[ViewVC] Diff of: group/trunk/openmdDocs/openmdDoc.tex

Comparing trunk/openmdDocs/openmdDoc.tex (file contents):
Revision 3709 by gezelter, Wed Nov 24 20:44:51 2010 UTC vs.
Revision 3793 by skuang, Mon Aug 20 21:03:35 2012 UTC

+\textwidth 6.5in
+\brokenpenalty=10000
+\renewcommand{\baselinestretch}{1.2}
-+
+\usepackage[square, comma, sort&compress]{natbib}
-+
+\bibpunct{[}{]}{,}{n}{}{;}
-+
+%\renewcommand\citemid{\ } % no comma in optional reference note
+\lstset{language=C,frame=TB,basicstyle=\tiny,basicstyle=\ttfamily, %
+        xleftmargin=0.25in, xrightmargin=0.25in,captionpos=b, %
+\newcolumntype{H}{p{0.75in}}
+\newcolumntype{I}{p{5in}}
-+
+\newcolumntype{J}{p{1.5in}}
-+
+\newcolumntype{K}{p{1.2in}}
-+
+\newcolumntype{L}{p{1.5in}}
-+
+\newcolumntype{M}{p{1.55in}}
-–
+\title{{\sc OpenMD}: Molecular Dynamics in the Open}
-<
+\author{Kelsey M. Stocker, Shenyu Kuang, Charles F. Vardeman II, \\
-<
+  Teng Lin, Christopher J. Fennell,  Xiuquan Sun, \\
->
+\title{{\sc OpenMD-2}: Molecular Dynamics in the Open}
->
->
+\author{Shenyu Kuang, Joseph Michalka, Kelsey Stocker, James Marr, \\
->
+  Teng Lin, Charles F. Vardeman II, Christopher J. Fennell, Xiuquan Sun, \\
+  Chunlei Li, Kyle Daily, Yang Zheng, Matthew A. Meineke, and \\
+  J. Daniel Gezelter \\
+  Department of Chemistry and Biochemistry\\
+\endhead
+\hline
+\endfoot
-<
+{\tt forceField} & string & Sets the force field. & Possible force
-<
+fields are DUFF, WATER, LJ, EAM, SC, and CLAY. \\
->
+{\tt forceField} & string & Sets the base name for the force field file &
->
+OpenMD appends a {\tt .frc} to the end of this to look for a force
->
+field file.\\
+{\tt component} & & Defines the molecular components of the system &
+Every {\tt $<$MetaData$>$} block must have a component statement. \\
+{\tt minimizer} & string & Chooses a minimizer & Possible minimizers
+\section{Constant Pressure without periodic boundary conditions (The LangevinHull)}
-<
+The Langevin Hull uses an external bath at a fixed constant pressure
->
+The Langevin Hull\cite{Vardeman2011} uses an external bath at a fixed constant pressure
+($P$) and temperature ($T$) with an effective solvent viscosity
+($\eta$).  This bath interacts only with the objects on the exterior
+hull of the system.  Defining the hull of the atoms in a simulation is
+\label{table:zconParams}
+\end{longtable}
-<
+\chapter{\label{section:restraints}Restraints}
-<
+Restraints are external potentials that are added to a system to keep
-<
+particular molecules or collections of particles close to some
-<
+reference structure.  A restraint can be a collective
->
+% \chapter{\label{section:restraints}Restraints}
->
+% Restraints are external potentials that are added to a system to
->
+% keep particular molecules or collections of particles close to some
->
+% reference structure.  A restraint can be a collective
+\chapter{\label{section:thermInt}Thermodynamic Integration}
+\mbox{rad}^{-2}$ & & spring constant for rotation around z-axis in
+Einstein crystal
+\label{table:thermIntParams}
-+
+\end{longtable}
-+
-+
+\chapter{\label{section:rnemd}RNEMD}
-+
-+
+There are many ways to compute transport properties from molecular
-+
+dynamics simulations.  Equilibrium Molecular Dynamics (EMD)
-+
+simulations can be used by computing relevant time correlation
-+
+functions and assuming linear response theory holds.  These approaches
-+
+are generally subject to noise and poor convergence of the relevant
-+
+correlation functions. Traditional Non-equilibrium Molecular Dynamics
-+
+(NEMD) methods impose a gradient (e.g. thermal or momentum) on a
-+
+simulation.  However, the resulting flux is often difficult to
-+
+measure. Furthermore, problems arise for NEMD simulations of
-+
+heterogeneous systems, such as phase-phase boundaries or interfaces,
-+
+where the type of gradient to enforce at the boundary between
-+
+materials is unclear.
-+
-+
+{\it Reverse} Non-Equilibrium Molecular Dynamics (RNEMD) methods adopt
-+
+a different approach in that an unphysical {\it flux} is imposed
-+
+between different regions or ``slabs'' of the simulation box.  The
-+
+response of the system is to develop a temperature or momentum {\it
-+
+  gradient} between the two regions. Since the amount of the applied
-+
+flux is known exactly, and the measurement of gradient is generally
-+
+less complicated, imposed-flux methods typically take shorter
-+
+simulation times to obtain converged results for transport properties.
-+
-+
+\begin{figure}
-+
+\includegraphics[width=\linewidth]{rnemdDemo}
-+
+\caption{The (VSS) RNEMD approach imposes unphysical transfer of both
-+
+  linear momentum and kinetic energy between a ``hot'' slab and a
-+
+  ``cold'' slab in the simulation box.  The system responds to this
-+
+  imposed flux by generating both momentum and temperature gradients.
-+
+  The slope of the gradients can then be used to compute transport
-+
+  properties (e.g. shear viscosity and thermal conductivity).}
-+
+\label{rnemdDemo}
-+
+\end{figure}
-+
-+
+The original ``swapping'' approaches by M\"{u}ller-Plathe {\it et
-+
+  al.}\cite{ISI:000080382700030,MullerPlathe:1997xw} can be understood
-+
+as a sequence of imaginary elastic collisions between particles in
-+
+opposite slabs.  In each collision, the entire momentum vectors of
-+
+both particles may be exchanged to generate a thermal
-+
+flux. Alternatively, a single component of the momentum vectors may be
-+
+exchanged to generate a shear flux.  This algorithm turns out to be
-+
+quite useful in many simulations. However, the M\"{u}ller-Plathe
-+
+swapping approach perturbs the system away from ideal
-+
+Maxwell-Boltzmann distributions, and this may leads to undesirable
-+
+side-effects when the applied flux becomes large.\cite{Maginn:2010}
-+
+This limits the application of the swapping algorithm, so in OpenMD,
-+
+we implement two additional algorithms for RNEMD in addition to the
-+
+original swapping approach.
-+
-+
+{\bf Non-Isotropic Velocity Scaling (NIVS):}\cite{kuang:164101}
-+
+Instead of having momentum exchange between {\it individual particles}
-+
+in each slab, the NIVS algorithm applies velocity scaling to all of
-+
+the selected particles in both slabs.  A combination of linear
-+
+momentum, kinetic energy, and flux constraint equations governs the
-+
+amount of velocity scaling performed at each step.  Interested readers
-+
+should consult ref. \citealp{kuang:164101} for further details on the
-+
+methodology.
-+
-+
+NIVS has been shown to be very effective at producing thermal
-+
+gradients and for computing thermal conductivities, particularly for
-+
+heterogeneous interfaces.  Although the NIVS algorithm can also be
-+
+applied to impose a directional momentum flux, thermal anisotropy was
-+
+observed in relatively high flux simulations, and the method is not
-+
+suitable for imposing a shear flux.
-+
-+
+{\bf Velocity Shearing and Scaling (VSS)}:\cite{2012MolPh.110..691K}
-+
+The third RNEMD algorithm implemented in OpenMD utilizes a series of
-+
+simultaneous velocity shearing and scaling exchanges between the two
-+
+slabs.  This method results in a set of simpler equations to satisfy
-+
+the conservation constraints while creating a desired flux between the
-+
+two slabs.
-+
-+
+The VSS approach is versatile in that it may be used to implement both
-+
+thermal and shear transport either separately or simultaneously.
-+
+Perturbations of velocities away from the ideal Maxwell-Boltzmann
-+
+distributions are minimal, and thermal anisotropy is kept to a
-+
+minimum.  This ability to generate simultaneous thermal and shear
-+
+fluxes has been utilized to map out the shear viscosity of SPC/E water
-+
+in a wide range of temperature (90~K) just with a single simulation.
-+
+VSS-RNEMD also allows the directional momentum flux to have quite
-+
+arbitary directions, which could aid in the study of anisotropic solid
-+
+surfaces in contact with liquid environments.
-+
-+
+{\bf What the user needs to specify:} To carry out a RNEMD simulation,
-+
+a user must specify a number of parameters in the MetaData (.md) file.
-+
+Because the RNEMD methods have a large number of parameters, these
-+
+must be enclosed in a {\tt RNEMD\{...\}} block.  The most important
-+
+parameters to specify are the {\tt useRNEMD}, {\tt fluxType} and flux
-+
+parameters. Most other parameters (summarized in table
-+
+\ref{table:rnemd}) have reasonable default values.  {\tt fluxType}
-+
+sets up the kind of exchange that will be carried out between the two
-+
+slabs (either Kinetic Energy ({\tt KE}) or momentum ({\tt Px, Py, Pz,
-+
+  Pvector}), or some combination of these).  The flux is specified
-+
+with the use of three possible parameters: {\tt kineticFlux} for
-+
+kinetic energy exchange, as well as {\tt momentumFlux} or {\tt
-+
+  momentumFluxVector} for simulations with directional exchange.
-+
-+
+{\bf How to process the results:} OpenMD will generate a {\tt .rnemd}
-+
+file with the same prefix as the original {\tt .md} file.  This file
-+
+contains a running average of properties of interest computed within a
-+
+set of bins that divide the simulation cell along the $z$-axis.  The
-+
+first column of the {\tt .rnemd} file is the $z$ coordinate of the
-+
+center of each bin, while following columns may contain the average
-+
+temperature, velocity, or density within each bin.  The output format
-+
+in the {\tt .rnemd} file can be altered with the {\tt outputFields},
-+
+{\tt outputBins}, and {\tt outputFileName} parameters.  A report at
-+
+the top of the {\tt .rnemd} file contains the current exchange totals
-+
+as well as the average flux applied during the simulation.  Using the
-+
+slope of the temperature or velocity gradient obtaine from the {\tt
-+
+  .rnemd} file along with the applied flux, the user can very simply
-+
+arrive at estimates of thermal conductivities ($\lambda$),
-+
+\begin{equation}
-+
+J_z = -\lambda \frac{\partial T}{\partial z},
-+
+\end{equation}
-+
+and shear viscosities ($\eta$),
-+
+\begin{equation}
-+
+j_z(p_x) = -\eta \frac{\partial \langle v_x \rangle}{\partial z}.
-+
+\end{equation}
-+
+Here, the quantities on the left hand side are the actual flux values
-+
+(in the header of the {\tt .rnemd} file), while the slopes are
-+
+obtained from linear fits to the gradients observed in the {\tt
-+
+  .rnemd} file.
-+
-+
+More complicated simulations (including interfaces) require a bit more
-+
+care.  Here the second derivative may be required to compute the
-+
+interfacial thermal conductance,
-+
+\begin{align}
-+
+  G^\prime &= \left(\nabla\lambda \cdot \mathbf{\hat{n}}\right)_{z_0} \\
-+
+  &= \frac{\partial}{\partial z}\left(-\frac{J_z}{
-+
+      \left(\frac{\partial T}{\partial z}\right)}\right)_{z_0} \\
-+
+  &= J_z\left(\frac{\partial^2 T}{\partial z^2}\right)_{z_0} \Big/
-+
+  \left(\frac{\partial T}{\partial z}\right)_{z_0}^2.
-+
+  \label{derivativeG}
-+
+\end{align}
-+
+where $z_0$ is the location of the interface between two materials and
-+
+$\mathbf{\hat{n}}$ is a unit vector normal to the interface.  We
-+
+suggest that users interested in interfacial conductance consult
-+
+reference \citealp{kuang:AuThl} for other approaches to computing $G$.
-+
+Users interested in {\it friction coefficients} at heterogeneous
-+
+interfaces may also find reference \citealp{2012MolPh.110..691K}
-+
+useful.
-+
-+
+\newpage
-+
-+
+\begin{longtable}[c]{JKLM}
-+
+\caption{The following keywords must be enclosed inside a {\tt RNEMD\{\}} block}
-+
+\\
-+
+{\bf keyword} & {\bf units} & {\bf use} & {\bf remarks}  \\ \hline
-+
+\endhead
-+
+\hline
-+
+\endfoot
-+
+{\tt useRNEMD} & logical & perform RNEMD? & default is ``false'' \\
-+
+{\tt objectSelection} & string & see section \ref{section:syntax}
-+
+for selection syntax & default is ``select all'' \\
-+
+{\tt method} & string & exchange method & one of the following:
-+
+{\tt Swap, NIVS,} or {\tt VSS}  (default is {\tt VSS}) \\
-+
+{\tt fluxType} & string & what is being exchanged between slabs? & one
-+
+of the following: {\tt KE, Px, Py, Pz, Pvector, KE+Px, KE+Py, KE+Pvector} \\
-+
+{\tt kineticFlux} & kcal mol$^{-1}$ \AA$^{-2}$ fs$^{-1}$ & specify the kinetic energy flux &  \\
-+
+{\tt momentumFlux} & amu \AA$^{-1}$ fs$^{-2}$ & specify the momentum flux & \\
-+
+{\tt momentumFluxVector} & amu \AA$^{-1}$ fs$^{-2}$ & specify the momentum flux when
-+
+{\tt Pvector} is part of the exchange & Vector3d input\\
-+
+{\tt exchangeTime} & fs & how often to perform the exchange & default is 100 fs\\
-+
-+
+{\tt slabWidth} & $\mbox{\AA}$ & width of the two exchange slabs & default is $\mathsf{H}_{zz} / 10.0$ \\
-+
+{\tt slabAcenter} & $\mbox{\AA}$ & center of the end slab & default is 0 \\
-+
+{\tt slabBcenter} & $\mbox{\AA}$ & center of the middle slab & default is $\mathsf{H}_{zz} / 2$ \\
-+
+{\tt outputFileName} & string & file name for output histograms & default is the same prefix as the
-+
+.md file, but with the {\tt .rnemd} extension \\
-+
+{\tt outputBins} & int & number of $z$-bins in the output histogram &
-+
+default is 20 \\
-+
+{\tt outputFields} & string & columns to print in the {\tt .rnemd}
-+
+file where each column is separated by a pipe ($\mid$) symbol. & Allowed column names are: {\sc z, temperature, velocity, density} \\
-+
+\label{table:rnemd}
+\end{longtable}
+DMR-0079647.
-<
+\bibliographystyle{jcc}
->
+\bibliographystyle{aip}
+\bibliography{openmdDoc}
+\end{document}

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Comparing trunk/openmdDocs/openmdDoc.tex (file contents): Revision 3709 by gezelter, Wed Nov 24 20:44:51 2010 UTC vs. Revision 3793 by skuang, Mon Aug 20 21:03:35 2012 UTC

Diff Legend

Comparing trunk/openmdDocs/openmdDoc.tex (file contents):
Revision 3709 by gezelter, Wed Nov 24 20:44:51 2010 UTC vs.
Revision 3793 by skuang, Mon Aug 20 21:03:35 2012 UTC