From 2f93b778791b09b09415128699e891ac8f822cf0 Mon Sep 17 00:00:00 2001 From: Daniel Bauer Date: Sat, 24 Oct 2020 20:35:06 +0200 Subject: [PATCH] update rand lib --- Cargo.lock | 69 ++++++++----- Cargo.toml | 2 +- example/1d_cyclic/wham.out | 200 ++++++++++++++++++------------------- src/error_analysis.rs | 2 +- src/main.rs | 2 +- 5 files changed, 148 insertions(+), 127 deletions(-) diff --git a/Cargo.lock b/Cargo.lock index 4d80ba9..10ea738 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -106,15 +106,6 @@ dependencies = [ "yaml-rust", ] -[[package]] -name = "cloudabi" -version = "0.0.3" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "ddfc5b9aa5d4507acaf872de71051dfd0e309860e88966e1051e462a077aac4f" -dependencies = [ - "bitflags", -] - [[package]] name = "crossbeam-channel" version = "0.4.4" @@ -179,10 +170,15 @@ dependencies = [ ] [[package]] -name = "fuchsia-cprng" -version = "0.1.1" +name = "getrandom" +version = "0.1.15" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "a06f77d526c1a601b7c4cdd98f54b5eaabffc14d5f2f0296febdc7f357c6d3ba" +checksum = "fc587bc0ec293155d5bfa6b9891ec18a1e330c234f896ea47fbada4cadbe47e6" +dependencies = [ + "cfg-if", + "libc", + "wasi", +] [[package]] name = "gimli" @@ -258,33 +254,52 @@ version = "0.3.18" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "d36492546b6af1463394d46f0c834346f31548646f6ba10849802c9c9a27ac33" +[[package]] +name = "ppv-lite86" +version = "0.2.9" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "c36fa947111f5c62a733b652544dd0016a43ce89619538a8ef92724a6f501a20" + [[package]] name = "rand" -version = "0.5.6" +version = "0.7.3" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "c618c47cd3ebd209790115ab837de41425723956ad3ce2e6a7f09890947cacb9" +checksum = "6a6b1679d49b24bbfe0c803429aa1874472f50d9b363131f0e89fc356b544d03" dependencies = [ - "cloudabi", - "fuchsia-cprng", + "getrandom", "libc", - "rand_core 0.3.1", - "winapi", + "rand_chacha", + "rand_core", + "rand_hc", ] [[package]] -name = "rand_core" -version = "0.3.1" +name = "rand_chacha" +version = "0.2.2" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "7a6fdeb83b075e8266dcc8762c22776f6877a63111121f5f8c7411e5be7eed4b" +checksum = "f4c8ed856279c9737206bf725bf36935d8666ead7aa69b52be55af369d193402" dependencies = [ - "rand_core 0.4.2", + "ppv-lite86", + "rand_core", ] [[package]] name = "rand_core" -version = "0.4.2" +version = "0.5.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "9c33a3c44ca05fa6f1807d8e6743f3824e8509beca625669633be0acbdf509dc" +checksum = "90bde5296fc891b0cef12a6d03ddccc162ce7b2aff54160af9338f8d40df6d19" +dependencies = [ + "getrandom", +] + +[[package]] +name = "rand_hc" +version = "0.2.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "ca3129af7b92a17112d59ad498c6f81eaf463253766b90396d39ea7a39d6613c" +dependencies = [ + "rand_core", +] [[package]] name = "rayon" @@ -356,6 +371,12 @@ version = "0.9.2" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "b5a972e5669d67ba988ce3dc826706fb0a8b01471c088cb0b6110b805cc36aed" +[[package]] +name = "wasi" +version = "0.9.0+wasi-snapshot-preview1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "cccddf32554fecc6acb585f82a32a72e28b48f8c4c1883ddfeeeaa96f7d8e519" + [[package]] name = "wham" version = "0.9.8" diff --git a/Cargo.toml b/Cargo.toml index da78b18..5b36ded 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -12,7 +12,7 @@ keywords = ["math", "statistics", "histogram", "bioinformatics", "molecular-dyna [dependencies] clap = {version="2.32.0", features=['yaml']} error-chain = "0.12.0" -rand = "0.5.5" +rand = "0.7.*" GSL = "1.1" rayon = "1.0.3" diff --git a/example/1d_cyclic/wham.out b/example/1d_cyclic/wham.out index 5e12e07..8c82afe 100644 --- a/example/1d_cyclic/wham.out +++ b/example/1d_cyclic/wham.out @@ -1,101 +1,101 @@ #coord1 Free Energy +/- Probability +/- --3.110177 7.158102 0.069244 0.003494 0.000067 --3.047345 5.365727 0.068503 0.007168 0.000135 --2.984513 3.873190 0.065883 0.013039 0.000226 --2.921681 2.953162 0.066856 0.018855 0.000334 --2.858849 1.949554 0.066705 0.028195 0.000501 --2.796017 1.391747 0.064012 0.035261 0.000576 --2.733186 1.128270 0.061522 0.039189 0.000598 --2.670354 0.839970 0.060810 0.043991 0.000653 --2.607522 0.624769 0.061888 0.047955 0.000733 --2.544690 0.663757 0.062566 0.047211 0.000736 --2.481858 1.051932 0.061093 0.040407 0.000616 --2.419026 1.463048 0.062547 0.034267 0.000543 --2.356194 1.990616 0.057022 0.027734 0.000373 --2.293363 2.190692 0.044029 0.025597 0.000202 --2.230531 2.553036 0.041867 0.022136 0.000157 --2.167699 2.572522 0.044817 0.021964 0.000184 --2.104867 2.472360 0.038778 0.022863 0.000155 --2.042035 2.517562 0.030296 0.022453 0.000150 --1.979203 2.469778 0.025852 0.022887 0.000167 --1.916372 2.223125 0.030799 0.025266 0.000411 --1.853540 2.080157 0.024928 0.026756 0.000365 --1.790708 1.793841 0.027529 0.030011 0.000475 --1.727876 1.458784 0.026130 0.034326 0.000462 --1.665044 0.914441 0.024774 0.042697 0.000576 --1.602212 0.303813 0.020400 0.054540 0.000701 --1.539380 0.268335 0.020423 0.055321 0.000733 --1.476549 0.000000 0.020271 0.061604 0.000835 --1.413717 0.537061 0.023895 0.049671 0.000735 --1.350885 1.439940 0.023678 0.034586 0.000528 --1.288053 2.391838 0.025951 0.023614 0.000386 --1.225221 3.779470 0.026215 0.013538 0.000224 --1.162389 5.685555 0.028543 0.006305 0.000109 --1.099557 7.661896 0.030579 0.002855 0.000051 --1.036726 9.946594 0.039243 0.001142 0.000022 --0.973894 12.359408 0.054067 0.000434 0.000009 --0.911062 14.954655 0.066597 0.000153 0.000004 --0.848230 17.742242 0.073582 0.000050 0.000002 --0.785398 20.555785 0.074644 0.000016 0.000001 --0.722566 22.811160 0.078503 0.000007 0.000000 --0.659734 25.178094 0.088961 0.000003 0.000000 --0.596903 26.442288 0.093509 0.000002 0.000000 --0.534071 27.897565 0.091353 0.000001 0.000000 --0.471239 29.062473 0.086244 0.000001 0.000000 --0.408407 30.384521 0.084285 0.000000 0.000000 --0.345575 31.638454 0.084871 0.000000 0.000000 --0.282743 32.817727 0.092750 0.000000 0.000000 --0.219911 33.770369 0.094479 0.000000 0.000000 --0.157080 34.505503 0.095774 0.000000 0.000000 --0.094248 35.431659 0.107598 0.000000 0.000000 --0.031416 35.615810 0.108959 0.000000 0.000000 -0.031416 35.561946 0.107382 0.000000 0.000000 -0.094248 35.382089 0.096643 0.000000 0.000000 -0.157080 34.934827 0.107624 0.000000 0.000000 -0.219911 33.673460 0.100231 0.000000 0.000000 -0.282743 32.731563 0.096604 0.000000 0.000000 -0.345575 31.261855 0.099036 0.000000 0.000000 -0.408407 29.717377 0.107915 0.000000 0.000000 -0.471239 28.076620 0.104513 0.000001 0.000000 -0.534071 26.481097 0.103164 0.000002 0.000000 -0.596903 24.487358 0.103039 0.000003 0.000000 -0.659734 22.344251 0.100666 0.000008 0.000000 -0.722566 20.241543 0.102150 0.000018 0.000001 -0.785398 18.341869 0.101957 0.000039 0.000002 -0.848230 16.261582 0.105391 0.000091 0.000005 -0.911062 14.301801 0.107389 0.000199 0.000010 -0.973894 12.603788 0.105487 0.000394 0.000020 -1.036726 11.249601 0.106308 0.000678 0.000035 -1.099557 10.087886 0.106741 0.001079 0.000055 -1.162389 9.443303 0.106957 0.001398 0.000071 -1.225221 9.152799 0.105940 0.001570 0.000079 -1.288053 9.331937 0.105860 0.001462 0.000074 -1.350885 9.905546 0.105389 0.001161 0.000058 -1.413717 11.042050 0.105466 0.000736 0.000037 -1.476549 12.598167 0.105119 0.000395 0.000020 -1.539380 14.520167 0.104367 0.000183 0.000009 -1.602212 16.569783 0.104184 0.000080 0.000004 -1.665044 18.687390 0.104276 0.000034 0.000002 -1.727876 20.775408 0.104944 0.000015 0.000001 -1.790708 22.905200 0.101547 0.000006 0.000000 -1.853540 24.643852 0.103914 0.000003 0.000000 -1.916372 26.301740 0.101973 0.000002 0.000000 -1.979203 27.372071 0.101762 0.000001 0.000000 -2.042035 28.697726 0.105177 0.000001 0.000000 -2.104867 29.417901 0.100003 0.000000 0.000000 -2.167699 30.008351 0.100038 0.000000 0.000000 -2.230531 30.406016 0.096233 0.000000 0.000000 -2.293363 30.171275 0.096428 0.000000 0.000000 -2.356194 29.884646 0.108339 0.000000 0.000000 -2.419026 29.428153 0.106679 0.000000 0.000000 -2.481858 28.546982 0.123259 0.000001 0.000000 -2.544690 27.757520 0.108526 0.000001 0.000000 -2.607522 26.505787 0.111134 0.000001 0.000000 -2.670354 24.491866 0.095963 0.000003 0.000000 -2.733186 22.320664 0.096576 0.000008 0.000000 -2.796017 20.052723 0.098813 0.000020 0.000001 -2.858849 17.655650 0.097052 0.000052 0.000002 -2.921681 15.471590 0.100497 0.000125 0.000005 -2.984513 13.138167 0.092102 0.000318 0.000011 -3.047345 11.092386 0.081862 0.000722 0.000020 -3.110177 9.065722 0.072111 0.001626 0.000034 +-3.110177 7.158102 0.071438 0.003494 0.000068 +-3.047345 5.365727 0.069449 0.007168 0.000135 +-2.984513 3.873190 0.067495 0.013039 0.000232 +-2.921681 2.953162 0.067589 0.018855 0.000343 +-2.858849 1.949554 0.064640 0.028195 0.000480 +-2.796017 1.391747 0.063570 0.035261 0.000584 +-2.733186 1.128270 0.061710 0.039189 0.000620 +-2.670354 0.839970 0.060445 0.043991 0.000667 +-2.607522 0.624769 0.060762 0.047955 0.000739 +-2.544690 0.663757 0.060786 0.047211 0.000731 +-2.481858 1.051932 0.059774 0.040407 0.000617 +-2.419026 1.463048 0.060422 0.034267 0.000527 +-2.356194 1.990616 0.055242 0.027734 0.000360 +-2.293363 2.190692 0.044458 0.025597 0.000210 +-2.230531 2.553036 0.042144 0.022136 0.000159 +-2.167699 2.572522 0.043313 0.021964 0.000165 +-2.104867 2.472360 0.039799 0.022863 0.000157 +-2.042035 2.517562 0.036792 0.022453 0.000203 +-1.979203 2.469778 0.036324 0.022887 0.000237 +-1.916372 2.223125 0.049496 0.025266 0.000565 +-1.853540 2.080157 0.039205 0.026756 0.000453 +-1.790708 1.793841 0.041488 0.030011 0.000558 +-1.727876 1.458784 0.042362 0.034326 0.000565 +-1.665044 0.914441 0.037561 0.042697 0.000682 +-1.602212 0.303813 0.028701 0.054540 0.000761 +-1.539380 0.268335 0.025765 0.055321 0.000771 +-1.476549 0.000000 0.023371 0.061604 0.000866 +-1.413717 0.537061 0.026370 0.049671 0.000715 +-1.350885 1.439940 0.025620 0.034586 0.000547 +-1.288053 2.391838 0.027653 0.023614 0.000393 +-1.225221 3.779470 0.027093 0.013538 0.000229 +-1.162389 5.685555 0.027762 0.006305 0.000111 +-1.099557 7.661896 0.028996 0.002855 0.000051 +-1.036726 9.946594 0.032118 0.001142 0.000021 +-0.973894 12.359408 0.042801 0.000434 0.000009 +-0.911062 14.954655 0.052443 0.000153 0.000004 +-0.848230 17.742242 0.063261 0.000050 0.000002 +-0.785398 20.555785 0.068133 0.000016 0.000001 +-0.722566 22.811160 0.075518 0.000007 0.000000 +-0.659734 25.178094 0.086226 0.000003 0.000000 +-0.596903 26.442288 0.091783 0.000002 0.000000 +-0.534071 27.897565 0.093175 0.000001 0.000000 +-0.471239 29.062473 0.096027 0.000001 0.000000 +-0.408407 30.384521 0.096855 0.000000 0.000000 +-0.345575 31.638454 0.099956 0.000000 0.000000 +-0.282743 32.817727 0.107689 0.000000 0.000000 +-0.219911 33.770369 0.108946 0.000000 0.000000 +-0.157080 34.505503 0.112902 0.000000 0.000000 +-0.094248 35.431659 0.120856 0.000000 0.000000 +-0.031416 35.615810 0.122046 0.000000 0.000000 +0.031416 35.561946 0.118225 0.000000 0.000000 +0.094248 35.382089 0.108652 0.000000 0.000000 +0.157080 34.934827 0.118384 0.000000 0.000000 +0.219911 33.673460 0.119195 0.000000 0.000000 +0.282743 32.731563 0.121592 0.000000 0.000000 +0.345575 31.261855 0.129698 0.000000 0.000000 +0.408407 29.717377 0.139789 0.000000 0.000000 +0.471239 28.076620 0.137289 0.000001 0.000000 +0.534071 26.481097 0.135712 0.000002 0.000000 +0.596903 24.487358 0.135156 0.000003 0.000000 +0.659734 22.344251 0.131027 0.000008 0.000000 +0.722566 20.241543 0.133145 0.000018 0.000001 +0.785398 18.341869 0.131952 0.000039 0.000002 +0.848230 16.261582 0.134676 0.000091 0.000006 +0.911062 14.301801 0.134417 0.000199 0.000013 +0.973894 12.603788 0.131018 0.000394 0.000024 +1.036726 11.249601 0.131276 0.000678 0.000043 +1.099557 10.087886 0.132498 0.001079 0.000070 +1.162389 9.443303 0.132990 0.001398 0.000092 +1.225221 9.152799 0.132250 0.001570 0.000104 +1.288053 9.331937 0.133178 0.001462 0.000099 +1.350885 9.905546 0.133357 0.001161 0.000078 +1.413717 11.042050 0.133807 0.000736 0.000051 +1.476549 12.598167 0.132722 0.000395 0.000027 +1.539380 14.520167 0.131816 0.000183 0.000012 +1.602212 16.569783 0.131773 0.000080 0.000005 +1.665044 18.687390 0.132601 0.000034 0.000002 +1.727876 20.775408 0.133867 0.000015 0.000001 +1.790708 22.905200 0.129265 0.000006 0.000000 +1.853540 24.643852 0.128894 0.000003 0.000000 +1.916372 26.301740 0.130266 0.000002 0.000000 +1.979203 27.372071 0.128620 0.000001 0.000000 +2.042035 28.697726 0.133263 0.000001 0.000000 +2.104867 29.417901 0.133513 0.000000 0.000000 +2.167699 30.008351 0.130925 0.000000 0.000000 +2.230531 30.406016 0.124398 0.000000 0.000000 +2.293363 30.171275 0.122493 0.000000 0.000000 +2.356194 29.884646 0.130278 0.000000 0.000000 +2.419026 29.428153 0.130844 0.000000 0.000000 +2.481858 28.546982 0.148114 0.000001 0.000000 +2.544690 27.757520 0.133045 0.000001 0.000000 +2.607522 26.505787 0.134364 0.000001 0.000000 +2.670354 24.491866 0.115061 0.000003 0.000000 +2.733186 22.320664 0.110036 0.000008 0.000000 +2.796017 20.052723 0.107894 0.000020 0.000001 +2.858849 17.655650 0.105964 0.000052 0.000002 +2.921681 15.471590 0.107005 0.000125 0.000005 +2.984513 13.138167 0.099378 0.000318 0.000012 +3.047345 11.092386 0.087770 0.000722 0.000022 +3.110177 9.065722 0.077092 0.001626 0.000038 diff --git a/src/error_analysis.rs b/src/error_analysis.rs index 1cce049..ce8bb9e 100644 --- a/src/error_analysis.rs +++ b/src/error_analysis.rs @@ -1,4 +1,4 @@ -use rand::{SeedableRng, StdRng, Rng}; +use rand::prelude::*; use super::histogram::{Dataset}; use super::perform_wham; use super::{Config,calc_free_energy}; diff --git a/src/main.rs b/src/main.rs index 913fa05..6764e7a 100644 --- a/src/main.rs +++ b/src/main.rs @@ -3,6 +3,7 @@ extern crate wham; extern crate clap; extern crate rand; +use rand::prelude::*; use clap::App; use wham::Config; use wham::errors::*; @@ -49,7 +50,6 @@ fn cli() -> Result { .chain_err(|| "Cannot parse bootstrap iteration.")?; let bootstrap_seed: u64 = matches.value_of("bootstrap_seed") .unwrap_or({ - use rand::Rng; let mut rng = rand::thread_rng(); &rng.gen::().to_string() }).parse()