pl.plot(alpha_min, f_alpha_min, 'o', color='red')
pl.show()
if __name__ == '__main__':
solver = ScipyAndersonOZsolver(port = 0)
#solver = ScipyNewtonKrylovOZsolver(port = 0)
#We only work with LJ or Yukawa potential since we want to avoid the trouble
#related to the 'jump' (discontinuity) at r = sigma
doLennardJonesExample = False
if doLennardJonesExample:
#LJ possible but with HMSA
solver.setPotentialByName('LennardJones', 0.1) #epsilon/kT = 0.1 is default in SASfit
print "Energy scale of Lennard Jones Potential in kT units:", solver.getEpsilonInkTUnits()
#Initialize HMSA with some (random) start alpha
solver.doHMSAclosure(1.0)
else:
#Yukawa possible with RY: With negative K (attractive besides HS) convergence may be reached for exp shift only (real HS-Yukawa)
#positive (repulsive as HS) K converges for fully shifted potential (1/r included)
solver.setPotentialByName('Yukawa', 1.0, -1.0, True) #lamda in SASfit is different; K = 0.1 is default in SASfit
print "Energy scale of Yukawa HS Potential in kT units:", solver.getInteractionStrengthInKTunits()
print "Length scale of Yukawa HS Potential in sigma units:", solver.getShieldingConstantInSigmaUnits()
#Initialize RY with some (random) start alpha
solver.doRYclosure(1.0)
solver.setVolumeDensity(0.3)
from andersonOZsolver import AndersonOZsolver
from scipyAndersonOZsolver import ScipyAndersonOZsolver
from scipyNewtonKrylovOZsolver import ScipyNewtonKrylovOZsolver
if __name__ == '__main__':
#Instantiate solver class (Picard iteration, etc.)
#For star potential, ScipyAndersonOZsolver gives best result
#s = PicardOZsolver(port = 0)
#s = AndersonOZsolver(port = 0)
s = ScipyAndersonOZsolver(port = 0)
#s = ScipyNewtonKrylovOZsolver(port = 0)
s.printPotentialSetterArguments()
#s.setPotentialByName('HardSphere')
#s.setPotentialByName('LennardJones', 0.2)
s.setPotentialByName('Star', 20)
#Define the density range to scan
densityRange = np.arange(0.3, 0.4, 0.1)
#densityRange = np.asarray([0.3])
#densityRange = np.asarray([0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5,0.5])
densityRDFdictionary = {}
#Start loop over densities and measure wall clock time
t_start = time.time()
for d in densityRange:
s.setVolumeDensity(float(d))
s.solve()
that a zero start value may be better than the previous.
'''
import numpy as np
#Solver
from scipyAndersonOZsolver import ScipyAndersonOZsolver
#plot
import matplotlib.pyplot as plt
import pylab as pl
if __name__ == '__main__':
solver = ScipyAndersonOZsolver(port = 0)
solver.setPotentialByName('HardSphere')
#solver.setNumberOfIterations(10*solver.getNumberOfIterations())
#Relaxing ConvergenceCriterion by a factor 1000
solver.setConvergenceCriterion(1.0e3*solver.getConvergenceCriterion())
#solver.setPotentialByName('LennardJones', 0.5)
startDensity = 0.58
targetDensity = 0.63
totalDeltaDensity = targetDensity - startDensity
density = startDensity
deltaDensity = totalDeltaDensity
decayFactor = 2.5
deltaDensity = 0.01
pl.plot(alpha_min, f_alpha_min, 'o', color='red')
pl.show()
if __name__ == '__main__':
solver = ScipyAndersonOZsolver(port=0)
#solver = ScipyNewtonKrylovOZsolver(port = 0)
#We only work with LJ or Yukawa potential since we want to avoid the trouble
#related to the 'jump' (discontinuity) at r = sigma
doLennardJonesExample = False
if doLennardJonesExample:
#LJ possible but with HMSA
solver.setPotentialByName('LennardJones',
0.1) #epsilon/kT = 0.1 is default in SASfit
print "Energy scale of Lennard Jones Potential in kT units:", solver.getEpsilonInkTUnits(
)
#Initialize HMSA with some (random) start alpha
solver.doHMSAclosure(1.0)
else:
#Yukawa possible with RY: With negative K (attractive besides HS) convergence may be reached for exp shift only (real HS-Yukawa)
#positive (repulsive as HS) K converges for fully shifted potential (1/r included)
solver.setPotentialByName(
'Yukawa', 1.0, -1.0,
True) #lamda in SASfit is different; K = 0.1 is default in SASfit
print "Energy scale of Yukawa HS Potential in kT units:", solver.getInteractionStrengthInKTunits(
)
print "Length scale of Yukawa HS Potential in sigma units:", solver.getShieldingConstantInSigmaUnits(
)
