pmf-enthalpy
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pmf-enthalpy: version 6.380.1d87074 (2021-07-26 16:36)
Name
pmf-enthalpy
Synopsis
pmf-enthalpy [OPTIONS] [--] accuname enthalpy
Description
The program provides enthalpy from the PMF accumulator.
Arguments
| accuname Name of file containing the PMF accumulator. If the name is '-' then the accumulator is read from the standard input.
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| enthalpy Name of file where results will be printed. If the name is '-' then the output will be written to the standard output.
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Options
| -r, --realm NAME Intended output: (Default: <Epot>)
** - enthalpy as the ensemble average of the potential energy (default) ** - the ensemble average of the kinetic energy (this should be a constant for simulations at a constant temperature) ** - the ensemble average of the PMFLib restrain energy ** - enthalpy as the ensemble average of the total energy |
| -m, --method NAME Supported methods are: raw (data taken directly from accumulator) and gpr (gaussian process filtered data). (Default: raw)
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| -a, --absolute absolute enthalpy.
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| -l, --limit LIMIT Only bins containing more samples than NUMBER are considered as properly sampled. (Default: 0)
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| -e, --witherror GPR: Estimate enthalpy errors from the GPR model. RAW: Print enthalpy errors from the PMF accumulator.
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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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| -s, --sigmaf2 NUMBER GPR: Variance of the reconstructed enthalpy surface (signal variance). (Default: 15)
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| -c, --ncorr VALUE Number of statistically correlated samples. (Default: 1)
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| -w, --wfac SPEC GPR: Factors influencing widths of 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 the GPR hyperparameters.
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| --slevel VALUE Sigma-level for confidence interval. (Default: 1)
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| --globalmin SPEC 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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| -o, --offset NUMBER Specify an integration constant. (Default: 0)
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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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| --includebinstat Include bin statuses (1=sampled, 0=unsampled, -1=glued) into resulting FES.
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| --output FORMAT Output FORMAT to print the enthalpy surface. Supported formats are: plain and gnuplot. (Default: gnuplot)
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| --noheader Do not print header to the output file.
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| --printall Print results for all bins even if not properly sampled.
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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 results. (Default: %15.7e)
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| --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), lu (LU factorization), ll (LL - Cholesky factorization). Possible combinations are: GPR(LU,SVD,SVD2,LL,default). (Default: default)
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| --rcond NUMBER 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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| -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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