Project ID: plumID:21.021
Source: meta_inputs/LJ-38/plumed.dat
Originally used with PLUMED version: 2.7-mod
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
UNITSThis command sets the internal units for the code. More details NATURAL use natural units
The UNITS action with label calculates somethingnsaThe COORDINATIONNUMBER action with label nsa calculates the following quantities:| Quantity | Type | Description |
| nsa | vector | the coordination numbers of the specified atoms |
: COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut. More details SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=1-38 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=1.25 D_MAX=1.5}
# nsa: COORDINATIONNUMBER SPECIES=1-38 SWITCH={CUBIC D_0=1.25 D_MAX=1.5} #MORE_THAN={GAUSSIAN R_0=0.5 D_0=6}
nsa_grpThe GROUP action with label nsa_grp calculates the following quantities:| Quantity | Type | Description |
| nsa_grp | atoms | indices of atoms specified in GROUP |
: 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=1-38
nsa_matThe CONTACT_MATRIX action with label nsa_mat calculates the following quantities:| Quantity | Type | Description |
| nsa_mat | matrix | a matrix containing the weights for the bonds between each pair of atoms |
: CONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details GROUPspecifies the list of atoms that should be assumed indistinguishable=1-38 SWITCHthe input for the switching function that acts upon the distance between each pair of atoms. Options for this keyword are explained in the documentation for LESS_THAN.={CUBIC D_0=1.25 D_MAX=1.5}
nsa_onesThe CONSTANT action with label nsa_ones calculates the following quantities:| Quantity | Type | Description |
| nsa_ones | vector | the constant value that was read from the plumed input |
: ONESCreate a constant vector with all elements equal to one More details SIZEthe number of ones that you would like to create=38
nsaThe MATRIX_VECTOR_PRODUCT action with label nsa calculates the following quantities:| Quantity | Type | Description |
| nsa | vector | the vector that is obtained by taking the product between the matrix and the vector that were input |
: MATRIX_VECTOR_PRODUCTCalculate the product of the matrix and the vector More details ARGthe label for the matrix and the vector/scalar that are being multiplied=nsa_mat,nsa_ones
nsa_caverageThe MEAN action with label nsa_caverage calculates the following quantities:| Quantity | Type | Description |
| nsa_caverage | scalar | the mean of all the elements in the input vector |
: MEANCalculate the arithmetic mean of the elements in a vector More details ARGthe values input to this function=nsa PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input ---
nsThe MATHEVAL action with label ns calculates the following quantities:| Quantity | Type | Description |
| ns | vector | the vector obtained by doing an element-wise application of an arbitrary function to the input vectors |
: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=nsa FUNCthe function you wish to evaluate=exp(-(x-6)*(x-6)/(2*0.5*0.5)) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
neThe MATHEVAL action with label ne calculates the following quantities:| Quantity | Type | Description |
| ne | vector | the vector obtained by doing an element-wise application of an arbitrary function to the input vectors |
: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=nsa FUNCthe function you wish to evaluate=exp(-(x-8)*(x-8)/(2*0.5*0.5)) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
mtThe METAD action with label mt calculates the following quantities:| Quantity | Type | Description |
| mt.bias | scalar | the instantaneous value of the bias potential |
: METADUsed to performed metadynamics on one or more collective variables. This action has hidden defaults. More details ...
ARGthe labels of the scalars on which the bias will act=ns,ne
PACEthe frequency for hill addition=500
SIGMAthe widths of the Gaussian hills=0.1,0.1
BIASFACTORuse well tempered metadynamics and use this bias factor=10 HEIGHTthe heights of the Gaussian hills=1.0 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=0.12
GRID_MINthe lower bounds for the grid=0.,0. GRID_MAXthe upper bounds for the grid=28,20 GRID_BINthe number of bins for the grid=300,300
...
mt: METADUsed to performed metadynamics on one or more collective variables. This action uses the defaults shown here. More details ...
ARGthe labels of the scalars on which the bias will act=ns,ne
PACEthe frequency for hill addition=500
SIGMAthe widths of the Gaussian hills=0.1,0.1
BIASFACTORuse well tempered metadynamics and use this bias factor=10 HEIGHTthe heights of the Gaussian hills=1.0 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=0.12
GRID_MINthe lower bounds for the grid=0.,0. GRID_MAXthe upper bounds for the grid=28,20 GRID_BINthe number of bins for the grid=300,300
FILE a file in which the list of added hills is stored=HILLS
...
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=ns,ne,mt.bias FMTthe format that should be used to output real numbers=%8.4f FILEthe name of the file on which to output these quantities=colvar STRIDE the frequency with which the quantities of interest should be output=500
