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Todd J Martinez - One of the best experts on this subject based on the ideXlab platform.
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Electronic Absorption Spectra from MM and ab Initio QM/MM Molecular Dynamics: Environmental Effects on the Absorption Spectrum of Photoactive Yellow Protein
2016Co-Authors: Christine M Isborn, Matthew A Clark, Ross C Walker, Andreas W. Götz, Todd J MartinezAbstract:*S Supporting Information ABSTRACT: We describe a new interface of the GPU parallelized TERACHEM electronic Structure Package and the AMBER molecular dynamics Package for quantum mechanical (QM) and mixed QM and molecular mechanical (MM) molecular dynamics simulations. This QM/MM interface is used for computation of the absorption spectra of the photoactive yellow protein (PYP) chromophore in vacuum, aqueous solution, and protein environments. The computed excitation energies of PYP require a very large QM region (hundreds of atoms) covalently bonded to the chromophore in order to achieve agreement with calculations that treat the entire protein quantum mechanically. We also show that 40 or more surrounding water molecules must be included in the QM region in order to obtain converged excitation energies of the solvated PYP chromophore. These results indicate that large QM regions (with hundreds of atoms) are a necessity in QM/MM calculations. Combining quantum mechanical (QM) and classical force field molecular mechanical (MM) methods creates the hybrid QM/ MM approach.1−9 This framework has been used to study many complex reactions including enzymatic catalysis,10−1
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electronic absorption spectra from mm and ab initio qm mm molecular dynamics environmental effects on the absorption spectrum of photoactive yellow protein
Journal of Chemical Theory and Computation, 2012Co-Authors: Christine M Isborn, Andreas W Gotz, Matthew A Clark, Ross C Walker, Todd J MartinezAbstract:We describe a new interface of the GPU parallelized Terachem electronic Structure Package and the Amber molecular dynamics Package for quantum mechanical (QM) and mixed QM and molecular mechanical (MM) molecular dynamics simulations. This QM/MM interface is used for computation of the absorption spectra of the photoactive yellow protein (PYP) chromophore in vacuum, aqueous solution, and protein environments. The computed excitation energies of PYP require a very large QM region (hundreds of atoms) covalently bonded to the chromophore in order to achieve agreement with calculations that treat the entire protein quantum mechanically. We also show that 40 or more surrounding water molecules must be included in the QM region in order to obtain converged excitation energies of the solvated PYP chromophore. These results indicate that large QM regions (with hundreds of atoms) are a necessity in QM/MM calculations.
Christine M Isborn - One of the best experts on this subject based on the ideXlab platform.
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Electronic Absorption Spectra from MM and ab Initio QM/MM Molecular Dynamics: Environmental Effects on the Absorption Spectrum of Photoactive Yellow Protein
2016Co-Authors: Christine M Isborn, Matthew A Clark, Ross C Walker, Andreas W. Götz, Todd J MartinezAbstract:*S Supporting Information ABSTRACT: We describe a new interface of the GPU parallelized TERACHEM electronic Structure Package and the AMBER molecular dynamics Package for quantum mechanical (QM) and mixed QM and molecular mechanical (MM) molecular dynamics simulations. This QM/MM interface is used for computation of the absorption spectra of the photoactive yellow protein (PYP) chromophore in vacuum, aqueous solution, and protein environments. The computed excitation energies of PYP require a very large QM region (hundreds of atoms) covalently bonded to the chromophore in order to achieve agreement with calculations that treat the entire protein quantum mechanically. We also show that 40 or more surrounding water molecules must be included in the QM region in order to obtain converged excitation energies of the solvated PYP chromophore. These results indicate that large QM regions (with hundreds of atoms) are a necessity in QM/MM calculations. Combining quantum mechanical (QM) and classical force field molecular mechanical (MM) methods creates the hybrid QM/ MM approach.1−9 This framework has been used to study many complex reactions including enzymatic catalysis,10−1
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electronic absorption spectra from mm and ab initio qm mm molecular dynamics environmental effects on the absorption spectrum of photoactive yellow protein
Journal of Chemical Theory and Computation, 2012Co-Authors: Christine M Isborn, Andreas W Gotz, Matthew A Clark, Ross C Walker, Todd J MartinezAbstract:We describe a new interface of the GPU parallelized Terachem electronic Structure Package and the Amber molecular dynamics Package for quantum mechanical (QM) and mixed QM and molecular mechanical (MM) molecular dynamics simulations. This QM/MM interface is used for computation of the absorption spectra of the photoactive yellow protein (PYP) chromophore in vacuum, aqueous solution, and protein environments. The computed excitation energies of PYP require a very large QM region (hundreds of atoms) covalently bonded to the chromophore in order to achieve agreement with calculations that treat the entire protein quantum mechanically. We also show that 40 or more surrounding water molecules must be included in the QM region in order to obtain converged excitation energies of the solvated PYP chromophore. These results indicate that large QM regions (with hundreds of atoms) are a necessity in QM/MM calculations.
Gediminas Gaigalas - One of the best experts on this subject based on the ideXlab platform.
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crystal field module for the general relativistic atomic Structure Package
Computer Physics Communications, 2021Co-Authors: Gediminas Gaigalas, Daiji KatoAbstract:Abstract The latest version of the grasp2018 Package [Froese Fischer et al. (2019)], based on the multiconfigurational Dirac–Hartree–Fock method, is extended to account for effects of crystal fields in complex systems. Instead of using the simplified treatment of the crystal field effects based on the Stevens’ operator-equivalent method the program uses the fully ab-initio method in which the external ions are treated as point charges at fixed positions. In addition, examples of how to use the CF_Hamiltonian program are given in source directory grasp2018/src/appl/CF_Hamiltonian/Sample_Runs . Program summary Program Title: CF_Hamiltonian CPC Library link to program files: https://doi.org/10.17632/fksxwwjbx6.1 Licensing provisions: MIT license Programming language: Fortran 95. External routines/libraries used: Grasp 2018 modules: Libmod , Lib 9290, Librang 90; Grasp 2018 routines: starttime , setdbg , getmixblock , getmixa , getmixc , setmc , factt , setcon , setcsla , stoptime ; and Lapack library. Nature of problem: The CF_Hamiltonian program is designed as a part of the Grasp 2018 Package for the computation of Stark splitting in crystal field in the point charge crystal field approximation. Solution method: The point charge crystal field approach is used. It allows user to include different Atomic State Functions (ASF) mixing such as ASF mix with the same total J values, ASF mixing with different total J values, ASF mixing with different parities. Additional comments including restrictions and unusual features: The restrictions of the program are coming from the restrictions of Grasp 2018 Package and it is suitable for systems for which the point charge crystal field approximation is appropriate. The Stark level splitting of the atomic energy terms in the point-charge crystal field approach is performed by the program CF_Hamiltonian .
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grasp2018 a fortran 95 version of the general relativistic atomic Structure Package
Computer Physics Communications, 2019Co-Authors: Froese C Fischer, P Jonsson, Gediminas Gaigalas, Jacek BieronAbstract:Abstract The present Grasp 2018 is an updated Fortran 95 version of the recommended block versions of programs from Grasp 2K Version 1_1 for large-scale calculations Jonsson et al. (2013). MPI programs are included so that all major tasks can be executed using parallel computers. Tools have been added that simplify the generation of configuration state function expansions for the multireference single- and double computational model. Names of programs have been changed to accurately reflect the task performed by the code. Modifications to the relativistic self-consistent field program have been made that, in some instances, greatly reduce the number of iterations needed for determining the requested eigenvalues and the memory required. Changes have been made to the relativistic configuration interaction program to substantially cut down on the time for constructing the Hamiltonian matrix for configuration state function expansions based on large orbital sets. In the case of a finite nucleus the grid points have been changed so that the first non-zero point is Z-dependent as for the point nucleus. A number of tools have been developed to generate LaTeX tables of eigenvalue composition, energies, transition data and lifetimes. Tools for plotting and analyzing computed properties along an iso-electronic sequence have also been added. A number of minor errors have been corrected. A detailed manual is included that describes different aspects of the Package as well as the steps needed in order to produce reliable results. Program summary Program Title: Grasp 2018 Program Files doi: http://dx.doi.org/10.17632/x574wpp2vg.1 Licensing provisions: MIT license Programming language: Fortran 95. Nature of problem: Prediction of atomic properties – atomic energy levels, isotope shifts, oscillator strengths, radiative decay rates, hyperfine Structure parameters, specific mass shift parameters, Zeeman effects – using a multiconfiguration Dirac–Hartree–Fock approach. Solution method: The computational method is the same as in the previous Grasp 2K [1,2] version except that only the latest recommended versions of certain routines are included. Restrictions: All calculations are for bound state solutions. Instead of relying on packing algorithms for specifying arguments of arrays of integrals, orbitals are designated by a “short integer” requiring one byte of memory for a maximum of 127 orbitals. The tables of reduced coefficients of fractional parentage used in this version are limited to sub-shells with j ≤ 9 ∕ 2 [3]; occupied sub-shells with j > 9 ∕ 2 are, therefore, restricted to a maximum of two electrons. Some other parameters, such as the maximum number of orbitals are determined in a parameter_def_M.f90 file that can be modified prior to compile time. Unusual features: Parallel versions are available for several applications. References • [[1]] P. Jonsson, X. He, C. Froese Fischer, and I. P. Grant, Comput. Phys. Commun. 176, 597 (2007). • [[2]] P. Jonsson, G. Gaigalas, J. Bieron, C. Froese Fischer, and I. P. Grant, Comput. Phys. Commun. 184, 2197 (2013). • [[3]] G. Gaigalas, S. Fritzsche, Z. Rudzikas, Atomic Data and Nuclear Data Tables 76, 235 (2000).
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new version grasp2k relativistic atomic Structure Package
Computer Physics Communications, 2013Co-Authors: P Jonsson, Gediminas Gaigalas, Jacek Bieron, Charlotte Froese Fischer, I P GrantAbstract:Abstract A revised version of Grasp 2 K [P. Jonsson, X. He, C. Froese Fischer, I.P. Grant, Comput. Phys. Commun. 177 (2007) 597] is presented. It supports earlier non-block and block versions of codes as well as a new block version in which the njgraf library module [A. Bar-Shalom, M. Klapisch, Comput. Phys. Commun. 50 (1988) 375] has been replaced by the librang angular Package developed by Gaigalas based on the theory of [G. Gaigalas, Z.B. Rudzikas, C. Froese Fischer, J. Phys. B: At. Mol. Phys. 30 (1997) 3747, G. Gaigalas, S. Fritzsche, I.P. Grant, Comput. Phys. Commun. 139 (2001) 263]. Tests have shown that errors encountered by njgraf do not occur with the new angular Package. The three versions are denoted v1 , v2 , and v3 , respectively. In addition, in v3 , the coefficients of fractional parentage have been extended to j = 9 / 2 , making calculations feasible for the lanthanides and actinides. Changes in v2 include minor improvements. For example, the new version of rci2 may be used to compute quantum electrodynamic (QED) corrections only from selected orbitals. In v3 , a new program, jj2lsj , reports the percentage composition of the wave function in L S J and the program rlevels has been modified to report the configuration state function (CSF) with the largest coefficient of an L S J expansion. The bioscl2 and bioscl3 application programs have been modified to produce a file of transition data with one record for each transition in the same format as in Atsp 2 K [C. Froese Fischer, G. Tachiev, G. Gaigalas, M.R. Godefroid, Comput. Phys. Commun. 176 (2007) 559], which identifies each atomic state by the total energy and a label for the CSF with the largest expansion coefficient in L S J intermediate coupling. All versions of the codes have been adapted for 64-bit computer architecture. Program Summary Program title: Grasp 2 K , version 1_1 Catalogue identifier: ADZL_v1_1 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/ADZL_v1_1.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 730252 No. of bytes in distributed program, including test data, etc.: 14808872 Distribution format: tar.gz Programming language: Fortran. Computer: Intel Xeon, 2.66 GHz. Operating system: Suse, Ubuntu, and Debian Linux 64-bit. RAM: 500 MB or more Classification: 2.1. Catalogue identifier of previous version: ADZL_v1_0 Journal reference of previous version: Comput. Phys. Comm. 177 (2007) 597 Does the new version supersede the previous version?: Yes Nature of problem: Prediction of atomic properties — atomic energy levels, oscillator strengths, radiative decay rates, hyperfine Structure parameters, Lande g J -factors, and specific mass shift parameters — using a multiconfiguration Dirac–Hartree–Fock approach. Solution method: The computational method is the same as in the previous Grasp 2 K [1] version except that for v3 codes the njgraf library module [2] for recoupling has been replaced by librang [3,4]. Reasons for new version: New angular libraries with improved performance are available. Also methodology for transforming from jj- to LSJ-coupling has been developed. Summary of revisions: New angular libraries where the coefficients of fractional parentage have been extended to j = 9 / 2 , making calculations feasible for the lanthanides and actinides. Inclusion of a new program jj2lsj, which reports the percentage composition of the wave function in LSJ. Transition programs have been modified to produce a file of transition data with one record for each transition in the same format as Atsp2K [C. Froese Fischer, G. Tachiev, G. Gaigalas and M.R. Godefroid, Comput. Phys. Commun. 176 (2007) 559], which identifies each atomic state by the total energy and a label for the CSF with the largest expansion coefficient in LSJ intermediate coupling. Updated to 64-bit architecture. A comprehensive user manual in pdf format for the program Package has been added. Restrictions: The packing algorithm restricts the maximum number of orbitals to be ≤ 214 . The tables of reduced coefficients of fractional parentage used in this version are limited to subshells with j ≤ 9 / 2 [5]; occupied subshells with j > 9 / 2 are, therefore, restricted to a maximum of two electrons. Some other parameters, such as the maximum number of subshells of a CSF outside a common set of closed shells are determined by a parameter.def file that can be modified prior to compile time. Unusual features: The bioscl3 program reports transition data in the same format as in Atsp2K [6], and the data processing program tables of the latter Package can be used. The tables program takes a name.lsj file, usually a concatenated file of all the .lsj transition files for a given atom or ion, and finds the energy Structure of the levels and the multiplet transition arrays. The tables posted at the website http://atoms.vuse.vanderbilt.edu are examples of tables produced by the tables program. With the extension of coefficients of fractional parentage to j = 9 / 2 , calculations for the lanthanides and actinides become possible. Running time: CPU time required to execute test cases: 70.5 s. References: [1] P. Jonsson, X. He, C. Froese Fischer, I.P. Grant, Comput. Phys. Commun. 177 (2007) 597. [2] A. Bar-Shalom, M. Klapisch, Comput. Phys. Commun. 50 (1988) 375. [3] G. Gaigalas, Z.B. Rudzikas, C. Froese Fischer, J. Phys. B: At. Mol. Phys. 30 (1997) 3747. [4] G. Gaigalas, S. Fritzsche, I.P. Grant, Comput. Phys. Commun. 139 (2001) 263. [5] G. Gaigalas, S. Fritzsche, Z. Rudzikas, At. Data Nucl. Data Tables 76 (2000) 235. [6] C. Froese Fischer, G. Tachiev, G. Gaigalas, M.R. Godefroid, Comput. Phys. Commun. 176 (2007) 559.
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an mchf atomic Structure Package for large scale calculations
Computer Physics Communications, 2007Co-Authors: Charlotte Froese Fischer, Gediminas Gaigalas, Georgio Tachiev, Michel GodefroidAbstract:Abstract An MCHF atomic-Structure Package is presented based on dynamic memory allocation, sparse matrix methods, and a recently developed angular library. It is meant for large-scale calculations in a basis of orthogonal orbitals for groups of LS terms of arbitrary parity. For Breit–Pauli calculations, all operators—spin–orbit, spin–other orbit, spin–spin, and orbit–orbit—may be included. For transition probabilities the orbitals of the initial and final state need not be orthogonal. A bi-orthogonal transformation is used for the evaluation of matrix elements in such cases. In addition to transition rates of all types, isotope shifts and hyperfine constants can be computed as well as g J factors. New version summary Title of program: atsp 2K Version number: 1.00 Catalogue identifier: ADLY_v2_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/ADLY_v2_0 Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Computer: Pentium III 500 MHz Installations: Vanderbilt University, Nashville, TN 37235, USA Operating systems under which the present version has been tested: Red Hat 8 Programming language used in the present version: FORTRAN 90 Memory required to execute with typical data: 256 Mbytes words No. of bits in a word: 32 Supplementary material: User manuals for the program atsp 2k and for the Spin-Angular library are available No. of lines in distributed program, including test data, etc.: 209 992 No. of bytes in distributed Package, including test data, etc.: 1 740 883 Distribution format: tar.gz CPC Program Library subprograms used: none Does the new version supersede the previous version?: Yes Nature of physical problem: This program determines energy levels and associated wave functions for states of atoms and ions in the MCHF ( LS ) or Breit–Pauli ( LSJ ) approximation. Given the wave function, various atomic properties can be computed such as electric (E k ) and magnetic (M k ) multipole radiative transition probabilities ( k max = 10 ) between LS or LSJ states, isotope shift constants, hyperfine parameters, and g J factors. Method of solution: The new version of the program closely follows the design and Structure of the previous one [C. Froese Fischer, Comput. Phys. Comm. 128 (2000) 635], except that a simultaneous optimization scheme has been introduced. This program uses the angular methodology of [G. Gaigalas, Lithuanian J. Phys. 41 (2000) 39] and has been extended to include partially filled f -subshells in wavefunction expansions but assumes all orbitals are orthonormal. The bi-orthogonal transformation method is used to deal with the non-orthogonality of orbitals between initial and final states of an electromagnetic radiative transition. Reasons for new version: The previous version of the MCHF atomic Structure Package [C. Froese Fischer, Comput. Phys. Comm. 128 (2000) 635] was intended for small calculations, ideal for someone not familiar with the code, producing extensive print-out of intermediate results. The codes for the calculation of spin-angular coefficients were often not the most efficient and could only treat configurations with open f -subshells containing at most two electrons or an almost filled shell with one hole. The present version is designed for large-scale computation using algorithms for angular integration that have been shown to be faster, and include the case of arbitrarily filled f -shells. In addition, the MCHF program has been modified to include optimization on an energy functional that is a weighted average of energy functionals for expansions of wavefunctions for different LS terms or parity, thus facilitating Breit–Pauli calculations for complex atomic systems and for computing targets in collision calculations. Summary of revisions: Programs have been modified to take advantage of the newly developed angular library [G. Gaigalas, Lithuanian J. Phys. 41 (2000) 39], extended to arbitrarily filled f -shells. New programs have been developed for simultaneous optimization and for the efficient calculation of atomic spectra and transition rates for an iso-electronic sequence. All applications now take advantage of dynamic memory allocation and sparse matrix methods. Restrictions on the complexity of the problem: All orbitals in a wave function expansion are assumed to be orthonormal. Configuration states are restricted to at most eight (8) subshells in addition to the closed shells common to all configuration states. The maximum size is limited by the available memory and disk space. Typical running time: Included with the code are scripts for calculating E2 and M1 transitions between levels of 3 s 2 3 p 2 for Si and P + . This calculation has two stages: LS and LSJ . The calculation of the former required 21 minutes for the LS calculation and 36.5 minutes for the Breit–Pauli configuration interaction calculation that determines the mixing of the terms. Unusual features of the program: The programming style is essentially F77 with extensions for the POINTER data type and associated memory allocation. These have been available on workstations for more than a decade but their implementations are compiler dependent. The present serial code has been installed and tested extensively using both the Portland Group, pgf90, compiler and the IBM SP2, xlf90, compiler. The former is compatible also with the Intel Fortran90 compiler. The MPI codes are included for completeness though testing has not been as extensive. Additional comments: Parallel versions (MPI) of the following programs are included in the distribution. Use of these is optional but can speed up the angular integration processing. Serial Parallel nonh nonh_mpi mchf mchf_mpi bp_ang, bp_mat, bp_eiv bp_ang_mpi, bp_mat_ang, bp_eiv_mpi biotr_ang, biotr_tr biotr_ang_mpi, biotr_tr_mpi
P Jonsson - One of the best experts on this subject based on the ideXlab platform.
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grasp2018 a fortran 95 version of the general relativistic atomic Structure Package
Computer Physics Communications, 2019Co-Authors: Froese C Fischer, P Jonsson, Gediminas Gaigalas, Jacek BieronAbstract:Abstract The present Grasp 2018 is an updated Fortran 95 version of the recommended block versions of programs from Grasp 2K Version 1_1 for large-scale calculations Jonsson et al. (2013). MPI programs are included so that all major tasks can be executed using parallel computers. Tools have been added that simplify the generation of configuration state function expansions for the multireference single- and double computational model. Names of programs have been changed to accurately reflect the task performed by the code. Modifications to the relativistic self-consistent field program have been made that, in some instances, greatly reduce the number of iterations needed for determining the requested eigenvalues and the memory required. Changes have been made to the relativistic configuration interaction program to substantially cut down on the time for constructing the Hamiltonian matrix for configuration state function expansions based on large orbital sets. In the case of a finite nucleus the grid points have been changed so that the first non-zero point is Z-dependent as for the point nucleus. A number of tools have been developed to generate LaTeX tables of eigenvalue composition, energies, transition data and lifetimes. Tools for plotting and analyzing computed properties along an iso-electronic sequence have also been added. A number of minor errors have been corrected. A detailed manual is included that describes different aspects of the Package as well as the steps needed in order to produce reliable results. Program summary Program Title: Grasp 2018 Program Files doi: http://dx.doi.org/10.17632/x574wpp2vg.1 Licensing provisions: MIT license Programming language: Fortran 95. Nature of problem: Prediction of atomic properties – atomic energy levels, isotope shifts, oscillator strengths, radiative decay rates, hyperfine Structure parameters, specific mass shift parameters, Zeeman effects – using a multiconfiguration Dirac–Hartree–Fock approach. Solution method: The computational method is the same as in the previous Grasp 2K [1,2] version except that only the latest recommended versions of certain routines are included. Restrictions: All calculations are for bound state solutions. Instead of relying on packing algorithms for specifying arguments of arrays of integrals, orbitals are designated by a “short integer” requiring one byte of memory for a maximum of 127 orbitals. The tables of reduced coefficients of fractional parentage used in this version are limited to sub-shells with j ≤ 9 ∕ 2 [3]; occupied sub-shells with j > 9 ∕ 2 are, therefore, restricted to a maximum of two electrons. Some other parameters, such as the maximum number of orbitals are determined in a parameter_def_M.f90 file that can be modified prior to compile time. Unusual features: Parallel versions are available for several applications. References • [[1]] P. Jonsson, X. He, C. Froese Fischer, and I. P. Grant, Comput. Phys. Commun. 176, 597 (2007). • [[2]] P. Jonsson, G. Gaigalas, J. Bieron, C. Froese Fischer, and I. P. Grant, Comput. Phys. Commun. 184, 2197 (2013). • [[3]] G. Gaigalas, S. Fritzsche, Z. Rudzikas, Atomic Data and Nuclear Data Tables 76, 235 (2000).
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new version grasp2k relativistic atomic Structure Package
Computer Physics Communications, 2013Co-Authors: P Jonsson, Gediminas Gaigalas, Jacek Bieron, Charlotte Froese Fischer, I P GrantAbstract:Abstract A revised version of Grasp 2 K [P. Jonsson, X. He, C. Froese Fischer, I.P. Grant, Comput. Phys. Commun. 177 (2007) 597] is presented. It supports earlier non-block and block versions of codes as well as a new block version in which the njgraf library module [A. Bar-Shalom, M. Klapisch, Comput. Phys. Commun. 50 (1988) 375] has been replaced by the librang angular Package developed by Gaigalas based on the theory of [G. Gaigalas, Z.B. Rudzikas, C. Froese Fischer, J. Phys. B: At. Mol. Phys. 30 (1997) 3747, G. Gaigalas, S. Fritzsche, I.P. Grant, Comput. Phys. Commun. 139 (2001) 263]. Tests have shown that errors encountered by njgraf do not occur with the new angular Package. The three versions are denoted v1 , v2 , and v3 , respectively. In addition, in v3 , the coefficients of fractional parentage have been extended to j = 9 / 2 , making calculations feasible for the lanthanides and actinides. Changes in v2 include minor improvements. For example, the new version of rci2 may be used to compute quantum electrodynamic (QED) corrections only from selected orbitals. In v3 , a new program, jj2lsj , reports the percentage composition of the wave function in L S J and the program rlevels has been modified to report the configuration state function (CSF) with the largest coefficient of an L S J expansion. The bioscl2 and bioscl3 application programs have been modified to produce a file of transition data with one record for each transition in the same format as in Atsp 2 K [C. Froese Fischer, G. Tachiev, G. Gaigalas, M.R. Godefroid, Comput. Phys. Commun. 176 (2007) 559], which identifies each atomic state by the total energy and a label for the CSF with the largest expansion coefficient in L S J intermediate coupling. All versions of the codes have been adapted for 64-bit computer architecture. Program Summary Program title: Grasp 2 K , version 1_1 Catalogue identifier: ADZL_v1_1 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/ADZL_v1_1.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 730252 No. of bytes in distributed program, including test data, etc.: 14808872 Distribution format: tar.gz Programming language: Fortran. Computer: Intel Xeon, 2.66 GHz. Operating system: Suse, Ubuntu, and Debian Linux 64-bit. RAM: 500 MB or more Classification: 2.1. Catalogue identifier of previous version: ADZL_v1_0 Journal reference of previous version: Comput. Phys. Comm. 177 (2007) 597 Does the new version supersede the previous version?: Yes Nature of problem: Prediction of atomic properties — atomic energy levels, oscillator strengths, radiative decay rates, hyperfine Structure parameters, Lande g J -factors, and specific mass shift parameters — using a multiconfiguration Dirac–Hartree–Fock approach. Solution method: The computational method is the same as in the previous Grasp 2 K [1] version except that for v3 codes the njgraf library module [2] for recoupling has been replaced by librang [3,4]. Reasons for new version: New angular libraries with improved performance are available. Also methodology for transforming from jj- to LSJ-coupling has been developed. Summary of revisions: New angular libraries where the coefficients of fractional parentage have been extended to j = 9 / 2 , making calculations feasible for the lanthanides and actinides. Inclusion of a new program jj2lsj, which reports the percentage composition of the wave function in LSJ. Transition programs have been modified to produce a file of transition data with one record for each transition in the same format as Atsp2K [C. Froese Fischer, G. Tachiev, G. Gaigalas and M.R. Godefroid, Comput. Phys. Commun. 176 (2007) 559], which identifies each atomic state by the total energy and a label for the CSF with the largest expansion coefficient in LSJ intermediate coupling. Updated to 64-bit architecture. A comprehensive user manual in pdf format for the program Package has been added. Restrictions: The packing algorithm restricts the maximum number of orbitals to be ≤ 214 . The tables of reduced coefficients of fractional parentage used in this version are limited to subshells with j ≤ 9 / 2 [5]; occupied subshells with j > 9 / 2 are, therefore, restricted to a maximum of two electrons. Some other parameters, such as the maximum number of subshells of a CSF outside a common set of closed shells are determined by a parameter.def file that can be modified prior to compile time. Unusual features: The bioscl3 program reports transition data in the same format as in Atsp2K [6], and the data processing program tables of the latter Package can be used. The tables program takes a name.lsj file, usually a concatenated file of all the .lsj transition files for a given atom or ion, and finds the energy Structure of the levels and the multiplet transition arrays. The tables posted at the website http://atoms.vuse.vanderbilt.edu are examples of tables produced by the tables program. With the extension of coefficients of fractional parentage to j = 9 / 2 , calculations for the lanthanides and actinides become possible. Running time: CPU time required to execute test cases: 70.5 s. References: [1] P. Jonsson, X. He, C. Froese Fischer, I.P. Grant, Comput. Phys. Commun. 177 (2007) 597. [2] A. Bar-Shalom, M. Klapisch, Comput. Phys. Commun. 50 (1988) 375. [3] G. Gaigalas, Z.B. Rudzikas, C. Froese Fischer, J. Phys. B: At. Mol. Phys. 30 (1997) 3747. [4] G. Gaigalas, S. Fritzsche, I.P. Grant, Comput. Phys. Commun. 139 (2001) 263. [5] G. Gaigalas, S. Fritzsche, Z. Rudzikas, At. Data Nucl. Data Tables 76 (2000) 235. [6] C. Froese Fischer, G. Tachiev, G. Gaigalas, M.R. Godefroid, Comput. Phys. Commun. 176 (2007) 559.
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the grasp2k relativistic atomic Structure Package
Computer Physics Communications, 2007Co-Authors: P Jonsson, Charlotte Froesefischer, I P GrantAbstract:This paper describes grasp2K, a general-purpose relativistic atomic Structure Package. It is a modification and extension of the GRASP92 Package by [F.A. Parpia, C. Froese Fischer, I.P. Grant, Comput. Phys. Comm. 94 (1996) 249]. For the sake of continuity, two versions are included. Version 1 retains the GRASP92 formats for wave functions and expansion coefficients, but no longer requires preprocessing and more default options have been introduced. Modifications have eliminated some errors, improved the stability, and simplified interactive use. The transition code has been extended to cases where the initial and final states have different orbital sets. Several utility programs have been added. Whereas Version 1 constructs a single interaction matrix for all the J's and parities, Version 2 treats each J and parity as a separate matrix. This block Structure results in a reduction of memory use and considerably shorter eigenvectors. Additional tools have been developed for this format. The CPU intensive parts of Version 2 have been parallelized using MPI. The Package includes a “make” facility that relies on environment variables. These make it easier to port the application to different platforms. The present version supports the 32-bit Linux and ibmSP environments where the former is compatible with many Unix systems. Descriptions of the features and the program/data flow of the Package will be given in some detail in this report.
I P Grant - One of the best experts on this subject based on the ideXlab platform.
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new version grasp2k relativistic atomic Structure Package
Computer Physics Communications, 2013Co-Authors: P Jonsson, Gediminas Gaigalas, Jacek Bieron, Charlotte Froese Fischer, I P GrantAbstract:Abstract A revised version of Grasp 2 K [P. Jonsson, X. He, C. Froese Fischer, I.P. Grant, Comput. Phys. Commun. 177 (2007) 597] is presented. It supports earlier non-block and block versions of codes as well as a new block version in which the njgraf library module [A. Bar-Shalom, M. Klapisch, Comput. Phys. Commun. 50 (1988) 375] has been replaced by the librang angular Package developed by Gaigalas based on the theory of [G. Gaigalas, Z.B. Rudzikas, C. Froese Fischer, J. Phys. B: At. Mol. Phys. 30 (1997) 3747, G. Gaigalas, S. Fritzsche, I.P. Grant, Comput. Phys. Commun. 139 (2001) 263]. Tests have shown that errors encountered by njgraf do not occur with the new angular Package. The three versions are denoted v1 , v2 , and v3 , respectively. In addition, in v3 , the coefficients of fractional parentage have been extended to j = 9 / 2 , making calculations feasible for the lanthanides and actinides. Changes in v2 include minor improvements. For example, the new version of rci2 may be used to compute quantum electrodynamic (QED) corrections only from selected orbitals. In v3 , a new program, jj2lsj , reports the percentage composition of the wave function in L S J and the program rlevels has been modified to report the configuration state function (CSF) with the largest coefficient of an L S J expansion. The bioscl2 and bioscl3 application programs have been modified to produce a file of transition data with one record for each transition in the same format as in Atsp 2 K [C. Froese Fischer, G. Tachiev, G. Gaigalas, M.R. Godefroid, Comput. Phys. Commun. 176 (2007) 559], which identifies each atomic state by the total energy and a label for the CSF with the largest expansion coefficient in L S J intermediate coupling. All versions of the codes have been adapted for 64-bit computer architecture. Program Summary Program title: Grasp 2 K , version 1_1 Catalogue identifier: ADZL_v1_1 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/ADZL_v1_1.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 730252 No. of bytes in distributed program, including test data, etc.: 14808872 Distribution format: tar.gz Programming language: Fortran. Computer: Intel Xeon, 2.66 GHz. Operating system: Suse, Ubuntu, and Debian Linux 64-bit. RAM: 500 MB or more Classification: 2.1. Catalogue identifier of previous version: ADZL_v1_0 Journal reference of previous version: Comput. Phys. Comm. 177 (2007) 597 Does the new version supersede the previous version?: Yes Nature of problem: Prediction of atomic properties — atomic energy levels, oscillator strengths, radiative decay rates, hyperfine Structure parameters, Lande g J -factors, and specific mass shift parameters — using a multiconfiguration Dirac–Hartree–Fock approach. Solution method: The computational method is the same as in the previous Grasp 2 K [1] version except that for v3 codes the njgraf library module [2] for recoupling has been replaced by librang [3,4]. Reasons for new version: New angular libraries with improved performance are available. Also methodology for transforming from jj- to LSJ-coupling has been developed. Summary of revisions: New angular libraries where the coefficients of fractional parentage have been extended to j = 9 / 2 , making calculations feasible for the lanthanides and actinides. Inclusion of a new program jj2lsj, which reports the percentage composition of the wave function in LSJ. Transition programs have been modified to produce a file of transition data with one record for each transition in the same format as Atsp2K [C. Froese Fischer, G. Tachiev, G. Gaigalas and M.R. Godefroid, Comput. Phys. Commun. 176 (2007) 559], which identifies each atomic state by the total energy and a label for the CSF with the largest expansion coefficient in LSJ intermediate coupling. Updated to 64-bit architecture. A comprehensive user manual in pdf format for the program Package has been added. Restrictions: The packing algorithm restricts the maximum number of orbitals to be ≤ 214 . The tables of reduced coefficients of fractional parentage used in this version are limited to subshells with j ≤ 9 / 2 [5]; occupied subshells with j > 9 / 2 are, therefore, restricted to a maximum of two electrons. Some other parameters, such as the maximum number of subshells of a CSF outside a common set of closed shells are determined by a parameter.def file that can be modified prior to compile time. Unusual features: The bioscl3 program reports transition data in the same format as in Atsp2K [6], and the data processing program tables of the latter Package can be used. The tables program takes a name.lsj file, usually a concatenated file of all the .lsj transition files for a given atom or ion, and finds the energy Structure of the levels and the multiplet transition arrays. The tables posted at the website http://atoms.vuse.vanderbilt.edu are examples of tables produced by the tables program. With the extension of coefficients of fractional parentage to j = 9 / 2 , calculations for the lanthanides and actinides become possible. Running time: CPU time required to execute test cases: 70.5 s. References: [1] P. Jonsson, X. He, C. Froese Fischer, I.P. Grant, Comput. Phys. Commun. 177 (2007) 597. [2] A. Bar-Shalom, M. Klapisch, Comput. Phys. Commun. 50 (1988) 375. [3] G. Gaigalas, Z.B. Rudzikas, C. Froese Fischer, J. Phys. B: At. Mol. Phys. 30 (1997) 3747. [4] G. Gaigalas, S. Fritzsche, I.P. Grant, Comput. Phys. Commun. 139 (2001) 263. [5] G. Gaigalas, S. Fritzsche, Z. Rudzikas, At. Data Nucl. Data Tables 76 (2000) 235. [6] C. Froese Fischer, G. Tachiev, G. Gaigalas, M.R. Godefroid, Comput. Phys. Commun. 176 (2007) 559.
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the grasp2k relativistic atomic Structure Package
Computer Physics Communications, 2007Co-Authors: P Jonsson, Charlotte Froesefischer, I P GrantAbstract:This paper describes grasp2K, a general-purpose relativistic atomic Structure Package. It is a modification and extension of the GRASP92 Package by [F.A. Parpia, C. Froese Fischer, I.P. Grant, Comput. Phys. Comm. 94 (1996) 249]. For the sake of continuity, two versions are included. Version 1 retains the GRASP92 formats for wave functions and expansion coefficients, but no longer requires preprocessing and more default options have been introduced. Modifications have eliminated some errors, improved the stability, and simplified interactive use. The transition code has been extended to cases where the initial and final states have different orbital sets. Several utility programs have been added. Whereas Version 1 constructs a single interaction matrix for all the J's and parities, Version 2 treats each J and parity as a separate matrix. This block Structure results in a reduction of memory use and considerably shorter eigenvectors. Additional tools have been developed for this format. The CPU intensive parts of Version 2 have been parallelized using MPI. The Package includes a “make” facility that relies on environment variables. These make it easier to port the application to different platforms. The present version supports the 32-bit Linux and ibmSP environments where the former is compatible with many Unix systems. Descriptions of the features and the program/data flow of the Package will be given in some detail in this report.
