Debroglie's repository for fedora

Update: platon-110104-1.fc12

Sat, 08 Jan 2011 16:17:09 +0000

Package: platon
Summary: PLATON is a versatile SHELX97 compatible multipurpose crystallographic tool

Description:
PLATON is a versatile SHELX97 compatible multipurpose crystallographic tool. Most PLATON features complement those available in the excellent and widely distributed SHELX97 package for crystal structure determination and refinement. Historically (1980) PLATON started out as a program for the automated calculation of derived geometrical data (i.e. bond distances, bond angles and torsion angles, including su's (esd's)) for structures refined with SHELX76. Since then, that basic function evolved into an automatic function to calculate everything of possible interest (both intra- and intermolecular)for a given structural parameter set (Instruction: CALC). Over time, various other tools were introduced (Molecular Graphics i.e. PLUTON & ORTEP, Absorption correction, Data Validation etc.), some of which requiring a reflection datafile as well. Several functions in PLATON (e.g. SPGR and EXOR) are there to implement calculations needed for datareduction, structure determination and refinement with a program system called 'SYSTEM-S'. Reference: A.L.Spek (2008) PLATON, A Multipurpose Crystallographic Tool, Utrecht University, Utrecht, The Netherlands. or A.L.Spek, J.Appl.Cryst. 2003, 36, 7-13 A.L.Spek Acta Cryst. 2009, D65, 148-155

Changes:

platon-110104-1.fc12.i686 [8.3 MiB]	Changelog by John (2011-01-08): - 110104 version - Update (New ALERTS _018 & _019)
platon-110104-1.fc12.x86_64 [8.4 MiB]	Changelog by John (2011-01-08): - 110104 version - Update (New ALERTS _018 & _019)
platon-101207-1.fc12.x86_64 [8.4 MiB]	Changelog by John (2010-12-14): - 101207 version - Minor Update(s) - Minor Update for Synchrotron data - 'CrystalStructure FCF format added' - Update R/S Assignments
platon-101207-1.fc12.i586 [8.3 MiB]	Changelog by John (2010-12-14): - 101207 version - Minor Update(s) - Minor Update for Synchrotron data - 'CrystalStructure FCF format added' - Update R/S Assignments
platon-101013-1.fc12.i686 [8.2 MiB]	Changelog by Pascal Parois (2010-10-17): - 101013 version - Minor Update, corrections - new feature: PAGEHEADER Toggle - new feature: NEW KEYBOARD INSTRUCTION: 'ANOM element_type wavelength' - new feature: New ALERT _303 + optimization issue solved - new feature: Angle calculation between crystal faces and netplanes added - new feature: New ALERT _934 added
platon-101013-1.fc12.x86_64 [8.3 MiB]	Changelog by Pascal Parois (2010-10-17): - 101013 version - Minor Update, corrections - new feature: PAGEHEADER Toggle - new feature: NEW KEYBOARD INSTRUCTION: 'ANOM element_type wavelength' - new feature: New ALERT _303 + optimization issue solved - new feature: Angle calculation between crystal faces and netplanes added - new feature: New ALERT _934 added
platon-100824-1.fc12.i386 [8.1 MiB]	Changelog by Pascal Parois (2010-08-26): - 100712 version - Minor Updates & Corrections
platon-100824-1.fc12.x86_64 [8.3 MiB]	Changelog by Pascal Parois (2010-08-26): - 100712 version - Minor Updates & Corrections
platon-100712-1.fc12.i686 [7.7 MiB]	Changelog by John (2010-07-12): - 100712 version - New ALERTS _980,_981,_982,_983 - Minor Updates - Minor Updates & Corrections - Minor Updates & Corrections
platon-100712-1.fc12.x86_64 [7.8 MiB]	Changelog by John (2010-07-12): - 100712 version - New ALERTS _980,_981,_982,_983 - Minor Updates - Minor Updates & Corrections - Minor Updates & Corrections
platon-100421-1.fc12.x86_64 [5.4 MiB]	Changelog by John (2010-04-21): - Changed spec to reflect doc path change - 100331 version - Minor Update - New Compare: platon -d file1.fcf file2.fcf - Corrections + Update - Fobs/Fcalc Scatterplot added (in Variance Analysis) - Minor Update - Minor Update
platon-100310-1.fc12.x86_64 [5.4 MiB]	Changelog by John (2010-03-10): - 100310 version - Handling of 'TITL data_' record in .res file - Minor Update - Minor Update
platon-100310-1.fc12.i586 [5.3 MiB]	Changelog by John (2010-03-10): - 100310 version - Handling of 'TITL data_' record in .res file - Minor Update - Minor Update
platon-100224-1.fc12.x86_64 [5.4 MiB]	Changelog by John (2010-02-24): - 24210 version - Minor Update - Minor Update - Platon source now in platon.f.gz (not Z) - SPEC file updated - Minor Update (CIF-VALIDATION.pdf) - Update SGSM routines
platon-100224-1.fc12.i586 [5.2 MiB]	Changelog by John (2010-02-24): - 24210 version - Minor Update - Minor Update - Platon source now in platon.f.gz (not Z) - SPEC file updated - Minor Update (CIF-VALIDATION.pdf) - Update SGSM routines
platon-100215-1.fc12.x86_64 [5.1 MiB]	Changelog by John (2010-02-09): - 12210 version - Minor Update (Intel-Ifort compiler compatible)
platon-100215-1.fc12.i586 [5.0 MiB]	Changelog by John (2010-02-09): - 12210 version - Minor Update (Intel-Ifort compiler compatible)
platon-100129-1.fc12.i586 [4.3 MiB]	Changelog by John (2010-01-31): - 29110 version - New ALERTS _973 & _974 - Minor Update - New _782 ALERT
platon-100129-1.fc12.x86_64 [4.4 MiB]	Changelog by John (2010-01-31): - 29110 version - New ALERTS _973 & _974 - Minor Update - New _782 ALERT
platon-100126-1.fc12.i586 [4.2 MiB]	Changelog by John (2010-01-26): - 20110 version - Non-standard space group settings P1 1 21:A & P 21 1 1:B added
platon-100126-1.fc12.x86_64 [4.3 MiB]	Changelog by John (2010-01-26): - 20110 version - Non-standard space group settings P1 1 21:A & P 21 1 1:B added
platon-100115-1.fc12.i586 [4.1 MiB]	Changelog by John (2010-01-15): - 13110 version - minor update/corrections
platon-100115-1.fc12.x86_64 [4.3 MiB]	Changelog by John (2010-01-15): - 13110 version - minor update/corrections
platon-091203-1.fc12.x86_64 [4.3 MiB]	Changelog by John (2009-12-03): - 03122009 version - mimor correction (Friedif)
platon-091203-1.fc12.i586 [4.1 MiB]	Changelog by John (2009-12-03): - 03122009 version - mimor correction (Friedif)
platon-091104-1.fc12.i586 [4.1 MiB]	Changelog by John (2009-11-04): - 27102009 version - minor update
platon-091104-1.fc12.x86_64 [4.3 MiB]	Changelog by John (2009-11-04): - 27102009 version - minor update

Update: edensgrid-0.3-1.fc12

Mon, 11 Oct 2010 08:07:38 +0000

Package: edensgrid
Summary: Electron density grid calculator

Description:
Edensgrid calulcates electron density grids, or difference electron density grids from shelx list 3 fcf files. The grid output is an ascii file.

Changes:

edensgrid-0.3-1.fc12.x86_64 [180 KiB]	Changelog by Pascal Parois (2010-10-11): - software update
edensgrid-0.3-1.fc12.i686 [161 KiB]	Changelog by Pascal Parois (2010-10-11): - software update
edensgrid-0.1-1.fc12.x86_64 [166 KiB]	Changelog by Pascal Parois (2010-09-16): - first public version
edensgrid-0.1-1.fc12.i686 [149 KiB]	Changelog by Pascal Parois (2010-09-16): - first public version

Update: ediffana-0.1-1.fc12

Thu, 16 Sep 2010 13:25:27 +0000

Package: ediffana
Summary: Tool to check the featureless of the difference electron density grids

Description:
Ediffana plot graphs of the distribution of difference electron density values in a grid. It also calculates some statistics to help to check the normality of the distribution.

Changes:

ediffana-0.1-1.fc12.noarch [20 KiB]

Changelog by Pascal Parois (2010-09-16):

- first public version

Update: superflip-20100415-1.fc12

Wed, 12 May 2010 09:38:23 +0000

Package: superflip
Summary: Application of the charge-flipping algorithm

Description:
Superflip is a computer program for application of the charge-flipping algorithm to structure solution of crystal structures from diffraction data. Superflip works in arbitrary dimension and can be therefore used for solution of normal periodic structures, modulated structures and also quasicrystals. Oszlanyi G., Suto A. (2004): Ab initio structure solution by charge flipping, Acta Crystallogr. A60, 134-141

Changes:

superflip-20100415-1.fc12.x86_64 [715 KiB]	Changelog by Pascal (2010-05-12): - Update of superflip to version 15/04/2010
superflip-20100415-1.fc12.i686 [681 KiB]	Changelog by Pascal (2010-05-12): - Update of superflip to version 15/04/2010
superflip-20100226-1.fc12.x86_64 [714 KiB]	Changelog by Pascal (2010-03-18): - Update of superflip to version 26/02/2010 - clen the spec file a bit
superflip-20100226-1.fc12.i386 [680 KiB]	Changelog by Pascal (2010-03-18): - Update of superflip to version 26/02/2010 - clen the spec file a bit
superflip-20090824-1.fc12.x86_64 [725 KiB]	Changelog by Pascal (2009-12-10): - Update of superflip
superflip-20090824-1.fc12.i386 [687 KiB]	Changelog by Pascal (2009-12-10): - Update of superflip
superflip-20090316-1.fc12.i686 [646 KiB]	Changelog by Pascal (2009-04-11): - Update of superflip
superflip-20090316-1.fc12.x86_64 [683 KiB]	Changelog by Pascal (2009-04-11): - Update of superflip

Update: superflip-debuginfo-20100415-1.fc12

Wed, 12 May 2010 09:38:23 +0000

Package: superflip-debuginfo
Summary: Debug information for package superflip

Description:
This package provides debug information for package superflip. Debug information is useful when developing applications that use this package or when debugging this package.

Changes:

superflip-debuginfo-20100415-1.fc12.x86_64 [3 KiB]	Changelog by Pascal (2010-05-12): - Update of superflip to version 15/04/2010
superflip-debuginfo-20100415-1.fc12.i686 [3 KiB]	Changelog by Pascal (2010-05-12): - Update of superflip to version 15/04/2010
superflip-debuginfo-20100226-1.fc12.x86_64 [2 KiB]	Changelog by Pascal (2010-03-18): - Update of superflip to version 26/02/2010 - clen the spec file a bit
superflip-debuginfo-20100226-1.fc12.i386 [2 KiB]	Changelog by Pascal (2010-03-18): - Update of superflip to version 26/02/2010 - clen the spec file a bit

Update: objcryst-fox-1.9.0.2-1.R1215.fc12

Mon, 01 Feb 2010 09:56:52 +0000

Package: objcryst-fox
Summary: Viewing and solving crystal structures from powder diffraction data

Description:
The FOX program was made for the ab initio crystal structure solution from diffraction data (mostly powder diffraction data). Its most interesting features for ab initio structure determination are: * a versatile description of the crystal contents: either isolated atoms, molecules described using a bond length, bond angles and dihedral angles, and polyhedra for inorganic compounds. You can describe your structure by using any combination of groups of atoms, using a chemist's or crystallographer knowledge about the connectivity in your sample to constrain possible solutions; * an automatic correction for special positions and shared atoms between polyhedra, suitable for global optimization algorithms; * the ability to use simultaneously multiple powder patterns (X-rays, neutrons), as well as single crystal data (e.g. extracted from a powder pattern); * smart global optimization algorithms which can get out of false minima; * a graphical interface with a 3D crystal structure view, with live updates during the optimization process. This program can be used also for educational purposes, to show a 3D display of Crystal structures, and the associated powder pattern(s) (see how adding atoms, changing the lattice, or changing the spacegroup affects the powder spectrum and the 3D structure).

Changes:

objcryst-fox-1.9.0.2-1.R1215.fc12.x86_64 [3.2 MiB]	Changelog by Pascal (2010-02-01): - Update to upstream version
objcryst-fox-1.9.0.2-1.R1215.fc12.i386 [3.2 MiB]	Changelog by Pascal (2010-02-01): - Update to upstream version
objcryst-fox-1.9.0.1-1.R1204.fc12.i686 [3.2 MiB]	Changelog by Pascal (2009-11-20): - Update to upstream version
objcryst-fox-1.9.0.1-1.R1204.fc12.x86_64 [3.2 MiB]	Changelog by Pascal (2009-11-20): - Update to upstream version

Update: objcryst-fox-debuginfo-1.9.0.2-1.R1215.fc12

Mon, 01 Feb 2010 09:56:52 +0000

Package: objcryst-fox-debuginfo
Summary: Debug information for package objcryst-fox

Description:
This package provides debug information for package objcryst-fox. Debug information is useful when developing applications that use this package or when debugging this package.

Changes:

objcryst-fox-debuginfo-1.9.0.2-1.R1215.fc12.x86_64 [2 KiB]	Changelog by Pascal (2010-02-01): - Update to upstream version
objcryst-fox-debuginfo-1.9.0.2-1.R1215.fc12.i386 [2 KiB]	Changelog by Pascal (2010-02-01): - Update to upstream version
objcryst-fox-debuginfo-1.9.0.1-1.R1204.fc12.i686 [2 KiB]	Changelog by Pascal (2009-11-20): - Update to upstream version
objcryst-fox-debuginfo-1.9.0.1-1.R1204.fc12.x86_64 [2 KiB]	Changelog by Pascal (2009-11-20): - Update to upstream version

Update: tonto-chem-2.3.20100131svn-1.fc12

Sun, 31 Jan 2010 16:26:38 +0000

Package: tonto-chem
Summary: Tonto is a free package for doing quantum chemistry simulations

Description:
Tonto is a free package for doing quantum chemistry simulations. The main objective of Tonto is to be simple--simple to understand, simple to use, and most importantly, simple to hack. Built using gfortran -O3 -ffast-math -fomit-frame-pointer -ftree-vectorize Tonto-DEFS = -DUSE_ERROR_MANAGEMENT

Changes:

tonto-chem-2.3.20100131svn-1.fc12.x86_64 [6.8 MiB]

Changelog by John (2010-01-31):

- SVN version 3432
- Lots of updates:
- fixed bug in bond angle derivatives
  (swapped b & c)
- added multi_t_adp code (untested)
  and additions for the type
- removed MO symmorthonormalisation on scf restart
- added read vector, matrix from cif file
- added to_outer_product in mat{real}
- removed normalisation factors in cartesian
  rortation code
- adjusted width in accurate output of atoms 
  to a cif
- multi_t_adp compiles without error (untested)
- added some connection routines in vec\{atom}
- contains the stuff that calculates electric dipole for geminal product
  wave functions.
- replaced deprecated -M option with -J
- corrected torsion angle code
- corrected atom label read to convert integer
  atom labels (atomic numbers) to chemical symbol label
- modified tests to work under gfortran
- some relativistic jobs still fail:
- energy_decomposition fails
- corrected minor output changes
- corrected IO file
- new test with read in MOs instead of Hartree-Fock MOs which are
  degenerate
- new input without sp-two-orthogonality and with readin MOs
- directory renamed to be consistent with what the test actually does
- cosmetic changes to geminal product dipole moment calculations and
  energy printout.
- now only copies the actual .bad output files
- added clean up of files and associated minor changes
- added delete: option explanation
- changed to remove scf integrals and MO's
- minor comparison change.
- check to see if output file exists before comparing
- delete added in the IO file
- new test but I forgot the stdout it seems...
- stdout added, delete added in IO
- this test is now hexagonal_H6_GMFCI
- fixed this to cope with multiple failures
  and if output file does not exist
- remove blankls from all input, output, delete files
- minor changes
- added copy output files even for program crash
- removed scg archives at the end
- fixed up atom label processing
- corrected look_for bug requiring a move_to_line
  beforehand to use it
- fixed occ array decl array
- fixed move_to_line(1) text file processing error
  should be fixed more generally in the look_for routines
- fixed up xcrysden plots
- added hirshfeld atom plots

tonto-chem-2.3.20100131svn-1.fc12.i586 [6.5 MiB]

Changelog by John (2010-01-31):

- SVN version 3432
- Lots of updates:
- fixed bug in bond angle derivatives
  (swapped b & c)
- added multi_t_adp code (untested)
  and additions for the type
- removed MO symmorthonormalisation on scf restart
- added read vector, matrix from cif file
- added to_outer_product in mat{real}
- removed normalisation factors in cartesian
  rortation code
- adjusted width in accurate output of atoms 
  to a cif
- multi_t_adp compiles without error (untested)
- added some connection routines in vec\{atom}
- contains the stuff that calculates electric dipole for geminal product
  wave functions.
- replaced deprecated -M option with -J
- corrected torsion angle code
- corrected atom label read to convert integer
  atom labels (atomic numbers) to chemical symbol label
- modified tests to work under gfortran
- some relativistic jobs still fail:
- energy_decomposition fails
- corrected minor output changes
- corrected IO file
- new test with read in MOs instead of Hartree-Fock MOs which are
  degenerate
- new input without sp-two-orthogonality and with readin MOs
- directory renamed to be consistent with what the test actually does
- cosmetic changes to geminal product dipole moment calculations and
  energy printout.
- now only copies the actual .bad output files
- added clean up of files and associated minor changes
- added delete: option explanation
- changed to remove scf integrals and MO's
- minor comparison change.
- check to see if output file exists before comparing
- delete added in the IO file
- new test but I forgot the stdout it seems...
- stdout added, delete added in IO
- this test is now hexagonal_H6_GMFCI
- fixed this to cope with multiple failures
  and if output file does not exist
- remove blankls from all input, output, delete files
- minor changes
- added copy output files even for program crash
- removed scg archives at the end
- fixed up atom label processing
- corrected look_for bug requiring a move_to_line
  beforehand to use it
- fixed occ array decl array
- fixed move_to_line(1) text file processing error
  should be fixed more generally in the look_for routines
- fixed up xcrysden plots
- added hirshfeld atom plots

Update: debroglie-release-12-1.fc12

Fri, 20 Nov 2009 16:46:10 +0000

Package: debroglie-release
Summary: YUM configuration for Debroglie repository

Description:
This package contains yum configuration for the "Debroglie" RPM Repository, as well as the public GPG keys used to sign them.

Changes:

debroglie-release-12-1.fc12.noarch [4 KiB]

Changelog by Pascal Parois (2009-11-20):

- Setup Fedora 12

Update: newmat-11-2.fc12

Fri, 20 Nov 2009 12:37:01 +0000

Package: newmat
Summary: C++ matrix library

Description:
This C++ library is intended for scientists and engineers who need to manipulate a variety of types of matrices using standard matrix operations. Emphasis is on the kind of operations needed in statistical calculations such as least squares, linear equation solve and eigenvalues.

Changes:

newmat-11-2.fc12.x86_64 [179 KiB]	Changelog by Pascal (2009-09-15): - Introduction a SONAME of libnewmat.so.0 using Ralf's patch
newmat-11-2.fc12.i686 [178 KiB]	Changelog by Pascal (2009-09-15): - Introduction a SONAME of libnewmat.so.0 using Ralf's patch

Update: newmat-debuginfo-11-2.fc12

Fri, 20 Nov 2009 12:37:01 +0000

Package: newmat-debuginfo
Summary: Debug information for package newmat

Description:
This package provides debug information for package newmat. Debug information is useful when developing applications that use this package or when debugging this package.

Changes:

newmat-debuginfo-11-2.fc12.x86_64 [350 KiB]	Changelog by Pascal (2009-09-15): - Introduction a SONAME of libnewmat.so.0 using Ralf's patch
newmat-debuginfo-11-2.fc12.i686 [335 KiB]	Changelog by Pascal (2009-09-15): - Introduction a SONAME of libnewmat.so.0 using Ralf's patch

Update: newmat-devel-11-2.fc12

Fri, 20 Nov 2009 12:37:01 +0000

Package: newmat-devel
Summary: Development files for newmat

Description:
The newmat-devel package contains libraries and header files for developing applications that use newmat.

Changes:

newmat-devel-11-2.fc12.x86_64 [31 KiB]	Changelog by Pascal (2009-09-15): - Introduction a SONAME of libnewmat.so.0 using Ralf's patch
newmat-devel-11-2.fc12.i686 [31 KiB]	Changelog by Pascal (2009-09-15): - Introduction a SONAME of libnewmat.so.0 using Ralf's patch

Update: jana-2000-1.fc12

Fri, 20 Nov 2009 12:26:29 +0000

Package: jana
Summary: Structure analysis of crystals periodics from diffraction data

Description:
Jana2006 is a crystallographic program focused to solution, refinement and interpretation of difficult, especially modulated structures. It calculates structures having up to three modulation vectors from powder as well as single crystal data measured with X-ray or neutron diffraction.

Changes:

jana-2000-1.fc12.x86_64 [3.3 MiB]	Changelog by Pascal Parois (2008-10-12): - First spec file
jana-2000-1.fc12.i686 [3.1 MiB]	Changelog by Pascal Parois (2008-10-12): - First spec file

Update: flipsmall-20090610-1.fc12

Fri, 20 Nov 2009 11:28:17 +0000

Package: flipsmall
Summary: Prepares input file for Superflip and EDMA

Description:
Flipsmall (FLIPping for SMALL molecules) is a C-shell script that reads a SHELX-style ins and hkl file, prepares input file for Superflip and EDMA, and runs the programs. The result is an .ins file with the structure that can be directly read by SHLEXL or other software. Flipsmall has been largely written by Arie van der Lee. It has been designed to allow an automated structure solution including the determination of symmetry. It is an ideal tool for quickly getting a solution from Superflip and EDMA, especially for crystallographers that are used to work with SHELX files.

Changes:

flipsmall-20090610-1.fc12.noarch [10 KiB]

Changelog by Pascal (2009-09-16):

- First spec file

Update: EDMA-20090927-1.fc12

Fri, 20 Nov 2009 11:20:31 +0000

Package: EDMA
Summary: Analysis of discrete elecron density maps

Description:
EDMA (Electron Density Map Analysis) is a program for analysis of discrete elecron density maps. It was developed at the University of Bayreuth for analysis of Maximum Entropy maps in arbitrary dimensions as a part of the program suite BayMEM. However, EDMA is also an excellent tool for analysis of other electron density maps, in particular of those obtained by Superflip. Therefore Prof. Sander van Smaalen kindly agreed to make EDMA available for public also separately from the rest of the BayMEM suite. EDMA shares the file format and many keywords with Superflip and therefore it is practical to have only one input file for both Superflip and EDMA. van Smaalen S., Palatinus L., Schneider M. (2003): The Maximum Entropy Method in superspace, Acta Crystallogr. A59, 459-469

Changes:

EDMA-20090927-1.fc12.x86_64 [301 KiB]	Changelog by Pascal (2009-09-27): - Update to upstream version, fixed compilation bug with gcc 4.4
EDMA-20090927-1.fc12.i686 [292 KiB]	Changelog by Pascal (2009-09-27): - Update to upstream version, fixed compilation bug with gcc 4.4