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* Merge branch 'circ_polarizations'Eugeniy Mikhailov2012-11-306-106/+136
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| * completed move of mathematica generated files to includesEugeniy Mikhailov2012-11-283-11/+13
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| * typo in makefileEugeniy Mikhailov2012-11-281-1/+2
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| * Makefile test properly works with included to xmds filesEugeniy Mikhailov2012-11-281-3/+17
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| * now we use proper xml includes in xmds file for generated codeEugeniy Mikhailov2012-11-284-94/+107
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* | move Maxwell distribution from computed vector to just a vectorEugeniy Mikhailov2012-11-271-8/+8
|/ | | | | | | | | | | | | Thanks to suggestion of Graham Dennis, this skip unnecessary calculations of the Maxwell probability distributions at every step since. Thus avoids recalculation. Below the original comment: Your computed_vector's "Maxwell_distribution_probabilities" and "Maxwell_distribution_probabilities_norm" are constant.  If you just change them to be <vector> elements changing the <evaluation> tags to <initialisation> tags, this will ensure that they are not evaluated every time they are needed.
* added code from newly regenerated mathematica->xmds filesEugeniy Mikhailov2012-09-281-113/+93
| | | | | * the main change is presense of the header and footer lines which allows to easily remove add this code at the right amount
* updated test cases since we use new etas separated for each transitionEugeniy Mikhailov2012-09-262-242/+56
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* use of mathematica generated etas normalized to the atomic densityEugeniy Mikhailov2012-09-261-18/+8
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* removed code related to unused density_matrix_averaged vectorEugeniy Mikhailov2012-09-261-112/+0
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* Replace Ec with conj(E) for E1,E2,E3,E4Eugeniy Mikhailov2012-09-261-41/+32
| | | | * this reduces the amount of hand introduced code
* fix typos in commentsEugeniy Mikhailov2012-09-251-2/+2
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* Modified tests callEugeniy Mikhailov2012-09-252-612/+5
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* added test case to the main xmds fileEugeniy Mikhailov2012-09-251-0/+6
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* updated test suite file according to new Mathematica definitionsEugeniy Mikhailov2012-09-251-102/+47
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* heavy use of Hermitian properties in dRho/dt calculationsEugeniy Mikhailov2012-09-251-86/+50
| | | | * also read constants from mathematica generated files
* added test files for simulationsEugeniy Mikhailov2012-09-255-0/+1719
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* Fixed dE/dz equations according to the latest Mathematica fileEugeniy Mikhailov2012-09-241-6/+6
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* added imaginary one to propagation equation into the polarizationEugeniy Mikhailov2012-09-201-4/+4
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* reflect new xmds file name in MakefilesEugeniy Mikhailov2012-09-202-25/+19
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* changed printed figures command to match new octaveEugeniy Mikhailov2012-09-201-0/+99
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* added some notes aboit optimization performanceEugeniy Mikhailov2012-09-061-0/+17
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* First draft of realistic Rb which compiles and runsEugeniy Mikhailov2012-08-211-112/+243
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* changed some substitution to better match our XMDSEugeniy Mikhailov2012-08-215-0/+699