fixed allot of warnings, and adde the molecule

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starting work on the molecule class

starting to add in the molecule class

the final copy went out this morning. YAYYYYYYYYY!!!!!!!!!!!!!!!

added a bunch of igures

finished the revisions of the first draft

now only lacks a complete results section, and a future Directions section

added command line arguments, and a time smoother

fixed a cosCorr and GofR flag bug, as well as the GofR scaling bug.

made some changes to the Makefile, and added the sections I think I should write

additions to the lipid model

added the ssd figure

just writing, not much editing yet

my Canidacy paper

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VS: ----------------------------------------------------------------------
added more figures, and fixed the slides. GFave a practice talk 6-16-02 with this.

fixed somebugs with start frame

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I think I have most of it the way I like it, just need to change the correlation functions, and the final pictures

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changed some of the figures, and put some more polish on the intro

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made a new figure. trying to add it to the slide

switched in Chuck's magic slide enviroment

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fixed the Makefile

getting there. Most everything but the motivation slide has been filled out. Lacks only pictures and Diagrams.

made some changes

Matt's canidacy presentation

little utility for catting together dump files.

got the GofR code working, and slimmed down the memory usage.

finished working on the command line options, and started working on the GofR

made a header directory, and fixed the Makefile to work with it

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fixed the ordering on the end of file test

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cleaned up the output a little

fixed a bug in getA( double the_A[3][3] );

adding the routines to the proogram
`

fixed some bugs in the Makefile

fixed a precision error in the calculation of the temperature.
Also fixed the order that dump file are written.

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nose hoover chains added

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initial checkin

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