Project ID: plumID:19.014
Source: mil-101_paper_setup/plumed_files/plumed_coordination.dat
Originally used with PLUMED version: 2.2
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
RESTARTActivate restart. More details
The RESTART action with label calculates somethingCOORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut and it has hidden defaults. More details LABELa label for the action so that its output can be referenced in the input to other actions=cnThe COORDINATIONNUMBER action with label cn calculates the following quantities:| Quantity | Type | Description |
| cn | vector | the coordination numbers of the specified atoms |
| cn_morethan | scalar | the number of colvars that have a value more than a threshold |
SPECIESAthe list of atoms for which the symmetry function is being calculated=1-3,61-63 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=23,24,39,40,55,56,83,84,99,100,115,116 R_0The r_0 parameter of the switching function=0.25 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=0.5 NN=2 MM=4 D_0=0}
COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut and uses the defaults shown here. More details LABELa label for the action so that its output can be referenced in the input to other actions=cn SPECIESAthe list of atoms for which the symmetry function is being calculated=1-3,61-63 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=23,24,39,40,55,56,83,84,99,100,115,116 R_0The r_0 parameter of the switching function=0.25 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=0.5 NN=2 MM=4 D_0=0} D_0 The d_0 parameter of the switching function=0.0 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=0
# COORDINATIONNUMBER LABEL=cn SPECIESA=1-3,61-63 SPECIESB=23,24,39,40,55,56,83,84,99,100,115,116 R_0=0.25 MORE_THAN={RATIONAL R_0=0.5 NN=2 MM=4 D_0=0}
cn_grpThe GROUP action with label cn_grp calculates the following quantities:| Quantity | Type | Description |
| cn_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=1-3,61-63
cn_matThe CONTACT_MATRIX action with label cn_mat calculates the following quantities:| Quantity | Type | Description |
| cn_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 GROUPAwhen you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPB=1-3,61-63 GROUPBwhen you are calculating the adjacency matrix between two sets of atoms this keyword is used to specify the atoms along with the keyword GROUPA=23,24,39,40,55,56,83,84,99,100,115,116 R_0The r_0 parameter of the switching function=0.25 D_0 The d_0 parameter of the switching function=0.0 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=0
cn_onesThe CONSTANT action with label cn_ones calculates the following quantities:| Quantity | Type | Description |
| cn_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=12
cnThe MATRIX_VECTOR_PRODUCT action with label cn calculates the following quantities:| Quantity | Type | Description |
| cn | 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=cn_mat,cn_ones
cn_caverageThe MEAN action with label cn_caverage calculates the following quantities:| Quantity | Type | Description |
| cn_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=cn PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cn_mtThe MORE_THAN action with label cn_mt calculates the following quantities:| Quantity | Type | Description |
| cn_mt | vector | the vector obtained by doing an element-wise application of a function that is one if the if the input is more than a threshold to the input vectors |
: MORE_THANUse a switching function to determine how many of the input variables are more than a certain cutoff. More details ARGthe values input to this function=cn SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={RATIONAL R_0=0.5 NN=2 MM=4 D_0=0}
cn_morethanThe SUM action with label cn_morethan calculates the following quantities:| Quantity | Type | Description |
| cn_morethan | scalar | the sum of all the elements in the input vector |
: SUMCalculate the sum of the arguments More details ARGthe values input to this function=cn_mt PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input ---
METADUsed to performed metadynamics on one or more collective variables. More details ...
ARGthe labels of the scalars on which the bias will act=cn.morethan SIGMAthe widths of the Gaussian hills=0.01 HEIGHTthe heights of the Gaussian hills=2.5 PACEthe frequency for hill addition=500
LABELa label for the action so that its output can be referenced in the input to other actions=metadThe METAD action with label metad calculates the following quantities:| Quantity | Type | Description |
| metad.bias | scalar | the instantaneous value of the bias potential |
TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=298 BIASFACTORuse well tempered metadynamics and use this bias factor=50 FILE a file in which the list of added hills is stored=hills
GRID_MINthe lower bounds for the grid=-0.5 GRID_MAXthe upper bounds for the grid=6 GRID_SPACINGthe approximate grid spacing (to be used as an alternative or together with GRID_BIN)=0.002 GRID_SPARSE use a sparse grid to store hills
... METAD
PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=100 ARGthe labels of the values that you would like to print to the file=cn.morethan,metad.bias FILEthe name of the file on which to output these quantities=colvar
ENDPLUMEDTerminate plumed input. More details
