Software
From CODECS-COST
Contents |
Goals
A particular goal of the COST action CODECS is to facilitate or enhance the interoperability of different quantum chemical programs to extend the range of spectroscopic applications that can be targeted.
Important aspects of this goal are:
- meta-programs driving quantum chemistry and/or molecular simulation software to enhance their functionality,
- interfaces connecting several of such packages, and
- a common data format for Quantum Chemistry codes
- Quantum Chemistry modules/codes for non-standard computations
- data analysis or supporting tools
Meta-Programs for Enhanced Functionality of Quantum Chemistry Codes
Several more specialized types of spectroscopic applications are not available as standard features in quantum chemistry software. Often, however, Quantum Chemistry groups have found smart solutions to work around such limitations.
As an example for vibrational spectroscopy, consider the calculation of the Hessian for a large molecular system. While most electronic-structure codes provide the possibility to do this without invoking external software, it may be advantageous to employ meta-programs such as SNF for improved parallelization or exploiting point-group symmetries not supported in your favorite electronic-structure code.
SNF also provides the possibility of a mode-wise calculation of intensities for vibrational spectra after an initial frequency analysis. In this way, the computational cost of Raman spectra calculations can considerably be reduced.
Also additional algorithmic features may be accessible through external programs, such as the optimization of selective Hessian eigenvectors (i.e., normal modes) within the so-called mode-tracking approach. This approach is implemented, e.g., in the program AKIRA, which is a meta-program that currently supports the electronic-structure codes DALTON, TURBOMOLE, ADF, and GAUSSIAN.
- MoViPac: Vibrational Spectroscopy with a Robust Meta-Program for Massively Parallel Standard and Inverse Calculations.
MoViPac unites the newest versions of both SNF and Akira alongside with a range of helpful add-ons to analyze and interpret the data obtained in the calculations. With its efficient parallelization scheme and meta-program design, it is particularly suited for the calculation of vibrational spectra of very large molecules.
Interfaces Connecting Several Quantum Chemistry Codes
One of the current efforts of COST-CODECS is to provide interface programs connecting several Quantum Chemistry packages. One example of such a tool is the PyADF scripting framework.
PyADF provides the possibility to define quantum-chemical workflows, in particular for multiscale simulations. Such applications generally require many individual quantum-chemical calculations, and the results of one calculation often serves as input subsequent ones. Moreover, different program packages might be necessary for different parts of the same workflow.
PyADF handles all steps of such workflows: In particular, it generates input files, runs the different program packages, extracts the results of these calculations and is able to transfer them between different programs. PyADF currently works with the software packages ADF, DALTON, and DIRAC.
Common Data Formats for Quantum Chemistry
Multiscale simulations using different quantum-chemical methods and program packages, such as those made possible by PyADF require the exchange of data between these different programs. This step would be greatly simplified by the definition of common data formats for quantum chemistry.
An important step towards a such a common Quantum Chemistry data format was achieved with Q5cost. It defines data formats based on XML and HDF5 for storing and exchanging information defining quantum-chemical calculations (e.g., geometry and basis set information) as well as for their results (e.g., molecular orbital coefficients). To facilitate multiscale simulations, work on using Q5cost within different quantum-chemical programs is in progress. To this end, tools are being developed for converting data in the programs' native format to Q5cost within PyADF.
Moreover, by annotating the programs' output file with XML tags it becomes possible to extract results of calculations easily. So far, this work has focused on the Dirac and Dalton program packages to establish best-practice guidelines for other codes.
Quantum Chemistry Modules/Codes
Gen1Int is a Fortran 90 library (with Python interface) to evaluate the derivatives of one-electron integrals with respect to the geometry perturbation, external electric and magnetic fields, and total rotational angular momentum at zero fields with contracted rotational London atomic orbitals (LAO). Relevant literature: B.Gao, A.J.Thorvaldsen, and K.Ruud: IJQC 2011 vol. 111 (4) pp. 858-872
XCFun is Arbitrary-Order Exchange-Correlation Functional Library. Relevant literature: U.Ekström, L.Visscher, R.Bast, A.J.Thorvaldsen, and K.Ruud, JCTC 2010 vol. 6 (7) pp. 1971-1980
The Gauge-Including Magnetically Induced Currents (GIMIC) program calculates, visualizes and analyzes magnetically induced currents in molecules. The GIMIC code implements the theory outlined in J.Juselius, D.Sundholm and J.Gauss, Calculation of Current Densities using Gauge-Including Atomic Orbitals, JCP 2004 vol. 121 (9) pp. 3952-3963. GIMIC is currently interfaced to CFOUR and Turbomole.
- FCclasses is a Fortran 77 code for the computation of vibrationally resolved electronic absorption, emission and circular dichroism spectra. The method works in harmonic approximation including the normal mode Duschinsky mixing. Equilibrium geometries, normal modes and their frequencies are read from input files and they can therefore be computed by any suitable electronic method. Vibronic transitions are partitioned in classes Cn, depending on the number "n" of modes simultaneously excited in the final state. For each class, the codes selects automatically the relevant vibronic transitions through an a priori estimate of their intensity, without imposing limitations on the spectral energy window. FCclasses includes the temperature effect and it is able to treat both Condon transitions (where the transition dipoles are independent of the nuclear coordinates) and Herzberg-Teller transitions (where the transition dipoles are assumed to be linearly dependent on the nuclear coordinates). In numerous tests the code has proved to be fast and efficient.
Data analysis or supporting tools
- MADAMM Multi stAged Docking with an Automated Molecular Modeling protocol allowing flexibilization of both the receptor and the ligand and including a graphical interface. The software uses standard docking software and molecular mechanics force fields in the core process and a set of scripts that automates the process without the intervention of the user. In order to simplify the use of MADAMM has also been developed. Relevant literature: N. M. Cerqueira, N. F. Bras, P. A. Fernandes, M. J. Ramos "MADAMM: a multistaged docking with an automated molecular modeling protocol". Proteins 74 (1): 192–206. (2009)
- vsLab – an easy-to-use graphical interface for the well known molecular docking software AutoGrid/AutoDock that has been included into VMD as a plug-in. This program allows almost anyone to use AutoDock and AutoGrid for simple docking or for virtual screening campaigns without requiring any deep knowledge about these techniques. The potential associated to this software makes it an attractive choice not only for educational purposes, but also for more advanced users that can use vsLab to increase workflow and productivity of everyday tasks. Relevant literature: N. M. F. S. A. Cerqueira, J. Ribeiro, P. A. Fernandes, M. J. Ramos vsLab—An implementation for virtual high-throughput screening using AutoDock and VMD, International Journal of Quantum Chemistry, 111, 1208–1212 (2012)
- JOYCE and ULYSSES - force field parametrization software.
- Joyce is a FORTRAN program which can be used to parametrize intramolecular force fields, using energy and its first and second derivative from QM calculations as reference. The parametrized force field and the optimization protocol, take into account the harmonic stretching, bendings and "hard" torsions, the "soft" torsional potentials which characterize flexible molecules, and the charge-charge and Lennard-Jones non-bonded interactions. Relevant literature: I. Cacelli, G. Prampolini Parametrization and Validation of Intramolecular Force Fields Derived from DFT Calculations, J. Chem. Theory Comput., 3, 1803–1817 (2007)
- Ulysses, is a Java/Java3D package which includes a GUI designed to make the usage of Joyce more user friendly. It also adds some useful features, like the topology generation wizard and the link to the CM5PAC tool for the calculation of partial atomic charges. Relevant literature: V. Barone; I. Cacelli; N. De Mitri; D. Licari; S. Monti; G. Prampolini, JOYCE and ULYSSES: integrated and user-friendly tools for the parameterization of intramolecular force fields from quantum mechanical data, Phys. Chem. Chem. Phys., 2013, just accepted, DOI:10.1039/C3CP44179B