April 2020 - firedrake - imperial.ac.uk

fd.derivative
by Onno Bokhove 14 Apr '20

14 Apr '20

Dear Firedrakers, When taking a Firedrake (functional/form) derivative, say the derivative of the functional int (du/dx)^2 dx (plus some bc's) is the outcome the functional derivative (i) with or (ii) without integration by parts? I.e. is it: (ii) 2 int du/dx dv/dx dx or (i) -2 int d^2u/d x^2 v dx, modulo bc's, and with v = delta u? https://www.firedrakeproject.org/firedrake.html#firedrake.ufl_expr.derivati… (I am trying to understand why the below would work, and it does, with CG1 for X, or in the above with CG1 for v and u, which only can work when no ibp is done. ) Kind regards, Onno PS: # Kinematics # Right Cauchy-Green tensor if self.nonlin: d = self.X.geometric_dimension() I = fd.Identity(d) # Identity tensor F = I + fd.grad(self.X) # Deformation gradient C = F.T*F E = (C-I)/2. # Green-Lagrangian strain # E = 1./2.*( fd.grad(self.X).T + fd.grad(self.X) + fd.grad(self.X).T * fd.grad(self.X) ) # alternative equivalent definition else: E = 1./2.*( fd.grad(self.X).T + fd.grad(self.X) ) # linear strain self.W = (self.lam/2.)*(fd.tr(E))**2 + self.mu*fd.tr( E*E ) # f = fd.Constant((0, 0, -self.g)) # body force / rho # T = self.surface_force() # Total potential energy Pi = self.W * fd.dx # Compute first variation of Pi (directional derivative about X in the direction of v) F_expr = fd.derivative(Pi, self.X, self.v)

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Re: [firedrake] BC's - 1D Hermite elements
by Lawrence Mitchell 07 Apr '20

07 Apr '20

[Adding firedrake back in to cc] > On 7 Apr 2020, at 22:25, Roberto Federico Ausas <rfausas(a)icmc.usp.br> wrote: > > File "/home/usuario/Codes/newfire/firedrake/src/firedrake/firedrake/functionspacedata.py", line 514, in lgmap > nodes.append(tmp + i) > TypeError: can only concatenate list (not "int") to list This is the proximate error. Your definition from Patrick has: class FixHermiteDerivativeValue(DirichletBC): @utils.cached_property def nodes(self): if V.mesh().mpi_comm().size > 1: raise NotImplementedError return [1] # the derivative component of the left endpoint I think it might work if you use from pyop2.datatypes import IntType and then return numpy.asarray([1], dtype=IntType) Thanks, Lawrence

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Re: [firedrake] BC's - 1D Hermite elements
by Roberto Federico Ausas 07 Apr '20

07 Apr '20

Dear Patrick, Thanks for your help! It essentially worked, however, for some reason the nonlinear solver does not allow me to use direct methods as the inner solver, i.e., ('ksp_type': 'preonly', 'pc_type': 'lu', 'pc_factor_mat_solver_type': 'mumps') produces some sort of error, possibly related to local_to_global_map, I do not understand the error actually. Thanks anyway! On Tue, Apr 7, 2020 at 8:00 AM <firedrake-request(a)imperial.ac.uk> wrote: > Send firedrake mailing list submissions to > firedrake(a)imperial.ac.uk > > To subscribe or unsubscribe via the World Wide Web, visit > https://mailman.ic.ac.uk/mailman/listinfo/firedrake > or, via email, send a message with subject or body 'help' to > firedrake-request(a)imperial.ac.uk > > You can reach the person managing the list at > firedrake-owner(a)imperial.ac.uk > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of firedrake digest..." > > > Today's Topics: > > 1. BC's - 1D Hermite elements (Roberto Federico Ausas) > 2. Re: BC's - 1D Hermite elements (Patrick Farrell) > 3. Problem installing Firedrake (Smail Merabet) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 6 Apr 2020 16:49:25 -0300 > From: Roberto Federico Ausas <rfausas(a)icmc.usp.br> > To: firedrake(a)imperial.ac.uk > Subject: [firedrake] BC's - 1D Hermite elements > Message-ID: > <CAH6Ec4nWnhmM=HeMtd8uU9VQ9NF0_hVdorMFdK= > p8Xc3Gus4xQ(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hello, > > My name is Roberto. I'm currently a professor in the Applied Mathematics > Department of Univ. of S?o Paulo at S?o Carlos. > > I'm working on some fluid-structure interaction problems in which the solid > will be modeled as a 1D beam. Our reference integration domain will be the > interval [0,L]. > > We are planning to use firedrake and Hermite elements. The problem is > nonlinear. > > I already have a working example. Values degrees of freedom are easy to > impose by using DirichletBC(), however I'm not figuring out how to enforce > derivatives degrees of freedom as boundary conditions (let say at x=0), > which I need for a clamped beam. > > Any help or trick would be appreciated > Regards > > -- > Roberto F. Ausas > Instituto de Ci?ncias Matem?ticas e de Computa??o - ICMC/USP > S?o Carlos, SP - Brasil > *http://www.lmacc.icmc.usp.br/~ausas* <http://www.lmacc.icmc.usp.br/~ausas > > >

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Problem installing Firedrake
by Smail Merabet 07 Apr '20

07 Apr '20

Hi firedrake users, I have a problem with the installation of firedrake, I work on Mojave 10.14.6 I did the following steps: url -O https://raw.githubusercontent.com/firedrakeproject/firedrake/master/scripts… unset PYTHONPATH unset PETSC_DIR unset PETSC_ARCH; python3 firedrake-install the installation see to be done, I attached the log file to this email, but when I excuse any script I get the following error message (firedrake) (base) Merabets-MacBook-Pro:examples merabet$ python3 fi.py Traceback (most recent call last): File "/Users/merabet/firedrake/src/h5py/h5py/__init__.py", line 26, in <module> from . import _errors ImportError: dlopen(/Users/merabet/firedrake/src/h5py/h5py/_ errors.cpython-37m-darwin.so, 2): Library not loaded: @rpath/libhdf5.103.dylib Referenced from: /Users/merabet/firedrake/src/h5py/h5py/_ errors.cpython-37m-darwin.so Reason: image not found During handling of the above exception, another exception occurred: Traceback (most recent call last): File "fi.py", line 1, in <module> import firedrake File "/Users/merabet/firedrake/src/firedrake/firedrake/__init__.py", line 53, in <module> from firedrake.checkpointing import * File "/Users/merabet/firedrake/src/firedrake/firedrake/checkpointing.py", line 3, in <module> from firedrake.cython import hdf5interface as h5i File "firedrake/cython/hdf5interface.pyx", line 2, in init firedrake.cython.hdf5interface File "/Users/merabet/firedrake/src/h5py/h5py/__init__.py", line 30, in <module> raise ImportError("You cannot import h5py from inside the install directory.\nChange to another directory first.") ImportError: You cannot import h5py from inside the install directory. Change to another directory first. (firedrake) (base) Merabets-MacBook-Pro:examples merabet$ Please, could any one help me to solve this problem ? Best regards

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BC's - 1D Hermite elements
by Roberto Federico Ausas 06 Apr '20

06 Apr '20

Hello, My name is Roberto. I'm currently a professor in the Applied Mathematics Department of Univ. of São Paulo at São Carlos. I'm working on some fluid-structure interaction problems in which the solid will be modeled as a 1D beam. Our reference integration domain will be the interval [0,L]. We are planning to use firedrake and Hermite elements. The problem is nonlinear. I already have a working example. Values degrees of freedom are easy to impose by using DirichletBC(), however I'm not figuring out how to enforce derivatives degrees of freedom as boundary conditions (let say at x=0), which I need for a clamped beam. Any help or trick would be appreciated Regards -- Roberto F. Ausas Instituto de Ciências Matemáticas e de Computação - ICMC/USP São Carlos, SP - Brasil *http://www.lmacc.icmc.usp.br/~ausas* <http://www.lmacc.icmc.usp.br/~ausas>

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Help me
by Emmanuel Yarleque Medina 05 Apr '20

05 Apr '20

Hi users, I have a problem installing Firedrake with Petsc. Initially install using the following steps: curl -O https://raw.githubusercontent.com/firedrakeproject/firedrake/master/scripts… unset PYTHONPATH; unset PETSC_DIR; unset PETSC_ARCH; python3 firedrake-install and it works on installation, only when testing my code with the discontinuous Galerkin hybrid method (HDG) it gave the following error: (firedrake) hpc@hpc:~/Downloads/Exemplos_Firedrake/HDG/poroso/MWE/SDHM$ python3 sdhm_monolithic.py Traceback (most recent call last): File "sdhm_monolithic.py", line 1, in <module> from firedrake import * File "/home/hpc/firedrake/src/firedrake/firedrake/__init__.py", line 8, in <module> raise ImportError("PETSC_DIR is set, but you did not install with --honour-petsc-dir.\n" ImportError: PETSC_DIR is set, but you did not install with --honour-petsc-dir. Please unset PETSC_DIR (and PETSC_ARCH) before using Firedrake. try installing with python3 firedrake-install --honor-petsc-dir, but I have the following error: hpc @ hpc: ~ $ python3 firedrake-install --honor-petsc-dir Running firedrake-install --honor-petsc-dir The --honor-petsc-dir is set, but PETSC_DIR environment variable is not defined. If you have compiled PETSc manually, set PETSC_DIR (and optionally PETSC_ARCH) variables to point to the build directory. could you help me on how to solve that problem, please. Best regards, Emmanuel Y. Medina Ph.D Student in UFJF-Brazil

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sprint to merge complex branch
by Sagiyama, Koki 01 Apr '20

01 Apr '20

Dear all, As we are ready to merge the `complex` branch to master except that we have yet to: * ensure type safety in each part of Firedrake, * reduce the size of tests to make complex tests run in a reasonable amount of time, we would like to run a sprint to have these efficiently done, each participant working on their favorite parts of Firedrake. We plan to have this sprint in the afternoons (UK time, GMT+1) of the week of 20th April on Webex. We will also be hosting a pre-sprint Webex meeting on Friday 17th April at 16:00 (UK time, GMT+1), to discuss the workflow. (We will provide the links to the sprint and the pre-sprint meeting on Slack http://firedrakeproject.slack.com beforehand.) I hope that many of you could attend and help us. If you could, please add your name to the list of participants on the github wiki page for this sprint: https://github.com/firedrakeproject/firedrake/wiki/MergeComplexSprint Any updates regarding this sprint will also be posted on this page. Regards, Koki

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