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 system's dimensionality. Subtracting ''d'' accounts for the center-of-mass motion of the system. This is incorrect if the system has a proper frame of reference, e.g., when using a Langevin thermostat in which all particles interact with a stationary background solvent. In this case it is necessary to ensure ''dof'' is used instead of ''dof'' – ''d''. To do this, use the command [http://lammps.sandia.gov/doc/compute_modify.html compute_modify] as follows


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Revision as of 18:14, 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 system's dimensionality. Subtracting d accounts for the center-of-mass motion of the system. This is incorrect if the system has a proper frame of reference, e.g., when using a Langevin thermostat in which all particles interact with a stationary background solvent. In this case it is necessary to ensure dof is used instead of dofd. To do this, use the command compute_modify as follows

compute myTemp all temp
compute_modify myTemp extra 0
thermo_modify temp myTemp

Monte Carlo simulations