{"title":"Polar Shift: Charge carrier polarization energies in organic electronic materials","authors":"K. Kaklamanis, D.G. Papageorgiou","doi":"10.1016/j.cpc.2025.109700","DOIUrl":null,"url":null,"abstract":"<div><div>Electronic polarization of charge carriers in the solid state plays an important role in organic electronics, as it alters the gas phase energy levels associated with phenomena such as charge transport, molecular doping, charge injection and charge separation at interfaces. In this article we present P<span>olar</span> S<span>hift</span>, a software package for calculating the polarization energy of an electron or hole charge carrier in organic electronic materials. The software uses an atomistic approach employing the microelectrostatics model. Molecular charge distributions are represented by atomic point charges, while the molecular polarizability is divided into distributed atomic contributions. The electrostatic and inductive components of the polarization energy are calculated separately. For the electrostatic interactions we propose an efficient cutoff–based scheme that allows fast yet accurate evaluation of the relevant energy. For the induction part we use a self–consistent iterative method based on modified field interaction tensors in the framework of the Thole model. P<span>olar</span> S<span>hift</span> can be applied to ideal molecular crystals, thermally disordered crystalline packings or completely amorphous materials. Many additional features are implemented such as calculation of the molecular polarizability tensor, fitting of molecular polarizabilities to reference values, different schemes for computing induction energies, and extrapolation of induction energies to the bulk limit. Special attention has been paid to the interoperability with other software packages, so P<span>olar</span> S<span>hift</span> can obtain the required input from various widely used file types such as pdb, mol2 or even binary dcd files. The software is parallelized using the MPI standard thus exploiting a wide range of shared and distributed memory computer architectures. P<span>olar</span> S<span>hift</span> is applied to eight different test cases of prototype organic electronics materials demonstrating its capabilities, and the results are compared with existing literature.</div></div><div><h3>Program summary</h3><div><em>Program Title:</em> P<span>olar</span> S<span>hift</span></div><div><em>CPC Library link to program files:</em> <span><span><span>https://doi.org/10.17632/26ck9stzh9.1</span></span><svg><path></path></svg></span></div><div><em>Developer's repository link:</em> <span><span><span>http://cmsl.materials.uoi.gr/polar-shift</span></span><svg><path></path></svg></span></div><div><em>Licensing provisions:</em> GPLv2</div><div><em>Programming language:</em> Fortran 2008</div><div><em>Supplementary material:</em> User manual (45 pages), 22 annotated examples with reference output, input and output files for the eight test cases described in the paper.</div><div><em>Nature of problem:</em> Electronic polarization of charge carriers in organic electronic materials is responsible for altering key quantities from their gas phase counterparts. In many molecular solids electron affinities and ionization potentials are severely affected, with the corresponding energy shifts reaching values of the order of ≈1 eV [1]. This suggests that polarization should be taken into account in phenomena such as charge transport, molecular doping, charge injection and charge separation at interfaces [2]. In addition, there is an ever–increasing demand for specialized, yet easy to use, computational tools to be used in the prediction and investigation of materials properties.</div><div><em>Solution method:</em> The classical atomistic microelectrostatics [3] (or alternatively known as polarizable point dipoles [4]) model is used. Atoms are represented by point charges reproducing the molecular electrostatic potential, while point dipoles are induced at each atomic site. The molecular polarizability tensor is represented by isotropic distributed atomic polarizabilities. By employing the zero overlap approximation the two contributions in polarization energy, namely electrostatic and induction, can be separately evaluated. Electrostatic interactions are calculated using a cutoff–based algorithm and automatic replication of the simulation cell where necessary. Induced dipole conformation in the system is determined self consistently using a successive over–relaxation algorithm, based on modified field interaction tensors in the framework of the Thole model [5]. The latter allows for short range interaction screening, thus avoiding the well known polarization catastrophe. Two different schemes are implemented to calculate induction in the condensed phase. (a) Dipole conformation is obtained by applying periodic boundary conditions and a truncation cutoff for intermolecular interactions. (b) A finite spherical cluster centered at the charged molecule is extracted from the simulation cell. Since in both cases the calculated induction energies depend on the truncation distance, an extrapolation method can be applied to retrieve the bulk limit.</div><div><em>Additional comments including restrictions and unusual features:</em> There are no restrictions on the number of molecules in the simulation cell, the only limit being computer memory. The software can read various widely used file formats, making it interoperable with other packages. Arbitrary simulation cells may be specified using cell lengths and angles. Assignment of atomic polarizabilities in large molecular structures can be assisted by selecting values from predefined sets, based on atomic element, type or index. Parallelization using MPI exploits shared or distributed memory computer architectures.</div></div><div><h3>References</h3><div><ul><li><span>[1]</span><span><div>N. Sato, K. Seki, H. Inokuchi, Polarization energies of organic solids determined by ultraviolet photoelectron spectroscopy, J. Chem. Soc. Faraday Trans. II 77 (1981) 1621, <span><span>https://doi.org/10.1039/F29817701621</span><svg><path></path></svg></span></div></span></li><li><span>[2]</span><span><div>G. D'Avino, L. Muccioli, F. Castet, C. Poelking, D. Andrienko, Z.G. Soos, J. Cornil, D. Beljonne, Electrostatic phenomena in organic semiconductors: fundamentals and implications for photovoltaics, J. Phys. Condens. Matter 28 (2016) 433002, <span><span>https://dx.doi.org/10.1088/0953-8984/28/43/433002</span><svg><path></path></svg></span></div></span></li><li><span>[3]</span><span><div>P. Ren, C. Wu, J.W. Ponder, Polarizable atomic multipole-based molecular mechanics for organic molecules, J. Chem. Theory Comput. 7 (2011) 3143–3161, <span><span>https://doi.org/10.1021/ct200304d</span><svg><path></path></svg></span>.</div></span></li><li><span>[4]</span><span><div>J. Sala, E. Guàrdia, M. Masia, The polarizable point dipoles method with electrostatic damping: implementation on a model system, J. Chem. Phys. 133 (2010) 234101, <span><span>https://doi.org/10.1063/1.3511713</span><svg><path></path></svg></span>.</div></span></li><li><span>[5]</span><span><div>B.T. Thole, Molecular polarizabilities calculated with a modified dipole interaction, Chem. Phys. 59 (1981) 341, <span><span>https://doi.org/10.1016/0301-0104(81)85176-2</span><svg><path></path></svg></span></div></span></li></ul></div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"315 ","pages":"Article 109700"},"PeriodicalIF":7.2000,"publicationDate":"2025-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Computer Physics Communications","FirstCategoryId":"101","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S0010465525002024","RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS","Score":null,"Total":0}
引用次数: 0
Abstract
Electronic polarization of charge carriers in the solid state plays an important role in organic electronics, as it alters the gas phase energy levels associated with phenomena such as charge transport, molecular doping, charge injection and charge separation at interfaces. In this article we present Polar Shift, a software package for calculating the polarization energy of an electron or hole charge carrier in organic electronic materials. The software uses an atomistic approach employing the microelectrostatics model. Molecular charge distributions are represented by atomic point charges, while the molecular polarizability is divided into distributed atomic contributions. The electrostatic and inductive components of the polarization energy are calculated separately. For the electrostatic interactions we propose an efficient cutoff–based scheme that allows fast yet accurate evaluation of the relevant energy. For the induction part we use a self–consistent iterative method based on modified field interaction tensors in the framework of the Thole model. Polar Shift can be applied to ideal molecular crystals, thermally disordered crystalline packings or completely amorphous materials. Many additional features are implemented such as calculation of the molecular polarizability tensor, fitting of molecular polarizabilities to reference values, different schemes for computing induction energies, and extrapolation of induction energies to the bulk limit. Special attention has been paid to the interoperability with other software packages, so Polar Shift can obtain the required input from various widely used file types such as pdb, mol2 or even binary dcd files. The software is parallelized using the MPI standard thus exploiting a wide range of shared and distributed memory computer architectures. Polar Shift is applied to eight different test cases of prototype organic electronics materials demonstrating its capabilities, and the results are compared with existing literature.
Program summary
Program Title: Polar Shift
CPC Library link to program files:https://doi.org/10.17632/26ck9stzh9.1
Supplementary material: User manual (45 pages), 22 annotated examples with reference output, input and output files for the eight test cases described in the paper.
Nature of problem: Electronic polarization of charge carriers in organic electronic materials is responsible for altering key quantities from their gas phase counterparts. In many molecular solids electron affinities and ionization potentials are severely affected, with the corresponding energy shifts reaching values of the order of ≈1 eV [1]. This suggests that polarization should be taken into account in phenomena such as charge transport, molecular doping, charge injection and charge separation at interfaces [2]. In addition, there is an ever–increasing demand for specialized, yet easy to use, computational tools to be used in the prediction and investigation of materials properties.
Solution method: The classical atomistic microelectrostatics [3] (or alternatively known as polarizable point dipoles [4]) model is used. Atoms are represented by point charges reproducing the molecular electrostatic potential, while point dipoles are induced at each atomic site. The molecular polarizability tensor is represented by isotropic distributed atomic polarizabilities. By employing the zero overlap approximation the two contributions in polarization energy, namely electrostatic and induction, can be separately evaluated. Electrostatic interactions are calculated using a cutoff–based algorithm and automatic replication of the simulation cell where necessary. Induced dipole conformation in the system is determined self consistently using a successive over–relaxation algorithm, based on modified field interaction tensors in the framework of the Thole model [5]. The latter allows for short range interaction screening, thus avoiding the well known polarization catastrophe. Two different schemes are implemented to calculate induction in the condensed phase. (a) Dipole conformation is obtained by applying periodic boundary conditions and a truncation cutoff for intermolecular interactions. (b) A finite spherical cluster centered at the charged molecule is extracted from the simulation cell. Since in both cases the calculated induction energies depend on the truncation distance, an extrapolation method can be applied to retrieve the bulk limit.
Additional comments including restrictions and unusual features: There are no restrictions on the number of molecules in the simulation cell, the only limit being computer memory. The software can read various widely used file formats, making it interoperable with other packages. Arbitrary simulation cells may be specified using cell lengths and angles. Assignment of atomic polarizabilities in large molecular structures can be assisted by selecting values from predefined sets, based on atomic element, type or index. Parallelization using MPI exploits shared or distributed memory computer architectures.
References
[1]
N. Sato, K. Seki, H. Inokuchi, Polarization energies of organic solids determined by ultraviolet photoelectron spectroscopy, J. Chem. Soc. Faraday Trans. II 77 (1981) 1621, https://doi.org/10.1039/F29817701621
[2]
G. D'Avino, L. Muccioli, F. Castet, C. Poelking, D. Andrienko, Z.G. Soos, J. Cornil, D. Beljonne, Electrostatic phenomena in organic semiconductors: fundamentals and implications for photovoltaics, J. Phys. Condens. Matter 28 (2016) 433002, https://dx.doi.org/10.1088/0953-8984/28/43/433002
[3]
P. Ren, C. Wu, J.W. Ponder, Polarizable atomic multipole-based molecular mechanics for organic molecules, J. Chem. Theory Comput. 7 (2011) 3143–3161, https://doi.org/10.1021/ct200304d.
[4]
J. Sala, E. Guàrdia, M. Masia, The polarizable point dipoles method with electrostatic damping: implementation on a model system, J. Chem. Phys. 133 (2010) 234101, https://doi.org/10.1063/1.3511713.
[5]
B.T. Thole, Molecular polarizabilities calculated with a modified dipole interaction, Chem. Phys. 59 (1981) 341, https://doi.org/10.1016/0301-0104(81)85176-2
固体载流子的电子极化在有机电子学中起着重要的作用,因为它改变了气相的能级,与界面上的电荷输运、分子掺杂、电荷注入和电荷分离等现象有关。在本文中,我们提出了一个计算有机电子材料中电子或空穴载流子极化能的软件包Polar Shift。该软件采用采用微静电模型的原子方法。分子的电荷分布由原子点电荷表示,而分子的极化率则分为分布的原子贡献。极化能的静电分量和感应分量分别计算。对于静电相互作用,我们提出了一种有效的基于截止的方案,可以快速而准确地评估相关能量。对于归纳部分,我们在Thole模型的框架下采用了基于修正场相互作用张量的自洽迭代方法。极移可以应用于理想分子晶体,热无序晶体填料或完全非晶材料。实现了许多附加功能,如分子极化张量的计算,分子极化率与参考值的拟合,感应能计算的不同方案,以及感应能到体极限的外推。特别注意与其他软件包的互操作性,因此Polar Shift可以从各种广泛使用的文件类型(如pdb, mol2甚至二进制dcd文件)中获得所需的输入。该软件使用MPI标准并行化,从而利用了广泛的共享和分布式内存计算机体系结构。将Polar Shift应用于八个不同的原型有机电子材料测试案例中,验证了其性能,并将结果与现有文献进行了比较。程序摘要程序标题:Polar ShiftCPC库链接到程序文件:https://doi.org/10.17632/26ck9stzh9.1Developer's存储库链接:http://cmsl.materials.uoi.gr/polar-shiftLicensing条款:gplv2编程语言:Fortran 2008补充材料:用户手册(45页),22个带注释的示例,其中包含本文中描述的八个测试用例的参考输出、输入和输出文件。问题性质:有机电子材料中载流子的电子极化负责改变其气相对应物的关键量。在许多分子固体中,电子亲和和电离势受到严重影响,相应的能量位移达到≈1 eV[1]数量级。这表明在界面[2]处的电荷输运、分子掺杂、电荷注入和电荷分离等现象中应考虑极化。此外,对专业的、易于使用的计算工具的需求也在不断增加,这些工具可用于预测和研究材料的特性。解决方法:使用经典的原子微静电[3](或称为极化点偶极子[4])模型。原子由再现分子静电势的点电荷表示,而在每个原子位置诱导点偶极子。分子极化张量由各向同性分布原子极化张量表示。利用零重叠近似,可以分别计算静电和感应对极化能的贡献。静电相互作用的计算使用基于截止的算法,并在必要时自动复制模拟单元。在Thole模型[5]的框架下,基于修正的场相互作用张量,采用逐次超松弛算法自一致地确定了系统中的诱导偶极子构象。后者允许近距离相互作用筛选,从而避免了众所周知的极化灾难。采用了两种不同的方案来计算凝聚相的感应强度。(a)偶极构象是通过应用周期性边界条件和分子间相互作用的截断截断得到的。(b)从模拟细胞中提取出以带电分子为中心的有限球形团簇。由于在这两种情况下计算的感应能都取决于截断距离,因此可以采用外推法来检索体积极限。附加说明,包括限制和不寻常的功能:模拟细胞中的分子数量没有限制,唯一的限制是计算机内存。该软件可以读取各种广泛使用的文件格式,使其与其他软件包互操作。可以使用单元长度和角度指定任意模拟单元。 可以根据原子元素、类型或索引,从预定义的集合中选择值来辅助大分子结构中原子极化率的赋值。使用MPI的并行化利用共享或分布式内存计算机体系结构。陈志强,刘志强,紫外光电子能谱法测定有机固体的极化能,化学学报。Soc。法拉第反式。II 77 (1981) 1621, https://doi.org/10.1039/F29817701621[2]G。D'Avino, L. Muccioli, F. Castet, C. Poelking, D. Andrienko, Z.G. Soos, J. Cornil, D. Beljonne,有机半导体的静电现象:基本原理及其对光电的影响,物理学报。提供者。Matter 28 (2016) 433002, https://dx.doi.org/10.1088/0953-8984/28/43/433002[3]P。理论计算,7 (2011)3143-3161,https://doi.org/10.1021/ct200304d.[4]J。Sala, E. Guàrdia, M. Masia,具有静电阻尼的极化点偶极子方法:在模型系统上的实现,J.化学。物理学报,133 (2010)234101,https://doi.org/10.1063/1.3511713.[5]B.T。用修正的偶极相互作用计算分子极化率,化学。物理学59 (1981)341,https://doi.org/10.1016/0301-0104(81)85176-2
期刊介绍:
The focus of CPC is on contemporary computational methods and techniques and their implementation, the effectiveness of which will normally be evidenced by the author(s) within the context of a substantive problem in physics. Within this setting CPC publishes two types of paper.
Computer Programs in Physics (CPiP)
These papers describe significant computer programs to be archived in the CPC Program Library which is held in the Mendeley Data repository. The submitted software must be covered by an approved open source licence. Papers and associated computer programs that address a problem of contemporary interest in physics that cannot be solved by current software are particularly encouraged.
Computational Physics Papers (CP)
These are research papers in, but are not limited to, the following themes across computational physics and related disciplines.
mathematical and numerical methods and algorithms;
computational models including those associated with the design, control and analysis of experiments; and
algebraic computation.
Each will normally include software implementation and performance details. The software implementation should, ideally, be available via GitHub, Zenodo or an institutional repository.In addition, research papers on the impact of advanced computer architecture and special purpose computers on computing in the physical sciences and software topics related to, and of importance in, the physical sciences may be considered.