Quantum Chemical Calculations by Parallel Computer from Commodity PC

Computational quantum chemistry helps us to determine, calculate, and study new concepts, compounds, reactions and mechanisms. Such way is very useful with compounds that require exceptionally care in their handling, such as explosives, decreasing risk to persons testing and maintenance costs in service. Computational quantum chemistry is the ground of molecular modeling, on prediction the behavior of individual molecules within a chemical system. The molecular modeling let us to obtain the molecular characteristics comparable with experimental date. In this way the molecular structures of for positional isomers of 2,4,6-trinitrotoluene (TNT) were calculated by an ab initio HF/6-31G∗ method using self made local area personal computer (PC) cluster TAURAS. The cluster was made from heterogeneous commodity hardware of teaching class and for high performance computing (HPC) was used the SCore cluster system software developed in Japan. The structure and the features of the cluster are described and the performance is evaluated during solving of linear algebra testing tasks. During the determination of the structures of the positional isomers of TNT, the deformation of the phenyl ring and the distortions of the nitro and methyl groups were concern. The calculations confirmed that both of these were affected by the positions of nitro groups. A comparison of the calculated energies of all the isomers revealed the tendency to form the stable isomers when the close contact effects of the nitro groups were reduced

PC Cluster Possibilities in Mathematical Modeling in Quantum Mechanical Molecular Computations

We present the PC cluster built in the Department of Applied Sciences of Lithuanian Military Academy. The structure of the cluster is described and the performance is evaluated by solving of linear algebra testing tasks and nonlinear quantum chemistry molecular electronic structure computations

On the Cholesky Decomposition for electron propagator methods: General aspects and application on C60

To treat the electronic structure of large molecules by electron propagator methods we developed a parallel computer program called P-RICD$\Sigma$. The program exploits the sparsity of the two-electron integral matrix by using Cholesky decomposition techniques. The advantage of these techniques is that the error introduced is controlled only by one parameter which can be chosen as small as needed. We verify the tolerance of electron propagator methods to the Cholesky decomposition threshold and demonstrate the power of the P-RICD$\Sigma$ program for a representative example (C60). All decomposition schemes addressed in the literature are investigated. Even with moderate thresholds the maximal error encountered in the calculated electron affinities and ionization potentials amount to a few meV only, and the error becomes negligible for small thresholds.Comment: 30 pages, 6 figures submitted to J.Chem. Phy

Scalable computational chemistry: new developments and applications

The computational part of the thesis is the investigation of titanium chloride (II) as a potential catalyst for the bis-silylation reaction of ethylene with hexaclorodisilane at different levels of theory. Bis-silylation is an important reaction for producing bis(silyl) compounds and new C-Si bonds, which can serve as monomers for silicon containing polymers and silicon carbides. Ab initio calculations on the steps involved in a proposed mechanism are presented. This choice of reactants allows us to study this reaction at reliable levels of theory without compromising accuracy. Our calculations indicate that this is a highly exothermic barrierless reaction. The TiCl 2 catalyst removes a 50 kcal/mol activation energy barrier required for the reaction without the catalyst. The first step is interaction of TiCl 2 with ethylene to form an intermediate that is 60 kcal/mol below the energy of the reactants. This is the driving force for the entire reaction. Dynamic correlation plays a significant role because RHF calculations indicate that the net barrier for the catalyzed reaction is 50 kcal/mol. We conclude that divalent Ti has the potential to become an important industrial catalyst for silylation reactions.;In the programming part of the thesis, parallelization of different quantum chemistry methods is presented. The parallelization of code is becoming important aspect of quantum chemistry code development. Two trends contribute to it: the overall desire to study large chemical systems and the desire to employ highly correlated methods which are usually computationally and memory expensive. In the presented distributed data algorithms computation is parallelized and the largest arrays are evenly distributed among CPUs. First, the parallelization of the Hartree-Fock self-consistent field (SCF) method is considered. SCF method is the most common starting point for more accurate calculations. The Fock build (sub step of SCF) from AO integrals is also often used to avoid MO integral computation. The presented distributed data SCF increases the size of chemical systems that can be calculated by using RHF and DFT. The important ab initio method to study bond formation and breaking as well as excited molecules is CASSCF. The presented distributed data CASSCF algorithm can significantly decrease computational time and memory requirements per node. Therefore, large CASSCF computations can be performed. The most time consuming operation to study potential energy surfaces of reactions and chemical systems is Hessian calculations. The distributed data parallelization of CPHF will allow scientists carry out large analytic Hessian calculations