niels-bohr-institute-xns-structbiophys / xndiff

X-ray and Neutron powder pattern simulation for nanocrystals in dispersion (SAXS, SANS)

/* folder structure: XNDiff/ : XNDiff.cpp mtrand.cpp mtrand.h compile_XNDiff.sh Makefile XNDiff/in/ : syminfo.lib (optional) f0_InterTables.dat DeBe_NeutronNews.dat atomweights.dat cif_core.dic further user-provided input files like cif-files (less common pdb-files), symmetry operation files, parameter files (less common, parameters can be provided upon call of XNDiff on cmd) XNDiff/out/ : XNDiff generated files for SAXS and SANS patterns, log-files, further output files for testing (distributions, (modified)cif-files, ...)

*/

/* mandatory and optional external libraries / installations to run XNDiff on GNU Linux and (with minor code modifcations) on other POSIX systems (FreeBSD, ...):

-MTRand PRNG (MANDATORY, might be replaced with a PRNG from GSL later), http://www.bedaux.net/mtrand/ just place mtrand.cpp and mtrand.h at the same location of XNDiff.cpp before compilation

-GSL (MANDATORY, tested with v1.15) http://www.gnu.org/software/gsl/ comes along with most GNU Linux distros and is installed on most HPC systems by default

-CCP4 (OPTIONAL, tested with v6.1.13, when using -sym <ccp4 ...> option) http://www.ccp4.ac.uk/ Note: CCP4 can be binary installation, since CCP4 is called via opening a shell

-Armadillo (OPTIONAL, tested with v3.0.3, mostly for test purposes, when using -bt <bt_twin, bt_double> option) */

/* compilation using g++, assuming everything is installed / put in the right place:

-without using optional Armadillo library, Optimization: DEBUG / O3-Level, no further architecture-specific optimization e.g. ./compile_XNDiff.sh g++ DEBUG 0 NONE e.g. ./compile_XNDiff.sh g++ 3 0 NONE -using optional Armadillo library, Optimization: DEBUG / O3-Level, no further architecture-specific optimization e.g. ./compile_XNDiff.sh g++ DEBUG 1 NONE e.g. ./compile_XNDiff.sh g++ 3 1 NONE

*/

/* further mandatory / optional parameter-files with physical constants and symmetry operations etc to run XNDiff:

-download from link below and save as syminfo.lib to in/ http://www.ccp4.ac.uk/cvs/viewvc.cgi/libccp4/data/syminfo.lib?view=co (OPTIONAL, symmetry operations, required when using -sym or -sym <ccp4 ...> option without providing a symopfile, see source code for further details) (further reading http://www.ccp4.ac.uk/html/symlib.html)

-download from link below and save as f0_InterTables.dat to in/ http://ftp.esrf.eu/pub/scisoft/xop2.3/DabaxFiles/f0_InterTables.dat (MANDATORY, Cromer-Mann coefficients for X-ray scattering)

-download from link below and save as DeBe_NeutronNews.dat to in/ http://ftp.esrf.eu/pub/scisoft/DabaxFiles/DeBe_NeutronNews.dat (MANDATORY, neutron coherent scattering lengths etc)

-save as atomweights.dat the ASCII table from link below into in/ and make some modifications (has been already done and included in your download of XNDiff!!!) http://physics.nist.gov/cgi-bin/Compositions/stand_alone.pl?ele=&ascii=ascii&isotype=some (MANDATORY, atom/isotope masses)

-download from link below the current version and save as cif_core.dic to in/ ftp://ftp.iucr.org/pub/cif_core.dic (MANDATORY, cif-dictionary required to read cif-files, tested with v2.4.3 from 2012-05-16) */