View source for Manual:Updating to a new version

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

==== Octopus 8 ====

===== Variables =====

* The {{variable|Species|System}} block can now take a {{emph|set}} option to choose which pseudopotential set to use.
* The default for {{variable|XCFunctional|Hamiltonian}} is now taken, when possible, from the pseudopotentials.

==== Octopus 7 ====

===== 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 {{code|1=Spacing = 0.25*angstrom}}.
* Now by default the code assumes XYZ files to be in Angstrom. This can be changed by using the {{variable|UnitsXYZFiles|Execution}} variable.

==== Octopus 6 ====

===== Installation =====

* A compiler supporting Fortran 2003 iso_c_binding is now required.
* The executable is always called {{file|octopus}}, no longer {{file|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 {{variable|Species|System}} block and the names of the species options have been revised.
* The variable OutputHow has been renamed to {{variable|OutputFormat|Output}}.
* The variable ParallelizationStrategy and ParallelizationGroupRanks have been replaced with {{variable|ParDomains|Execution}}, {{variable|ParStates|Execution}}, {{variable|ParKPoints|Execution}}, and {{variable|ParOther|Execution}}.

===== Utilities =====

The {{file|oct-rotatory_strength}} utility has been removed. This utility is replaced by a new {{variable|PropagationSpectrumType|Utilities}} in {{file|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 {{file|restart/casida}}, and a file {{file|kernel}} or {{file|kernel_triplet}}. One then needs to create the directory and rename the files.
* The format of the {{file|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 {{emph|fft_alpha}} was removed from the {{file|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.

The datasets feature was removed. The input file of a calculation using datasets needs to be split into several independent input files.

==== 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 =====

* TDEvolutionMethod is now called {{variable|TDPropagator|Time-Dependent}}.

===== Utilities =====

* {{file|oct-cross_section}} was renamed to {{file|oct-propagation_spectrum}}.
* {{file|oct-broad}} was renamed to {{file|oct-casida_spectrum}}.
* The format for {{file|oct-help}} has changed. Now {{file|-s}} is used instead of {{file|search}}, {{file|-p}} instead of {{file|show}}, and  {{file|-l}} instead of {{file|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.

* {{variable|Units|Execution}}, {{variable|UnitsInput|Execution}} and {{variable|UnitsOutput|Execution}} now take a named option as argument instead of a string. So

 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 {{variable|XCFunctional|Hamiltonian}}, for example

 XFunctional = lda_x
 CFunctional = lda_c_vwn

must be replaced with

 XCFunctional = lda_x + lda_c_vwn

* TDLasers was replaced by {{variable|TDExternalFields|Time-Dependent}}.
* Some options for {{variable|CalculationMode|Calculation_Modes}} were renamed.

===== Output directories =====

Some directories in {{octopus}} output were renamed, restart files now are stored under {{file|restart/}} instead of {{file|tmp/}}. Files previously found under {{file|status/}} are now located in {{file|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 {{file|tmp/}} directory to {{file|restart/}} and remove the {{file|restart_}} prefix from its subdirectories, for example {{file|tmp/restart_gs/}} now should be called {{file|restart/gs/}}.

Now you can run {{octopus}} 3.0 and it will find your restart information.


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