Simulations: Difference between revisions

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===Special Usage Notes===
===Special Usage Notes===
By default, LAMMPS normalizes the temperature by an amount (dof - d), where dof is the system's total number of degrees of freedom and d is the dimensionality of the simulation. Subtracting d accounts for the center-of-mass motion of the system. This is correct except when there is a proper frame of reference for the system, e.g., in a Langevin dynamics simulation in which the implicit background solvent has zero average velocity. In this case it is necessary to use the command [http://lammps.sandia.gov/doc/compute_modify.html compute_modify] to ensure dof is used instead of (dof - d). For instance one can use
By default, LAMMPS normalizes the temperature by an amount ''dof'' ''d'', where ''dof'' is the system's total number of degrees of freedom and ''d'' is the dimensionality of the simulation. Subtracting ''d'' accounts for the center-of-mass motion of the system. This is correct except when there is a proper frame of reference for the system, e.g., in a Langevin dynamics simulation in which the implicit background solvent has zero average velocity. In this case it is necessary to use the command [http://lammps.sandia.gov/doc/compute_modify.html compute_modify] to ensure ''dof'' is used instead of ''dof'' - ''d''. For instance one can use


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Revision as of 19:02, 7 June 2014

Introduction

Assorted topics relevant to programming particle-based simulation codes and to using these codes for the modeling of a wide range of systems, notably complex fluids.

Molecular dynamics simulations

Special Usage Notes

By default, LAMMPS normalizes the temperature by an amount dofd, where dof is the system's total number of degrees of freedom and d is the dimensionality of the simulation. Subtracting d accounts for the center-of-mass motion of the system. This is correct except when there is a proper frame of reference for the system, e.g., in a Langevin dynamics simulation in which the implicit background solvent has zero average velocity. In this case it is necessary to use the command compute_modify to ensure dof is used instead of dof - d. For instance one can use

compute myTemp all temp
compute_modify myTemp extra 0
thermo_modify temp myTemp

Monte Carlo simulations