Simulations: Difference between revisions
Jump to navigation
Jump to search
Line 6: | Line 6: | ||
===Special Usage Notes=== |
===Special Usage Notes=== |
||
By default LAMMPS normalizes the temperature by an amount |
By default LAMMPS normalizes the temperature by an amount <math>n_\text{dof} - d</math>, where <math>n_\text{dof}</math> is the system's total number of degrees of freedom and <math>d</math> is the system's dimensionality. Subtracting <math>d</math> 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 <math>n_\text{dof}</math> is used instead of <math>n_\text{dof} - d</math>. To do this, use the command [http://lammps.sandia.gov/doc/compute_modify.html compute_modify] as follows |
||
<pre> |
<pre> |
Revision as of 16:59, 12 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 , where is the system's total number of degrees of freedom and is the system's dimensionality. Subtracting 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 is used instead of . To do this, use the command compute_modify as follows
compute myTemp all temp compute_modify myTemp extra 0 thermo_modify temp myTemp