Add Reaction Dynamics to BD Code#19

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sarahsandholtz wants to merge 12 commits intoSpakowitzLab:masterfrom

sarahsandholtz:master

Commits on Aug 18, 2016

First version: tracking methylation profile during BD simulations
sarahsandholtz
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Merge remote-tracking branch 'upstream/master'
sarahsandholtz
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Commits on Aug 20, 2016

fixed bugs: seg faults, i/o issues
Sarah Sandholtz
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Commits on Aug 30, 2016

fixed bugs: declaring variables and passing them between subroutines
sarahsandholtz
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added new variable and updated output to screen
sarahsandholtz
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Commits on Aug 31, 2016

fixed bug in how methylation profile was updated
Sarah Sandholtz
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Commits on Sep 1, 2016

fixed error in selecting site where methyl mark will spread
Sarah Sandholtz
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Commits on Sep 11, 2016

fixed bug with demethylation scheme
Sarah Sandholtz
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Commits on Sep 21, 2016

fixed bugs with modified timestep and demethylation scheme
Sarah Sandholtz
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Commits on Oct 8, 2016

fixed bug with finding which pairs of beads could react; also fixed problems with how to skip MC initialization and with initializing configuration as straight chain
Sarah Sandholtz
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Commits on Oct 10, 2016

moved methyl profile code from Brownian Dynamics subroutine into main simulation
Sarah Sandholtz
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Commits on Oct 26, 2016

Moved methylation algorithm back into BD subroutine; added toggle to turn dynamics on/off
Sarah Sandholtz
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