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Rita Prosmiti - One of the best experts on this subject based on the ideXlab platform.

  • finite systems under pressure assessing volume definition models from parallel tempering monte carlo simulations
    Journal of Physical Chemistry A, 2020
    Co-Authors: Ales Vitek, Daniel J Arismendiarrieta, Rene Kalus, Martina Sarmanova, Rita Prosmiti
    Abstract:

    We have investigated different approaches to handling parallel-tempering Monte Carlo (PTMC) simulations in the Isothermal-Isobaric Ensemble of molecular cluster/nanoparticle systems for predicting structural phase diagram transitions. We have implemented various methodologies that consist of treating pressure implicitly through its effect on the volume. Thus, the main problem in the simulations under nonzero pressure becomes the volume definition of the finite nonperiodic system, and we considered approaches based on the particles' coordinates. Various volume models, namely container-volume, particle-volume, average-volume, ellipsoids-volume, and convex hull-volume, were employed, and the required corrections for each of them in the Monte Carlo computations were introduced. Finally, we explored the effects of volume/pressure changes for all models on structural phase transitions of a test system, such as the small "icelike" (H2O)12 water cluster. The temperature and pressure dependence of the cluster's heat capacity and energy-volume Pearson correlation coefficient were studied, phase diagrams were constructed using a multiple-histogram method, and attempts were made to identify phase transitions to particular cluster structures. Our results show significant differences between the employed volume models, and we discuss all pressure-induced, such as solid-solid-, solid-liquid-, and liquid-gas-like, phase transformations in the present study.

  • computational investigations of the thermodynamic properties of size selected water and ar water clusters high pressure transitions
    Physical Chemistry Chemical Physics, 2015
    Co-Authors: Ales Vitek, Daniel J Arismendiarrieta, Rocio Rodriguezcantano, Rita Prosmiti, Pablo Villarreal, Rene Kalus, G Delgadobarrio
    Abstract:

    Classical parallel-tempering Monte Carlo simulations in the isothermal–isobaric Ensemble were carried out for the (H2O)20 and Ar(H2O)20 clusters, over a wide range of temperatures (30–1000 K) and pressures (3 kPa–10 GPa) in order to study their thermodynamic properties and structural changes. The TIP4P/ice water model is employed for the water–water interactions, while both semiempirical and ab initio-based potentials are used to model the interaction between the rare-gas atoms and the water molecules. Temperature–pressure phase diagrams for these cluster systems were constructed by employing a two-dimensional multiple-histogram method. Structural changes were detected by analyzing the heat capacity landscape and the Pearson correlation coefficient profile for the interaction energy and volume. Those at high pressure correspond to solid-to-solid transitions and are found to be related to clathrate-like cages around the Ar atom. It is also shown that the formation and thermodynamic stability of such structures are determined by the intermolecular interaction between the rare-gas atoms and the host water molecules.

Daniel J Arismendiarrieta - One of the best experts on this subject based on the ideXlab platform.

  • finite systems under pressure assessing volume definition models from parallel tempering monte carlo simulations
    Journal of Physical Chemistry A, 2020
    Co-Authors: Ales Vitek, Daniel J Arismendiarrieta, Rene Kalus, Martina Sarmanova, Rita Prosmiti
    Abstract:

    We have investigated different approaches to handling parallel-tempering Monte Carlo (PTMC) simulations in the Isothermal-Isobaric Ensemble of molecular cluster/nanoparticle systems for predicting structural phase diagram transitions. We have implemented various methodologies that consist of treating pressure implicitly through its effect on the volume. Thus, the main problem in the simulations under nonzero pressure becomes the volume definition of the finite nonperiodic system, and we considered approaches based on the particles' coordinates. Various volume models, namely container-volume, particle-volume, average-volume, ellipsoids-volume, and convex hull-volume, were employed, and the required corrections for each of them in the Monte Carlo computations were introduced. Finally, we explored the effects of volume/pressure changes for all models on structural phase transitions of a test system, such as the small "icelike" (H2O)12 water cluster. The temperature and pressure dependence of the cluster's heat capacity and energy-volume Pearson correlation coefficient were studied, phase diagrams were constructed using a multiple-histogram method, and attempts were made to identify phase transitions to particular cluster structures. Our results show significant differences between the employed volume models, and we discuss all pressure-induced, such as solid-solid-, solid-liquid-, and liquid-gas-like, phase transformations in the present study.

  • computational investigations of the thermodynamic properties of size selected water and ar water clusters high pressure transitions
    Physical Chemistry Chemical Physics, 2015
    Co-Authors: Ales Vitek, Daniel J Arismendiarrieta, Rocio Rodriguezcantano, Rita Prosmiti, Pablo Villarreal, Rene Kalus, G Delgadobarrio
    Abstract:

    Classical parallel-tempering Monte Carlo simulations in the isothermal–isobaric Ensemble were carried out for the (H2O)20 and Ar(H2O)20 clusters, over a wide range of temperatures (30–1000 K) and pressures (3 kPa–10 GPa) in order to study their thermodynamic properties and structural changes. The TIP4P/ice water model is employed for the water–water interactions, while both semiempirical and ab initio-based potentials are used to model the interaction between the rare-gas atoms and the water molecules. Temperature–pressure phase diagrams for these cluster systems were constructed by employing a two-dimensional multiple-histogram method. Structural changes were detected by analyzing the heat capacity landscape and the Pearson correlation coefficient profile for the interaction energy and volume. Those at high pressure correspond to solid-to-solid transitions and are found to be related to clathrate-like cages around the Ar atom. It is also shown that the formation and thermodynamic stability of such structures are determined by the intermolecular interaction between the rare-gas atoms and the host water molecules.

Ales Vitek - One of the best experts on this subject based on the ideXlab platform.

  • finite systems under pressure assessing volume definition models from parallel tempering monte carlo simulations
    Journal of Physical Chemistry A, 2020
    Co-Authors: Ales Vitek, Daniel J Arismendiarrieta, Rene Kalus, Martina Sarmanova, Rita Prosmiti
    Abstract:

    We have investigated different approaches to handling parallel-tempering Monte Carlo (PTMC) simulations in the Isothermal-Isobaric Ensemble of molecular cluster/nanoparticle systems for predicting structural phase diagram transitions. We have implemented various methodologies that consist of treating pressure implicitly through its effect on the volume. Thus, the main problem in the simulations under nonzero pressure becomes the volume definition of the finite nonperiodic system, and we considered approaches based on the particles' coordinates. Various volume models, namely container-volume, particle-volume, average-volume, ellipsoids-volume, and convex hull-volume, were employed, and the required corrections for each of them in the Monte Carlo computations were introduced. Finally, we explored the effects of volume/pressure changes for all models on structural phase transitions of a test system, such as the small "icelike" (H2O)12 water cluster. The temperature and pressure dependence of the cluster's heat capacity and energy-volume Pearson correlation coefficient were studied, phase diagrams were constructed using a multiple-histogram method, and attempts were made to identify phase transitions to particular cluster structures. Our results show significant differences between the employed volume models, and we discuss all pressure-induced, such as solid-solid-, solid-liquid-, and liquid-gas-like, phase transformations in the present study.

  • computational investigations of the thermodynamic properties of size selected water and ar water clusters high pressure transitions
    Physical Chemistry Chemical Physics, 2015
    Co-Authors: Ales Vitek, Daniel J Arismendiarrieta, Rocio Rodriguezcantano, Rita Prosmiti, Pablo Villarreal, Rene Kalus, G Delgadobarrio
    Abstract:

    Classical parallel-tempering Monte Carlo simulations in the isothermal–isobaric Ensemble were carried out for the (H2O)20 and Ar(H2O)20 clusters, over a wide range of temperatures (30–1000 K) and pressures (3 kPa–10 GPa) in order to study their thermodynamic properties and structural changes. The TIP4P/ice water model is employed for the water–water interactions, while both semiempirical and ab initio-based potentials are used to model the interaction between the rare-gas atoms and the water molecules. Temperature–pressure phase diagrams for these cluster systems were constructed by employing a two-dimensional multiple-histogram method. Structural changes were detected by analyzing the heat capacity landscape and the Pearson correlation coefficient profile for the interaction energy and volume. Those at high pressure correspond to solid-to-solid transitions and are found to be related to clathrate-like cages around the Ar atom. It is also shown that the formation and thermodynamic stability of such structures are determined by the intermolecular interaction between the rare-gas atoms and the host water molecules.

Mark E Tuckerman - One of the best experts on this subject based on the ideXlab platform.

  • ab initio molecular dynamics study of water at constant pressure using converged basis sets and empirical dispersion corrections
    Journal of Chemical Physics, 2012
    Co-Authors: Yanli Zhang, Mark E Tuckerman
    Abstract:

    It is generally believed that studies of liquid water using the generalized gradient approximation to density functional theory require dispersion corrections in order to obtain reasonably accurate structural and dynamical properties. Here, we report on an ab initio molecular dynamics study of water in the Isothermal-Isobaric Ensemble using a converged discrete variable representation basis set and an empirical dispersion correction due to Grimme [J. Comp. Chem. 27, 1787 (2006)]10.1002/jcc.20495. At 300 K and an applied pressure of 1 bar, the density obtained without dispersion corrections is approximately 0.92 g/cm3 while that obtained with dispersion corrections is 1.07 g/cm3, indicating that the empirical dispersion correction overestimates the density by almost as much as it is underestimated without the correction for this converged basis. Radial distribution functions exhibit a loss of structure in the second solvation shell. Comparison of our results with other studies using the same empirical corr...

  • measure preserving integrators for molecular dynamics in the isothermal isobaric Ensemble derived from the liouville operator
    Chemical Physics, 2010
    Co-Authors: Jose Alejandre, G. Martyna, Roberto Lopezrendon, Mark E Tuckerman
    Abstract:

    Abstract The Liouville operator approach is employed to derive a new measure-preserving geometric integrator for molecular dynamics simulations in the isothermal–isobaric ( NPT ) Ensemble. Recently, we introduced such a scheme for NPT simulations with isotropic cell fluctuations in the absence of holonomic constraints [M.E. Tuckerman et al., J. Phys. A 39 (2006) 5629]. Here, we extend this approach to include both fully flexible cell fluctuations and holonomic constraints via a new and simpler formulation of the ROLL algorithm of Martyna et al. [Martyna et al., Mol. Phys. 87 (1996) 1117]. The new algorithm improves on earlier schemes in that it possesses a simpler mathematical structure and rigorously preserves the phase space metric. The new algorithm is illustrated on two example systems, ice and liquid n -decane.

  • a liouville operator derived measure preserving integrator for molecular dynamics simulations in the isothermal isobaric Ensemble
    Journal of Physics A, 2006
    Co-Authors: Roberto Lopezrendon, Jose Alejandre, Mark E Tuckerman, Andrea L Jochim, G. Martyna
    Abstract:

    The constant-pressure, constant-temperature (NPT) molecular dynamics approach is re-examined from the viewpoint of deriving a new measure-preserving reversible geometric integrator for the equations of motion. The underlying concepts of non-Hamiltonian phase-space analysis, measure-preserving integrators and the symplectic property for Hamiltonian systems are briefly reviewed. In addition, current measure-preserving schemes for the constant-volume, constant-temperature Ensemble are also reviewed. A new geometric integrator for the NPT method is presented, is shown to preserve the correct phase-space volume element and is demonstrated to perform well in realistic examples. Finally, a multiple time-step version of the integrator is presented for treating systems with motion on several time scales.

Joachim Gross - One of the best experts on this subject based on the ideXlab platform.

  • phase equilibria of solid and fluid phases from molecular dynamics simulations with equilibrium and nonequilibrium free energy methods
    Journal of Chemical Theory and Computation, 2019
    Co-Authors: Gernot Bauer, Joachim Gross
    Abstract:

    In this work, we present a methodology to determine phase coexistence lines for atomic and rigid molecular systems with an emphasis on solid–fluid and on solid–solid equilibria. Phase coexistence points are found by computing the absolute free energy for each candidate phase separately. For solid phases, a combination of the extended Einstein crystal and the Einstein molecule method is presented which constitutes a convenient way to compute the absolute free energy with fixed center of mass. We compare results from equilibrium methods—thermodynamic integration and reweighting using the multistate Bennett acceptance ratio estimator (MBAR)—with simulations using a nonequilibrium method and discuss their advantages and disadvantages. Once absolute free energies of different phases are available, they are combined with simulations performed in the isothermal isobaric Ensemble and MBAR, which enables efficient, iterative tracing of coexistence lines. The method is applicable to both liquid–solid as well as sol...

  • Phase Equilibria of Solid and Fluid Phases from Molecular Dynamics Simulations with Equilibrium and Nonequilibrium Free Energy Methods
    2019
    Co-Authors: Gernot Bauer, Joachim Gross
    Abstract:

    In this work, we present a methodology to determine phase coexistence lines for atomic and rigid molecular systems with an emphasis on solid–fluid and on solid–solid equilibria. Phase coexistence points are found by computing the absolute free energy for each candidate phase separately. For solid phases, a combination of the extended Einstein crystal and the Einstein molecule method is presented which constitutes a convenient way to compute the absolute free energy with fixed center of mass. We compare results from equilibrium methodsthermodynamic integration and reweighting using the multistate Bennett acceptance ratio estimator (MBAR)with simulations using a nonequilibrium method and discuss their advantages and disadvantages. Once absolute free energies of different phases are available, they are combined with simulations performed in the isothermal isobaric Ensemble and MBAR, which enables efficient, iterative tracing of coexistence lines. The method is applicable to both liquid–solid as well as solid–solid transitions and is comparably simple and convenient to apply since the same method (MBAR) is used to compute free energies and to trace the coexistence line. Furthermore, statistical uncertainties can readily be computed in a transparent manner. We apply the method to an atomic solid (fcc argon) as well as small molecular systems (methanol and water) using the LAMMPS simulation package. Our study shows that all methods can be used to reliably compute the absolute free energy of solid phases, while MBAR is the most flexible method with high statistical efficiency. We find the nonequilibrium method is an attractive choice since it is simple to set up and to postprocess and is, hence, less prone to errors. The presented workflow provides a flexible, efficient, and robust way to compute phase diagrams using openly available software