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].
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.
d1: DENSITYSPECIES=1-50 s1: GRADIENTthis keyword is used for colvars such as coordination number.ORIGIN=1we will use the position of this atom as the origin in our calculation.DATA=d1compulsory keyword The multicolvar that calculates the set of base quantities that we are interested inDIR=xcompulsory keyword ( default=xyz ) the directions in which we are calculating the gradient.NBINS=4compulsory keyword number 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=s1the input for this action is the scalar output from one or more other actions.FILE=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.
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} s2: GRADIENTcalculate the number of variables more than a certain target value.ORIGIN=1we will use the position of this atom as the origin in our calculation.DATA=d2compulsory keyword The multicolvar that calculates the set of base quantities that we are interested inDIR=xcompulsory keyword ( default=xyz ) the directions in which we are calculating the gradient.NBINS=4compulsory keyword number 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=s2the input for this action is the scalar output from one or more other actions.FILE=colvarthe name of the file on which to output these quantities
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 |
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 |
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 |