BOND_DIRECTIONS

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 vectors connecting atoms that are within cutoff defined using a switching function.

- Examples

- Glossary of keywords and components

- Description of components

When the label of this action is used as the input for a second you are not referring to a scalar quantity as you are in regular collective variables. The label is used to reference the full set of vectors calculated by the action. This is usual when using MultiColvar functions. Generally when doing this the previously calculated multicolvar will be referenced using the DATA keyword rather than ARG.

This Action can be used to calculate the following scalar quantities directly. These quantities are calculated by employing the keywords listed below. These quantities can then be referenced elsewhere in the input file by using this Action's label followed by a dot and the name of the quantity. All of them can be calculated multiple times with different parameters. In this case the quantities calculated can be referenced elsewhere in the input by using the name of the quantity followed by a numerical identifier e.g. *label*.lessthan-1, *label*.lessthan-2 etc. When doing this and, for clarity we have made it so that the user can set the label for the components. As such by using the LABEL keyword in the description of the keyword input you can customize the component name. In addition, you can calculate all of these scalar functions for one particular component of the calculated vector by making use of the COMPONENT keyword. The first component is used to refer to the norm of the vector. The individual components can then be referenced using the numbers 2, 3, and so on. So as an example MEAN1={COMPONENT=1} calculates the average vector norm. MEAN2={COMPONENT=2} by contrast calculates the mean for all of the first components of the vectors.

Quantity | Keyword | Description |

vmean | VMEAN | the norm of the mean vector. The output component can be referred to elsewhere in the input file by using the label.vmean |

vsum | VSUM | the norm of sum of vectors. The output component can be referred to elsewhere in the input file by using the label.vsum |

- The atoms involved can be specified using

ATOMS | the atoms involved in each of the vectors you wish to calculate. Keywords like ATOMS1, ATOMS2, ATOMS3,... should be listed and one vector will be calculated for each ATOM keyword you specify (all ATOM keywords should specify the indices of two atoms). The eventual number of quantities calculated by this action will depend on what functions of the distribution you choose to calculate. You can use multiple instances of this keyword i.e. ATOMS1, ATOMS2, ATOMS3... |

- Or alternatively by using

GROUP | Calculate the distance between each distinct pair of atoms in the group |

- Or alternatively by using

GROUPA | Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB. This must be used in conjunction with GROUPB. |

GROUPB | Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB. This must be used in conjunction with GROUPA. |

- Compulsory keywords

NN | ( default=12 ) The n parameter of the switching function |

MM | ( default=0 ) The m parameter of the switching function; 0 implies 2*NN |

D_0 | ( default=0.0 ) The d_0 parameter of the switching function |

R_0 | The r_0 parameter of the switching function |

- 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 |

SWITCH | This keyword is used if you want to employ an alternative to the continuous switching function defined above. The following provides information on the switchingfunction that are available. When this keyword is present you no longer need the NN, MM, D_0 and R_0 keywords. |

VMEAN | calculate the norm of the mean vector. The final value can be referenced using label.vmean. You can use multiple instances of this keyword i.e. VMEAN1, VMEAN2, VMEAN3... The corresponding values are then referenced using label.vmean-1, label.vmean-2, label.vmean-3... |

VSUM | calculate the norm of the sum of vectors. The final value can be referenced using label.vsum. You can use multiple instances of this keyword i.e. VSUM1, VSUM2, VSUM3... The corresponding values are then referenced using label.vsum-1, label.vsum-2, label.vsum-3... |