Computing resources
Last Update
15.09.2016 |

**La**tvian **S**uper**C**luster (LASC), installed at the Institute of Solid State Physics of the University of Latvia (ISSP UL).

The LASC system is a heterogenous Beowulf-type cluster, based on reliable Intel multiprocessor servers, connected together via Gigabit Ethernet networks and running Linux RedHat operating system.

The LASC system conforms to the following criteria:

- High Productivity - high speed processing of relatively huge data volumes
- High Availability - reliable system, accessible from Internet, Dial-Up and local terminals
- Scalability - possibility to increase computational power in the future
- Low Cost - for hardware and software (initial, upgrade, repairing)
- Easy Maintenance - no special personal required
- Security - free access on pre-registration basis

For more information please visit LASC homepage here.

# Available software

# 1. CRYSTAL

The **CRYSTAL** program computes the electronic structure of periodic systems within the methods of Hartree-Fock, Density Functional Theory or various hybrid approximations. The Bloch functions of the periodic systems are expanded as linear combinations of atom centered Gaussian functions. Powerful screening techniques are used to exploit the real space locality.

Restricted (Closed Shell) and Unrestricted (Spin-polarized) calculations can be performed with all-electron and valence-only basis sets with effective core pseudo-potentials.

The program can automatically handle space symmetry (230 space groups, 80 two-sided plane groups, 99 rod groups, 45 point groups are available ). Point symmetries compatible with translation symmetry are provided for molecules. Rotohelical symmetry options, which can be applied for construction of 1D nanotubes, are available in CRYSTAL-2009 code (up to order 48).

Input tools allow the generation of a slab (2D system), or a cluster (0D system), from a 3D crystalline structure, or the creation of a supercell with a defect, or nanotubes (1D system) from a single-layer slab model (2D system).

The code may be used to perform consistent studies of the physical and chemical properties of molecules, polymers, surfaces and crystalline solids:

- Structural features
- Vibrational properties
- Electronic structure
- Magnetic properties
- Dielectric properties
- Elastic properties

# 2. VASP

**The Vienna Ab initio** Simulation Package (VASP) is a computer program for atomic scale materials modeling, *e.g.,* electronic structure calculations and quantum-mechanical molecular dynamics, from the first principles.

VASP computes an approximate solution to the many-body Schrödinger equation, either within the Density Functional Theory (DFT), solving the Kohn-Sham equations, or within the Hartree-Fock (HF) approximation, solving the Roothaan equations. Hybrid functionals that mix the Hartree-Fock approach with density functional theory are implemented as well. Furthermore, Green's functions methods (GW quasi-particles, and ACFDT-RPA, *i.e.*, Adiabatic-Connection Fluctuation-Dissipation Theorem within the Random Phase Approximation) as well as many-body perturbation theory (2^{nd}-order Møller-Plesset) are available in VASP.

VASP key quantities, like the one-electron orbitals, the electronic charge density, and the local potential, are expressed in the Plane Wave basis sets. The interactions between the electrons and ions are described using norm-conserving or ultrasoft pseudopotentials (US-PP), or the Projector-Augmented-Wave (PAW) method.

To determine the electronic ground state, VASP makes use of efficient iterative matrix diagonalization techniques, like the Residual Minimization Method with Direct Inversion of the Iterative Subspace (RMM-DIIS) or blocked Davidson algorithms. These are coupled to highly efficient Broyden and Pulay density mixing schemes to speed up the self-consistency cycle.

# 3. NWChem

**NWChem** aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters.

NWChem software can handle:

- Biomolecules, nanostructures, and solid-state
- From quantum to classical, and all combinations
- Ground and excited-states
- Gaussian basis functions or plane-waves
- Scaling from one to thousands of processors
- Properties and relativistic effects

The NWChem development strategy is focused on providing new and essential scientific capabilities to its users in the areas of kinetics and dynamics of chemical transformations, chemistry at interfaces and in the condensed phase, and enabling innovative and integrated research at EMSL. At the same time continued development is needed to enable NWChem to effectively utilize architectures of tens of petaflops (thousand trillion floating point operations per second) and beyond.

# 4. ABINIT

**ABINIT** is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within the Density Functional Theory, using pseudopotentials and a plane-wave or wavelet basis. ABINIT also includes options to optimize the geometry according to the DFT forces and stresses, or to perform molecular dynamics simulations using these forces, or to generate dynamical matrices, Born effective charges, and dielectric tensors, based on Density-Functional Perturbation Theory, and many more properties. Excited states can be computed within the Many-Body Perturbation Theory (the GW approximation and the Bethe-Salpeter equation) and Time-Dependent Density Functional Theory, *i.e.*, TD-DFT (for molecules). In addition to the main ABINIT code, different utility programs are provided.

# 5. Quantum ESPRESSO

**Quantum ESPRESSO** is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale.

It is based on density-functional theory, plane waves, and pseudopotentials.

Quantum ESPRESSO has evolved into a distribution of independent and inter-operable codes in the spirit of an open-source project. The Quantum ESPRESSO distribution consists of a “historical” core set of components, and a set of plug-ins that perform more advanced tasks, plus a number of third-party packages designed to be inter-operable with the core components.

# 6. SIESTA

**SIESTA** is both a method and its computer program implementation, to perform efficient electronic structure calculations and *ab initio* molecular dynamics simulations of molecules and solids. SIESTA's efficiency stems from the use of strictly localized basis sets and from the implementation of linear-scaling algorithms which can be applied to suitable systems. A very important feature of the code is that its accuracy and cost can be tuned in a wide range, from quick exploratory calculations to highly accurate simulations matching the quality of other approaches, such as plane-wave and all-electron methods.

The possibility of treating large systems with some first-principles electronic-structure methods has opened up new opportunities in many disciplines.

# 7. DFTB+

**DFTB+** is an implementation of the Density Functional based Tight Binding (DFTB) method, containing many extensions to the original method. The development is supported by various groups, resulting in a code which is probably the most versatile DFTB-implementation, with some unique features not available in other implementations so far.

DFTB+ offers an approximate density functional theory based quantum simulation tool with functionalities similar to *ab initio* quantum mechanical packages while being one or two orders of magnitude faster. One can optimize the structure of molecules and solids as well as extract one electron spectra, band structures and various other useful quantities. Additionally, one can calculate electron transport under non-equilibrium conditions.

# 8. GAMESS

**GAMESS** is a program for *ab initio* molecular quantum chemistry. Briefly, GAMESS can compute SCF wave functions ranging from RHF, ROHF, UHF, GVB, and MC SCF. Correlation corrections to these SCF wave functions include Configuration Interaction (CI), second order perturbation Theory, and Coupled-Cluster approaches, as well as the Density Functional Theory approximation. Excited states can be computed by CI, EOM, or TD-DFT procedures. Nuclear gradients are available, for automatic geometry optimization, transition state searches, or reaction path following. Computation of the energy hessian permits prediction of vibrational frequencies, with IR or Raman intensities. Solvent effects may be modeled by the discrete Effective Fragment potentials, or continuum models such as the Polarizable Continuum Model. Numerous relativistic computations are available, including infinite order two component scalar corrections, with various spin-orbit coupling options. The Fragment Molecular Orbital method permits use of many of these sophisticated treatments to be used on very large systems, by dividing the computation into small fragments. Nuclear wave functions can also be computed, in VSCF, or with explicit treatment of nuclear orbitals by the NEO code.

A variety of molecular properties, ranging from simple dipole moments to frequency dependent hyperpolarizabilities may be computed. Many basis sets are stored internally, together with effective core potentials or model core potentials, so that essentially the entire periodic table can be considered.

# 9. FEFF

**FEFF9** is an *ab initio* self-consistent multiple-scattering code for simultaneous calculations of excitation spectra and electronic structure. The approach builds in core-hole effects and can include local fields (TD-LDA). Output includes extended X-ray-absorption fine structure (EXAFS), full multiple scattering calcula-tions of various X-ray absorption spectra (XAS) and projected local densities of states (LDOS).The spectra include X-ray absorption near edge structure (XANES), X-ray natural and magnetic circular dichroism (XNCD and XMCD), spin polarized X-ray absorption spectra (SPXAS and SPEXAFS), non-resonant X-ray emission spectra (XES), the X-ray scattering amplitude(Thomson and anomalous parts), and electron energy loss spectroscopy (EELS).

# 10. GULP

**GULP** is a program for performing a variety of types of simulation on materials using boundary conditions of 0-D (molecules and clusters), 1-D (polymers), 2-D (surfaces, slabs and grain boundaries), or 3-D (periodic solids). The focus of the code is on analytical solutions, through the use of lattice dynamics, where possible, rather than on molecular dynamics. A variety of force fields can be used within GULP spanning the shell model for ionic materials, molecular mechanics for organic systems, the embedded atom model for metals and the reactive REBO potential for hydrocarbons. Analytic derivatives are included up to at least second order for most force fields, and to third order for many.

# 11. LAMMPS

**LAMMPS** is a classical molecular dynamics code that models an ensemble of particles in a liquid, solid, or gaseous state. It can model atomic, polymeric, biological, metallic, granular, and coarse-grained systems using a variety of force fields and boundary conditions.

In the most general sense, LAMMPS integrates Newton's equations of motion for collections of atoms, molecules, or macroscopic particles that interact via short- or long-range forces with a variety of initial and/or boundary conditions. For computational efficiency LAMMPS uses neighbor lists to keep track of nearby particles. The lists are optimized for systems with particles that are repulsive at short distances, so that the local density of particles never becomes too large. On parallel machines, LAMMPS uses spatial-decomposition techniques to partition the simulation domain into small 3d sub-domains, one of which is assigned to each processor. Processors communicate and store "ghost" atom information for atoms that border their sub-domain. LAMMPS is most efficient (in a parallel sense) for systems whose particles fill a 3d rectangular box with roughly uniform density.