Action: METAD
| Module | bias |
|---|---|
| Description | Usage |
| Used to performed metadynamics on one or more collective variables. |   |
Output components
This action can calculate the values in the following table when the associated keyword is included in the input for the action. These values can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the value required from the list below.
| Name | Type | Keyword | Description |
|---|---|---|---|
| bias | scalar | default | the instantaneous value of the bias potential |
| rbias | scalar | CALC_RCT | the instantaneous value of the bias normalized using the c(t) reweighting factor [rbias=bias-rct] |
| rct | scalar | CALC_RCT | the reweighting factor c(t) |
| work | scalar | CALC_WORK | accumulator for work |
| acc | scalar | ACCELERATION | the metadynamics acceleration factor |
| maxbias | scalar | CALC_MAX_BIAS | the maximum of the metadynamics V(s, t) |
| transbias | scalar | CALC_TRANSITION_BIAS | the metadynamics transition bias V*(t) |
| pace | scalar | FREQUENCY_ADAPTIVE | the hill addition frequency when employing frequency adaptive metadynamics |
| nlker | scalar | NLIST | number of hills in the neighbor list |
| nlsteps | scalar | NLIST | number of steps from last neighbor list update |
Input
The arguments that serve as the input for this action are specified using one or more of the keywords in the following table.
| Keyword | Type | Description |
|---|---|---|
| ARG | scalar | the labels of the scalars on which the bias will act |
Further details and examples
Text from manual goes here
Syntax
The following table describes the keywords and options that can be used with this action
| Keyword | Type | Default | Description |
|---|---|---|---|
| ARG | input | none | the labels of the scalars on which the bias will act |
| SIGMA | compulsory | none | the widths of the Gaussian hills |
| PACE | compulsory | none | the frequency for hill addition |
| FILE | compulsory | HILLS | a file in which the list of added hills is stored |
| NUMERICAL_DERIVATIVES | optional | false | calculate the derivatives for these quantities numerically |
| HEIGHT | optional | not used | the heights of the Gaussian hills |
| FMT | optional | not used | specify format for HILLS files (useful for decrease the number of digits in regtests) |
| BIASFACTOR | optional | not used | use well tempered metadynamics and use this bias factor |
| CALC_WORK | optional | false | calculate the total accumulated work done by the bias since last restart |
| RECT | optional | not used | list of bias factors for all the replicas |
| DAMPFACTOR | optional | not used | damp hills with exp(-max(V)/(kT*DAMPFACTOR) |
| TTBIASFACTOR | optional | not used | use transition tempered metadynamics with this bias factor |
| TTBIASTHRESHOLD | optional | not used | use transition tempered metadynamics with this bias threshold |
| TTALPHA | optional | not used | use transition tempered metadynamics with this hill size decay exponent parameter |
| TARGET | optional | not used | target to a predefined distribution |
| TEMP | optional | not used | the system temperature - this is only needed if you are doing well-tempered metadynamics |
| TAU | optional | not used | in well tempered metadynamics, sets height to (k_B Delta Tpacetimestep)/tau |
| CALC_RCT | optional | false | calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct] |
| RCT_USTRIDE | optional | not used | the update stride for calculating the c(t) reweighting factor |
| GRID_MIN | optional | not used | the lower bounds for the grid |
| GRID_MAX | optional | not used | the upper bounds for the grid |
| GRID_BIN | optional | not used | the number of bins for the grid |
| GRID_SPACING | optional | not used | the approximate grid spacing (to be used as an alternative or together with GRID_BIN) |
| GRID_SPARSE | optional | false | use a sparse grid to store hills |
| GRID_NOSPLINE | optional | false | don't use spline interpolation with grids |
| GRID_WSTRIDE | optional | not used | write the grid to a file every N steps |
| GRID_WFILE | optional | not used | the file on which to write the grid |
| GRID_RFILE | optional | not used | a grid file from which the bias should be read at the initial step of the simulation |
| STORE_GRIDS | optional | false | store all the grid files the calculation generates |
| NLIST | optional | false | Use neighbor list for kernels summation, faster but experimental |
| NLIST_PARAMETERS | optional | not used | the two cutoff parameters for the Gaussians neighbor list |
| ADAPTIVE | optional | not used | use a geometric (=GEOM) or diffusion (=DIFF) based hills width scheme |
| SIGMA_MAX | optional | not used | the upper bounds for the sigmas (in CV units) when using adaptive hills |
| SIGMA_MIN | optional | not used | the lower bounds for the sigmas (in CV units) when using adaptive hills |
| WALKERS_ID | optional | not used | walker id |
| WALKERS_N | optional | not used | number of walkers |
| WALKERS_DIR | optional | not used | shared directory with the hills files from all the walkers |
| WALKERS_RSTRIDE | optional | not used | stride for reading hills files |
| WALKERS_MPI | optional | false | Switch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIR |
| INTERVAL | optional | not used | one dimensional lower and upper limits, outside the limits the system will not feel the biasing force |
| FLYING_GAUSSIAN | optional | false | Switch on flying Gaussian method, must be used with WALKERS_MPI |
| ACCELERATION | optional | false | Set to TRUE if you want to compute the metadynamics acceleration factor |
| ACCELERATION_RFILE | optional | not used | a data file from which the acceleration should be read at the initial step of the simulation |
| CALC_MAX_BIAS | optional | false | Set to TRUE if you want to compute the maximum of the metadynamics V(s, t) |
| CALC_TRANSITION_BIAS | optional | false | Set to TRUE if you want to compute a metadynamics transition bias V*(t) |
| TRANSITIONWELL | optional | not used | This keyword appears multiple times as TRANSITIONWELL followed by an integer |
| FREQUENCY_ADAPTIVE | optional | false | Set to TRUE if you want to enable frequency adaptive metadynamics such that the frequency for hill addition to change dynamically based on the acceleration factor |
| FA_UPDATE_FREQUENCY | optional | not used | the frequency for updating the hill addition pace in frequency adaptive metadynamics, by default this is equal to the value given in PACE |
| FA_MAX_PACE | optional | not used | the maximum hill addition frequency allowed in frequency adaptive metadynamics |
| FA_MIN_ACCELERATION | optional | not used | only update the hill addition pace in frequency adaptive metadynamics after reaching the minimum acceleration factor given here |
| RESTART | optional | not used | allows per-action setting of restart (YES/NO/AUTO) |
| UPDATE_FROM | optional | not used | Only update this action from this time |
| UPDATE_UNTIL | optional | not used | Only update this action until this time |