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The output of pyOZ can be divided into several parts. It will be described on an outcome of a test calculation for charged particles interacting via potential defined by PMF read from separate files (test case **pmf_sep**), started as

pyoz.py -i pmf_sep.in -name pmf_sep -o pmf_sep.log

Note that by using the **-o** command line switch, all output (including error messages) after the header (program name and version)

pyOZ - iterative solver of the Ornstein-Zernike equation version 0.2, Lubos Vrbka, 2008-2009

is redirected to the selected output file.

First part of the output file contains a summary of control statements, as specified by the ctrl section of the input file. For example, number of discretization points, step size in real and Fourier space, variables related to the iteration scheme and others are given.

control statements number of points 4096 deltar, maximum r 0.040000, 163.800000 deltak, maximum k 0.019179, 78.539816 max iterations 5000 convergence criterion 1.000000e-09 maximal allowed DSQN 1.000000e+02 Picard iteration method will be used Picard mix parameter 1.000000 graphic output won't be used

This is follows by the section devoted to the system settings – number of components, their names, desired temperature, concentration, but also the value of fundamental physical constants.

system information constants and factors temperature 300.000000 K relative permittivity 72.000000 Bjerrum length 7.736146 A Avogadro constant 6.022141e+23 1/mol Boltzmann constant 1.380650e-23 J/K kT 4.141951e-21 J 1/kT = beta 2.414321e+20 1/J elementary charge 1.602176e-19 C vacuum permittivity 8.854188e-12 C^2/Jm conversion kcal/mol to kT 1.677397 conversion kJ/mol to kT 0.400907 conversion eV to kT 38.681684 number of components 2 closure relation HNC constituent names P M concentrations mol/L 0.500000 0.500000 particle densities part/A3 0.000301 0.000301 total particle density 0.000602 molar fractions 0.500000 0.500000

Then, all interaction parameters (as specified in the parm section) are summarized. In this case, Coulombic interaction and external PMFs are used.

potential parameters potential type Coulomb potential (coulomb) title coulomb charges (elementary) 1.000000 -1.000000 alpha for Ng (from kappa) 0.060 0.060 0.060 potential type PMF from external file(s) (pmf) title pmf pmf units kT pmf distance units nm interpolation scheme cosine values added (r->0) inf values added (r->inf) 0.000000 attempting load of pmf individual pmf 0 (pmf_sep1) individual pmf 1 (pmf_sep2) individual pmf 2 (pmf_sep3) data processing combination 1 of 3 (file pmf_sep1, columns 1 and 2) combination 2 of 3 (file pmf_sep2, columns 1 and 2) combination 3 of 3 (file pmf_sep3, columns 1 and 2) loaded pmf data succesfully

Output-related information (handling of the Gamma function, pair correlation functions , …) is summarized in the next section of the output file.

output controls Gamma function will not be written! g(r) will be saved to file pmf_sep-gr.dat total potential will be saved to file pmf_sep-ur.dat

As a next step, information regarding the Fourier transforms is printed out.

initializing DFT routines FT set up for 4095 points FT prefactor 0.050661 iFT prefactor 25729.643833 factor involved in convolution 248.050213

PMF data are processed at this point, when requested in input file. Missing data are filled with predefined values (in this case infinity and zero for small and large separations, respectively). The exact value of the potential at discretization points is calculated using linear or cosine interpolation.

processing pmf data cosine interpolation will be used combination pmf(1,1) added before pmf 72 interpolated 422 added after pmf 3601 combination pmf(1,2) added before pmf 63 interpolated 431 added after pmf 3601 combination pmf(2,2) added before pmf 94 interpolated 400 added after pmf 3601

When graphical output is requested, a short message is written out at this point and the respective windows are created. Please note that this may take some time, specially on slower computers, or when the computer is accessed over a slow network.

`initializing graphic subsystem`

When requested, the total interaction potential is saved to file. Furthermore (if requested by the -g command line parameter), load of the Gamma function from an external file is attempted. Please note that even if it is unsuccesful, the calculation carries on (with zero Gamma function).

writing pair potential (pmf_sep-ur.dat) using zero Gamma function

Afterwards, the iteration procedure is started. The used solver is indicated. Then, for every iteration, its number, some time statistics, the quadratic norm, and information whether the convergence was achieved is printed out. At the end it is indicated where the calculation has converged or the maximum number of iteration cycles has been reached. Requested output procedures are performed during the iterative process and also afterwards.

using optimized solver for 2 components starting iteration ... main 12 0.220477 sec - DSQN 1.031253e-08 - not converged main 13 0.219964 sec - DSQN 1.868795e-09 - not converged main 14 0.220347 sec - DSQN 3.386760e-10 - converged iteration process completed after iteration 14 calculation converged saving outputs pair correlation function (hs-gr.dat)

In this case, the calculation converged in 14 iterations. When the NR/CG algorithm is used, there are several nr/cg sub-iterations after each main iteration, but the output looks the same otherwise (the extra information about the NR parameters is then given in the ctrl part of the output as well).

The program carries on with the calculation of thermodynamical properties. For some purposes (isothermal compressibilities, excess chemical potentials), short ranged potentials need to be used. Furthermore, the Kirkwood-Buff factors are evaluated and their values for unique pairs (i.e., 1-1, 1-2, …, 1-n, 2-2, …) are printed.

calculation of (thermodynamic) properties testing for long-ranged potentials found, using short-ranged c(r) Kirkwood-Buff integrals unique comb. -1614.801864 1710.420596 -1607.875761

For osmotic coefficient, the total osmotic coefficient is given, and furthermore the contributions from all individual potentials. These are listed in the same order as in the input file.

osmotic coefficient 0.93895 contributions of individual potentials potential title given in brackets coulomb -0.17128 (coulomb) pmf 0.11024 (pmf)

Excess chemical potentials of all components, their activity coefficients and the mean activity coefficient (only for binary electrolyte) are then calculated.

excess chemical potential (using sr-c(r)) mu/kT -0.374528 -0.373254 activity coefficients exp(mu/kT) 0.687614 0.688490 mean 0.688052

As a next step, isothermal compressibility is calculated. Normal and reciprocal values for excess, ideal and absolute compressibility is given.

isothermal compressibility (using sr-c(r)) excess chi, chi^(-1) 1.029837 0.971027 ideal chi, chi^(-1) 4.00907e-07 2494341.621249 absolute, chi, chi^(-1) 4.12869e-07 2422073.240606

The succesful end of the calculation is indicated by the words

`calculation finished`

To completely quit the program when graphic output is used, it is necessary to press enter at this point, as indicated by the program output.

`press enter to close the graphics window and exit`

In case there is a problem, pyOZ should print out helpful error messages (I hope to have done my best). In the worst case, you can always consult the source code, which should have all the information you need to sort out what is going on.

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