'''
   MFEM example 10p

      This examples solves a time dependent nonlinear elasticity
      problem of the form dv/dt = H(x) + S v, dx/dt = v, where H is a
      hyperelastic model and S is a viscosity operator of Laplacian
      type.

   How to run:
      mpirun -np 4 python <arguments>

   Example of arguments:
      ex10p.py -m beam-quad.mesh -s 3 -rs 2 -dt 3
      ex10p.py -m beam-tri.mesh -s 3 -rs 2 -dt 3
      ex10p.py -m beam-hex.mesh -s 2 -rs 1 -dt 3
      ex10p.py -m beam-tet.mesh -s 2 -rs 1 -dt 3
      ex10p.py -m beam-quad.mesh -s 14 -rs 2 -dt 0.03 -vs 20
      ex10p.py -m beam-hex.mesh -s 14 -rs 1 -dt 0.05 -vs 20

   See c++ version in the MFEM library for more detail 
'''
import sys
import mfem.par as mfem

from mfem.common.arg_parser import ArgParser
from os.path import expanduser, join
import numpy as np
from numpy import sqrt, pi, cos, sin, hypot, arctan2
from scipy.special import erfc

from mfem import path
from mfem.par import intArray, add_vector
from mpi4py import MPI

num_procs = MPI.COMM_WORLD.size
myid      = MPI.COMM_WORLD.rank

parser = ArgParser(description='Ex10p')
parser.add_argument('-m', '--mesh',
                    default = 'beam-quad.mesh', 
                    action = 'store', type = str,
                    help='Mesh file to use.')
parser.add_argument('-rs', '--refine-serial',
                    action = 'store', default = 2, type=int,
       help = "Number of times to refine the mesh uniformly before parallel")
parser.add_argument('-rp', '--refine-parallel',
                    action = 'store', default = 0, type=int,
       help = "Number of times to refine the mesh uniformly after parallel")
parser.add_argument('-o', '--order',
                    action = 'store', default = 2, type=int,
                    help = "Finite element order (polynomial degree)");
help_ode = "\n".join(["ODE solver: 1 - Backward Euler, 2 - SDIRK2, 3 - SDIRK3",
                      "\t11 - Forward Euler, 12 - RK2",
                      "\t13 - RK3 SSP, 14 - RK4."])
parser.add_argument('-s', '--ode-solver',
                    action = 'store', default = 3, type=int,
                    help = help_ode)
parser.add_argument('-tf', '--t-final',
                    action = 'store', default = 300.0, type=float,
                    help = "Final time; start time is 0.")
parser.add_argument('-dt', '--time-step',
                    action = 'store', default = 3.0, type=float,
                    help = "Time step")

parser.add_argument("-v", "--viscosity",
                    action = 'store', default = 1e-2, type=float,
                    help = "Viscosity coefficient.")
parser.add_argument("-mu", "--shear-modulus",
             action = 'store', default = 0.25, type=float,                    
             help = "Shear modulus in the Neo-Hookean hyperelastic model.")
parser.add_argument("-K", "--bulk-modulus",
             action = 'store', default = 5.0, type=float,                    
             help = "Bulk modulus in the Neo-Hookean hyperelastic model.");
parser.add_argument('-vis', '--visualization',
                    action = 'store_true', default = True, 
                    help='Enable GLVis visualization')
parser.add_argument("-vs", "--visualization-steps",
                    action = 'store', default = 1,  type = int,
                    help = "Visualize every n-th timestep.");
args = parser.parse_args()

ser_ref_levels = args.refine_serial
par_ref_levels = args.refine_parallel
order = args.order
ode_solver_type = args.ode_solver
t_final = args.t_final
dt = args.time_step
visc = args.viscosity
mu = args.shear_modulus
K = args.bulk_modulus
visualization = args.visualization
vis_steps = args.visualization_steps
if (myid == 0): parser.print_options(args)

# 3. Read the serial mesh from the given mesh file on all processors. We can
#    handle triangular, quadrilateral, tetrahedral and hexahedral meshes
#    with the same code.
meshfile = expanduser(join(path, 'data', args.mesh))
mesh = mfem.Mesh(meshfile, 1,1)
dim = mesh.Dimension()

# 4. Define the ODE solver used for time integration. Several implicit
#    singly diagonal implicit Runge-Kutta (SDIRK) methods, as well as
#    explicit Runge-Kutta methods are available.
if   ode_solver_type == 1:   ode_solver = BackwardEulerSolver()
elif ode_solver_type == 2:   ode_solver = mfem.SDIRK23Solver(2)
elif ode_solver_type == 3:   ode_solver = mfem.SDIRK33Solver()
elif ode_solver_type == 11:  ode_solver = ForwardEulerSolver()
elif ode_solver_type == 12:  ode_solver = mfem.RK2Solver(0.5); 
elif ode_solver_type == 13:  ode_solver = mfem.RK3SSPSolver()
elif ode_solver_type == 14:  ode_solver = mfem.RK4Solver()
elif ode_solver_type == 22:  ode_solver = mfem.ImplicitMidpointSolver()
elif ode_solver_type == 23:  ode_solver = mfem.SDIRK23Solver()
elif ode_solver_type == 24:  ode_solver = mfem.SDIRK34Solver()
else:
    if myid == 0: print( "Unknown ODE solver type: " + str(ode_solver_type))
    sys.exit()

# 5. Refine the mesh in serial to increase the resolution. In this example
#    we do 'ser_ref_levels' of uniform refinement, where 'ser_ref_levels' is
#    a command-line parameter.
for lev in range(ser_ref_levels):
    mesh.UniformRefinement()

# 6. Define a parallel mesh by a partitioning of the serial mesh. Refine
#    this mesh further in parallel to increase the resolution. Once the
#    parallel mesh is defined, the serial mesh can be deleted.
pmesh = mfem.ParMesh(MPI.COMM_WORLD, mesh)
del mesh
for x in range(par_ref_levels):
    pmesh.UniformRefinement();

# 7. Define the parallel vector finite element spaces representing the mesh
#    deformation x_gf, the velocity v_gf, and the initial configuration,
#    x_ref. Define also the elastic energy density, w_gf, which is in a
#    discontinuous higher-order space. Since x and v are integrated in time
#    as a system, we group them together in block vector vx, on the unique
#    parallel degrees of freedom, with offsets given by array true_offset.

fec = mfem.H1_FECollection(order, dim)
fespace = mfem.ParFiniteElementSpace(pmesh, fec, dim)
glob_size = fespace.GlobalTrueVSize()
if (myid == 0):
    print('Number of velocity/deformation unknowns: '+ str(glob_size))

true_size = fespace.TrueVSize()
true_offset = mfem.intArray(3)
true_offset[0] = 0;
true_offset[1] = true_size;
true_offset[2] = 2*true_size;

vx = mfem.BlockVector(true_offset)

v_gf  = mfem.ParGridFunction(fespace)
x_gf  = mfem.ParGridFunction(fespace)

x_ref = mfem.ParGridFunction(fespace)
pmesh.GetNodes(x_ref)

w_fec = mfem.L2_FECollection(order + 1, dim)
w_fespace = mfem.ParFiniteElementSpace(pmesh, w_fec)
w_gf = mfem.ParGridFunction(w_fespace)

# 8. Set the initial conditions for v_gf, x_gf and vx, and define the
#    boundary conditions on a beam-like mesh (see description above).
class InitialVelocity(mfem.VectorPyCoefficient):
   def EvalValue(self, x):
       dim = len(x)
       s = 0.1/64.
       
       v = np.zeros(len(x))
       v[-1]  = s*x[0]**2*(8.0-x[0])
       v[0]   = -s*x[0]**2
       return v
class InitialDeformation(mfem.VectorPyCoefficient):
   def EvalValue(self, x):
       return x.copy()

velo = InitialVelocity(dim)
v_gf.ProjectCoefficient(velo)
deform =  InitialDeformation(dim)
x_gf.ProjectCoefficient(deform)
   
v_gf.GetTrueDofs(vx.GetBlock(0));
x_gf.GetTrueDofs(vx.GetBlock(1));

ess_bdr = mfem.intArray(fespace.GetMesh().bdr_attributes.Max())
ess_bdr.Assign(0)
ess_bdr[0] = 1; 


# 9. Initialize the hyperelastic operator, the GLVis visualization and print
#    the initial energies.
class ElasticEnergyCoefficient(mfem.PyCoefficient):
    def __init__(self, model, x):
        self.x = x
        self.model = model
        self.J = mfem.DenseMatrix()
        mfem.PyCoefficient.__init__(self)
       
    def Eval(self, T, ip):
        self.model.SetTransformation(T)
        self.x.GetVectorGradient(T, self.J)
        return self.model.EvalW(self.J)/(self.J.Det())
    
class ReducedSystemOperator(mfem.PyOperator):
    def __init__(self, M, S, H, ess_tdof_list):
        mfem.PyOperator.__init__(self, M.ParFESpace().TrueVSize())
        self.M = M
        self.S = S
        self.H = H
        self.Jacobian = None
        h = M.ParFESpace().TrueVSize()
        self.w = mfem.Vector(h)
        self.z = mfem.Vector(h)
        self.dt = 0.0
        self.ess_tdof_list = ess_tdof_list
        
    def SetParameters(self, dt, v, x):
        self.dt = dt
        self.v = v
        self.x = x

    def Mult(self, k, y):
        add_vector(self.v, self.dt, k, self.w)
        add_vector(self.x, self.dt, self.w, self.z)
        self.H.Mult(self.z, y)
        self.M.TrueAddMult(k, y)
        self.S.TrueAddMult(self.w, y)
        y.SetSubVector(self.ess_tdof_list, 0.0);
   
    def GetGradient(self, k):
        localJ = mfem.Add(1.0, self.M.SpMat(), self.dt, self.S.SpMat());
        add_vector(self.v, self.dt, k, self.w)
        add_vector(self.x, self.dt, self.w, self.z)
        localJ.Add(self.dt * self.dt,  self.H.GetLocalGradient(self.z))
        Jacobian = self.M.ParallelAssemble(localJ)
        Jacobian.EliminateRowsCols(self.ess_tdof_list)        
        return Jacobian
    
class HyperelasticOperator(mfem.PyTimeDependentOperator):
    def __init__(self, fespace, ess_bdr, visc, mu, K):
        mfem.PyTimeDependentOperator.__init__(self, 2*fespace.TrueVSize(), 0.0)
       
        rel_tol = 1e-8;
        skip_zero_entries = 0;
        ref_density = 1.0
        
        self.ess_tdof_list = intArray()
        self.z = mfem.Vector(self.Height()//2)
        self.fespace =  fespace
        self.viscosity = visc
        self.newton_solver = mfem.NewtonSolver(fespace.GetComm())
       
        M = mfem.ParBilinearForm(fespace)
        S = mfem.ParBilinearForm(fespace)
        H = mfem.ParNonlinearForm(fespace)
        self.M = M
        self.H = H
        self.S = S
       
        rho = mfem.ConstantCoefficient(ref_density)
        M.AddDomainIntegrator(mfem.VectorMassIntegrator(rho))
        M.Assemble(skip_zero_entries)
        M.EliminateEssentialBC(ess_bdr)
        M.Finalize(skip_zero_entries)
        self.Mmat = M.ParallelAssemble()
        
        fespace.GetEssentialTrueDofs(ess_bdr, self.ess_tdof_list)
        self.Mmat.EliminateRowsCols(self.ess_tdof_list)

        M_solver = mfem.CGSolver(fespace.GetComm())
        M_prec = mfem.HypreSmoother()
        M_solver.iterative_mode = False
        M_solver.SetRelTol(rel_tol)
        M_solver.SetAbsTol(0.0)
        M_solver.SetMaxIter(30)
        M_solver.SetPrintLevel(0)
        M_prec.SetType(mfem.HypreSmoother.Jacobi)
        M_solver.SetPreconditioner(M_prec)
        M_solver.SetOperator(self.Mmat)
       
        self.M_solver = M_solver
        self.M_prec = M_prec

        model = mfem.NeoHookeanModel(mu, K)
        H.AddDomainIntegrator(mfem.HyperelasticNLFIntegrator(model))
        H.SetEssentialTrueDofs(self.ess_tdof_list)
        self.model = model

        visc_coeff = mfem.ConstantCoefficient(visc)
        S.AddDomainIntegrator(mfem.VectorDiffusionIntegrator(visc_coeff))
        S.Assemble(skip_zero_entries)
        S.EliminateEssentialBC(ess_bdr)
        S.Finalize(skip_zero_entries)

        self.reduced_oper = ReducedSystemOperator(M, S, H, self.ess_tdof_list)        

        J_hypreSmoother= mfem.HypreSmoother()
        J_hypreSmoother.SetType(mfem.HypreSmoother.l1Jacobi)
        J_hypreSmoother.SetPositiveDiagonal(True)
        J_prec = J_hypreSmoother;
        
        J_minres = mfem.MINRESSolver(fespace.GetComm())
        J_minres.SetRelTol(rel_tol);
        J_minres.SetAbsTol(0.0);
        J_minres.SetMaxIter(300);
        J_minres.SetPrintLevel(-1);
        J_minres.SetPreconditioner(J_prec)

        self.J_solver = J_minres
        self.J_prec  =  J_prec

        newton_solver = mfem.NewtonSolver(fespace.GetComm())
        newton_solver.iterative_mode = False
        newton_solver.SetSolver(self.J_solver);
        newton_solver.SetOperator(self.reduced_oper)
        newton_solver.SetPrintLevel(1); #print Newton iterations
        newton_solver.SetRelTol(rel_tol);
        newton_solver.SetAbsTol(0.0);
        newton_solver.SetMaxIter(10);
        self.newton_solver = newton_solver
       
    def Mult(self, vx, vx_dt):    
        sc = self.Height()//2
        v = mfem.Vector(vx, 0,  sc)
        x = mfem.Vector(vx, sc,  sc)
        dv_dt = mfem.Vector(dvx_dt, 0, sc)
        dx_dt = mfem.Vector(dvx_dt, sc,  sc)

        self.H.Mult(x, z);
        if (self.viscosity != 0.0):
            S.TrueAddMult(v, z)
            z.SetSubVector(self.ess_tdof_list, 0.0)
        z.Neg()
        self.M_solver.Mult(z, dv_dt);
        dx_dt = v
        
    def ImplicitSolve(self, dt, vx, dvx_dt):
        sc = self.Height()//2
        v = mfem.Vector(vx, 0,  sc)
        x = mfem.Vector(vx, sc,  sc)
        dv_dt = mfem.Vector(dvx_dt, 0, sc)
        dx_dt = mfem.Vector(dvx_dt, sc,  sc)

        # By eliminating kx from the coupled system:
        # kv = -M^{-1}*[H(x + dt*kx) + S*(v + dt*kv)]
        # kx = v + dt*kv
        # we reduce it to a nonlinear equation for kv, represented by the
        # backward_euler_oper. This equation is solved with the newton_solver
        # object (using J_solver and J_prec internally).
        self.reduced_oper.SetParameters(dt, v, x)
        zero = mfem.Vector() # empty vector is interpreted as
                             # zero r.h.s. by NewtonSolver
        self.newton_solver.Mult(zero, dv_dt)
        add_vector(v, dt, dv_dt, dx_dt);

    def ElasticEnergy(self, x):
        return self.H.GetEnergy(x)

    def KineticEnergy(self, v):
        local_energy  = 0.5*self.M.InnerProduct(v, v)
        energy = MPI.COMM_WORLD.allreduce(local_energy, op = MPI.SUM)
        return energy
    
    def GetElasticEnergyDensity(self, x, w):
        w_coeff = ElasticEnergyCoefficient(self.model, x)
        w.ProjectCoefficient(w_coeff)
        
def visualize(out, pmesh, deformed_nodes, field,
              field_name = '', init_vis = False):
   nodes = deformed_nodes;
   owns_nodes = 0

   nodes, owns_nodes = pmesh.SwapNodes(nodes, owns_nodes);

   out.send_text("parallel " + str(num_procs) +  " " + str(myid))            
   out.send_solution(pmesh, field)
    
   nodes, owns_nodes = pmesh.SwapNodes(nodes, owns_nodes);

   if (init_vis):
      out.send_text("window_size 400 400")
      out.send_text( "window_title '"  + field_name)
      if (pmesh.SpaceDimension() == 2):
         out.send_text("view 0 0")
         out.send_text("keys jl")
      out.send_text("keys cm")         # show colorbar and mesh
      out.send_text("autoscale value") # update value-range; keep mesh-extents fixed
      out.send_text("pause")
   out.flush()
       
oper = HyperelasticOperator(fespace, ess_bdr, visc,  mu, K)
if (visualization):
    vis_v = mfem.socketstream("localhost", 19916)
    vis_v.precision(8)
    visualize(vis_v, pmesh, x_gf, v_gf, "Velocity", True)
                    
    MPI.COMM_WORLD.Barrier()
    vis_w = mfem.socketstream("localhost", 19916)
    oper.GetElasticEnergyDensity(x_gf, w_gf)
    vis_w.precision(8)
    visualize(vis_w, pmesh, x_gf, w_gf, "Elastic energy density", True)

ee0 = oper.ElasticEnergy(x_gf)
ke0 = oper.KineticEnergy(v_gf)

if myid == 0:
    print("initial elastic energy (EE) = " + str(ee0)) 
    print("initial kinetic energy (KE) = " + str(ke0)) 
    print("initial   total energy (TE) = " + str(ee0 + ke0))
                    
# 8. Perform time-integration (looping over the time iterations, ti, with a
#    time-step dt).
t = 0. ; ti = 1

oper.SetTime(t);
ode_solver.Init(oper)
last_step = False;

while not last_step:
    dt_real = min(dt, t_final -t)
    t, dt = ode_solver.Step(vx, t, dt_real)

    if (t >= t_final - 1e-8*dt): last_step = True    
    
    if (last_step or (ti % vis_steps) == 0):
        v_gf.Distribute(vx.GetBlock(0))
        x_gf.Distribute(vx.GetBlock(1))
        
        ee = oper.ElasticEnergy(x_gf)
        ke = oper.KineticEnergy(v_gf)
        
        text = ("step " + str(ti) + ", t = " + str(t) + ", EE = " +
                str(ee) +  ", KE = " + str(ke) + 
                ", dTE = " + str((ee+ke)-(ee0+ke0)))

        if myid == 0: print(text)
        if visualization:
            visualize(vis_v, pmesh, x_gf, v_gf)
            oper.GetElasticEnergyDensity(x_gf, w_gf)
            visualize(vis_w, pmesh, x_gf, w_gf)
    
    ti = ti + 1

#
# if i translate c++ line-by-line, ti seems the second swap does not work...
#

smyid = '{:0>6d}'.format(myid)
mesh_name  =  "deformed."+smyid
velo_name   =  "velocity."+smyid
ee_name   =  "elastic_energy."+smyid

nodes = x_gf
owns_nodes = 0
nodes, owns_nodes = pmesh.SwapNodes(nodes, owns_nodes)
pmesh.Print(mesh_name, 8)
pmesh.SwapNodes(nodes, owns_nodes)
    
v_gf.Save(velo_name, 8)
oper.GetElasticEnergyDensity(x_gf, w_gf)
w_gf.Save(ee_name,  8)







'''
   MFEM example 10p

      This examples solves a time dependent nonlinear elasticity
      problem of the form dv/dt = H(x) + S v, dx/dt = v, where H is a
      hyperelastic model and S is a viscosity operator of Laplacian
      type.

   How to run:
      mpirun -np 4 python <arguments>

   Example of arguments:
      ex10p.py -m beam-quad.mesh -s 3 -rs 2 -dt 3
      ex10p.py -m beam-tri.mesh -s 3 -rs 2 -dt 3
      ex10p.py -m beam-hex.mesh -s 2 -rs 1 -dt 3
      ex10p.py -m beam-tet.mesh -s 2 -rs 1 -dt 3
      ex10p.py -m beam-quad.mesh -s 14 -rs 2 -dt 0.03 -vs 20
      ex10p.py -m beam-hex.mesh -s 14 -rs 1 -dt 0.05 -vs 20

   See c++ version in the MFEM library for more detail 
'''
import sys
import mfem.par as mfem

from mfem.common.arg_parser import ArgParser
from os.path import expanduser, join
import numpy as np
from numpy import sqrt, pi, cos, sin, hypot, arctan2
from scipy.special import erfc

from mfem import path
from mfem.par import intArray, add_vector
from mpi4py import MPI

num_procs = MPI.COMM_WORLD.size
myid      = MPI.COMM_WORLD.rank

parser = ArgParser(description='Ex10p')
parser.add_argument('-m', '--mesh',
                    default = 'beam-quad.mesh', 
                    action = 'store', type = str,
                    help='Mesh file to use.')
parser.add_argument('-rs', '--refine-serial',
                    action = 'store', default = 2, type=int,
       help = "Number of times to refine the mesh uniformly before parallel")
parser.add_argument('-rp', '--refine-parallel',
                    action = 'store', default = 0, type=int,
       help = "Number of times to refine the mesh uniformly after parallel")
parser.add_argument('-o', '--order',
                    action = 'store', default = 2, type=int,
                    help = "Finite element order (polynomial degree)");
help_ode = "\n".join(["ODE solver: 1 - Backward Euler, 2 - SDIRK2, 3 - SDIRK3",
                      "\t11 - Forward Euler, 12 - RK2",
                      "\t13 - RK3 SSP, 14 - RK4."])
parser.add_argument('-s', '--ode-solver',
                    action = 'store', default = 3, type=int,
                    help = help_ode)
parser.add_argument('-tf', '--t-final',
                    action = 'store', default = 300.0, type=float,
                    help = "Final time; start time is 0.")
parser.add_argument('-dt', '--time-step',
                    action = 'store', default = 3.0, type=float,
                    help = "Time step")

parser.add_argument("-v", "--viscosity",
                    action = 'store', default = 1e-2, type=float,
                    help = "Viscosity coefficient.")
parser.add_argument("-mu", "--shear-modulus",
             action = 'store', default = 0.25, type=float,                    
             help = "Shear modulus in the Neo-Hookean hyperelastic model.")
parser.add_argument("-K", "--bulk-modulus",
             action = 'store', default = 5.0, type=float,                    
             help = "Bulk modulus in the Neo-Hookean hyperelastic model.");
parser.add_argument('-vis', '--visualization',
                    action = 'store_true', default = True, 
                    help='Enable GLVis visualization')
parser.add_argument("-vs", "--visualization-steps",
                    action = 'store', default = 1,  type = int,
                    help = "Visualize every n-th timestep.");
args = parser.parse_args()

ser_ref_levels = args.refine_serial
par_ref_levels = args.refine_parallel
order = args.order
ode_solver_type = args.ode_solver
t_final = args.t_final
dt = args.time_step
visc = args.viscosity
mu = args.shear_modulus
K = args.bulk_modulus
visualization = args.visualization
vis_steps = args.visualization_steps
if (myid == 0): parser.print_options(args)

# 3. Read the serial mesh from the given mesh file on all processors. We can
#    handle triangular, quadrilateral, tetrahedral and hexahedral meshes
#    with the same code.
meshfile = expanduser(join(path, 'data', args.mesh))
mesh = mfem.Mesh(meshfile, 1,1)
dim = mesh.Dimension()

# 4. Define the ODE solver used for time integration. Several implicit
#    singly diagonal implicit Runge-Kutta (SDIRK) methods, as well as
#    explicit Runge-Kutta methods are available.
if   ode_solver_type == 1:   ode_solver = BackwardEulerSolver()
elif ode_solver_type == 2:   ode_solver = mfem.SDIRK23Solver(2)
elif ode_solver_type == 3:   ode_solver = mfem.SDIRK33Solver()
elif ode_solver_type == 11:  ode_solver = ForwardEulerSolver()
elif ode_solver_type == 12:  ode_solver = mfem.RK2Solver(0.5); 
elif ode_solver_type == 13:  ode_solver = mfem.RK3SSPSolver()
elif ode_solver_type == 14:  ode_solver = mfem.RK4Solver()
elif ode_solver_type == 22:  ode_solver = mfem.ImplicitMidpointSolver()
elif ode_solver_type == 23:  ode_solver = mfem.SDIRK23Solver()
elif ode_solver_type == 24:  ode_solver = mfem.SDIRK34Solver()
else:
    if myid == 0: print( "Unknown ODE solver type: " + str(ode_solver_type))
    sys.exit()

# 5. Refine the mesh in serial to increase the resolution. In this example
#    we do 'ser_ref_levels' of uniform refinement, where 'ser_ref_levels' is
#    a command-line parameter.
for lev in range(ser_ref_levels):
    mesh.UniformRefinement()

# 6. Define a parallel mesh by a partitioning of the serial mesh. Refine
#    this mesh further in parallel to increase the resolution. Once the
#    parallel mesh is defined, the serial mesh can be deleted.
pmesh = mfem.ParMesh(MPI.COMM_WORLD, mesh)
del mesh
for x in range(par_ref_levels):
    pmesh.UniformRefinement();

# 7. Define the parallel vector finite element spaces representing the mesh
#    deformation x_gf, the velocity v_gf, and the initial configuration,
#    x_ref. Define also the elastic energy density, w_gf, which is in a
#    discontinuous higher-order space. Since x and v are integrated in time
#    as a system, we group them together in block vector vx, on the unique
#    parallel degrees of freedom, with offsets given by array true_offset.

fec = mfem.H1_FECollection(order, dim)
fespace = mfem.ParFiniteElementSpace(pmesh, fec, dim)
glob_size = fespace.GlobalTrueVSize()
if (myid == 0):
    print('Number of velocity/deformation unknowns: '+ str(glob_size))

true_size = fespace.TrueVSize()
true_offset = mfem.intArray(3)
true_offset[0] = 0;
true_offset[1] = true_size;
true_offset[2] = 2*true_size;

vx = mfem.BlockVector(true_offset)

v_gf  = mfem.ParGridFunction(fespace)
x_gf  = mfem.ParGridFunction(fespace)

x_ref = mfem.ParGridFunction(fespace)
pmesh.GetNodes(x_ref)

w_fec = mfem.L2_FECollection(order + 1, dim)
w_fespace = mfem.ParFiniteElementSpace(pmesh, w_fec)
w_gf = mfem.ParGridFunction(w_fespace)

# 8. Set the initial conditions for v_gf, x_gf and vx, and define the
#    boundary conditions on a beam-like mesh (see description above).
class InitialVelocity(mfem.VectorPyCoefficient):
   def EvalValue(self, x):
       dim = len(x)
       s = 0.1/64.
       
       v = np.zeros(len(x))
       v[-1]  = s*x[0]**2*(8.0-x[0])
       v[0]   = -s*x[0]**2
       return v
class InitialDeformation(mfem.VectorPyCoefficient):
   def EvalValue(self, x):
       return x.copy()

velo = InitialVelocity(dim)
v_gf.ProjectCoefficient(velo)
deform =  InitialDeformation(dim)
x_gf.ProjectCoefficient(deform)
   
v_gf.GetTrueDofs(vx.GetBlock(0));
x_gf.GetTrueDofs(vx.GetBlock(1));

ess_bdr = mfem.intArray(fespace.GetMesh().bdr_attributes.Max())
ess_bdr.Assign(0)
ess_bdr[0] = 1; 


# 9. Initialize the hyperelastic operator, the GLVis visualization and print
#    the initial energies.
class ElasticEnergyCoefficient(mfem.PyCoefficient):
    def __init__(self, model, x):
        self.x = x
        self.model = model
        self.J = mfem.DenseMatrix()
        mfem.PyCoefficient.__init__(self)
       
    def Eval(self, T, ip):
        self.model.SetTransformation(T)
        self.x.GetVectorGradient(T, self.J)
        return self.model.EvalW(self.J)/(self.J.Det())
    
class ReducedSystemOperator(mfem.PyOperator):
    def __init__(self, M, S, H, ess_tdof_list):
        mfem.PyOperator.__init__(self, M.ParFESpace().TrueVSize())
        self.M = M
        self.S = S
        self.H = H
        self.Jacobian = None
        h = M.ParFESpace().TrueVSize()
        self.w = mfem.Vector(h)
        self.z = mfem.Vector(h)
        self.dt = 0.0
        self.ess_tdof_list = ess_tdof_list
        
    def SetParameters(self, dt, v, x):
        self.dt = dt
        self.v = v
        self.x = x

    def Mult(self, k, y):
        add_vector(self.v, self.dt, k, self.w)
        add_vector(self.x, self.dt, self.w, self.z)
        self.H.Mult(self.z, y)
        self.M.TrueAddMult(k, y)
        self.S.TrueAddMult(self.w, y)
        y.SetSubVector(self.ess_tdof_list, 0.0);
   
    def GetGradient(self, k):
        localJ = mfem.Add(1.0, self.M.SpMat(), self.dt, self.S.SpMat());
        add_vector(self.v, self.dt, k, self.w)
        add_vector(self.x, self.dt, self.w, self.z)
        localJ.Add(self.dt * self.dt,  self.H.GetLocalGradient(self.z))
        Jacobian = self.M.ParallelAssemble(localJ)
        Jacobian.EliminateRowsCols(self.ess_tdof_list)        
        return Jacobian
    
class HyperelasticOperator(mfem.PyTimeDependentOperator):
    def __init__(self, fespace, ess_bdr, visc, mu, K):
        mfem.PyTimeDependentOperator.__init__(self, 2*fespace.TrueVSize(), 0.0)
       
        rel_tol = 1e-8;
        skip_zero_entries = 0;
        ref_density = 1.0
        
        self.ess_tdof_list = intArray()
        self.z = mfem.Vector(self.Height()//2)
        self.fespace =  fespace
        self.viscosity = visc
        self.newton_solver = mfem.NewtonSolver(fespace.GetComm())
       
        M = mfem.ParBilinearForm(fespace)
        S = mfem.ParBilinearForm(fespace)
        H = mfem.ParNonlinearForm(fespace)
        self.M = M
        self.H = H
        self.S = S
       
        rho = mfem.ConstantCoefficient(ref_density)
        M.AddDomainIntegrator(mfem.VectorMassIntegrator(rho))
        M.Assemble(skip_zero_entries)
        M.EliminateEssentialBC(ess_bdr)
        M.Finalize(skip_zero_entries)
        self.Mmat = M.ParallelAssemble()
        
        fespace.GetEssentialTrueDofs(ess_bdr, self.ess_tdof_list)
        self.Mmat.EliminateRowsCols(self.ess_tdof_list)

        M_solver = mfem.CGSolver(fespace.GetComm())
        M_prec = mfem.HypreSmoother()
        M_solver.iterative_mode = False
        M_solver.SetRelTol(rel_tol)
        M_solver.SetAbsTol(0.0)
        M_solver.SetMaxIter(30)
        M_solver.SetPrintLevel(0)
        M_prec.SetType(mfem.HypreSmoother.Jacobi)
        M_solver.SetPreconditioner(M_prec)
        M_solver.SetOperator(self.Mmat)
       
        self.M_solver = M_solver
        self.M_prec = M_prec

        model = mfem.NeoHookeanModel(mu, K)
        H.AddDomainIntegrator(mfem.HyperelasticNLFIntegrator(model))
        H.SetEssentialTrueDofs(self.ess_tdof_list)
        self.model = model

        visc_coeff = mfem.ConstantCoefficient(visc)
        S.AddDomainIntegrator(mfem.VectorDiffusionIntegrator(visc_coeff))
        S.Assemble(skip_zero_entries)
        S.EliminateEssentialBC(ess_bdr)
        S.Finalize(skip_zero_entries)

        self.reduced_oper = ReducedSystemOperator(M, S, H, self.ess_tdof_list)        

        J_hypreSmoother= mfem.HypreSmoother()
        J_hypreSmoother.SetType(mfem.HypreSmoother.l1Jacobi)
        J_hypreSmoother.SetPositiveDiagonal(True)
        J_prec = J_hypreSmoother;
        
        J_minres = mfem.MINRESSolver(fespace.GetComm())
        J_minres.SetRelTol(rel_tol);
        J_minres.SetAbsTol(0.0);
        J_minres.SetMaxIter(300);
        J_minres.SetPrintLevel(-1);
        J_minres.SetPreconditioner(J_prec)

        self.J_solver = J_minres
        self.J_prec  =  J_prec

        newton_solver = mfem.NewtonSolver(fespace.GetComm())
        newton_solver.iterative_mode = False
        newton_solver.SetSolver(self.J_solver);
        newton_solver.SetOperator(self.reduced_oper)
        newton_solver.SetPrintLevel(1); #print Newton iterations
        newton_solver.SetRelTol(rel_tol);
        newton_solver.SetAbsTol(0.0);
        newton_solver.SetMaxIter(10);
        self.newton_solver = newton_solver
       
    def Mult(self, vx, vx_dt):    
        sc = self.Height()//2
        v = mfem.Vector(vx, 0,  sc)
        x = mfem.Vector(vx, sc,  sc)
        dv_dt = mfem.Vector(dvx_dt, 0, sc)
        dx_dt = mfem.Vector(dvx_dt, sc,  sc)

        self.H.Mult(x, z);
        if (self.viscosity != 0.0):
            S.TrueAddMult(v, z)
            z.SetSubVector(self.ess_tdof_list, 0.0)
        z.Neg()
        self.M_solver.Mult(z, dv_dt);
        dx_dt = v
        
    def ImplicitSolve(self, dt, vx, dvx_dt):
        sc = self.Height()//2
        v = mfem.Vector(vx, 0,  sc)
        x = mfem.Vector(vx, sc,  sc)
        dv_dt = mfem.Vector(dvx_dt, 0, sc)
        dx_dt = mfem.Vector(dvx_dt, sc,  sc)

        # By eliminating kx from the coupled system:
        # kv = -M^{-1}*[H(x + dt*kx) + S*(v + dt*kv)]
        # kx = v + dt*kv
        # we reduce it to a nonlinear equation for kv, represented by the
        # backward_euler_oper. This equation is solved with the newton_solver
        # object (using J_solver and J_prec internally).
        self.reduced_oper.SetParameters(dt, v, x)
        zero = mfem.Vector() # empty vector is interpreted as
                             # zero r.h.s. by NewtonSolver
        self.newton_solver.Mult(zero, dv_dt)
        add_vector(v, dt, dv_dt, dx_dt);

    def ElasticEnergy(self, x):
        return self.H.GetEnergy(x)

    def KineticEnergy(self, v):
        local_energy  = 0.5*self.M.InnerProduct(v, v)
        energy = MPI.COMM_WORLD.allreduce(local_energy, op = MPI.SUM)
        return energy
    
    def GetElasticEnergyDensity(self, x, w):
        w_coeff = ElasticEnergyCoefficient(self.model, x)
        w.ProjectCoefficient(w_coeff)
        
def visualize(out, pmesh, deformed_nodes, field,
              field_name = '', init_vis = False):
   nodes = deformed_nodes;
   owns_nodes = 0

   nodes, owns_nodes = pmesh.SwapNodes(nodes, owns_nodes);

   out.send_text("parallel " + str(num_procs) +  " " + str(myid))            
   out.send_solution(pmesh, field)
    
   nodes, owns_nodes = pmesh.SwapNodes(nodes, owns_nodes);

   if (init_vis):
      out.send_text("window_size 400 400")
      out.send_text( "window_title '"  + field_name)
      if (pmesh.SpaceDimension() == 2):
         out.send_text("view 0 0")
         out.send_text("keys jl")
      out.send_text("keys cm")         # show colorbar and mesh
      out.send_text("autoscale value") # update value-range; keep mesh-extents fixed
      out.send_text("pause")
   out.flush()
       
oper = HyperelasticOperator(fespace, ess_bdr, visc,  mu, K)
if (visualization):
    vis_v = mfem.socketstream("localhost", 19916)
    vis_v.precision(8)
    visualize(vis_v, pmesh, x_gf, v_gf, "Velocity", True)
                    
    MPI.COMM_WORLD.Barrier()
    vis_w = mfem.socketstream("localhost", 19916)
    oper.GetElasticEnergyDensity(x_gf, w_gf)
    vis_w.precision(8)
    visualize(vis_w, pmesh, x_gf, w_gf, "Elastic energy density", True)

ee0 = oper.ElasticEnergy(x_gf)
ke0 = oper.KineticEnergy(v_gf)

if myid == 0:
    print("initial elastic energy (EE) = " + str(ee0)) 
    print("initial kinetic energy (KE) = " + str(ke0)) 
    print("initial   total energy (TE) = " + str(ee0 + ke0))
                    
# 8. Perform time-integration (looping over the time iterations, ti, with a
#    time-step dt).
t = 0. ; ti = 1

oper.SetTime(t);
ode_solver.Init(oper)
last_step = False;

while not last_step:
    dt_real = min(dt, t_final -t)
    t, dt = ode_solver.Step(vx, t, dt_real)

    if (t >= t_final - 1e-8*dt): last_step = True    
    
    if (last_step or (ti % vis_steps) == 0):
        v_gf.Distribute(vx.GetBlock(0))
        x_gf.Distribute(vx.GetBlock(1))
        
        ee = oper.ElasticEnergy(x_gf)
        ke = oper.KineticEnergy(v_gf)
        
        text = ("step " + str(ti) + ", t = " + str(t) + ", EE = " +
                str(ee) +  ", KE = " + str(ke) + 
                ", dTE = " + str((ee+ke)-(ee0+ke0)))

        if myid == 0: print(text)
        if visualization:
            visualize(vis_v, pmesh, x_gf, v_gf)
            oper.GetElasticEnergyDensity(x_gf, w_gf)
            visualize(vis_w, pmesh, x_gf, w_gf)
    
    ti = ti + 1

#
# if i translate c++ line-by-line, ti seems the second swap does not work...
#

smyid = '{:0>6d}'.format(myid)
mesh_name  =  "deformed."+smyid
velo_name   =  "velocity."+smyid
ee_name   =  "elastic_energy."+smyid

nodes = x_gf
owns_nodes = 0
nodes, owns_nodes = pmesh.SwapNodes(nodes, owns_nodes)
pmesh.Print(mesh_name, 8)
pmesh.SwapNodes(nodes, owns_nodes)
    
v_gf.Save(velo_name, 8)
oper.GetElasticEnergyDensity(x_gf, w_gf)
w_gf.Save(ee_name,  8)







MFEM example 10p        This examples solves a time dependent nonlinear elasticity       problem of the form dv/dt = H(x) + S v, dx/dt = v, where H is a       hyperelastic model and S is a viscosity operator of Laplacian       type.     How to run:       mpirun -np 4 python <arguments>     Example of arguments:       ex10p.py -m beam-quad.mesh -s 3 -rs 2 -dt 3       ex10p.py -m beam-tri.mesh -s 3 -rs 2 -dt 3       ex10p.py -m beam-hex.mesh -s 2 -rs 1 -dt 3       ex10p.py -m beam-tet.mesh -s 2 -rs 1 -dt 3       ex10p.py -m beam-quad.mesh -s 14 -rs 2 -dt 0.03 -vs 20       ex10p.py -m beam-hex.mesh -s 14 -rs 1 -dt 0.05 -vs 20     See c++ version in the MFEM library for more detail # 3. Read the serial mesh from the given mesh file on all processors. We can #    handle triangular, quadrilateral, tetrahedral and hexahedral meshes #    with the same code. # 4. Define the ODE solver used for time integration. Several implicit #    singly diagonal implicit Runge-Kutta (SDIRK) methods, as well as #    explicit Runge-Kutta methods are available. # 5. Refine the mesh in serial to increase the resolution. In this example #    we do 'ser_ref_levels' of uniform refinement, where 'ser_ref_levels' is #    a command-line parameter. # 6. Define a parallel mesh by a partitioning of the serial mesh. Refine #    this mesh further in parallel to increase the resolution. Once the #    parallel mesh is defined, the serial mesh can be deleted. # 7. Define the parallel vector finite element spaces representing the mesh #    deformation x_gf, the velocity v_gf, and the initial configuration, #    x_ref. Define also the elastic energy density, w_gf, which is in a #    discontinuous higher-order space. Since x and v are integrated in time #    as a system, we group them together in block vector vx, on the unique #    parallel degrees of freedom, with offsets given by array true_offset. # 8. Set the initial conditions for v_gf, x_gf and vx, and define the #    boundary conditions on a beam-like mesh (see description above). # 9. Initialize the hyperelastic operator, the GLVis visualization and print #    the initial energies. #print Newton iterations # By eliminating kx from the coupled system: # kv = -M^{-1}*[H(x + dt*kx) + S*(v + dt*kv)] # kx = v + dt*kv # we reduce it to a nonlinear equation for kv, represented by the # backward_euler_oper. This equation is solved with the newton_solver # object (using J_solver and J_prec internally). # empty vector is interpreted as # zero r.h.s. by NewtonSolver # show colorbar and mesh # update value-range; keep mesh-extents fixed # 8. Perform time-integration (looping over the time iterations, ti, with a #    time-step dt). # # if i translate c++ line-by-line, ti seems the second swap does not work... #