Project ID: plumID:21.044
Source: plumed.dat
Originally used with PLUMED version: 2.5.1
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
pThe FIXEDATOM action with label p calculates the following quantities:| Quantity | Type | Description |
| p | atoms | virtual atom calculated by FIXEDATOM action |
: FIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More details ATcoordinates of the virtual atom=2.,2.,2.
p: FIXEDATOMAdd a virtual atom in a fixed position. This action uses the defaults shown here. More details ATcoordinates of the virtual atom=2.,2.,2. SET_MASS mass of the virtual atom=1 SET_CHARGE charge of the virtual atom=0
gnaThe GROUP action with label gna calculates the following quantities:| Quantity | Type | Description |
| gna | 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=4501-4870
gclThe GROUP action with label gcl calculates the following quantities:| Quantity | Type | Description |
| gcl | 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=4871-5240
cn0The COORDINATIONNUMBER action with label cn0 calculates the following quantities:| Quantity | Type | Description |
| cn0 | 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 SPECIESAthe list of atoms for which the symmetry function is being calculated=gna SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=gcl 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=0.38 D_MAX=1.0}
# cn0: COORDINATIONNUMBER SPECIESA=gna SPECIESB=gcl SWITCH={RATIONAL R_0=0.38 D_MAX=1.0}
cn0_grpThe GROUP action with label cn0_grp calculates the following quantities:| Quantity | Type | Description |
| cn0_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=gna
cn0_matThe CONTACT_MATRIX action with label cn0_mat calculates the following quantities:| Quantity | Type | Description |
| cn0_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=gna 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=gcl 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.={RATIONAL R_0=0.38 D_MAX=1.0}
cn0_onesThe CONSTANT action with label cn0_ones calculates the following quantities:| Quantity | Type | Description |
| cn0_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=370
cn0The MATRIX_VECTOR_PRODUCT action with label cn0 calculates the following quantities:| Quantity | Type | Description |
| cn0 | 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=cn0_mat,cn0_ones
cn0_caverageThe MEAN action with label cn0_caverage calculates the following quantities:| Quantity | Type | Description |
| cn0_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=cn0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- cn1The COORDINATIONNUMBER action with label cn1 calculates the following quantities:| Quantity | Type | Description |
| cn1 | 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 SPECIESAthe list of atoms for which the symmetry function is being calculated=gcl SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=gna 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=0.38 D_MAX=1.0}
# cn1: COORDINATIONNUMBER SPECIESA=gcl SPECIESB=gna SWITCH={RATIONAL R_0=0.38 D_MAX=1.0}
cn1_grpThe GROUP action with label cn1_grp calculates the following quantities:| Quantity | Type | Description |
| cn1_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=gcl
cn1_matThe CONTACT_MATRIX action with label cn1_mat calculates the following quantities:| Quantity | Type | Description |
| cn1_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=gcl 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=gna 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.={RATIONAL R_0=0.38 D_MAX=1.0}
cn1_onesThe CONSTANT action with label cn1_ones calculates the following quantities:| Quantity | Type | Description |
| cn1_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=370
cn1The MATRIX_VECTOR_PRODUCT action with label cn1 calculates the following quantities:| Quantity | Type | Description |
| cn1 | 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=cn1_mat,cn1_ones
cn1_caverageThe MEAN action with label cn1_caverage calculates the following quantities:| Quantity | Type | Description |
| cn1_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=cn1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input ---
sphere0The INSPHERE action with label sphere0 calculates the following quantities:| Quantity | Type | Description |
| sphere0_morethan | scalar | the number of cvs in the region of interest that are more than a certain threshold |
: INSPHEREThis quantity can be used to calculate functions of the distribution of collective variables for the atoms that lie in a particular, user-specified part of of the cell. This action is a shortcut. More details ATOMthe atom whose vicinity we are interested in examining=p DATAthe label of an action that calculates multicolvars=cn0 RADIUSthe switching function that tells us the extent of the sphereical region of interest. Options for this keyword are explained in the documentation for LESS_THAN.={TANH R_0=1.5} MORE_THANcalcualte the number of colvars that are inside the region of interest and that are greater that a certain threshold={RATIONAL R_0=5.0}
# sphere0: INSPHERE ATOM=p DATA=cn0 RADIUS={TANH R_0=1.5} MORE_THAN={RATIONAL R_0=5.0}
sphere0_grpThe GROUP action with label sphere0_grp calculates the following quantities:| Quantity | Type | Description |
| sphere0_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=cn0
cn0_sphere0_mtThe MORE_THAN action with label cn0_sphere0_mt calculates the following quantities:| Quantity | Type | Description |
| cn0_sphere0_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=cn0 SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={RATIONAL R_0=5.0}
sphere0_mtThe CUSTOM action with label sphere0_mt calculates the following quantities:| Quantity | Type | Description |
| sphere0_mt | 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=cn0_sphere0_mt,sphere0 FUNCthe function you wish to evaluate=x*y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
sphere0_morethanThe SUM action with label sphere0_morethan calculates the following quantities:| Quantity | Type | Description |
| sphere0_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=sphere0_mt PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- sphere1The INSPHERE action with label sphere1 calculates the following quantities:| Quantity | Type | Description |
| sphere1_morethan | scalar | the number of cvs in the region of interest that are more than a certain threshold |
: INSPHEREThis quantity can be used to calculate functions of the distribution of collective variables for the atoms that lie in a particular, user-specified part of of the cell. This action is a shortcut. More details ATOMthe atom whose vicinity we are interested in examining=p DATAthe label of an action that calculates multicolvars=cn1 RADIUSthe switching function that tells us the extent of the sphereical region of interest. Options for this keyword are explained in the documentation for LESS_THAN.={TANH R_0=1.5} MORE_THANcalcualte the number of colvars that are inside the region of interest and that are greater that a certain threshold={RATIONAL R_0=5.0}
# sphere1: INSPHERE ATOM=p DATA=cn1 RADIUS={TANH R_0=1.5} MORE_THAN={RATIONAL R_0=5.0}
sphere1_grpThe GROUP action with label sphere1_grp calculates the following quantities:| Quantity | Type | Description |
| sphere1_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=cn1
cn1_sphere1_mtThe MORE_THAN action with label cn1_sphere1_mt calculates the following quantities:| Quantity | Type | Description |
| cn1_sphere1_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=cn1 SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={RATIONAL R_0=5.0}
sphere1_mtThe CUSTOM action with label sphere1_mt calculates the following quantities:| Quantity | Type | Description |
| sphere1_mt | 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=cn1_sphere1_mt,sphere1 FUNCthe function you wish to evaluate=x*y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
sphere1_morethanThe SUM action with label sphere1_morethan calculates the following quantities:| Quantity | Type | Description |
| sphere1_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=sphere1_mt PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input ---
COMBINECalculate a polynomial combination of a set of other variables. More details LABELa label for the action so that its output can be referenced in the input to other actions=ncrystThe COMBINE action with label ncryst calculates the following quantities:| Quantity | Type | Description |
| ncryst | scalar | a linear compbination |
ARGthe values input to this function=sphere0.morethan,sphere1.morethan POWERS the powers to which you are raising each of the arguments in your function=1,1 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
COMBINECalculate a polynomial combination of a set of other variables. More details LABELa label for the action so that its output can be referenced in the input to other actions=vcrystThe COMBINE action with label vcryst calculates the following quantities:| Quantity | Type | Description |
| vcryst | scalar | a linear compbination |
ARGthe values input to this function=ncryst POWERS the powers to which you are raising each of the arguments in your function=0.333 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
metadThe METAD action with label metad calculates the following quantities:| Quantity | Type | Description |
| metad.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=vcryst SIGMAthe widths of the Gaussian hills=0.01 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=298 PACEthe frequency for hill addition=1000 BIASFACTORuse well tempered metadynamics and use this bias factor=200.0 HEIGHTthe heights of the Gaussian hills=2.5 GRID_MINthe lower bounds for the grid=-1. GRID_MAXthe upper bounds for the grid=10.
metad: 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=vcryst SIGMAthe widths of the Gaussian hills=0.01 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=298 PACEthe frequency for hill addition=1000 BIASFACTORuse well tempered metadynamics and use this bias factor=200.0 HEIGHTthe heights of the Gaussian hills=2.5 GRID_MINthe lower bounds for the grid=-1. GRID_MAXthe upper bounds for the grid=10. 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=ncryst,vcryst,metad.bias STRIDE the frequency with which the quantities of interest should be output=10 FILEthe name of the file on which to output these quantities=COLVAR
