pmf-integrate
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pmf-integrate: version 6.380.1d87074 (2021-07-26 16:36)
Name
pmf-integrate
Synopsis
pmf-integrate [OPTIONS] [--] accuname fename [fullfename]
Description
The program numerically integrates data from the PMF calculations. The integration is performed either by the reverse finite difference (RFD) method, radial basis functions (RBF), or Gaussian process (GPR).
Arguments
accuname Name of file containing the ABF accumulator. If the name is '-' then the accumulator is read from the standard input.
fename 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.
fullfename Optional name of file with free energy surface containing all regions (sampled and unsampled).
fename 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.
fullfename Optional name of file with free energy surface containing all regions (sampled and unsampled).
Options
| -r, --realm NAME Intended output from the integration: (Default: dG)
** dG - free energy (default) ** -TdS - entropy contribution to the free energy ** dG_p - free energy (potential part) - ABF ** dG_k - free energy (kinetic part) - ABF ** -TdS_PP - entropy contribution to the free energy, cov(dH_p/dx,Epot) - ABF ** -TdS_PK - entropy contribution to the free energy, cov(dH_p/dx,Ekin) - ABF ** -TdS_PR - entropy contribution to the free energy, cov(dH_p/dx,Erst) - ABF ** -TdS_KP - entropy contribution to the free energy, cov(dH_k/dx,Epot) - ABF ** -TdS_KK - entropy contribution to the free energy, cov(dH_k/dx,Ekin) - ABF ** -TdS_KR - entropy contribution to the free energy, cov(dH_k/dx,Erst) - ABF ** -TdS_HP - entropy contribution to the free energy, cov(dH/dx,Epot) - CST ** -TdS_HK - entropy contribution to the free energy, cov(dH/dx,Ekin) - CST ** -TdS_HR - entropy contribution to the free energy, cov(dH/dx,Erst) - CST |
| -m, --method NAME Integration method. Supported methods are: rfd (reverse finite differences via csparse), rbf (radial basis functions), and gpr (gaussian process). (Default: rfd)
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| --emethod NAME Integration method for energy cut-off. Supported methods are: rfd (reverse finite differences via csparse), rbf (radial basis functions), and gpr (gaussian process). (Default: rfd)
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| -a, --lmethod NAME 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), RBF(QR,SVD,default), and GPR(LU,SVD,SVD2,LL,default). (Default: default)
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| --rcond NUMBER RBF+GPR: Rank condition for SVD. Used value must be carefully tested. Calculation at computer precision is requested with -1 (not recommended). (Default: 1e-06)
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| -l, --limit NUMBER Only bins containing more samples than NUMBER are considered as properly sampled. (Default: 100)
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| --skipfftest Skip flood fill test for discontinuous regions.
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| -q, --energylimit NUMBER Integrate data only if the free energy is below NUMBER. This limit enforces two integration runs. Negative value disables the limit. (Default: -1)
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| --rmnegene Remove regions with negative free energy.
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| --skiplastelimit Skip energy limit filter after final integration.
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| --mfmaxzscore NUMBER 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. (Default: -1)
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| --mfnumofztests NUMBER RBF+GPR: Repeat z-score test for mean force errrors NUMBER times. (Default: 1)
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| -s, --sigmaf2 NUMBER GPR: Variance of the reconstructed free energy surface (signal variance). (Default: 15)
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| -c, --ncorr NUMBER GPR: Number of statistically correlated samples. (Default: 1)
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| -w, --wfac SPEC 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. (Default: 3.0)
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| --loadhyprms NAME GPR: Name of file with GPR hyperparameters.
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| -t, --rfac SPEC 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. (Default: 1.0)
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| -g, --overhang NUMBER RBFs overhang to properly integrate areas near sampled edges. Ignored for periodic CVs. (Default: 2)
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| --includeglued RBF+GPR: Explicitly include glued regions. This options is set ON when --glueing > 0.
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| --glueing NUMBER RBF+GPR: Calculate energy also for unsampled bins in close vicinity to sampled ones. (Default: 0)
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| --glueholes RBF+GPR: Calculate energy also for unsampled regions inside the FES.
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| -p, --periodic RFD: Switch on periodicity for collective variables that are periodic.
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| --globalmin SPEC 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.
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| --userealglbmin RBF+GPR: ignore --globalmin in the final integration step
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| -o, --offset NUMBER Specify an integration constant. (Default: 0)
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| -e, --witherror GPR: Estimate free energy errors.
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| --noenergy GPR: Skip calculation of energy and errors (it can save some time when only logML is required).
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| --saveabf NAME Save the final ABF accumulator into the file with NAME.
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| --mfinfo NAME RBF+GPR: name of file with input and predicted mean forces.
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| --output FORMAT Output FORMAT to print the free energy surface. Supported formats are: plain, and gnuplot. (Default: gnuplot)
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| --printall Print results for all bins even if not properly sampled.
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| --unsampledasmax Set energy values in unsampled region to maximum energy from sampled region or to value provided by --maxenergy.
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| --maxenergy NUMBER If set, this is the energy used of unsampled regions. (Default: 0)
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| --noheader Do not print header to the output file.
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| --includebinstat Include bin statuses (1=sampled, 0=unsampled, -1=glued) into resulting FES.
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| --oldrfd RFD: Use old RFD implementation.
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| --fdpoints NUMBER RFD: Determine number of points employed in differenciation scheme (three or four is upported) in RFD method. (Default: 3)
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| --fx FORMAT Output FORMAT, which will be used to print values of collective variables. (Default: %15.7e)
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| --fe FORMAT Output FORMAT, which will be used to print values of free energy. (Default: %15.7e)
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| --kernel NAME GPR: Kernel type. Supported types: ardse (ARD squared exponential), ardmc52 (ARD Matern class 5/2), default(=ardse) (Default: default)
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| --numdiff GPR: Use numerical differentiation of kernel function (for testing only).
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| --useinv GPR: Use matrix inversion pathway (for testing only).
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| --calclogpl GPR: Calculate logPL.
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| --inczpe GPR: Include zero-point energy at position specified by --globalmin.
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| --nofasterror GPR: Do not use faster algorithm for error calculation.
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| --slevel VALUE Sigma-level for confidence interval. (Default: 1)
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| --keepcvs SPEC 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. (Default: T)
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| --reducedfes NAME Name of file for FES reduced by statistical reweighting containing only kept CVs.
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| -v, --verbose Increase output verbosity.
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| --version Output version information and exit.
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| -h, --help Display this help and exit.
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