Skip to main content

Advertisement

Log in

Calcite–magnesite solid solutions: using genetic algorithms to understand non-ideality

  • Original Paper
  • Published:
Physics and Chemistry of Minerals Aims and scope Submit manuscript

Abstract

We show how a genetic algorithm (GA) generates efficiently the energy landscape of the equimolar calcite–magnesite (CaCO3—MgCO3) solid solution. Starting from a random configuration of cations and a supercell containing 480 atoms, the lowest energy form of ordered dolomite was found in all runs, in 94% of which it was located with less than 20,000 fitness evaluations. Practical implementation and operation of the GA are discussed in detail. The method can also generate both low-lying and high-lying excited states. Detailed analysis of the energy-minimised structures of the different configurations reveals that low energies are associated with reduction of strain associated with rotation of the carbonate groups, a mechanism possible only when a carbonate layer lies between a layer of just Ca and a layer of just Mg. Such strain relief is not possible in the equimolar MgO–CaO solid solution despite the similarity of the crystal structures of these binary oxides to calcite–magnesite, and therefore, the enthalpy of mixing is very high. Implications for thermodynamic configurational averaging over the minima in the energy landscape are briefly considered. Overall, the genetic algorithm is shown to be a powerful tool in probing non-ideality in solid solutions and revealing the ordering patterns that give rise to such behaviour.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

References

  • Allan NL, Barrera GD, Fracchia RM, Lavrentiev MY, Taylor MB, Todorov IT, Purton JA (2001) Free energy of solid solutions and phase diagrams via quasiharmonic lattice dynamics. Phys Rev B 63:094203

    Article  Google Scholar 

  • Althoff PL (1977) Structural refinements of dolomite and a magnesian calcite and implications for Dolomite formation in marine-environment. Am Mineral 62:772–783

    Google Scholar 

  • Burton BP (1987) Theoretical analysis of cation ordering in binary rhombohedral carbonate systems. Am Mineral 72:329–336

    Google Scholar 

  • Burton BP, Kikuchi R (1984) Thermodynamic analysis of the system CaCO3–MgCO3 in the tetrahedron approximation. Am Mineral 69:165–175

    Google Scholar 

  • Burton BP, Van de Walle A (2003) First principles based calculations of the CaCO3–MgCO3 subsolidus phase diagrams. Phys Chem Miner 30:88–97

    Article  Google Scholar 

  • Bakken E, Allan NL, Barron THK, Mohn CE, Todorov IT, Stølen S (2003) Order-disorder in grossly non-stoichiometric SrFeO 2.50—a simulation study. Phys Chem Chem Phys 5:2237–2243

    Article  Google Scholar 

  • Catti M, Dovesi R, Pavese A, Saunders VR (1991) Elastic constants and electronic structure of fluorite (CaF2): an ab initio Hartree–Fock study. J Phys Condens Matter 3:4151–4164

    Article  Google Scholar 

  • Catti M, Pavese A, Dovesi R, Saunders VR (1993) Static lattice and electron properties of MgCO3 (magnesite) calculated by ab initio periodic Hartree–Fock methods. Phys Rev B 47:9189–9198

    Article  Google Scholar 

  • Chai L, Navrotsky A (1996) Synthesis, characterization, and energetics of solid solution along the CaMg(CO3)2–CaFe(CO3)2 join and implication for the stability of ordered CaFe(CO3)2. Am Mineral 81:1141–1147

    Article  Google Scholar 

  • Chai L, Navrotsky A, Dooley D (1995) Energetics of calcium–rich dolomite. Geochim Cosmochim Acta 59:939–944

    Article  Google Scholar 

  • Chan JA, Zunger A (2009) II–VI oxides phase separate whereas the corresponding carbonates order: the stabilizing role of anionic groups. Phys Rev B 80:165201

    Article  Google Scholar 

  • Chen FY, Curley BC, Rossi G, Johnston RL (2007) Structure, melting, and thermal stability of 55 atom Ag–Au nanoalloys. J Phys Chem C111:9157–9165

    Google Scholar 

  • Chua AL-S, Benedek NA, Chen L, Finnis MW, Sutton AP (2010) A genetic algorithm for predicting the structures of interfaces in multicomponent systems. Nat Mater 9:418–422

    Article  Google Scholar 

  • Chuang FC, Ciobanu CV, Shenoy VB, Wang CZ, Ho KM (2004) Finding the reconstructions of semiconductor surfaces via a genetic algorithm. Surf Sci 573:L375–L381

    Article  Google Scholar 

  • Davidson PM (1994) Ternary iron, magnesium, calcium carbonates: a thermodynamic model for dolomite as an ordered derivative of calcite structure solutions. Am Mineral 79:332–339

    Google Scholar 

  • Deaven DM, Ho KM (1995) Molecular-geometry optimization with a genetic algorithm. Phys Rev Lett 75:288–291

    Article  Google Scholar 

  • Deelman JC (1999) Low temperature nucleation of magnesite and dolomite. Neues Jahrbuch für Mineralogic Monatshefte 7:289–302

    Google Scholar 

  • Dick BG, Overhauser AW (1958) Theory of the dielectric constants of alkali halide crystals. Phys Rev 112:90

    Article  Google Scholar 

  • Dovesi R, Orlando R, Civalleri B, Roetti C, Saunders VR, Zicovich-Wilson CM (2005) Z Kristallogr 220:571–573

    Google Scholar 

  • Dovesi R, Saunders VR, Roetti C, Orlando R, Zicovich-Wilson CM, Pascale F, Civalleri B, Doll K, Harrison NM, Bush IJ, D’Arco P, Llunell M (2009) CRYSTAL09 user’s manual. University of Torino, Torino

    Google Scholar 

  • Dudiy SV, Zunger A (2006) Searching for alloy configurations with target physical properties: impurity design via a genetic algorithm inverse band structure approach. Phys Rev Lett 97:046401

    Article  Google Scholar 

  • Ferrando R, Fortunelli A, Johnston RL (2008) Searching for the optimum structures of alloy nanoclusters. Phys Chem Chem Phys 10:640–649

    Article  Google Scholar 

  • Fisler DK, Gale JD, Cygan RT (2000) Am Mineral 85:217–224

    Article  Google Scholar 

  • Freeman CL, Allan NL, van Westrenen W (2006) Local cation environments in the pyrope-grossular Mg3Al2Si3O12–Ca3Al2Si3O12 garnet solid solution. Phys Rev B 74:134203

    Article  Google Scholar 

  • Gale JD (1997) The general utility lattice program GULP—a computer program for the symmetry adapted simulation of solids. J Chem Soc Faraday Trans 93:629–637

    Article  Google Scholar 

  • Gale JD (2005) GULP: capabilities and prospects. Z Krist 220:552–554

    Google Scholar 

  • Gale JD, Rohl AL (1997) Mol Simul 29:291–234

    Article  Google Scholar 

  • Goldberg DE (1989) Genetic algorithms in search, optimization and machine learning. Addison Wesley, Reading

    Google Scholar 

  • Holland JH (1975) Adaption in natural and artificial systems. University of Michigan Press, Ann Arbor

    Google Scholar 

  • Johnston RL (2003) Evolving better nanoparticles: genetic algorithms for optimising cluster geometries. Dalton Trans 22:4193–4207

    Article  Google Scholar 

  • Lavrentiev M, Yu, van Westrenen W, Allan NL, Freeman CL, Purton JA (2006) Simulation of thermodynamic mixing properties of garnet solid solutions at high temperatures and pressures. Chem Geol 225:336–346

    Article  Google Scholar 

  • Lyakhov AO, Oganov AR, Valle M (2010) How to predict very large and complex crystal structures. Comput Phys Commun 181:1623–1632

    Article  Google Scholar 

  • Lyakhov AO, Oganov AR, Stokes HT, Zhu Q (2013) New developments in evolutionary structure prediction algorithm USPEX. Comput Phys Commun 184:1172–1182

    Article  Google Scholar 

  • McCarthy MI, Harrison NM (1994) Ab initio determination of the bulk properties of MgO. Phys Rev B 49:8574–8582

    Article  Google Scholar 

  • Mohn CE, Kob W (2009) A genetic algorithm for the atomistic design and global optimisation of substitutionally disordered materials. Comput Mater Sci 45:111–117

    Article  Google Scholar 

  • Mohn CE, Kob W (2015) Predicting complex mineral structures using genetic algorithms. J Phys Condens Matter 47:425201

    Article  Google Scholar 

  • Mohn CE, Stølen S (2005) Genetic mapping of the distribution of minima on the potential energy surface of disordered systems. J Chem Phys 123:114104

    Article  Google Scholar 

  • Mohn CE, Lavrentiev MY, Allan NL, Bakken E, Stølen S (2005) Size mismatch effects in oxide solid solutions using Monte Carlo and configurational averaging. Phys Chem Chem Phys 7:1127–1135

    Article  Google Scholar 

  • Mohn CE, Stølen S, Kob W (2011) Predicting the structure of alloys using genetic algorithms. Mater Manuf Process 26:348–353

    Article  Google Scholar 

  • Navrotsky A (1987) Models of crystalline solutions. In: Reeder RJ (ed) Reviews in mineralogy, vol 17. Mineralogical Society of America, Washington, DC

    Google Scholar 

  • Navrotsky A, Capobianco C (1987) Enthalpies of formation of dolomite and of magnesian calcites. Am Mineral 72:782–787

    Google Scholar 

  • Navrotsky A, Dooley D, Reeder R, Brady P (1999) Calorimetric studies of the energetics of order–disorder in the system MgxFe1−xCa(CO3)2. Am Mineral 84:1622–1626

    Article  Google Scholar 

  • Oganov AR, Stokes HT, Zhu Q (2006) Crystal structure prediction using ab initio evolutionary techniques: principles and applications. J Chem Phys 124:244704

    Article  Google Scholar 

  • Oganov AR, Chen J, Gatti C, Ma Y-Z, Ma Y-M, Glass CW, Liu Z, Yu T, Kurakevych OO, Solozhenko VL (2009) Ionic highpressure form of elemental boron. Nature 457:863–867

    Article  Google Scholar 

  • Oganov AR, Ma Y, Lyakhov AO, Valle M, Gatti C (2010) Evolutionary crystal structure prediction as a method for the discovery of minerals and materials. Rev Miner Geochem 71:271–298

    Article  Google Scholar 

  • Oganov AR, Lyakhov AO, Valle M (2011) How evolutionary crystal structure prediction works—and why. Acc Chem Res 44:227–233

    Article  Google Scholar 

  • Purton JA, Blundy JD, Taylor MB, Barrera GD, Allan NL (1998a) Hybrid Monte Carlo and lattice dynamics simulations: the enthalpy of mixing of binary oxides. Chem Commun. https://doi.org/10.1039/A708907D

    Article  Google Scholar 

  • Purton JA, Parker SC, Allan NL (1998b) Monte Carlo and hybrid Monte Carlo/molecular dynamics approaches to order–disorder in alloys, oxides and silicates. J Phys Chem B 102:5202–5207

    Article  Google Scholar 

  • Purton JA, Allan NL, Lavrentiev MYu, Todorov IT, Freeman CL (2006) Computer simulation of mineral solid solutions. Chem Geol 225:176–188

    Article  Google Scholar 

  • Purton JA, Lavrentiev MY, Allan NL (2007) Monte Carlo simulation of GaN/AlN and AlN/InN mixtures. Mater Chem Phys 105:179–184

    Article  Google Scholar 

  • Purton JA, Parker SC, Allan NL (2013) Monte Carlo simulation and free energies of mixed oxide nanoparticles. Phys Chem Chem Phys 15:6219–6225

    Article  Google Scholar 

  • Putnis A (1992) Introduction to mineral science. Cambridge University Press, Cambridge

    Book  Google Scholar 

  • Shannon RD (1976) Revised effective ionic radii and systematic studies of interatomic distances in halides and chalcogenides. Acta Crystallogr A32, 751–767

    Article  Google Scholar 

  • Sluiter MHF, Vinograd V, Kawazoe Y (2004) Intermixing tendencies in garnets: pyrope and grossular. Phys Rev B 70:184120

    Article  Google Scholar 

  • Smith RW (1992) Energy minimization of binary alloy models via genetic algorithms. Comput Phys Commun 71:134–146

    Article  Google Scholar 

  • Taylor MB, Barrera GD, Allan NL, Barron THK, Mackrodt WC (1997a) The free energy of formation of defects in polar solids. Faraday Discuss 106:377–387

    Article  Google Scholar 

  • Taylor MB, Barrera GD, Allan NL, Barron THK (1997b) Free energy derivatives and structure optimisation within quasiharmonic lattice dynamics. Phys Rev B56:14380–14390

    Article  Google Scholar 

  • Taylor MB, Barrera GD, Allan NL, Barron THK, Mackrodt WC (1998) SHELL—a code for lattice dynamics and structure optimisation of ionic crystals. Comput Phys Commun 109:135–143

    Article  Google Scholar 

  • Todorov IT, Allan NL, Lavrentiev MYu, Freeman CL, Mohn CE, Purton JA (2004) Computer simulation of mineral solid solutions. J Phys Condens Matter 16:S2751–S2770

    Article  Google Scholar 

  • Towler MD, Allan NL, Harrison NM, Saunders VR, Mackrodt WC, Aprà E (1994) Ab initio Hartree–Fock study of MnO and NiO. Phys Rev B 50:5041–5054

    Article  Google Scholar 

  • van Westrenen W, Allan NL, Blundy JD, Lavrentiev MYu, Lucas BR, Purton JA (2003) Trace element incorporation into pyrope-grossular solid solutions: an atomistic simulation study. Phys Chem Minerals 30, 217–229

    Article  Google Scholar 

  • Vinograd VL, Burton BP, Gale JD, Allan NL, Winkler B (2007) Activity–composition relations in the system CaCO3–MgCO3 predicted from static structure energy calculations and Monte Carlo simulations. Geochim Cosmochim Acta 71:974–983

    Article  Google Scholar 

  • Vinograd VL, Sluiter M, Winkler B (2009) Subsolidus phase relations in the CaCO3–MgCO3 system predicted from the excess enthalpies of supercell structures with single and double defects. Phys Rev B 79:104201

    Article  Google Scholar 

  • Woodley SM (2009) Structure prediction of ternary oxide subnanoparticles. Mater Manuf Process 24:255–264

    Article  Google Scholar 

  • Woodley SM, Catlow CRA (2008) Crystal structure prediction from first principles. Nat Mater 7:937–946

    Article  Google Scholar 

  • Woodley SM, Battle PD, Gale JD, Catlow CRA (1999) The prediction of inorganic crystal structures using a genetic algorithm and energy minimisation. Phys Chem Chem Phys 1:2535–2542

    Article  Google Scholar 

  • Zhang J, Reeder RJ (1999) Comparative compressibilities of calcite-structure carbonates; deviations from empirical relations. Am Mineral 84(5–6):861–870

    Article  Google Scholar 

  • Zhang J, Wang CZ, Ho KM (2009) Finding the low-energy structures of Si[001] symmetric tilted grain boundaries with a genetic algorithm. Phys Rev B 80:174102

    Article  Google Scholar 

  • Zhu Q, Oganov AR, Glass CW, Stokes HT (2012) Structure prediction for molecular crystals using evolutionary algorithms: methodology and applications. Acta Cryst B 68:215–226

    Article  Google Scholar 

Download references

Acknowledgements

NLA is grateful for valuable discussions with Victor Vinograd which prompted this work. This work was, in part, performed on the Abel Cluster, owned by the University of Oslo and the Norwegian metacenter for High Performance Computing (NOTUR), and operated by the Department for Research Computing at the University of Oslo IT-department. CM acknowledges support from the Research Council of Norway through its Centres of Excellence funding scheme, project number 223272.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to C. E. Mohn.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Allan, N.L., Thomas, L., Hart, J.N. et al. Calcite–magnesite solid solutions: using genetic algorithms to understand non-ideality. Phys Chem Minerals 46, 193–202 (2019). https://doi.org/10.1007/s00269-018-0997-3

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00269-018-0997-3

Keywords

Navigation