numpy.savetxt('RHS.txt', F)
setup_time = toc - TIC
print 'List time : %fs' % list_time
print 'Data transfer time : %fs' % transfer_time
print 'RHS generation time: %fs' % rhs_time
print '------------------------------'
print 'Total setup time : %fs\n' % setup_time
tic = time.time()
### Solve
print 'Solve'
phi = numpy.zeros(param.Neq)
phi = gmres_solver(surf_array, field_array, phi, F, param, ind0, timing,
kernel)
toc = time.time()
solve_time = toc - tic
print 'Solve time : %fs' % solve_time
numpy.savetxt('phi.txt', phi)
#phi = loadtxt('phi.txt')
# Put result phi in corresponding surfaces
fill_phi(phi, surf_array)
### Calculate solvation energy
print '\nCalculate Esolv'
tic = time.time()
E_solv = calculateEsolv(surf_array, field_array, param, kernel)
toc = time.time()
print 'Time Esolv: %fs' % (toc - tic)
numpy.savetxt('RHS.txt',F)
setup_time = toc-TIC
print 'List time : %fs'%list_time
print 'Data transfer time : %fs'%transfer_time
print 'RHS generation time: %fs'%rhs_time
print '------------------------------'
print 'Total setup time : %fs\n'%setup_time
tic = time.time()
### Solve
print 'Solve'
phi = numpy.zeros(param.Neq)
phi = gmres_solver(surf_array, field_array, phi, F, param, ind0, timing, kernel)
toc = time.time()
solve_time = toc-tic
print 'Solve time : %fs'%solve_time
numpy.savetxt('phi.txt',phi)
#phi = loadtxt('phi.txt')
# Put result phi in corresponding surfaces
fill_phi(phi, surf_array)
### Calculate solvation energy
print '\nCalculate Esolv'
tic = time.time()
E_solv = calculateEsolv(surf_array, field_array, param, kernel)
toc = time.time()
print 'Time Esolv: %fs'%(toc-tic)
if type(MM[0, 0]) != numpy.complex128:
savetxt('RHS_matrix.txt', FF)
print '\nSolve system'
tec = time.time()
phi = zeros(len(F))
if type(MM[0, 0]) == numpy.complex128:
phi = gmres(MM,
FF,
tol=param.tol,
restart=param.restart,
maxiter=param.max_iter)[0]
else:
phi = gmres_solver(MM, phi, FF, param.restart, param.tol, param.max_iter)
converged = -1
toc = time.time()
if type(MM[0, 0]) != numpy.complex128:
savetxt('phi_matrix.txt', phi)
print '\nEnergy calculation'
fill_phi(phi, surf_array)
Esolv, field_Esolv = solvationEnergy(surf_array, field_array, param)
Ecoul, field_Ecoul = coulombicEnergy(field_array, param)
Esurf, surf_Esurf = surfaceEnergy(surf_array, param)
MM = Ainv*M
FF = Ainv*F
#MM = M
#FF = F
if type(MM[0,0]) != numpy.complex128:
savetxt('RHS_matrix.txt',FF)
print '\nSolve system'
tec = time.time()
phi = zeros(len(F))
if type(MM[0,0]) == numpy.complex128:
phi = gmres(MM, FF, tol=param.tol, restart=param.restart, maxiter=param.max_iter)[0]
else:
phi = gmres_solver(MM, phi, FF, param.restart, param.tol, param.max_iter)
converged = -1
toc = time.time()
if type(MM[0,0]) != numpy.complex128:
savetxt('phi_matrix.txt',phi)
print '\nEnergy calculation'
fill_phi(phi, surf_array)
Esolv, field_Esolv = solvationEnergy(surf_array, field_array, param)
Ecoul, field_Ecoul = coulombicEnergy(field_array, param)
print '\n\nGenerate preconditioner'
Ainv = generatePreconditioner(surf_array)
print 'preconditioner generated'
MM = Ainv*M
FF = Ainv*F
#MM = M
#FF = F
savetxt('RHS_matrix.txt',FF)
print '\nCalculation for both spheres'
tec = time.time()
phi = zeros(len(F))
phi = gmres_solver(MM, phi, FF, param.restart, param.tol, param.max_iter) # Potential both spheres
converged = -1
toc = time.time()
savetxt('phi_matrix.txt',phi)
print '\nEnergy calculation'
fill_phi(phi, surf_array)
Esolv, field_Esolv = solvationEnergy(surf_array, field_array, param)
Ecoul, field_Ecoul = coulombicEnergy(field_array, param)
Esurf, surf_Esurf = surfaceEnergy(surf_array, param)
toc = time.time()
