mirror of
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Compare commits
10 Commits
| Author | SHA1 | Date | |
|---|---|---|---|
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7b39d603bd | ||
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5390b089ac |
3
.gitignore
vendored
3
.gitignore
vendored
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target
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target
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reference
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reference
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.idea
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.idea
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*bench.*
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*bench.*
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*.sublime*
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183
Cargo.lock
generated
183
Cargo.lock
generated
@@ -11,6 +11,21 @@ dependencies = [
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|||||||
"pkg-config",
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"pkg-config",
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]
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]
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||||||
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||||||
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[[package]]
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||||||
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name = "addr2line"
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||||||
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version = "0.13.0"
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||||||
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source = "registry+https://github.com/rust-lang/crates.io-index"
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||||||
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checksum = "1b6a2d3371669ab3ca9797670853d61402b03d0b4b9ebf33d677dfa720203072"
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||||||
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dependencies = [
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||||||
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"gimli",
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||||||
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]
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||||||
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[[package]]
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name = "adler"
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version = "0.2.3"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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||||||
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checksum = "ee2a4ec343196209d6594e19543ae87a39f96d5534d7174822a3ad825dd6ed7e"
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||||||
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||||||
[[package]]
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[[package]]
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||||||
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name = "ansi_term"
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@@ -20,6 +35,12 @@ dependencies = [
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|||||||
"winapi",
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"winapi",
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]
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]
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[[package]]
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||||||
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||||||
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||||||
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||||||
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@@ -33,32 +54,24 @@ dependencies = [
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[[package]]
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[[package]]
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||||||
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[[package]]
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[[package]]
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checksum = "ad235dabf00f36301792cfe82499880ba54c6486be094d1047b02bacb67c14e8"
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dependencies = [
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dependencies = [
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"backtrace-sys",
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"addr2line",
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"cfg-if",
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"cfg-if",
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"libc",
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"libc",
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"miniz_oxide",
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"object",
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"rustc-demangle",
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"rustc-demangle",
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]
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||||||
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||||||
[[package]]
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||||||
name = "backtrace-sys"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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dependencies = [
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"cc",
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"libc",
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]
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[[package]]
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[[package]]
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@@ -71,12 +84,6 @@ version = "1.0.12"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "aa9e1d9f7d49e289f36f19effbf3d5a5e30163ecf9c7a3c9be94d5374dec5b9a"
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checksum = "aa9e1d9f7d49e289f36f19effbf3d5a5e30163ecf9c7a3c9be94d5374dec5b9a"
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||||||
[[package]]
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||||||
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "95e28fa049fda1c330bcf9d723be7663a899c4679724b34c81e9f5a326aab8cd"
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[[package]]
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[[package]]
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@@ -85,9 +92,9 @@ checksum = "4785bdd1c96b2a846b2bd7cc02e86b6b3dbf14e7e53446c4f54c92a361040822"
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|||||||
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||||||
[[package]]
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[[package]]
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||||||
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||||||
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||||||
source = "registry+https://github.com/rust-lang/crates.io-index"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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||||||
checksum = "5067f5bb2d80ef5d68b4c87db81601f0b75bca627bc2ef76b141d7b846a3c6d9"
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||||||
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dependencies = [
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||||||
"ansi_term",
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"ansi_term",
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"atty",
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"atty",
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@@ -108,6 +115,16 @@ dependencies = [
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"bitflags",
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"bitflags",
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||||||
]
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]
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||||||
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||||||
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[[package]]
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||||||
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name = "crossbeam-channel"
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||||||
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version = "0.4.4"
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||||||
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source = "registry+https://github.com/rust-lang/crates.io-index"
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||||||
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checksum = "b153fe7cbef478c567df0f972e02e6d736db11affe43dfc9c56a9374d1adfb87"
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||||||
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dependencies = [
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||||||
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"crossbeam-utils",
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||||||
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"maybe-uninit",
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||||||
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]
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[[package]]
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[[package]]
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||||||
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name = "crossbeam-deque"
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version = "0.7.3"
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@@ -134,16 +151,6 @@ dependencies = [
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"scopeguard",
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"scopeguard",
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||||||
]
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]
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||||||
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||||||
[[package]]
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||||||
name = "crossbeam-queue"
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||||||
version = "0.2.1"
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||||||
source = "registry+https://github.com/rust-lang/crates.io-index"
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||||||
checksum = "c695eeca1e7173472a32221542ae469b3e9aac3a4fc81f7696bcad82029493db"
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||||||
dependencies = [
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||||||
"cfg-if",
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"crossbeam-utils",
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]
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||||||
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[[package]]
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[[package]]
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||||||
name = "crossbeam-utils"
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name = "crossbeam-utils"
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||||||
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@@ -157,15 +164,15 @@ dependencies = [
|
|||||||
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||||||
[[package]]
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[[package]]
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||||||
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name = "either"
|
||||||
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|
||||||
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||||||
checksum = "bb1f6b1ce1c140482ea30ddd3335fc0024ac7ee112895426e0a629a6c20adfe3"
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checksum = "cd56b59865bce947ac5958779cfa508f6c3b9497cc762b7e24a12d11ccde2c4f"
|
||||||
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||||||
[[package]]
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[[package]]
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||||||
name = "error-chain"
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|
||||||
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version = "0.12.4"
|
||||||
source = "registry+https://github.com/rust-lang/crates.io-index"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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||||||
checksum = "d371106cc88ffdfb1eabd7111e432da544f16f3e2d7bf1dfe8bf575f1df045cd"
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||||||
dependencies = [
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|
||||||
"backtrace",
|
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|
||||||
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"version_check",
|
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@@ -178,10 +185,16 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
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|
|
||||||
[[package]]
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[[package]]
|
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|
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checksum = "1010591b26bbfe835e9faeabeb11866061cc7dcebffd56ad7d0942d0e61aefd8"
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checksum = "aaf91faf136cb47367fa430cd46e37a788775e7fa104f8b4bcb3861dc389b724"
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[[package]]
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@@ -194,9 +207,9 @@ checksum = "e2abad23fbc42b3700f2f279844dc832adb2b2eb069b2df918f455c4e18cc646"
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|||||||
|
|
||||||
[[package]]
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|
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||||||
[[package]]
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@@ -206,28 +219,44 @@ checksum = "60302e4db3a61da70c0cb7991976248362f30319e88850c487b9b95bbf059e00"
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|
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|
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||||||
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|
||||||
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"adler",
|
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"autocfg",
|
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|
||||||
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|
||||||
[[package]]
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|
||||||
"hermit-abi",
|
"hermit-abi",
|
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"libc",
|
"libc",
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|
||||||
|
|
||||||
[[package]]
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[[package]]
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|
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|
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@@ -259,10 +288,11 @@ checksum = "9c33a3c44ca05fa6f1807d8e6743f3824e8509beca625669633be0acbdf509dc"
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"either",
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"rayon-core",
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@@ -270,12 +300,12 @@ dependencies = [
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|||||||
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"crossbeam-deque",
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"crossbeam-queue",
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@@ -287,36 +317,12 @@ version = "0.1.16"
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||||||
[[package]]
|
[[package]]
|
||||||
name = "scopeguard"
|
name = "scopeguard"
|
||||||
version = "1.1.0"
|
version = "1.1.0"
|
||||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||||
checksum = "d29ab0c6d3fc0ee92fe66e2d99f700eab17a8d57d1c1d3b748380fb20baa78cd"
|
checksum = "d29ab0c6d3fc0ee92fe66e2d99f700eab17a8d57d1c1d3b748380fb20baa78cd"
|
||||||
|
|
||||||
[[package]]
|
|
||||||
name = "semver"
|
|
||||||
version = "0.9.0"
|
|
||||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
||||||
checksum = "1d7eb9ef2c18661902cc47e535f9bc51b78acd254da71d375c2f6720d9a40403"
|
|
||||||
dependencies = [
|
|
||||||
"semver-parser",
|
|
||||||
]
|
|
||||||
|
|
||||||
[[package]]
|
|
||||||
name = "semver-parser"
|
|
||||||
version = "0.7.0"
|
|
||||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
||||||
checksum = "388a1df253eca08550bef6c72392cfe7c30914bf41df5269b68cbd6ff8f570a3"
|
|
||||||
|
|
||||||
[[package]]
|
[[package]]
|
||||||
name = "strsim"
|
name = "strsim"
|
||||||
version = "0.8.0"
|
version = "0.8.0"
|
||||||
@@ -334,27 +340,28 @@ dependencies = [
|
|||||||
|
|
||||||
[[package]]
|
[[package]]
|
||||||
name = "unicode-width"
|
name = "unicode-width"
|
||||||
version = "0.1.7"
|
version = "0.1.8"
|
||||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||||
checksum = "caaa9d531767d1ff2150b9332433f32a24622147e5ebb1f26409d5da67afd479"
|
checksum = "9337591893a19b88d8d87f2cec1e73fad5cdfd10e5a6f349f498ad6ea2ffb1e3"
|
||||||
|
|
||||||
[[package]]
|
[[package]]
|
||||||
name = "vec_map"
|
name = "vec_map"
|
||||||
version = "0.8.1"
|
version = "0.8.2"
|
||||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||||
checksum = "05c78687fb1a80548ae3250346c3db86a80a7cdd77bda190189f2d0a0987c81a"
|
checksum = "f1bddf1187be692e79c5ffeab891132dfb0f236ed36a43c7ed39f1165ee20191"
|
||||||
|
|
||||||
[[package]]
|
[[package]]
|
||||||
name = "version_check"
|
name = "version_check"
|
||||||
version = "0.9.1"
|
version = "0.9.2"
|
||||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||||
checksum = "078775d0255232fb988e6fccf26ddc9d1ac274299aaedcedce21c6f72cc533ce"
|
checksum = "b5a972e5669d67ba988ce3dc826706fb0a8b01471c088cb0b6110b805cc36aed"
|
||||||
|
|
||||||
[[package]]
|
[[package]]
|
||||||
name = "wham"
|
name = "wham"
|
||||||
version = "0.9.6"
|
version = "0.9.8"
|
||||||
dependencies = [
|
dependencies = [
|
||||||
"GSL",
|
"GSL",
|
||||||
|
"assert_approx_eq",
|
||||||
"clap",
|
"clap",
|
||||||
"error-chain",
|
"error-chain",
|
||||||
"rand",
|
"rand",
|
||||||
@@ -363,9 +370,9 @@ dependencies = [
|
|||||||
|
|
||||||
[[package]]
|
[[package]]
|
||||||
name = "winapi"
|
name = "winapi"
|
||||||
version = "0.3.8"
|
version = "0.3.9"
|
||||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||||
checksum = "8093091eeb260906a183e6ae1abdba2ef5ef2257a21801128899c3fc699229c6"
|
checksum = "5c839a674fcd7a98952e593242ea400abe93992746761e38641405d28b00f419"
|
||||||
dependencies = [
|
dependencies = [
|
||||||
"winapi-i686-pc-windows-gnu",
|
"winapi-i686-pc-windows-gnu",
|
||||||
"winapi-x86_64-pc-windows-gnu",
|
"winapi-x86_64-pc-windows-gnu",
|
||||||
|
|||||||
@@ -1,6 +1,6 @@
|
|||||||
[package]
|
[package]
|
||||||
name = "wham"
|
name = "wham"
|
||||||
version = "0.9.6"
|
version = "0.9.8"
|
||||||
authors = ["Daniel Bauer <bauer@cbs.tu-darmstadt.de>"]
|
authors = ["Daniel Bauer <bauer@cbs.tu-darmstadt.de>"]
|
||||||
description = "An implementation of the weighted histogram analysis method"
|
description = "An implementation of the weighted histogram analysis method"
|
||||||
license = "GPL-3.0"
|
license = "GPL-3.0"
|
||||||
@@ -13,6 +13,9 @@ rand = "0.5.5"
|
|||||||
GSL = "1.0.0"
|
GSL = "1.0.0"
|
||||||
rayon = "1.0.3"
|
rayon = "1.0.3"
|
||||||
|
|
||||||
|
[dev-dependencies]
|
||||||
|
assert_approx_eq = "1.1.0"
|
||||||
|
|
||||||
[profile.release]
|
[profile.release]
|
||||||
opt-level = 2
|
opt-level = 2
|
||||||
|
|
||||||
|
|||||||
@@ -81,8 +81,8 @@ one can estimate the error as standard deviation between the N bootstrapping run
|
|||||||
Autocorrelation Estimates, JCTC, 6(12), 3713-3720*.
|
Autocorrelation Estimates, JCTC, 6(12), 3713-3720*.
|
||||||
|
|
||||||
To perform bayesian bootstrapping in WHAM, use the ```-bt <RUNS>``` flag to perform <RUNS> individual bootstrapping
|
To perform bayesian bootstrapping in WHAM, use the ```-bt <RUNS>``` flag to perform <RUNS> individual bootstrapping
|
||||||
runs. The error estimates of bin probabilities and free energy will be given as separate column (+/-) in the output file.
|
runs. The error estimates of bin probabilities and free energy will be given as standard error (SE) in a
|
||||||
If no error analysis is performed, these columns are set to 0.0.
|
separate column (+/-) in the output file. If no error analysis is performed, these columns are set to 0.0.
|
||||||
|
|
||||||
Examples
|
Examples
|
||||||
---
|
---
|
||||||
|
|||||||
@@ -1,101 +1,101 @@
|
|||||||
#coord1 Free Energy +/- Probability +/-
|
#coord1 Free Energy +/- Probability +/-
|
||||||
-3.110177 7.158102 0.476037 0.003494 0.000667
|
-3.110177 7.158102 0.069244 0.003494 0.000067
|
||||||
-3.047345 5.365727 0.470738 0.007168 0.001353
|
-3.047345 5.365727 0.068503 0.007168 0.000135
|
||||||
-2.984513 3.873190 0.433120 0.013039 0.002264
|
-2.984513 3.873190 0.065883 0.013039 0.000226
|
||||||
-2.921681 2.953162 0.441412 0.018855 0.003337
|
-2.921681 2.953162 0.066856 0.018855 0.000334
|
||||||
-2.858849 1.949554 0.443549 0.028195 0.005014
|
-2.858849 1.949554 0.066705 0.028195 0.000501
|
||||||
-2.796017 1.391747 0.407397 0.035261 0.005759
|
-2.796017 1.391747 0.064012 0.035261 0.000576
|
||||||
-2.733186 1.128270 0.380789 0.039189 0.005983
|
-2.733186 1.128270 0.061522 0.039189 0.000598
|
||||||
-2.670354 0.839970 0.370008 0.043991 0.006526
|
-2.670354 0.839970 0.060810 0.043991 0.000653
|
||||||
-2.607522 0.624769 0.381081 0.047955 0.007326
|
-2.607522 0.624769 0.061888 0.047955 0.000733
|
||||||
-2.544690 0.663757 0.389082 0.047211 0.007364
|
-2.544690 0.663757 0.062566 0.047211 0.000736
|
||||||
-2.481858 1.051932 0.379999 0.040407 0.006156
|
-2.481858 1.051932 0.061093 0.040407 0.000616
|
||||||
-2.419026 1.463048 0.394914 0.034267 0.005425
|
-2.419026 1.463048 0.062547 0.034267 0.000543
|
||||||
-2.356194 1.990616 0.335141 0.027734 0.003726
|
-2.356194 1.990616 0.057022 0.027734 0.000373
|
||||||
-2.293363 2.190692 0.196497 0.025597 0.002016
|
-2.293363 2.190692 0.044029 0.025597 0.000202
|
||||||
-2.230531 2.553036 0.177045 0.022136 0.001571
|
-2.230531 2.553036 0.041867 0.022136 0.000157
|
||||||
-2.167699 2.572522 0.208798 0.021964 0.001839
|
-2.167699 2.572522 0.044817 0.021964 0.000184
|
||||||
-2.104867 2.472360 0.168929 0.022863 0.001548
|
-2.104867 2.472360 0.038778 0.022863 0.000155
|
||||||
-2.042035 2.517562 0.166774 0.022453 0.001501
|
-2.042035 2.517562 0.030296 0.022453 0.000150
|
||||||
-1.979203 2.469778 0.182308 0.022887 0.001673
|
-1.979203 2.469778 0.025852 0.022887 0.000167
|
||||||
-1.916372 2.223125 0.405294 0.025266 0.004105
|
-1.916372 2.223125 0.030799 0.025266 0.000411
|
||||||
-1.853540 2.080157 0.340376 0.026756 0.003651
|
-1.853540 2.080157 0.024928 0.026756 0.000365
|
||||||
-1.790708 1.793841 0.394974 0.030011 0.004752
|
-1.790708 1.793841 0.027529 0.030011 0.000475
|
||||||
-1.727876 1.458784 0.335956 0.034326 0.004623
|
-1.727876 1.458784 0.026130 0.034326 0.000462
|
||||||
-1.665044 0.914441 0.336724 0.042697 0.005764
|
-1.665044 0.914441 0.024774 0.042697 0.000576
|
||||||
-1.602212 0.303813 0.320695 0.054540 0.007012
|
-1.602212 0.303813 0.020400 0.054540 0.000701
|
||||||
-1.539380 0.268335 0.330495 0.055321 0.007330
|
-1.539380 0.268335 0.020423 0.055321 0.000733
|
||||||
-1.476549 0.000000 0.338143 0.061604 0.008351
|
-1.476549 0.000000 0.020271 0.061604 0.000835
|
||||||
-1.413717 0.537061 0.369220 0.049671 0.007352
|
-1.413717 0.537061 0.023895 0.049671 0.000735
|
||||||
-1.350885 1.439940 0.381006 0.034586 0.005283
|
-1.350885 1.439940 0.023678 0.034586 0.000528
|
||||||
-1.288053 2.391838 0.407306 0.023614 0.003856
|
-1.288053 2.391838 0.025951 0.023614 0.000386
|
||||||
-1.225221 3.779470 0.413629 0.013538 0.002245
|
-1.225221 3.779470 0.026215 0.013538 0.000224
|
||||||
-1.162389 5.685555 0.432485 0.006305 0.001093
|
-1.162389 5.685555 0.028543 0.006305 0.000109
|
||||||
-1.099557 7.661896 0.446994 0.002855 0.000512
|
-1.099557 7.661896 0.030579 0.002855 0.000051
|
||||||
-1.036726 9.946594 0.489990 0.001142 0.000224
|
-1.036726 9.946594 0.039243 0.001142 0.000022
|
||||||
-0.973894 12.359408 0.544847 0.000434 0.000095
|
-0.973894 12.359408 0.054067 0.000434 0.000009
|
||||||
-0.911062 14.954655 0.622373 0.000153 0.000038
|
-0.911062 14.954655 0.066597 0.000153 0.000004
|
||||||
-0.848230 17.742242 0.747233 0.000050 0.000015
|
-0.848230 17.742242 0.073582 0.000050 0.000002
|
||||||
-0.785398 20.555785 0.921773 0.000016 0.000006
|
-0.785398 20.555785 0.074644 0.000016 0.000001
|
||||||
-0.722566 22.811160 1.179343 0.000007 0.000003
|
-0.722566 22.811160 0.078503 0.000007 0.000000
|
||||||
-0.659734 25.178094 1.484376 0.000003 0.000002
|
-0.659734 25.178094 0.088961 0.000003 0.000000
|
||||||
-0.596903 26.442288 1.565063 0.000002 0.000001
|
-0.596903 26.442288 0.093509 0.000002 0.000000
|
||||||
-0.534071 27.897565 1.418232 0.000001 0.000000
|
-0.534071 27.897565 0.091353 0.000001 0.000000
|
||||||
-0.471239 29.062473 1.246738 0.000001 0.000000
|
-0.471239 29.062473 0.086244 0.000001 0.000000
|
||||||
-0.408407 30.384521 1.231662 0.000000 0.000000
|
-0.408407 30.384521 0.084285 0.000000 0.000000
|
||||||
-0.345575 31.638454 1.209295 0.000000 0.000000
|
-0.345575 31.638454 0.084871 0.000000 0.000000
|
||||||
-0.282743 32.817727 1.291637 0.000000 0.000000
|
-0.282743 32.817727 0.092750 0.000000 0.000000
|
||||||
-0.219911 33.770369 1.323362 0.000000 0.000000
|
-0.219911 33.770369 0.094479 0.000000 0.000000
|
||||||
-0.157080 34.505503 1.396454 0.000000 0.000000
|
-0.157080 34.505503 0.095774 0.000000 0.000000
|
||||||
-0.094248 35.431659 1.662548 0.000000 0.000000
|
-0.094248 35.431659 0.107598 0.000000 0.000000
|
||||||
-0.031416 35.615810 1.766523 0.000000 0.000000
|
-0.031416 35.615810 0.108959 0.000000 0.000000
|
||||||
0.031416 35.561946 1.799603 0.000000 0.000000
|
0.031416 35.561946 0.107382 0.000000 0.000000
|
||||||
0.094248 35.382089 1.374764 0.000000 0.000000
|
0.094248 35.382089 0.096643 0.000000 0.000000
|
||||||
0.157080 34.934827 1.659669 0.000000 0.000000
|
0.157080 34.934827 0.107624 0.000000 0.000000
|
||||||
0.219911 33.673460 1.317449 0.000000 0.000000
|
0.219911 33.673460 0.100231 0.000000 0.000000
|
||||||
0.282743 32.731563 1.191975 0.000000 0.000000
|
0.282743 32.731563 0.096604 0.000000 0.000000
|
||||||
0.345575 31.261855 1.199834 0.000000 0.000000
|
0.345575 31.261855 0.099036 0.000000 0.000000
|
||||||
0.408407 29.717377 1.339899 0.000000 0.000000
|
0.408407 29.717377 0.107915 0.000000 0.000000
|
||||||
0.471239 28.076620 1.303458 0.000001 0.000000
|
0.471239 28.076620 0.104513 0.000001 0.000000
|
||||||
0.534071 26.481097 1.281459 0.000002 0.000001
|
0.534071 26.481097 0.103164 0.000002 0.000000
|
||||||
0.596903 24.487358 1.251139 0.000003 0.000002
|
0.596903 24.487358 0.103039 0.000003 0.000000
|
||||||
0.659734 22.344251 1.233967 0.000008 0.000004
|
0.659734 22.344251 0.100666 0.000008 0.000000
|
||||||
0.722566 20.241543 1.251834 0.000018 0.000009
|
0.722566 20.241543 0.102150 0.000018 0.000001
|
||||||
0.785398 18.341869 1.241684 0.000039 0.000020
|
0.785398 18.341869 0.101957 0.000039 0.000002
|
||||||
0.848230 16.261582 1.281159 0.000091 0.000047
|
0.848230 16.261582 0.105391 0.000091 0.000005
|
||||||
0.911062 14.301801 1.294427 0.000199 0.000103
|
0.911062 14.301801 0.107389 0.000199 0.000010
|
||||||
0.973894 12.603788 1.270069 0.000394 0.000200
|
0.973894 12.603788 0.105487 0.000394 0.000020
|
||||||
1.036726 11.249601 1.273360 0.000678 0.000346
|
1.036726 11.249601 0.106308 0.000678 0.000035
|
||||||
1.099557 10.087886 1.280795 0.001079 0.000554
|
1.099557 10.087886 0.106741 0.001079 0.000055
|
||||||
1.162389 9.443303 1.266983 0.001398 0.000710
|
1.162389 9.443303 0.106957 0.001398 0.000071
|
||||||
1.225221 9.152799 1.255009 0.001570 0.000790
|
1.225221 9.152799 0.105940 0.001570 0.000079
|
||||||
1.288053 9.331937 1.256822 0.001462 0.000736
|
1.288053 9.331937 0.105860 0.001462 0.000074
|
||||||
1.350885 9.905546 1.251237 0.001161 0.000583
|
1.350885 9.905546 0.105389 0.001161 0.000058
|
||||||
1.413717 11.042050 1.263816 0.000736 0.000373
|
1.413717 11.042050 0.105466 0.000736 0.000037
|
||||||
1.476549 12.598167 1.275325 0.000395 0.000202
|
1.476549 12.598167 0.105119 0.000395 0.000020
|
||||||
1.539380 14.520167 1.280735 0.000183 0.000094
|
1.539380 14.520167 0.104367 0.000183 0.000009
|
||||||
1.602212 16.569783 1.295384 0.000080 0.000042
|
1.602212 16.569783 0.104184 0.000080 0.000004
|
||||||
1.665044 18.687390 1.309518 0.000034 0.000018
|
1.665044 18.687390 0.104276 0.000034 0.000002
|
||||||
1.727876 20.775408 1.356414 0.000015 0.000008
|
1.727876 20.775408 0.104944 0.000015 0.000001
|
||||||
1.790708 22.905200 1.308568 0.000006 0.000003
|
1.790708 22.905200 0.101547 0.000006 0.000000
|
||||||
1.853540 24.643852 1.425870 0.000003 0.000002
|
1.853540 24.643852 0.103914 0.000003 0.000000
|
||||||
1.916372 26.301740 1.362138 0.000002 0.000001
|
1.916372 26.301740 0.101973 0.000002 0.000000
|
||||||
1.979203 27.372071 1.391716 0.000001 0.000001
|
1.979203 27.372071 0.101762 0.000001 0.000000
|
||||||
2.042035 28.697726 1.504676 0.000001 0.000000
|
2.042035 28.697726 0.105177 0.000001 0.000000
|
||||||
2.104867 29.417901 1.369019 0.000000 0.000000
|
2.104867 29.417901 0.100003 0.000000 0.000000
|
||||||
2.167699 30.008351 1.409081 0.000000 0.000000
|
2.167699 30.008351 0.100038 0.000000 0.000000
|
||||||
2.230531 30.406016 1.240128 0.000000 0.000000
|
2.230531 30.406016 0.096233 0.000000 0.000000
|
||||||
2.293363 30.171275 1.179444 0.000000 0.000000
|
2.293363 30.171275 0.096428 0.000000 0.000000
|
||||||
2.356194 29.884646 1.219365 0.000000 0.000000
|
2.356194 29.884646 0.108339 0.000000 0.000000
|
||||||
2.419026 29.428153 1.177281 0.000000 0.000000
|
2.419026 29.428153 0.106679 0.000000 0.000000
|
||||||
2.481858 28.546982 1.351057 0.000001 0.000000
|
2.481858 28.546982 0.123259 0.000001 0.000000
|
||||||
2.544690 27.757520 1.238695 0.000001 0.000000
|
2.544690 27.757520 0.108526 0.000001 0.000000
|
||||||
2.607522 26.505787 1.308430 0.000001 0.000001
|
2.607522 26.505787 0.111134 0.000001 0.000000
|
||||||
2.670354 24.491866 1.039660 0.000003 0.000001
|
2.670354 24.491866 0.095963 0.000003 0.000000
|
||||||
2.733186 22.320664 0.927893 0.000008 0.000003
|
2.733186 22.320664 0.096576 0.000008 0.000000
|
||||||
2.796017 20.052723 0.894483 0.000020 0.000007
|
2.796017 20.052723 0.098813 0.000020 0.000001
|
||||||
2.858849 17.655650 0.893580 0.000052 0.000019
|
2.858849 17.655650 0.097052 0.000052 0.000002
|
||||||
2.921681 15.471590 0.930897 0.000125 0.000047
|
2.921681 15.471590 0.100497 0.000125 0.000005
|
||||||
2.984513 13.138167 0.837026 0.000318 0.000107
|
2.984513 13.138167 0.092102 0.000318 0.000011
|
||||||
3.047345 11.092386 0.674785 0.000722 0.000195
|
3.047345 11.092386 0.081862 0.000722 0.000020
|
||||||
3.110177 9.065722 0.521230 0.001626 0.000340
|
3.110177 9.065722 0.072111 0.001626 0.000034
|
||||||
|
|||||||
@@ -1,7 +1,7 @@
|
|||||||
use rand::{SeedableRng, StdRng, Rng};
|
use rand::{SeedableRng, StdRng, Rng};
|
||||||
use super::histogram::{Dataset};
|
use super::histogram::{Dataset};
|
||||||
use super::perform_wham;
|
use super::perform_wham;
|
||||||
use super::Config;
|
use super::{Config,calc_free_energy};
|
||||||
use rgsl::statistics;
|
use rgsl::statistics;
|
||||||
|
|
||||||
// returns a set of num_windows continious weights by
|
// returns a set of num_windows continious weights by
|
||||||
@@ -20,7 +20,7 @@ fn generate_random_weights(num_windows: usize, rng: &mut StdRng) -> Vec<f64> {
|
|||||||
for i in 0..num_windows {
|
for i in 0..num_windows {
|
||||||
weights[i] = rnds[i+1] - rnds[i]
|
weights[i] = rnds[i+1] - rnds[i]
|
||||||
}
|
}
|
||||||
return weights
|
weights
|
||||||
}
|
}
|
||||||
|
|
||||||
// Generate a random weighted dataset from the given dataset by changing the weights
|
// Generate a random weighted dataset from the given dataset by changing the weights
|
||||||
@@ -32,7 +32,7 @@ fn generate_random_weighted_dataset(ds: Dataset, rng: &mut StdRng) -> Dataset {
|
|||||||
// Perform bootstrap error analysis. This runs the WHAM analysis num_runs times on random weighted
|
// Perform bootstrap error analysis. This runs the WHAM analysis num_runs times on random weighted
|
||||||
// datasets. The standard deviation is calculated on the bootstrapped probabilities of each bin. The
|
// datasets. The standard deviation is calculated on the bootstrapped probabilities of each bin. The
|
||||||
// standard deviation of the free eneergy is then deduced by error propagation (A_std = kT*1/P*P_std)
|
// standard deviation of the free eneergy is then deduced by error propagation (A_std = kT*1/P*P_std)
|
||||||
pub fn run_bootstrap(cfg: &Config, ds: Dataset, P: &[f64], num_runs: usize) -> (Vec<f64>,Vec<f64>) {
|
pub fn run_bootstrap(cfg: &Config, ds: Dataset, num_runs: usize) -> (Vec<f64>,Vec<f64>) {
|
||||||
// seed the rng
|
// seed the rng
|
||||||
let mut rng: StdRng = SeedableRng::seed_from_u64(cfg.bootstrap_seed);
|
let mut rng: StdRng = SeedableRng::seed_from_u64(cfg.bootstrap_seed);
|
||||||
|
|
||||||
@@ -43,16 +43,27 @@ pub fn run_bootstrap(cfg: &Config, ds: Dataset, P: &[f64], num_runs: usize) -> (
|
|||||||
perform_wham(cfg, &rnd_weighted_dataset).unwrap().0
|
perform_wham(cfg, &rnd_weighted_dataset).unwrap().0
|
||||||
}).collect();
|
}).collect();
|
||||||
|
|
||||||
// Evaulate standard deviation of P per bin
|
// Standard error (SE) of P per bin
|
||||||
let mut P_std = vec![0.0; ds.num_bins];
|
// SE = SD/sqrt(n)
|
||||||
|
let mut P_se = vec![0.0; ds.num_bins];
|
||||||
for bin in 0..ds.num_bins {
|
for bin in 0..ds.num_bins {
|
||||||
let Ps = bootstrapped_Ps.iter().map(|window| window[bin]).collect::<Vec<f64>>();
|
let Ps = bootstrapped_Ps.iter().map(|window| window[bin]).collect::<Vec<f64>>();
|
||||||
P_std[bin] = statistics::sd(&Ps, 1, num_runs);
|
P_se[bin] = statistics::sd(&Ps, 1, num_runs)/(num_runs as f64).sqrt();
|
||||||
}
|
}
|
||||||
|
|
||||||
// A_std by error propagation
|
// SE of A
|
||||||
let A_std = P_std.iter().zip(P.iter()).map(|(std,P)| ds.kT*1.0/P*std).collect();
|
let bootstrapped_As: Vec<Vec<f64>> = (0..num_runs).map(|x| {
|
||||||
(P_std, A_std)
|
let run_Ps = &bootstrapped_Ps[x];
|
||||||
|
calc_free_energy(&ds, run_Ps)
|
||||||
|
}).collect();
|
||||||
|
|
||||||
|
let mut A_se = vec![0.0; ds.num_bins];
|
||||||
|
for bin in 0..ds.num_bins {
|
||||||
|
let As = bootstrapped_As.iter().map(|window| window[bin]).collect::<Vec<f64>>();
|
||||||
|
A_se[bin] = statistics::sd(&As, 1, num_runs)/(num_runs as f64).sqrt();
|
||||||
|
}
|
||||||
|
|
||||||
|
(P_se, A_se)
|
||||||
}
|
}
|
||||||
|
|
||||||
#[cfg(tests)]
|
#[cfg(tests)]
|
||||||
|
|||||||
@@ -61,7 +61,9 @@ pub struct Dataset {
|
|||||||
|
|
||||||
impl Dataset {
|
impl Dataset {
|
||||||
|
|
||||||
pub fn new(num_bins: usize, dimens_lengths: Vec<usize>, bin_width: Vec<f64>, hist_min: Vec<f64>, hist_max: Vec<f64>, bias_pos: Vec<f64>, bias_fc: Vec<f64>, kT: f64, histograms: Vec<Histogram>, cyclic: bool) -> Dataset {
|
pub fn new(num_bins: usize, dimens_lengths: Vec<usize>, bin_width: Vec<f64>,
|
||||||
|
hist_min: Vec<f64>, hist_max: Vec<f64>, bias_pos: Vec<f64>,
|
||||||
|
bias_fc: Vec<f64>, kT: f64, histograms: Vec<Histogram>, cyclic: bool) -> Dataset {
|
||||||
let num_windows = histograms.len();
|
let num_windows = histograms.len();
|
||||||
let bias: Vec<f64> = vec![0.0; num_bins*num_windows];
|
let bias: Vec<f64> = vec![0.0; num_bins*num_windows];
|
||||||
let weights = vec![1.0; num_windows];
|
let weights = vec![1.0; num_windows];
|
||||||
@@ -92,7 +94,7 @@ impl Dataset {
|
|||||||
|
|
||||||
pub fn new_weighted(ds: Dataset, weights: Vec<f64>) -> Dataset {
|
pub fn new_weighted(ds: Dataset, weights: Vec<f64>) -> Dataset {
|
||||||
Dataset {
|
Dataset {
|
||||||
weights: weights,
|
weights,
|
||||||
..ds
|
..ds
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
@@ -105,9 +107,9 @@ impl Dataset {
|
|||||||
let mut tmp = bin;
|
let mut tmp = bin;
|
||||||
let mut idx = vec![0; lengths.len()];
|
let mut idx = vec![0; lengths.len()];
|
||||||
for dimen in (1..lengths.len()).rev() {
|
for dimen in (1..lengths.len()).rev() {
|
||||||
let denom = lengths.iter().take(dimen).fold(1, |s,&x| s*x);
|
let denom: usize = lengths.iter().take(dimen).product();
|
||||||
idx[dimen] = tmp / denom;
|
idx[dimen] = tmp / denom;
|
||||||
tmp = tmp % denom;
|
tmp %= denom;
|
||||||
}
|
}
|
||||||
idx[0] = tmp;
|
idx[0] = tmp;
|
||||||
idx
|
idx
|
||||||
@@ -151,8 +153,7 @@ impl Dataset {
|
|||||||
// store exp(U/kT) for better performance
|
// store exp(U/kT) for better performance
|
||||||
bias_sum += 0.5 * bias_fc[i] * dist * dist
|
bias_sum += 0.5 * bias_fc[i] * dist * dist
|
||||||
}
|
}
|
||||||
let bias_sum = (-bias_sum/self.kT).exp();
|
(-bias_sum/self.kT).exp()
|
||||||
bias_sum
|
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
@@ -205,13 +206,13 @@ mod tests {
|
|||||||
let ds = build_hist_set(); // k = 10
|
let ds = build_hist_set(); // k = 10
|
||||||
|
|
||||||
// 3th element -> x=3.5, x0=3.5
|
// 3th element -> x=3.5, x0=3.5
|
||||||
assert_delta!(0.134722337796, ds.calc_bias(3, 0), 0.00000001);
|
assert_delta!(0.134_722_337_796, ds.calc_bias(3, 0), 0.000_000_01);
|
||||||
|
|
||||||
// 8th element -> x=8.5, x0=3.5
|
// 8th element -> x=8.5, x0=3.5
|
||||||
assert_delta!(1.0, ds.calc_bias(4,0), 0.00000001);
|
assert_delta!(1.0, ds.calc_bias(4,0), 0.000_000_01);
|
||||||
|
|
||||||
// 1st element -> x=0.5, x0=3.5. non-cyclic!
|
// 1st element -> x=0.5, x0=3.5. non-cyclic!
|
||||||
assert_delta!(0.0, ds.calc_bias(0,0), 0.0000001);
|
assert_delta!(0.0, ds.calc_bias(0,0), 0.000_000_1);
|
||||||
}
|
}
|
||||||
|
|
||||||
#[test]
|
#[test]
|
||||||
@@ -220,28 +221,28 @@ mod tests {
|
|||||||
ds.cyclic = true;
|
ds.cyclic = true;
|
||||||
|
|
||||||
// 7th element -> x=3.5, x0=3.5
|
// 7th element -> x=3.5, x0=3.5
|
||||||
assert_delta!(0.134722337796, ds.calc_bias(3, 0), 0.00000001);
|
assert_delta!(0.134_722_337_796, ds.calc_bias(3, 0), 0.000_000_01);
|
||||||
|
|
||||||
// 8th element -> x=4.5, x0=3.5
|
// 8th element -> x=4.5, x0=3.5
|
||||||
assert_delta!(1.0, ds.calc_bias(4, 0), 0.00000001);
|
assert_delta!(1.0, ds.calc_bias(4, 0), 0.000_000_01);
|
||||||
|
|
||||||
|
|
||||||
// 1th element -> x=0.5, x0=3.5
|
// 1th element -> x=0.5, x0=3.5
|
||||||
// cyclic flag makes bin 0 neighboring bin 9, so the distance is actually 2
|
// cyclic flag makes bin 0 neighboring bin 9, so the distance is actually 2
|
||||||
assert_delta!(0.0000000000000117769, ds.calc_bias(0, 0), 0.00000001);
|
assert_delta!(0.000_000_000_000_011_776_9, ds.calc_bias(0, 0), 0.000_000_01);
|
||||||
|
|
||||||
// 2nd element -> x=1.5, x0=3.5
|
// 2nd element -> x=1.5, x0=3.5
|
||||||
assert_delta!(0.00000001, ds.calc_bias(1, 0), 0.00000001);
|
assert_delta!(0.000_000_01, ds.calc_bias(1, 0), 0.000_000_01);
|
||||||
}
|
}
|
||||||
|
|
||||||
#[test]
|
#[test]
|
||||||
fn get_x_for_bin() {
|
fn get_x_for_bin() {
|
||||||
let ds = build_hist_set();
|
let ds = build_hist_set();
|
||||||
let expected: Vec<f64> = vec![0,1,2,3,4,5,6,7,8].iter()
|
let expected: Vec<f64> = vec![0,1,2,3,4,5,6,7,8].iter()
|
||||||
.map(|x| *x as f64 + 0.5).collect();
|
.map(|x| *x as f64 + 0.5).collect();
|
||||||
for i in 0..9 {
|
expected.iter().enumerate().for_each(|(i, exp)| {
|
||||||
assert_eq!(expected[i], ds.get_coords_for_bin(i)[0]);
|
assert_approx_eq!(exp, &ds.get_coords_for_bin(i)[0]);
|
||||||
}
|
})
|
||||||
}
|
}
|
||||||
|
|
||||||
#[test]
|
#[test]
|
||||||
@@ -258,10 +259,10 @@ mod tests {
|
|||||||
vec![build_hist(), build_hist()], // hists
|
vec![build_hist(), build_hist()], // hists
|
||||||
false // cyclic
|
false // cyclic
|
||||||
);
|
);
|
||||||
assert_delta!(2.0, ds.get_weighted_bin_count(0), 0.0000000001);
|
assert_delta!(2.0, ds.get_weighted_bin_count(0), 0.000_000_000_1);
|
||||||
assert_delta!(2.0, ds.get_weighted_bin_count(1), 0.0000000001);
|
assert_delta!(2.0, ds.get_weighted_bin_count(1), 0.000_000_000_1);
|
||||||
assert_delta!(6.0, ds.get_weighted_bin_count(2), 0.0000000001);
|
assert_delta!(6.0, ds.get_weighted_bin_count(2), 0.000_000_000_1);
|
||||||
assert_delta!(10.0, ds.get_weighted_bin_count(3), 0.0000000001);
|
assert_delta!(10.0, ds.get_weighted_bin_count(3), 0.000_000_000_1);
|
||||||
assert_delta!(24.0, ds.get_weighted_bin_count(4), 0.0000000001);
|
assert_delta!(24.0, ds.get_weighted_bin_count(4), 0.000_000_000_1);
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
57
src/io.rs
57
src/io.rs
@@ -35,7 +35,7 @@ pub fn read_data(cfg: &Config) -> Result<Dataset> {
|
|||||||
let bin_width: Vec<f64> = (0..cfg.dimens).map(|idx| {
|
let bin_width: Vec<f64> = (0..cfg.dimens).map(|idx| {
|
||||||
(cfg.hist_max[idx] - cfg.hist_min[idx])/(cfg.num_bins[idx] as f64)
|
(cfg.hist_max[idx] - cfg.hist_min[idx])/(cfg.num_bins[idx] as f64)
|
||||||
}).collect();
|
}).collect();
|
||||||
let num_bins = cfg.num_bins.iter().fold(1, |state, &bins| state*bins);
|
let num_bins = cfg.num_bins.iter().product();
|
||||||
let dimens_length = cfg.num_bins.clone();
|
let dimens_length = cfg.num_bins.clone();
|
||||||
|
|
||||||
let f = File::open(&cfg.metadata_file).chain_err(|| "Failed to open metadata file")?;
|
let f = File::open(&cfg.metadata_file).chain_err(|| "Failed to open metadata file")?;
|
||||||
@@ -46,7 +46,7 @@ pub fn read_data(cfg: &Config) -> Result<Dataset> {
|
|||||||
let line = l.chain_err(|| "Failed to read line")?;
|
let line = l.chain_err(|| "Failed to read line")?;
|
||||||
|
|
||||||
// skip comments and empty lines
|
// skip comments and empty lines
|
||||||
if line.starts_with("#") || line.len() == 0 {
|
if line.starts_with('#') || line.is_empty() {
|
||||||
continue;
|
continue;
|
||||||
}
|
}
|
||||||
|
|
||||||
@@ -67,19 +67,19 @@ pub fn read_data(cfg: &Config) -> Result<Dataset> {
|
|||||||
histograms.last().unwrap().num_points), cfg.verbose);
|
histograms.last().unwrap().num_points), cfg.verbose);
|
||||||
|
|
||||||
// parse bias force constants and positions
|
// parse bias force constants and positions
|
||||||
for i in 1..cfg.dimens+1 {
|
for val in split.iter().skip(1).take(cfg.dimens) {
|
||||||
let pos = split[i].parse()
|
let pos = val.parse()
|
||||||
.chain_err(|| format!("Failed to read bias position in line {} of metadata file", line_num+1))?;
|
.chain_err(|| format!("Failed to read bias position in line {} of metadata file", line_num+1))?;
|
||||||
bias_pos.push(pos);
|
bias_pos.push(pos);
|
||||||
}
|
}
|
||||||
for i in (1+cfg.dimens)..(1+2*cfg.dimens) {
|
for val in split.iter().skip(1+cfg.dimens).take(cfg.dimens) {
|
||||||
let fc = split[i].parse()
|
let fc = val.parse()
|
||||||
.chain_err(|| format!("Failed to read bias fc in line {} of metadata file", line_num+1))?;
|
.chain_err(|| format!("Failed to read bias fc in line {} of metadata file", line_num+1))?;
|
||||||
bias_fc.push(fc);
|
bias_fc.push(fc);
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
if histograms.len() > 0 {
|
if !histograms.is_empty() {
|
||||||
Ok(Dataset::new(num_bins, dimens_length, bin_width, cfg.hist_min.clone(), cfg.hist_max.clone(), bias_pos, bias_fc, kT, histograms, cfg.cyclic))
|
Ok(Dataset::new(num_bins, dimens_length, bin_width, cfg.hist_min.clone(), cfg.hist_max.clone(), bias_pos, bias_fc, kT, histograms, cfg.cyclic))
|
||||||
} else {
|
} else {
|
||||||
bail!("Histogram has no datapoints.")
|
bail!("Histogram has no datapoints.")
|
||||||
@@ -91,13 +91,10 @@ pub fn read_data(cfg: &Config) -> Result<Dataset> {
|
|||||||
// lengths: length of the matrix in each dimension
|
// lengths: length of the matrix in each dimension
|
||||||
// returns an index if the matrix is flattened to a one dimensional vector
|
// returns an index if the matrix is flattened to a one dimensional vector
|
||||||
// example for 3 dimensions N,M,O: idx = i_O + l_O*l_M*i_M + l_O*l_M*l_N*i_N
|
// example for 3 dimensions N,M,O: idx = i_O + l_O*l_M*i_M + l_O*l_M*l_N*i_N
|
||||||
fn flat_index(indeces: &Vec<usize>, lengths: &Vec<usize>) -> usize {
|
fn flat_index(indeces: &[usize], lengths: &[usize]) -> usize {
|
||||||
let mut idx = 0;
|
indeces.iter().enumerate().map(|(i, idx)| {
|
||||||
for i in 0..indeces.len() {
|
idx * lengths.iter().take(i).product::<usize>()
|
||||||
idx += indeces[i]*lengths[0..i].iter()
|
}).sum()
|
||||||
.fold(1, |state, &l| { state * l });
|
|
||||||
}
|
|
||||||
idx
|
|
||||||
}
|
}
|
||||||
|
|
||||||
// returns true if the values are inside the histogram boundaries defined by cfg
|
// returns true if the values are inside the histogram boundaries defined by cfg
|
||||||
@@ -118,14 +115,14 @@ fn is_in_time_boundaries(time: f64, cfg: &Config) -> bool {
|
|||||||
false
|
false
|
||||||
}
|
}
|
||||||
|
|
||||||
// parse a timeseries file into a histogram
|
// parse a time series file into a histogram
|
||||||
fn read_window_file(window_file: &str, cfg: &Config) -> Result<Histogram> {
|
fn read_window_file(window_file: &str, cfg: &Config) -> Result<Histogram> {
|
||||||
let f = File::open(window_file)
|
let f = File::open(window_file)
|
||||||
.chain_err(|| format!("Failed to open sample data file {}.", window_file))?;
|
.chain_err(|| format!("Failed to open sample data file {}.", window_file))?;
|
||||||
let mut buf = BufReader::new(&f);
|
let mut buf = BufReader::new(&f);
|
||||||
|
|
||||||
// total number of bins is the product of all dimensions length
|
// total number of bins is the product of all dimensions length
|
||||||
let total_bins = cfg.num_bins.iter().fold(1, |s, &x| { s*x });
|
let total_bins = cfg.num_bins.iter().product();
|
||||||
let mut hist = vec![0.0; total_bins];
|
let mut hist = vec![0.0; total_bins];
|
||||||
|
|
||||||
// bin width for each dimension: (max-min)/bins
|
// bin width for each dimension: (max-min)/bins
|
||||||
@@ -139,7 +136,7 @@ fn read_window_file(window_file: &str, cfg: &Config) -> Result<Histogram> {
|
|||||||
while buf.read_line(&mut line).chain_err(|| "Failed to read line")? > 0 {
|
while buf.read_line(&mut line).chain_err(|| "Failed to read line")? > 0 {
|
||||||
linecount += 1;
|
linecount += 1;
|
||||||
// skip comments and empty lines
|
// skip comments and empty lines
|
||||||
if line.starts_with("#") || line.starts_with("@") || line.len() == 0 {
|
if line.starts_with('#') || line.starts_with('@') || line.is_empty() {
|
||||||
line.clear();
|
line.clear();
|
||||||
continue;
|
continue;
|
||||||
}
|
}
|
||||||
@@ -158,7 +155,7 @@ fn read_window_file(window_file: &str, cfg: &Config) -> Result<Histogram> {
|
|||||||
}
|
}
|
||||||
|
|
||||||
if is_in_hist_boundaries(&values[1..], cfg) && is_in_time_boundaries(values[0], cfg) {
|
if is_in_hist_boundaries(&values[1..], cfg) && is_in_time_boundaries(values[0], cfg) {
|
||||||
let bin_indeces = (0..cfg.dimens).map(|dimen: usize| {
|
let bin_indeces: Vec<usize> = (0..cfg.dimens).map(|dimen: usize| {
|
||||||
let val = values[dimen+1];
|
let val = values[dimen+1];
|
||||||
((val - cfg.hist_min[dimen]) / bin_width[dimen]) as usize
|
((val - cfg.hist_min[dimen]) / bin_width[dimen]) as usize
|
||||||
}).collect();
|
}).collect();
|
||||||
@@ -174,20 +171,22 @@ fn read_window_file(window_file: &str, cfg: &Config) -> Result<Histogram> {
|
|||||||
}
|
}
|
||||||
|
|
||||||
// Write WHAM calculation results to out_file.
|
// Write WHAM calculation results to out_file.
|
||||||
pub fn write_results(out_file: &str, ds: &Dataset, free: &Vec<f64>, free_std: &Vec<f64>, prob: &Vec<f64>, prob_std: &Vec<f64>) -> Result<()> {
|
pub fn write_results(out_file: &str, ds: &Dataset, free: &[f64],
|
||||||
|
free_std: &[f64], prob: &[f64], prob_std: &[f64]) -> Result<()> {
|
||||||
let output = File::create(out_file)
|
let output = File::create(out_file)
|
||||||
.chain_err(|| format!("Failed to create file with path {}", out_file))?;
|
.chain_err(|| format!("Failed to create file with path {}", out_file))?;
|
||||||
let mut buf = BufWriter::new(output);
|
let mut buf = BufWriter::new(output);
|
||||||
|
|
||||||
let header: String = (0..ds.dimens_lengths.len()).map(|d| format!("coord{}", d+1))
|
let header: String = (0..ds.dimens_lengths.len()).map(|d| format!("coord{}", d+1))
|
||||||
.collect::<Vec<String>>().join(" ");
|
.collect::<Vec<String>>().join(" ");
|
||||||
writeln!(buf, "#{} {} {} {} {}", header, "Free Energy", "+/-", "Probability", "+/-");
|
writeln!(buf, "#{} Free Energy +/- Probability +/-", header).unwrap();
|
||||||
|
|
||||||
for bin in 0..free.len() {
|
for bin in 0..free.len() {
|
||||||
let coords = ds.get_coords_for_bin(bin);
|
let coords = ds.get_coords_for_bin(bin);
|
||||||
let coords_str: String = coords.iter().map(|c| {format!("{:8.6} ", c)})
|
let coords_str: String = coords.iter().map(|c| {format!("{:8.6} ", c)})
|
||||||
.collect::<Vec<String>>().join("\t");
|
.collect::<Vec<String>>().join("\t");
|
||||||
writeln!(buf, "{}{:8.6} {:8.6} {:8.6} {:8.6}", coords_str, free[bin], free_std[bin], prob[bin], prob_std[bin])
|
writeln!(buf, "{}{:8.6} {:8.6} {:8.6} {:8.6}", coords_str,
|
||||||
|
free[bin], free_std[bin], prob[bin], prob_std[bin])
|
||||||
.chain_err(|| "Failed to write to file.")?;
|
.chain_err(|| "Failed to write to file.")?;
|
||||||
}
|
}
|
||||||
Ok(())
|
Ok(())
|
||||||
@@ -196,10 +195,12 @@ pub fn write_results(out_file: &str, ds: &Dataset, free: &Vec<f64>, free_std: &V
|
|||||||
#[cfg(test)]
|
#[cfg(test)]
|
||||||
mod tests {
|
mod tests {
|
||||||
use super::*;
|
use super::*;
|
||||||
|
use assert_approx_eq::assert_approx_eq;
|
||||||
|
|
||||||
fn cfg() -> Config {
|
fn cfg() -> Config {
|
||||||
Config {
|
Config {
|
||||||
metadata_file: "example/1d_cyclic/metadata.dat".to_string(),
|
metadata_file: "example/1d_cyclic/metadata.dat".to_string(),
|
||||||
|
|
||||||
hist_min: vec![-3.14],
|
hist_min: vec![-3.14],
|
||||||
hist_max: vec![3.14],
|
hist_max: vec![3.14],
|
||||||
num_bins: vec![10],
|
num_bins: vec![10],
|
||||||
@@ -224,12 +225,12 @@ mod tests {
|
|||||||
let h = super::read_window_file(&f, &cfg).unwrap();
|
let h = super::read_window_file(&f, &cfg).unwrap();
|
||||||
println!("{:?}", h);
|
println!("{:?}", h);
|
||||||
assert_eq!(5000, h.num_points);
|
assert_eq!(5000, h.num_points);
|
||||||
assert_eq!(0.0, h.bins[2]);
|
assert_approx_eq!(0.0, h.bins[2]);
|
||||||
assert_eq!(11.0, h.bins[3]);
|
assert_approx_eq!(11.0, h.bins[3]);
|
||||||
assert_eq!(2236.0, h.bins[4]);
|
assert_approx_eq!(2236.0, h.bins[4]);
|
||||||
assert_eq!(2714.0, h.bins[5]);
|
assert_approx_eq!(2714.0, h.bins[5]);
|
||||||
assert_eq!(39.0, h.bins[6]);
|
assert_approx_eq!(39.0, h.bins[6]);
|
||||||
assert_eq!(0.0, h.bins[7]);
|
assert_approx_eq!(0.0, h.bins[7]);
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
@@ -241,7 +242,7 @@ mod tests {
|
|||||||
assert_eq!(25, ds.num_windows);
|
assert_eq!(25, ds.num_windows);
|
||||||
assert_eq!(cfg.num_bins.len(), ds.dimens_lengths.len());
|
assert_eq!(cfg.num_bins.len(), ds.dimens_lengths.len());
|
||||||
assert_eq!(cfg.num_bins[0], ds.dimens_lengths[0]);
|
assert_eq!(cfg.num_bins[0], ds.dimens_lengths[0]);
|
||||||
assert_eq!(cfg.temperature * k_B, ds.kT);
|
assert_approx_eq!(cfg.temperature * k_B, ds.kT);
|
||||||
assert_eq!(25, ds.histograms.len())
|
assert_eq!(25, ds.histograms.len())
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|||||||
149
src/lib.rs
149
src/lib.rs
@@ -5,6 +5,10 @@ extern crate error_chain;
|
|||||||
extern crate rand;
|
extern crate rand;
|
||||||
extern crate rgsl;
|
extern crate rgsl;
|
||||||
extern crate rayon;
|
extern crate rayon;
|
||||||
|
#[cfg(test)]
|
||||||
|
#[macro_use]
|
||||||
|
extern crate assert_approx_eq;
|
||||||
|
|
||||||
|
|
||||||
pub mod io;
|
pub mod io;
|
||||||
pub mod histogram;
|
pub mod histogram;
|
||||||
@@ -21,7 +25,7 @@ pub mod errors { error_chain!{} }
|
|||||||
use errors::*;
|
use errors::*;
|
||||||
|
|
||||||
#[allow(non_upper_case_globals)]
|
#[allow(non_upper_case_globals)]
|
||||||
static k_B: f64 = 0.0083144621; // kJ/mol*K
|
static k_B: f64 = 0.008_314_462_1; // kJ/mol*K
|
||||||
|
|
||||||
// Application config
|
// Application config
|
||||||
#[derive(Debug)]
|
#[derive(Debug)]
|
||||||
@@ -45,7 +49,9 @@ pub struct Config {
|
|||||||
|
|
||||||
impl fmt::Display for Config {
|
impl fmt::Display for Config {
|
||||||
fn fmt(&self, f: &mut fmt::Formatter) -> fmt::Result {
|
fn fmt(&self, f: &mut fmt::Formatter) -> fmt::Result {
|
||||||
write!(f, "Metadata={}, hist_min={:?}, hist_max={:?}, bins={:?} verbose={}, tolerance={}, iterations={}, temperature={}, cyclic={:?}, bootstrap={:?}, seed={:?}",
|
write!(f, "Metadata={}, hist_min={:?}, hist_max={:?}, bins={:?},
|
||||||
|
verbose={}, tolerance={}, iterations={}, temperature={},
|
||||||
|
cyclic={:?}, bootstrap={:?}, seed={:?}",
|
||||||
self.metadata_file, self.hist_min, self.hist_max, self.num_bins,
|
self.metadata_file, self.hist_min, self.hist_max, self.num_bins,
|
||||||
self.verbose, self.tolerance, self.max_iterations, self.temperature,
|
self.verbose, self.tolerance, self.max_iterations, self.temperature,
|
||||||
self.cyclic, self.bootstrap, self.bootstrap_seed)
|
self.cyclic, self.bootstrap, self.bootstrap_seed)
|
||||||
@@ -56,25 +62,34 @@ impl fmt::Display for Config {
|
|||||||
// converged if the maximal difference for the calculated bias offsets is
|
// converged if the maximal difference for the calculated bias offsets is
|
||||||
// smaller then a tolerance value.
|
// smaller then a tolerance value.
|
||||||
fn is_converged(old_F: &[f64], new_F: &[f64], tolerance: f64) -> bool {
|
fn is_converged(old_F: &[f64], new_F: &[f64], tolerance: f64) -> bool {
|
||||||
!new_F.iter().zip(old_F.iter())
|
// calculates abs diff between every old and new F and checks if any
|
||||||
.map(|x| { (x.0-x.1).abs() })
|
// is larger than tolerance
|
||||||
.any(|diff| { diff > tolerance })
|
!new_F.iter()
|
||||||
|
.zip(old_F.iter())
|
||||||
|
.map(|x| { (x.0-x.1).abs() })
|
||||||
|
.any(|diff| { diff > tolerance })
|
||||||
}
|
}
|
||||||
|
|
||||||
// estimate the probability of a bin of the histogram set based on given bias offsets (F)
|
// estimate the probability of a bin of the histogram set based on given bias
|
||||||
// This evaluates the first WHAM equation for each bin.
|
// offsets (F). This evaluates the first WHAM equation for each bin:
|
||||||
|
// P(x) = \frac {\sum_{i=1}^N{n_i(x)}}
|
||||||
|
// {\sum_{i=1}^N{ N_i exp(\beta [F_i - U_{bias,i}(x)])}}
|
||||||
fn calc_bin_probability(bin: usize, dataset: &Dataset, F: &[f64]) -> f64 {
|
fn calc_bin_probability(bin: usize, dataset: &Dataset, F: &[f64]) -> f64 {
|
||||||
let mut denom_sum: f64 = 0.0;
|
let mut denom_sum: f64 = 0.0;
|
||||||
let bin_count: f64 = dataset.get_weighted_bin_count(bin);
|
let bin_count: f64 = dataset.get_weighted_bin_count(bin);
|
||||||
for (window, h) in dataset.histograms.iter().enumerate() {
|
for (window, h) in dataset.histograms.iter().enumerate() {
|
||||||
let bias = dataset.get_bias(bin, window);
|
let bias = dataset.get_bias(bin, window);
|
||||||
denom_sum += (dataset.weights[window] * h.num_points as f64) * bias * F[window];
|
denom_sum += (dataset.weights[window] * h.num_points as f64)
|
||||||
|
* bias * F[window];
|
||||||
}
|
}
|
||||||
bin_count / denom_sum
|
bin_count / denom_sum
|
||||||
}
|
}
|
||||||
|
|
||||||
// estimate the bias offset F of the histogram based on given probabilities.
|
// estimate the bias offset F of the histogram based on given probabilities.
|
||||||
// This evaluates the second WHAM equation for each window and returns exp(F/kT)
|
// This evaluates the second WHAM equation for each window and returns exp(F/kT).
|
||||||
|
// exp(F/kT) is not required in intermediate steps so we save some time by not
|
||||||
|
// calculating it for every iteration.
|
||||||
|
// F_i = - 1/\beta ln[\sum_{X_{bins}}{P(x)exp(-\beta U_{bias,i}(x))}]
|
||||||
fn calc_window_F(window: usize, dataset: &Dataset, P: &[f64]) -> f64 {
|
fn calc_window_F(window: usize, dataset: &Dataset, P: &[f64]) -> f64 {
|
||||||
let f: f64 = (0..dataset.num_bins).zip(P.iter()) // zip bins and P
|
let f: f64 = (0..dataset.num_bins).zip(P.iter()) // zip bins and P
|
||||||
.map(|bin_and_prob: (usize, &f64)| {
|
.map(|bin_and_prob: (usize, &f64)| {
|
||||||
@@ -84,16 +99,18 @@ fn calc_window_F(window: usize, dataset: &Dataset, P: &[f64]) -> f64 {
|
|||||||
1.0/f
|
1.0/f
|
||||||
}
|
}
|
||||||
|
|
||||||
// One full WHAM iteration includes calculation of new probabilities P and
|
// One full WHAM iteration: calculation of new probabilities P and new bias
|
||||||
// new bias offsets F based on previous bias offsets F_prev. This updates
|
// offsets F based on previous bias offsets F_prev. This updates the values in
|
||||||
// the values in vectors F and P
|
// vectors F and P.
|
||||||
fn perform_wham_iteration(dataset: &Dataset, F_prev: &[f64], F: &mut Vec<f64>, P: &mut Vec<f64>) {
|
fn perform_wham_iteration(dataset: &Dataset, F_prev: &[f64], F: &mut Vec<f64>, P: &mut Vec<f64>) {
|
||||||
// evaluate first WHAM equation for each bin to
|
// Update P
|
||||||
// estimage probabilities based on previous offsets (F_prev))
|
// evaluate first WHAM equation for each bin to
|
||||||
(0..dataset.num_bins).into_par_iter()
|
// estimate probabilities based on previous offsets (F_prev))
|
||||||
|
(0..dataset.num_bins).into_par_iter()
|
||||||
.map(|bin| { calc_bin_probability(bin, dataset, F_prev) })
|
.map(|bin| { calc_bin_probability(bin, dataset, F_prev) })
|
||||||
.collect_into_vec(P);
|
.collect_into_vec(P);
|
||||||
|
|
||||||
|
// Update F
|
||||||
// evaluate second WHAM equation for each window to
|
// evaluate second WHAM equation for each window to
|
||||||
// estimate new bias offsets from propabilities
|
// estimate new bias offsets from propabilities
|
||||||
(0..dataset.num_windows).into_par_iter()
|
(0..dataset.num_windows).into_par_iter()
|
||||||
@@ -101,12 +118,20 @@ fn perform_wham_iteration(dataset: &Dataset, F_prev: &[f64], F: &mut Vec<f64>, P
|
|||||||
.collect_into_vec(F);
|
.collect_into_vec(F);
|
||||||
}
|
}
|
||||||
|
|
||||||
pub fn perform_wham(cfg: &Config, dataset: &Dataset) -> Result<(Vec<f64>, Vec<f64>, Vec<f64>)> {
|
// Full WHAM calculation. Calls `perform_wham_iteration` until convergence
|
||||||
|
// criteria are met or max iterations reached.
|
||||||
|
pub fn perform_wham(cfg: &Config, dataset: &Dataset)
|
||||||
|
-> Result<(Vec<f64>, Vec<f64>, Vec<f64>)> {
|
||||||
// allocate required vectors.
|
// allocate required vectors.
|
||||||
let mut P: Vec<f64> = vec![f64::NAN; dataset.num_bins]; // bin probability
|
|
||||||
let mut F: Vec<f64> = vec![1.0; dataset.num_windows]; // bias offset exp(F/kT)
|
// bin probability
|
||||||
let mut F_prev: Vec<f64> = vec![f64::NAN; dataset.num_windows]; // previous bias offset
|
let mut P: Vec<f64> = vec![f64::NAN; dataset.num_bins];
|
||||||
let mut F_tmp: Vec<f64> = vec![f64::NAN; dataset.num_windows]; // temp storage for F
|
// bias offset exp(F/kT)
|
||||||
|
let mut F: Vec<f64> = vec![1.0; dataset.num_windows];
|
||||||
|
// previous bias offset
|
||||||
|
let mut F_prev: Vec<f64> = vec![f64::NAN; dataset.num_windows];
|
||||||
|
// temp storage for F
|
||||||
|
let mut F_tmp: Vec<f64> = vec![f64::NAN; dataset.num_windows];
|
||||||
|
|
||||||
let mut iteration = 0;
|
let mut iteration = 0;
|
||||||
let mut converged = false;
|
let mut converged = false;
|
||||||
@@ -118,33 +143,32 @@ pub fn perform_wham(cfg: &Config, dataset: &Dataset) -> Result<(Vec<f64>, Vec<f6
|
|||||||
// store F values before the next iteration
|
// store F values before the next iteration
|
||||||
F_prev.copy_from_slice(&F);
|
F_prev.copy_from_slice(&F);
|
||||||
|
|
||||||
// perform wham iteration (this updates F and P)
|
// perform wham iteration (this updates F and P).
|
||||||
perform_wham_iteration(&dataset, &F_prev, &mut F, &mut P);
|
perform_wham_iteration(&dataset, &F_prev, &mut F, &mut P);
|
||||||
|
|
||||||
// convergence check
|
// convergence check
|
||||||
if iteration % 10 == 0 {
|
if iteration % 10 == 0 {
|
||||||
// This backups exp(F/kT) in a temporary vector and calculates true F and F_prev for
|
// This backups exp(F/kT) in a temporary vector and calculates
|
||||||
// convergence. Finally, F is restored. F_prev does not need to be restored because
|
// true F and F_prev for convergence. Finally, F is restored.
|
||||||
// its overwritten for the next iteration.
|
// F_prev does not need to be restored because its overwritten
|
||||||
|
// for the next iteration.
|
||||||
F_tmp.copy_from_slice(&F);
|
F_tmp.copy_from_slice(&F);
|
||||||
for f in F.iter_mut() { *f = -dataset.kT * f.ln() }
|
for f in F.iter_mut() { *f = -dataset.kT * f.ln() }
|
||||||
for f in F_prev.iter_mut() { *f = -dataset.kT * f.ln() }
|
for f in F_prev.iter_mut() { *f = -dataset.kT * f.ln() }
|
||||||
converged = is_converged(&F_prev, &F, cfg.tolerance);
|
converged = is_converged(&F_prev, &F, cfg.tolerance);
|
||||||
|
|
||||||
println!("Iteration {}: dF={}", &iteration, &diff_avg(&F_prev, &F));
|
if cfg.verbose {
|
||||||
|
println!("Iteration {}: dF={}", &iteration, &diff_avg(&F_prev, &F));
|
||||||
|
}
|
||||||
F.copy_from_slice(&F_tmp);
|
F.copy_from_slice(&F_tmp);
|
||||||
}
|
}
|
||||||
|
|
||||||
// Dump free energy and bias offsets
|
|
||||||
//if iteration % 100 == 0 {
|
|
||||||
// free_energy(&histograms, &mut P, &mut A);
|
|
||||||
// dump_state(&histograms, &F, &F_prev, &P, &A);
|
|
||||||
//}
|
|
||||||
}
|
}
|
||||||
|
|
||||||
// Normalize P to sum(P) = 1.0
|
// Normalize P to sum(P) = 1.0
|
||||||
let P_sum: f64 = P.iter().sum();
|
let P_sum: f64 = P.iter().sum();
|
||||||
P.iter_mut().map(|p| *p /= P_sum).count();
|
for p in P.iter_mut() {
|
||||||
|
*p /= P_sum;
|
||||||
|
}
|
||||||
|
|
||||||
if iteration == cfg.max_iterations {
|
if iteration == cfg.max_iterations {
|
||||||
bail!("WHAM not converged! (max iterations reached)");
|
bail!("WHAM not converged! (max iterations reached)");
|
||||||
@@ -161,17 +185,14 @@ pub fn run(cfg: &Config) -> Result<()>{
|
|||||||
println!("{}", &dataset);
|
println!("{}", &dataset);
|
||||||
|
|
||||||
let (P, F, F_prev) = perform_wham(&cfg, &dataset)?;
|
let (P, F, F_prev) = perform_wham(&cfg, &dataset)?;
|
||||||
|
println!("WHAM converged.");
|
||||||
|
|
||||||
let P_std: Vec<f64>;
|
let (P_std, free_energy_std) = if cfg.bootstrap > 0 {
|
||||||
let free_energy_std: Vec<f64>;
|
println!("Bootstrapping..");
|
||||||
if cfg.bootstrap > 0 {
|
error_analysis::run_bootstrap(&cfg, dataset.clone(), cfg.bootstrap)
|
||||||
let error_est = error_analysis::run_bootstrap(&cfg, dataset.clone(), &P, cfg.bootstrap);
|
|
||||||
P_std = error_est.0;
|
|
||||||
free_energy_std = error_est.1;
|
|
||||||
} else {
|
} else {
|
||||||
P_std = vec![0.0; P.len()];
|
(vec![0.0; P.len()], vec![0.0; P.len()])
|
||||||
free_energy_std = vec![0.0; P.len()];
|
};
|
||||||
}
|
|
||||||
|
|
||||||
// calculate free energy and dump state
|
// calculate free energy and dump state
|
||||||
println!("Finished. Dumping final PMF");
|
println!("Finished. Dumping final PMF");
|
||||||
@@ -214,19 +235,23 @@ fn calc_free_energy(dataset: &Dataset, P: &[f64]) -> Vec<f64> {
|
|||||||
free_energy
|
free_energy
|
||||||
}
|
}
|
||||||
|
|
||||||
fn dump_state(dataset: &Dataset, F: &[f64], F_prev: &[f64], P: &[f64], P_std: &[f64], A: &[f64], A_std: &[f64]) {
|
// Print the current WHAM iteration state. Dumps the PMF and associated vectors
|
||||||
|
fn dump_state(dataset: &Dataset, F: &[f64], F_prev: &[f64], P: &[f64],
|
||||||
|
P_std: &[f64], A: &[f64], A_std: &[f64]) {
|
||||||
// TODO fix output of F/F_prev
|
// TODO fix output of F/F_prev
|
||||||
let out = std::io::stdout();
|
let out = std::io::stdout();
|
||||||
let mut lock = out.lock();
|
let mut lock = out.lock();
|
||||||
writeln!(lock, "# PMF");
|
writeln!(lock, "# PMF").unwrap();
|
||||||
writeln!(lock, "#bin\t\tFree Energy\t\t+/-\t\tP(x)\t\t+/-");
|
writeln!(lock, "#bin\t\tFree Energy\t\t+/-\t\tP(x)\t\t+/-").unwrap();
|
||||||
for bin in 0..dataset.num_bins {
|
for bin in 0..dataset.num_bins {
|
||||||
writeln!(lock, "{:9.5}\t{:9.5}\t{:9.5}\t{:9.5}\t{:9.5}", bin, A[bin], A_std[bin], P[bin], P_std[bin]);
|
writeln!(lock, "{:9.5}\t{:9.5}\t{:9.5}\t{:9.5}\t{:9.5}",
|
||||||
|
bin, A[bin], A_std[bin], P[bin], P_std[bin]).unwrap();
|
||||||
}
|
}
|
||||||
writeln!(lock, "# Bias offsets");
|
writeln!(lock, "# Bias offsets").unwrap();
|
||||||
writeln!(lock, "#Window\t\tF\t\tF_prev");
|
writeln!(lock, "#Window\t\tF\t\tF_prev").unwrap();
|
||||||
for window in 0..dataset.num_windows {
|
for window in 0..dataset.num_windows {
|
||||||
writeln!(lock, "{}\t{:9.5}\t{:8.8}", window, F[window], (F[window]-F_prev[window]).abs());
|
writeln!(lock, "{}\t{:9.5}\t{:8.8}",
|
||||||
|
window, F[window], (F[window]-F_prev[window]).abs()).unwrap();
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
@@ -268,23 +293,23 @@ mod tests {
|
|||||||
fn calc_bin_probability() {
|
fn calc_bin_probability() {
|
||||||
let dataset = create_test_dataset();
|
let dataset = create_test_dataset();
|
||||||
let F = vec![1.0; dataset.num_bins] ;
|
let F = vec![1.0; dataset.num_bins] ;
|
||||||
let expected = vec!(0.0, 0.0825296687031316, 40.92355847097493,
|
let expected = vec!(0.0, 0.082_529_668_703_131_6, 40.923_558_470_974_93,
|
||||||
124226.70003377, 2308526035.5283747);
|
124_226.700_033_77, 2_308_526_035.528_374_7);
|
||||||
for b in 0..dataset.num_bins {
|
expected.iter().enumerate().for_each(|(i, exp)| {
|
||||||
let p = super::calc_bin_probability(b, &dataset, &F);
|
let p = super::calc_bin_probability(i, &dataset, &F);
|
||||||
assert_delta!(expected[b], p, 0.0000001);
|
assert_delta!(exp, p, 0.000_000_1);
|
||||||
}
|
})
|
||||||
}
|
}
|
||||||
|
|
||||||
#[test]
|
#[test]
|
||||||
fn calc_bias_offset() {
|
fn calc_bias_offset() {
|
||||||
let dataset = create_test_dataset();
|
let dataset = create_test_dataset();
|
||||||
let probability = vec!(0.0, 0.1, 0.2, 0.3, 0.4);
|
let probability = vec!(0.0, 0.1, 0.2, 0.3, 0.4);
|
||||||
let expected = vec!(15.927477169990633, 15.927477169990633);
|
let expected = vec!(15.927_477_169_990_633, 15.927_477_169_990_633);
|
||||||
for window in 0..dataset.num_windows {
|
expected.iter().enumerate().for_each(|(i, exp)| {
|
||||||
let F = super::calc_window_F(window, &dataset, &probability);
|
let F = super::calc_window_F(i, &dataset, &probability);
|
||||||
assert_delta!(expected[window], F, 0.0000001);
|
assert_delta!(exp, F, 0.000_000_1);
|
||||||
}
|
})
|
||||||
}
|
}
|
||||||
|
|
||||||
#[test]
|
#[test]
|
||||||
@@ -295,8 +320,8 @@ mod tests {
|
|||||||
let mut P = vec![f64::NAN; dataset.num_bins];
|
let mut P = vec![f64::NAN; dataset.num_bins];
|
||||||
super::perform_wham_iteration(&dataset, &prev_F, &mut F, &mut P);
|
super::perform_wham_iteration(&dataset, &prev_F, &mut F, &mut P);
|
||||||
let expected_F = vec!(1.0, 1.0);
|
let expected_F = vec!(1.0, 1.0);
|
||||||
let expected_P = vec!(0.0, 0.0825296687031316, 40.92355847097493,
|
let expected_P = vec!(0.0, 0.082_529_668_703_131_6, 40.923_558_470_974_93,
|
||||||
124226.70003377, 2308526035.5283747);
|
124_226.700_033_77, 2_308_526_035.528_374_7);
|
||||||
for bin in 0..dataset.num_bins {
|
for bin in 0..dataset.num_bins {
|
||||||
assert_delta!(expected_P[bin], P[bin], 0.01)
|
assert_delta!(expected_P[bin], P[bin], 0.01)
|
||||||
}
|
}
|
||||||
|
|||||||
@@ -2,8 +2,6 @@ mod command;
|
|||||||
|
|
||||||
#[cfg(test)]
|
#[cfg(test)]
|
||||||
mod integration {
|
mod integration {
|
||||||
|
|
||||||
use std::process::Command;
|
|
||||||
use super::command::get_command;
|
use super::command::get_command;
|
||||||
|
|
||||||
#[test]
|
#[test]
|
||||||
|
|||||||
Reference in New Issue
Block a user