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Generating derivative superstructures for systems with high configurational freedom Wiley S. Morgan Department of Physics and Astronomy, Brigham Young University, Provo Utah 84602 USA Gus L. W. Hart Department of Physics and Astronomy Brigham Young University, Provo Utah 84602 USA Rodney W. Forcade Department of Mathematics Brigham Young University, Provo Utah 84602 USA Modeling potential alloys requires the exploration of all possible configurations of atoms. Ad- 7 ditionally, modeling the thermal properties of materials requires knowledge of the possible ways 1 of displacing the atoms. One solution to finding all symmetrically unique configurations and dis- 0 placements is to generate the complete list of possible configurations and remove those that are 2 symmetrically equivalent. This approach, however, suffers from the combinatorial explosion that n happens when the supercell size is large, when there are more than two atom types, or when a there are multiple displaced atoms. This problem persists even when there are only a relatively J small number of unique arrangements that survive the elimination process. Here, we extend an 9 existing algorithm1–3 to include the extra configurational degree of freedom from the inclusion of displacement directions. The algorithm uses group theory to eliminate large classes of configura- ] tions, avoiding the combinatoric explosion. With this approach we can now enumerate previously i c inaccessible systems, including atomic displacements. s - l r I. INTRODUCTION of freedom, such as phonon models.13,14 There are nu- t m merous techniques available for modeling these systems including cluster expansion (CE)15 and a recently devel- . In computational material science, one frequently t oped“smallsetoforderedstructures”(SSOS)method.16 a needs to list the “derivative superstructures”4 of a given m However, the accuracy of these methods is still linked to lattice. A derivative superstructure is a structure with the number of unique configurations being modeled. In - lattice vectors that are multiples of a “parent lattice” d other words, if the model is trained on a small set of and have atomic basis vectors constructed from the the n configurations then it will not be able to make accurate lattice points of the parent lattice. For example, many o predictions. Increasingthenumberofconfigurationsused c phases in metal alloys are merely “superstructures” of to train the models can improve their predictive powers. [ fcc,bcc,orhcplattices(L1 ,L1 ,B2,D0 ,etc.). When 0 2 19 Increasing the number of structures being used requires modelingalloysitisnecessarytoexploreallpossiblecon- 1 a more efficient enumeration technique than those cur- figurations and concentrations of atoms within these su- v rently available. 2 perstructures. Whendeterminingifamaterialisthermo- Leveraging the basic concepts of the algorithm pre- 8 dynamically stable, the energies of the unique arrange- sented in Ref. 3, we altered the algorithm to have more 3 ments are compared to determine which has the lowest favorable scaling in multinary cases. The basic idea is to 2 energy. 0 imaginetheenumerationasatreesearchandemploytwo Derivative superstructures are found using combina- . new ideas: (1) “partial colorings” and (2) stabilizer sub- 1 toric searches1–3,5–8, comparing every possible combina- groups. Sec. III illustrates the algorithm with a concrete 0 tion of atoms to determine which are unique. However, 7 example. these searches can be computationally expensive for sys- 1 The concept of partial colorings is to skip entire tems with high configurational freedom and are some- : branches of the tree that are symmetrically equivalent v times impractical due to the large number of possible i to previously visited branches. A partial coloring is an X arrangements. intermediate level in the tree (see Fig. 1) where config- r Theinefficiencyofcombinatoricsearchesmakesfinding urations are not yet completely specified. It frequently a theuniquederivativesuperstructuresalimitingfactorin happensthat symmetric redundancy can be identified at searches for high entropy alloys (HEA)9–11. The config- an early, “partially colored” stage, avoiding the need to urational complexity of HEAs prevents them from phase descend further down the tree. separating;thissamecomplexitymakeslistingeverypos- Stabilizer subgroups further increase the efficiency of sible arrangement of atoms impractical with current al- the new algorithm. Any symmetrically-equivalent full gorithms. colorings further down the current branch will have the Otherproblemsimpairedbytheinefficiencyofcurrent same partial coloring. Thus, the only symmetries that enumeration methods include modeling materials that are relevant are those that leave the current partial col- have disorder in their structures, such as site-disordered oring unchanged. These symmetries form a (stabilizing) solids12 orthatincludeatomicdisplacementsasadegree subgroupofthefullgroup. Thissignificantlyimpactsthe 2 efficiency because the stabilizer subgroup is often much III. TREE SEARCH smaller than the full group. Once a supercell has been selected, the remainder of the enumeration algorithm resembles a tree search in which each branch corresponds to a specific configura- II. SUPERCELL SELECTION AND THE tion of atoms within the supercell, many of which are SYMMETRY GROUP not fully populated and are called partial colorings (see Fig. 2). The partial colorings are identified using a vec- The first step in enumerating derivative superstruc- tor that indicates their locations within the tree. Once tures is the enumeration of unique supercells. This step a partial coloring is constructed, the stabilizer subgroup has already been solved by Hart and Forcade1, but due forthatpartialcoloringisfound. Thestabilizersubgroup to its importance to the algorithm we provide a brief allowsforthecomparisonofbrancheswithinthetreeina overview. manner that minimizes the number of group operations The supercells, of size n, are found by constructing all used. These tools, (partial colorings and the stabilizer Hermite Normal Form (HNF) matrices whose determi- subgroup), are used to “prune” branches of the tree as nant is n. An HNF matrix is an integer matrix with the they are being constructed, eliminating large classes of following form and relations: arrangements at once. We will use a 2D lattice of 9 atoms as an illustrative   a 0 0 example of the algorithm. The lattice will be populated b c 0,0≤b<c,0≤d<f,e<f (1) with the following atomic species; 2 red atoms, 3 yel- d e f low atoms, and 4 purple atoms. A subset of the possible arrangementsofthissystemisshowninFig. 2. Thecon- where acf = n. The HNFs determine all possible the cepts illustrated with this 2D example are equally appli- supercellsforthesystem. Forexample,considera9-atom cable in 3D. cell, then n = 9 and a, c, f are limited to permutations of (1,3,3) and (1,1,9). Then following the rules for the values of b, d, and e, every HNF for this system can A. Partial Colorings be constructed. These HNFs represent all the possible supercells of size n of the selected lattice. Some of these Whensearchingforalluniqueconfigurations,itisuse- are equivalent by symmetry, so the symmetry group of ful to know, a priori, how many configurations are ex- the parent lattice is used to eliminate any duplicates. pected. Arecentlydevelopednumericalalgorithmforthe Next, we convert the symmetries of the lattice to a P´olyaenumerationtheorem17–19allowsonetoquicklyde- list of permutations of atomic sites. There is a one-to- termine the memory requirements of storing the unique one mapping between the symmetries of the lattice and arrangements. For the 9 atom system considered here, atomicsitepermutations,i.e.,thegroupsareisomorphic. the P´olya algorithm predicts that there are 24 unique The mapping from the symmetry operations to the per- arrangements to be found. mutationgroupisaccomplishedusingthequotientgroup The algorithm places atomic species on the lattice ac- G = L/L(cid:48), where L is the lattice, constructed from the cording to their concentrations. In this case, the red unitcell,andL(cid:48) isthesuperlattice,constructedfromthe atoms have the lowest concentration and are placed in supercell. The quotient group G is found directly from the first two sites of the cell creating the first 1-partial the Smith Normal Form (SNF) matrices, which can be coloring (a partial coloring is a configuration with only a constructed fromthe HNFs via astandard algorithm us- subsetoftheatomsdecoratingthelattice). Thisisshown ing integer row and column operations. Thus S =UHV in the leftmost configuration, labeled (0,•,•), in the sec- whereU andV areintegermatriceswithdeterminant±1 ond row of Fig. 1. The general procedure is to apply and S is the diagonal SNF matrix, where each positive the symmetry group to each partial coloring in order to integer diagonal entry divides the next one down. The make comparisons between partial colorings and deter- (cid:76) (cid:76) group, G, is then G = Zs1 Zs2 Zs3, where si is ith mine if they are symmetrically equivalent. For example, diagonal of the SNF and Zsi represents the cyclic group in Fig. 1, the configuration labeled (1,•,•) is equivalent of order n. to configuration (0,•,•) by a translation of the lattice. Oncethesupercellshavebeenfoundandtheirsymme- At this stage we only have one partial coloring so it is trygroupshavebeenconvertedtotheisomorphicpermu- unique and no comparisons need to be made, however tation group, the algorithm can begin finding the unique the symmetry group is still applied to find the stabilizer arrangements of atoms within each supercell in a tree subgroup described in section IIIB. searchframework. Thisisaccomplishedbytreatingeach Comparisons between configurations are made by us- supercellwithitssymmetrygroupasaseparateenumer- ing a hash function. In computer science, any data set ation problem. The results of the enumeration across all canbeplacedina hashtablewhichassociatesa hash, or supercellsarethencombinedtoproducethefullenumer- label, with the data. In our case, the configurations are ation. listedwithinthehashtableintheordertheyarecreated. 3 ( , , ) (0, , ) (1, , ) (2, , ) (3, , ) (11, , ) (16, , ) (24, , ) (35, , ) (0, , ) (0, , ) (3, , ) (3, , ) (3, , ) (0, , ) A B FIG.1. (Coloronline)Theemptylatticeand8ofthe36configurationswithonlyredatomsareshownfortheexamplediscussed in section III. Above each partial coloring is a vector that indicates it’s location in the tree, i.e. (x ,x ,x ), where the x s r y p i are integers that indicate which arrangement of that color is on the lattice and a • means that no atoms of that color have beenplacedyet. Beloweachconfigurationiseitherthelabelofasymmetricallyequivalentconfiguration,alongwiththegroup operation that makes them equivalent, or the letters A and B. A and B are the branches that are built from the 1-partial colorings that are unique and are displayed in Fig. 2 The hash function then maps the configuration to a vec- assigned yet then the x s are replaced by dots indicating i tor of integers with an entry for each species, color, in an empty vector site. the system. The hash function used is similar to the one Thehashfunctionisaone-to-onemappingbetweenthe described in Ref. 3. However, due to its importance in configurations to the location vectors. These numbers this algorithm, we provide an overview of how the hash are constructed by considering each color separately and function works. building a binary string of the color and the remaining The hash function for the algorithm uses the princi- empty lattice sites, where the color is a 1 and the empty ples of combinatorics to uniquely identify each partial site is a 0 within the string. From the binary string, we coloring using an integer vector. Its construction starts can then use a series of binomial coefficients to find the by determining the number of possible ways to arrange x ’s. Thebinomialcoefficientsarefoundbytakingeach0 i the colors on the lattice. The number of possible config- inthestringthathas1’stotherightofitandcomputing urations can be found using the multinomial coefficient, (cid:0) p (cid:1), where p is the number of digits to the right and q−1 whichisequivalenttotheproductofbinomialcoefficients q is the number of 1’s to the right of the 0. Summing for each individual color: thebinomialsforqualifyingzeroproducesanumberthat tellsushowmanyconfigurationscamebeforethecurrent (cid:18) (cid:19) n C = =C C ...C = one. a ,a ,..,a 1 2 k 1 2 k Asanexampleofthehashfunctionthatconstructsthe (2) (cid:18) (cid:19)(cid:18) (cid:19) (cid:18) (cid:19) n n−a n−a −a −...−a location vector, consider configuration (3,19,0) of Fig. 1 ... 1 2 k , a a a 2B. The construction begins with the red atoms repre- 1 2 k sented as the following binary string (1,0,0,0,1,0,0,0,0), where n is the number of sites in the unit cell and where every atom that is not red has been represented a ,a ,...,a are the number of atoms of species i such by a 0 and the red atoms by a 1. This string has 3 zeros 1 2 k that (cid:80) a =n. The binomials determine the number of that have a single 1 to their right, the first zero has 7 i i ways to place the atoms of each color within the lattice digitstoitsright,thesecondhas6atomstoitsrightand once the previous colors have been placed. By assigning the third has 5 atoms to its right. The resultant sum of each partial coloring an integer, xi, from 0 to Ci − 1, binomials is xr = (cid:0)70(cid:1)+(cid:0)60(cid:1)+(cid:0)50(cid:1) = 1+1+1 = 3. This where i is the color, we can build a vector that identifies result is the first entry in our location vector. the location, (x ,x ,...,x ), of the configuration within The second entry in the location vector is constructed 1 2 k the tree. For example, there are C = (cid:0)9(cid:1) = 36 ways to for the yellow atoms. The bit string representation of r 2 place the red atoms on the empty lattice. After the red theyellowatomsis(0,1,0,1,1,0,0), thereareonly7digits atoms are placed then there remain C =(cid:0)7(cid:1)=35 ways because the 2 red atoms have already been placed, so to place the yellow atoms on the remayining3lattice sites. x = (cid:0)6(cid:1)+(cid:0)4(cid:1) = 15+4 = 19. The last entry in the This leaves C =(cid:0)4(cid:1)=1 way to place the purple atoms loycation2vecto1r is built for the purple atoms which have p 4 on the lattice. Within Fig. 1 and 2, the vector locations the bit string (1,1,1,1), so x = 0. The location vector p have the form (x ,x ,x ) and if the color has not been is complete once all atoms within a configuration have r y p 4 (0, , ) A (0,0, ) (0,1, ) (0,2, ) (0,3, ) (0,4, ) (0,5, ) (0,11, ) (0,15, ) (0,16, ) (0,17, ) (0,18, ) (0,19, ) (0,20, ) (0,21, ) (0,22, ) (0,34, ) (0,1, ) (0,16, ) (0,16, ) (0,15, ) (0,0,0) (0,1,0) (0,2,0) (0,3,0) (0,4,0) (0,11,0) (0,15,0)(0,16,0) (0,18,0) (0,19,0) (0,20,0) (0,21,0) (3, , ) B (3,0, ) (3,1, ) (3,2, ) (3,3, ) (3,4, ) (3,6, ) (3,8, ) (3,9, ) (3,11, ) (3,19, )(3,20, ) (3,21, ) (3,23, )(3,24, ) (3,26, ) (3,34, ) (3,0, ) (3,19, ) (3,2, ) (3,21, ) (3,0,0) (3,1,0) (3,2,0) (3,3,0)(3,4,0) (3,8,0) (3,9,0) (3,11,0) (3,19,0) (3,21,0) (3,23,0)(3,24,0) FIG. 2. (Color online) Here the A and B branches of the tree from Fig. 1 are shown. Each branch starts with the initial 1- partialcoloringthebranchisbuiltfrom((0,•,•)and(3,•,•)respectively). Thebranchesthenshowaselectionofthe2-partial coloringsforthatbranch,andtheuniquefullcoloringsthatarefound. AsinFig. 1thevectorsthatindicatetheconfigurations location in the tree are displayed above the configurations and the symmetrically equivalent labels appears beneath them. In thisfiguretheactionsthatmaketheconfigurationshavebeenexcludedduetotheircomplexity. Forexample,Theconfiguration labeled (0,5,•) is equivalent to the (0,1,•) configuration by a rotation about the vertical followed by a translation to the left. In the B branch configuration (3,19,0) is outlined for reference because it is used as an example later in the text. been included. then the corresponding configuration has already been The location vectors allow us to determine if a config- visited. uration is unique by checking if an element of the sym- metry group maps the configuration to a configuration withasmallerlocationvector. Thesymmetryoperations B. The Stabilizer Subgroup map a configuration’s location to a second, equivalent location. Uniqueness is determined by comparing the original and mapped locations for the configuration; if Thealgorithmisefficientbecausetheentiresymmetry the mapped configuration has already been enumerated, group does not need to be applied to a partial coloring, that is, if x > x , then the configuration is only the stabilizer subgroup of the partial coloring one original mapped not unique because it is equivalent to one we have al- level up the tree is needed. The stabilizer subgroup is ready visited. For example, configuration (2,•,•) shown found when the symmetry group was applied to the par- in Fig. 1 can be turned into configuration (0,•,•) by a tial coloring one level higher up the tree, so finding the 180 degree rotation about the diagonal. Since (2,•,•) stabilizersubgroupcostsnothingcomputationally. Asan and (0,•,•) are equivalent we conclude that (2,•,•) is example of an element of the stabilizer subgroup, con- notuniquebecause2>0. Insummary, ifanyelementof sider the cell (3,•,•), displayed in Fig. 1, and reflect it thesymmetrygroupmakesthelocationvector“smaller”, about the diagonal; the red atoms are unaffected. This 5 also unique, and records its stabilizer subgroup. Next, it places the purple atoms to get the configuration at (0,0,0); this configuration is saved, then the algorithm backs up to the 2-partial coloring level to consider the configuration (0,1,•) and find its stabilizer subgroup. Once this process has been repeated for all 34 partial FIG. 3. (Color online) The configuration (3,0,•), shown on colorings in the vector (0,xy,•) (0≤xy ≤34=Cy), the the left, is acted on by a reflection about the diagonal re- algorithm retreats to the 1-partial coloring level shown sultinginconfiguration(3,6,•),shownontheright. Because in the second row of Fig. 1 and finds that (1,•,•) and the symmetry group operation is a stabilizer for the configu- (2,•,•)areequivalentto(0,•,•). Itthenbeginstobuild ration (3,•,•) the red atoms were not affected. A stabilizer the (3,•,•) branch, of Fig. 2 B, in the same manner as is a group element that leaves the set invariant. The yellow the (0,•,•) branch. atoms, however, were mapped to a different configuration. Since there are only two unique 1-partial colorings for This means we can use just the stabilizer subgroup for the thissystemthealgorithmiscompleteoncebothbranches (3,•,•)configurationtocompareallthe2-partialcoloringsof that originate from these 1-partial colorings have been the form (3,x ,•), where (0 ≤ x ≤ C −1), because any y y y other group operation would map us to a different branch of explored. In the end, 24 unique configurations are found the tree. (shown in Fig. 2A and 2B), in agreement with the pre- diction from the P`olya enumeration algorithm. means that a reflection about the diagonal is a mem- ber of the stabilizer subgroup for the 1-partial coloring C. Extension to Include Additional Degrees of (3,•,•). In general, only a small subset of the symmetry Freedom group will be in the stabilizer subgroup for any partial coloring. Having established the algorithm, we will now ad- The stabilizer subgroup leaves the desired n-partial dress its extension to include displacement directions. coloring unchanged, where n is the depth in the tree. These enumerations are more difficult because includ- Once another color is added (making an (n+1)-partial ing displacement directions changes the action of the coloring) the stabilizer subgroup for the n-partial color- group. Displacement directions simply indicate the di- ing becomes the only group operations that can be ap- rection that an atom could be displaced off the lattice. plied without affecting the n-partial coloring. In other Theenumerationofstructuresthatincludedisplacement words, if we were to use any other group elements we directions can be used to build databases20 of possible wouldbecomparingconfigurationsthatwealreadyknow structures with displacements included. are equivalent on the n-partial coloring level. Our algorithm changes only slightly if displacement Onceauniquen-partialcoloringanditsstabilizersub- directions are included in the enumeration. First, the grouphavebeenfound,thealgorithmproceedsdownthe atoms that will be displaced are treated as a different branch to the (n+1)-partial colorings, see Fig. 2. To atomicspeciessothateachdisplacedatom’suniqueloca- check the uniqueness of the (n+1)-partial colorings, the tionscanbedetermined(seeFig. 4foranexamplewhere stabilizer subgroup from the n-partial coloring are used yellow displaced atoms are replaced with the red atoms and the stabilizer subgroup for the (n+1)-partial color- from the example system used above). Once the arrows ingsarestored. Whenauniqueconfigurationisfoundon havebeenreplacedbyatomicspecies,thealgorithmpro- the(n+1)levelanothercolorisadded,makingthe(n+2)- ceeds as normal until a full configuration is found. The partial colorings, and the process starts over again. algorithmthenrestoresthearrowsandusesthestabilizer The algorithm proceeds down a branch of the tree un- subgroupofthefullconfigurationtocheckforequivalent til a unique full configuration is found, such as (0,0,0) of arrow configurations. Fig. 2. When the full configuration is found, the algo- In order to determine if the combined arrow and color rithm backs up one level and considers the next partial configuration is unique, each group element has to be coloring. When no partial colorings are available on a paired with a second set of permutations that determine level, the algorithm backs up until it finds a level with how the symmetry operation affects the arrows. The ef- untestedpartialcolorings. Inthismanner,theentiretree fect on the arrows is represented as a permutation of is explored but only sections with unique configurations the numbers 0 to d−1, where each number represents are explored in detail. a different displacement direction up to the d directions For an example of the complete algorithm, consider beingconsidered. Forexample,ifweconsiderthesystem Figs. 1 and 2. The algorithm starts at (•,•,•) then in Fig. 4, we have two atoms being displaced along one builds the 1-partial coloring at (0,•,•), which is unique of the 6 cardinal directions, then any arrow could have by virtue of being the first partial coloring considered values of between 0 and 5 where each integer has an as- on this level, and records its stabilizer subgroup. The sociated direction; up=0, right=1, down=2, left=3, into yellowatomsarethenaddedtotheconfigurationtobuild the page=4, and out of the page=5. The initial arrow the 2-partial coloring at (0,0,•), of Fig. 2 A, which is vector, shown in the figure, is (up,up) and is represented 6 as (0,5) has been considered. At this point all possible arrangements that have the first arrow pointing up have been considered, so the second arrow is set to point up andfirstarrowisrotatedtomakethearrangement(1,0). Wethengobacktoincreasingthelastentryinthevector to create new arrangements in order to determine if any FIG. 4. (Color online) To include displacement directions of them are unique until (1,5) is reached. The process to the algorithm we represent the atoms to be displaced by is repeated until all possible the arrangements, i.e., all a unique color and then convert them back once a unique 2-tuplesof0...(d−1),havebeenconsidered. Onceallthe configuration is found. In this figure two displaced yellow vectorshavebeenconsidered,thealgorithmgoesbackup atomsarerepresentedbyredatomsuntilthepreviousportion the tree to find the next unique configuration of colors. ofthealgorithmiscomplete,thentheyarereplacedbyarrows In this manner, discrete displacement directions can again for the arrow enumeration. be added to the configurations. In this example, adding arrows to the system increases the number of possible arrangements to 45360 (the number of possible arrange- as (0,0). mentsforjusttheatomsis1260). However,theresultant The comparison of the rotated and unrotated arrows number of unique arrangements is only 663. is achieved using a hash function. This function gives eacharrowconfigurationauniquelabelthatcorresponds to the order it is constructed within the algorithm. IV. CONCLUSION This hash function takes a vector of arrow directions (a0,a1,a2,....,ak), where ai is an integer from 0 to d−1 Our previous algorithms1–3 explored configuration indicating the direction of the ith arrow and k+1 is the space by comparing all possible configurations of the number of arrows, and finds: atoms to eliminate those that were symmerically equiva- lent. These algorithms were only effective for systems k with relatively small amounts configurational freedom (cid:88) xa = aidi (3) duetothecombinatoricexplosionthatoccurforsystems i=0 with high configurational freedom and were incapable of enumerating systems that included displacement direc- Thisgiveseacharrowarrangementauniqueintegerlabel tions. thatwecanthencomparebetweensymmetryoperations. With this new algorithm, it is now possible to find As was the case for the configurations, if the effect of a the unique arrangements of systems with high configu- symmetry operation results in a relationship of x > rational freedom. The systems now accessible include k- old x , then the the arrow configuration is not unique and nary alloys and structures with displacement directions. new can be ignored. This is accomplished by using an approach which closely The stabilizer subgroup for the unique color configu- resembles a tree search, in which large classes of config- ration are used to map the arrows to new directions and urations are eliminated at a time. In this manner, we the hash function is used to compare the original and are able to avoid the combinatoric explosion which im- mapped arrows. After an arrow arrangement is checked, pedes the performance of the previous algorithms. This thealgorithmthenincreasesthemagnitudeofthelasta algorithm’sabilitytoefficientlydeterminetheuniquear- k in the vector by 1 and checks it for uniqueness with the rangements of these systems enables more effective com- stabilizer subgroup. If increasing the magnitude of a putational studies. k would cause it to be greater than the value of d−1 then This research was funded by ONR grant MURI a becomes0againanda isincreasedby1. Thispro- N00014-13-1-0635. Thisalgorithmhasbeenimplemented k k−1 cess is repeated until all the entries in the arrow vector in the enumlib package and is available for public use21. are equal to d−1. For example, the initial arrow vector for the system V. ACKNOWLEDGEMENTS shown in Fig. 4 is (up,up) and is represented as (0,0). It isfoundtobeuniquesinceitisthefirstarrangement. For thenextarrangementthearrowontherightisrotatedto Thisworkwassupportedunder: ONR(MURIN00014- point to the right creating the arrangement represented 13-1-0635). as (0,1). 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