Project ID: plumID:23.026
Source: plumed_model_2D_WTD.dat
Originally used with PLUMED version: 2.5.2
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
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# LOAD FILE=PythonCV.dylib grp: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=1-421 cv1: PYTHONCVThis action is not part of PLUMED and was included by using a LOAD command More details ATOMS=1-421 IMPORT=model_2D FUNCTION=cv1 COMPONENTS=ncl,nq6 cn: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=grp 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.={RATIONAL R_0=7.0 D_MAX=8.0} LOWMEM this flag does nothing and is present only to ensure back-compatibility MORE_THANcalculate the number of variables that are more than a certain target value. Options for this keyword are explained in the documentation for MORE_THAN.={RATIONAL R_0=3.0 D_MAX=13.0} ### calculate the number of particles with crystalline order (first shell geometries) q6: Q6Calculate sixth order Steinhardt parameters. More details SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=grp 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.={RATIONAL R_0=7.0 D_MAX=8.0} LOWMEM this flag does nothing and is present only to ensure back-compatibility lq6: LOCAL_Q6Calculate the local degree of order around an atoms by taking the average dot product between the q_6 vector on the central atom and the q_6 vector on the atoms in the first coordination sphere. More details SPECIESthe label of the action that computes the Steinhardt parameters for which you would like to calculate local steinhardt parameters=q6 SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={RATIONAL R_0=7.0 D_MAX=8.0} LOWMEM this flag does nothing and is present only to ensure back-compatibility flq6: MFILTER_MOREApply one minus a switching function to the input vector. More details DATAthe vector you wish to transform=lq6 SWITCHthe switching function that transform={GAUSSIAN R_0=0.69 D_MAX=0.70}
### calculate the coordination number distributions for these crystalline particles and count them cnq6: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=flq6 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.={RATIONAL R_0=7.0 D_MAX=8.0} MEAN calculate the mean of all the quantities MORE_THANcalculate the number of variables that are more than a certain target value. Options for this keyword are explained in the documentation for MORE_THAN.={RATIONAL R_0=11.0 D_MAX=13.0}
n: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=cn.morethan POWERS the powers to which you are raising each of the arguments in your function=0.33333333 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO nq6: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=cnq6.morethan POWERS the powers to which you are raising each of the arguments in your function=0.333333 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO lwall: LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=cv1.nq6 ATthe positions of the wall=-0.5 KAPPAthe force constant for the wall=150.0 EXP the powers for the walls=4 EPS the values for s_i in the expression for a wall=1 OFFSET the offset for the start of the wall=0 res: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=cv1.ncl,cv1.nq6 SIGMAthe widths of the Gaussian hills=0.18,0.05 HEIGHTthe heights of the Gaussian hills=0.1 PACEthe frequency for hill addition=1000 BIASFACTORuse well tempered metadynamics and use this bias factor=50 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=2 GRID_MINthe lower bounds for the grid=-0.5,-1.5 GRID_MAXthe upper bounds for the grid=10,8 GRID_BINthe number of bins for the grid=200,200 PRINTPrint quantities to a file. More details FILEthe name of the file on which to output these quantities=colvar.out ARGthe labels of the values that you would like to print to the file=cv1.ncl,cv1.nq6,res.bias,res.work,cn.morethan,cnq6.morethan STRIDE the frequency with which the quantities of interest should be output=500