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+{{DISPLAYTITLE:abf-integrate}}
 Navigation: [[Documentation]] / [[Methods]] / [[Adaptive Biasing Force Method]] / [[ABF:Utilities]] / [[abf-integrate]]
 ----
 {{ABFUtils}}
-'''Name'''
+<div style="text-align: center">abf-integrate: version 5.271.40980cf (2020-03-02 15:18)</div>'''Name'''
-abf-integrate
+<span style="margin-left: 15px;">abf-integrate</span>
 '''Synopsis'''
-<span style="color: maroon;">abf-integrate</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">accuname</span> <span style="color: purple;">fename</span>
+<span style="color: maroon; margin-left: 15px;">abf-integrate</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">accuname fename [fullfename]</span>
 '''Description'''
-It numericaly integrates data from the ABF calculation. The integration is performed by reverse finite difference method with order either 3 or 4.
+<p style="text-indent: 1em; text-align: justify;">The program numericaly integrates data from the ABF calculation. The integration is performed either by reverse finite difference (RFD or RFD2) method, employing radial basis functions (RBF), or gaussian process (GPR).</p>
 '''Arguments'''
-{| style="margin-left: 2em; width: 75%;"
+<div style="margin-left: 2em;"><span style="color: darkcyan;"><span style="font-style: bold;">accuname</span></span>                   Name of file containing the ABF accumulator. If the name is '-' then the accumulator is read from the standard input.<br /><span style="color: darkcyan;"><span style="font-style: bold;">fename</span></span>                     Name of file where the resulting free energy surface will be printed. If the name is '-' then the output will be written to the standard output.<br /><span style="color: darkcyan;"><span style="font-style: bold;">fullfename</span></span>                 Optional name of file with free energy surface containing all rigions (sampled and unsampled).</div>
-|- style="vertical-align: top; background-color: #e6e6e6;"
-| <span style="color: purple;">accuname</span><br/>
-<span style="margin-left: 30px;">Name of file containing the ABF accumulator. If the name is '-' then the accumulator is read from the standard input.</span>
-|- style="vertical-align: top;"
-| <span style="color: purple;">fename</span><br/>
-<span style="margin-left: 30px;">Name of file where the resulting free energy surface will be printed. If the name is '-' then the output will be written to the standard output.</span>
-|}
 '''Options'''
@@ Line 29: / Line 23: @@
 {| style="margin-left: 2em; width: 95%;"
 |- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">-l, --limit NUMBER</span><br/><span style="margin-left: 30px;">Only bins containing more samples than NUMBER are considered as properly sampled.</span><br/><span style="color:purple; margin-left: 30px;">(Default: 100)</span>
+|<span style="color: blue;">-m, --method NAME</span><br/><div style="margin-left: 30px;">Integration method. Supported methods are: rfd (reverse finite differences via csparse), rfd2 (reverse finite differences via lapack), rbf (radial basis functions), and gpr (gaussian process).</div><span style="color:purple; margin-left: 30px;">(Default: rfd)</span>
+|- style="vertical-align: top;"
+|<span style="color: blue;">--emethod NAME</span><br/><div style="margin-left: 30px;">Integration method for energy cut-off. Supported methods are: rfd (reverse finite differences via csparse), rfd2 (reverse finite differences via lapack), rbf (radial basis functions), and gpr (gaussian process).</div><span style="color:purple; margin-left: 30px;">(Default: rfd)</span>
+|- style="vertical-align: top; background-color: #e6e6e6;"
+|<span style="color: blue;">-a, --lmethod NAME</span><br/><div style="margin-left: 30px;">Linear algebra method for LLS solution or matrix inversion. Supported algorithms are: default, svd (SVD - singular value decomposition, divide and conquer driver), svd2 (SVD - singular value decomposition, simple driver), qr (QR factorization), lu (LU factorization), ll (LL - Cholesky factorization). Possible combinations are: RFD(LU,default), RFD2(QR,SVD,default), RBF(QR,SVD,default), and GPR(LU,SVD,SVD2,LL,default).</div><span style="color:purple; margin-left: 30px;">(Default: default)</span>
+|- style="vertical-align: top;"
+|<span style="color: blue;">-r, --rcond NUMBER</span><br/><div style="margin-left: 30px;">RFD2+RBF+GPR: 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; background-color: #e6e6e6;"
+|<span style="color: blue;">-l, --limit NUMBER</span><br/><div style="margin-left: 30px;">Only bins containing more samples than NUMBER are considered as properly sampled.</div><span style="color:purple; margin-left: 30px;">(Default: 100)</span>
+|- style="vertical-align: top;"
+|<span style="color: blue;">--skipfftest</span><br/><div style="margin-left: 30px;">Skip flood fill test for discountinous regions.</div>
+|- style="vertical-align: top; background-color: #e6e6e6;"
+|<span style="color: blue;">-q, --energylimit NUMBER</span><br/><div style="margin-left: 30px;">Integrate data only if the free energy is below NUMBER. This limit enforces two integration runs. Negative value disables the limit.</div><span style="color:purple; margin-left: 30px;">(Default: -1)</span>
+|- style="vertical-align: top;"
+|<span style="color: blue;">--rmnegene</span><br/><div style="margin-left: 30px;">Remove regions with negative free energy.</div>
+|- style="vertical-align: top; background-color: #e6e6e6;"
+|<span style="color: blue;">--skiplastelimit</span><br/><div style="margin-left: 30px;">Skip energy limit filter after final integration.</div>
+|- style="vertical-align: top;"
+|<span style="color: blue;">--mfmaxzscore NUMBER</span><br/><div style="margin-left: 30px;">RBF+GPR: Reject mean forces whose errors in prediction have z-score above NUMBER. In the test, it is assumend that mean force errors have zero mean and they follow normal distribution. This limit is aplied in the each pass. Negative value disables the limit.</div><span style="color:purple; margin-left: 30px;">(Default: -1)</span>
+|- style="vertical-align: top; background-color: #e6e6e6;"
+|<span style="color: blue;">--mfnumofztests NUMBER</span><br/><div style="margin-left: 30px;">RBF+GPR: Repeat z-score test for mean force errrors NUMBER times.</div><span style="color:purple; margin-left: 30px;">(Default: 1)</span>
+|- style="vertical-align: top;"
+|<span style="color: blue;">-s, --sigmaf2 NUMBER</span><br/><div style="margin-left: 30px;">GPR: 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;">RBF+GPR: 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;">--loadhyprms NAME</span><br/><div style="margin-left: 30px;">GPR: Name of file with GPR hyperparameters.</div>
+|- style="vertical-align: top; background-color: #e6e6e6;"
+|<span style="color: blue;">-t, --rfac SPEC</span><br/><div style="margin-left: 30px;">RBF: Reduction factor for number of RBFs. Number of RBFs in given direction is number of bins in that direction divided by this factor in the form RFac1[xRFac2x...]. The last value pads the rest.</div><span style="color:purple; margin-left: 30px;">(Default: 1.0)</span>
+|- style="vertical-align: top;"
+|<span style="color: blue;">-g, --overhang NUMBER</span><br/><div style="margin-left: 30px;">RBFs overhang to properly integrate areas near sampled edges. Ignored for periodic CVs.</div><span style="color:purple; margin-left: 30px;">(Default: 2)</span>
+|- style="vertical-align: top; background-color: #e6e6e6;"
+|<span style="color: blue;">--includeglued</span><br/><div style="margin-left: 30px;">RBF+GPR: Explicitly include glued regions. This options is set ON when --glueing > 0.</div>
+|- style="vertical-align: top;"
+|<span style="color: blue;">--glueing NUMBER</span><br/><div style="margin-left: 30px;">RBF+GPR: Calculate energy also for unsampled bins in close vicinity to sampled ones.</div><span style="color:purple; margin-left: 30px;">(Default: 0)</span>
+|- style="vertical-align: top; background-color: #e6e6e6;"
+|<span style="color: blue;">--glueholes</span><br/><div style="margin-left: 30px;">RBF+GPR: Calculate energy also for unsampled regions inside the FES.</div>
+|- style="vertical-align: top;"
+|<span style="color: blue;">-p, --periodic</span><br/><div style="margin-left: 30px;">RFD: Switch on periodicity for collective variables that are periodic.</div>
+|- style="vertical-align: top; background-color: #e6e6e6;"
+|<span style="color: blue;">--globalmin SPEC</span><br/><div style="margin-left: 30px;">RBF+GPR: 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;"
+|<span style="color: blue;">--userealglbmin</span><br/><div style="margin-left: 30px;">RBF+GPR: ignore --globalmin in the final integration step</div>
+|- style="vertical-align: top; background-color: #e6e6e6;"
+|<span style="color: blue;">-o, --offset NUMBER</span><br/><div style="margin-left: 30px;">Specify an integration constant.</div><span style="color:purple; margin-left: 30px;">(Default: 0)</span>
+|- style="vertical-align: top;"
+|<span style="color: blue;">-e, --witherror</span><br/><div style="margin-left: 30px;">GPR: Estimate free energy errors.</div>
+|- style="vertical-align: top; background-color: #e6e6e6;"
+|<span style="color: blue;">--noenergy</span><br/><div style="margin-left: 30px;">GPR: Skip calculation of energy and errors (it can save some time when only logML is required).</div>
+|- style="vertical-align: top;"
+|<span style="color: blue;">--saveabf NAME</span><br/><div style="margin-left: 30px;">Save the final ABF accumulator into the file with NAME.</div>
+|- style="vertical-align: top; background-color: #e6e6e6;"
+|<span style="color: blue;">--mfinfo NAME</span><br/><div style="margin-left: 30px;">RBF+GPR: name of file with input and predicted mean forces.</div>
+|- style="vertical-align: top;"
+|<span style="color: blue;">--output FORMAT</span><br/><div style="margin-left: 30px;">Output FORMAT to print the free energy surface. Supported formats are: plain, gnuplot, fes.</div><span style="color:purple; margin-left: 30px;">(Default: gnuplot)</span>
+|- style="vertical-align: top; background-color: #e6e6e6;"
+|<span style="color: blue;">--printall</span><br/><div style="margin-left: 30px;">Print results for all bins even if not properly sampled.</div>
+|- style="vertical-align: top;"
+|<span style="color: blue;">--unsampledasmax</span><br/><div style="margin-left: 30px;">Set energy values in unsampled region to maximum energy from sampled region or to value provided by --maxenergy.</div>
+|- style="vertical-align: top; background-color: #e6e6e6;"
+|<span style="color: blue;">--maxenergy NUMBER</span><br/><div style="margin-left: 30px;">If set, this is the energy used of unsampled regions.</div><span style="color:purple; margin-left: 30px;">(Default: 0)</span>
+|- style="vertical-align: top;"
+|<span style="color: blue;">--noheader</span><br/><div style="margin-left: 30px;">Do not print header to the output file.</div>
+|- style="vertical-align: top; background-color: #e6e6e6;"
+|<span style="color: blue;">--includebinstat</span><br/><div style="margin-left: 30px;">Include bin statuses (1=sampled, 0=unsampled, -1=glued) into resulting FES.</div>
+|- style="vertical-align: top;"
+|<span style="color: blue;">--oldrfd</span><br/><div style="margin-left: 30px;">RFD: Use old RFD implementation.</div>
+|- style="vertical-align: top; background-color: #e6e6e6;"
+|<span style="color: blue;">--fdpoints NUMBER</span><br/><div style="margin-left: 30px;">RFD: Determine number of points employed in differenciation scheme (three or four is upported) in RFD method.</div><span style="color:purple; margin-left: 30px;">(Default: 3)</span>
+|- style="vertical-align: top;"
+|<span style="color: blue;">--fx FORMAT</span><br/><div style="margin-left: 30px;">Output FORMAT, which will be used to print values of collective variables.</div><span style="color:purple; margin-left: 30px;">(Default: %15.7e)</span>
+|- style="vertical-align: top; background-color: #e6e6e6;"
+|<span style="color: blue;">--fe FORMAT</span><br/><div style="margin-left: 30px;">Output FORMAT, which will be used to print values of free energy.</div><span style="color:purple; margin-left: 30px;">(Default: %15.7e)</span>
 |- style="vertical-align: top;"
-|<span style="color: blue;">--fdorder ORDER</span><br/><span style="margin-left: 30px;">Determines differenciation scheme. Currently implemented schemes use either three or four points.</span><br/><span style="color:purple; margin-left: 30px;">(Default: 3)</span>
+|<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; background-color: #e6e6e6;"
-|<span style="color: blue;">-o, --offset NUMBER</span><br/><span style="margin-left: 30px;">Specify an integration constant.</span><br/><span style="color:purple; margin-left: 30px;">(Default: 0)</span>
+|<span style="color: blue;">--numdiff</span><br/><div style="margin-left: 30px;">GPR: Use numerical differentiation of kernel function (for testing only).</div>
 |- style="vertical-align: top;"
-|<span style="color: blue;">-p, --periodic</span><br/><span style="margin-left: 30px;">Switch on periodicity for collective variables that are periodic.</span>
+|<span style="color: blue;">--useinv</span><br/><div style="margin-left: 30px;">GPR: Use matrix inversion pathway (for testing only).</div>
 |- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">-e, --errors</span><br/><span style="margin-left: 30px;">Integrate errors of derivatives.</span>
+|<span style="color: blue;">--calclogpl</span><br/><div style="margin-left: 30px;">GPR: Calculate logPL.</div>
 |- style="vertical-align: top;"
-|<span style="color: blue;">--output FORMAT</span><br/><span style="margin-left: 30px;">Output FORMAT, which will be used to print free energy surface. Supported formats are: plain, gnuplot, fes.</span><br/><span style="color:purple; margin-left: 30px;">(Default: gnuplot)</span>
+|<span style="color: blue;">--inczpe</span><br/><div style="margin-left: 30px;">GPR: Include zero-point energy at position specified by --globalmin.</div>
 |- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">--printwithlimit</span><br/><span style="margin-left: 30px;">Print results from bins that were adequately sampled.</span>
+|<span style="color: blue;">--fasterror</span><br/><div style="margin-left: 30px;">GPR: Use faster algorithm for error calculation.</div>
 |- style="vertical-align: top;"
-|<span style="color: blue;">--noheader</span><br/><span style="margin-left: 30px;">Do not print header to the output file.</span>
+|<span style="color: blue;">--keepcvs SPEC</span><br/><div style="margin-left: 30px;">Which CVs should be kept during statistical reweighting of FES. Flags are specified in the form CV1[xCV2x...] with F and T for skip and kept CV, respectively. The last value pads the rest.</div><span style="color:purple; margin-left: 30px;">(Default: T)</span>
 |- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">--fx FORMAT</span><br/><span style="margin-left: 30px;">Output FORMAT, which will be used to print values of collective variables.</span><br/><span style="color:purple; margin-left: 30px;">(Default: %15.7e)</span>
+|<span style="color: blue;">--reducedfes NAME</span><br/><div style="margin-left: 30px;">Name of file for FES reduced by statistical reweighting containing only kept CVs.</div>
 |- style="vertical-align: top;"
-|<span style="color: blue;">--fe FORMAT</span><br/><span style="margin-left: 30px;">Output FORMAT, which will be used to print values of free energy.</span><br/><span style="color:purple; margin-left: 30px;">(Default: %15.7e)</span>
+|<span style="color: blue;">--temperature NUMBER</span><br/><div style="margin-left: 30px;">Absolute temperature for reduction of FES in [K].</div><span style="color:purple; margin-left: 30px;">(Default: 300)</span>
 |- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">-v, --verbose</span><br/><span style="margin-left: 30px;">Increase output verbosity.</span>
+|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">Increase output verbosity.</div>
 |- style="vertical-align: top;"
-|<span style="color: blue;">--version</span><br/><span style="margin-left: 30px;">Output version information and exit.</span>
+|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">Output version information and exit.</div>
 |- style="vertical-align: top; background-color: #e6e6e6;"
-|<span style="color: blue;">-h, --help</span><br/><span style="margin-left: 30px;">Display this help and exit.</span>
+|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">Display this help and exit.</div>
 |}