def test_check(self):
'''Can we validate a system object?'''
types = ['A', 'B', 'C']
sys = pyPRISM.System(types)
self.assertRaises(ValueError, sys.check)
# These values make no sense but their sufficient
# for this 'check'
sys.domain = pyPRISM.Domain(dr=0.1, length=1024)
sys.density[sys.types] = 1.0
sys.diameter[sys.types] = 1.0
sys.potential.setUnset(1.0)
sys.closure.setUnset(1.0)
sys.omega.setUnset(1.0)
#test should fail if this raises
try:
sys.check()
except ValueError:
self.fail('Check failed when it should have passed...')
def test_createPRISM(self):
'''Can we construct a simple but fully specified PRISM problem?'''
sys = pyPRISM.System(['A', 'B'])
sys.domain = pyPRISM.Domain(dr=0.1, length=1024)
sys.density['A'] = 0.45
sys.density['B'] = 0.35
sys.diameter[sys.types] = 1.0
sys.closure.setUnset(pyPRISM.closure.PercusYevick())
sys.potential.setUnset(pyPRISM.potential.HardSphere(sigma=1.0))
sys.omega['A', 'A'] = pyPRISM.omega.SingleSite()
sys.omega['A', 'B'] = pyPRISM.omega.NoIntra()
sys.omega['B', 'B'] = pyPRISM.omega.Gaussian(sigma=1.0, length=100)
PRISM = sys.createPRISM()
self.assertIsInstance(PRISM, pyPRISM.core.PRISM.PRISM)
def setup(self):
'''Construct a simple but fully specified PRISM problem'''
sys = pyPRISM.System(['A', 'B'])
sys.domain = pyPRISM.Domain(dr=0.1, length=1024)
sys.density['A'] = 0.1
sys.density['B'] = 0.75
sys.diameter[sys.types] = 1.0
sys.closure.setUnset(pyPRISM.closure.PercusYevick())
sys.potential.setUnset(pyPRISM.potential.HardSphere(sigma=1.0))
sys.omega['A', 'A'] = pyPRISM.omega.SingleSite()
sys.omega['A', 'B'] = pyPRISM.omega.NoIntra()
sys.omega['B', 'B'] = pyPRISM.omega.Gaussian(sigma=1.0, length=10000)
PRISM = sys.createPRISM()
return PRISM
#sys.path.append(os.path.join(cwd,'pyPRISMpackage/pyPRISM'))
import pyPRISM
import pyPRISM
print(pyPRISM.__file__)
import numpy as np
import matplotlib.pyplot as plt
import scipy as sp
sigma = 1.
scale = 1
kbT = 1.
dr = 0.003
power = 14 # 2**power == # grid points; therefore length = dr*2**power
sys = pyPRISM.System(['A'], kT=kbT)
sys.domain = pyPRISM.Domain(dr=dr, length=2**power)
print('r =', sys.domain.r)
print('k = ', sys.domain.k)
sys.diameter['A'] = dr
sys.omega['A', 'A'] = pyPRISM.omega.SingleSite()
def cust_norm(_GammaIn, _GammaOut):
_diff = np.subtract(_GammaOut, _GammaIn)
_diff = np.sum(_diff**2)
_diff = np.divide(_diff, np.sum(_GammaOut**2))
return _diff
def test_create(self):
'''Can we create a system?'''
types = ['A', 'B', 'C']
sys = pyPRISM.System(types)