Commit f07719e9 authored by Axel Kohlmeyer's avatar Axel Kohlmeyer
Browse files

make fix rhok examples more consistent with LAMMPS conventions: 

- move example folder to examples/USER/misc/
- comment out writing of trajectory files
- reduce run length (for easier testing for regressions)
- record example outputs for 1 and 4 MPI processes
- rename readme.md to README.md for visibility
parent 5f527091

examples/USER/pinning/in.crystal→examples/USER/misc/pinning/in.crystal

+4 −3
Original line number Diff line number Diff line
@@ -29,7 +29,8 @@ fix bias all rhok 16 0 0 0.0 0.0 
# output

thermo 50

thermo_style custom step temp press density f_bias[3]

dump dumpXYZ all xyz 2000 traj.xyz

# dump dumpXYZ all xyz 2000 traj.xyz



# run

run 100000
 
# NOTE: this is cut short to 5000 steps for demonstration purposes

# run 100000

run 5000

examples/USER/pinning/in.pinning→examples/USER/misc/pinning/in.pinning

+4 −3
Original line number Diff line number Diff line
@@ -26,7 +26,8 @@ fix bias all rhok 16 0 0 4.0 26.00 
# output                                U_bias rho_k_RE  rho_k_IM |rho_k| 

thermo_style custom step temp pzz pe lz f_bias f_bias[1] f_bias[2] f_bias[3]

thermo 50

dump dumpXYZ all xyz 500 traj.xyz

# dump dumpXYZ all xyz 500 traj.xyz



# run

run 50000
 
# NOTE: run reduced for demonstration purposes

# run 50000

run 5000

examples/USER/pinning/in.setup→examples/USER/misc/pinning/in.setup

+4 −3
Original line number Diff line number Diff line
@@ -33,8 +33,9 @@ fix langevin left langevin 3.0 0.8 100.0 2017 
# outout

thermo_style custom step temp pzz pe lz

thermo 100

dump dumpXYZ all xyz 100 traj.xyz

# dump dumpXYZ all xyz 100 traj.xyz



# run

run 10000

# run reduced for demonstration purposes

# run 10000

run 5000

write_data data.halfhalf

examples/USER/misc/pinning/log.22Sep2017.crystal.g++.1

0 → 100644
+187 −0
Original line number Diff line number Diff line 
LAMMPS (22 Sep 2017)

  using 1 OpenMP thread(s) per MPI task

units		lj

dimension	3

boundary	p p p

atom_style  atomic



# truncated and shifted LJ potential

pair_style	lj/cut 2.5

pair_modify	shift yes

lattice	fcc 0.9731

Lattice spacing in x,y,z = 1.6019 1.6019 1.6019

region	my_box block 0 8.0   0 8.0   0 20.0

create_box 1 my_box

Created orthogonal box = (0 0 0) to (12.8152 12.8152 32.0379)

  1 by 1 by 1 MPI processor grid

region particles block 0 8.0 0 8.0 0 20.0

create_atoms 1 region particles

Created 5120 atoms

pair_coeff 1 1 1.0 1.0 2.5

pair_modify tail no

pair_modify shift yes

mass 1 1.0

velocity all create 1.6 1 mom yes rot yes



# simulation parameters

neighbor	0.6 bin

timestep	0.004

run_style 	verlet

fix ensemble all npt temp 0.8 0.8 4.0 aniso 2.185 2.185 8.0 pchain 32



# computing long-range order (no bias is added since k=0)

fix bias all rhok 16 0 0 0.0 0.0



# output

thermo 50

thermo_style custom step temp press density f_bias[3]

# dump dumpXYZ all xyz 2000 traj.xyz



# NOTE: this is cut short to 5000 steps for demonstration purposes

# run 100000

run 5000

Neighbor list info ...

  update every 1 steps, delay 10 steps, check yes

  max neighbors/atom: 2000, page size: 100000

  master list distance cutoff = 3.1

  ghost atom cutoff = 3.1

  binsize = 1.55, bins = 9 9 21

  1 neighbor lists, perpetual/occasional/extra = 1 0 0

  (1) pair lj/cut, perpetual

      attributes: half, newton on

      pair build: half/bin/atomonly/newton

      stencil: half/bin/3d/newton

      bin: standard

Per MPI rank memory allocation (min/avg/max) = 4.523 | 4.523 | 4.523 Mbytes

Step Temp Press Density f_bias[3] 

       0          1.6   -2.7568106       0.9731    71.554175 

      50   0.78457786    3.1029192   0.97362639    54.327705 

     100   0.85528971    2.4670259   0.97213457    55.189308 

     150   0.85241818    2.3210306    0.9698027    56.138125 

     200   0.82301385    2.3448692   0.96708227    55.735326 

     250   0.83076383    2.0890816   0.96425763    55.320625 

     300   0.81602823    2.0118796   0.96173925    54.095736 

     350   0.81084006    1.9122192   0.95979392    54.526429 

     400   0.80776593    1.8502174   0.95869117    54.434901 

     450   0.80694697    1.8435873   0.95851085     53.20809 

     500   0.81384248    1.8111331   0.95917305    53.419395 

     550   0.81027072    1.9222272   0.96056019     54.36723 

     600   0.81199582    2.0291945   0.96248486    54.888582 

     650   0.82507964    2.0706462   0.96467227    55.807137 

     700     0.832562    2.1471442    0.9668913    56.721267 

     750   0.83358138    2.2674672     0.968984    56.723838 

     800   0.83477542    2.3658275   0.97072603    56.234689 

     850   0.84722921    2.3506233   0.97189674    56.262424 

     900   0.83526965    2.4532068   0.97248856    56.219103 

     950   0.83174583    2.4763958   0.97249527    56.409813 

    1000   0.83022557    2.4334341   0.97194093    55.890858 

    1050   0.83208978    2.3478416   0.97092452    54.934691 

    1100   0.82789545     2.272404    0.9696152     54.90894 

    1150   0.82678617    2.1798046   0.96819776    54.927782 

    1200    0.8088841    2.1960256   0.96687735    54.914327 

    1250   0.81512784    2.0736261   0.96579008    53.927291 

    1300   0.81271067    2.0297138   0.96504188    54.289698 

    1350    0.8201767    1.9493976   0.96464115    55.342131 

    1400   0.80880489    2.0016987   0.96468463    55.757758 

    1450    0.8114196    2.0282699   0.96514115    55.865676 

    1500   0.81085664    2.0838361   0.96591869    56.553425 

    1550   0.81257075    2.1283157   0.96694549    56.921544 

    1600   0.82617645    2.1017986   0.96817075    56.858808 

    1650   0.82616141    2.1885582   0.96941073    56.717917 

    1700   0.81634174    2.2996967   0.97047447    56.453745 

    1750   0.82447573    2.2924266   0.97128663    56.916813 

    1800   0.83610432     2.236456   0.97178453    56.400752 

    1850   0.82479203    2.3103493   0.97197318    55.891368 

    1900   0.82298992    2.3059289   0.97181084    55.680563 

    1950   0.82098556    2.2801003   0.97138609    55.754406 

    2000    0.8181203    2.2480175   0.97078591    55.801363 

    2050   0.82822293    2.1208884   0.97004107       55.687 

    2100    0.7976818    2.2711199   0.96930169    55.459844 

    2150   0.81817848    2.0680351   0.96860201    56.514731 

    2200   0.80707457    2.1112141   0.96810519    55.504308 

    2250   0.81651111    2.0077603   0.96781161    55.635702 

    2300   0.80634534    2.0662241   0.96777177    56.051086 

    2350   0.80892831    2.0619333   0.96799037    56.548711 

    2400   0.82454203    1.9585394    0.9684672    56.695235 

    2450   0.81517178     2.075283   0.96921622    56.613082 

    2500   0.80969595    2.1624581   0.97010528     56.57516 

    2550   0.80862964    2.2088622   0.97100774    57.072594 

    2600   0.81468816    2.2293973   0.97192868    56.879212 

    2650   0.82063107    2.2244887   0.97269715    55.454502 

    2700   0.81691618    2.2789954   0.97319841    54.421943 

    2750    0.8141787    2.2981247   0.97340453    54.469921 

    2800   0.81973871    2.2422136    0.9733278    55.959235 

    2850   0.82037399     2.201016   0.97302727    56.685826 

    2900   0.80650164    2.2672955    0.9726128    56.574395 

    2950   0.81752783    2.1317541   0.97207545    56.809412 

    3000   0.80836945    2.1461483   0.97151192    57.205206 

    3050   0.80785109    2.1189056   0.97103049    57.418763 

    3100   0.79835058     2.146416   0.97069705    57.329383 

    3150   0.79792089    2.1388267   0.97051679    57.279852 

    3200   0.79934603    2.1049562   0.97046851    56.351494 

    3250   0.79523232    2.1549779   0.97063956     56.00356 

    3300    0.8004458    2.1145975   0.97096375    55.725509 

    3350   0.79772742     2.166292   0.97143785    55.558075 

    3400   0.80621087    2.1309217   0.97198456    55.816704 

    3450   0.80540626    2.1727557   0.97263267    55.671283 

    3500   0.80867606    2.1905129   0.97321538    55.390086 

    3550   0.80917896    2.2144872   0.97370472    55.742085 

    3600   0.80930722    2.2288938     0.974093     56.23064 

    3650   0.80390523    2.2777327   0.97431886    56.084731 

    3700   0.79620093    2.3143541   0.97435103    55.942797 

    3750   0.80252393    2.2564638    0.9741875    56.042055 

    3800   0.78981264    2.3156481    0.9739121    55.971352 

    3850   0.80391951    2.1804938   0.97351088    55.855858 

    3900   0.81268129    2.0855818   0.97308521    56.288315 

    3950    0.7958182     2.175259   0.97273088    56.140141 

    4000   0.80054484    2.1163279   0.97243129    56.366818 

    4050   0.79760187     2.105362   0.97225308    56.684619 

    4100   0.79283424    2.1357603     0.972206    56.203341 

    4150   0.79543088    2.1036951   0.97227608    56.606315 

    4200   0.79410999    2.1402049   0.97253758    56.277478 

    4250    0.7985469    2.1285154   0.97293622    56.356076 

    4300   0.79700387    2.1470614   0.97337091    56.722298 

    4350   0.80479321    2.1403244   0.97384674    57.212574 

    4400   0.79505512     2.224463   0.97434415    56.561877 

    4450   0.78346648    2.3347865   0.97478611    56.681362 

    4500   0.79811284     2.259123   0.97510069    57.365929 

    4550   0.80015561    2.2345254   0.97523653     57.34799 

    4600   0.79648318    2.2651869   0.97525975    57.502318 

    4650   0.80524865    2.1943025   0.97507638    57.702488 

    4700   0.80397778    2.1758629   0.97478268    57.162107 

    4750   0.78914913    2.2470191    0.9744625    56.849565 

    4800   0.79324889    2.2028993   0.97408817    57.572344 

    4850   0.78993209     2.181763   0.97373372    57.683552 

    4900   0.79041263    2.1604768   0.97348692    56.922312 

    4950   0.79741332    2.1105901   0.97332545    57.488932 

    5000    0.7891178     2.163416   0.97328963    57.365252 

Loop time of 33.6467 on 1 procs for 5000 steps with 5120 atoms



Performance: 51357.258 tau/day, 148.603 timesteps/s

99.7% CPU use with 1 MPI tasks x 1 OpenMP threads



MPI task timing breakdown:

Section |  min time  |  avg time  |  max time  |%varavg| %total

---------------------------------------------------------------

Pair    | 24.699     | 24.699     | 24.699     |   0.0 | 73.41

Neigh   | 2.8894     | 2.8894     | 2.8894     |   0.0 |  8.59

Comm    | 0.34907    | 0.34907    | 0.34907    |   0.0 |  1.04

Output  | 0.0056     | 0.0056     | 0.0056     |   0.0 |  0.02

Modify  | 5.5718     | 5.5718     | 5.5718     |   0.0 | 16.56

Other   |            | 0.1319     |            |       |  0.39



Nlocal:    5120 ave 5120 max 5120 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Nghost:    7594 ave 7594 max 7594 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Neighs:    323081 ave 323081 max 323081 min

Histogram: 1 0 0 0 0 0 0 0 0 0



Total # of neighbors = 323081

Ave neighs/atom = 63.1018

Neighbor list builds = 248

Dangerous builds = 0



Please see the log.cite file for references relevant to this simulation



Total wall time: 0:00:33

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