Numba tutorial

conftest.py

@@ -1,3 +1,5 @@
+import multiprocessing
+
 import numpy
 
 try:
@@ -30,6 +32,8 @@ def setup_sybil_tests(namespace):
     # Common imports.
     namespace["numpy"] = numpy
     namespace["lammpsio"] = lammpsio
+    namespace["multiprocessing"] = multiprocessing
+    namespace["Pool"] = multiprocessing.Pool
 
     if has_lammps:
         namespace["lammps"] = lammps

doc/source/tutorials.rst

@@ -6,6 +6,7 @@ Tutorials
 
     ./tutorials/dimer_lattice_tutorial
     ./tutorials/analysis_tutorial/analysis_tutorial
+    ./tutorials/numba_tutorial/numba_tutorial
     ./tutorials/ethanol-water-tutorial/ethanol_water_mixture
 
 .. grid:: 2
@@ -29,3 +30,10 @@ Tutorials
         :link-type: doc
 
         Use Snapshot to create a LAMMPS data file for an ethanol-water mixture.
+
+    .. grid-item-card:: Analysis speedup using Numba
+        :link: ./tutorials/numba_tutorial/numba_tutorial
+        :link-type: doc
+
+        Read and analyze a LAMMPS dump file to study a 100-mer polymer
+        using the NumPy and Numba library for accelerated computation.

doc/source/tutorials/numba_tutorial/init.data

@@ -0,0 +1,218 @@
+LAMMPS init.data
+
+100 atoms
+99 bonds
+1 atom types
+1 bond types
+0.0 200.0 xlo xhi
+0.0 200.0 ylo yhi
+0.0 200.0 zlo zhi
+
+Masses
+
+   1         1.0
+
+Atoms # molecular
+
+1 0 1 41.07031216 98.97420857 107.59355066
+2 0 1 42.07031216 98.97420857 107.59355066
+3 0 1 43.07031216 98.97420857 107.59355066
+4 0 1 44.07031216 98.97420857 107.59355066
+5 0 1 45.07031216 98.97420857 107.59355066
+6 0 1 46.07031216 98.97420857 107.59355066
+7 0 1 47.07031216 98.97420857 107.59355066
+8 0 1 48.07031216 98.97420857 107.59355066
+9 0 1 49.07031216 98.97420857 107.59355066
+10 0 1 50.07031216 98.97420857 107.59355066
+11 0 1 51.07031216 98.97420857 107.59355066
+12 0 1 52.07031216 98.97420857 107.59355066
+13 0 1 53.07031216 98.97420857 107.59355066
+14 0 1 54.07031216 98.97420857 107.59355066
+15 0 1 55.07031216 98.97420857 107.59355066
+16 0 1 56.07031216 98.97420857 107.59355066
+17 0 1 57.07031216 98.97420857 107.59355066
+18 0 1 58.07031216 98.97420857 107.59355066
+19 0 1 59.07031216 98.97420857 107.59355066
+20 0 1 60.07031216 98.97420857 107.59355066
+21 0 1 61.07031216 98.97420857 107.59355066
+22 0 1 62.07031216 98.97420857 107.59355066
+23 0 1 63.07031216 98.97420857 107.59355066
+24 0 1 64.07031216 98.97420857 107.59355066
+25 0 1 65.07031216 98.97420857 107.59355066
+26 0 1 66.07031216 98.97420857 107.59355066
+27 0 1 67.07031216 98.97420857 107.59355066
+28 0 1 68.07031216 98.97420857 107.59355066
+29 0 1 69.07031216 98.97420857 107.59355066
+30 0 1 70.07031216 98.97420857 107.59355066
+31 0 1 71.07031216 98.97420857 107.59355066
+32 0 1 72.07031216 98.97420857 107.59355066
+33 0 1 73.07031216 98.97420857 107.59355066
+34 0 1 74.07031216 98.97420857 107.59355066
+35 0 1 75.07031216 98.97420857 107.59355066
+36 0 1 76.07031216 98.97420857 107.59355066
+37 0 1 77.07031216 98.97420857 107.59355066
+38 0 1 78.07031216 98.97420857 107.59355066
+39 0 1 79.07031216 98.97420857 107.59355066
+40 0 1 80.07031216 98.97420857 107.59355066
+41 0 1 81.07031216 98.97420857 107.59355066
+42 0 1 82.07031216 98.97420857 107.59355066
+43 0 1 83.07031216 98.97420857 107.59355066
+44 0 1 84.07031216 98.97420857 107.59355066
+45 0 1 85.07031216 98.97420857 107.59355066
+46 0 1 86.07031216 98.97420857 107.59355066
+47 0 1 87.07031216 98.97420857 107.59355066
+48 0 1 88.07031216 98.97420857 107.59355066
+49 0 1 89.07031216 98.97420857 107.59355066
+50 0 1 90.07031216 98.97420857 107.59355066
+51 0 1 91.07031216 98.97420857 107.59355066
+52 0 1 92.07031216 98.97420857 107.59355066
+53 0 1 93.07031216 98.97420857 107.59355066
+54 0 1 94.07031216 98.97420857 107.59355066
+55 0 1 95.07031216 98.97420857 107.59355066
+56 0 1 96.07031216 98.97420857 107.59355066
+57 0 1 97.07031216 98.97420857 107.59355066
+58 0 1 98.07031216 98.97420857 107.59355066
+59 0 1 99.07031216 98.97420857 107.59355066
+60 0 1 100.07031216 98.97420857 107.59355066
+61 0 1 101.07031216 98.97420857 107.59355066
+62 0 1 102.07031216 98.97420857 107.59355066
+63 0 1 103.07031216 98.97420857 107.59355066
+64 0 1 104.07031216 98.97420857 107.59355066
+65 0 1 105.07031216 98.97420857 107.59355066
+66 0 1 106.07031216 98.97420857 107.59355066
+67 0 1 107.07031216 98.97420857 107.59355066
+68 0 1 108.07031216 98.97420857 107.59355066
+69 0 1 109.07031216 98.97420857 107.59355066
+70 0 1 110.07031216 98.97420857 107.59355066
+71 0 1 111.07031216 98.97420857 107.59355066
+72 0 1 112.07031216 98.97420857 107.59355066
+73 0 1 113.07031216 98.97420857 107.59355066
+74 0 1 114.07031216 98.97420857 107.59355066
+75 0 1 115.07031216 98.97420857 107.59355066
+76 0 1 116.07031216 98.97420857 107.59355066
+77 0 1 117.07031216 98.97420857 107.59355066
+78 0 1 118.07031216 98.97420857 107.59355066
+79 0 1 119.07031216 98.97420857 107.59355066
+80 0 1 120.07031216 98.97420857 107.59355066
+81 0 1 121.07031216 98.97420857 107.59355066
+82 0 1 122.07031216 98.97420857 107.59355066
+83 0 1 123.07031216 98.97420857 107.59355066
+84 0 1 124.07031216 98.97420857 107.59355066
+85 0 1 125.07031216 98.97420857 107.59355066
+86 0 1 126.07031216 98.97420857 107.59355066
+87 0 1 127.07031216 98.97420857 107.59355066
+88 0 1 128.07031216 98.97420857 107.59355066
+89 0 1 129.07031216 98.97420857 107.59355066
+90 0 1 130.07031216 98.97420857 107.59355066
+91 0 1 131.07031216 98.97420857 107.59355066
+92 0 1 132.07031216 98.97420857 107.59355066
+93 0 1 133.07031216 98.97420857 107.59355066
+94 0 1 134.07031216 98.97420857 107.59355066
+95 0 1 135.07031216 98.97420857 107.59355066
+96 0 1 136.07031216 98.97420857 107.59355066
+97 0 1 137.07031216 98.97420857 107.59355066
+98 0 1 138.07031216 98.97420857 107.59355066
+99 0 1 139.07031216 98.97420857 107.59355066
+100 0 1 140.07031216 98.97420857 107.59355066
+
+Bonds
+
+1 1 1 2
+2 1 2 3
+3 1 3 4
+4 1 4 5
+5 1 5 6
+6 1 6 7
+7 1 7 8
+8 1 8 9
+9 1 9 10
+10 1 10 11
+11 1 11 12
+12 1 12 13
+13 1 13 14
+14 1 14 15
+15 1 15 16
+16 1 16 17
+17 1 17 18
+18 1 18 19
+19 1 19 20
+20 1 20 21
+21 1 21 22
+22 1 22 23
+23 1 23 24
+24 1 24 25
+25 1 25 26
+26 1 26 27
+27 1 27 28
+28 1 28 29
+29 1 29 30
+30 1 30 31
+31 1 31 32
+32 1 32 33
+33 1 33 34
+34 1 34 35
+35 1 35 36
+36 1 36 37
+37 1 37 38
+38 1 38 39
+39 1 39 40
+40 1 40 41
+41 1 41 42
+42 1 42 43
+43 1 43 44
+44 1 44 45
+45 1 45 46
+46 1 46 47
+47 1 47 48
+48 1 48 49
+49 1 49 50
+50 1 50 51
+51 1 51 52
+52 1 52 53
+53 1 53 54
+54 1 54 55
+55 1 55 56
+56 1 56 57
+57 1 57 58
+58 1 58 59
+59 1 59 60
+60 1 60 61
+61 1 61 62
+62 1 62 63
+63 1 63 64
+64 1 64 65
+65 1 65 66
+66 1 66 67
+67 1 67 68
+68 1 68 69
+69 1 69 70
+70 1 70 71
+71 1 71 72
+72 1 72 73
+73 1 73 74
+74 1 74 75
+75 1 75 76
+76 1 76 77
+77 1 77 78
+78 1 78 79
+79 1 79 80
+80 1 80 81
+81 1 81 82
+82 1 82 83
+83 1 83 84
+84 1 84 85
+85 1 85 86
+86 1 86 87
+87 1 87 88
+88 1 88 89
+89 1 89 90
+90 1 90 91
+91 1 91 92
+92 1 92 93
+93 1 93 94
+94 1 94 95
+95 1 95 96
+96 1 96 97
+97 1 97 98
+98 1 98 99
+99 1 99 100

doc/source/tutorials/numba_tutorial/lammps_input.in

@@ -0,0 +1,29 @@
+# Initialize simulation
+units lj
+atom_style molecular
+boundary p p p
+
+# Read data file
+read_data init.data
+
+# Neighbor list settings
+neighbor        0.4 bin
+
+# Pair potential (LJ with cutoff at 2^(1/6))
+pair_style lj/cut 1.122462048309373
+pair_coeff 1 1 1.0 1.0 1.122462048309373
+
+# Bond potential (FENE)
+bond_style fene
+bond_coeff 1 30.0 1.5 1.0 1.0
+special_bonds fene
+
+# Integrator settings
+timestep 0.005
+fix 1 all nvt temp 1.0 1.0 1.0
+fix 2 all langevin 1.0 1.0 1.0 5
+
+# Run simulation
+run 10000
+dump 2 all custom 1000 traj.lammpstrj id type x y z ix iy iz vx vy vz
+run 100000