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23.0 16.0 17.0 14.51 MB

3D unaveraged FEL simulation code

License: Other

Python 15.87% Fortran 51.68% CMake 29.09% Shell 0.77% Makefile 0.03% C++ 0.23% MATLAB 2.10% sed 0.04% Dockerfile 0.18%

physics-simulation fel free-electron-laser particle-accelerator

puffin's People

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gzhoutd fhabib jfmorgan mightylorenzo zengli0910 werin99 qjohn2017 zeugaushh larshuebner-lhnw lostmyhat gharib85 nanshawn lilybstrath mu-yuchen liuzhuoy 1778393206 shrouding

puffin's Issues

Include test for particles slipping out of bounds during puffin start up

Create unit test for 1D particle dataset separate write

Cmake and Bilder Issue

Recently the Bilder updated Cmake to ver 3.7.x which causes me a lot of trouble - I just can't pass through cmake. The message I see in cmake is stating that it can't find fftw3 libs although the paths are defined properly - this is not happening in cmake 3.4.x (bilder downloaded on 2nd December 2016). Same machine+system (Ubuntu mate 16.04) used.

cmake_script.txt

cmake_run.txt

Fix sdds / qseparateFiles bug...

Sdds writing doesn't work when qseparateFiles = .true. ....

Init qSimple as .false.

By not explicitly initializing the simple flag, some compilers may have it set to true when the simple input method is not used, causing problems in initialization.

Steady state simulation

... something similar to the ability in Genesis to swtich on a flag for ITDP (basically run 'steady state' through as much undulator as it takes to saturate).

Maybe this is a capability we should look up.

Can we change back to aw, gamma_r from eta, k_beta?

Not sure about this one. The Puffin paper uses eta, k_beta in the final eqns. But aw, gamma_r are more intuitive to all other FEL physicists.

HDF5 errors when in first parallel structure

HDF5 prints errors when writing field files (collectively or separately). This only happens if writing data before the first resorting of parallel field data. The errors appear in the call to write the front section of the field - and the front section of the field will be empty at this stage. Once the front field size is non-zero, the errors go away.

The errors do not stop the code or affect the output results.

Messages:

HDF5-DIAG: Error detected in HDF5 (1.8.16) MPI-process 0:
#000: ../../../src/H5S.c line 392 in H5Sclose(): not a dataspace
major: Invalid arguments to routine
minor: Inappropriate type

HDF5-DIAG: Error detected in HDF5 (1.8.16) MPI-process 1:
#000: ../../../src/H5S.c line 392 in H5Sclose(): not a dataspace
major: Invalid arguments to routine
minor: Inappropriate type

Fix sparse beam bug

When the beam has 'holes' in it, or large spaces, then the communication buffers for the parallel field are calculated to be at a node of index less than the final node on the process, causing the program to crash.

Integer overflow for iNumberNodes_G when field mesh is large (> 2x10^9 nodes)

Need to change precision of iNumberNodes_G. Currently it means that field files have the wrong metadata written to them.

Ensure that correct output is written for 1D input files

I've really been concentrating on parallel IO for 3D files. We need to make sure the correct output is written for 1D files too.

Allow input in unscaled units

Create unit test for 3D particle dataset collective write

.vs not using derived meshes.

In vizSchema files in Visit, variables told to be plotted on a derived mesh are instead shown on the original mesh.

Update comments in .f90 files to doxygen standards

See formatting of comments for function descriptions in .f90.in file for hdf5 writing.

This will allow us to autogenerate puffin developer documentation.

Also see
https://www.stack.nl/~dimitri/doxygen/manual/docblocks.html#fortranblocks

Determine feature set in demo Puffin release

Seed allocated wrong length

The seed field in z2 is being allocated with the incorrect size, causing crashes in some case. It is unclear why it works at all, actually - it should always crash. Regardless, it worked fine except in a very few cases. This almost invisible bug has now been identified.

1D cases crash with new random beam algorithm...

Add particle tags

Tag each particle with a unique integer, to allow tracking through the FEL process.

Need more example files

Planar case, gaussian pulse case.

Add random beam generation to dist input option.

Create unit test for 1D hdf5 field I/O (Jonny)

Need test 3D file (can be run on 8 cores in a few minutes)

Something with modest mesh, producing modest files, that can be run with updated software to check all is well in 3D as it is in 1D.

qRndEj_G = .true. when using simple gaussian beam causes strange issues

Especially when qScaled = .false. . This may not affect things when using qScaled = .true. - it seems to depend on the size of the tail specified...

Update hdf5_puff.f90.in so that new fields are written (parallel write)

What it says on the tin. Fortran ordering is to be used here.

Reading large (>~2GB) files with MASPin broken

When attempting to read large files with the MASP routine, on the final rank readin I get the error:

forrtl: severe (24): end-of-file during read, unit 132, file /nfs/slac/g/beamphysics/bryantg/FERMI_HGHG_2012/electron_dist.pufin

Again, the error only appears on the final readin step, not at some intermediate location (Corresponding to ~2GB read, for example).

Reducing file size to below ~2GB by using fewer particles solves the problem, so I suspect it is some type of weird memory issue (related to 32bit?)

The following python scripts produce input files which give the error (note: with 4E7 particles, the python script to generate the distribution takes some time).

MASPerror.tar.gz

Create unit test for 3D hdf5 field I/O (Jonny)

Update README text (here, then port to release branch)

Ensure hdf5_puff.f90.in has correct algorithms to write slice emittance integrated output

We could postprocess this, or calculate potentially on a more frequent basis along with the other integrated quantities. Ultimately slice emittance (and potentially other quantities TBD) are probably going to want to be available both ways.

More sophisticated active field layouts.

The field layouts could be constructed in alternative ways. For example, one could construct the layout so that the number of macroparticles was equal on each process. This would even out the computational load more, but it would also make the MEMORY load uneven.

Add focusing quadrupoles to Puffin

This should be relatively simple to do, given the undulator-chicane lattice is already present. We just need to work out the transforms in the scaled notation, and modify the input file format.

3D undulator

Test whether the 3D undulator code simulates the 'vanilla' Puffin undulator properly.

Update hdf5_puff.f90.in so that electrons are written (parallel write)

Create unit test for 1D integrated quantity hdf5 field I/O

Send notes on chunking (or link to hdf5 group's notes)

Read electrons output files as initial macroparticle distribution.

Provide doxygen infrastructure to turn comments into developer documentation

Refer to
https://www.stack.nl/~dimitri/doxygen/manual/starting.html
https://www.stack.nl/~dimitri/doxygen/manual/doxygen_usage.html
https://www.stack.nl/~dimitri/doxygen/manual/docblocks.html#fortranblocks

So - probably use doxywizard to create a conf file, then test it out! But need a bit more content in the .f90 files first!

Zero local electrons bug

If the beam has large spaces in it, or holes, in the temporal z2 frame, then the parallel field algorithm will crash. Need to set some operations to work only when the number of electrons on the local process is > 0.

Add Hammersley or other low-discrepency sequences to the 'random' beam generation

Flag for writing data at ends of undulator modules

Currently, data is written at the end of every module, which can be quite a lot of data for lattices with many separate components. An option to disable this functionality, (and probably then just write when the global # of steps hits the counter) would be useful for such circumstances.

Determine featureset of final EPSRC SFTF Puffin release

Create unit test for 3D particle dataset separate write

HDF5 errors (warnings) need removal

Looks like this:

HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 0:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 1:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 31:
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 2:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 33:
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 16:
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 3:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 42HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 28:
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 21:
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 4:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 45:
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 24:
HDF5-DIAG: Error detected in HDF5 (1.8.13) HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 5:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
MPI-process 22:
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 6:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 46:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 7:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 8:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 26:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 13:
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 9:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 41:
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 25:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 10:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 11:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 27:
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 17:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 43:
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 30:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 39:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 23:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
MPI-process 20:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 36:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 32:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 19 major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 29:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 14:
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 38:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 34:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 37:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 35:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 44:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 15:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 47:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 12:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 18:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 40:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 11:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 3:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 10:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 36:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 42:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 15:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 6:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 9:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 5:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 7:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 43:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 1:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 2:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 8:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 4:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 13:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 23:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 20:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 46:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 24:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 19:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 41:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 44:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 34:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 18:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 38:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 21:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 39:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 47:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 16:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 37:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 40:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 45:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 22:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 12:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 17:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 14:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 26:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 27:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 25:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 29:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 28:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 35:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 33:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 30:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 31:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 32:
  #000: /gpfs/stfc/local/HCP084/bwm06/pxt69-bwm06/FXFEL_BUILD/builddir-intel/hdf5-1.8.13/src/H5S.c line 391 in H5Sclose(): not a data
space
    major: Invalid arguments to routine
    minor: Inappropriate type

Python script for constructing simple input still produces old input files

New form of input files in dev branch, due to 3D undulator updates. Need to update example inputs.

Update hdf5_puff.f90.in so that new fields are written (separate files for ranks)

.vs plotting labels don't work in visit for curve plots

When using Visit to visualize the data from Puffin, none of the line plots label
the axes with the labels specified by Puffin.

Using pyTables to examine any of the integrated files, e.g. after opening one
of them as 'h5file' and doing

h5file.root.power._v_attrs

it shows the contents as

/power._v_attrs (AttributeSet), 23 attributes:
   [iChic_cr := 1,
    iCsteps := 210,
    iDrift_cr := 1,
    iL := 1,
    iModulation_cr := 1,
    iQuad_cr := 1,
    iUnd_cr := 1,
    istep := 210,
    time := 0.87964596748352286,
    vsAxisLabels := 'z2, Power (Scaled)',
    vsCentering := 'nodal',
    vsIndexOrder := 'compMinorF',
    vsLabels := 'power',
    vsLimits := 'globalLimitsSI',
    vsMesh := 'intFieldMeshSc',
    vsTimeGroup := 'time',
    vsType := 'variable',
    zInter := 0.28000000000000075,
    zLocal := 0.28000000000000075,
    zTotal := 0.28000000000000075,
    zbarInter := 0.87964596748352286,
    zbarLocal := 0.87964596748352286,
    zbarTotal := 0.87964596748352286]

This shows the mesh to draw the line on as 'intFieldMeshSc'. Looking at this mesh in the
file, so doing

h5file.root.intFieldMeshSc._v_attrs

we get

/intFieldMeshSc._v_attrs (AttributeSet), 9 attributes:
   [vsAxisLabels := 'z2,scaled parameter',
    vsCentering := 'nodal',
    vsIndexOrder := 'compMajorF',
    vsKind := 'uniform',
    vsLowerBounds := 0.0,
    vsNumCells := 1657,
    vsStartCell := 0,
    vsType := 'mesh',
    vsUpperBounds := 13.005309677124023]

which contains labels for the .vs mesh. However, the plot which is shown by Visit has labels "X-Axis" and "Y-Axis."

The above example is for the power plots, but this happens for ALL the integrated data. Furthermore, there seems to be no documentation for labelling plots using vizSchema online.

FFTW 3 upgrade

Now the weakest link, as far as speed goes, is the FT's, by far. We are currently using FFTW v2.1.5, since this was previously the latest version supporting MPI. The more recent versions have now returned the MPI functionality, but the interfaces are different. Since v2.1.5 was released in 1999, it may be that v3.x is faster. It may be worth upgrading. FFTW v3.x is also usually more readily available.

Create unit test for 1D particle dataset collective write

FFT's for large mesh (>10^9 nodes) are very slow...

...either use less diffraction steps, less nodes, or both, for now.

In the longer term, may need to switch to something like finite difference method. Considering 3 options:

Fully finite difference
1D Fourier transforms in z2, and finite difference in the transverse plane
Finite difference method, ignoring frequency dependence of diffraction - just use dispersion coefficient of 'central' frequency.
Solve using 2D Fourier transforms for each slice, losing frequency dependence. Just assume dispersion coefficient of 'central' frequency.
is best. 4) is easiest.

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