interpolation_type=params['interpolation_type'],
inv_power=params['inv_power'],
energy_thresh=params['energy_thresh'],
scaling_property='test_charge')
print "With C"
universe.setForceField(ForceField)
universe.atom1.setPosition(Vector(x[0],0.5,1.5))
# print 'Energy Terms:'
# print universe.energyTerms()
# e, g = universe.energyAndGradients()
print 'Gradient Test'
gradientTest(universe)
import time
start_time = time.time()
for n in range(steps):
universe.atom1.setPosition(Vector(x[n],0.5,1.5))
e, g = universe.energyAndGradients()
print 'Time to do %d energy and gradient evaluations: %f s'%(\
steps, time.time()-start_time)
print "Without C"
ForceField.use_C = False
universe.setForceField(ForceField)
universe = InfiniteUniverse()
universe.atom1 = Atom('C', position=Vector(1.02, 0.512, 1.513))
universe.atom1.test_charge = 1.
universe.atom2 = Atom('C', position=Vector(1.553, 1.724, 1.464))
universe.atom2.test_charge = -0.2
ForceField = TrilinearThreshGrid.TrilinearThreshGridForceField(
'../../../Example/grids/LJa.nc', 1.0, 'test_charge', Ethresh=100.)
universe.setForceField(ForceField)
print 'Energy Terms:'
print universe.energyTerms()
e, g = universe.energyAndGradients()
print 'Gradient on Atom 1'
print g[universe.atom1]
print 'Gradient on Atom 2'
print g[universe.atom2]
print 'Gradient Test'
gradientTest(universe)
import time
start_time = time.time()
for t in range(100000):
e, g = universe.energyAndGradients()
print 'Time to do 100000 energy and gradient evaluations'
print time.time() - start_time
import AlGDock
from MMTK import *
from Cylinder import CylinderForceField
from MMTK.ForceFields.ForceFieldTest import gradientTest, forceConstantTest
import numpy as N
try:
from Scientific._vector import Vector
except:
from Scientific.Geometry.VectorModule import Vector
universe = InfiniteUniverse()
universe.atom1 = Atom('C', position=Vector((2, 4.1, 2.1)))
ff1 = CylinderForceField(\
origin=N.array((2., 2., 1.)), \
direction=N.array((0,0,1.0)), \
max_Z=2., max_R=2.)
universe.setForceField(ff1)
e, g = universe.energyAndGradients()
print universe.energyTerms()
print e
gradientTest(universe, delta=0.001)
#forceConstantTest(universe)