From 36fd76ef9d9689fc99170cd2fa363617ce4c1281 Mon Sep 17 00:00:00 2001
From: Gareth Tribello <gareth.tribello@gmail.com>
Date: Wed, 2 Nov 2016 21:15:16 +0000
Subject: [PATCH] Hopefully added more reliable test for sketch-map out of
sample
---
regtest/dimred/rt-smap-osample/Makefile | 1 +
regtest/dimred/rt-smap-osample/config | 3 +
regtest/dimred/rt-smap-osample/plumed.dat | 22 +
regtest/dimred/rt-smap-osample/plumed.in | 507 ++++++++++++++++++
.../rt-smap-osample/projections.reference | 501 +++++++++++++++++
5 files changed, 1034 insertions(+)
create mode 100644 regtest/dimred/rt-smap-osample/Makefile
create mode 100644 regtest/dimred/rt-smap-osample/config
create mode 100644 regtest/dimred/rt-smap-osample/plumed.dat
create mode 100644 regtest/dimred/rt-smap-osample/plumed.in
create mode 100644 regtest/dimred/rt-smap-osample/projections.reference
diff --git a/regtest/dimred/rt-smap-osample/Makefile b/regtest/dimred/rt-smap-osample/Makefile
new file mode 100644
index 000000000..3703b27ce
--- /dev/null
+++ b/regtest/dimred/rt-smap-osample/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
diff --git a/regtest/dimred/rt-smap-osample/config b/regtest/dimred/rt-smap-osample/config
new file mode 100644
index 000000000..bc4e14b1c
--- /dev/null
+++ b/regtest/dimred/rt-smap-osample/config
@@ -0,0 +1,3 @@
+type=driver
+# this is to test a different name
+arg="--plumed plumed.dat --noatoms"
diff --git a/regtest/dimred/rt-smap-osample/plumed.dat b/regtest/dimred/rt-smap-osample/plumed.dat
new file mode 100644
index 000000000..068d284a6
--- /dev/null
+++ b/regtest/dimred/rt-smap-osample/plumed.dat
@@ -0,0 +1,22 @@
+d1: READ FILE=plumed.in VALUES=c1
+d2: READ FILE=plumed.in VALUES=c2
+d3: READ FILE=plumed.in VALUES=c3
+
+oo: EUCLIDEAN_DISSIMILARITIES ARG=d1,d2,d3 USE_ALL_DATA
+ll: LANDMARK_SELECT_STRIDE USE_OUTPUT_DATA_FROM=oo NLANDMARKS=250
+
+CLASSICAL_MDS ...
+ USE_OUTPUT_DATA_FROM=ll
+ NLOW_DIM=2
+ LABEL=mds
+... CLASSICAL_MDS
+
+SKETCHMAP_CONJGRAD ...
+ USE_OUTPUT_DATA_FROM=mds
+ HIGH_DIM_FUNCTION={SMAP R_0=4 A=3 B=2}
+ LOW_DIM_FUNCTION={SMAP R_0=4 A=1 B=2}
+ CGTOL=1E-4 LABEL=smap
+... SKETCHMAP_CONJGRAD
+
+pp: PROJECT_ALL_ANALYSIS_DATA PROJECTION=smap USE_OUTPUT_DATA_FROM=oo CGTOL=1E-3
+OUTPUT_ANALYSIS_DATA_TO_COLVAR USE_OUTPUT_DATA_FROM=pp FMT=%8.2f FILE=projections
diff --git a/regtest/dimred/rt-smap-osample/plumed.in b/regtest/dimred/rt-smap-osample/plumed.in
new file mode 100644
index 000000000..1c96756a4
--- /dev/null
+++ b/regtest/dimred/rt-smap-osample/plumed.in
@@ -0,0 +1,507 @@
+#! FIELDS time c1 c2 c3 c.bias x
+#! SET min_c1 -pi
+#! SET max_c1 pi
+#! SET min_c2 -pi
+#! SET max_c2 pi
+#! SET min_c3 -pi
+#! SET max_c3 pi
+1 -1.63647 -2.19448 1.145 19 1
+2 1.47231 0.983589 -2.05682 11 2
+3 1.47989 2.70527 1.23769 6 3
+4 -1.66607 1.28149 -0.842482 30 4
+5 -2.57117 -1.66954 -1.95307 6 5
+6 -1.75009 1.06779 2.29045 12 6
+7 0.552083 -1.96243 -1.59225 8 7
+8 1.42691 -0.474587 1.43612 6 8
+9 1.72338 -2.00472 2.97464 2 9
+10 1.89071 -1.7752 -0.0245318 3 10
+11 -1.29551 -3.10719 -1.36093 7 11
+12 0.0654693 1.3653 1.47119 12 12
+13 -1.42348 -1.2069 2.83669 4 13
+14 1.98618 1.57369 -0.28893 3 14
+15 -1.24978 -0.330908 -1.73867 6 15
+16 2.64491 1.30507 1.6579 8 16
+17 3.01208 2.00737 -1.77873 2 17
+18 2.92017 -1.75878 1.56299 6 18
+19 1.8789 -0.709893 -1.50219 12 19
+20 -0.0326084 -1.53443 1.57965 7 20
+21 0.0280411 1.65644 -1.22987 4 21
+22 -1.82688 2.15514 0.911059 7 22
+23 1.43649 2.81711 -1.39397 8 23
+24 -1.86112 -0.353627 1.31613 9 24
+25 -1.72389 -1.40666 -0.482592 7 25
+26 1.28044 1.66349 2.63232 6 26
+27 -1.22956 1.76731 -2.58239 2 27
+28 -1.04164 -1.82081 -2.14735 9 28
+29 1.47117 -1.9116 1.31689 18 29
+30 1.34394 0.884897 1.49173 23 30
+31 1.91058 -2.20125 -1.52227 11 31
+32 -1.977 0.824297 -2.0655 10 32
+33 -0.891642 2.06399 2.01779 6 33
+34 -1.37642 0.819211 1.09606 10 34
+35 -2.58168 1.94737 1.90133 8 35
+36 -0.541078 -1.31761 -1.16741 6 36
+37 -1.64394 3.14031 1.88571 6 37
+38 -2.22261 -1.64303 2.03879 17 38
+39 -2.09535 2.1275 -1.63039 9 39
+40 2.7014 -1.4336 -1.09538 3 40
+41 1.72741 1.9851 -2.57642 4 41
+42 1.08422 1.25062 -0.936592 13 42
+43 1.4905 -1.20877 -2.468 8 43
+44 -1.12808 -1.22831 1.63709 11 44
+45 1.2005 1.53337 0.515166 6 45
+46 2.2992 1.14057 -1.27738 4 46
+47 1.38347 -1.1783 2.29012 18 47
+48 1.29951 0.164676 -1.31851 7 48
+49 -1.07504 1.91924 -1.4454 22 49
+50 -1.89997 -2.25987 -1.29817 17 50
+51 1.2073 -1.36815 -1.04265 19 51
+52 -2.07319 -0.982366 -1.35099 10 52
+53 -0.994843 0.775998 -1.78413 5 53
+54 0.897226 1.88556 -1.99939 8 54
+55 -1.30664 1.69025 0.0148277 4 55
+56 0.953204 1.81632 1.62528 12 56
+57 -1.4296 -1.4063 0.552758 7 57
+58 -1.34139 -2.14991 2.09122 13 58
+59 -0.83184 1.68383 1.11277 8 59
+60 1.98763 2.01562 1.81554 12 60
+61 2.19586 -1.12566 1.74186 14 61
+62 1.84723 1.94637 -1.57797 23 62
+63 1.36218 -1.11518 0.717682 7 63
+64 1.15504 -2.7246 1.69724 5 64
+65 -2.23464 1.07777 1.4829 15 65
+66 -1.59746 -2.01002 -2.98904 3 66
+67 -2.2027 -1.31505 1.1635 15 67
+68 -2.15063 1.69416 -2.47704 3 68
+69 -2.78959 1.26451 -1.49435 5 69
+70 -1.43132 -1.05526 -2.50049 4 70
+71 2.05708 1.70377 0.947851 16 71
+72 2.01027 0.226763 1.52926 8 72
+73 1.56602 -2.10779 -2.40217 7 73
+74 0.92587 -1.21746 1.50768 19 74
+75 -1.671 2.85028 -2.0909 2 75
+76 -1.59495 1.67909 1.65932 26 76
+77 -1.81944 0.349547 -1.35265 2 77
+78 1.94921 -3.0354 -1.94266 5 78
+79 2.21765 -2.10399 1.92621 7 79
+80 2.19097 -1.45093 -2.02965 19 80
+81 -1.08339 -1.98184 -1.30493 19 81
+82 -1.79406 -0.881555 2.04358 11 82
+83 1.85927 1.2931 3.13794 6 83
+84 -1.72866 1.61997 2.9389 5 84
+85 -2.63929 -1.87572 -1.12806 3 85
+86 0.957133 -1.89722 2.16235 10 86
+87 1.29135 2.19124 -0.84659 4 87
+88 2.29316 -1.66207 1.00964 4 88
+89 -1.42978 -2.60048 -2.01651 4 89
+90 1.96159 -2.90094 1.611 9 90
+91 1.91366 -1.73615 -0.844004 9 91
+92 0.979138 -1.17623 -1.80628 7 92
+93 -1.72056 0.42656 1.78245 10 93
+94 -0.443805 1.7454 -1.92402 6 94
+95 -1.61635 -3.05639 1.08494 4 95
+96 -1.29194 2.53722 1.48399 14 96
+97 -0.953079 1.24863 1.88431 9 97
+98 -2.05528 -2.45779 1.80107 10 98
+99 -0.221246 2.10434 1.50952 2 99
+100 -0.182818 -1.60361 -1.81456 5 100
+101 -1.51945 2.05797 -0.784709 9 101
+102 1.37743 0.893437 2.28249 4 102
+103 1.28997 -1.33648 3.06037 3 103
+104 2.79069 -1.95302 -1.6802 4 104
+105 -0.833397 -1.91489 1.40003 9 105
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+124 1.1174 -0.529666 -1.3615 3 124
+125 1.34577 -2.57169 -1.89917 3 125
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+127 -2.00568 1.85456 2.31326 13 127
+128 0.461747 1.36519 -1.78053 7 128
+129 -1.10835 -1.71029 -0.301155 2 129
+130 1.98188 1.4412 2.42983 9 130
+131 1.3738 2.02601 1.07898 14 131
+132 -3.12153 -1.12406 -1.52863 3 132
+133 0.973417 0.798397 -1.5984 7 133
+134 -1.02673 -1.58574 2.40129 9 134
+135 2.03247 -1.59806 2.37249 6 135
+136 0.813446 1.40205 2.1708 10 136
+137 -2.32255 -1.98138 0.993494 7 137
+138 1.5136 2.41477 2.13363 6 138
+139 1.7459 0.913934 0.928745 12 139
+140 1.29831 1.4599 -1.58554 18 140
+141 0.734143 -1.78676 1.16545 5 141
+142 2.52419 2.0284 1.38121 8 142
+143 -1.12957 -0.601763 1.34766 9 143
+144 -1.13036 2.53482 -1.7449 7 144
+145 1.32697 0.201305 1.43499 11 145
+146 -2.85856 -1.50355 1.17584 6 146
+147 -1.92607 1.45763 -0.237063 1 147
+148 0.256291 1.75664 1.99598 2 148
+149 -1.97437 3.11764 -1.38718 4 149
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+154 1.83809 1.35882 0.355813 4 154
+155 -1.13911 1.39804 -2.01585 25 155
+156 1.58172 -2.15484 2.20519 16 156
+157 -1.38611 1.52142 0.66538 4 157
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+212 -0.957329 2.018 -2.00569 9 212
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+345 -0.00285021 -1.21727 -1.63241 4 345
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+347 2.09469 -1.91202 -1.83194 9 347
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diff --git a/regtest/dimred/rt-smap-osample/projections.reference b/regtest/dimred/rt-smap-osample/projections.reference
new file mode 100644
index 000000000..1876554fe
--- /dev/null
+++ b/regtest/dimred/rt-smap-osample/projections.reference
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--
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