Add new random number generators - #882

Merged

drroe merged 98 commits into

Amber-MD:masterfrom

Feb 27, 2021

Commits on Feb 19, 2021

Add ABC for random number generators.
drroe
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dbf4f4e
Make rn_set a base class function that can call clock() if needed; then call specific RNG setup SetupRng()
drroe
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310c85c
Add Marsaglia RNG
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8408e6e
Change to Generate()
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a965e93
Change to Set_Seed()
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5012da5
Change to GenerateGauss
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6061980
Make Random_Number an interface
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3963497
Enable interface for RNG
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228872b
Start adding stdlib rng
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973c736
Allocate based on what the current default RNG is
drroe
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8f7fed3

Commits on Feb 20, 2021

Remove unused default rng seed set
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9b87972
Fix variable names
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54b424a
Random routines can be const
drroe
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50296da
Start adding a RNG test
drroe
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655c083
Add random number stream generation compatible with dieharder
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5f136d3
Add test script
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a313e45
Add missing object rule
drroe
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59f67ef
Merge branch 'rng' of github.com:drroe/cpptraj into rng
drroe
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acb3ab9

Commits on Feb 21, 2021

Increase size of the stream. Remove final extra newline.
drroe
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4978deb
Start adding Mersenne twister
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ee5c832
Capture set seed errors
drroe
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3b73467
Enable Mersenne twister
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62621f3
Increase the number of values tested. Add missing depend
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61c2e4a
Redirect results to files for easier comparison
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ae18971
Add a mode to just generate a random integer directly
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e5f4421
Add PCG from Melissa O'Neill
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a933aab
Enable PCG32
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1d23f36
Test the pcg32 implementation
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967e614
First attempt adding xoshiro 128++ rng
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fa8726c
Add Xoshiro 128++ RNG class
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3a85d58
Test new generator
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854dbb9

Commits on Feb 22, 2021

Move Gaussian PRNG to Random
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c77623b
Improve code docs
drroe
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c11855a
Add function to generate random number on an interval
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09be000
Add signed/unsigned versions of interval function
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c07fc4b
Add Fisher Yates shuffle to random
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f510756
Add test for shuffle
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c2173c4
Add description. Add debug mode compile
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50adf87
Move constructor to cpp source
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d410adc
Check for seed error
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e6c3994
Change the way linking is done. Not sure why the other way was giving me memory issues.
drroe
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8e40d37
Print RNG string
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8d27531
Start adding new random command
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80cfdf9
Start adding ability to create data sets
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0d21fd0
Add C11_SUPPORT to defines
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1cdcdea
Start adding rng test
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b0b9f01
Test mersenne twister with c++11 support
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dcbc724
Add help
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8ac226b
Do not list mt as a rng option if no c11 support
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0e9612c
Add missing bracket to help text
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e43213d
Add unsigned integer DataSet type
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efe94b4
Have random use unsigned int set
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a0747d3
Add test saves
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c644183
Add missing comma
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ad1688f
Add float01 mode
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c5ef288
Move RNG change to CpptrajState
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0d8729d
Add --rng command line arg
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19f1f17
Add links for PCG32 and Xoshiro RNGs
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795c23e

Commits on Feb 24, 2021

Add range tests
drroe
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d6d43ca
The Marsaglia generate max is 24 bits, adjust Number() accordingly
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2b3a54b
Allow max to be changed. Calculate average and absolute average
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e5f45aa
Update Marsaglia results for fixed max value
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9bed6f5
Add help text
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c29afd6
Add entry for random command
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9c74129
Set default RNG back to Marsaglia so tests pass.
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86d37ba
Enable random tests. Ensure CPPTRAJ_RNG is exported
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3b0c462

Commits on Feb 25, 2021

Add file which will contain functions that only pytraj needs.
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83d47bd
Rename, make more general
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c12e1fc
Change to ExternalFxn
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5d33202
Convert to c++ file; has c++-like syntax anyway.
Daniel R. Roe
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c7fdc09
Merge remote-tracking branch 'origin/rng' into rng
drroe
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4526c0b
Add URL and note about interface people know I am to blame for that
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1b3fe6e
Go back to Marsaglia as default RNG until more testing can be done.
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85aa639
Replace defunct Travis status with GitHub actions status
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9608eb9
Comment out defaultSeed for now, not used. Change MARSAGLIAS to MARSAGLIA
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b342d44
Remove leading bracket
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e74ca5e
Add actions URL
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0a65a5e
Start adding TestU01 tests
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94cd2ba
Add link options and clean target
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e7fd46e
Do correct C/C++ mixing
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95dbf90
Use main config.h file
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2fe3e65
Use env var
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99b9a21

Commits on Feb 26, 2021

Add volmap volume test
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eb99bf5
Add ability to run regular crush tests
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e0434f6
Add TestU01 results
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11f9146
Add citations for RNG to manual
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2cf09fa
Dont hide evalplateau; published now.
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eebf178
Add evalplateau command to manual. Add citations for volmap speedup and evalplateau.
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bfcebf6
Revision bump for added RNGs, rng command, making evalplateau not hidden. Default RNG not changing yet.
drroe
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154c203
Fix formatting
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30d5f83
Add dieharder results.
drroe
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8284ea2
Do not test volume yet, not ready for prime time.
drroe
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28a8f14
Split out stdlib rand test and do not run on windows, which seems to have a different implementation.
drroe
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bb054d8
Try to fix visual studio compilation by adding some defines.
drroe
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e13a15d
Split off pcg32 test; does not compile for windows
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8dd0f68
PCG32 does not currently compile under visual studio
drroe
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ff4a3d3
Try to fix the tzdata issue with libcpptraj
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3dbdb74

Commits on Feb 27, 2021

Second try to fix tzdata
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29d5ba8