.52      -15174.217      28.696914    
+     21000   295.69633     -36910.395     -16942.206      28.720366    
+     21250   304.50195     -36820.533     -15684.019      28.586479    
+     21500   294.27848     -36897.687     -15504.534      28.453431    
+     21750   307.8989      -36855.62      -16126.539      28.297444    
+     22000   296.87866     -36933.722     -15843.975      28.126083    
+     22250   305.12031     -36909.05      -16665.104      27.914203    
+     22500   303.6656      -36882.759     -15782.095      27.649354    
+     22750   303.19051     -36957.99      -13737.512      27.517987    
+     23000   289.068       -37004.639     -16860.431      27.408123    
+     23250   307.10849     -36902.97      -13575.588      27.362659    
+     23500   301.9796      -36964.7       -16138.705      27.341708    
+     23750   302.04615     -36943.06      -14682.908      27.446369    
+     24000   303.55071     -36916.648     -15769.225      27.638065    
+     24250   299.28723     -36921.37      -16222.902      27.728968    
+     24500   291.5983      -37019.435     -15465.817      27.80032     
+     24750   298.12473     -36935.211     -15972.57       27.873797    
+     25000   285.7955      -36987.666     -15532.856      27.865816    
+     25250   303.25167     -36884.418     -16895.863      27.812628    
+     25500   291.64331     -36948.742     -15313.099      27.825571    
+     25750   303.21897     -36909.115     -15854.083      27.814838    
+     26000   302.53357     -36939.146     -14137.918      27.861024    
+     26250   295.26883     -36989.282     -16115.572      27.868712    
+     26500   305.17131     -36897.871     -14681.182      27.92563     
+     26750   288.76941     -36986.603     -16103.981      27.91584     
+     27000   291.80769     -36984.93      -15484.922      27.923419    
+     27250   304.23374     -36892.366     -14278.612      27.953653    
+     27500   299.41784     -36991.213     -15858.494      27.918312    
+     27750   308.39833     -36923.553     -14879.879      27.943377    
+     28000   302.77869     -36943.642     -15824.154      27.961717    
+     28250   301.42839     -36967.04      -14710.463      27.923713    
+     28500   303.69052     -36998.79      -16159.865      27.934355    
+     28750   313.40796     -36935.563     -15593.739      27.906203    
+     29000   314.33693     -36945.419     -15453.239      27.919606    
+     29250   297.23048     -36988.607     -15800.301      27.909852    
+     29500   317.0411      -36907.326     -13785.11       27.916182    
+     29750   306.62569     -36988.639     -16055.811      27.931907    
+     30000   284.41998     -37029.035     -15326.199      27.92206     
+Loop time of 671.775 on 8 procs for 30000 steps with 1680 atoms
+
+Performance: 3.858 ns/day, 6.220 hours/ns, 44.658 timesteps/s, 75.025 katom-step/s
+812.1% CPU use with 1 MPI tasks x 8 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 277.08     | 277.08     | 277.08     |   0.0 | 41.25
+Bond    | 0.63486    | 0.63486    | 0.63486    |   0.0 |  0.09
+Kspace  | 338.5      | 338.5      | 338.5      |   0.0 | 50.39
+Neigh   | 19.484     | 19.484     | 19.484     |   0.0 |  2.90
+Comm    | 4.1445     | 4.1445     | 4.1445     |   0.0 |  0.62
+Output  | 13.359     | 13.359     | 13.359     |   0.0 |  1.99
+Modify  | 18.077     | 18.077     | 18.077     |   0.0 |  2.69
+Other   |            | 0.4928     |            |       |  0.07
+
+Nlocal:           1680 ave        1680 max        1680 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:           6841 ave        6841 max        6841 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:         795654 ave      795654 max      795654 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 795654
+Ave neighs/atom = 473.60357
+Ave special neighs/atom = 1.45
+Neighbor list builds = 1443
+Dangerous builds = 0
+System init for write_data ...
+PPPM initialization ...
+  extracting TIP4P info from pair style
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
+  G vector (1/distance) = 0.25237451
+  grid = 18 18 60
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.0034985124
+  estimated relative force accuracy = 1.0535666e-05
+  using double precision KISS FFT
+  3d grid and FFT values/proc = 39375 19440
+Generated 9 of 10 mixed pair_coeff terms from geometric mixing rule
+Last active /omp style is kspace_style pppm/tip4p/omp

files/tutorial4/solution/equilibrate.log

@@ -0,0 +1,8 @@
+# Time-averaged data for fix myat1
+# TimeStep f_mysf1[1] f_mysf2[1]
+1000 -4.37215 2.286
+2000 1.86016 8.2834
+3000 -1.98866 3.10032
+4000 -3.03073 4.76226
+5000 -2.74076 0.585792
+6000 -3.11492 -0.888404

files/tutorial4/solution/shearing-forces.dat

@@ -8,7 +8,7 @@ pair_style lj/cut/tip4p/long O H O−H H−O−H 0.1546 12.0
 kspace_style pppm/tip4p 1.0e−5
 kspace_modify slab 3.0
 
-read_data minimize.data
+read_data equilibrate.data
 
 include parameters.inc
 include groups.inc
@@ -23,13 +23,14 @@ fix_modify mynvt2 temp Twall
 
 fix myshk H2O shake 1.0e−5 200 0 b O−H a H−O−H
 fix myrct all recenter NULL NULL 0
+timestep 1.0
 
 fix mysf1 walltop setforce 0 NULL NULL
 fix mysf2 wallbot setforce 0 NULL NULL
 velocity wallbot set −2e−4 NULL NULL
 velocity walltop set 2e−4 NULL NULL
 
-dump mydmp all image 200 myimage-*.ppm type type &
+dump mydmp all image 250 myimage-*.ppm type type &
   shiny 0.1 box no 0.01 view 90 0 zoom 1.8
 dump_modify mydmp backcolor white &
   acolor O red adiam O 2 &
@@ -38,22 +39,19 @@ dump_modify mydmp backcolor white &
   acolor Cl− cyan adiam Cl− 3 &
   acolor WALL gray adiam WALL 3
 
-thermo 500
+thermo 250
 thermo_modify temp Tfluid
 thermo_style custom step temp etotal f_mysf1[1] f_mysf2[1] 
 
 compute cc1 H2O chunk/atom bin/1d z 0.0 1.0
 compute cc2 wall chunk/atom bin/1d z 0.0 1.0
 compute cc3 ions chunk/atom bin/1d z 0.0 1.0
+
 fix myac1 H2O ave/chunk 10 15000 200000 &
   cc1 density/mass vx file shearing-water.dat
 fix myac2 wall ave/chunk 10 15000 200000 &
   cc2 density/mass vx file shearing-wall.dat
 fix myac3 ions ave/chunk 10 15000 200000 &
   cc3 density/mass vx file shearing-ions.dat
-fix myat1 all ave/time 10 100 1000 f_mysf1[1] &
-  f_mysf2[1] file shearing-forces.dat
 
-timestep 1.0
 run 200000
-write_data system.data nocoeff

files/tutorial4/solution/shearing.lmp

@@ -735,3 +735,14 @@ @article{kadaoluwa2021systematic
   year={2021},
   publisher={ACS Publications}
 }
+
+@article{mills1955remeasurement,
+  title={A remeasurement of the self-diffusion coefficients of sodium ion in aqueous sodium chloride solutions},
+  author={Mills, Reginald},
+  journal={Journal of the American Chemical Society},
+  volume={77},
+  number={23},
+  pages={6116--6119},
+  year={1955},
+  publisher={ACS Publications}
+}