Calculating long-range particle interactions with numpy (handmade mesh grid)

Too slow

import random
import math
import time
import numpy as np

np.set_printoptions(threshold=np.inf)
random.seed(1)

XX = 0
YY = 1
ZZ = 2

#total particle num
PN = 300

xyzV = [[0 for i in range(3)] for j in range(PN)]
xyzP = np.zeros((PN,3))
xyzF = np.zeros((PN,3))


def find_pair():
  global PN
  global xyzF
  global xyzP

  x1 = np.empty(0)
  y1 = np.empty(0)

  for mm in range(1,PN):
    for nn in range(mm,PN):
      x1 = np.append(x1,[nn],axis=0)
      y1 = np.append(y1,[mm-1],axis=0)

  x1 = x1.astype(np.int32)
  x1 = x1.reshape(x1.shape[0],1)
  y1 = y1.astype(np.int32)
  y1 = y1.reshape(y1.shape[0],1)

  dd = np.linalg.norm(xyzP[x1]-xyzP[y1], axis=2)

  distances = np.zeros((PN,PN))
  ly = 0
  lx = ly + 1
  for kk in range(0,dd.shape[0]):
    distances[lx][ly] = dd[kk]
    distances[ly][lx] = dd[kk]
    lx = lx + 1
    if lx == PN:
      ly = ly + 1
      lx = ly + 1

  tmp_index = np.arange(xyzP.shape[0])
  xx, yy = np.meshgrid(tmp_index, tmp_index)

  dxyz = xyzP[xx] - xyzP[yy]

  distances = distances[:,:,np.newaxis]
  tmp_force = dxyz/distances
  tmp_force = np.nan_to_num(tmp_force,0)

  mmm = tmp_force.sum(axis=1)
  xyzF = xyzF + mmm

def init_lattice():
  global xyzF
  global xyzP

  pnum = 0
  while pnum < PN:
    xyzP[pnum][XX] = random.uniform(-1,1)
    xyzP[pnum][YY] = random.uniform(-1,1)
    xyzP[pnum][ZZ] = random.uniform(-1,1)
    xyzF[pnum][XX] = random.uniform(-1,1)
    xyzF[pnum][YY] = random.uniform(-1,1)
    xyzF[pnum][ZZ] = random.uniform(-1,1)
    pnum += 1

def results_sum():
  #global xyzF
  pnum = 0
  total_F = 0
  while pnum < PN:
    total_F = total_F + xyzF[pnum][XX]
    total_F = total_F + xyzF[pnum][YY]
    total_F = total_F + xyzF[pnum][ZZ]
    pnum += 1

  print (total_F)


if __name__ == "__main__":

  init_lattice()
  find_pair()
  results_sum()

import random

import math

import time

import numpy as np

np.set_printoptions(threshold=np.inf)

random.seed(1)

XX = 0

YY = 1

ZZ = 2

#total particle num

PN = 300

xyzV = [[0 for i in range(3)] for j in range(PN)]

xyzP = np.zeros((PN,3))

xyzF = np.zeros((PN,3))

def find_pair():

global PN

global xyzF

global xyzP

x1 = np.empty(0)

y1 = np.empty(0)

for mm in range(1,PN):

for nn in range(mm,PN):

x1 = np.append(x1,[nn],axis=0)

y1 = np.append(y1,[mm-1],axis=0)

x1 = x1.astype(np.int32)

x1 = x1.reshape(x1.shape[0],1)

y1 = y1.astype(np.int32)

y1 = y1.reshape(y1.shape[0],1)

dd = np.linalg.norm(xyzP[x1]-xyzP[y1], axis=2)

distances = np.zeros((PN,PN))

ly = 0

lx = ly + 1

for kk in range(0,dd.shape[0]):

distances[lx][ly] = dd[kk]

distances[ly][lx] = dd[kk]

lx = lx + 1

if lx == PN:

ly = ly + 1

lx = ly + 1

tmp_index = np.arange(xyzP.shape[0])

xx, yy = np.meshgrid(tmp_index, tmp_index)

dxyz = xyzP[xx] - xyzP[yy]

distances = distances[:,:,np.newaxis]

tmp_force = dxyz/distances

tmp_force = np.nan_to_num(tmp_force,0)

mmm = tmp_force.sum(axis=1)

xyzF = xyzF + mmm

def init_lattice():

global xyzF

global xyzP

pnum = 0

while pnum < PN:

xyzP[pnum][XX] = random.uniform(-1,1)

xyzP[pnum][YY] = random.uniform(-1,1)

xyzP[pnum][ZZ] = random.uniform(-1,1)

xyzF[pnum][XX] = random.uniform(-1,1)

xyzF[pnum][YY] = random.uniform(-1,1)

xyzF[pnum][ZZ] = random.uniform(-1,1)

pnum += 1

def results_sum():

#global xyzF

pnum = 0

total_F = 0

while pnum < PN:

total_F = total_F + xyzF[pnum][XX]

total_F = total_F + xyzF[pnum][YY]

total_F = total_F + xyzF[pnum][ZZ]

pnum += 1

print (total_F)

if __name__ == "__main__":

init_lattice()

find_pair()

results_sum()

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