GRADIENT

This is part of the crystallization module | |

It is only available if you configure PLUMED with ./configure –enable-modules=crystallization . Furthermore, this feature is still being developed so take care when using it and report any problems on the mailing list. |

Calculate the gradient of the average value of a multicolvar value

This command allows you to calculate the collective variable discussed in [49].

- Examples

The input below calculates the gradient of the density of atoms in the manner described in [49] in order to detect whether or not atoms are distributed uniformly along the x-axis of the simulation cell.

Click on the labels of the actions for more information on what each action computes

d1:DENSITYSPECIES=1-50this keyword is used for colvars such as coordination number.s1:GRADIENTORIGIN=1we will use the position of this atom as the origin in our calculation.DATA=compulsory keywordThe multicolvar that calculates the set of base quantities that we are interested ind1DIR=xcompulsory keyword ( default=xyz )the directions in which we are calculating the gradient.NBINS=4compulsory keywordnumber of bins to use in each direction for the calculation of the gradientSIGMA=1.0 PRINTcompulsory keyword ( default=1.0 )the width of the function to be used for kernel density estimationARG=the input for this action is the scalar output from one or more other actions.s1FILE=colvarthe name of the file on which to output these quantities

The input below calculates the coordination numbers of the 50 atoms in the simulation cell. The gradient of this quantity is then evaluated in the manner described using the equation above to detect whether the average values of the coordination number are uniformly distributed along the x-axis of the simulation cell.

Click on the labels of the actions for more information on what each action computes

d2:COORDINATIONNUMBERSPECIES=1-50this keyword is used for colvars such as coordination number.SWITCH={RATIONAL R_0=2.0}This keyword is used if you want to employ an alternative to the continuous switching function defined above.MORE_THAN={EXP R_0=4.0}calculate the number of variables more than a certain target value.s2:GRADIENTORIGIN=1we will use the position of this atom as the origin in our calculation.DATA=compulsory keywordThe multicolvar that calculates the set of base quantities that we are interested ind2DIR=xcompulsory keyword ( default=xyz )the directions in which we are calculating the gradient.NBINS=4compulsory keywordnumber of bins to use in each direction for the calculation of the gradientSIGMA=1.0 PRINTcompulsory keyword ( default=1.0 )the width of the function to be used for kernel density estimationARG=the input for this action is the scalar output from one or more other actions.s2FILE=colvarthe name of the file on which to output these quantities

- Glossary of keywords and components

- The atoms involved can be specified using

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

- Compulsory keywords

DATA | The multicolvar that calculates the set of base quantities that we are interested in |

DIR | ( default=xyz ) the directions in which we are calculating the gradient. Should be x, y, z, xy, xz, yz or xyz |

NBINS | number of bins to use in each direction for the calculation of the gradient |

SIGMA | ( default=1.0 ) the width of the function to be used for kernel density estimation |

KERNEL | ( default=gaussian ) the type of kernel function to be used |

- Options

NUMERICAL_DERIVATIVES | ( default=off ) calculate the derivatives for these quantities numerically |

NOPBC | ( default=off ) ignore the periodic boundary conditions when calculating distances |

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

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

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