cube1 = Cube(0,0,0,30,mesh_size)
x_extent = cube1.x_extent
z_extent = cube1.z_extent
start = time.time()
timeList,dList = [],numpy.concatenate((numpy.linspace(0,10,101),range(11,101)))
Uside2sideArray = numpy.zeros((len(dList), 5))
outFile1 = open(join(root, 'interactionPotential_{0}(finalWith-Z&HP-{1}nm).dat'.format(name, mesh_size)), 'w')
outFile1.write("Separation Potential\n")
print "Cube ..."
for n,d in tqdm(enumerate(dList)):
d_vector = numpy.array([0,0,z_extent + d])
cube2 = cube1.shift(d_vector)
U,Vdw = interactionPotential(cube1, cube2,conc,A)
hp1 = hydrophobic_potential(d, 0.5)
hp2 = hydrophobic_potential(d, 1)
hp3 = hydrophobic_potential(d, 2)
Uside2sideArray[n] = [U, Vdw, hp1, hp2, hp3]
outFile1.write("%f %.18e %.18e %.18e %.18e %.18e\n" %(d, U, Vdw, hp1, hp2, hp3))
end = time.time()
print "Total number of runs = ", len(dList)
print "Time for full run = {0} minutes".format((end-start) / 60.)
print "Time for each run = {0} minutes".format((end-start)/(60. * len(dList)))
outFile1.close()
#fig, (ax1, ax2) = plt.subplots(2, figsize=(5,7))
#ax1.plot(dList, Uside2sideArray[:,0], color='steelblue')
start = time.time()
timeList, dList = [], numpy.concatenate((numpy.linspace(1, 10,
91), range(11, 101)))
Uside2sideArray = numpy.zeros((len(dList), 2))
outFile1 = open(
join(root,
'interactionPotential_s2s_{0}({1}nm).dat'.format(name, mesh_size)),
'w')
outFile1.write("Separation Potential\n")
for n, d in tqdm(enumerate(dList)):
d_vector = numpy.array([0, 0, d])
new_bp = bp.shift(d_vector)
U, Vdw = interactionPotential(new_bp, sheet, conc, A)
Uside2sideArray[n] = [U, Vdw]
outFile1.write("%f %.18e %.18e\n" % (d, U, Vdw))
end = time.time()
print "Total number of runs = ", 2 * len(dList)
print "Time for full run = {0} minutes".format((end - start) / 60.)
print "Time for each run = {0} minutes".format(
(end - start) / (60. * len(dList)))
outFile1.close()
fig, (ax1, ax2) = plt.subplots(2, figsize=(5, 7))
ax1.plot(dList, Uside2sideArray[:, 0], color='steelblue')
ax1.set_yscale('log')
ax1.set_ylabel('Coulomb potential')
start = time.time()
timeList, dList = [], numpy.concatenate((numpy.linspace(0, 10,
101), range(11, 101)))
Uside2sideArray = numpy.zeros((len(dList), 2))
outFile1 = open(
join(
root, 'interactionPotential_{0}(finalzeta-{1}nm).dat'.format(
name, mesh_size)), 'w')
outFile1.write("Separation Potential\n")
print "Sphere ..."
for n, d in tqdm(enumerate(dList)):
d_vector = numpy.array([0, 0, z_extent + d])
sphere2 = sphere1.shift(d_vector)
U, Vdw = interactionPotential(sphere1, sphere2, conc, A)
Uside2sideArray[n] = [U, Vdw]
outFile1.write("%f %.18e %.18e\n" % (d, U, Vdw))
end = time.time()
print "Total number of runs = ", len(dList)
print "Time for full run = {0} minutes".format((end - start) / 60.)
print "Time for each run = {0} minutes".format(
(end - start) / (60. * len(dList)))
outFile1.close()
fig, (ax1, ax2) = plt.subplots(2, figsize=(5, 7))
ax1.plot(dList, Uside2sideArray[:, 0], color='steelblue')
ax1.set_yscale('log')
ax1.set_ylabel('Coulomb potential')
outFile1 = open(
join(
root, 'interactionPotential_s2s_{0}(final-{1}nm).dat'.format(
name, mesh_size)), 'w')
outFile2 = open(
join(
root, 'interactionPotential_t2t_{0}(final-{1}nm).dat'.format(
name, mesh_size)), 'w')
outFile1.write("Separation Potential\n")
outFile2.write("Separation Potential\n")
print "Side by side"
for n, d in tqdm(enumerate(dList)):
d_vector = numpy.array([x_extent + d, 0, 0])
rod2 = rod1.shift(d_vector)
U, Vdw = interactionPotential(rod1, rod2, conc, A)
Uside2sideArray[n] = [U, Vdw]
outFile1.write("%f %.18e %.18e\n" % (d, U, Vdw))
print "Tip to tip"
for n, d in tqdm(enumerate(dList)):
d_vector = numpy.array([0, 0, z_extent + d])
rod2 = rod1.shift(d_vector)
U, Vdw = interactionPotential(rod1, rod2, conc, A)
Utip2tipArray[n] = [U, Vdw]
outFile2.write("%f %.18e %.18e\n" % (d, U, Vdw))
end = time.time()
print "Total number of runs = ", 2 * len(dList)
print "Time for full run = {0} minutes".format((end - start) / 60.)
print "Time for each run = {0} minutes".format(
outFile1 = open(
join(
root, 'interactionPotential_s2s_{0}(final-{1}nm).dat'.format(
name, mesh_size)), 'w')
outFile2 = open(
join(
root, 'interactionPotential_t2t_{0}(final-{1}nm).dat'.format(
name, mesh_size)), 'w')
outFile1.write("Separation Potential\n")
outFile2.write("Separation Potential\n")
print "Side by side"
for n, d in tqdm(enumerate(dList)):
d_vector = numpy.array([x_extent + d, 0, 0])
bp2 = bp1.shift(d_vector)
U, Vdw = interactionPotential(bp1, bp2, conc, A)
Uside2sideArray[n] = [U, Vdw]
outFile1.write("%f %.18e %.18e\n" % (d, U, Vdw))
print "Tip to tip"
for n, d in tqdm(enumerate(dList)):
d_vector = numpy.array([0, 0, z_extent + d])
bp2 = bp1.shift(d_vector)
U, Vdw = interactionPotential(bp1, bp2, conc, A)
Utip2tipArray[n] = [U, Vdw]
outFile2.write("%f %.18e %.18e\n" % (d, U, Vdw))
end = time.time()
print "Total number of runs = ", 2 * len(dList)
print "Time for full run = {0} minutes".format((end - start) / 60.)
print "Time for each run = {0} minutes".format(
