1.4.1. USPEX Changelog

v.1 — Evolutionary algorithm without local optimization. Real-space representation, interface with VASP. Experimental version. October 2004.

v.2 — CMA-ES implementation (CMA-ES is a powerful global optimization method developed by N. Hansen). Experimental version. January 2005.

v.3 — Evolutionary algorithm with local optimization.

v.3.1 — Working versions, sequential. Major basic developments.

3.1.4-3.1.5 — First production version. Based largely on heredity with slice-shifting and with minimum-parent contribution (hard-coded to be 0.25). May 2005.

3.1.8 — Adaptive \(k\)-point grids. 15/10/2005.

3.1.11 — Restart from arbitrary generation. Experimental version. 04/11/2005.

3.1.12 — Production version based on v.3.1.11, variable slice-shift mutation. 11/11/2005.

3.1.13 — Adaptive scaling volume. 29/11/2005.

3.1.14 — Basic seed technique. 29/11/2005 (debugged 6/12/2005).

v.3.2 — Massively parallel version.

v.4 — Unified parallel/sequential version.

4.1.1 — Lattice mutation. 20/12/2005 (debugged 10/01/2006).

4.2.1 — Interfaced with SIESTA. Initial population size allowed to differ from the running population size. 24/01/2006 (debugged 20/04/2006).

4.2.3 — Relaxation of best structures made optional. Version with fully debugged parallelism. 25/04/2006.

4.4.1 — Interfaced with GULP. 08/05/2006.

v.5 — Completely rewritten and debugged version, clear modular structure of the code.

5.1.1 — Atom-specific permutation, code interoperability, on-the-fly reading of parameters from . 20/12/2006.

5.2.1 — SIESTA-interface for Z-matrix, rotational mutation operator. 01/03/2007.

v.6 — Production version.

6.1.3 — To efficiently fulfill hard constraints for large systems, an optimizer was implemented within USPEX. 07/06/2007.

6.2 — Development version.

6.3.1–6.3.2 — Introduced angular constraints for cell diagonals. Completely rewritten remote submission. Improved input format. Further extended standard tests. 07/12/2007.

6.3.3 — X-com grid interface (with participation of S. Tikhonov and S. Sobolev). 05/03/2008.

6.4.1 — Fingerprint functions for niching. 07/04/2008.

6.4.4 — Space group recognition. Fast fingerprints (from tables). 05/05/2008.

6.5.1 — Split-cell method for large systems. Easy remote submission. Variable number of best structures (clustering). 16/07/2008.

6.6.1 — A very robust version — improved fingerprint and split-cell implementations. 13/08/2008.

6.6.3 — Heredity with multiple parents implemented. 01/10/2008.

6.6.4 — Added a threshold for parents participating in heredity (niching). 03/10/2008.

6.6.6 — First implementation of multicomponent fingerprints. 04/12/2008.

6.6.7, 6.7.1 and 6.7.2 — Implemented quasi-entropy to measure the diversity of the population. 10/12/2008.

v.7 — Production version, written to include variable composition.

7.1.1–7.1.7 — Series of improved versions. Version 7.1.7 has been distributed to \(\sim\)200 users. Variable composition partly coded, most known bugs fixed, improved tricks based on energy landscapes. Improved cell splitting, implemented pseudo-subcells. Implemented multicomponent fingerprints (much more sensitive to the structure than one-component fingerprints). 28/04/2009 (version finalized 28/05/2009).

7.2.5 — First fully functional version of the variable-composition method. Introduced transmutation operator and compositional entropy. 06/09/2009.

7.2.7 — Thoroughly debugged, improved restart capabilities, improved seeding, introduced perturbations within structure relaxation. 25/09/2009, further improved in versions 7.2.8/9.

7.3.0 — Full fingerprint support in the variable-composition code, including niching. “Fair” algorithm for producing the first generation of compositions. 22/10/2009.

7.4.1 — Introduced coordinate mutation based on local order ¹⁹. Heredity and transmutation are also biased by local order. Introduced computation of the hardness and new types of optimization by hardness and density. 04/01/2010.

7.4.2 — Implementation of multiple-parents heredity biased by local order. 15/01/2010.

7.4.3 — Implementation of new types of optimization (to maximize structural order and diversity of the population). Implemented antiseeds, eliminated parameters , . 24/01/2010.

v.8 — Production version, written to include new types of optimization.

8.1.1–8.2.8 — Development versions. Local order and coordinate mutation operator. Softmutation operator. Calculation and optimization of the hardness. Optimization of the dielectric susceptibility. Prediction of the structure of nanoparticles and surfaces. Implementation of point groups. Greatly improved overall performance. Option to perform PSO simulations (not recommended for applications, due to PSO’s inferior efficiency — so use only for testing purposes). Parameter transformed into a matrix and used for building nanoparticles. 22/09/2010.

8.3.1 — Optimization of dielectric constants, cleaned-up input. 08/10/2010.

8.3.2 — For clusters, introduced a check on connectivity (extremely useful), =2 option improved, as well as mechanism for producing purely softmutated generations. Improved fingerprints for clusters. Interface to Quantum Espresso and CP2K codes. 11/10/2010.

8.4 — Improved antiseed functionalities and several improvements for nanoparticles. Development branches for surface reconstructions, pseudo-metadynamics, molecular crystals.

8.5.0 — Initialization of the first random generation using the space group code of H. Stokes added. New formulation of metadynamics implemented and finalized, for now in a separate code. Several debugs for varcomp, antiseeds, nanoparticles, computation of hardness. 18/03/2011.

8.5.1 — Space group initialization implemented for cases of fixed unit cell, variable composition, and subcells. 20/04/2011.

8.6.0 — Added space group determination program from H. Stokes. Merger with the updated code for molecular crystals (including space group initialization). Fixed a bug for SIESTA (thanks to D. Skachkov). 06/05/2011.

8.6.1–8.7.2 — Improved symmetric initialization for the case of a fixed cell. Implemented optimization of dielectric constants (using GULP and VASP), band gap (using VASP), and DOS at the Fermi level (VASP). Graphical output enabled. Improved softmutation (by using better criteria for mode and directional degeneracies) and heredity (by using energy-order correlation coefficient and cosine formula for the number of trial slabs) operators. Most variables now have default values, which enables the use of very short input files. Shortened and improved the format of log-files. 13/11/2011.

8.7.5 — Graphical output now includes many extra figures. Added utility to extract all structures close to convex hull for easier post-processing. 21/03/2012.

v.9 — Production version, made more user-friendly and written to include new types of functionality and to set the new standard in the field.

9.0.0 — Evolutionary metadynamics and VCNEB codes added to USPEX package, added tensor version of metadynamics, added additional figures and post-processing tools, cleaned the code output. A few parameters removed from the input. Improved softmutation. April 2012.

9.1.0 — Release version. Cleaned up, documented. The user community is >800 people. Released 28/05/2012.

9.2.0 — Working GEM. Constant development of the GEM code. Space group determination tolerance is now an input parameter. Improved default for number of permutations. July-August 2012.

9.2.1–9.2.3 — Improved GEM, more diverse populations and supercell sizes, improved mode selection. September-October 2012.

9.2.4–9.2.6 — (9.2.4 is a release version). Intelligent defaults for most input parameters. Improved symmetric initialization for clusters. Order-enhanced heredity for nanoparticles. New parameter to tune the tolerance for the space group determination. New property (quasientropy) can be optimized. Fully integrated VCNEB code. November-December 2012.

9.2.7. — Release version. Enabled optimization of order for alloys, without structure relaxation (for easy creation of quasirandom structures, based on the more general definition than the so-called “special quasi-random structures”). Symmetry generation was improved (particularly important for fixed-cell calculations). For fixed-cell calculations, one can now specify the cell parameters, not only in the form of a 3 \(\times\) 3 matrix, but also as a row of six values (three lengths in Angstroms and three angles in degrees). For the maximum number of permutation swaps (parameter ), we have introduced an intelligent default. Added new tests, and cleaned and reran the old ones. Added interface to CASTEP (thanks to Z. Raza, X. Dong and AL). User community 1160 people. 30/12/2012.

9.3.0–9.3.3 — Fixed a bug in generation of random symmetric structures (this bug appeared in 9.2.7). Significantly simplified input and output. Created file with the most important information. Enabled split-cell trick for molecular crystals. Improved variable-composition calculations by allowing one to specify initial compositions. Added interface to CASTEP and LAMMPS. Added new test cases. 20/03/2013.

9.3.4 — Release version, cleaned up. 25/03/2013.

9.3.5 — Added code for prediction of 2D-crystals. 19/04/2013.

9.3.6 — Incorporated plane groups for 2D-crystals. 29/04/2013.

9.3.8 — Incorporated plane groups for 1D-polymer crystals, improved variables of stoichiometry for surfaces. 19/06/2013.

9.3.9 — Released version. Significantly improved version, improved user-friendliness, new functionalities (2D-crystals, GEM) made more robust, improvements in the variable-composition algorithm (and enabled support for single-block calculations, i.e. fixed-composition searches with variable number of atoms in the cell), fully functional surface calculations, new optimization types (can optimize band gaps, dielectric constants, and newly invented figure of merit of dielectric materials). Interfaces with LAMMPS and ATK are documented in new test cases. Continuously updated with minor debugs (last debug 10/02/2014). 19/07/2013.

9.4.1 — A major upgrade, greatly improved user-friendliness (automatic estimate of volumes and of percentages of variation operators for each case), new functionalities (optimization of elastic properties and Chen’s model of hardness, prediction of polymeric structures, anti-compositions, automatic analysis of statistics, improved seed technique), first release of GEM (generalized evolutionary metadynamics), provided a set of real-life examples of USPEX calculations, test cases, documentation. More than 2100 users. Released 30/12/2014.

9.4.2 — Release version, compatible with Octave 3.4. Convex hull code rewritten. Interface with MOPAC implemented. Default values for , , enabled. More robust for ternary, quaternary, and more complex variable-composition searches. Robust TPS implementation (only for developers, will be available for users soon). More than 2200 users. Released 21/03/2015.

9.4.3 — Release version. It includes fixing a number of bugs (which should slightly speed up performance), interface with MOPAC, improved documentation. Released 10/08/2015.

9.4.4 — Release version. It includes fix for space group determination and other problems reported by users, improved documentation and examples, full Octave 3.4 compatibility and partial Octave 3.6/3.8/4.0 support. This version should be nearly bug-free and is a milestone towards a very major upgrade, which will be made available in version 10. Released 05/10/2015.

10.1 - Experimental version, released as a virtual machine on 01/08/2018.

10.2 - Release version. Distributed as a compiled code, so users no longer need to have Matlab. Has no known bugs and contains a very large number of new features and improvements. Random topological structure generator and automatic parameter control greatly speed up calculations. Prediction of (collinear) magnetic materials is enabled. Many new types of fitness implemented: magnetization, birefringence, thermoelectric figure of merit ZT, fracture toughness. Fitness can be minimized or maximized, and we can input mathematical expressions as fitness. Pareto optimization of several fitnesses is enabled. USPEX has been interfaced with Gaussian, MOPAC, DFTB, ORCA, FHI-aims, ABINIT. Symmetry determination is now done using SPGLIB. Symmetrization can also be optionally performed during calculation of physical properties, making it cheaper and more robust. 80 layer symmetry groups are utilized for generating initial population of 2D-structures. Variable-composition prediction of 2D-crystals is enabled. For surface structure prediction, we have enabled all possible surface supercells and output the surface phase diagram. Variable-cell NEB method has been greatly improved (made a few times faster). Utility “pmpaths” of V. Stevanovic has been added to predict the likeliest phase transition mechanisms (which can then be directly input into the VCNEB code). Released 19/01/2019.

10.3 - Similar to version 10.2, with some critical fixed-bugs in job submission, and some minor fixed-bugs in the code. Released 15/10/2019.

10.4 - Several improvements, bug fixes, new features. Local and remote submission files are improved. VCNEB and PSO codes are improved. Interfaces to QE, DMACRYS, VASP, and DFTB+ are improved. Interfaces to Abinit and CRYSTAL codes are added. Half-metallicity fitness is added. Added Mazhnik-Oganov model for calculation of hardness and fracture toughness. All python scripts are translated to python3 - no more python2 needed for USPEX. Released 05/11/2020.

10.5 - minor bug fixes. Added optimization of more than one quantity expressed by formula. Improved interface with DFTB+ and GULP5.2. Added “USPEX -u” feature, which allows one to update the package to the latest version without downloading the entire USPEX distribution. Enabled machine learning calculation of the elastic moduli (their optimization is available as optType=1201-1207), using graph convolutional neural network, and added Example35 to show how to use this feature. Released 08/07/2021.

2021.0 - This version is a beginning of reimplementation of previously developed techniques (with improvements, bug fixes, and more transparent code structure to facilitate further developments). In this version we have reimplemented structure/compound prediction for bulk crystals. Released 27/10/2021.

2022.0 - Continuation of USPEX pythonization effort. In this version we bring structure prediction of films, surfaces and nanoparticles. Realeased 20/08/2022.

2022.1 - Continuation of USPEX pythonization effort. New approach to calculating distance between atomic structures utilizing the same atomic fingerprints. Implemented global parent pool option. Introduced auxiliary *.uspex files, which allows to use seeds for molecular crystals. New optimization types. Realeased 14/11/2022.

Note

All regimes of 10.5 version will be reimplemented in subsequent releases.