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README
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README
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******************* PSDsolv v.1.0 **********************
Author of psd.cpp: Supriyo Bhattacharya
solvopt.cpp and solvopt.h were included upon permission
from Prof. Franz Kappel. ran_nr.cpp is taken from
"Numerical Recipes in C++"
Feel free to modify / distribute the original code for
nonprofit / academic purposes. I give permission for
commercial use of my own code, however solvopt is
forbidden from being used commercially. Therefore
commercial users can use the code as long as they
provide their own nonlinear optimization routine and
give proper credits to the author and cite the reference
given at the end of this document. Also, commercial
establishments may not prohibit others from modifying
/ distributing the original codes either for nonprofit
or for commercial purposes.
GENERAL DESCRIPTION
This program calculates the pore size distribution
from a structure file. The program does not need the
connect records, only the locations and atom types,
so the xyz format is the simplest to work with. If
your structure is in a pdb or mol2 format, use babel
to convert: i.e. openbabel -ipdb struc.pdb -oxyz struc.xyz
The atoms are modeled as hard spheres (vdW radii).
The program uses a nonlinear optimization routine (SOLVOPT)
INSTALL
Run the install script (./install)
Then place the executable (psd) somewhere in your path or
create a link in /usr/local/bin.
Place radii_list.dat in the same directory where you run
the program. This file contains the vdW radii of the
common atom types used by the program. New user defined
atom types can be added to radii_list.dat.
RUN
psd <xyz file> <test particle radius (A)> <histogram bin width (A)>
A bin width of 0.25A seems to be the optimum. The output produces
three files: psd_diff.dat (the actual distribution), psd_cumm.dat
(cummulative PSD, see paper for explanation) and error.dat (shows
the average error over time / MC steps).
Once you start the program, a rough profile can be seen within an hour.
However, it may take upto 24 hours to get a smooth profile
(depending on the system size). Please continue to monitor the
distribution and the estimated error. Once you are satisfied with the results,
just kill the process, simple!!
OTHER INFO
Please cite the following:
psd calculation:
S. Bhattacharya and K. E. Gubbins, fast Method for Computing
Pore Size Distributions of Model Materials, Langmuir 2006, 22, 7726.
solvopt:
F. Kappel and A. V. Kuntsevich, Comput. Optim. Appl. 2000, 15, 193.
Send all comments to [email protected]