Inverse Design of Crystals Using Generalized Invertible Crystallographic Representation - Danny - 2020
Inverse Design of Crystals Using Generalized Invertible Crystallographic Representation - Danny - 2020
representation
Zekun Ren 1 2 Juhwan Noh 3 Siyu Tian 1 2 Felipe Oviedo 4 Guangzong Xing 5 Qiaohao Liang 4 Armin Aberle 2
arXiv:2005.07609v1 [physics.comp-ph] 15 May 2020
Yi Liu 6 Qianxiao Li 7 Senthilnath Jayavelu 8 Kedar Hippalgaonkar 9 10 Yousung Jung 3 Tonio Buonassisi 1 4
space to material properties, inverse design with a targeted tion of new materials is expensive, local perturbation is used
property can be realized. for new crystal generation.
Prior work on inverse design using generative models has We demonstrate three success cases to design new crystals
been extensively studied in molecules (Gmez-Bombarelli with desired properties that are not in the training database
et al., 2018; Liu et al., 2018; Jin et al., 2018; Samanta et al., (Materials Project). As we trained our model with DFT
2018; Assouel et al., 2018; Kusner et al., 2017; Polykovskiy calculations only, we believe performing independent DFT
et al., 2018). Those invertible molecular descriptors are calculations of new crystals is an adequate and actionable
either represented in a 1D string (SMILES representation) validation procedure. In the first demonstration, we gen-
or 2D graphs. However, they are not suitable to describe a erated 97 unique ternary crystals with various targets of
3D periodic lattice, such as the one in a crystal. Building formation energy per atom (Ef ). We perform additional
generative models for crystals is challenging due to lim- DFT calculations to validate those crystals and find 27 crys-
ited available data and its 3D periodic structure (Noh et al., tals have targeted Ef within -0.1 eV/atom error. In the
2020). Several specialized inverse design tools for solid- second demonstration, we generate 16 new crystals with
state materials have been proposed, with limited structural targeted bandgap (EG ) and Ef . 6 out of 16 generated crys-
and chemical range (Zhao et al., 2017; Nouira et al., 2018; tals are validated to have EG close to the target within the
Noh et al., 2019a; Kim et al., 2020). Noh et al. featurizes a model prediction accuracy while the majority of the unique
single unit cell in a 3D grid and builds a hierarchical image- crystals meet the Ef target. Lastly, we extend our gener-
based VAE to generate new vanadium oxides. Beyond au- ative model to predict good thermoelectric crystals. An
toencoders, Generative Adversarial Neural Networks have additional challenge for such a demonstration is the small
been investigated to inverse design new crystals with differ- dataset. The application-relevant properties such as effective
ent elemental compositions (Sawada et al., 2019; Dan et al., mass, Seebeck coefficient and power factor are computa-
2019; Nouira et al., 2018; Kim et al., 2020). Kim and Noh tionally expensive to compute with DFT or require different
et al. represent the crystal as a set of atomic coordinates and computation platforms (Madsen & Singh, 2006), and ex-
cell parameters. The crystal generation in the above inverse isting data is limited. We tackle this data scarcity problem
design methods is achieved by selecting a subset of elements by jointly training a large unlabelled dataset with a small
from the periodic table. Moreover, the periodic nature of the labelled subset via a semi-supervised VAE. We show that
crystals is not reflected in the current crystal representations. 2 out of a total 27 predicted unique crystals have state-of-
To account for crystal periodicity, Hoffmann et al. directly the-art power factor validated using Boltzmann Transport
encode the repeated unit cells in a 3D cube to train a VAE calculations. In summary, in this work:
(Hoffmann et al., 2019). Training the model using a 3D
representation of the repeating unit can be computationally 1. We present a generalized invertible crystallographic
inefficient, and limited to specific crystal symmetries. representation for 3D crystals.
In this work, we propose an efficient and invertible 2D repre-
2. We build a VAE that allows the generation of new
sentation for 3D crystals that accounts for crystal periodicity
crystals with targeted materials properties.
and accesses the full periodic table. The motion of electrons
for crystals in Quantum Mechanics is generally described in 3. We demonstrate three successful applications of in-
both the real space e.g. surface energy, and the momentum verse design of unique functional crystals.
space (k space) e.g. E-k diagram. We embed this domain
knowledge to construct a crystallographic representation
that can be used to train a generative model by combin-
2. Invertible crystallographic representation
ing the atomic and structural properties in both real space for crystals
and momentum space (also called k space, Fourier space Atoms in a crystal are arranged in a periodic pattern. Ac-
or frequency space). We build a VAE (Kingma & Welling, cording to Bloch’s theorem in solid-state physics, the wave
2013) using these 2D crystallographic representations with function can be expressed as the product of a plane wave
the latent space organized according to different material and a function that has the same periodicity as the crystal
properties. This material-semantic latent representation al- (Martn-Palma et al., 2006). The energy of electrons in the
lows the generation of new crystals with targeted materials crystal is both studied in the real space (energy surface) and
properties. We investigate different sampling strategies to momentum space (energy dispersion relation). We embed
generate new crystals from the latent space. The compari- such physics knowledge to construct the crystallographic
son is assessed by the reconstruction error in rediscovered descriptors for the 3D periodic crystal. Figure 1 shows the
crystals from the test dataset. We find that applying a local schematic of our crystallographic representation. Firstly, we
perturbation to existing crystals yields the lowest crystal represent the unit cell (the basic building block of the crystal)
reconstruction error in rediscovered crystals. Given evalua- using the length and angles of the three fundamental trans-
Inverse design of crystals using generalized invertible crystallographic representation
Figure 1. Invertible crystal representation using both real space and Fourier space crystal properties
lation vectors (lattice vectors) and all atomic coordinates matrix, the basis matrix and the element matrix.
in the real space. Then, we introduce Fourier-transformed
crystal properties (FTCP) to capture the elemental and struc- 2.2. Momentum space representation:
tural information in the momentum space. We construct the
crystallographic representations by concatenating both real The most common momentum space representation of a
space and momentum space crystal representations. crystal is its diffraction pattern. X-ray crystallography is
the primary method to study periodic crystals (Ladd et al.,
1985). Modified diffraction images for periodic crystals
2.1. Real space representation
have been shown to classify its geometry accurately (Ziletti
To represent the crystals in the real space, we extract the text et al., 2018). We enrich the information in diffraction im-
information in the crystallographic information file (CIF) ages in the momentum space by projecting one-hot encoded
of 3D crystals. The text primarily corresponds to two ma- elemental properties Z to different crystal planes (h, k, l)
trices: cell matrix (the length and angle of three translation using a discrete Fourier transform.
lattice vectors), with size (2, 3), and basis matrix (all atom
coordinates in the unit cell) with size Nsites . Nsites is the N
X
upper bound of the number of atoms in the unit cell. We F(h, k, l) = Zi ∗ e(−j2π(hx+ky+lz)) (1)
use zero padding in crystals with less atoms. In addition, i=1
we bin and one-hot encode each element in the unit cell
as a vector Z which has K features which are the number where i is the atom in the unit cell, x, y, z is the atom co-
of atomic properties such as group number, electronegativ- ordinates in real space and h, k, l is the Miller index of a
ity, first ionization energy, etc. (Xie & Grossman, 2018). crystal plane (a point in momentum space). F(h, k, l) is
For featurizing the elements in ternary compounds, we con- the Fourier transformed crystal properties for plane (h, k, l),
catenate Z into a (K, 3) matrix. Hereafter, we construct which is the projection of atomic properties in one plane in
the real space representation by further concatenating the the crystal lattice and a point in the reciprocal lattice. As
atomic vector Z of each element, the cell matrix, the ba- the unit cells are defined as the repeating unit in the crys-
sis matrix and the one-hot encoded element matrix. The tal, there exist an infinite number of planes. We limit the
concatenated real space representation matrix is V(x, y, z) number of planes by applying a filter of the sum of (h, k, l)
with size (m, 3) where m is the sum of the length of the cell less than 4. The Fourier-transformed properties F(h, k, l)
are arranged according to orders of their Miller index and
Inverse design of crystals using generalized invertible crystallographic representation
become a (c, K) matrix where c is the number of planes gradient by material property values (Figure S1) and allows
with the sum of (h, k, l) less than 4 and K is the number to generate new crystals with targeted material properties.
of atomic features. Lastly, we concatenate the real space
R(z) = σ(g(z) · h(z)) (2)
crystal representation (V with size (m, 3)) and momentum
space representation (F with size (c, K)) with zero padding.
3.3. Decoder
The combined representation has a matrix size of (m, K).
The decoder mirrors the encoder using transposed convo-
3. Generative model and inverse design lutional layers. Lengths, angles of the three translational
vectors and coordinates of atoms in the unit cell are part of
Hereafter, we build a generative model to encode and de- the decoded crystallographic descriptors. Therefore, the 3D
code the concatenated crystallographic descriptors shown structure of the unit cell can be fully reconstructed.
in Figure 2. The detailed structure of the neural network is
shown in Supplementary S6. 3.4. Loss
Training of the model is done by optimization of the
3.1. Encoder
tractable evidence lower bound (ELBO) of VAE and re-
We treat the concatenated crystallographic representation as gression loss for material properties prediction. The overall
a 1D signals with K channels. The signal in each channel loss is
represents the atomic property projection such as electroneg- L = Lreconstruct βLKL + λLreg (3)
ativity, ionization energy, etc., in both real and momentum
space. We use the 1D convolutional neural network (CNN) where Lreconstruct is the reconstruction loss, LKL is the
as the sequence of atoms and crystal planes are contained distribution loss, Lreg is the regression loss, β and λ are
in the 1D signal. The 1D CNN in this work is inspired by the coefficients. To learn a disentangled representation, we
point clouds used for 3D image classification (Kim et al., allow heavy penalization of the latent distribution (β > 1)
2020; Qi et al., 2017). There is a spatial 1D relationship (Higgins et al., 2017).
in our crystal representation. Along this spatial axis, our
Fourier space descriptor is arranged according to symmetry
points F(h, k, l) that are universal in describing the elec-
tronic band structure. Because of the pooling operations in
CNNs, the arrangement of those geometry points becomes
translationally invariant (Gu et al., 2018; Liu et al., 2019).
However, there is no universal order for the real space de-
scriptor and thus the real space representation has neither
translational or rotational invariance. Kim et al (Kim et al.,
2020) have shown that performing data augmentation for
the real space descriptors will lead to a more balanced gen- Figure 2. VAE architecture using invertible crystal representations
eration of crystal structures for Mg-Mn-O systems. Given of both real space and Fourier space crystal properties.
a much larger chemical range is considered in this study,
data augmentation is not feasible. Instead, we encode 1D
signals with K channels into a normal distribution with a 3.5. Inverse design
diagonal covariance matrix using 1D CNN. The latent vec-
tor is sampled from those distributions and is regularized As the latent space of the VAE is mapped to material proper-
by the KullbackLeibler (KL) divergence between the latent ties using the regression model, the latent space or reduced
distribution and the standard Gaussian prior. material space becomes an organized and continuous crys-
tal representation with different material properties (Figure
3.2. Latent to material property regression S1). Inverse design of new crystals leverages this structured
latent space by sampling in regions with desired properties.
In addition to constraining the latent distribution to the mul- To avoid the possibility that generated crystals with minor
tivariant normal distribution with diagonal covariance, we structural change is considered as a new crystal, we only con-
train a gated regression model to map the latent space to sider generated crystals whose chemical formula changes
material properties (Gmez-Bombarelli et al., 2018). The as unique samples. To ensure the correctness of inverse-
regression is shown in Eq.2 where g and h are neural net- designed crystals, we investigate three different sampling
works and σ(.) is the sigmoid function, z is the encoded strategies to the latent space. The comparison is assessed by
latent. We use the L2 loss between R(z) and the materials the crystal reconstruction errors for the crystals in the test
properties. The regression shapes the latent space with a dataset.
Inverse design of crystals using generalized invertible crystallographic representation
E LEMENT
C ATEGORICAL
ACCURACY [%] 99.1 97.9
L ATTICE CONSTANT
PMAE[%] 7.41 12.5
L ATTICE ANGLES
PMAE[%] 3.99 6.75
ATOM FRACTIONAL
COORDINATES
MAE [ A . U .] 0.001 0.002
Figure 3. Examples of VAE-generated 3D crystals with targeted Ef =-0.5 eV after DFT relaxation. There are 8 different crystal structures
with more than 30 different elements in those 17 crystals (Figure S2). This shows the VAE can generate crystals accessing a wide range of
structures and chemistries.
Figure 4. DFT calculated material properties for inverse designed unique crystals (a) Case 1: ternary crystals with a targeted Ef =-0.5 eV.
The black dashed line is the target of Ef . 7 out of 17 generated crystals have Ef close to the target (-0.5eV) within 0.1 eV accuracy (b)
Case 2: ternary and quarternary crystals with targeted Ef <-1.5 eV and EG =1.5 eV. Most of the generated crystals satisfies Ef <-1.5 eV
requirement and the median EG of those crystals is around 1.5 eV
Figure 5. (a) and (b) show the predicted ternary crystals generated by our inverse design algorithm. These materials dont exist in any
database. Their power factor values (divided by the relaxation time) are plotted as a function of doping level at room temperature, both
for n- and p-doping. (c) shows the comparison to state-of-the-art high-performance thermoelectric material, cubic germanium telluride
(GeTe), with comparable results.
tions is much more challenging because of data scarcity: we properties (EG , Ehull ). Only 4,284 crystal have calculated
use the database from (Ricci et al., 2017) where the con- power factor labels. We tackle this limited data problem
stant relaxation time approximation under the Boltzmann by jointly training the VAE and mapping its latent space
Transport Equations is used to calculate the thermoelectric to ground-state property labels, and a small labelled subset
properties of inorganic crystals from Materials Project. The with thermoelectric property labels. The training loss of the
final dataset has 34,784 crystal structures with ground-state semi-supervised VAE is shown in Eq.4. We demonstrate
Inverse design of crystals using generalized invertible crystallographic representation
that our method can generate crystal structures that meet 7. Conclusions
those objectives. Here, the doping level and temperature are
treated as user inputs. The ability to dope the material to We present a generalized invertible crystallographic repre-
the desired carrier concentration is beyond the scope of our sentation for 3D periodic crystals. An ablation study of
approach. our crystallographic representation suggests an advantage
of using both real space crystal representations and momen-
tum space representations for material property prediction
and new crystal generation. We propose an inverse design
paradigm for generating new solid-state materials with tar-
X X X X geted material properties using VAE. We demonstrated three
L= Lrec β LKL + λ1 Lreg1 + λ2 Lreg2 unique applications of our model by generating new chem-
n∈P n∈P n∈P m∈Q istry formulas that are not in the database and validate them
(4) using DFT and Boltzmann Transport Calculations. Our fu-
P P
where n∈P Lrec , n∈P LKL is the reconstruction and ture work will be experimentally synthesizing the predicted
KullbackLeibler divergence for all crystals in the data, crystals, and bridging the synthesizability gap between the-
P
L is the regression loss for ground oretically generated crystals and experimental crystals by
n∈P reg1 Pstate material using semi-supervised learning of experimental datasets.
properties (EG ,Ef ,Ehull ) of all crystals and m∈Q Lreg2 is
the regression loss for 4,284 crystals that have calculated
power factor labels. 8. Acknowledgement
Based on domain expertise, we select 100 ternary and qua- We acknowledge Shijing Sun from MIT and Vladan Ste-
ternary crystals with the following section criteria: high vanovic from Colorado School of Mines for helpful dis-
power factors, energy above convex hull less than 0.03 eV, cussions. This research is supported by the National Re-
and bandgap between 0.3 and 1.5 eV. Applying local pertur- search Foundation, Prime Ministers Office, Singapore un-
bation to those compounds generates 27 unique crystals that der its Campus for Research Excellence and Technologi-
are not in the database. To test the quality of the crystals cal Enterprise (CREATE) program through the Singapore
generated, we performed DFT calculations of the predicted Massachusetts Institute of Technology (MIT) Alliance for
materials. We also performed thermal relaxation to obtain Research and Technologys Low Energy Electronic Sys-
the final atomic coordinates and then performed Boltztrap tems research program. J.N. and Y.J. acknowledge sup-
calculations (Madsen & Singh, 2006). We find that 2 out of port from NRF Korea (NRF-2017R1A2B3010176). Y.L.
the 27 crystals show state-of-the-art power factors, compa- is supported by the National Key Research and Develop-
rable to the best thermoelectric materials. The results are ment Program of China (Grant Nos. 2017YFB0702901
shown in Figure 5, as a function of doping concentration. and 2017YFB0701502) and the National Nature Science
Foundation of China (Grant No. 91641128). Q.L., S.J. and
6. Future work K.H. acknowledge funding from the Accelerated Materials
Development for Manufacturing Program at A*STAR via
Despite many recent studies reporting great results through the AME Programmatic Fund by the Agency for Science,
theoretical screening using forward prediction and inverse Technology and Research under Grant No. A1898b0043.
design using generative methods in the realm of computa-
tions, the synthesizability of these newly found materials
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