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小木虫论坛-学术科研互动平台 » 计算模拟区 » 第一性原理 » 其他 » 【分享】DFT计算软件OPENMX
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molech

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[交流] 【分享】DFT计算软件OPENMX

日本研究者开发的DFT计算软件，GNU开源软件，更新的比较快，现在是3.5版本。http://www.openmx-square.org/
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1楼 2009-10-16 21:28:41
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aylayl08

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珍惜拥有，快乐人生!欢迎光临计算模拟区(*^__^*)。。。。。。。。。。。。。。
2楼2009-10-16 21:31:42
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wuli8

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小木虫(金币+0.5):给个红包，谢谢回帖交流
aylayl08(金币+2,VIP+0):谢谢介绍OpenMX 10-16 21:44
What is OpenMX?
OpenMX (Open source package for Material eXplorer) is a software package for nano-scale material simulations based on density functional theories (DFT) [1], norm-conserving pseudopotentials [2,20,21], and pseudo-atomic localized basis functions [23]. Since the code is designed for the realization of large-scale ab initio calculations on parallel computers, it is anticipated that OpenMX can be a useful and powerful tool for nano-scale material sciences in a wide variety of systems such as bio-materials, carbon nanotubes, magnetic materials, and nanoscale conductors. The distribution of the program package and the source codes follow the practice of the GNU General Public License (GPL) [47], and they are downloadable from http:http://www.openmx-square.org/


Features and capabilities of OpenMX Ver. 3.5 are as follows:

Total energy and forces by cluster, band, and O(N) methods
Local density approximation (LDA, LSDA) [2,3,4] and generalized gradient approximation (GGA) [5] to the exchange-correlation potential
Norm-conserving pseudopotentials [2,20,21]
Variationally optimized pseudo-atomic basis functions [23]
Fully and scalar relativistic treatment within pseudopotential scheme [10,19,13]
Non-collinear DFT [6,7,8,9]
Constraint DFT for non-collinear spin and orbital orientation [11]
Collinear LDA+U and non-collinear LDA+U methods [16]
Macroscopic polarization by Berry's phase [12]
Divide-conquer (DC) method [28], generalized DC method, and Krylov subspace method for O(N) eigenvalue solver
Simple, RMM-DIIS [31], GR-Pulay [30], Kerker [32], and RMM-DIIS with Kerker's metric [31] charge mixing schemes
Exchange coupling parameter [14,15]
Optical conductivity
Charge doping
Uniform electric field
Full and constrained geometry optimization
Electric transport calculation by a non-equilibrium Green's function method
Construction of maximally localized wannier functions
NVE ensemble molecular dynamics
NVT ensemble molecular dynamics by a velocity scaling [17] and the Nose-Hoover methods [18]
Mulliken, Voronoi, and ESP fitting analysis of charge and spin densities
Analysis of wave functions and electron (spin) densities
Dispersion analysis by the band calculation
Density of states (DOS) and projected DOS
Flexible data format for the input
Completely dynamic memory allocation
Parallel execution by Message Passing Interface (MPI)
Parallel execution by OpenMP
Useful user interface for developers
Evaluation of two-center integrals using Fourier transformation [27]
Evaluation of three-center integrals by a projector expansion method [24]
Solution of Poisson's equation using FFT [26]
Considerable functionalities are available for calculations of physical properties such as magnetic, dielectric, electric transport properties as listed above. Not only conventional diagonalization schemes are provided for clusters, molecules, slab, and solids, but also linear scaling methods are supported as the eigenvalue solver. Three calculation parts in OpenMX are mainly time-consuming:

Evaluation of Hamiltonian matrix elements
Solution of Poisson's equation
Diagonalization of the generalized secular equation
For the first and second parts, the computational time always scales as O(N) and O(Nlog(N)) for any eigenvalue solver, where N is the number of atoms, basis functions, or grid points. When the conventional diagonalization scheme (cluster and band methods) is used, the computational time for the third part scales as O(N). On the other hand, the O(N) methods can solve the eigenvalue problem in O(N) operation in exchange for accuracy. For large scale calculations parallel execution by MPI or OpenMX is supported for parallel machines. The hybrid parallelization by OpenMP/MPI is also supported which is suitable for PC cluster consisting of multicore processors. All work arrays in the program codes are dynamically allocated with the minimum memory size required by an input file. The execution environment is unix and linux. For the execution of OpenMX, you are required to possess pseudo-atomic basis orbitals and pseudopotentials. These input data can be calculated using ADPACK which is a program package for atomic density functional calculations. Conveniently, the data for several elements and ADPACK are available from a web site (http://www.openmx-square.org/). We are continuously working toward development. Motivated contributors who want to develop the open source codes are welcome. If so, the contact information is available in the above website.
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3楼2009-10-16 21:35:37
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wuli8

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fegg7502(金币+1,VIP+0):thank you very much! 10-17 17:46
Anisotropic exchange interactions of spin-orbit-integrated states in Sr2IrO4
H. Jin, H. Jeong, T. Ozaki, and J. Yu, Phys. Rev. B 80, 075112 (5 pages) (2009).


Revisiting magnetic coupling in transition-metal-benzene complexes with maximally localized Wannier functions
H. Weng, T. Ozaki, and K. Terakura, Phys. Rev. B 79, 235118 (8 pages) (2009).


Graphene nanoribbon array in a cellular automata architecture for propagation of binary information
A. Leon, Z. Barticevic, and M. Pacheco, Appl. Phys. Lett. 94, 173111 (3 pages) (2009).


Competition between structural distortion and magnetic moment formation in fullerene C20
M. J. Han, G. Kim, J.-I. Lee, and J. Yu, J. Chem. Phys. 130, 184107 (2009).


Band Structures of Narrow Zigzag Silicon Carbon Nanoribbons
P. Lou and J.Y. Lee, J. Phys. Chem. C 113, 12637 (4 pages) (2009).


Frustrated magnetic interactions, giant magneto-elastic coupling, and magnetic phonons in iron-pnictides
T. Yildirim, Physica C 469, 425 (17 pages) (2009).


Numerical evaluation of electron repulsion integrals for pseudoatomic orbitals and their derivatives
M. Toyoda and T. Ozaki, J. Chem. Phys. 130, 124114 (7 pages) (2009).


Substrate-mediated interactions of Pt atoms adsorbed on single-wall carbon nanotubes: Density functional calculations
H.C. Dam, N.T. Cuong, A. Sugiyama, T. Ozaki, A. Fujiwara, T. Mitani, and S. Okada, Phys. Rev. B 79, 115426 (6 pages) (2009).


Localized electronic states induced by defects and possible origin of ferroelectricity in strontium titanate thin films
Y. S. Kim, J. Kim, S. J. Moon, W. S. Choi, Y. J. Chang, J.-G. Yoon, J. Yu, J.-S. Chung, and T. W. Noh, Appl. Phys. Lett. 94, 202906 (3 pages) (2009).


Calculation of electronic structures and magnetic moments of Nd2Fe14B and Dy2Fe14B by using linear-combination-of-pseudo-atomic-orbital method
I. Kitagawa, J. Appl. Phys. 105, 07E502 (3 pages) (2009).


Equilibrium structure of delta-Bi2O3 from first principles
D. Music, S. Konstantinidis, and J. M. Schneider, J. Phys.: Condens. Matter 21, 175403 (7 pages) (2009).


Carrier-induced noncollinear magnetism in perovskite manganites by first-principles calculations
K. Sawada and F. Ishii, J. Phys.: Condens. Matter 21, 064246 (4 pages) (2009).


Reduction-Controlled Viologen in Bisolvent as an Environmentally Stable n-Type Dopant for Carbon Nanotubes
S.M. Kim, J.H. Jang, K.K. Kim, H.K. Park, J.J. Bae, W.J. Yu, Il Ha Lee, G. Kim, D.D. Loc, U.J. Kim, E.-H. Lee, H.-J. Shin, J.-Y. Choi, and Y.H. Lee, J. Am. Chem. Soc. 131, 327 (5 pages) (2009).


Phase Control of Graphene Nanoribbon by Carrier Doping: Appearance of Noncollinear Magnetism
K. Sawada, F. Ishii, M. Saito, S. Okada, and T. Kawai, Nano Lett. 9, 269 (4 pages) (2009).
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4楼2009-10-16 21:37:40
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xirainbow

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小木虫(金币+0.5):给个红包，谢谢回帖交流
引用回帖:
Originally posted by aylayl08 at 2009-10-16 21:31:
无法显示该网页

啊哈，
我一直以为只有我这里才无法打开
原来你能来也打不开；）
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5楼2009-10-16 21:42:38
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xirainbow

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小木虫(金币+0.5):给个红包，谢谢回帖交流
fegg7502(金币+2,VIP+0):thank you very much! 10-17 17:46
引用回帖:
Originally posted by molech at 2009-10-16 21:28:
日本研究者开发的DFT计算软件，GNU开源软件，更新的比较快，现在是3.5版本。http://www.openmx-square.org/

恩；）
这个东西我已经学习了一周了；）
国内用这个的好像不多，
希望以后可以多多请教和交流；）
这是我的博客http://blog.sina.com.cn/nkasir，欢迎有空瞅瞅；）
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6楼2009-10-16 22:02:03
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molech

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fegg7502(金币+2,VIP+0):thank you very much! 10-17 17:46
看了你的博客，不错。我没有用它来正经做计算，只是试了试3.5之前的一个版本，我当时编译的时候也遇到麻烦，我当时记得有几点要注意: 1)要安装fftw3-dev, 2) 去掉 -lg2c 来编译, 3) 用mkl em64t (opteron CPU). 另外，他们的论坛也是比较活跃的，看看帮助不少。
引用回帖:
Originally posted by xirainbow at 2009-10-16 22:02:

恩；）
这个东西我已经学习了一周了；）
国内用这个的好像不多，
希望以后可以多多请教和交流；）
这是我的博客http://blog.sina.com.cn/nkasir，欢迎有空瞅瞅；）

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7楼2009-10-16 23:14:22
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xirainbow

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小木虫(金币+0.5):给个红包，谢谢回帖交流
fegg7502(金币+2,VIP+0):thank you very much! 10-17 17:46
引用回帖:
Originally posted by molech at 2009-10-16 23:14:
看了你的博客，不错。我没有用它来正经做计算，只是试了试3.5之前的一个版本，我当时编译的时候也遇到麻烦，我当时记得有几点要注意: 1)要安装fftw3-dev, 2) 去掉 -lg2c 来编译, 3) 用mkl em64t (opteron CPU). 另 ...

谢谢您的指点；）
我确实在使用fftw2的时候遇到了麻烦，最后被迫用的fftw3：）
我刚开始学习，估计半年内还没能力用它来做正经计算；）

其实最令我郁闷的是，我这里无法登陆它的主页和论坛
不知道为什么；（
aylayl08  也无法登陆
估计国内很多地方都无法登陆啊；）

[ Last edited by xirainbow on 2009-10-17 at 09:31 ]
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8楼2009-10-17 09:30:17
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lz830617

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小木虫(金币+0.5):给个红包，谢谢回帖交流
fegg7502(金币+2,VIP+0):thank you very much! 10-17 17:46
各位虫友，我使用这个软件已经一年多了。谈谈自己的个人感受吧。
openmx与siesta属于同一类程序，只不过基组产生的软件不同。从速度上说openmx要快于siesta，从功能上说各有千秋。openmx增加了瓦尼尔函数，siesta增加了transiesta用于计算电子输运。精度上来说siesta要好于openmx，因为基组的选择较多。而openmx直接是赝势。我用openmx做过一篇文章，但是学习型的。计算结果通过比较与ab initio有一定的可比性。
所以根据你的课题将openmx与其他程序组合使用。小日本也是组合使用。因为程序相对较小，所以速度快，但功能就有所缺失。
以上是我的个人经验之谈。
这个网站是可以登录的。免费下载。
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9楼2009-10-17 10:32:17
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xirainbow

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小木虫(金币+0.5):给个红包，谢谢回帖交流
fegg7502(金币+2,VIP+0):thank you very much! 10-17 17:47
引用回帖:
Originally posted by lz830617 at 2009-10-17 10:32:
各位虫友，我使用这个软件已经一年多了。谈谈自己的个人感受吧。
openmx与siesta属于同一类程序，只不过基组产生的软件不同。从速度上说openmx要快于siesta，从功能上说各有千秋。openmx增加了瓦尼尔函数，siest ...

啊哈；）
又一位战友哦；）

非常感谢您分享自己的经验；）

您上面的帖子有三个小问题请教您；）
1：”而openmx直接是赝势。“
这句话我没看懂，这个“而”是相对于哪句话的：）？
2：“计算结果通过比较与ab initio有一定的可比性。”
能否给些更详细的对比数据；）
3：“小日本也是组合使用。”
您所指的组合使用是什么意思？

本人愚钝，还望见谅：）

另：无法登陆是分地区的：）
我这里翻墙都上不去；（
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10楼2009-10-17 10:45:24
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