Manual:Updating to a new version

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This page lists the issues that may appear when updating to a new version of Octopus and how to solve them.

Octopus 7.0

Variables
  • The UnitsInput and Units variables have been removed. Input file values are now always in atomic units, unless explicitly stated otherwise in the corresponding variable description. A few constants are available to help using eV/Angstrom units in the input file, such that one can write Spacing = 0.25*angstrom.
  • Now by default the code assumes XYZ files to be in Angstrom. This can be changed by using the UnitsXYZFiles variable.

Octopus 6.0

Installation
  • A compiler supporting Fortran 2003 iso_c_binding is now required.
  • The executable is always called octopus, no longer octopus_mpi when compiled in parallel.
  • This version supports libxc 3.0.0. Although it is still possible to use libxc 2.0.0 or any of the 2.x versions, updating to libxc 3.0.0 is highly recommended.
Variables
  • There is a new format for the Species block and the names of the species options have been revised.
  • The variable OutputHow has been renamed to OutputFormat.
  • The variable ParallelizationStrategy and ParallelizationGroupRanks have been replaced with ParDomains, ParStates, ParKPoints, and ParOther.
Utilities

The oct-rotatory_strength utility has been removed. This utility is replaced by a new PropagationSpectrumType in oct-propagation_spectrum.

Octopus 5.0

Restart files

This version breaks the backwards compatibility of the restart files. Nevertheless, it is not too difficult to update the restart files generated with a previous version. Here is a summary of the changes and how to update the files:

  • Casida restart data now goes to a directory restart/casida, and a file kernel or kernel_triplet. One then needs to create the directory and rename the files.
  • The format of the occs file changed with the addition of an extra field for the imaginary part of the eigenvalues. To update the file one needs to add a column of zeros by hand after the column of eigenvalues.
  • The line starting with fft_alpha was removed from the mesh file.

Note that the mesh partition restart is also not compatible any more. In this case the partition needs to be recalculated, which is usually not a problem.

Variables

Some variables changed name or changed format. If an obsolete variable is found, Octopus will stop and will tell you the variable that replaces it.

Octopus 4.1

Installation

This version requires libxc 2.0.0 or higher, so it might be necessary to update libxc before installing Octopus.

Restart files

Casida restart file is incompatible with that generated by version 4.0. The new format avoids problems with restarting with a different number of states.

Octopus 4.0

Installation
  • Libxc is now an independent library. To compile Octopus 4.0.0 you will have to compile libxc 1.1.0 first. These are the short instructions to compile it (we assume that libxc will be installed in $DIR, this can be the same directory where Octopus is going to be installed):
tar -xvzf libxc-1.1.0.tar.gz
cd libxc-1.1.0 
./configure --prefix=$DIR
make
make install

Now, when configuring Octopus pass the option --with-libxc-prefix=$DIR.

  • The configure option for the location of netcdf and etsf_io are --with-netcdf-prefix and --with-etsf-io-prefix.
Variables
Utilities
  • oct-cross_section was renamed to oct-propagation_spectrum.
  • oct-broad was renamed to oct-casida_spectrum.
  • The format for oct-help has changed. Now -s is used instead of search, -p instead of show, and -l instead of list.

Octopus 3.0

Input variables

Some variables changed name or changed format. If an obsolete variable is found, Octopus will stop and will tell you the variable that replaces it.

Units = "eVA"

should be replaced by

Units = eV_Angstrom

The code will stop if the old format is encountered.

  • XFunctional and CFunctional were replaced by XCFunctional, for example
XFunctional = lda_x
CFunctional = lda_c_vwn

must be replaced with

XCFunctional = lda_x + lda_c_vwn
Output directories

Some directories in Octopus output were renamed, restart files now are stored under restart/ instead of tmp/. Files previously found under status/ are now located in exec/.

Restart file format

Octopus writes restart files in a binary format, this format has been updated and improved. As a result Octopus is no longer able to restart automatically the calculation of a run performed with older versions.

Recovering old restart files

If you really need to recover your old restart files, first you have to generate NetCDF restart files with your old version of Octopus. Then you will have to rename the tmp/ directory to restart/ and remove the restart_ prefix from its subdirectories, for example tmp/restart_gs/ now should be called restart/gs/.

Now you can run Octopus 3.0 and it will find your restart information.



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