The time-dependent density functional-based tight-bind （TD-DFTB） method is implemented on the multi-core and the graphical processing unit （GPU） system for excited state calcu-lations of large system with hundreds...The time-dependent density functional-based tight-bind （TD-DFTB） method is implemented on the multi-core and the graphical processing unit （GPU） system for excited state calcu-lations of large system with hundreds or thousands of atoms. Sparse matrix and OpenMP multithreaded are used for building the Hamiltonian matrix. The diagonal of the eigenvalue problem in the ground state is implemented on the GPUs with double precision. The GPU- based acceleration fully preserves all the properties, and a considerable total speedup of 8.73 can be achieved. A Krylov-space-based algorithm with the OpenMP parallel and CPU acceleration is used for finding the lowest eigenvalue and eigenvector of the large TDDFT matrix, which greatly reduces the iterations taken and the time spent on the excited states eigenvalue problem. The Krylov solver with the GPU acceleration of matrix-vector product can converge quickly to obtain the final result and a notable speed-up of 206 times can be observed for system size of 812 atoms. The calculations on serials of small and large systems show that the fast TD-DFTB code can obtain reasonable result with a much cheaper computational requirement compared with the first-principle results of CIS and full TDDFT calculation.展开更多
The adsorption of a 1-pyrenebutanoic acid, succinimidyl ester (PSE) interacting with metallic armchair (n, n) carbon nanotubes (CNTs) (n= 3-13) was investigated by using a density-functional tight-binding method with ...The adsorption of a 1-pyrenebutanoic acid, succinimidyl ester (PSE) interacting with metallic armchair (n, n) carbon nanotubes (CNTs) (n= 3-13) was investigated by using a density-functional tight-binding method with an empirical van der Waals force correction. In this study of large systems involving weak interactions, our calculations showed that the pyrene ring of PSE could be spontaneously absorbed onto the CNTs surface through π-π stacking at the physisorption distances. Increasing of the CNTs diameter leads to a higher adsorption energy. After adsorption of PSE on its sidewall, the geometric and electronic structures of CNTs are basically undamaged. CNTs contribute to the main peak of the electron excitation procedure in the UV/vis spectrum, with a slight red shift after adsorption of PSE.展开更多
Based on density functional theory and electronegativity equalization principle, a σπ model, which considers the structure of double bond for the first time, is developed. In this model the double bond is partitione...Based on density functional theory and electronegativity equalization principle, a σπ model, which considers the structure of double bond for the first time, is developed. In this model the double bond is partitioned into one σ bond region and four π bond regions. The atom bond electronegativity equalization method plus σπ model(ABEEM σπ ) is then proposed for the calculation of charge distribution and charge polarization in large molecules. It has been shown that the results of charge distribution in large molecules obtained by ABEEM σπ model agree with those obtained by ab initio method very well. In addition, the model can be used to explain the region selectivity of Diels Alder reaction successfully. All these indicate that ABEEM σπ model is reasonable and reliable.展开更多
Using density functional methods,some properties were studied such as the energies and compositions of frontier molecular orbitals and the atomic charges,which are related to the reactive behavior of thioureas contain...Using density functional methods,some properties were studied such as the energies and compositions of frontier molecular orbitals and the atomic charges,which are related to the reactive behavior of thioureas containing different N-substituent groupings.The calculation results indicate that the N-substituent groupings have significant effect on the flotation performance of thiourea collectors.The order of electron-donating ability is N-propyl-N'-benzyl-thiourea(PBZYTU)>N-propyl-N'-ethyl-thiourea (PETU)>N-propyl-N'-allyl-thiourea(PALTU)>>N-propyl-N'-acetyl-thiourea(PACTU)>N-propyl-N'-ethoxycarbonyl-thiourea (PECTU)>N-propyl-N'-benzoyl-thiourea(PBZOYTU),and the order of feedback-electron-accepting ability is PBZOYTU> PACTU>PECTU>>PALTU>PETU>PBZYTU.This implies that PBZOYTU,PACTU or PECTU can react with copper atoms having(t2g) 6 (eg) 3Cu(II)or t 6e 4Cu(I)configuration on the surfaces of copper sulfide minerals through normal covalent bond and back donation covalent bond,and exhibit excellently collecting performance for copper sulfide minerals.These are consistent with the experimental data reported in the literatures.展开更多
文摘The time-dependent density functional-based tight-bind （TD-DFTB） method is implemented on the multi-core and the graphical processing unit （GPU） system for excited state calcu-lations of large system with hundreds or thousands of atoms. Sparse matrix and OpenMP multithreaded are used for building the Hamiltonian matrix. The diagonal of the eigenvalue problem in the ground state is implemented on the GPUs with double precision. The GPU- based acceleration fully preserves all the properties, and a considerable total speedup of 8.73 can be achieved. A Krylov-space-based algorithm with the OpenMP parallel and CPU acceleration is used for finding the lowest eigenvalue and eigenvector of the large TDDFT matrix, which greatly reduces the iterations taken and the time spent on the excited states eigenvalue problem. The Krylov solver with the GPU acceleration of matrix-vector product can converge quickly to obtain the final result and a notable speed-up of 206 times can be observed for system size of 812 atoms. The calculations on serials of small and large systems show that the fast TD-DFTB code can obtain reasonable result with a much cheaper computational requirement compared with the first-principle results of CIS and full TDDFT calculation.
基金Supported by the Research Grants Council of Hong Kong SAR (Project No. CityU 103907)the National Basic Research Program of China (Grant No. 2006CB933000)Centre for Applied Computing and Interactive Media (ACIM)
文摘The adsorption of a 1-pyrenebutanoic acid, succinimidyl ester (PSE) interacting with metallic armchair (n, n) carbon nanotubes (CNTs) (n= 3-13) was investigated by using a density-functional tight-binding method with an empirical van der Waals force correction. In this study of large systems involving weak interactions, our calculations showed that the pyrene ring of PSE could be spontaneously absorbed onto the CNTs surface through π-π stacking at the physisorption distances. Increasing of the CNTs diameter leads to a higher adsorption energy. After adsorption of PSE on its sidewall, the geometric and electronic structures of CNTs are basically undamaged. CNTs contribute to the main peak of the electron excitation procedure in the UV/vis spectrum, with a slight red shift after adsorption of PSE.
基金Supported by Education Department of Heilongjiang Province(11533046)the Academic Scientific and Technological Innovative Projects of Heilongjiang University University Students
文摘Based on density functional theory and electronegativity equalization principle, a σπ model, which considers the structure of double bond for the first time, is developed. In this model the double bond is partitioned into one σ bond region and four π bond regions. The atom bond electronegativity equalization method plus σπ model(ABEEM σπ ) is then proposed for the calculation of charge distribution and charge polarization in large molecules. It has been shown that the results of charge distribution in large molecules obtained by ABEEM σπ model agree with those obtained by ab initio method very well. In addition, the model can be used to explain the region selectivity of Diels Alder reaction successfully. All these indicate that ABEEM σπ model is reasonable and reliable.
基金Project(50604016)supported by the National Natural Science Foundation of ChinaProject(2007B52)supported by the Foundation for the Author of National Excellent Doctoral Dissertation of China+3 种基金Project(NCET-08-0568)supported by the Program for New Century Excellent Talents in Chinese UniversityProject(2007CB613602)supported by the National Basic Research Program of ChinaProject(2007AA06Z122)supported by the National High-tech Research and Development Program of ChinaProject(2007BAB22B01)supported by the National Science and Technology Support Project of China
文摘Using density functional methods,some properties were studied such as the energies and compositions of frontier molecular orbitals and the atomic charges,which are related to the reactive behavior of thioureas containing different N-substituent groupings.The calculation results indicate that the N-substituent groupings have significant effect on the flotation performance of thiourea collectors.The order of electron-donating ability is N-propyl-N'-benzyl-thiourea(PBZYTU)>N-propyl-N'-ethyl-thiourea (PETU)>N-propyl-N'-allyl-thiourea(PALTU)>>N-propyl-N'-acetyl-thiourea(PACTU)>N-propyl-N'-ethoxycarbonyl-thiourea (PECTU)>N-propyl-N'-benzoyl-thiourea(PBZOYTU),and the order of feedback-electron-accepting ability is PBZOYTU> PACTU>PECTU>>PALTU>PETU>PBZYTU.This implies that PBZOYTU,PACTU or PECTU can react with copper atoms having(t2g) 6 (eg) 3Cu(II)or t 6e 4Cu(I)configuration on the surfaces of copper sulfide minerals through normal covalent bond and back donation covalent bond,and exhibit excellently collecting performance for copper sulfide minerals.These are consistent with the experimental data reported in the literatures.
