Project ID: plumID:19.052
Source: plumed.dat
Originally used with PLUMED version: not specified
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr

Click on the labels of the actions for more information on what each action computes
tested onv2.10
tested onmaster
UNITSThis command sets the internal units for the code. More details NATURAL use natural units 
# Record the volume of the simulation cell.
cell: CELLGet the components of the simulation cell More details
# We first compute the local order parameter for each atom using the cubic harmonic function “FCCUBIC”. The sigmoid switching function “SMAP” is used to transform these quantities with a non-linear mapping on. 
# We compute the sum of these transformed order parameters using the keyword “MORE THAN”. The value of “cub.morethan” is thus proportional to the number of atoms in the fcc crystal.
# The system contains a total of 23328 real atoms, The first atom is a “ghost” atom that stays stationary at the center of the supercell. This ghost atom is only used as a reference point
cub: FCCUBICMeasure how similar the environment around atoms is to that found in a FCC structure. More details SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=2-23329 SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={CUBIC D_0=1.2 D_MAX=1.5} ALPHA The alpha parameter of the angular function that is used for FCCUBIC=27 MEAN calculate the mean of all the quantities MORE_THAN1calculate the number of variables that are more than a certain target value. Options for this keyword are explained in the documentation for MORE_THAN.={SMAP R_0=0.45 D_0=0.0 A=8 B=8}

# Perform a metadynamics simulation
metad: METADUsed to performed metadynamics on one or more collective variables. More details ...
ARGthe labels of the scalars on which the bias will act=cub.morethan-1
PACEthe frequency for hill addition=1000 HEIGHTthe heights of the Gaussian hills=0.3 SIGMAthe widths of the Gaussian hills=600 FILE a file in which the list of added hills is stored=HILLS TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=0.58 BIASFACTORuse well tempered metadynamics and use this bias factor=400
ADAPTIVEuse a geometric (=GEOM) or diffusion (=DIFF) based hills width scheme=DIFF SIGMA_MAXthe upper bounds for the sigmas (in CV units) when using adaptive hills=300 SIGMA_MINthe lower bounds for the sigmas (in CV units) when using adaptive hills=0.1 
... 

fixmax: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=cub.morethan-1 ATthe positions of the wall=2500 KAPPAthe force constant for the wall=0.1
# monitor the two variables and the metadynamics bias potential 
PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=10 ARGthe labels of the values that you would like to print to the file=cell.ax,cub.*,metad.bias,fixmax.bias FILEthe name of the file on which to output these quantities=COLVAR
ENDPLUMEDTerminate plumed input. More details