Project ID: plumID:24.000
Source: scripts/LAMMPS/plumed_LAMMPS/plumed.dat
Originally used with PLUMED version: 2.8.1
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
UNITSThis command sets the internal units for the code. More details LENGTHthe units of lengths=A
The UNITS action with label calculates somethingHThe GROUP action with label H calculates the following quantities:| Quantity | Type | Description |
| H | 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=1,2,3
NThe GROUP action with label N calculates the following quantities:| Quantity | Type | Description |
| N | 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=4,5,6
LiThe GROUP action with label Li calculates the following quantities:| Quantity | Type | Description |
| Li | 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=7,8,9
ghostaThe FIXEDATOM action with label ghosta calculates the following quantities:| Quantity | Type | Description |
| ghosta | 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=0,0,15
ghosta: FIXEDATOMAdd a virtual atom in a fixed position. This action uses the defaults shown here. More details ATcoordinates of the virtual atom=0,0,15 SET_MASS mass of the virtual atom=1 SET_CHARGE charge of the virtual atom=0
max_nnThe COORDINATIONNUMBER action with label max_nn calculates the following quantities:| Quantity | Type | Description |
| max_nn | vector | the coordination numbers of the specified atoms |
| max_nn_max | scalar | the maximum colvar |
: 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=N SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=N 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=1.6 D_MAX=5} MAXcalculate the maximum value={BETA=0.01}
# max_nn: COORDINATIONNUMBER SPECIESA=N SPECIESB=N SWITCH={RATIONAL R_0=1.6 D_MAX=5} MAX={BETA=0.01}
max_nn_grpThe GROUP action with label max_nn_grp calculates the following quantities:| Quantity | Type | Description |
| max_nn_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=N
max_nn_matThe CONTACT_MATRIX action with label max_nn_mat calculates the following quantities:| Quantity | Type | Description |
| max_nn_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=N 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=N 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=1.6 D_MAX=5}
max_nn_onesThe CONSTANT action with label max_nn_ones calculates the following quantities:| Quantity | Type | Description |
| max_nn_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=3
max_nnThe MATRIX_VECTOR_PRODUCT action with label max_nn calculates the following quantities:| Quantity | Type | Description |
| max_nn | 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=max_nn_mat,max_nn_ones
max_nn_caverageThe MEAN action with label max_nn_caverage calculates the following quantities:| Quantity | Type | Description |
| max_nn_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=max_nn PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
max_nn_me_maxThe CUSTOM action with label max_nn_me_max calculates the following quantities:| Quantity | Type | Description |
| max_nn_me_max | 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=max_nn FUNCthe function you wish to evaluate=exp(x/0.01) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
max_nn_mec_maxThe SUM action with label max_nn_mec_max calculates the following quantities:| Quantity | Type | Description |
| max_nn_mec_max | 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=max_nn_me_max PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
max_nn_maxThe CUSTOM action with label max_nn_max calculates the following quantities:| Quantity | Type | Description |
| max_nn_max | scalar | an arbitrary function |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=max_nn_mec_max FUNCthe function you wish to evaluate=0.01*log(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input ---
max_nn_focusThe COORDINATIONNUMBER action with label max_nn_focus calculates the following quantities:| Quantity | Type | Description |
| max_nn_focus | vector | the coordination numbers of the specified atoms |
| max_nn_focus_max | scalar | the maximum colvar |
: 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=4 SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=1 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=1.6 D_MAX=5} MAXcalculate the maximum value={BETA=0.01}
# max_nn_focus: COORDINATIONNUMBER SPECIESA=4 SPECIESB=1 SWITCH={RATIONAL R_0=1.6 D_MAX=5} MAX={BETA=0.01}
max_nn_focus_grpThe GROUP action with label max_nn_focus_grp calculates the following quantities:| Quantity | Type | Description |
| max_nn_focus_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=4
max_nn_focus_matThe CONTACT_MATRIX action with label max_nn_focus_mat calculates the following quantities:| Quantity | Type | Description |
| max_nn_focus_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=4 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 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=1.6 D_MAX=5}
max_nn_focus_onesThe CONSTANT action with label max_nn_focus_ones calculates the following quantities:| Quantity | Type | Description |
| max_nn_focus_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
max_nn_focusThe MATRIX_VECTOR_PRODUCT action with label max_nn_focus calculates the following quantities:| Quantity | Type | Description |
| max_nn_focus | 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=max_nn_focus_mat,max_nn_focus_ones
max_nn_focus_caverageThe MEAN action with label max_nn_focus_caverage calculates the following quantities:| Quantity | Type | Description |
| max_nn_focus_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=max_nn_focus PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
max_nn_focus_me_maxThe CUSTOM action with label max_nn_focus_me_max calculates the following quantities:| Quantity | Type | Description |
| max_nn_focus_me_max | 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=max_nn_focus FUNCthe function you wish to evaluate=exp(x/0.01) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
max_nn_focus_mec_maxThe SUM action with label max_nn_focus_mec_max calculates the following quantities:| Quantity | Type | Description |
| max_nn_focus_mec_max | 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=max_nn_focus_me_max PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
max_nn_focus_maxThe CUSTOM action with label max_nn_focus_max calculates the following quantities:| Quantity | Type | Description |
| max_nn_focus_max | scalar | an arbitrary function |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=max_nn_focus_mec_max FUNCthe function you wish to evaluate=0.01*log(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- d1The DISTANCE action with label d1 calculates the following quantities:| Quantity | Type | Description |
| d1 | scalar | the DISTANCE between this pair of atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,4
dis_GHThe ZDISTANCES action with label dis_GH calculates the following quantities:| Quantity | Type | Description |
| dis_GH_max | scalar | the maximum colvar |
: ZDISTANCESCalculate the z components of the vectors connecting one or many pairs of atoms. This action is a shortcut. More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=ghosta GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=H MAXcalculate the maximum value={BETA=0.5}
# dis_GH: ZDISTANCES GROUPA=ghosta GROUPB=H MAX={BETA=0.5}
dis_GHThe DISTANCE action with label dis_GH calculates the following quantities:| Quantity | Type | Description |
| dis_GH.x | vector | the x-component of the vector connecting the two atoms |
| dis_GH.y | vector | the y-component of the vector connecting the two atoms |
| dis_GH.z | vector | the z-component of the vector connecting the two atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details COMPONENTS calculate the x, y and z components of the distance separately and store them as label ATOMS1the pair of atom that we are calculating the distance between=ghosta,1 ATOMS2the pair of atom that we are calculating the distance between=ghosta,2 ATOMS3the pair of atom that we are calculating the distance between=ghosta,3
dis_GH_me_maxThe CUSTOM action with label dis_GH_me_max calculates the following quantities:| Quantity | Type | Description |
| dis_GH_me_max | 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=dis_GH.z FUNCthe function you wish to evaluate=exp(x/0.5) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
dis_GH_mec_maxThe SUM action with label dis_GH_mec_max calculates the following quantities:| Quantity | Type | Description |
| dis_GH_mec_max | 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=dis_GH_me_max PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
dis_GH_maxThe CUSTOM action with label dis_GH_max calculates the following quantities:| Quantity | Type | Description |
| dis_GH_max | scalar | an arbitrary function |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=dis_GH_mec_max FUNCthe function you wish to evaluate=0.5*log(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- uwall1The UPPER_WALLS action with label uwall1 calculates the following quantities:| Quantity | Type | Description |
| uwall1.bias | scalar | the instantaneous value of the bias potential |
| uwall1.force2 | scalar | the instantaneous value of the squared force due to this bias potential |
: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dis_GH.max ATthe positions of the wall=12.0 KAPPAthe force constant for the wall=2000.0 EXP the powers for the walls=2
dis_GNThe ZDISTANCES action with label dis_GN calculates the following quantities:| Quantity | Type | Description |
| dis_GN_max | scalar | the maximum colvar |
: ZDISTANCESCalculate the z components of the vectors connecting one or many pairs of atoms. This action is a shortcut. More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=ghosta GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=N MAXcalculate the maximum value={BETA=0.5}
# dis_GN: ZDISTANCES GROUPA=ghosta GROUPB=N MAX={BETA=0.5}
dis_GNThe DISTANCE action with label dis_GN calculates the following quantities:| Quantity | Type | Description |
| dis_GN.x | vector | the x-component of the vector connecting the two atoms |
| dis_GN.y | vector | the y-component of the vector connecting the two atoms |
| dis_GN.z | vector | the z-component of the vector connecting the two atoms |
: DISTANCECalculate the distance/s between pairs of atoms. More details COMPONENTS calculate the x, y and z components of the distance separately and store them as label ATOMS1the pair of atom that we are calculating the distance between=ghosta,4 ATOMS2the pair of atom that we are calculating the distance between=ghosta,5 ATOMS3the pair of atom that we are calculating the distance between=ghosta,6
dis_GN_me_maxThe CUSTOM action with label dis_GN_me_max calculates the following quantities:| Quantity | Type | Description |
| dis_GN_me_max | 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=dis_GN.z FUNCthe function you wish to evaluate=exp(x/0.5) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
dis_GN_mec_maxThe SUM action with label dis_GN_mec_max calculates the following quantities:| Quantity | Type | Description |
| dis_GN_mec_max | 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=dis_GN_me_max PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
dis_GN_maxThe CUSTOM action with label dis_GN_max calculates the following quantities:| Quantity | Type | Description |
| dis_GN_max | scalar | an arbitrary function |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=dis_GN_mec_max FUNCthe function you wish to evaluate=0.5*log(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- uwall2The UPPER_WALLS action with label uwall2 calculates the following quantities:| Quantity | Type | Description |
| uwall2.bias | scalar | the instantaneous value of the bias potential |
| uwall2.force2 | scalar | the instantaneous value of the squared force due to this bias potential |
: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dis_GN.max ATthe positions of the wall=12.0 KAPPAthe force constant for the wall=2000.0 EXP the powers for the walls=2
OPES_METADOn-the-fly probability enhanced sampling with metadynamics-like target distribution. This action has hidden defaults. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=opes2The OPES_METAD action with label opes2 calculates the following quantities:| Quantity | Type | Description |
| opes2.bias | scalar | the instantaneous value of the bias potential |
| opes2.rct | scalar | estimate of c(t). log(exp(beta V)/beta, should become flat as the simulation converges. Do NOT use for reweighting |
| opes2.zed | scalar | estimate of Z_n. should become flat once no new CV-space region is explored |
| opes2.neff | scalar | effective sample size |
| opes2.nker | scalar | total number of compressed kernels used to represent the bias |
ARGthe labels of the scalars on which the bias will act=max_nn.max
PACEthe frequency for kernel deposition=250
BARRIERthe free energy barrier to be overcome=200
TEMP temperature=750
FILE a file in which the list of all deposited kernels is stored=Kernels_Bb200.data.data
STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=State_Bb200.data
STATE_WSTRIDEnumber of MD steps between writing the STATE_WFILE=2000
SIGMA_MINnever reduce SIGMA below this value=0.001
STORE_STATES append to STATE_WFILE instead of ovewriting it each time
... OPES_METAD
OPES_METADOn-the-fly probability enhanced sampling with metadynamics-like target distribution. This action 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=opes2
ARGthe labels of the scalars on which the bias will act=max_nn.max
PACEthe frequency for kernel deposition=250
BARRIERthe free energy barrier to be overcome=200
TEMP temperature=750
FILE a file in which the list of all deposited kernels is stored=Kernels_Bb200.data.data
STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=State_Bb200.data
STATE_WSTRIDEnumber of MD steps between writing the STATE_WFILE=2000
SIGMA_MINnever reduce SIGMA below this value=0.001
STORE_STATES append to STATE_WFILE instead of ovewriting it each time
SIGMA the initial widths of the kernels=ADAPTIVE COMPRESSION_THRESHOLD merge kernels if closer than this threshold, in units of sigma=1
... OPES_METAD
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=* FILEthe name of the file on which to output these quantities=COLVAR STRIDE the frequency with which the quantities of interest should be output=400
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=400
