Output
Minima hopping produces several output files.
Depending on the parameters set the output can vary.
This section is explaining how the output of Minima Hopping is structured and which output files are generated.
Minima Hopping is generating two output folders one is called minima and the other one output.
Minima folder
In the minima folder the lowest minima are output ordered from lowest to highest energy.
The number of how many lowest minima are written is given by the parameter output_n_lowest_minima.
In the case of periodic simulations the files are in .ascii format in the non-periodic case the files are written in the .xyz format.
The same folder also contains tow more files, namely all_minima.extxyz and all_minima_no_duplicates.extxyz.
As the filenames indicate contains former all minima found by Minima Hopping and latter contains only all unique minima.
Output folder
Standard output
The minimal output in the output folder contains the following files:
Filename |
Description |
|---|---|
accepted_minima.extxyz |
Contains all accepted minima |
all_minima.extxyz |
Contains all minima |
all_minima_no_duplicates.extxyz |
Contains all unique minima (accepted/rejected) |
history.dat |
Information summary of all minima found |
minimahopping.log |
Log file of the current minimahopping run |
Caution
Be aware that in the case of a restart the minimahopping.log file is overwritten.
If you require any information contained in this file copy it to a different folder before the restart.
The file is not needed for performing the restart.
If the parameter verbose_output is set to True each step of the MD and the geometry optimization is written.
Hence, the following files are written:
Filename |
Description |
|---|---|
MD_log.dat |
Contains information about the current MD run e.g. energy conservation |
MD.extxyz |
Contains the structure of each MD step |
geometry_optimization_log |
Contains information about each geometry optimization step |
geometry_optimization_trajectory.extxyz |
Contains the structure of each geometry optimization step |
Caution
Be aware that in each MD-geometry optimization cycle these files are overwritten in order to keep the output minimal.
If it is desired to collect the structures generated during each MD e.g. for the construction of machine learning potentials the parameter collect_md_data can be set to true.
This generates a file named MD_collection.extxyz where the structure is added if two structures in the MD differ on average by 0.2 Angstroem.
This file is not overwritten during a restart and can get very large during a Minima Hopping run.
The output folder also contains a restart subfolder containing all the restart files required for restarting Minima Hopping.
It contains the params.json file where all the current parameters are stored and the poscur.extxyz file which is the last accepted minimum.
In the minima.pickle.shelve.dat the database is stored including also fingerprints as well as the structures.
If the parameter write_graph_output is set to True a trajectory.dat and graph.dat file is written containing information about the paths the algorithm is taking.
Caution
Changing files in the restart folder can lead to corrupted restarts or even makes restarts of the Minima Hopping impossible.
Therefore, no changes in the files of the restart files should be made.
MPI parallelization
In the case of MPI parallelized Minima Hopping runs the output directory contains subdirectories for each worker and a master directory.
The same files as described above are written, however, for each worker seperately.
The graph output is written in the restart subdirectory in the master directory.
Furthermore contains the master directory also a minimahopping.log file where the communication between the workers is written.
This information can be very helpful if a MPI-parallelized Minima Hopping run is crashing and detecting the worker which is crashed.