Module: ves
| Description | Usage |
|---|---|
| implementations of methods based on Variationally Enhanced Sampling (VES) | |
| Authors: Omar Valsson, Michele Invernizzi, Pablo Piaggi and Benjamin Pampel |   |
Details
The VES code is a module for PLUMED that implements enhanced sampling methods based on Variationally Enhanced Sampling (VES) (see paper cited below). The VES code is developed by Omar Valsson, see the homepage of the VES code for further information.
The VES code is an optional module that needs to be enabled when configuring the
compilation of PLUMED by using the --enable-modules=ves
(or --enable-modules=all) flag when running the 'configure' script.
Actions
The following actions are part of this module
| Name | Description | Tags |
|---|---|---|
| BF_CHEBYSHEV | Chebyshev polynomial basis functions. | VES_BASISF |
| BF_COMBINED | Combining other basis functions types | VES_BASISF |
| BF_COSINE | Fourier cosine basis functions. | VES_BASISF |
| BF_CUBIC_B_SPLINES | Cubic B spline basis functions. | VES_BASISF |
| BF_CUSTOM | Basis functions given by arbitrary mathematical expressions. | VES_BASISF |
| BF_FOURIER | Fourier basis functions. | VES_BASISF |
| BF_GAUSSIANS | Gaussian basis functions. | VES_BASISF |
| BF_LEGENDRE | Legendre polynomials basis functions. | VES_BASISF |
| BF_POWERS | Polynomial power basis functions. | VES_BASISF |
| BF_SINE | Fourier sine basis functions. | VES_BASISF |
| BF_WAVELETS | Daubechies Wavelets basis functions. | VES_BASISF |
| OPT_ADAM | Adaptive moment estimation (ADAM) optimizer. | VES_OPTIMIZER |
| OPT_AVERAGED_SGD | Averaged stochastic gradient decent with fixed step size. | VES_OPTIMIZER |
| OPT_DUMMY | Dummy optimizer for debugging. | VES_OPTIMIZER |
| OPT_ROBBINS_MONRO_SGD | Robbins-Monro stochastic gradient decent. | VES_OPTIMIZER |
| TD_CHI | Chi distribution (static). | VES_TARGETDIST |
| TD_CHISQUARED | Chi-squared distribution (static). | VES_TARGETDIST |
| TD_CUSTOM | Target distribution given by an arbitrary mathematical expression (static or dynamic). | VES_TARGETDIST |
| TD_EXPONENTIAL | Exponential distribution (static). | VES_TARGETDIST |
| TD_EXPONENTIALLY_MODIFIED_GAUSSIAN | Target distribution given by a sum of exponentially modified Gaussian distributions (static). | VES_TARGETDIST |
| TD_GAUSSIAN | Target distribution given by a sum of Gaussian kernels (static). | VES_TARGETDIST |
| TD_GENERALIZED_EXTREME_VALUE | Generalized extreme value distribution (static). | VES_TARGETDIST |
| TD_GENERALIZED_NORMAL | Target distribution given by a sum of generalized normal distributions (static). | VES_TARGETDIST |
| TD_GRID | Target distribution from an external grid file (static). | VES_TARGETDIST |
| TD_LINEAR_COMBINATION | Target distribution given by linear combination of distributions (static or dynamic). | VES_TARGETDIST |
| TD_MULTICANONICAL | Multicanonical target distribution (dynamic). | VES_TARGETDIST |
| TD_MULTITHERMAL_MULTIBARIC | Multithermal-multibaric target distribution (dynamic). | VES_TARGETDIST |
| TD_PRODUCT_COMBINATION | Target distribution given by product combination of distributions (static or dynamic). | VES_TARGETDIST |
| TD_PRODUCT_DISTRIBUTION | Target distribution given by a separable product of one-dimensional distributions (static or dynamic). | VES_TARGETDIST |
| TD_UNIFORM | Uniform target distribution (static). | VES_TARGETDIST |
| TD_VONMISES | Target distribution given by a sum of Von Mises distributions (static). | VES_TARGETDIST |
| TD_WELLTEMPERED | Well-tempered target distribution (dynamic). | VES_TARGETDIST |
| VES_DELTA_F | Implementation of VES Delta F method | VES_BIAS |
| VES_LINEAR_EXPANSION | Linear basis set expansion bias. | VES_BIAS |
| VES_OUTPUT_BASISFUNCTIONS | Output basis functions to file. | VES_UTILS |
| VES_OUTPUT_FES | Tool to output biases and free energy surfaces for VES biases from previously obtained coefficients. | VES_UTILS |
| VES_OUTPUT_TARGET_DISTRIBUTION | Output target distribution to file. | VES_UTILS |
Command line tools
The following command line tools are part of this module
| Name | Description |
|---|---|
| ves_md_linearexpansion | MD of a one particle on a linear expansion PES |
References
More information about this module is available in the following articles: