MULTICOLVARDENS

This is part of the multicolvar module |

Evaluate the average value of a multicolvar on a grid.

This keyword allows one to construct a phase field representation for a symmetry function from an atomistic description. If each atom has an associated order parameter, \(\phi_i\) then a smooth phase field function \(\phi(r)\) can be computed using:

\[ \phi(\mathbf{r}) = \frac{\sum_i K(\mathbf{r}-\mathbf{r}_i) \phi_i }{ \sum_i K(\mathbf{r} - \mathbf{r}_i )} \]

where \(\mathbf{r}_i\) is the position of atom \(i\), the sums run over all the atoms input and \(K(\mathbf{r} - \mathbf{r}_i)\) is one of the kernelfunctions implemented in plumed. This action calculates the above function on a grid, which can then be used in the input to further actions.

- The atoms involved can be specified using

ORIGIN | we will use the position of this atom as the origin. For more information on how to specify lists of atoms see Groups and Virtual Atoms |

- Compulsory keywords

STRIDE | ( default=1 ) the frequency with which the data should be collected and added to the quantity being averaged |

CLEAR | ( default=0 ) the frequency with which to clear all the accumulated data. The default value of 0 implies that all the data will be used and that the grid will never be cleared |

BANDWIDTH | the bandwidths for kernel density esimtation |

KERNEL | ( default=gaussian ) the kernel function you are using. More details on the kernels available in plumed plumed can be found in kernelfunctions. |

DATA | the multicolvar which you would like to calculate the density profile for |

DIR | the direction in which to calculate the density profile |

- Options

SERIAL | ( default=off ) do the calculation in serial. Do not parallelize |

LOWMEM | ( default=off ) lower the memory requirements |

TIMINGS | ( default=off ) output information on the timings of the various parts of the calculation |

UNORMALIZED | ( default=off ) output the unaveraged quantity/quantities. |

FRACTIONAL | ( default=off ) use fractional coordinates for the various axes |

XREDUCED | ( default=off ) limit the calculation of the density/average to a portion of the z-axis only |

YREDUCED | ( default=off ) limit the calculation of the density/average to a portion of the y-axis only |

ZREDUCED | ( default=off ) limit the calculation of the density/average to a portion of the z-axis only |

LOGWEIGHTS | list of actions that calculates log weights that should be used to weight configurations when calculating averages |

NBINS | the number of bins to use to represent the density profile |

SPACING | the approximate grid spacing (to be used as an alternative or together with NBINS) |

XLOWER | this is required if you are using XREDUCED. It specifes the lower bound for the region of the x-axis that for which you are calculating the density/average |

XUPPER | this is required if you are using XREDUCED. It specifes the upper bound for the region of the x-axis that for which you are calculating the density/average |

YLOWER | this is required if you are using YREDUCED. It specifes the lower bound for the region of the y-axis that for which you are calculating the density/average |

YUPPER | this is required if you are using YREDUCED. It specifes the upper bound for the region of the y-axis that for which you are calculating the density/average |

ZLOWER | this is required if you are using ZREDUCED. It specifes the lower bound for the region of the z-axis that for which you are calculating the density/average |

ZUPPER | this is required if you are using ZREDUCED. It specifes the upper bound for the region of the z-axis that for which you are calculating the density/average |

- Examples

The following example shows perhaps the simplest way in which this action can be used. The following input computes the density of atoms at each point on the grid and ouptuts this quantity to a file. In other words this input instructs plumed to calculate \(\rho(\mathbf{r}) = \sum_i K(\mathbf{r} - \mathbf{r}_i )\)

dens: DENSITY SPECIES=1-100 grid: MULTICOLVARDENS DATA=dens ORIGIN=1 DIR=xyz NBINS=100,100,100 BANDWIDTH=0.05,0.05,0.05 STRIDE=1 DUMPGRID GRID=grid STRIDE=500 FILE=density

In the above example density is added to the grid on every step. The PRINT_GRID instruction thus tells PLUMED to output the average density at each point on the grid every 500 steps of simulation. Notice that the that grid output on step 1000 is an average over all 1000 frames of the trajectory. If you would like to analyse these two blocks of data separately you must use the CLEAR flag.

This second example computes an order parameter (in this case FCCUBIC) and constructs a phase field model for this order parameter using the equation above.

fcc: FCCUBIC SPECIES=1-5184 SWITCH={CUBIC D_0=1.2 D_MAX=1.5} ALPHA=27 dens: MULTICOLVARDENS DATA=fcc ORIGIN=1 DIR=xyz NBINS=14,14,28 BANDWIDTH=1.0,1.0,1.0 STRIDE=1 CLEAR=1 DUMPCUBE GRID=dens STRIDE=1 FILE=dens.cube

In this example the phase field model is computed and output to a file on every step of the simulation. Furthermore, because the CLEAR=1 keyword is set on the MULTICOLVARDENS line each Gaussian cube file output is a phase field model for a particular trajectory frame. The average value accumulated thus far is cleared at the start of every single timestep and there is no averaging over trajectory frames in this case.