| This is part of the adjmat module |
| It is only available if you configure PLUMED with ./configure –enable-modules=adjmat . Furthermore, this feature is still being developed so take care when using it and report any problems on the mailing list. |
Adjacency matrix in which two atoms are adjacent if they are connected topologically
- Examples
- Glossary of keywords and components
- The atoms involved can be specified using
- Compulsory keywords
DENSITY_THRESHOLD | |
SIGMA | 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 |
TIMINGS | ( default=off ) output information on the timings of the various parts of the calculation |
HIGHMEM | ( default=off ) use a more memory intensive version of this collective variable
|
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. You can use multiple instances of this keyword i.e. SWITCH1, SWITCH2, SWITCH3... |
RADIUS | You can use multiple instances of this keyword i.e. RADIUS1, RADIUS2, RADIUS3... |
CYLINDER_SWITCH | a switching function on \((r_{ij}\cdot r_{ik}-1)/r_{ij}\) You can use multiple instances of this keyword i.e. CYLINDER_SWITCH1, CYLINDER_SWITCH2, CYLINDER_SWITCH3... |
BIN_SIZE | the size to use for the bins You can use multiple instances of this keyword i.e. BIN_SIZE1, BIN_SIZE2, BIN_SIZE3... |