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{{DISPLAYTITLE:abf-admin}}
{{DISPLAYTITLE:abf-optgprhyprms}}
Navigation: [[Documentation]] / [[Methods]] / [[Adaptive Biasing Force Method]] / [[ABF:Utilities]] / [[abf-admin]]
Navigation: [[Documentation]] / [[Methods]] / [[Adaptive Biasing Force Method]] / [[ABF:Utilities]] / [[abf-optgprhyprms]]
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{{ABFUtils}}
{{ABFUtils}}
<div style="text-align: center">abf-admin: version 5.271.40980cf (2020-03-02 15:18)</div>'''Name'''
<div style="text-align: center">abf-optgprhyprms: version 5.271.40980cf (2020-03-02 15:18)</div>'''Name'''


<span style="margin-left: 15px;">abf-admin</span>
<span style="margin-left: 15px;">abf-optgprhyprms</span>


'''Synopsis'''
'''Synopsis'''


<span style="color: maroon; margin-left: 15px;">abf-admin</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">abf://server[:port]/command</span>
<span style="color: maroon; margin-left: 15px;">abf-optgprhyprms</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">accuname1 [accuname2 [..]] hyprmsname</span>


'''Description'''
'''Description'''


<p style="text-indent: 1em; text-align: justify;">The utility that controls the behaviour and state of the server implementing the multiple walkers extension of the ABF method.</p>
<p style="text-indent: 1em; text-align: justify;">abf-optgprhyprms finds optimal GPR hyperparameters, which maximize logarithm of marginal likelihood. The optimization is performed by the L-BFGS optimizer employing either analytical or numerical gradients of logML w.r.t. hyperparameters.</p>


'''Arguments'''
'''Arguments'''


{| style="margin-left: 2em; width: 95%;"
<div style="margin-left: 2em;"><span style="color: darkcyan;"><span style="font-style: bold;">accuname1</span></span>                 Name of file containing the ABF accumulator.<br /><span style="color: darkcyan;"><span style="font-style: bold;">hyprmsname</span></span>                 Name of file where the optimized GPR hyperparameters are saved. If the name is '-' then the output will be written to the standard output.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
| <span style="color: purple;">abf://server[:port]/command</span><br/><div style="margin-left: 30px;">It provides the action specification. The server is either the DNS name or IP address of the server or word 'serverkey' or 'key'. In the later case, the information about the server is read from the server key file. The port number, on which the server is listen, may be optionally provided. Finally, the command is administration task, which can be one of the following:<br />info          = print information about registered clients<br />flush          = save the accumulated ABF data on the server side<br />get?file=NAME  = get the accumulated ABF data and saves them locally to the NAME file (the default name is _abfserver.rst)<br />shutdown      = stop the server execution (use --force to skip protection by passphrase)<br />errors        = print errors from the server stack</div>
|}


'''Options'''
'''Options'''
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{| style="margin-left: 2em; width: 95%;"
{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-s, --serverkey FILE</span><br/><div style="margin-left: 30px;">Name of file containing the server key. The server key contains the server name, port, and password. This option is mutually exclusive with 'password' option.</div><span style="color:purple; margin-left: 30px;">(Default: server.key)</span>
|<span style="color: blue;">-t, --target NAME</span><br/><div style="margin-left: 30px;">Specify optimized targed, which can be either logml (log of marginal likelihood) or logpl (log of pseudo-likelihood from leave-one-out cross-validation (LOO-CV)).</div><span style="color:purple; margin-left: 30px;">(Default: logml)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">-a, --lmethod NAME</span><br/><div style="margin-left: 30px;">Linear algebra method for matrix inversion. Supported algorithms are: default, svd (SVD - singular value decomposition, divide and conquer driver), svd2 (SVD - singular value decomposition, simple driver), lu (LU factorization), and ll (LL - Cholesky factorization).</div><span style="color:purple; margin-left: 30px;">(Default: default)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-r, --rcond NUMBER</span><br/><div style="margin-left: 30px;">Rank condition for SVD. Used value must be carefully tested. Calculation at computer precision is requested with -1 (not recommended).</div><span style="color:purple; margin-left: 30px;">(Default: 1e-06)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">-s, --sigmaf2 NUMBER</span><br/><div style="margin-left: 30px;">Variance of the reconstructed free energy surface (signal variance).</div><span style="color:purple; margin-left: 30px;">(Default: 15)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-c, --ncorr SPEC</span><br/><div style="margin-left: 30px;">GPR: Number of statistically correlated samples in the form NCorr1[xNCorr2x...]. The last value pads the rest. Split ncorr mode is enabled by the --splitncorr option.</div><span style="color:purple; margin-left: 30px;">(Default: 1.0)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--splitncorr</span><br/><div style="margin-left: 30px;">Use indepenedent ncorr for each CV.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-w, --wfac SPEC</span><br/><div style="margin-left: 30px;">Factors influencing widths of RBFs or square exponential kernels. The width is distance between the adjacent square exponential functions multiplied by this factors in the form WFac1[xWFac2x...]. The last value pads the rest.</div><span style="color:purple; margin-left: 30px;">(Default: 3.0)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--enablesigmaf2</span><br/><div style="margin-left: 30px;">Enable optimization of SigmaF2 hyperparameter.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--enablencorr SPEC</span><br/><div style="margin-left: 30px;">Enable optimization of NCorr hyperparameter. Flags are specified in the form Ncorr1Enabled[xNcorr2Enabledx...] with F and T for disabled and enabled, respectively. The last value pads the rest.</div><span style="color:purple; margin-left: 30px;">(Default: F)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--enablewfac SPEC</span><br/><div style="margin-left: 30px;">Enable optimization of Wfac hyperparamters. Flags are specified in the form WFac1Enabled[xWFac2Enabledx...] with F and T for disabled and enabled, respectively. The last value pads the rest.</div><span style="color:purple; margin-left: 30px;">(Default: F)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--numeric</span><br/><div style="margin-left: 30px;">Use numeric gradients.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--noptsteps NUMBER</span><br/><div style="margin-left: 30px;">Maximum number of optimization steps.</div><span style="color:purple; margin-left: 30px;">(Default: 100)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--nresets NUMBER</span><br/><div style="margin-left: 30px;">Maximum number of resets due to insufficient optimization progress.</div><span style="color:purple; margin-left: 30px;">(Default: 3)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--termeps NUMBER</span><br/><div style="margin-left: 30px;">Termination criteria for L-BFGS optimizer (see L-BFGS code).</div><span style="color:purple; margin-left: 30px;">(Default: 1e-05)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--termval NUMBER</span><br/><div style="margin-left: 30px;">Termination criteria for L-BFGS optimizer. Minimum change of optimized property.</div><span style="color:purple; margin-left: 30px;">(Default: 1e-06)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--nlbfgscorr NUMBER</span><br/><div style="margin-left: 30px;">Number of corrections used in an L-BFGS update.</div><span style="color:purple; margin-left: 30px;">(Default: 10)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--test</span><br/><div style="margin-left: 30px;">Compare analytical and numerical gradient for input hyperparameters.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--cd5</span><br/><div style="margin-left: 30px;">Use 5-point stencil for numerical differentiation.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--loadhyprms NAME</span><br/><div style="margin-left: 30px;">Name of file with GPR hyperparameters.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--stat</span><br/><div style="margin-left: 30px;">Calculate detailed GPR status employing found hyperparameters.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--sptype</span><br/><div style="margin-left: 30px;">Determine type of stationary point.</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--numdiff</span><br/><div style="margin-left: 30px;">Use numerical differentiation of kernel function (for testing only).</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--kernel NAME</span><br/><div style="margin-left: 30px;">GPR: Kernel type. Supported types: ardse (ARD squared exponential), ardmc52 (ARD Matern class 5/2), default(=ardse)</div><span style="color:purple; margin-left: 30px;">(Default: default)</span>
|- style="vertical-align: top;"
|<span style="color: blue;">--useinv</span><br/><div style="margin-left: 30px;">Use matrix inversion pathway (for testing only).</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">--calclogpl</span><br/><div style="margin-left: 30px;">Calculate logPL for --stat if --target is not logpl.</div>
|- style="vertical-align: top;"
|- style="vertical-align: top;"
|<span style="color: blue;">-p, --password FILE</span><br/><div style="margin-left: 30px;">Name of file containing the server magic word. If the pasword is not provided via this option or via the server key then it is read interactively from the keyboard. This option is mutually exclusive with 'serverkey' option.</div>
|<span style="color: blue;">--globalmin SPEC</span><br/><div style="margin-left: 30px;">position of global minimum provided as a single string in the form CV1xCV2x...xCVn (relevant for error determination), if not set the position is determined automatically.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-f, --force</span><br/><div style="margin-left: 30px;">Skip protection of server shutdown by passphrase.</div>
|<span style="color: blue;">--inczpe</span><br/><div style="margin-left: 30px;">Include zero-point energy at position specified by --globalmin.</div>
|- style="vertical-align: top;"
|- style="vertical-align: top;"
|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">Increase output verbosity.</div>
|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">Increase output verbosity.</div>
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