Action: OPES_METAD
| Module | opes |
|---|---|
| Description | Usage |
| On-the-fly probability enhanced sampling with metadynamics-like target distribution. |   |
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 |
| rct | scalar | default | estimate of c(t) |
| zed | scalar | default | estimate of Z_n |
| neff | scalar | default | effective sample size |
| nker | scalar | default | total number of compressed kernels used to represent the bias |
| work | scalar | CALC_WORK | total accumulated work done by the bias |
| nlker | scalar | NLIST | number of kernels 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 |
| EXCLUDED_REGION | scalar | kernels are not deposited when the action provided here has a nonzero value, see example above |
| EXTRA_BIAS | scalar | consider also these other bias potentials for the internal reweighting |
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 |
| EXCLUDED_REGION | input | none | kernels are not deposited when the action provided here has a nonzero value, see example above |
| EXTRA_BIAS | input | none | consider also these other bias potentials for the internal reweighting |
| TEMP | compulsory | -1 | temperature |
| PACE | compulsory | none | the frequency for kernel deposition |
| SIGMA | compulsory | ADAPTIVE | the initial widths of the kernels |
| BARRIER | compulsory | none | the free energy barrier to be overcome |
| COMPRESSION_THRESHOLD | compulsory | 1 | merge kernels if closer than this threshold, in units of sigma |
| FILE | compulsory | KERNELS | a file in which the list of all deposited kernels is stored |
| NUMERICAL_DERIVATIVES | optional | false | calculate the derivatives for these quantities numerically |
| ADAPTIVE_SIGMA_STRIDE | optional | not used | number of steps for measuring adaptive sigma |
| SIGMA_MIN | optional | not used | never reduce SIGMA below this value |
| BIASFACTOR | optional | not used | the gamma bias factor used for the well-tempered target distribution |
| EPSILON | optional | not used | the value of the regularization constant for the probability |
| KERNEL_CUTOFF | optional | not used | truncate kernels at this distance, in units of sigma |
| NLIST_PARAMETERS | optional | not used | the two cutoff parameters for the kernels neighbor list |
| NLIST | optional | false | use neighbor list for kernels summation, faster but experimental |
| NLIST_PACE_RESET | optional | false | force the reset of the neighbor list at each PACE |
| FIXED_SIGMA | optional | false | do not decrease sigma as the simulation proceeds |
| RECURSIVE_MERGE_OFF | optional | false | do not recursively attempt kernel merging when a new one is added |
| NO_ZED | optional | false | do not normalize over the explored CV space, Z_n=1 |
| FMT | optional | not used | specify format for KERNELS file |
| STATE_RFILE | optional | not used | read from this file the compressed kernels and all the info needed to RESTART the simulation |
| STATE_WFILE | optional | not used | write to this file the compressed kernels and all the info needed to RESTART the simulation |
| STATE_WSTRIDE | optional | not used | number of MD steps between writing the STATE_WFILE |
| STORE_STATES | optional | false | append to STATE_WFILE instead of ovewriting it each time |
| CALC_WORK | optional | false | calculate the total accumulated work done by the bias since last restart |
| WALKERS_MPI | optional | false | switch on MPI version of multiple walkers |
| SERIAL | optional | false | perform calculations in serial |
| 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 |