Facing problem with binning

LAMMPS LAMMPS Beginners
1 
fix             6b all ave/spatial 1 4000000 4000000 x lower 20.0 v_atemp file 20Temperature4.txt units box

this fix generated below output file (only a portion):

# Spatial-averaged data for fix 6b and group all
# Timestep Number-of-bins
# Bin Coord Ncount v_atemp
4000000 201
  1 6.58935 13695.5 299.197
  2 26.5893 14196 299.322
  3 46.5893 13168.9 299.29
  4 66.5893 14131.1 299.407
  5 86.5893 14193.4 299.452
  6 106.589 13108.4 299.646
  7 126.589 14194.2 299.71
  8 146.589 14110.7 299.821
  9 166.589 13189.3 299.859
  10 186.589 14196 300.018
  11 206.589 13633.5 300.09
  12 226.589 13666.5 300.133
  13 246.589 14196 300.244
  14 266.589 13179.1 300.416
  15 286.589 14120.9 300.547
  16 306.589 14193.7 300.577
  17 326.589 13108.7 300.694
  18 346.589 14193.6 300.932
  19 366.589 14122.7 300.918
  20 386.589 13177.3 301.026
  21 406.589 14196 301.168
  22 426.589 13674.1 301.44
  23 446.589 13625.9 301.553
  24 466.589 14196 301.636
  25 486.589 13194.8 301.737
  26 506.589 14105.2 301.835
  27 526.589 14194.2 302.03
  28 546.589 13109 302.268
  29 566.589 14192.8 302.283
  30 586.589 14132.2 302.421
  31 606.589 13167.8 302.612
  32 626.589 14196 302.633
  33 646.589 13711.4 302.692
  34 666.589 13588.6 302.831
  35 686.589 14196 302.892
  36 706.589 13210.6 302.938
  37 726.589 14089.4 303.177
  38 746.589 14194.5 303.275
  39 766.589 13109.4 303.495
  40 786.589 14192.1 303.594
  41 806.589 14140.1 303.743
  42 826.589 13160 303.848
  43 846.589 14196 304.138
  44 866.589 13743.5 304.3
  45 886.589 13556.5 304.72
  46 906.589 14196 305.018
  47 926.589 13229.3 305.276
  48 946.589 14070.7 305.655
  49 966.589 14194.8 306.11
  50 986.589 13110.6 306.944
  51 1006.59 14190.6 307.325
  52 1026.59 14150.8 306.195
  53 1046.59 13149.2 305.62
  54 1066.59 14195.9 305.218
  55 1086.59 13793.1 304.973
  56 1106.59 13506.9 304.681
  57 1126.59 14196 304.439
  58 1146.59 13252.7 304.313
  59 1166.59 14047.3 304.125
  60 1186.59 14195.2 303.923
  61 1206.59 13111.7 303.665
  62 1226.59 14189.1 303.462
  63 1246.59 14161.5 303.363
  64 1266.59 13138.6 303.156
  65 1286.59 14195.9 303.061
  66 1306.59 13829 302.873
  67 1326.59 13471 302.68
  68 1346.59 14196 302.625
  69 1366.59 13269.3 302.455
  70 1386.59 14030.7 302.346
  71 1406.59 14195.4 302.147
  72 1426.59 13112.5 302.039
  73 1446.59 14188.1 301.971
  74 1466.59 14165.7 301.786
  75 1486.59 13134.4 301.646
  76 1506.59 14195.9 301.522
  77 1526.59 13851.4 301.446
  78 1546.59 13448.6 301.327
  79 1566.59 14196 301.184
  80 1586.59 13280.7 301.065
  81 1606.59 14019.3 301.066
  82 1626.59 14195.5 301.05
  83 1646.59 13113.2 301.007
  84 1666.59 14187.3 300.767
  85 1686.59 14169.6 300.607
  86 1706.59 13130.5 300.44
  87 1726.59 14195.9 300.322
  88 1746.59 13872.8 300.294
  89 1766.59 13427.2 300.169
  90 1786.59 14196 299.998
  91 1806.59 13295.8 299.972
  92 1826.59 14004.2 299.815
  93 1846.59 14195.6 299.662
  94 1866.59 13113.7 299.576
  95 1886.59 14186.6 299.446
  96 1906.59 14172.6 299.436
  97 1926.59 13127.5 299.386
  98 1946.59 14195.9 299.315
  99 1966.59 13887.8 299.307
  100 1986.59 13412.2 299.133
  101 2006.59 14196 298.975
  102 2026.59 13304.2 298.954
  103 2046.59 13995.8 298.868
  104 2066.59 14195.7 298.81
  105 2086.59 13114.9 298.795
  106 2106.59 14185.4 298.615
  107 2126.59 14174.8 298.515
  108 2146.59 13125.3 298.391
  109 2166.59 14195.9 298.345
  110 2186.59 13904.6 298.202
  111 2206.59 13395.4 298.053
  112 2226.59 14196 298.016
  113 2246.59 13316.8 297.901
  114 2266.59 13983.2 297.851
  115 2286.59 14195.7 297.727
  116 2306.59 13116.5 297.677
  117 2326.59 14183.8 297.558
  118 2346.59 14177.3 297.523
  119 2366.59 13122.9 297.391
  120 2386.59 14195.8 297.29
  121 2406.59 13923.9 297.257
  122 2426.59 13376.1 297.055
  123 2446.59 14196 296.873
  124 2466.59 13338.1 296.807
  125 2486.59 13961.9 296.634
  126 2506.59 14195.8 296.526
  127 2526.59 13118.9 296.415
  128 2546.59 14181.3 296.288
  129 2566.59 14178.8 296.14
  130 2586.59 13121.4 296.139
  131 2606.59 14195.8 295.999
  132 2626.59 13939.1 295.715
  133 2646.59 13360.9 295.636
  134 2666.59 14196 295.572
  135 2686.59 13355.1 295.481
  136 2706.59 13944.9 295.277
  137 2726.59 14195.8 295.065
  138 2746.59 13120.5 294.979
  139 2766.59 14179.7 294.804
  140 2786.59 14179.9 294.608
  141 2806.59 13120.3 294.417
  142 2826.59 14195.8 294.242
  143 2846.59 13945.9 294.07
  144 2866.59 13354.1 293.922
  145 2886.59 14196 293.703
  146 2906.59 13364.4 293.485
  147 2926.59 13935.6 293.172
  148 2946.59 14195.8 292.754
  149 2966.59 13122 292.251
  150 2986.59 14178.2 291.36
  151 3006.59 14180.7 290.956
  152 3026.59 13119.5 292.079
  153 3046.59 14195.8 292.736
  154 3066.59 13957.4 293.164
  155 3086.59 13342.6 293.463
  156 3106.59 14196 293.602
  157 3126.59 13373.1 293.886
  158 3146.59 13926.9 294.022
  159 3166.59 14195.8 294.228
  160 3186.59 13123.4 294.401
  161 3206.59 14176.8 294.586
  162 3226.59 14182.2 294.761
  163 3246.59 13118.1 294.814
  164 3266.59 14195.7 295.003
  165 3286.59 13968.5 295.102
  166 3306.59 13331.5 295.224
  167 3326.59 14196 295.266
  168 3346.59 13385.1 295.452
  169 3366.59 13914.9 295.543
  170 3386.59 14195.8 295.745
  171 3406.59 13124 295.792
  172 3426.59 14176.1 295.946
  173 3446.59 14183.6 296.152
  174 3466.59 13116.7 296.282
  175 3486.59 14195.7 296.339
  176 3506.59 13978.9 296.426
  177 3526.59 13321.1 296.481
  178 3546.59 14196 296.672
  179 3566.59 13392.4 296.888
  180 3586.59 13907.6 296.92
  181 3606.59 14195.9 297.104
  182 3626.59 13125 297.111
  183 3646.59 14175.1 297.174
  184 3666.59 14184.9 297.316
  185 3686.59 13115.5 297.455
  186 3706.59 14195.7 297.553
  187 3726.59 13988.8 297.657
  188 3746.59 13311.2 297.84
  189 3766.59 14196 297.945
  190 3786.59 13408.6 297.991
  191 3806.59 13891.4 298.069
  192 3826.59 14195.9 298.171
  193 3846.59 13127 298.222
  194 3866.59 14173.1 298.416
  195 3886.59 14186.1 298.549
  196 3906.59 13114.3 298.66
  197 3926.59 14195.7 298.688
  198 3946.59 14001.6 298.828
  199 3966.59 13298.4 298.897
  200 3986.59 14196 298.994
  201 4006.59 4868.48 299.062

since ave/spatial in no longer in work, trying to recreate this for my triclinic system which has 121.06 angstrom in z axis using below fix is only giving number of bin= 1.

compute 	myChunk all chunk/atom bin/1d z lower 10.0 units reduced
fix 		4a all ave/chunk 1 100 100 myChunk v_atemp file temp_profile2.txt

output:

# Chunk-averaged data for fix 4a and group all
# Timestep Number-of-chunks Total-count
# Chunk Coord1 Ncount v_atemp
100 1 3840
  1 5 3840 301.7
200 1 3840
  1 5 3840 302.634
300 1 3840
  1 5 3840 299.188
400 1 3840
  1 5 3840 300.742
500 1 3840
  1 5 3840 299.889
600 1 3840
  1 5 3840 299.981

how do i bin my whole system along z direction while bin thickness=10 units

2

Why do you use “units reduced”?

3

For orthogonal simulation boxes, any of the 3 options may be used. For non-orthogonal (triclinic) simulation boxes, only the reduced option may be used.

A reduced value means normalized unitless values between 0 and 1, which represent the lower and upper faces of the simulation box respectively. Thus an origin value of 0.5 means the center of the box in any dimension. A delta value of 0.1 means 10 bins span the box in that dimension.

Fixed it.

One thing I’d like clarification about. Does bin/1d z takes a cubic region of given thickness along z direction in account? Documentation says it represents a slab. Then what bin/3d x y z would represent?

4

No. It will be cubic only in reduced units.

Sub-volumes representing fractions of the whole simulation cell with the same tilt.