8000 Add TICA, max/min distance calc, and data projection commands by drroe · Pull Request #1075 · Amber-MD/cpptraj · GitHub

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Add TICA, max/min distance calc, and data projection commands#1075

Merged

drroe merged 200 commits intoAmber-MD:masterfrom

Apr 25, 2024

Commits on Mar 26, 2024

Another reorganization since full covar array needs separate
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Commits on Mar 29, 2024

Commits on Apr 1, 2024

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Commits on Apr 5, 2024

Use typedef
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Commits on Apr 8, 2024

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Commits on Apr 11, 2024

Start thinking about how to implement the general eigenvalue calc
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Commits on Apr 13, 2024

Commits on Apr 15, 2024

Commits on Apr 16, 2024

Ensure avg coords are set for TICA modes
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If precision of file is set/reset, indicate file needs to be written
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Add cumulative variance calculation
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Commits on Apr 17, 2024

Commits on Apr 18, 2024

Start new function to calculate matrices in a single pass
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Change var
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Do XXYY matrix
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Further simplify the calculation
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Slight reorganize
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Calculate means in a single pass
Daniel R. Roe
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Reorganize new functions into a separate umbrella function
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Normalize matrices in new function
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Put the TICA modes calculation in its own function
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Switch to the new function
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Put all the debug print functions in the same location
Daniel R. Roe
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Reorganize so that old functions are all grouped together
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Add sum for periodic sets
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Start COORDS set sum calc
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Add sum for COORDS sets
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Check if data sets are periodic
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Commits on Apr 23, 2024

Commits on Apr 24, 2024

Commits on Apr 25, 2024

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