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Documentation: outputs

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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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