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164
Collective variables
TOL
SWITCH
this keyword can be used to speed up your
calculation. When accumulating sums in which the
individual terms are numbers inbetween zero and one
it is assumed that terms less than a certain tolerance
make only a small contribution to the sum. They can
thus be safely ignored as can the the derivatives wrt
these small quantities.
This keyword is used if you want to employ an
alternative to the continuous swiching 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. You can use multiple
instances of this keyword i.e. SWITCH1, SWITCH2,
SWITCH3...
Examples
This example input calculates the 7 SPRINT coordinates for a 7 atom cluster of Lennard-Jones atoms and prints
their values to a file. In this input the SPRINT coordinates are calculated in the manner described in ?? so two
atoms are adjacent if they are within a cutoff:
DENSITY SPECIES=1-7 LABEL=d1
SPRINT ARG=d1 SWITCH={RATIONAL R_0=0.1} LABEL=ss
PRINT ARG=ss.* FILE=colvar
This example input calculates the 14 SPRINT coordinates foa a molecule composed of 7 hydrogen and 7 carbon
atoms. Once again two atoms are adjacent if they are within a cutoff:
DENSITY SPECIES=1-7 LABEL=c
DENSITY SPECIES=8-14 LABEL=h
SPRINT ...
ARG=c,h
SWITCH11={RATIONAL R_0=2.6 NN=6 MM=12}
SWITCH12={RATIONAL R_0=2.2 NN=6 MM=12}
SWITCH22={RATIONAL R_0=2.2 NN=6 MM=12}
LABEL=ss
... SPRINT
PRINT ARG=ss.* FILE=colvar
5.5.26
UWALLS
This is part of the manyrestraints module
Add UPPER_WALLS restraints on all the multicolvar values
This action takes the set of values calculated by the colvar specified by label in the DATA keyword and places a
restraint on each quantity, x, with the following functional form:
k((x − a + o)/s)e
k (KAPPA) is an energy constant in internal unit of the code, s (EPS) a rescaling factor and e (EXP) the exponent
determining the power law. By default: EXP = 2, EPS = 1.0, OFF = 0.
Description of components
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