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adjmodel.py
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adjmodel.py
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import numpy as np
import numexpr as ne
import time
import sys
import agents
import correlations
import orderParameterStatistics
import plottingFunctions
from pylab import *
#############################################################################################
### Adjustable range model: ###
### Collective motion model in 2d, with periodic boundary conditions. ###
### Each agent co-aligns with agents in its interacting group ###
### The interacting groups is an ordered list containing n members ###
### each at successive distances from the agent. ###
### With the closest member at a topological distance alpha. ###
### ###
### Here: n = numNayHigh - numNayLow ###
### alpha = numNayLow ###
### ###
### Arthur King 9/9/19 ###
#############################################################################################
def main(N, T, dt, numNayLow, numNayHigh, L, eta, speed, numBins, burnInTime,saveCorrEvery,calculateCorrelations, showAnimation, resultsFolder):
start = time.time()
print(" #################################################################################################")
print(" START ")
print("N = ", N, " T = ", T, " dt = ", dt, " numNayLow =", numNayLow," numNayHigh = ", numNayHigh, " L = ", L, " eta = ", eta, " speed = ", speed, " numBins = ", numBins, "burnInTime = ", burnInTime," saveCorrEvery = ", saveCorrEvery,"calculateCorrelations" ,calculateCorrelations, " showAnimation = ",showAnimation)
################################################################
########### initialise
#############################################################
numexprNumCores = ne.detect_number_of_cores()
ne.set_num_threads(numexprNumCores)
resultsCompletePath = resultsFolder + '/N%s/n%s/alpha%s'% (str(N), str(numNayHigh-numNayLow),str(numNayLow))
positionsQ = np.zeros((N,2))
anglesQ = np.zeros(N)
inRangeIndexQ = np.zeros((N, 1+numNayHigh - numNayLow),dtype=np.int)
allNearAngles = np.zeros((N, 1+numNayHigh - numNayLow))
meanSinAllNearAngles = np.zeros(N)
meanCosAllNearAngles = np.zeros(N)
meanDirectionsQ = np.zeros(N)
velocitiesQ = np.zeros((N,2))
velocities_uQ = np.zeros((N,2))
mean_velocityQ = np.zeros((1,2))
noisesQ = np.zeros(N)
if calculateCorrelations == True:
binMatrix = np.zeros((N,N),dtype=int)
binMatrixVU = np.zeros((N,N),dtype=int)
correlationList = np.zeros((0,2))
maxDist = np.sqrt(pow(L/2.0,2)+pow(L/2.0,2))
binWidth = maxDist/numBins
distanceMatrix = np.zeros((N,N))
velocityDotProductMatrixVU = np.zeros((N,N))
correlationSumHistogramVU = np.zeros(numBins)
correlationCountsHistogramVU = np.zeros(numBins)
sqVelocityDotProductMatrixVU = np.zeros((N,N))
sqCorrelationSumHistogramVU = np.zeros(numBins)
onesMatrix =np.ones(np.shape(velocityDotProductMatrixVU[np.triu_indices(N,1)]))
runCount = int(1)
sumVelocities_U = 0.0
dotProdVelocities_U = 0.0
sumDotProdVelocities_U = 0.0
orderParameter= 0.0
sumOrderParameter = 0.0
positionsQ = agents.initialiseRandomPositions(L,positionsQ)
anglesQ = agents.initialiseRandomAngles(anglesQ)
noisesQ = agents.updateRandomNoises(noisesQ,eta)
velocitiesQ = agents.updateVelocities(velocitiesQ,anglesQ,speed)
velocities_uQ = agents.updateVelocities_u(velocitiesQ,velocities_uQ)
inRangeIndexQ = agents.initialise_inRangeIndex(inRangeIndexQ)
if showAnimation == True:
figVelocityAnimation = plt.figure(1,figsize=(6,6))
axVel = figVelocityAnimation.add_subplot(111)
plt.ion()
wframe = None
figVelocityAnimation.set_visible(False)
pause(0.00000000001)
################################################################
########### simulation loop
#############################################################
for i in range(T):
if showAnimation == True:
if i < burnInTime:
pass
elif i >= burnInTime:
oldcol = wframe
wframe = plottingFunctions.plot_grid(axVel,positionsQ, velocitiesQ)
figVelocityAnimation.set_visible(True)
########### timestep
inRangeIndexQ[:,1:] = agents.calculateParticleInRange(positionsQ, L, numNayLow, numNayHigh)
anglesQ = agents.calculateAngles(anglesQ, inRangeIndexQ, allNearAngles, meanSinAllNearAngles, meanCosAllNearAngles, meanDirectionsQ, noisesQ)
velocitiesQ = agents.updateVelocities(velocitiesQ, anglesQ, speed)
positionsQ = agents.updatePositions(positionsQ, velocitiesQ, L, dt)
velocities_uQ = agents.updateVelocities_u(velocitiesQ, velocities_uQ)
noisesQ = agents.updateRandomNoises(noisesQ,eta)
if i < burnInTime:
pass
elif i >= burnInTime:
if showAnimation == True:
if oldcol:
axVel.collections.remove(oldcol)
figVelocityAnimation.canvas.draw()
axVel.autoscale(enable=True, axis='both', tight=True)
axVel.set_xticks([])
axVel.set_yticks([])
plt.pause(0.00000000000001)
################################################################
########### correlations
#############################################################
if i < burnInTime:
pass
elif i >= burnInTime:
if calculateCorrelations == True:
########### save correlations
if i % saveCorrEvery==0:
if np.sum(correlationSumHistogramVU) != 0.0:
print("i ",i)
correlations.saveArray(resultsCompletePath + '/Correlations/sums/Correlation Velocity_U Sum Histogram_run%s'% (str(runCount)) ,correlationSumHistogramVU,N, T, dt, numNayLow, numNayHigh, L, eta, speed, numBins, burnInTime, saveCorrEvery)
correlations.saveArray(resultsCompletePath +'/Correlations/counts/Correlation Velocity_U Counts Histogram_run%s'% ( str(runCount)) ,correlationCountsHistogramVU,N, T, dt, numNayLow, numNayHigh, L, eta, speed, numBins, burnInTime, saveCorrEvery)
correlations.saveArray(resultsCompletePath +'/Correlations/sqSums/Square Correlation Velocity_U Sum Histogram_run%s'% ( str(runCount)) ,sqCorrelationSumHistogramVU,N, T, dt, numNayLow, numNayHigh, L, eta, speed, numBins, burnInTime, saveCorrEvery)
correlations.saveArray(resultsCompletePath +'/Correlations/sumvUdotvU/sum dot prod velocities_U_run%s'% ( str(runCount)) ,np.array([sumDotProdVelocities_U]), N, T, dt, numNayLow, numNayHigh, L, eta, speed, numBins, burnInTime, saveCorrEvery)
correlations.saveArray(resultsCompletePath +'/OrderParameter/sum of OrderParameter_run%s'% ( str(runCount)) ,np.array([sumOrderParameter]), N, T, dt, numNayLow, numNayHigh, L, eta, speed, numBins,burnInTime, saveCorrEvery)
print("saving correlationCountsHistogramVU", correlationCountsHistogramVU)
print("total counts" , np.sum(correlationCountsHistogramVU))
########### reset correlations arrays
distanceMatrix = np.zeros((N,N))
velocityDotProductMatrixVU = np.zeros((N,N))
correlationSumHistogramVU = np.zeros(numBins)
correlationCountsHistogramVU = np.zeros(numBins)
sqVelocityDotProductMatrixVU = np.zeros((N,N))
sqCorrelationSumHistogramVU = np.zeros(numBins)
sumDotProdVelocities_U = 0.0
binMatrixVU = np.zeros((N,N),dtype=int)
upperTriangleIndicesMask = np.triu_indices(np.size(binMatrixVU, axis=0),1)
runCount +=1
########### calculate correlations
distanceMatrix = correlations.calculateDistMatrixWithPeriodicBoundary(positionsQ, L)
velocityDotProductMatrixVU = correlations.calculateMatrixDotProduct(velocities_uQ)
sqVelocityDotProductMatrixVU = correlations.calcSquareMatrix(velocityDotProductMatrixVU)
binMatrixVU = correlations.calculateBinMatrix(distanceMatrix, binWidth,binMatrixVU)
upperTriangleIndicesMask = np.triu_indices(np.size(binMatrixVU, axis=0),1)
correlationSumHistogramVU += correlations.calcCorrelationHistoSum(binMatrixVU, velocityDotProductMatrixVU,numBins,upperTriangleIndicesMask)
correlationCountsHistogramVU += correlations.calcCorrelationHistoCounts(binMatrixVU, onesMatrix,numBins,upperTriangleIndicesMask)
sqCorrelationSumHistogramVU += correlations.calcCorrelationHistoSum(binMatrixVU, sqVelocityDotProductMatrixVU,numBins,upperTriangleIndicesMask)
################################################################
########### order parameter
#############################################################
orderParameter= orderParameterStatistics.calculateOrderParameter(velocitiesQ,speed)
sumOrderParameter += orderParameter
sumVelocities_U = orderParameterStatistics.calculateSumVelocities_U(velocities_uQ)
dotProdVelocities_U = orderParameterStatistics.calculateDotProductVelocities_U(velocities_uQ)
sumDotProdVelocities_U += dotProdVelocities_U
################################################################
########### correlations
#############################################################
if calculateCorrelations==True:
correlations.saveArray(resultsCompletePath +'/Correlations/sums/Correlation Velocity_U Sum Histogram_run%s'% ( str(runCount)) ,correlationSumHistogramVU,N, T, dt, numNayLow, numNayHigh, L, eta, speed, numBins, burnInTime, saveCorrEvery)
correlations.saveArray(resultsCompletePath +'/Correlations/counts/Correlation Velocity_U Counts Histogram_run%s'% ( str(runCount)) ,correlationCountsHistogramVU,N, T, dt, numNayLow, numNayHigh, L, eta, speed, numBins, burnInTime, saveCorrEvery)
correlations.saveArray(resultsCompletePath +'/Correlations/sqSums/Square Correlation Velocity_U Sum Histogram_run%s'% ( str(runCount)) ,sqCorrelationSumHistogramVU,N, T, dt, numNayLow, numNayHigh, L, eta, speed, numBins, burnInTime, saveCorrEvery)
correlations.saveArray(resultsCompletePath +'/Correlations/sumvUdotvU/sum dot prod velocities_U_run%s'% ( str(runCount)) ,np.array([sumDotProdVelocities_U]), N, T, dt, numNayLow, numNayHigh, L, eta, speed, numBins, burnInTime, saveCorrEvery)
correlations.saveArray(resultsCompletePath +'/OrderParameter/sum of OrderParameter_run%s'% ( str(runCount)) ,np.array([sumOrderParameter]), N, T, dt, numNayLow, numNayHigh, L, eta, speed, numBins,burnInTime, saveCorrEvery)
end = time.time()
meanOrderParameter = sumOrderParameter/(T-burnInTime)
print(" #################################################################################################")
print(" END ")
print(" Simulation statistics")
print('eta = ', eta)
print('mean order parameter = ', meanOrderParameter)
print('mean DotProdVelocities_U = ', sumDotProdVelocities_U/(T-burnInTime))
print ("time taken = ", end - start)
return meanOrderParameter
if __name__ == "__main__":
import cmdLineParsingAdjmodel
parser = cmdLineParsingAdjmodel.createParser()
args = parser.parse_args()
main(N=args.N, T=args.T, dt=args.dt, numNayLow=args.numNayLow, numNayHigh = args.numNayHigh, L=args.L, eta=args.eta, speed=args.speed, numBins=args.numBins, burnInTime=args.burnInTime, saveCorrEvery=args.saveCorrEvery, calculateCorrelations=args.calculateCorrelations, showAnimation=args.showAnimation, resultsFolder=args.resultsFolder)