Accepted Manuscript

Z-MEM, Maximum Entropy Method software for electron/nuclear density distribution in

Z-Code

Yoshihisa Ishikawa, Junrong Zhang, Ryoji Kiyanagi, Masao Yonemura, Takeshi

Matsukawa, Akinori Hoshikawa, Toru Ishigaki, Shuki Torii, Ryoko Oishi-Tomiyasu,
Takashi Kamiyama
PII: S0921-4526(18)30235-7
DOI: 10.1016/j.physb.2018.03.034
Reference: PHYSB 310795

To appear in: Physica B: Physics of Condensed Matter

Received Date: 30 August 2017

Revised Date: 17 March 2018
Accepted Date: 19 March 2018

Please cite this article as: Y. Ishikawa, J. Zhang, R. Kiyanagi, M. Yonemura, T. Matsukawa, A.
Hoshikawa, T. Ishigaki, S. Torii, R. Oishi-Tomiyasu, T. Kamiyama, Z-MEM, Maximum Entropy Method
software for electron/nuclear density distribution in Z-Code, Physica B: Physics of Condensed Matter
(2018), doi: 10.1016/j.physb.2018.03.034.

This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to
our customers we are providing this early version of the manuscript. The manuscript will undergo
copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please
note that during the production process errors may be discovered which could affect the content, and all
legal disclaimers that apply to the journal pertain.
 ACCEPTED MANUSCRIPT

Z-MEM, Maximum Entropy Method Software for

Electron/Nuclear Density Distribution in Z-Code

Yoshihisa Ishikawa a, Junrong Zhang a, b, Ryoji Kiyanagi c, Masao Yonemura a, d,

Takeshi Matsukawa e, Akinori Hoshikawa e, Toru Ishigaki e,

PT
Shuki Torii a, Ryoko Oishi-Tomiyasu a, f and Takashi Kamiyama a, d

RI
a
Institute of Materials Structure Science, KEK, Tokai, Ibaraki 319-1106, Japan
b
Institute of High Energy Physics, China Spallation Neutron Source, YuquanLu,

SC
Shijingshan District, Beijing, 100049, People's Republic of China
c
J-PARC Center, JAEA, Tokai, Ibaraki, 319-1195, Japan
d

U
Department of Materials Structure Science, The Graduate University for Advanced
Studies, Tokai, Ibaraki 319-1106, Japan
AN
e
Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Shirakata,
Tokai,Ibaraki, 319-1106, Japan
M

f
Department of Mathematial Science, Faculty of Science, Yamagata University,
Kojirakawa-machi, Yamagata-shi, 990-8560 Japan
D

Email: yoshihisa.ishikawa@j-parc.jp
TE

Abstract
EP

Maximum Entropy Method (MEM) is one of powerful tools for material science. We
developed the program Z-MEM for evaluation of electron and nuclear density
distribution by MEM analysis and Fourier synthesis. This code is designed by the
C

multi-threading library OpenMP, so that the calculation performance is significantly

AC

improvements for MEM analysis. Z-MEM is bundled in Z-Rietveld, which is Rietveld

software for X-ray and neutron powder diffraction, via the application programming
interface (API). Since Z-MEM have equipped with the graphical user interface
operations, users can perform from Rietveld refinement to MEM analysis seamlessly.

1
 ACCEPTED MANUSCRIPT

1. Introduction

Maximum Entropy Method (MEM) for crystallography has yielded widely

evolution in material science [1]. MEM analysis enables to image electron and nuclear
density distributions without assumption of the spherical independent atom model

PT
(IAM). Electron and nuclear densities at lower distribution level play an important
role with regard to physical and chemical properties, compared with IAM by the crystal

RI
structure analysis. In particular, progress of synchrotron X-ray technologies makes it
possible to reveal the precise electron density map such as a charge ordering and a

SC
chemical bonding [2, 3]. Indeed, recent MEM approaches have applied to electrostatic
potential calculation [4] and the modulated structure using the super space group [5, 6].

U
Neutron diffraction has strong advantages to elucidate properties of light weight
atoms in substances. Moreover, the neutron coherent scattering length bc is independent
AN
from the scattering vector |Q| = sinθ/λ, so that neutron diffraction data becomes high
accuracy for the atomic displacement parameters (ADPs) based on the atomic vibration
M

or static small displacement. MEM analysis was applied to many investigations, such as
organic materials [7], anharmonic ADPs [8], structural disorder with phase transition [9]
D

and the diffusion pathway in ionic conductor [10-12], respectively.

A precision of crystal structure factor F(h) with the standard deviation σ(h) is often
TE

discussed in MEM analysis. In case of single crystal diffraction, Bragg peaks become
independent of each other, and F(h) and σ(h) satisfy one by one corresponding relations.
EP

In contrast, powder diffraction is likely to arise peak overlaps at high Q-range, so that it
is difficult to obtain highly precise intensities, especially for low symmetry crystals.
MEM/Rietveld method deals with peak overlapping as a single data set using
C

G-constraint to avoid the contribution of IAM bias from Rietveld analysis [13].
AC

Moreover, the feedback process between Rietveld analysis and MEM has established as
the REMEDY cycle [14].
In material science and industry, powder diffraction has much broader application
than single crystal diffraction. Since majority of functional materials are solid-solution
ceramics, as preprocess of MEM analysis, it is necessary to identify the total electron
number or the sum of scattering neutron length from the Wyckoff site occupancy using
Rietveld refinement [15]. Such crystal structural parameters have already included in
program for the crystal structure analysis, and the seamless cooperation with MEM

2
 ACCEPTED MANUSCRIPT

analysis is essential in practical applications. Therefore, MEM software is required not

only the stand-alone program but also to bundle in Rietveld software. For instance,
Jana2006 [16] equips with export functions for BayMEM [5, 6] and PRIMA [17]. In
addition, Fullprof [18] can connect to Dysnomia [19].
Z-code is the software suite to analyze for powder diffraction, total scattering and

PT
small angle scattering data. In particular, Z-Rietveld includes the error propagation
algorithm not only angle dispersion measuring but also time of flight (TOF) neutron

RI
diffraction [20, 21]. Accordingly, a combination of Z-Rietveld and MEM analysis
enables to derive high reliable electron and nuclear density distributions. From above

SC
reasons, we developed the new program Z-MEM which implements the MEM analysis
and Fourier synthesis, utilizing advantages of Z-Code. Z-MEM can execute seamlessly

U
via the graphical user interface (GUI) in Z-Rietveld. In this paper, we introduce the new
program Z-MEM and describe features and performance.
AN
2. Algorithm of Maximum Entropy Method
M

From the transformation of the density distribution ρ(x) and the crystal structure
D

factor F(h) as Fourier relations, electron and nuclear density distributions are obtained
by X-ray and neutron diffraction, respectively. Similarly, electron diffraction data
TE

converts to the distributions of electrostatic potential. Maximum Entropy Method can be

applied same algorithm against each Fourier relations.
EP

The Shannon's information entropy S (ρk) is defined as the Jaynes’s representation,

(1)
C

where N (= Na × Nb × Nc) is number of divided pixels in a unit cell. τ’k and ρ’k mean
AC

prior and posterior probability distributions, respectively [22]. Electron and nuclear
density ρ(x) in MEM analysis equals to the expected value of normalized posterior
probability density distributions. Hence, ρ(x) is defined as the multiplied value between
the posterior probability density distribution ρ'(x) and the summation of element (i.e.
total electron number or sum of scattering length) in a unit cell.
In MEM analysis for crystallography, the electron/nuclear density ρ(x), which
maximizes the information entropy (1), is calculated under two conditions as below:

3
 ACCEPTED MANUSCRIPT

(2)

(3)

where NF is number of crystal structure factor F(h), and σ(h) is the standard deviation of

PT
observed Fobs(h). Here, (2) means the total probability density distribution is conserved
after MEM calculation. Accordingly, this condition ensures that the chemical formula,

RI
which is given from expected value ρ(x), is maintained in all calculation processes. The
constraint equation (3) means that the calculated structure factors FMEM(h) converge

SC
against the observed structure factors Fobs(h) within standard deviation σ(h), and it is so
called F-constraint.

U
Crystal structure factor from MEM analysis FMEM(h) has the relation of Fourier
transformation of density distribution ρ(x), and it is represented by
AN
(4)
M

where V is a volume of unit cell.

The program Z-MEM introduces the formulas of (1) to (4) by Collins's method
D

using the Lagrange multiplier λ [23]. These relations are formed as the constrained
extreme value problem to maximize the information entropy,
TE

(5)
EP

The relation can compute as the iterative calculation of (5) using Sakata-Sato method
[24, 25]. Hence, the recurrence equation between n and n+1 cycles is defined as
(6)
C
AC

The formula (6) is assumed that ρ’(n+1)k approximately equals to ρ’(n)k, and it is called
the 0th order single pixel approximation (ZSPA) [26]. When the initial probability
distribution ρ’(0)k set the uniform distribution, which is constructed by the mean element
̅̅̅̅̅̅̅, the equation (6) is corresponding to the mathematical induction method. Though
𝜌′(𝒙)
this algorithm in Z-MEM is known as the old-fashioned calculation style, compared
with recent non-linear optimization methods, it is well verified to obtain enough
solution and the high-speed calculation [6, 19].
Some atoms such as H, Li, Ti etc. have the negative neutron scattering length due

4
 ACCEPTED MANUSCRIPT

to the phase inversion of incident neutron beam, whereas the information entropy (1)
cannot define negative value in principle. In algorithm by Z-MEM, positive and
negative density distributions, ρ+(x) and ρ-(x), perform independent analysis each other,
then both density distributions composite in visualization stages [27].
The constraint equation (3) assumes the random error of ΔF/σ(h) = [Fobs(h) -

PT
Fcal(h)]/σ(h), and the histogram is expected to form a normal distribution. However,
X-ray powder diffraction often occurs the large difference of ΔF in low Q-range, so that

RI
such mismatches are likely to cause the bias problem in MEM analysis. In Z-MEM, the
weighting approach by de Vries has adopted to avoid the bias problem [28].

SC
3. Overview of the Program, Z-MEM

U
The maximum iteration number in MEM analysis has no limitation, until the
AN
constraint-F value CF satisfies the condition (3). Moreover, the calculation volume in
one cycle is proportional to the number of crystal structure factor and the total pixel size
M

from the equation (4). Accordingly, the reduction of time-consuming process is crucial
to the practical MEM application.
D

Z-MEM succeeded to improve calculation performance, because of the parallel

computing, reduction of total cycle number for convergence and shrink of calculation
TE

volume. Information of the bench-mark test for Z-MEM are shown in Table 1. Single
crystal data were analyzed by Jana2006 [16] and powder diffraction data was utilized
EP

by Z-Rietveld [20, 21]. All analyses were carried out Macintosh PC with Intel Core
i7-5557U processor (3.1 GHz, 2 core and 4 threads) and 16 GB RAM of DDR3.
C

3-1. Multi-Thread calculation

AC

Z-MEM was written in the C++ language with the OpenMP library. OpenMP is the
shared memory typed multi-threading library, and majority of commercial computers
can be available multi-threading calculation using this library. Z-MEM is designed for
multi-thread MEM analysis, so that all modules are optimized as object classes which is
utilized dynamic array of the standard template libraries (STL). Figure 1 shows the
elapsed time till convergence by Z-MEM, compared with the single and multi-core CPU.
The calculation time by OpenMP indicates high parallel efficiency in proportion to
thread number.

5
 ACCEPTED MANUSCRIPT

3-2. Automatically optimization of Lagrange multiplier

It is known that the MEM solution by ZSPA algorithm does not depend on the
Lagrange multiplier λ, if the λ would be small value not zero [26]. Z-MEM is equipped
the automatically optimization function of Lagrange multiplier λ, and any users can

PT
execute the two functions. One is the automatic initial λ, and the other is automatic
optimization λ for each iteration. Figure 2 shows the iteration number dependence of

RI
constraint-F value CF of Al2O3. The feature of automatic initial λ seeks the minimum CF
in the preprocess of MEM calculation. This function enable to start calculation using the

SC
suitable Lagrange multiplier λ. Second, the automatic optimization means that λ value is
increasing for each cycle by compound interest calculation. Compared with fixed λ, this

U
optimization becomes significantly decreasing cycle number until convergence of MEM
calculation.
AN
3-3. Look Up Table method of phase term
M

In a general numerical computing, the standard mathematical library, such as the

trigonometric function and the exponential function, often becomes a bottleneck in
D

iteration calculation. The Look Up Table method (LUT) is well known as one of
effective way to solve this problem. In LUT method, coefficients of sine and cosine
TE

functions are stored in the numerical table as preprocess of main computing part, then
this table is called by the sequential access for every iteration processes. The phase term
EP

exp(2πi h・r) in (4) is fixed value, and each real and imaginary parts are calculated
before iteration process in Z-MEM [29]. Although it is pointed out that LUT needs large
size of the random-access memory (RAM), the memory technology is progress with
C

improvement of the computer architecture. Consequently, LUT achieves superior

AC

computing performance under the recent 64bit architecture, compared with applying
triangular functions for each iteration.

4. Interface

The present Z-MEM is provided two version. One is the character user interface
(CUI) for single crystal data and the other is the graphical user interface (GUI) with
bundled in Z-Rietveld. In addition, Z-MEM is supported MEM analysis and Fourier

6
 ACCEPTED MANUSCRIPT

synthesis.
In CUI version, users need to prepare two input text files. Crystal information, such
as lattice parameters, space group (Hermann–Mauguin notation) and crystal structure
factors, are defined as *.zm or *.zf file, which *.zm file is used for MEM analysis and
*.zf file is applied for Fourier synthesis. The other input text file is prepared as the

PT
configuration file which extension is *.cf.
Figure 3 shows the screen shot of GUI version of Z-MEM. In GUI version, any

RI
objects of MEM analysis are linked to Z-Rietveld via an application programming
interface (API), and all input and output data store on RAM memory. Thereby, the

SC
calculation performance is reliable almost same as CUI version. Compared with CUI
version, some automatically calculation is supported in GUI. For instance, total electron

U
number (or sum of neutron scattering length) is derived from F(000) by Z-Rietveld. And,
the recommended pixel number can estimate from lattice parameters and symmetry
AN
operation. Additionally, estimation formulas of standard deviation are equipped to check
referred value from some references [5, 19].
M

Output format can select two text format. One is all grid typed text file, and
extension is *.grd. The other output file is *.den, which is applied asymmetric unit.
D

Since both format is the conventional format in MEM/Fourier program, these are
supported by majority of visualization software.
TE

5. Conclusion
EP

We developed the new program Z-MEM in Z-Code, which analyzes electron and
nuclear density distributions from X-ray/Neutron diffraction data by MEM and Fourier
C

synthesis. Z-MEM is designed for multi-thread calculation by OpenMP library, and the
AC

calculation performance is significantly improved. Moreover, the object classes are

bundled in Z-Rietveld via API, and we can use from Rietveld refinement to MEM
analysis seamlessly. Z-Rietveld is available to use broad probes such as X-ray and
neutron, and has already obtained high reliable. Therefore, combination Z-MEM and
Z-Rietveld will be strong tools for material science.

7
 ACCEPTED MANUSCRIPT

Acknowledgements

This work was financially supported by the Neutron Scattering Program Advisory
Committee of IMSS, KEK (2014S05, 2014S10), Ibaraki Prefecture (16D01, 17D23), by
Grant-in-Aid for Young Scientists B (JP17K14135), and collaboration with Ibaraki

PT
University (16C109, 17C113).

RI
References

SC
[1] C. J. Gilmore, Acta Crystallogr., A52 (1996) 561–589.

U
[2] E. Nishibori, E. Sunaoshi, A. Yoshida, S. Aoyagi, K. Kato, M. Takata, M. Sakata,
Acta Crystallogr., A63 (2007) 43 – 52.
AN
[3] H. Svendsen, J. Overgaard, R. Busselez, B. Arnaud, P. Rabiller, A. Kurita, E.
Nishibori, M. Sakata, M. Takatad and B. B. Iversen, Acta Crystallogr., A66 (2010) 458 -
M

469.
[4] H. Tanaka, Y. Kuroiwa, M. Takata, Phys. Rev. B., 74, (2006) 172105-1 - 172105-4.
D

[5] L. Palatinus and S. Smaalen, Acta Crystallogr., A58 (2002) 559-567.

[6] S. Smaalen, L. Palatinus, M. Schneider, Acta Crystallogr., A59 (2003) 459-469.
TE

[7] T. Matsukawa, A. Hoshikawa, Y. Ishikawa, T. Ishigaki, J. Mol. Struct., 1134 (2017)

835 - 839.
EP

[8] S. Christensen, M. A. Avila, K. Suekuni, R. Piltz, T. Takabatakeb, M. Christensen,

Dalton Trans., 42 (2013) 14766–14775.
[9] M. Yashima, Solid State Ionics, 179 (2008) 797–803.
C

[10] Y. Kato, S. Hori, T. Saito, K. Suzuki, M. Hirayama, A. Mitsui, M. Yonemura, H.

AC

Iba, R. Kanno, Nature Energy, 1 (2016) 16030-1 - 16030-7.

[11] S. Hori, S. Taminato, K. Suzuki, M. Hirayama, Y. Kato, R. Kanno, Acta
Crystallogr., B71 (2015) 727–736.
[12] M. Yashima, K. Nomura, H. Kageyama, Y. Miyazaki, N. Chitose, K. Adachi, Chem.
Phys. Lett., 380 (2003) 391–396.
[13] M. Sakata, R. Mori, S. Kumazawza, M. Takata, H. Toraya, J. Appl. Cryst. 23, 526–
534 (1990).
[14] F. Izumi and K. Momma, IOP Conf. Series.: Materials Science and Engineering,

8
 ACCEPTED MANUSCRIPT

18 (2011) 022011-1 – 022011-6.

[15] Th. Hahn, International Tables for Crystallography, Vol. A : Space-group
symmetry, 5th edition (2006).
[16] V. Petricek, M. Dusek, L. Palatinus, Z. Kristallogr., 229 (2014). 345-352.
[17] F. Izumi and R. A. Dilanian, “Recent Research Developments in Physics,” Vol. 3,

PT
Part II, Transworld Research Network, Trivandrum (2002) 699–726.
[18] J. Rodriguez-Carvajal, Physica B, 192 (1993) 55-69.

RI
[19] K. Momma, T. Ikeda, A.A. Belik and F. Izumi, Powder Diffraction, 28, (2013)
184-193.

SC
[20] R. Oishi, M. Yonemura, Y. Nishimaki, S. Torii, A. Hoshikawa, T. Ishigaki, T.
Morishima, K. Mori and T. Kamiyama, Nucl. Instrum. Methods., A600 (2009) 94–96.

U
[21] R. Oishi-Tomiyasu, M. Yonemura, T. Morishima, A. Hoshikawa, S. Torii, T.
Ishigaki, T. Kamiyama, J. Appl. Cryst., 45 (2012) 299–308.
AN
[22] E. T. Jaynes, Phys. Rev., 106 (1957) 620 - 630.
[23] D. M. Collins, Nature, 298 (1982) 49-51.
M

[24] M. Sakata and M. Sato, Acta Crystallogr., A46 (1990) 263–270.

[25] S. Kumazawa, Y. Kubota, M. Takata, M. Sakata and Y. Ishibashi, J. Appl. Cryst., 26,
D

(1993) 453–457.
[26] S. Kumazawa, M, Takata and M. Sakata, Acta Crystallogr., A51 (1995) 47-53.
TE

[27] M. Sakata, T. Uno, M. Takata, J. Appl. Cryst., 26 (1993) 159 – 165.

[28] R. Y. de Vries, W. J. Briels, D. Feil, Acta Crystallogr., A50 (1994) 383–391.
EP

[29] H. Tanaka, M. Takata, E. Nishibori, K. Kato, T. Iishi and M. Sakata, J. Appl. Cryst.,
35 (2002) 282 - 286.
C
AC

9
 ACCEPTED MANUSCRIPT

Figures and Tables

Table 1. Examples for the bench-mark test by Z-MEM

PT
RI
U SC
AN
M
D
TE
C EP
AC

Figure 1. Comparison elapsed times against multi-threading by Z-MEM of (a) Al2O3, (b)
C2H7NO3S and (c) MnF2. Blue mesh bars mean single CPU calculation, red bars are
multi-threading calculation using OpenMP.

10
 ACCEPTED MANUSCRIPT

1x106
1.0E6
O
Al
1.0E5
100000

1.0E4
constraint CF

10000

PT
1.0E3
1000

RI
1.0E2
100

SC
1.0E110 auto λ

U
Fixed λ
1.0 1
AN
11 10
10 100
100 1000
1000

iteration number
M

Figure 2. Cycle dependence on CF (see. equation (3)) value of Al2O3 (logarithmic scale).
Blue dash line is used the fixed Lagrange multiplier. Red line means the result by
D

automatically optimization λ equipped in Z-MEM.

TE
C EP
AC

Figure 3. Screen shot of GUI Z-MEM bundled in Z-Rietveld.

11