Project ID: plumID:21.013
Source: ch4-base/symm-param/plumed.inp
Originally used with PLUMED version: 2.6
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 LENGTHthe units of lengths=A TIMEthe units of time=fs ENERGYthe units of energy=kcal/mol
The UNITS action with label calculates somethingCOORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=1 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=2 D_0 The d_0 parameter of the switching function=0.85 R_0The r_0 parameter of the switching function=0.25 NN The n parameter of the switching function =1 LABELa label for the action so that its output can be referenced in the input to other actions=vib1The COORDINATION action with label vib1 calculates the following quantities:| Quantity | Type | Description |
| vib1 | scalar | the value of the coordination |
COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=1 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=2 D_0 The d_0 parameter of the switching function=0.85 R_0The r_0 parameter of the switching function=0.25 NN The n parameter of the switching function =1 LABELa label for the action so that its output can be referenced in the input to other actions=vib1 MM The m parameter of the switching function; 0 implies 2*NN=0
COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=1 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=3 D_0 The d_0 parameter of the switching function=0.85 R_0The r_0 parameter of the switching function=0.25 NN The n parameter of the switching function =1 LABELa label for the action so that its output can be referenced in the input to other actions=vib2The COORDINATION action with label vib2 calculates the following quantities:| Quantity | Type | Description |
| vib2 | scalar | the value of the coordination |
COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=1 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=3 D_0 The d_0 parameter of the switching function=0.85 R_0The r_0 parameter of the switching function=0.25 NN The n parameter of the switching function =1 LABELa label for the action so that its output can be referenced in the input to other actions=vib2 MM The m parameter of the switching function; 0 implies 2*NN=0
COORDINATIONNUMBERCalculate 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 SPECIESAthe list of atoms for which the symmetry function is being calculated=2-5 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=1 D_0 The d_0 parameter of the switching function=0.85 R_0The r_0 parameter of the switching function=0.25 NN The n parameter of the switching function =1 MEAN calculate the mean of all the quantities MOMENTSthe list of moments that you would like to calculate=2 LABELa label for the action so that its output can be referenced in the input to other actions=nmThe COORDINATIONNUMBER action with label nm calculates the following quantities:| Quantity | Type | Description |
| nm | vector | the coordination numbers of the specified atoms |
| nm_mean | scalar | the mean of the colvars |
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 SPECIESAthe list of atoms for which the symmetry function is being calculated=2-5 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=1 D_0 The d_0 parameter of the switching function=0.85 R_0The r_0 parameter of the switching function=0.25 NN The n parameter of the switching function =1 MEAN calculate the mean of all the quantities MOMENTSthe list of moments that you would like to calculate=2 LABELa label for the action so that its output can be referenced in the input to other actions=nm MM The m parameter of the switching function; 0 implies 2*NN=0
# COORDINATIONNUMBER SPECIESA=2-5 SPECIESB=1 D_0=0.85 R_0=0.25 NN=1 MEAN MOMENTS=2 LABEL=nm
nm_grpThe GROUP action with label nm_grp calculates the following quantities:| Quantity | Type | Description |
| nm_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=2-5
nm_matThe CONTACT_MATRIX action with label nm_mat calculates the following quantities:| Quantity | Type | Description |
| nm_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=2-5 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=1 R_0The r_0 parameter of the switching function=0.25 D_0 The d_0 parameter of the switching function=0.85 NN The n parameter of the switching function =1 MM The m parameter of the switching function; 0 implies 2*NN=0
nm_onesThe CONSTANT action with label nm_ones calculates the following quantities:| Quantity | Type | Description |
| nm_ones | scalar | 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=1
nmThe MATRIX_VECTOR_PRODUCT action with label nm calculates the following quantities:| Quantity | Type | Description |
| nm | 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=nm_mat,nm_ones
nm_caverageThe MEAN action with label nm_caverage calculates the following quantities:| Quantity | Type | Description |
| nm_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=nm PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
nm_diffpow-2The CUSTOM action with label nm_diffpow-2 calculates the following quantities:| Quantity | Type | Description |
| nm_diffpow-2 | vector | the vector obtained by doing an element-wise application of an arbitrary function to the input vectors |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=nm,nm_caverage PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO FUNCthe function you wish to evaluate=(x-y)^2
nm_moment-2The MEAN action with label nm_moment-2 calculates the following quantities:| Quantity | Type | Description |
| nm_moment-2 | 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=nm_diffpow-2 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
nm_meanThe MEAN action with label nm_mean calculates the following quantities:| Quantity | Type | Description |
| nm_mean | 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=nm PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input ---
bf1: BF_CHEBYSHEVChebyshev polynomial basis functions. More details MINIMUMThe minimum of the interval on which the basis functions are defined=0.0 MAXIMUMThe maximum of the interval on which the basis functions are defined=1.0 ORDERThe order of the basis function expansion=96
The BF_CHEBYSHEV action with label bf1 calculates somethingtd: TD_GRIDTarget distribution from an external grid file (static). More details FILEThe name of the external grid file to be used as a target distribution=histo
The TD_GRID action with label td calculates somethingVES_LINEAR_EXPANSIONLinear basis set expansion bias. This action has hidden defaults. More details ...
ARGthe labels of the scalars on which the bias will act=nm.mean
BASIS_FUNCTIONSthe label of the one dimensional basis functions that should be used=bf1
TEMPthe system temperature - this is needed if the MD code does not pass the temperature to PLUMED=500
GRID_BINSthe number of bins used for the grid=2000
TARGET_DISTRIBUTIONthe label of the target distribution to be used=td
LABELa label for the action so that its output can be referenced in the input to other actions=externalThe VES_LINEAR_EXPANSION action with label external calculates the following quantities:| Quantity | Type | Description |
| external.bias | scalar | the instantaneous value of the bias potential |
| external.force2 | scalar | the instantaneous value of the squared force due to this bias potential. |
... VES_LINEAR_EXPANSION
VES_LINEAR_EXPANSIONLinear basis set expansion bias. This action uses the defaults shown here. More details ...
ARGthe labels of the scalars on which the bias will act=nm.mean
BASIS_FUNCTIONSthe label of the one dimensional basis functions that should be used=bf1
TEMPthe system temperature - this is needed if the MD code does not pass the temperature to PLUMED=500
GRID_BINSthe number of bins used for the grid=2000
TARGET_DISTRIBUTIONthe label of the target distribution to be used=td
LABELa label for the action so that its output can be referenced in the input to other actions=external
GRID_FMT the format to use when outputting the numbers in the grids=%14.9f
... VES_LINEAR_EXPANSION
OPT_AVERAGED_SGDAveraged stochastic gradient decent with fixed step size. This action has hidden defaults. More details ...
BIASthe label of the VES bias to be optimized=external
STRIDEthe frequency of updating the coefficients given in the number of MD steps=5000
LABELa label for the action so that its output can be referenced in the input to other actions=o1
STEPSIZEthe step size used for the optimization=0.5
FES_OUTPUThow often the FES(s) should be written out to file=10000
BIAS_OUTPUThow often the bias(es) should be written out to file=100
FES_PROJ_OUTPUThow often the projections of the FES(s) should be written out to file=20
COEFFS_OUTPUT how often the coefficients should be written to file=1
... OPT_AVERAGED_SGD
The OPT_AVERAGED_SGD action with label o1 calculates the following quantities:| Quantity | Description |
| o1.value | a scalar |
OPT_AVERAGED_SGDAveraged stochastic gradient decent with fixed step size. This action uses the defaults shown here. More details ...
BIASthe label of the VES bias to be optimized=external
STRIDEthe frequency of updating the coefficients given in the number of MD steps=5000
LABELa label for the action so that its output can be referenced in the input to other actions=o1
STEPSIZEthe step size used for the optimization=0.5
FES_OUTPUThow often the FES(s) should be written out to file=10000
BIAS_OUTPUThow often the bias(es) should be written out to file=100
FES_PROJ_OUTPUThow often the projections of the FES(s) should be written out to file=20
COEFFS_OUTPUT how often the coefficients should be written to file=1
COEFFS_FILE the name of output file for the coefficients=coeffs.data
... OPT_AVERAGED_SGD
FLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More details STRIDEthe frequency with which all the open files should be flushed=100000
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=vib1,vib2,nm.moment-2,nm.mean,external.bias STRIDE the frequency with which the quantities of interest should be output=10000 FILEthe name of the file on which to output these quantities=colvar
