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USPEX

Release Notes for the v.9.4.4 - October 5, 2015

This is a minor release. With the help of users (especially Ah Hui), and with our own testing, we found and fixed 19 bugs and improved Examples and Tests. This version is, to the best of our knowledge, bug-free. It is fully compatible with Octave 3.4 and partially compatible with Octave 3.6/3.8/4.0. Contributors to version 9.4.4: M.S. Rakitin, Q. Zhu, M. Davari, S. Wang, F. Qi, G.R. Qian, A.R. Oganov.

This version is intended to be the current “golden standard” in computational materials discovery. Please switch to version 9.4.4, all previous versions of USPEX are obsolete.

Also, stay tuned – we are working hard on the new major release (version 10.1), which will take some time, but will feature major speedups and new functionalities.

Release Notes for the v.9.4.3 - August 10, 2015

It includes fixing a number of bugs (which should slightly speed up performance), extending functionalities, and improving documentation. This version should be nearly bug-free and is a milestone towards a very major upgrade, which will be made available in version 10.

Contributors to v. 9.4.3: Q. Zhu, G.R. Qian, M. Rakitin, F. Qi, Z. Allahyari, P. Bushlanov, Q.F. Zeng, D. Dong, J. Zhang, A.R. Oganov.

  1. User-friendliness:
    1. The Manual has been updated.

    2. A Chinese version of the Manual has been created, available online at: http://han.ess.sunysb.edu/uspex_manual/USPEXManualChinese942.pdf

    3. Several examples have been added: illustrating surface calculations, evolutionary metadynamics, generalized evolutionary metadynamics, use of USPEX in conjunction with MOPAC.

  2. Interfaces with external codes:
    1. Improved interface with MOPAC for nanoparticles and crystals.

  3. Internal machinery of the code, defaults, file names:
    1. Improved handling of space group symmetry and unit cell relaxation.

    2. Changed defaults for space group determination to more reliable ones: default general tolerance is now 0.08, and defaults for HIGH/MEDIUM/LOW = 0.04/0.08/0.15. We remind the users that obtained structures must be checked for the presence/absence of imaginary phonon frequencies.

    3. File non_optimized_structures renamed to gatheredPOSCARS_unrelaxed

    4. Changed default values for ionDistances, making them more robust.

    5. Softmutation rewritten and improved.

  4. Debugs:
    1. A number of bugs have been fixed – for handling symmetry, restart from previous generation, distance calculations for molecular crystals, reading of band gaps, calculation of structural quasientropies and degrees of order. Some bugs affected performance of the code, so the new version should be slightly faster. No known bugs remain in the code (which is now fully compatible also with Octave3.4).

  5. New methodological publication:
    1. Generalized evolutionary metadynamics (GEM) method and its applications to the discovery of novel allotropes of boron and silicon has been presented in the paper:

      Zhu, Q., Oganov, A. R., Lyakhov, A. O., and Yu, X. (2015). Generalized evolutionary metadynamics for sampling the energy landscapes and its applications. Phys. Rev. B, 92, 024106 (available at http://uspex.stonybrook.edu/pdfs/PhysRevB.92.024106.pdf).

Release Notes for the v.9.4.2 - March 21, 2015

This is a minor release with mostly bug fixes, full Octave compatibility, compatibility with 32-bit architectures, updated Manual, and several new features. Contributors to this version: Q. Zhu, Z. Allahyari and G.R. Qian.

  1. New features:
    1. Re-written convex hull code, making variable-composition calculations more robust.

    2. Improved variable-composition searches for ternary, quaternary, and more complex systems.

    3. Interface with MOPAC (abinitioCode=13).

    4. To make use of the code even more convenient, we implemented intelligent defaults for several parameters, and thanks to these defaults you don’t need to specify these parameters explicitly anymore: goodBonds, valences, IonDistances.

    5. Added Example 17 for optimization of elastic properties of carbon, and Example 18 for a ternary variable-composition search for the Zn-O-H system.

Release Notes for the v.9.4.1 - December 30, 2014

New major release of USPEX, v.9.4.1. The list of changes is very large, and makes all previous versions obsolete. More than 800 modifications were introduced into the code. Contributors to this version: Q. Zhu, G.R. Qian, M. Rakitin, H.Y. Niu, F. Qi, S. Athar, M. Davari, A. Masunov, B.X. Li, A.R. Oganov.

  1. New features:
    1. Optimization of the elastic properties – now users can optimize the bulk, shear, Young’s and Poisson’s moduli, Pugh’s ratio, and hardness from the Chen model, as well as the Debye temperature and acoustic wave velocities.

    2. Prediction of polymeric crystal structures is now enabled (calculationType=110).

    3. Now USPEX calculations for solids (calculationType= 300, 310, 301 and the as yet unreleased 311, which will be distributed in the next release) and surfaces (as yet unreleased calculationType=201, which will be distributed in the next release) give in the output not only the most stable structures at given conditions, but also phase diagrams. For solids they give you an idea (crude one – needs to be checked!) of what the new phases may be at higher and lower pressures, and a rough idea of transition pressures. For surfaces you get exact phase diagrams in terms of chemical potentials.

    4. Automated analysis for statistics. This is mainly needed for developers, but curious users may try this to see by how many times USPEX is faster and how much higher its success rate is, compared to another code. This feature is available only when stop_fitness is specified in INPUT.txt.

    5. Anti-composition feature enabled.

    6. Automatic evolution of variation operators (parameter control, enabled by option “1 : AutoFrac”), which speeds up the calculation by ~2 times.

    7. More powerful seeds technique: we now can organize seeds for specific generation, and more flexible of the sequence of different types of atoms in VASP5 format POSCAR file.

  2. User-friendliness:
    1. Users no longer need to specify the unit cell or atomic volumes in the keyblock Latticevalues – we have implemented a special algorithm that accurately estimates it at the pressure of interest, without the need for the user to specify it. You can also use online program. The users are still able to input the volumes manually.

    2. To create INPUT.txt files, you can also use online program - we recommend this for first-time users, to learn the meaning of all keywords (volume estimation algorithm is implemented here as well).

    3. Now pressure value (in GPa) is set by the tag ExternalPressure in the INPUT.txt file. Please NO LONGER specify it in relaxation files in the Specific folder.

    4. Single-block calculations now enabled in calculationType= 300/310.

    5. Now the code comes with a number of tests (to very quickly check that the code performs all key operations) and examples (realistic accurate calculations, which users can take as templates for new calculations). In particular, there are examples of calculations for 2D- crystals, surfaces, polymers, and for the vc-NEB method (to predict phase transition pathways).

    6. New data set (USPEX.mat) which can be used for post data analysis.

    7. Re-organized output files, which are more logical and easier to analyze.

    8. More detailed Warning messages during the calculation.

    9. High-resolution pdf-format convex hull figures are now output.

    10. For all USPEX calculation interfaced with VASP, the INCAR files can be edited and made effect during the calculations.

    11. Compositions statistics enabled in calculationType=301, fitness profile in 300 and 310.

    12. Now can move the calculation folder freely, without errors (when all jobs are done).

    13. Safer Matlab data files (.mat files) saving method for unstable file systems, which can easily recover the interrupted data file from backup (.mat.backup).

    14. The Manual has been updated.

    15. USPEX installation procedure has been implemented, as well as Python-based USPEX runner. Use 'USPEX -h' to see all available options and 'USPEX -r' to run USPEX calculation.

  3. Interfaces with external codes:
    1. Structures are now represented in VASP5 POSCAR format (which differs from the previous format by the presence of an extra line with element names). STM4 code for visualization is now able to read this format (please update it at http://mariovalle.name/STM4/kits/index.html)

    2. Interfaced with FHI-aims for calculation type 000 (nanoparticles).

    3. Interfaced with Tinker for calculation type 310 (molecular crystals).

    4. Improved interfaces for ATK, CASTEP, CP2K, DMACRYS, GULP, LAMMPS, Quantum Espresso, SIESTA, VASP.

  4. Internal machinery of the code:
    1. Automatic testing system has been created, to help fast and deep debugging. This will help to keep 9.4.1 and all future versions reasonably bug-free.

    2. A number of bugs was fixed.

    3. Source code folders hierarchy has been updated.

    4. Global variables have been updated and unified.

    5. Python-based INPUT.txt parser has been added.

Release Notes for the v.9.3.9 - August 6, 2013

This is a significantly improved version. We have made numerous updates, introduced major new functionalities and features, debugs. Improved user-friendliness (better output, easier input for molecular crystals, easier setup for remote calculations). Please download it from our new website http://uspex.stonybrook.edu

  1. New functionalities:
    1. Fully debugged codes for 2D crystals and GEM. GEM is a totally new method that is under final testing and will become available soon.

    2. Variable-cell Nudged Elastic Band method (Qian et al., Comp. Phys. Comm., 2013) for predicting phase transition pathways is under final testing and will become available very soon.

    3. Updates for variable-composition algorithm. More robust algorithm. More versatile too, now we have two types of varcomp calculations: single-block and multiple-blocks.

    4. For single block:

      • % numSpecices
      • 1 2
      • % EndNumSpecices
      • % atomType
      • Si O
      • % EndAtomType

      It means we sample structures of compound SiO2 (with the ratio of 1:2) with a variable number of formula units.

    5. Fully functional surface calculations (calculation types 200, 201; see Zhu et al.,Phys. Rev. B, 2013

    6. New calculation type (110), to study the packing of polymers. Will become available for users shortly.

    7. New optimization types – now it is possible to optimize band gaps, dielectric constants, and newly invented figure of merit of dielectric materials (for all these types of optimizations, see Zeng et al., http://arxiv.org/abs/1307.6358)

    8. Interfaced USPEX with LAMMPS and ATK. Added new tests to illustrate the use of these codes. Improved setup of many old test cases.

  2. Technical changes:
    1. For vasp calculations, one can prepare POTCAR in the same way for fixed- and variable-composition calculations. For instance, you can just put POTCAR_Mg and POTCAR_O in the specific folder if you do Mg-O variable-composition or MgO fixed-composition calculations. USPEX will by default search if there exist POTCAR_1,2,.... If there is no POTCAR_1 file, USPEX will prepare it from POTCAR_Mg and POTCAR_O.

    2. Seeds. We no longer specify them as POSCARS_1, _2, .etc. Instead, we just put POSCARS during the calculation. USPEX will read this file and use it for the next genereation. All the seeds files will be recorded into the file named 'Seeds/Seeds_history'.

    3. Simplified MOL_* files for (310) and (110) types of calculations.

    4. 301 calculations now prepare “lattice values” according to blocks – these will be volumes not of atoms, but of the compositional blocks. For the case of MgO-SiO2 system, you should put volumes of MgO and SiO2 formula units in the INPUT.txt

    5. For 301, we also support single block calculation. For the case of elemental boron, one just need to put one block in the INPUT.txt

      • % numSpecices
      • 1
      • % EndNumSpecices

      Summary:

      Calculation Types:

      • 000- clusters, nanoparticles
      • 110: prediction of packing of 1D polymers
      • 200: surface reconstructions (fixed composition)
      • 201: surface reconstructions (variable composition, up to binary systems)
      • 300: fixed composition for 3D crystal structures
      • 310: fixed composition for 3D crystal structures (from molecular building blocks)
      • 301: variable composition for 3D crystal structures
      • 311: variable composition for 3D molecular compounds (co-crystals)
      • -200: 2D crystal structures (user defined thickness)

    Release Notes - March 2013

    Release of the USPEX code version 9.3.4 is now available. All previous versions are obsolete. The input and output formats have been made simpler and more informative. Improvements in variable-composition calculations, seed technique, molecular structure prediction, massively parallel calculations. Added interface to CASTEP and LAMMPS. Several bugs fixed. Updated documentation and added new test cases.

    Release Notes - December 31, 2012

    New version (v.9.2.7) is available for download. There are significant improvements, but unless you need these improvements, you can continue using version 9.1.7.

    1. New major features:
    2. A major new feature is released: an 'ageing' (antiseeds) technique, aimed at improving population diversity and the ability of the algorithm to find the global minimum. For more details, see http://dx.doi.org/10.1016/j.cpc.2012.12.009

    3. Improved features:
      1. Optimization of order (minimization or maximization of the order or quasientropy) for alloys, without structure relaxation (for which, we introduced a new value abinitioCode=0). This allows, among many other things, an easy creation of quasirandom structures (based on the more general definition than the so-called “special quasi-random structures”). Since structure relaxation is not needed here, these calculations can be extremely fast, even on large supercells.

      2. An improvement was made in the handling of symmetry. This improvement is particularly important for fixed-cell calculations.

      3. For fixed-cell calculations, you can specify now the cell parameters, not only in the form of a 3 x 3 matrix, but also as a role of six values (three length in Angstrom and three angles in degrees), e.g.: 10.010 8.756 4.789 90.0 90.0 90.0. The former use all 3 x 3 matrices is also allowed.

      4. For the maximum number of permutations swaps (parameter howManySwaps), would have introduced an intelligent default, so that in virtually all cases, you can avoid manually setting this parameter and just rely on the default.

      5. Added interface to CASTEP (contribution of Zamaan Raza) and new test cases:

        • Generation of quasirandom structures

        • Antiseed technique (two tests, illustrating different uses of this technique)

        • Example of USPEX calculation with Quantum Espresso

    Examples of USPEX calculation with CASTEP and ATK are in preparation.


    Some of the recent publications done with (or about) USPEX:

    1. Chen Y, Hu Q-M, Yang R. (2012) Predicted suppression of the superconducting transition of new high-pressure yttrium phases with increasing pressure from first-principles calculations. Phys. Rev. Lett., 109, 157004.

    2. Zhou XF, Oganov AR, Qian GR and Zhu Q (2012) First-principles determination of the structure of magnesium borohydride. Phys. Rev. Lett., 109, 245503.

    3. Zhu Q, Jung DY, Oganov AR, Glass CW, Gatti C and Lyakhov AO (2013) Stability of xenon oxides at high pressures. Nature Chemistry 5, 61-65.

    4. Zhang W, Oganov AR, Goncharov AF, Zhu Q, Boufelfel SE, Lyakhov AO, Somayazulu M and Prakapenka VB (2012) Unexpected stable stoichiometries of sodium chlorides. Submitted. See http://arxiv.org/abs/1211.3644

    5. Zhu Q, Oganov AR, Lyakhov AO (2012) Unexpected stoichiometries in Mg-O system under high pressure. Submitted. See http://arxiv.org/abs/1211.6521.

    6. Lyakhov AO, Oganov AR, Stokes H, Zhu Q, (2013) New developments in evolutionary structure prediction algorithm USPEX. Comp. Phys. Comm., in press http://dx.doi.org/10.1016/j.cpc.2012.12.009

     

    Release Notes - December 2012

    New version (v.9.2.4) is available for download. Some of the new features include:

    1. Improved symmetrical initialization for nanoparticles (clusters).

    2. Order enhanced heredity for nanoparticles.

    3. New parameter to tune the tolerance for the space group determination.

    4. Better defaults, various minor bugs fixed.

    5. New property (quasientropy) can be optimized.

     

    Release Notes - June 2012

    We proudly announce the new version, v.9.1.7 - a major new release, which makes all previous versions obsolete and sets a new standard in the field. You will find major new functionalities and improvements, updated documentation and set of tests.

    1. New major features:
      1. Evolutionary metadynamics (ref. [1]), a very powerful method for predicting stable structures, which also gives a large number of metastable structures that can be reached from a particular user-chosen state. For instance, you can find all carbon structures that can be made by compressing graphite (ref. [2]), carbon nanotubes, etc. This method also gives transition pathways between the structures, so in many ways it is complementary to USPEX. Test case is added as an illustration.

      2. Extension of our evolutionary algorithm to molecular crystals (ref. [3]), which enables affordable and reliable predictions. Test case is added as an illustration.

      3. PSO (Particle Swarm Optimization) method - the original version for crystal structure prediction, developed by A.Boldyrev in early 2000s and its 2010 Wang-Lv-Zhu-Ma reimplementation, was improved by us by removing some unphysicalities. This corrected PSO algorithm was implemented with minor programming work on the basis of USPEX. However, the performance is generally inferior compared to USPEX - and the same is true of the older PSO versions (e.g., PSO relies on symmetry being used, its success rates and efficiency are lower, etc.). Use for testing purposes only.

    2. Improved features:
      1. Debugged the softmutation operator.

      2. Improved variable-composition functionalities. Created utility extendedConvexHull.m for easy analysis of the results.

      3. Debugged the cluster (nanoparticles) prediction code.

      4. Improved symmetry features of the code.

      5. Greatly improved and updated documentation (README and Manual).

      6. Enlarged and refreshed set of tests.

      7. Graphical output, which enables rapid pre-analysis.

      8. Additional property can be optimized now - magnetic moment (thankts to R. Agarwal).

     

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