_____________________________________________________________________________________________ ************************ SIMulation to EXPeriment comparison ******************************** (C) Norbert.Kucerka@nrc.gc.ca _____________________________________________________________________________________________ ******* *ABOUT* ******* Program 'SIMtoEXP' (originally 'VolProb') is for converting SIMulated data to scattering form factors and comparing those to experimental data. It also calculates the Volume Probability Distributions according to space filling volumetric model. _____________________________________________________________________________________________ ************** *INSTALLATION* ************** Download the SIMtoEXP.tgz package and unpack it, or download the ready for use directory SIMtoEXP while keeping the relative paths of all files. Within the files: Manual.doc is a walk-through user manual. Executable files are located in bin directory. There is a windows version SIMtoEXP.exe together with Mac OS X version SIMtoEXP.mac (compiled under Leopard) and linux version SIMtoEXP.lnx (compiled under Fedora Core 11). Note, that only windows version is provided as a stand-alone package, while other two executables require X-windows framework and Tcl/Tk/Blt v8.4 to be installed by the user (e.g. through MacPorts or Fink on Mac OS, and yum on Linux distros). lib and bin directories include tcl/tk related libraries and dependencies for windows version. The minimal package was extracted from version 8.4.13, however any patch to version 8.4 can be used (NK can provide windows installation packages). test directory includes the examples of input files as explained in user manual. _____________________________________________________________________________________________ ********* *History* ********* 07/2015 introduction of a new setting parameter (relError) that defines the way of treating experimental uncertainties. They are considered relative (i.e. will be scaled with form factors) when relError=1, otherwise they are considered absolute (not-for-scaling) by default (relEror=0). The parameter can be changed in a new window: Experiment Specifics. 12/2013 SIMtoEXP now allows to see multiple FT as corresponding to multiple samples (e.g., FTs for various neutron contrasts can be displayed all at once) 12/2013 X atom has been defined as an Xperc mixture of D and H to be used for exchangeable protons and neutron contrast variation in water. 12/2013 Y united atom has been defined as a Yperc mixture of D2O and H2O. 05/2013 The constraint on number of atoms in simulation being up to 999 was lifted. 11/2012 The parameters for X-ray atomic form factors of united atoms CH2, CH and CH3 were devised by John Nagle as a reasonable combinations of the individual atoms. 12/2011 Improved control of manipulating the scattering densities of water. While "set xWat (or nWat)" changes them at every re-calculation, new "setRHO_wat X (or N)" changes them only when it is not fixed in GUI. !!! change the experimental data files accordingly (i.e., "set xWat" -> setRHO_wat X") !!! 10/2011 Additional window that allows to perform some analysis has been added (GUI-->Tools-->Analysis). One can combine volume probabilities of various components, and then canculate the Gibb's dividing surface of a resulting distribution. 10/2011 Checking 'symmetrized' box inside FT subpanel results now in symmetrizing the simulation too, in addition to form factors only as done previously. 10/2011 Additional 2 parameters have been added to manipulate the simulation, Z axis in particular. These are 'Zcentre' for shifting off-centred simulations, and 'Zdirection' for arranging the Z values in ascending order. Note that Zdirection may also be used to rescale the Z axis, e.g. transforming units between Angstroems and nm. Both of the parameters can be entered in the header of *.sim file or in GUI Simulation Specifics window. 05/2011 Clean-up. 03/2011 SIMtoEXP now includes partial charges correction in a calculation of x-ray form factors, which can be defined for each atom in the second row (starting with “partial”) of *.sim file. 03/2011 The option to select a symmetrized Fourier Transform (utilizing cosine term only) has been added. 03/2011 Various *.tcl and *.txt files were moved to the separate directory called tcl. 01/2010 Margins delimiter was introduced (another good idea of Frank). 01/2010 Option of loading 2 experimental data files (ULV and ORI) was expanded to 5 different data files (SAM1 to SAM5). 01/2010 Incomplete and/or overloaded space filling volumetric model can be loaded (i.e., model that does not comprise all of the atoms and/or uses some atoms in several component groups). The warning messages will pop up for such models. Further clean up of GUI's menu, which now includes advanced options to configurate the axis of various graphs. 12/2009 GUI was rearranged to emphesize following order of importance: simulated scattering densities -> Fourier transforms -> comparison to exp. profiles -> volumetric calculation 12/2009 The issue of loading files with empty lines throughout the file and not at the end was fixed (thanks to Frank Heinrich for pointing this out). Option to manipulate NumEl/gr and NeutSl/gr was disabled to avoid confusion. These quantities are calculated based on the NumEl and NeutSl of each atom automatically. All the shown curves are now recalculated after changing any of these parameters. 11/2009 **** BETA version **** X-ray form factor calculation now includes atomic form factors. 11/2009 Further clean-up. The user can now define their own atom types (identifier and scattering length densities). 06/2009 **** SIMtoEXP - GAMMA version **** Data loading and manipulation was cleaned up and program was renamed to SIMtoEXP 05/2009 Program was expanded to calculate Fourier transform and to be capable to load EDP, NSLDP, eFF, and nFF from external files 03/2009 **** SIMtoSDP **** Program was expanded to include handling all-atom simulation files and renamed to SIMulation to SDP 04/2008 **** VolumeProb **** Volume analysis program by Norbert.Kucerka@nrc.gc.ca