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remove 1d test because of cargo size limit

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This commit is contained in:
Daniel Bauer
2020-03-08 12:52:55 +01:00
parent 1a95f222eb
commit 133234706e
41 changed files with 103 additions and 3400272 deletions
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1
README.md
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@@ -88,7 +88,6 @@ Examples
---
The example folder contains input and output files for two simple test systems:
- 1d: Hyaluronan-CD44 binding (See https://doi.org/10.1371/journal.pcbi.1005663)
- 1d_cyclic: Phi torsion angle of dialanine in vaccum
- 2d_cyclic: Phi and psi torsion angles of the same system

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example/1d/README.txt
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Data is a subset of the umbrella simulation run in 10.1371/journal.pcbi.1005663
"Atomisticfingerprintofhyaluronan–CD44binding" by Vuirio et al.
Only a subset of the original files was used to reduce file size. Please
refer to the publication for more information and original files.
wham.out was produced with the following settings:
wham --min 0.7 --max 4.5
--bins 100
-T 310
-f metadata.dat
-o wham.out
--bt 100 --seed 1234

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example/1d/metadata.dat
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pullx2_1.xvg 0.828578 1000
pullx2_2.xvg 0.894372 1000
pullx2_3.xvg 0.947997 1000
pullx2_4.xvg 1.04427 1000
pullx2_5.xvg 1.14278 1000
pullx2_6.xvg 1.24436 1000
pullx2_7.xvg 1.35144 1000
pullx2_8.xvg 1.46899 1000
pullx2_9.xvg 1.55697 1000
pullx2_10.xvg 1.67643 1000
pullx2_11.xvg 1.78437 1000
pullx2_12.xvg 1.88324 1000
pullx2_13.xvg 1.99181 1000
pullx2_14.xvg 2.10115 1000
pullx2_15.xvg 2.2161 1000
pullx2_16.xvg 2.32359 1000
pullx2_17.xvg 2.43421 1000
pullx2_18.xvg 2.55202 1000
pullx2_19.xvg 2.66111 1000
pullx2_20.xvg 2.77218 1000
pullx2_21.xvg 2.88181 1000
pullx2_22.xvg 2.99595 1000
pullx2_23.xvg 3.10619 1000
pullx2_24.xvg 3.22407 1000
pullx2_25.xvg 3.36352 1000
pullx2_26.xvg 3.47609 1000
pullx2_27.xvg 3.59642 1000
pullx2_28.xvg 3.71407 1000
pullx2_29.xvg 3.83224 1000
pullx2_30.xvg 3.94643 1000
pullx2_31.xvg 4.06551 1000
pullx2_32.xvg 4.18997 1000
pullx2_33.xvg 4.30464 1000
pullx2_34.xvg 4.42024 1000

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example/1d/wham.out
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@@ -1,101 +0,0 @@
#coord1 Free Energy +/- Probability +/-
0.719000 1.045338 0.321200 0.066227 0.008253
0.757000 0.672310 0.222353 0.076540 0.006603
0.795000 0.065559 0.230235 0.096855 0.008652
0.833000 0.000000 0.182864 0.099351 0.007049
0.871000 0.282147 0.148002 0.089049 0.005113
0.909000 0.924141 0.168668 0.069416 0.004542
0.947000 1.323815 0.162417 0.059445 0.003746
0.985000 1.442141 0.280480 0.056777 0.006178
1.023000 1.073149 0.292704 0.065516 0.007440
1.061000 2.039293 0.205105 0.045036 0.003584
1.099000 2.832833 0.485185 0.033102 0.006231
1.137000 3.617244 0.494607 0.024416 0.004685
1.175000 3.777235 0.365153 0.022947 0.003251
1.213000 3.545897 0.401465 0.025102 0.003910
1.251000 3.643923 0.552450 0.024165 0.005179
1.289000 3.557849 0.432776 0.024986 0.004195
1.327000 3.224783 0.374562 0.028432 0.004132
1.365000 3.198185 0.416317 0.028727 0.004640
1.403000 3.763371 0.387518 0.023071 0.003469
1.441000 5.694733 0.906405 0.010905 0.003835
1.479000 8.471156 2.270583 0.003714 0.003272
1.517000 9.120397 2.753665 0.002887 0.003084
1.555000 8.577757 2.485357 0.003563 0.003436
1.593000 8.949441 2.362706 0.003085 0.002828
1.631000 9.644386 2.307293 0.002356 0.002109
1.669000 10.543809 2.245210 0.001662 0.001448
1.707000 11.638565 2.324056 0.001087 0.000980
1.745000 11.727627 2.441482 0.001050 0.000994
1.783000 11.509311 2.409432 0.001143 0.001068
1.821000 11.313359 2.334143 0.001233 0.001116
1.859000 11.721043 2.449600 0.001053 0.001000
1.897000 12.615357 2.783721 0.000744 0.000803
1.935000 13.299266 2.848500 0.000571 0.000631
1.973000 13.836843 2.827743 0.000463 0.000508
2.011000 14.316781 2.825248 0.000384 0.000421
2.049000 14.543168 2.823627 0.000352 0.000386
2.087000 15.323904 2.933211 0.000260 0.000296
2.125000 16.367099 2.988800 0.000174 0.000201
2.163000 16.735406 2.807647 0.000150 0.000164
2.201000 17.146281 2.897707 0.000128 0.000144
2.239000 17.364666 2.873502 0.000118 0.000131
2.277000 17.891935 2.834906 0.000096 0.000106
2.315000 19.227582 2.889229 0.000057 0.000064
2.353000 20.338560 3.069783 0.000037 0.000044
2.391000 20.637523 3.047712 0.000033 0.000039
2.429000 20.069809 2.851374 0.000041 0.000046
2.467000 19.848484 2.855731 0.000045 0.000050
2.505000 19.822881 2.844711 0.000045 0.000050
2.543000 20.129721 2.854239 0.000040 0.000045
2.581000 19.990620 2.919055 0.000043 0.000048
2.619000 19.604754 2.939284 0.000049 0.000056
2.657000 19.331539 2.913951 0.000055 0.000062
2.695000 19.587411 2.957803 0.000050 0.000057
2.733000 19.636026 2.984551 0.000049 0.000057
2.771000 19.235521 2.915148 0.000057 0.000064
2.809000 18.808370 2.862071 0.000067 0.000075
2.847000 18.942317 2.995976 0.000064 0.000074
2.885000 19.363329 3.149785 0.000054 0.000066
2.923000 20.012558 3.222680 0.000042 0.000053
2.961000 20.173058 3.483178 0.000040 0.000054
2.999000 19.493923 3.474644 0.000052 0.000070
3.037000 18.820421 3.366128 0.000067 0.000087
3.075000 18.588460 3.697340 0.000073 0.000105
3.113000 19.068952 5.486258 0.000061 0.000129
3.151000 19.784238 6.431829 0.000046 0.000115
3.189000 19.419418 6.015023 0.000053 0.000124
3.227000 19.213801 5.954792 0.000058 0.000133
3.265000 19.048981 6.052074 0.000061 0.000144
3.303000 18.495011 5.872284 0.000076 0.000173
3.341000 18.575906 5.905808 0.000074 0.000169
3.379000 18.640359 5.879135 0.000072 0.000164
3.417000 18.735273 5.961066 0.000069 0.000160
3.455000 18.560215 5.990485 0.000074 0.000172
3.493000 18.252678 5.598918 0.000083 0.000181
3.531000 18.385414 5.511423 0.000079 0.000170
3.569000 18.418889 5.598271 0.000078 0.000170
3.607000 18.264799 5.683568 0.000083 0.000183
3.645000 18.323700 5.595971 0.000081 0.000176
3.683000 18.641658 5.610043 0.000072 0.000156
3.721000 18.883225 5.571318 0.000065 0.000141
3.759000 18.541955 5.619887 0.000075 0.000163
3.797000 18.427003 5.703009 0.000078 0.000173
3.835000 18.702330 5.755803 0.000070 0.000157
3.873000 18.551516 5.564812 0.000074 0.000161
3.911000 18.576866 5.252332 0.000074 0.000150
3.949000 18.549014 5.335647 0.000074 0.000154
3.987000 18.281190 5.354827 0.000083 0.000172
4.025000 18.262245 5.399367 0.000083 0.000174
4.063000 18.194917 5.243337 0.000085 0.000174
4.101000 18.071906 5.147383 0.000090 0.000179
4.139000 18.163805 5.139820 0.000086 0.000172
4.177000 18.436910 5.221989 0.000078 0.000157
4.215000 18.342570 5.178258 0.000081 0.000162
4.253000 18.575576 5.112701 0.000074 0.000146
4.291000 19.150807 5.139988 0.000059 0.000118
4.329000 19.466559 5.140555 0.000052 0.000104
4.367000 19.752741 5.185732 0.000047 0.000094
4.405000 19.690472 5.045691 0.000048 0.000094
4.443000 19.469823 5.053329 0.000052 0.000102
4.481000 19.315088 5.057310 0.000055 0.000108

3
example/1d_cyclic/README.txt
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@@ -5,4 +5,5 @@ wham --max pi --min -pi --cyclic\
--bins 100 \
-T 300 \
-f metadata.dat \
-o wham.out
-o wham.out \
--bt 100 --seed 1234

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example/1d_cyclic/wham.out
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#coord1 Free Energy +/- Probability +/-
-3.110177 7.158102 0.000000 0.003494 0.000000
-3.047345 5.365727 0.000000 0.007168 0.000000
-2.984513 3.873190 0.000000 0.013039 0.000000
-2.921681 2.953162 0.000000 0.018855 0.000000
-2.858849 1.949554 0.000000 0.028195 0.000000
-2.796017 1.391747 0.000000 0.035261 0.000000
-2.733186 1.128270 0.000000 0.039189 0.000000
-2.670354 0.839970 0.000000 0.043991 0.000000
-2.607522 0.624769 0.000000 0.047955 0.000000
-2.544690 0.663757 0.000000 0.047211 0.000000
-2.481858 1.051932 0.000000 0.040407 0.000000
-2.419026 1.463048 0.000000 0.034267 0.000000
-2.356194 1.990616 0.000000 0.027734 0.000000
-2.293363 2.190692 0.000000 0.025597 0.000000
-2.230531 2.553036 0.000000 0.022136 0.000000
-2.167699 2.572522 0.000000 0.021964 0.000000
-2.104867 2.472360 0.000000 0.022863 0.000000
-2.042035 2.517562 0.000000 0.022453 0.000000
-1.979203 2.469778 0.000000 0.022887 0.000000
-1.916372 2.223125 0.000000 0.025266 0.000000
-1.853540 2.080157 0.000000 0.026756 0.000000
-1.790708 1.793841 0.000000 0.030011 0.000000
-1.727876 1.458784 0.000000 0.034326 0.000000
-1.665044 0.914441 0.000000 0.042697 0.000000
-1.602212 0.303813 0.000000 0.054540 0.000000
-1.539380 0.268335 0.000000 0.055321 0.000000
-1.476549 0.000000 0.000000 0.061604 0.000000
-1.413717 0.537061 0.000000 0.049671 0.000000
-1.350885 1.439940 0.000000 0.034586 0.000000
-1.288053 2.391838 0.000000 0.023614 0.000000
-1.225221 3.779470 0.000000 0.013538 0.000000
-1.162389 5.685555 0.000000 0.006305 0.000000
-1.099557 7.661896 0.000000 0.002855 0.000000
-1.036726 9.946594 0.000000 0.001142 0.000000
-0.973894 12.359408 0.000000 0.000434 0.000000
-0.911062 14.954655 0.000000 0.000153 0.000000
-0.848230 17.742242 0.000000 0.000050 0.000000
-0.785398 20.555785 0.000000 0.000016 0.000000
-0.722566 22.811160 0.000000 0.000007 0.000000
-0.659734 25.178094 0.000000 0.000003 0.000000
-0.596903 26.442288 0.000000 0.000002 0.000000
-0.534071 27.897565 0.000000 0.000001 0.000000
-0.471239 29.062473 0.000000 0.000001 0.000000
-0.408407 30.384521 0.000000 0.000000 0.000000
-0.345575 31.638454 0.000000 0.000000 0.000000
-0.282743 32.817727 0.000000 0.000000 0.000000
-0.219911 33.770369 0.000000 0.000000 0.000000
-0.157080 34.505503 0.000000 0.000000 0.000000
-0.094248 35.431659 0.000000 0.000000 0.000000
-0.031416 35.615810 0.000000 0.000000 0.000000
0.031416 35.561946 0.000000 0.000000 0.000000
0.094248 35.382089 0.000000 0.000000 0.000000
0.157080 34.934827 0.000000 0.000000 0.000000
0.219911 33.673460 0.000000 0.000000 0.000000
0.282743 32.731563 0.000000 0.000000 0.000000
0.345575 31.261855 0.000000 0.000000 0.000000
0.408407 29.717377 0.000000 0.000000 0.000000
0.471239 28.076620 0.000000 0.000001 0.000000
0.534071 26.481097 0.000000 0.000002 0.000000
0.596903 24.487358 0.000000 0.000003 0.000000
0.659734 22.344251 0.000000 0.000008 0.000000
0.722566 20.241543 0.000000 0.000018 0.000000
0.785398 18.341869 0.000000 0.000039 0.000000
0.848230 16.261582 0.000000 0.000091 0.000000
0.911062 14.301801 0.000000 0.000199 0.000000
0.973894 12.603788 0.000000 0.000394 0.000000
1.036726 11.249601 0.000000 0.000678 0.000000
1.099557 10.087886 0.000000 0.001079 0.000000
1.162389 9.443303 0.000000 0.001398 0.000000
1.225221 9.152799 0.000000 0.001570 0.000000
1.288053 9.331937 0.000000 0.001462 0.000000
1.350885 9.905546 0.000000 0.001161 0.000000
1.413717 11.042050 0.000000 0.000736 0.000000
1.476549 12.598167 0.000000 0.000395 0.000000
1.539380 14.520167 0.000000 0.000183 0.000000
1.602212 16.569783 0.000000 0.000080 0.000000
1.665044 18.687390 0.000000 0.000034 0.000000
1.727876 20.775408 0.000000 0.000015 0.000000
1.790708 22.905200 0.000000 0.000006 0.000000
1.853540 24.643852 0.000000 0.000003 0.000000
1.916372 26.301740 0.000000 0.000002 0.000000
1.979203 27.372071 0.000000 0.000001 0.000000
2.042035 28.697726 0.000000 0.000001 0.000000
2.104867 29.417901 0.000000 0.000000 0.000000
2.167699 30.008351 0.000000 0.000000 0.000000
2.230531 30.406016 0.000000 0.000000 0.000000
2.293363 30.171275 0.000000 0.000000 0.000000
2.356194 29.884646 0.000000 0.000000 0.000000
2.419026 29.428153 0.000000 0.000000 0.000000
2.481858 28.546982 0.000000 0.000001 0.000000
2.544690 27.757520 0.000000 0.000001 0.000000
2.607522 26.505787 0.000000 0.000001 0.000000
2.670354 24.491866 0.000000 0.000003 0.000000
2.733186 22.320664 0.000000 0.000008 0.000000
2.796017 20.052723 0.000000 0.000020 0.000000
2.858849 17.655650 0.000000 0.000052 0.000000
2.921681 15.471590 0.000000 0.000125 0.000000
2.984513 13.138167 0.000000 0.000318 0.000000
3.047345 11.092386 0.000000 0.000722 0.000000
3.110177 9.065722 0.000000 0.001626 0.000000
-3.110177 7.158102 0.476037 0.003494 0.000667
-3.047345 5.365727 0.470738 0.007168 0.001353
-2.984513 3.873190 0.433120 0.013039 0.002264
-2.921681 2.953162 0.441412 0.018855 0.003337
-2.858849 1.949554 0.443549 0.028195 0.005014
-2.796017 1.391747 0.407397 0.035261 0.005759
-2.733186 1.128270 0.380789 0.039189 0.005983
-2.670354 0.839970 0.370008 0.043991 0.006526
-2.607522 0.624769 0.381081 0.047955 0.007326
-2.544690 0.663757 0.389082 0.047211 0.007364
-2.481858 1.051932 0.379999 0.040407 0.006156
-2.419026 1.463048 0.394914 0.034267 0.005425
-2.356194 1.990616 0.335141 0.027734 0.003726
-2.293363 2.190692 0.196497 0.025597 0.002016
-2.230531 2.553036 0.177045 0.022136 0.001571
-2.167699 2.572522 0.208798 0.021964 0.001839
-2.104867 2.472360 0.168929 0.022863 0.001548
-2.042035 2.517562 0.166774 0.022453 0.001501
-1.979203 2.469778 0.182308 0.022887 0.001673
-1.916372 2.223125 0.405294 0.025266 0.004105
-1.853540 2.080157 0.340376 0.026756 0.003651
-1.790708 1.793841 0.394974 0.030011 0.004752
-1.727876 1.458784 0.335956 0.034326 0.004623
-1.665044 0.914441 0.336724 0.042697 0.005764
-1.602212 0.303813 0.320695 0.054540 0.007012
-1.539380 0.268335 0.330495 0.055321 0.007330
-1.476549 0.000000 0.338143 0.061604 0.008351
-1.413717 0.537061 0.369220 0.049671 0.007352
-1.350885 1.439940 0.381006 0.034586 0.005283
-1.288053 2.391838 0.407306 0.023614 0.003856
-1.225221 3.779470 0.413629 0.013538 0.002245
-1.162389 5.685555 0.432485 0.006305 0.001093
-1.099557 7.661896 0.446994 0.002855 0.000512
-1.036726 9.946594 0.489990 0.001142 0.000224
-0.973894 12.359408 0.544847 0.000434 0.000095
-0.911062 14.954655 0.622373 0.000153 0.000038
-0.848230 17.742242 0.747233 0.000050 0.000015
-0.785398 20.555785 0.921773 0.000016 0.000006
-0.722566 22.811160 1.179343 0.000007 0.000003
-0.659734 25.178094 1.484376 0.000003 0.000002
-0.596903 26.442288 1.565063 0.000002 0.000001
-0.534071 27.897565 1.418232 0.000001 0.000000
-0.471239 29.062473 1.246738 0.000001 0.000000
-0.408407 30.384521 1.231662 0.000000 0.000000
-0.345575 31.638454 1.209295 0.000000 0.000000
-0.282743 32.817727 1.291637 0.000000 0.000000
-0.219911 33.770369 1.323362 0.000000 0.000000
-0.157080 34.505503 1.396454 0.000000 0.000000
-0.094248 35.431659 1.662548 0.000000 0.000000
-0.031416 35.615810 1.766523 0.000000 0.000000
0.031416 35.561946 1.799603 0.000000 0.000000
0.094248 35.382089 1.374764 0.000000 0.000000
0.157080 34.934827 1.659669 0.000000 0.000000
0.219911 33.673460 1.317449 0.000000 0.000000
0.282743 32.731563 1.191975 0.000000 0.000000
0.345575 31.261855 1.199834 0.000000 0.000000
0.408407 29.717377 1.339899 0.000000 0.000000
0.471239 28.076620 1.303458 0.000001 0.000000
0.534071 26.481097 1.281459 0.000002 0.000001
0.596903 24.487358 1.251139 0.000003 0.000002
0.659734 22.344251 1.233967 0.000008 0.000004
0.722566 20.241543 1.251834 0.000018 0.000009
0.785398 18.341869 1.241684 0.000039 0.000020
0.848230 16.261582 1.281159 0.000091 0.000047
0.911062 14.301801 1.294427 0.000199 0.000103
0.973894 12.603788 1.270069 0.000394 0.000200
1.036726 11.249601 1.273360 0.000678 0.000346
1.099557 10.087886 1.280795 0.001079 0.000554
1.162389 9.443303 1.266983 0.001398 0.000710
1.225221 9.152799 1.255009 0.001570 0.000790
1.288053 9.331937 1.256822 0.001462 0.000736
1.350885 9.905546 1.251237 0.001161 0.000583
1.413717 11.042050 1.263816 0.000736 0.000373
1.476549 12.598167 1.275325 0.000395 0.000202
1.539380 14.520167 1.280735 0.000183 0.000094
1.602212 16.569783 1.295384 0.000080 0.000042
1.665044 18.687390 1.309518 0.000034 0.000018
1.727876 20.775408 1.356414 0.000015 0.000008
1.790708 22.905200 1.308568 0.000006 0.000003
1.853540 24.643852 1.425870 0.000003 0.000002
1.916372 26.301740 1.362138 0.000002 0.000001
1.979203 27.372071 1.391716 0.000001 0.000001
2.042035 28.697726 1.504676 0.000001 0.000000
2.104867 29.417901 1.369019 0.000000 0.000000
2.167699 30.008351 1.409081 0.000000 0.000000
2.230531 30.406016 1.240128 0.000000 0.000000
2.293363 30.171275 1.179444 0.000000 0.000000
2.356194 29.884646 1.219365 0.000000 0.000000
2.419026 29.428153 1.177281 0.000000 0.000000
2.481858 28.546982 1.351057 0.000001 0.000000
2.544690 27.757520 1.238695 0.000001 0.000000
2.607522 26.505787 1.308430 0.000001 0.000001
2.670354 24.491866 1.039660 0.000003 0.000001
2.733186 22.320664 0.927893 0.000008 0.000003
2.796017 20.052723 0.894483 0.000020 0.000007
2.858849 17.655650 0.893580 0.000052 0.000019
2.921681 15.471590 0.930897 0.000125 0.000047
2.984513 13.138167 0.837026 0.000318 0.000107
3.047345 11.092386 0.674785 0.000722 0.000195
3.110177 9.065722 0.521230 0.001626 0.000340

23
tests/examples.rs
View File

@@ -8,31 +8,10 @@ mod integration {
use super::command::get_command;
#[test]
#[ignore] // expensive
fn wham_1d() {
get_command()
.args(&["--bins", "100", "--max", "4.5", "--min", "0.7", "-T", "310"])
.args(&["--bt", "100", "--seed", "1234"])
.args(&["-f", "example/1d/metadata.dat"])
.args(&["-o", "/tmp/wham_test_1d.out"])
.output()
.expect("failed to execute process");
assert!(fs::metadata("/tmp/wham_test_1d.out").is_ok());
let output = Command::new("diff")
.arg("/tmp/wham_test_1d.out")
.arg("example/1d/wham.out")
.output()
.expect("failed to run diff");
let output_len = String::from_utf8_lossy(&output.stdout).len();
assert_eq!(output_len, 0);
}
#[test]
#[ignore] // expensive
fn wham_1d_cyclic() {
get_command()
.args(&["--bins", "100", "--max", "pi", "--min", "-pi", "-T", "300", "--cyclic"])
.args(&["--bt", "100", "--seed", "1234"])
.args(&["-f", "example/1d_cyclic/metadata.dat"])
.args(&["-o", "/tmp/wham_test_1d_cyclic.out"])
.output()