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| This is part of the ves module | |
| It is only available if you configure PLUMED with ./configure –enable-modules=ves . Furthermore, this feature is still being developed so take care when using it and report any problems on the mailing list. |
Multithermal-multibaric target distribution (dynamic).
Use the target distribution to sample the multithermal-multibaric ensemble [106] [99]. In this way, in a single molecular dynamics simulation one can obtain information about the simulated system in a range of temperatures and pressures. This range is determined through the keywords MIN_TEMP, MAX_TEMP, MIN_PRESSURE, and MAX_PRESSURE. One should also specified the target pressure of the barostat with the keyword PRESSURE.
The collective variables (CVs) used to construct the bias potential must be:
Other choices of CVs or a different order of the above mentioned CVs are nonsensical. The third CV, the order parameter, must be used when the region of the phase diagram under study is crossed by a first order phase transition [107] .
The algorithm will explore the free energy at each temperature and pressure up to a predefined free energy threshold \(\epsilon\) specified through the keyword THRESHOLD (in kT units). If only the energy and the volume are being biased, i.e. no phase transition is considered, then THRESHOLD can be set to around 5. If also an order parameter is used then the THRESHOLD should be greater than the barrier for the transformation in kT. For small systems undergoing a freezing transition THRESHOLD is typically between 20 and 50.
It is also important to specify the number of intermediate temperatures and pressures to consider. This is done through the keywords STEPS_TEMP and STEPS_PRESSURE. If the number of intermediate temperature and pressures is too small, then holes might appear in the target distribution. If it is too large, the performance will deteriorate with no additional advantage.
We now describe the algorithm more rigorously. The target distribution is given by
\[ p(E,\mathcal{V},s)= \begin{cases} 1/\Omega_{E,\mathcal{V},s} & \text{if there is at least one } \beta',P' \text{ such} \\ & \text{that } \beta' F_{\beta',P'}(E,\mathcal{V},s)<\epsilon \text{ with} \\ & \beta_1>\beta'>\beta_2 \text{ and } P_1<P'<P_2 \\ 0 & \text{otherwise} \end{cases} \]
with \(F_{\beta',P'}(E,\mathcal{V},s)\) the free energy as a function of energy \(E\) and volume \(\mathcal{V}\) (and optionally the order parameter \(s\)) at temperature \(\beta'\) and pressure \(P'\), \(\Omega_{E,\mathcal{V},s}\) is a normalization constant, and \(\epsilon\) is the THRESHOLD. In practice the condition \(\beta' F_{\beta',P'}(E,\mathcal{V},s)<\epsilon\) is checked in equally spaced points in each dimension \(\beta'\) and \(P'\). The number of points is determined with the keywords STEPS_TEMP and STEPS_PRESSURE. In practice the target distribution is never set to zero but rather to a small value controlled by the keyword EPSILON. The small value is e^-EPSILON.
Much like in the Wang-Landau algorithm [140] or in the multicanonical ensemble [14] , a flat histogram is targeted. The idea behind this choice of target distribution is that all regions of potential energy and volume (and optionally order parameter) that are relevant at all temperatures \(\beta_1<\beta'<\beta_2\) and pressure \(P_1<P'<P_2\) are included in the distribution.
The free energy at temperature \(\beta'\) and pressure \(P'\) is calculated from the free energy at \(\beta\) and \(P\) using:
\[ \beta' F_{\beta',P'}(E,\mathcal{V},s) = \beta F_{\beta,P}(E,\mathcal{V},s) + (\beta' - \beta) E + (\beta' P' - \beta P ) \mathcal{V} + C \]
with \(C\) such that \(F_{\beta',P'}(E_m,\mathcal{V}_m,s_m)=0\) with \(E_{m},\mathcal{V}_m,s_m\) the position of the free energy minimum. \( \beta F_{\beta,P}(E,\mathcal{V},s) \) is not know from the start and is instead found during the simulation. Therefore \( p(E,\mathcal{V},s) \) is determined iteratively as done in the well tempered target distribution [138].
The output of these simulations can be reweighted in order to obtain information at all temperatures and pressures in the targeted region of Temperature-Pressure plane. The reweighting can be performed using the action REWEIGHT_TEMP_PRESS.
The multicanonical ensemble (fixed volume) can be targeted using TD_MULTICANONICAL.
The following input can be used to run a simulation in the multithermal-multibaric ensemble. The region of the temperature-pressure plane that will be explored is 260-350 K and 1 bar- 300 MPa. The energy and the volume are used as collective variables. Legendre polynomials are used to construct the two dimensional bias potential. The averaged stochastic gradient descent algorithm is chosen to optimize the VES functional. The target distribution is updated every 100 optimization steps (200 ps here) using the last estimation of the free energy.
# Use energy and volume as CVs energy: ENERGY vol: VOLUME # Basis functions bf1: BF_LEGENDRE ORDERcompulsory keyword The order of the basis function expansion. =10 MINIMUMcompulsory keyword The minimum of the interval on which the basis functions are defined. =-14750 MAXIMUMcompulsory keyword The maximum of the interval on which the basis functions are defined. =-12250 bf2: BF_LEGENDRE ORDERcompulsory keyword The order of the basis function expansion. =10 MINIMUMcompulsory keyword The minimum of the interval on which the basis functions are defined. =6.5 MAXIMUMcompulsory keyword The maximum of the interval on which the basis functions are defined. =8.25 # Target distribution - 1 bar = 0.06022140857 and 300 MPa = 180.66422571 td_multi: TD_MULTITHERMAL_MULTIBARIC ... MIN_TEMPcompulsory keyword Minimum energy. =260 MAX_TEMPcompulsory keyword Maximum energy. =350 MAX_PRESSUREcompulsory keyword Maximum pressure. =180.66422571 MIN_PRESSUREcompulsory keyword Minimum pressure. =0.06022140857 PRESSUREcompulsory keyword Target pressure of the barostat used in the MD engine. =0.06022140857 ... # Bias expansion b1: VES_LINEAR_EXPANSION ... ARGthe input for this action is the scalar output from one or more other actions. =energy,vol BASIS_FUNCTIONScompulsory keyword the label of the one dimensional basis functions that should be used. =bf1,bf2 TEMPthe system temperature - this is needed if the MD code does not pass the temperature to PLUMED. =300.0 GRID_BINSthe number of bins used for the grid. =200,200 TARGET_DISTRIBUTIONthe label of the target distribution to be used. =td_multi ... # Optimization algorithm o1: OPT_AVERAGED_SGD ... BIAScompulsory keyword the label of the VES bias to be optimized =b1 STRIDEcompulsory keyword the frequency of updating the coefficients given in the number of MD steps. =500 STEPSIZEcompulsory keyword the step size used for the optimization =1.0 FES_OUTPUThow often the FES(s) should be written out to file. =500 BIAS_OUTPUThow often the bias(es) should be written out to file. =500 TARGETDIST_OUTPUThow often the dynamic target distribution(s) should be written out to file. =500 COEFFS_OUTPUTcompulsory keyword ( default=100 ) how often the coefficients should be written to file. =100 TARGETDIST_STRIDEstride for updating a target distribution that is iteratively updated during the optimization. =100... OPT_AVERAGED_SGD
The multithermal-multibaric target distribution can also be used to explore regions of the phase diagram crossed by first order phase transitions. Consider a system of 250 atoms that crystallizes in the FCC crystal structure. The region of the temperature-pressure plane that will be explored is 350-450 K and 1bar-1GPa. We assume that inside this region we can find the liquid-FCC coexistence line that we would like to obtain. In this case in addition to the energy and volume, an order parameter must also be biased. The energy, volume, and an order parameter are used as collective variables to construct the bias potential. We choose as order parameter the FCCUBIC. Legendre polynomials are used to construct the three dimensional bias potential. The averaged stochastic gradient descent algorithm is chosen to optimize the VES functional. The target distribution is updated every 100 optimization steps (200 ps here) using the last estimation of the free energy.
# Use energy, volume and FCCUBIC as CVs energy: ENERGY vol: VOLUME fcc: FCCUBIC SPECIESthis keyword is used for colvars such as coordination number. =1-256 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. ={CUBIC D_0=0.4 D_MAX=0.5} MORE_THANcalculate the number of variables more than a certain target value. ={RATIONAL R_0=0.45 NN=12 MM=24} # Basis functions bf1: BF_LEGENDRE ORDERcompulsory keyword The order of the basis function expansion. =8 MINIMUMcompulsory keyword The minimum of the interval on which the basis functions are defined. =-26500 MAXIMUMcompulsory keyword The maximum of the interval on which the basis functions are defined. =-23500 bf2: BF_LEGENDRE ORDERcompulsory keyword The order of the basis function expansion. =8 MINIMUMcompulsory keyword The minimum of the interval on which the basis functions are defined. =8.0 MAXIMUMcompulsory keyword The maximum of the interval on which the basis functions are defined. =11.5 bf3: BF_LEGENDRE ORDERcompulsory keyword The order of the basis function expansion. =8 MINIMUMcompulsory keyword The minimum of the interval on which the basis functions are defined. =0.0 MAXIMUMcompulsory keyword The maximum of the interval on which the basis functions are defined. =256.0 # Target distribution td_multitp: TD_MULTITHERMAL_MULTIBARIC ... MIN_TEMPcompulsory keyword Minimum energy. =350.0 MAX_TEMPcompulsory keyword Maximum energy. =450.0 MIN_PRESSUREcompulsory keyword Minimum pressure. =0.06022140857 MAX_PRESSUREcompulsory keyword Maximum pressure. =602.2140857 PRESSUREcompulsory keyword Target pressure of the barostat used in the MD engine. =301.10704285 SIGMAThe standard deviation parameters of the Gaussian kernels used for smoothing the target distribution. =250.0,0.1,10.0 THRESHOLDcompulsory keyword ( default=5 ) Maximum exploration free energy in kT. =15 STEPS_TEMPcompulsory keyword ( default=20 ) Number of temperature steps. =20 STEPS_PRESSUREcompulsory keyword ( default=20 ) Number of pressure steps. =20 ... # Expansion b1: VES_LINEAR_EXPANSION ... ARGthe input for this action is the scalar output from one or more other actions. =energy,vol,fcc.morethan BASIS_FUNCTIONScompulsory keyword the label of the one dimensional basis functions that should be used. =bf1,bf2,bf3 TEMPthe system temperature - this is needed if the MD code does not pass the temperature to PLUMED. =400.0 GRID_BINSthe number of bins used for the grid. =40,40,40 TARGET_DISTRIBUTIONthe label of the target distribution to be used. =td_multitp ... # Optimization algorithm o1: OPT_AVERAGED_SGD ... BIAScompulsory keyword the label of the VES bias to be optimized =b1 STRIDEcompulsory keyword the frequency of updating the coefficients given in the number of MD steps. =500 STEPSIZEcompulsory keyword the step size used for the optimization =1.0 FES_OUTPUThow often the FES(s) should be written out to file. =500 BIAS_OUTPUThow often the bias(es) should be written out to file. =500 TARGETDIST_OUTPUThow often the dynamic target distribution(s) should be written out to file. =500 COEFFS_OUTPUTcompulsory keyword ( default=100 ) how often the coefficients should be written to file. =100 TARGETDIST_STRIDEstride for updating a target distribution that is iteratively updated during the optimization. =500... OPT_AVERAGED_SGD
| THRESHOLD | ( default=5 ) Maximum exploration free energy in kT. |
| EPSILON | ( default=10 ) The zeros of the target distribution are changed to e^-EPSILON. |
| MIN_TEMP | Minimum energy. |
| MAX_TEMP | Maximum energy. |
| MIN_PRESSURE | Minimum pressure. |
| MAX_PRESSURE | Maximum pressure. |
| PRESSURE | Target pressure of the barostat used in the MD engine. |
| STEPS_TEMP | ( default=20 ) Number of temperature steps. |
| STEPS_PRESSURE | ( default=20 ) Number of pressure steps. |
| SIGMA | The standard deviation parameters of the Gaussian kernels used for smoothing the target distribution. One value must be specified for each argument, i.e. one value per CV. A value of 0.0 means that no smoothing is performed, this is the default behavior. |
1.8.17