diff --git a/regtest/analysis/rt-reselect-land/data.reference b/regtest/analysis/rt-reselect-land/data.reference
index ad74b29f731a2ab1c0eca13f0f968bcf33f50abe..d685c75d692f862f192823409bd53802cc8a74e6 100644
--- a/regtest/analysis/rt-reselect-land/data.reference
+++ b/regtest/analysis/rt-reselect-land/data.reference
@@ -1,3 +1,3 @@
-#! FIELDS dist
- 1.2626
- 1.3934
+#! FIELDS dist weight
+ 1.2626 2.0000
+ 1.3934 3.0000
diff --git a/regtest/analysis/rt-store-print/analysis.0.output-half.pdb.reference b/regtest/analysis/rt-store-print/analysis.0.output-half.pdb.reference
index bf99439cf74b2563e4e1d30e92e3c20d14199c82..59f120ceae90b57c22d8ae68fe8f853944101ccf 100644
--- a/regtest/analysis/rt-store-print/analysis.0.output-half.pdb.reference
+++ b/regtest/analysis/rt-store-print/analysis.0.output-half.pdb.reference
@@ -1,7 +1,7 @@
-#! FIELDS d1
-0.000000
-1.000000
-2.000000
-3.000000
-4.000000
-5.000000
+#! FIELDS d1 weight
+0.000000 1.000000
+1.000000 1.000000
+2.000000 1.000000
+3.000000 1.000000
+4.000000 1.000000
+5.000000 1.000000
diff --git a/regtest/analysis/rt-store-print/analysis.0.output-stride2.pdb.reference b/regtest/analysis/rt-store-print/analysis.0.output-stride2.pdb.reference
index 59f916c90079db43135ad0b155387f1faac29313..457d66b29f0d298f8ae8953aafa0259f3449f155 100644
--- a/regtest/analysis/rt-store-print/analysis.0.output-stride2.pdb.reference
+++ b/regtest/analysis/rt-store-print/analysis.0.output-stride2.pdb.reference
@@ -1,4 +1,4 @@
-#! FIELDS d1
-0.000000
-2.000000
-4.000000
+#! FIELDS d1 weight
+0.000000 1.000000
+2.000000 1.000000
+4.000000 1.000000
diff --git a/regtest/analysis/rt-store-print/output-all.pdb.reference b/regtest/analysis/rt-store-print/output-all.pdb.reference
index 28cf6f1a23b24dfc22ed57587cdf10b36ca69a0a..fb5a52798223ca4462f7b011cadcc5aa55f22d3f 100644
--- a/regtest/analysis/rt-store-print/output-all.pdb.reference
+++ b/regtest/analysis/rt-store-print/output-all.pdb.reference
@@ -1,14 +1,14 @@
-#! FIELDS d1
-0.000000
-0.000000
-1.000000
-2.000000
-3.000000
-4.000000
-5.000000
-6.000000
-7.000000
-8.000000
-9.000000
-10.000000
-11.000000
+#! FIELDS d1 weight
+0.000000 1.000000
+0.000000 1.000000
+1.000000 1.000000
+2.000000 1.000000
+3.000000 1.000000
+4.000000 1.000000
+5.000000 1.000000
+6.000000 1.000000
+7.000000 1.000000
+8.000000 1.000000
+9.000000 1.000000
+10.000000 1.000000
+11.000000 1.000000
diff --git a/regtest/analysis/rt-store-print/output-half.pdb.reference b/regtest/analysis/rt-store-print/output-half.pdb.reference
index 894fea15fcb0ad0949d484b0e12e2a981f26c41c..5890cf725a0430fe5aab8f605bd314b9d87290ee 100644
--- a/regtest/analysis/rt-store-print/output-half.pdb.reference
+++ b/regtest/analysis/rt-store-print/output-half.pdb.reference
@@ -1,7 +1,7 @@
-#! FIELDS d1
-6.000000
-7.000000
-8.000000
-9.000000
-10.000000
-11.000000
+#! FIELDS d1 weight
+6.000000 1.000000
+7.000000 1.000000
+8.000000 1.000000
+9.000000 1.000000
+10.000000 1.000000
+11.000000 1.000000
diff --git a/regtest/analysis/rt-store-print/output-reuse.pdb.reference b/regtest/analysis/rt-store-print/output-reuse.pdb.reference
index 28cf6f1a23b24dfc22ed57587cdf10b36ca69a0a..fb5a52798223ca4462f7b011cadcc5aa55f22d3f 100644
--- a/regtest/analysis/rt-store-print/output-reuse.pdb.reference
+++ b/regtest/analysis/rt-store-print/output-reuse.pdb.reference
@@ -1,14 +1,14 @@
-#! FIELDS d1
-0.000000
-0.000000
-1.000000
-2.000000
-3.000000
-4.000000
-5.000000
-6.000000
-7.000000
-8.000000
-9.000000
-10.000000
-11.000000
+#! FIELDS d1 weight
+0.000000 1.000000
+0.000000 1.000000
+1.000000 1.000000
+2.000000 1.000000
+3.000000 1.000000
+4.000000 1.000000
+5.000000 1.000000
+6.000000 1.000000
+7.000000 1.000000
+8.000000 1.000000
+9.000000 1.000000
+10.000000 1.000000
+11.000000 1.000000
diff --git a/regtest/analysis/rt-store-print/output-stride.pdb.reference b/regtest/analysis/rt-store-print/output-stride.pdb.reference
index 9af0c7c91dc443faf6ef5ab71aed39e67ced3cb5..460a23a01dea551690cfb8203412a22c1b75f72b 100644
--- a/regtest/analysis/rt-store-print/output-stride.pdb.reference
+++ b/regtest/analysis/rt-store-print/output-stride.pdb.reference
@@ -1,6 +1,6 @@
-#! FIELDS d1
-0.000000
-1.000000
-3.000000
-5.000000
-7.000000
+#! FIELDS d1 weight
+0.000000 1.000000
+1.000000 1.000000
+3.000000 1.000000
+5.000000 1.000000
+7.000000 1.000000
diff --git a/regtest/analysis/rt-store-print/output-stride2.pdb.reference b/regtest/analysis/rt-store-print/output-stride2.pdb.reference
index 4e9c140cda4f2303e8b1e90804a8e55a3c90b5f0..f25543be338ad60241210c0d9c697fb46c9e1e7b 100644
--- a/regtest/analysis/rt-store-print/output-stride2.pdb.reference
+++ b/regtest/analysis/rt-store-print/output-stride2.pdb.reference
@@ -1,4 +1,4 @@
-#! FIELDS d1
-6.000000
-8.000000
-10.000000
+#! FIELDS d1 weight
+6.000000 1.000000
+8.000000 1.000000
+10.000000 1.000000
diff --git a/regtest/dimred/rt-mds/analysis.0.list_embed.reference b/regtest/dimred/rt-mds/analysis.0.list_embed.reference
index 185b19ed5558aa853b2fd67022b2c0c1250983a2..8cf06ed57a8e5c07a59db04c7270ed3c015a9f77 100644
--- a/regtest/dimred/rt-mds/analysis.0.list_embed.reference
+++ b/regtest/dimred/rt-mds/analysis.0.list_embed.reference
@@ -1,101 +1,101 @@
-#! FIELDS mds.1 mds.2
- 0.0873 0.0013
- 0.0535 0.0044
- 0.0150 0.0044
- -0.0136 0.0019
- -0.0308 -0.0012
- -0.0355 -0.0018
- -0.0090 -0.0015
- 0.0145 0.0004
- 0.0191 0.0022
- 0.0278 0.0015
- 0.0091 -0.0004
- -0.0359 -0.0012
- -0.0540 0.0004
- -0.0322 -0.0034
- -0.0205 -0.0150
- -0.0282 -0.0289
- -0.0530 -0.0358
- -0.0769 -0.0312
- -0.0893 -0.0259
- -0.0697 -0.0246
- -0.0302 -0.0196
- 0.0093 -0.0072
- 0.0274 0.0009
- 0.0301 0.0016
- 0.0265 -0.0033
- 0.0433 -0.0053
- 0.0514 -0.0019
- 0.0222 0.0031
- -0.0129 0.0061
- -0.0322 0.0084
- -0.0355 0.0080
- -0.0337 0.0067
- -0.0308 0.0047
- -0.0253 0.0016
- -0.0132 -0.0021
- 0.0040 -0.0031
- 0.0107 0.0011
- 0.0299 0.0060
- 0.0540 0.0070
- 0.0650 0.0039
- 0.0415 0.0025
- 0.0074 0.0033
- -0.0185 0.0059
- -0.0413 0.0073
- -0.0548 0.0074
- -0.0385 0.0041
- -0.0383 -0.0006
- -0.0584 -0.0008
- -0.0584 0.0023
- -0.0553 0.0090
- -0.0772 0.0146
- -0.0757 0.0157
- -0.0644 0.0144
- -0.0816 0.0141
- -0.1045 0.0148
- -0.0867 0.0111
- -0.0365 0.0014
- 0.0113 -0.0067
- 0.0272 -0.0074
- 0.0381 -0.0012
- 0.0548 0.0021
- 0.0470 0.0012
- 0.0227 -0.0019
- 0.0132 -0.0022
- 0.0040 0.0004
- -0.0045 0.0008
- -0.0145 0.0006
- -0.0116 0.0025
- -0.0031 0.0044
- -0.0148 0.0086
- -0.0318 0.0109
- -0.0166 0.0078
- 0.0154 0.0036
- 0.0451 0.0018
- 0.0364 0.0021
- 0.0125 0.0036
- 0.0330 0.0045
- 0.0605 0.0048
- 0.0417 0.0041
- 0.0115 0.0011
- 0.0257 -0.0018
- 0.0451 -0.0029
- 0.0387 -0.0032
- 0.0254 -0.0017
- 0.0311 -0.0001
- 0.0448 0.0006
- 0.0499 0.0020
- 0.0543 0.0037
- 0.0486 0.0054
- 0.0459 0.0051
- 0.0715 -0.0001
- 0.0764 -0.0063
- 0.0603 -0.0119
- 0.0378 -0.0153
- 0.0214 -0.0124
- 0.0063 -0.0091
- -0.0095 -0.0016
- -0.0259 0.0036
- -0.0234 0.0061
- 0.0012 0.0060
+#! FIELDS mds.1 mds.2 weight
+ 0.0873 0.0013 1.0000
+ 0.0535 0.0044 1.0000
+ 0.0150 0.0044 1.0000
+ -0.0136 0.0019 1.0000
+ -0.0308 -0.0012 1.0000
+ -0.0355 -0.0018 1.0000
+ -0.0090 -0.0015 1.0000
+ 0.0145 0.0004 1.0000
+ 0.0191 0.0022 1.0000
+ 0.0278 0.0015 1.0000
+ 0.0091 -0.0004 1.0000
+ -0.0359 -0.0012 1.0000
+ -0.0540 0.0004 1.0000
+ -0.0322 -0.0034 1.0000
+ -0.0205 -0.0150 1.0000
+ -0.0282 -0.0289 1.0000
+ -0.0530 -0.0358 1.0000
+ -0.0769 -0.0312 1.0000
+ -0.0893 -0.0259 1.0000
+ -0.0697 -0.0246 1.0000
+ -0.0302 -0.0196 1.0000
+ 0.0093 -0.0072 1.0000
+ 0.0274 0.0009 1.0000
+ 0.0301 0.0016 1.0000
+ 0.0265 -0.0033 1.0000
+ 0.0433 -0.0053 1.0000
+ 0.0514 -0.0019 1.0000
+ 0.0222 0.0031 1.0000
+ -0.0129 0.0061 1.0000
+ -0.0322 0.0084 1.0000
+ -0.0355 0.0080 1.0000
+ -0.0337 0.0067 1.0000
+ -0.0308 0.0047 1.0000
+ -0.0253 0.0016 1.0000
+ -0.0132 -0.0021 1.0000
+ 0.0040 -0.0031 1.0000
+ 0.0107 0.0011 1.0000
+ 0.0299 0.0060 1.0000
+ 0.0540 0.0070 1.0000
+ 0.0650 0.0039 1.0000
+ 0.0415 0.0025 1.0000
+ 0.0074 0.0033 1.0000
+ -0.0185 0.0059 1.0000
+ -0.0413 0.0073 1.0000
+ -0.0548 0.0074 1.0000
+ -0.0385 0.0041 1.0000
+ -0.0383 -0.0006 1.0000
+ -0.0584 -0.0008 1.0000
+ -0.0584 0.0023 1.0000
+ -0.0553 0.0090 1.0000
+ -0.0772 0.0146 1.0000
+ -0.0757 0.0157 1.0000
+ -0.0644 0.0144 1.0000
+ -0.0816 0.0141 1.0000
+ -0.1045 0.0148 1.0000
+ -0.0867 0.0111 1.0000
+ -0.0365 0.0014 1.0000
+ 0.0113 -0.0067 1.0000
+ 0.0272 -0.0074 1.0000
+ 0.0381 -0.0012 1.0000
+ 0.0548 0.0021 1.0000
+ 0.0470 0.0012 1.0000
+ 0.0227 -0.0019 1.0000
+ 0.0132 -0.0022 1.0000
+ 0.0040 0.0004 1.0000
+ -0.0045 0.0008 1.0000
+ -0.0145 0.0006 1.0000
+ -0.0116 0.0025 1.0000
+ -0.0031 0.0044 1.0000
+ -0.0148 0.0086 1.0000
+ -0.0318 0.0109 1.0000
+ -0.0166 0.0078 1.0000
+ 0.0154 0.0036 1.0000
+ 0.0451 0.0018 1.0000
+ 0.0364 0.0021 1.0000
+ 0.0125 0.0036 1.0000
+ 0.0330 0.0045 1.0000
+ 0.0605 0.0048 1.0000
+ 0.0417 0.0041 1.0000
+ 0.0115 0.0011 1.0000
+ 0.0257 -0.0018 1.0000
+ 0.0451 -0.0029 1.0000
+ 0.0387 -0.0032 1.0000
+ 0.0254 -0.0017 1.0000
+ 0.0311 -0.0001 1.0000
+ 0.0448 0.0006 1.0000
+ 0.0499 0.0020 1.0000
+ 0.0543 0.0037 1.0000
+ 0.0486 0.0054 1.0000
+ 0.0459 0.0051 1.0000
+ 0.0715 -0.0001 1.0000
+ 0.0764 -0.0063 1.0000
+ 0.0603 -0.0119 1.0000
+ 0.0378 -0.0153 1.0000
+ 0.0214 -0.0124 1.0000
+ 0.0063 -0.0091 1.0000
+ -0.0095 -0.0016 1.0000
+ -0.0259 0.0036 1.0000
+ -0.0234 0.0061 1.0000
+ 0.0012 0.0060 1.0000
diff --git a/regtest/dimred/rt-mds/list_embed.reference b/regtest/dimred/rt-mds/list_embed.reference
index b24c465dfceac9021d1e5b3dec7800870f408522..583254a00b55764b6973300fb6bd335e41e3e26c 100644
--- a/regtest/dimred/rt-mds/list_embed.reference
+++ b/regtest/dimred/rt-mds/list_embed.reference
@@ -1,101 +1,101 @@
-#! FIELDS mds.1 mds.2
- 0.0594 0.0053
- 0.0683 0.0034
- 0.0705 0.0006
- 0.0729 -0.0019
- 0.0874 -0.0069
- 0.0961 -0.0095
- 0.0867 -0.0062
- 0.0719 -0.0008
- 0.0575 0.0031
- 0.0552 0.0034
- 0.0682 -0.0002
- 0.0781 -0.0024
- 0.0785 -0.0025
- 0.0763 -0.0027
- 0.0755 -0.0041
- 0.0792 -0.0069
- 0.0778 -0.0062
- 0.0727 -0.0025
- 0.0726 0.0014
- 0.0756 0.0030
- 0.0821 0.0017
- 0.0816 0.0001
- 0.0774 0.0008
- 0.0766 0.0008
- 0.0838 -0.0005
- 0.0931 -0.0016
- 0.0936 -0.0010
- 0.0923 -0.0009
- 0.0906 -0.0008
- 0.0706 0.0025
- 0.0664 0.0050
- 0.0901 0.0019
- 0.1059 -0.0015
- 0.0917 0.0006
- 0.0876 0.0021
- 0.1008 -0.0001
- 0.0955 -0.0014
- 0.0858 -0.0018
- 0.0894 -0.0005
- 0.0922 0.0014
- 0.0917 0.0010
- 0.0925 -0.0043
- 0.0967 -0.0102
- 0.1073 -0.0096
- 0.1065 -0.0047
- 0.0935 -0.0003
- 0.0668 0.0049
- 0.0410 0.0086
- 0.0264 0.0110
- 0.0254 0.0125
- 0.0503 0.0085
- 0.0855 0.0007
- 0.0975 -0.0028
- 0.0983 -0.0035
- 0.0997 -0.0044
- 0.0877 -0.0021
- 0.0501 0.0053
- 0.0104 0.0140
- -0.0199 0.0221
- -0.0416 0.0277
- -0.0688 0.0338
- -0.0858 0.0354
- -0.0897 0.0313
- -0.0920 0.0254
- -0.1168 0.0227
- -0.1447 0.0227
- -0.1636 0.0221
- -0.1461 0.0182
- -0.1212 0.0139
- -0.0775 0.0056
- -0.0008 -0.0041
- 0.0469 -0.0038
- 0.0771 -0.0004
- 0.0917 0.0005
- 0.0656 0.0042
- -0.0034 0.0115
- -0.0901 0.0141
- -0.1784 0.0069
- -0.2253 -0.0077
- -0.2372 -0.0248
- -0.2415 -0.0448
- -0.2562 -0.0539
- -0.2901 -0.0433
- -0.3173 -0.0215
- -0.3117 0.0096
- -0.2787 0.0317
- -0.2319 0.0372
- -0.1897 0.0305
- -0.1592 0.0142
- -0.1212 -0.0049
- -0.0960 -0.0150
- -0.0842 -0.0162
- -0.0813 -0.0187
- -0.0823 -0.0193
- -0.0773 -0.0179
- -0.0621 -0.0202
- -0.0449 -0.0215
- -0.0269 -0.0307
- -0.0075 -0.0368
- 0.0266 -0.0342
+#! FIELDS mds.1 mds.2 weight
+ 0.0594 0.0053 1.0000
+ 0.0683 0.0034 1.0000
+ 0.0705 0.0006 1.0000
+ 0.0729 -0.0019 1.0000
+ 0.0874 -0.0069 1.0000
+ 0.0961 -0.0095 1.0000
+ 0.0867 -0.0062 1.0000
+ 0.0719 -0.0008 1.0000
+ 0.0575 0.0031 1.0000
+ 0.0552 0.0034 1.0000
+ 0.0682 -0.0002 1.0000
+ 0.0781 -0.0024 1.0000
+ 0.0785 -0.0025 1.0000
+ 0.0763 -0.0027 1.0000
+ 0.0755 -0.0041 1.0000
+ 0.0792 -0.0069 1.0000
+ 0.0778 -0.0062 1.0000
+ 0.0727 -0.0025 1.0000
+ 0.0726 0.0014 1.0000
+ 0.0756 0.0030 1.0000
+ 0.0821 0.0017 1.0000
+ 0.0816 0.0001 1.0000
+ 0.0774 0.0008 1.0000
+ 0.0766 0.0008 1.0000
+ 0.0838 -0.0005 1.0000
+ 0.0931 -0.0016 1.0000
+ 0.0936 -0.0010 1.0000
+ 0.0923 -0.0009 1.0000
+ 0.0906 -0.0008 1.0000
+ 0.0706 0.0025 1.0000
+ 0.0664 0.0050 1.0000
+ 0.0901 0.0019 1.0000
+ 0.1059 -0.0015 1.0000
+ 0.0917 0.0006 1.0000
+ 0.0876 0.0021 1.0000
+ 0.1008 -0.0001 1.0000
+ 0.0955 -0.0014 1.0000
+ 0.0858 -0.0018 1.0000
+ 0.0894 -0.0005 1.0000
+ 0.0922 0.0014 1.0000
+ 0.0917 0.0010 1.0000
+ 0.0925 -0.0043 1.0000
+ 0.0967 -0.0102 1.0000
+ 0.1073 -0.0096 1.0000
+ 0.1065 -0.0047 1.0000
+ 0.0935 -0.0003 1.0000
+ 0.0668 0.0049 1.0000
+ 0.0410 0.0086 1.0000
+ 0.0264 0.0110 1.0000
+ 0.0254 0.0125 1.0000
+ 0.0503 0.0085 1.0000
+ 0.0855 0.0007 1.0000
+ 0.0975 -0.0028 1.0000
+ 0.0983 -0.0035 1.0000
+ 0.0997 -0.0044 1.0000
+ 0.0877 -0.0021 1.0000
+ 0.0501 0.0053 1.0000
+ 0.0104 0.0140 1.0000
+ -0.0199 0.0221 1.0000
+ -0.0416 0.0277 1.0000
+ -0.0688 0.0338 1.0000
+ -0.0858 0.0354 1.0000
+ -0.0897 0.0313 1.0000
+ -0.0920 0.0254 1.0000
+ -0.1168 0.0227 1.0000
+ -0.1447 0.0227 1.0000
+ -0.1636 0.0221 1.0000
+ -0.1461 0.0182 1.0000
+ -0.1212 0.0139 1.0000
+ -0.0775 0.0056 1.0000
+ -0.0008 -0.0041 1.0000
+ 0.0469 -0.0038 1.0000
+ 0.0771 -0.0004 1.0000
+ 0.0917 0.0005 1.0000
+ 0.0656 0.0042 1.0000
+ -0.0034 0.0115 1.0000
+ -0.0901 0.0141 1.0000
+ -0.1784 0.0069 1.0000
+ -0.2253 -0.0077 1.0000
+ -0.2372 -0.0248 1.0000
+ -0.2415 -0.0448 1.0000
+ -0.2562 -0.0539 1.0000
+ -0.2901 -0.0433 1.0000
+ -0.3173 -0.0215 1.0000
+ -0.3117 0.0096 1.0000
+ -0.2787 0.0317 1.0000
+ -0.2319 0.0372 1.0000
+ -0.1897 0.0305 1.0000
+ -0.1592 0.0142 1.0000
+ -0.1212 -0.0049 1.0000
+ -0.0960 -0.0150 1.0000
+ -0.0842 -0.0162 1.0000
+ -0.0813 -0.0187 1.0000
+ -0.0823 -0.0193 1.0000
+ -0.0773 -0.0179 1.0000
+ -0.0621 -0.0202 1.0000
+ -0.0449 -0.0215 1.0000
+ -0.0269 -0.0307 1.0000
+ -0.0075 -0.0368 1.0000
+ 0.0266 -0.0342 1.0000
diff --git a/regtest/dimred/rt-mds2/analysis.0.list_embed.reference b/regtest/dimred/rt-mds2/analysis.0.list_embed.reference
index 185b19ed5558aa853b2fd67022b2c0c1250983a2..8cf06ed57a8e5c07a59db04c7270ed3c015a9f77 100644
--- a/regtest/dimred/rt-mds2/analysis.0.list_embed.reference
+++ b/regtest/dimred/rt-mds2/analysis.0.list_embed.reference
@@ -1,101 +1,101 @@
-#! FIELDS mds.1 mds.2
- 0.0873 0.0013
- 0.0535 0.0044
- 0.0150 0.0044
- -0.0136 0.0019
- -0.0308 -0.0012
- -0.0355 -0.0018
- -0.0090 -0.0015
- 0.0145 0.0004
- 0.0191 0.0022
- 0.0278 0.0015
- 0.0091 -0.0004
- -0.0359 -0.0012
- -0.0540 0.0004
- -0.0322 -0.0034
- -0.0205 -0.0150
- -0.0282 -0.0289
- -0.0530 -0.0358
- -0.0769 -0.0312
- -0.0893 -0.0259
- -0.0697 -0.0246
- -0.0302 -0.0196
- 0.0093 -0.0072
- 0.0274 0.0009
- 0.0301 0.0016
- 0.0265 -0.0033
- 0.0433 -0.0053
- 0.0514 -0.0019
- 0.0222 0.0031
- -0.0129 0.0061
- -0.0322 0.0084
- -0.0355 0.0080
- -0.0337 0.0067
- -0.0308 0.0047
- -0.0253 0.0016
- -0.0132 -0.0021
- 0.0040 -0.0031
- 0.0107 0.0011
- 0.0299 0.0060
- 0.0540 0.0070
- 0.0650 0.0039
- 0.0415 0.0025
- 0.0074 0.0033
- -0.0185 0.0059
- -0.0413 0.0073
- -0.0548 0.0074
- -0.0385 0.0041
- -0.0383 -0.0006
- -0.0584 -0.0008
- -0.0584 0.0023
- -0.0553 0.0090
- -0.0772 0.0146
- -0.0757 0.0157
- -0.0644 0.0144
- -0.0816 0.0141
- -0.1045 0.0148
- -0.0867 0.0111
- -0.0365 0.0014
- 0.0113 -0.0067
- 0.0272 -0.0074
- 0.0381 -0.0012
- 0.0548 0.0021
- 0.0470 0.0012
- 0.0227 -0.0019
- 0.0132 -0.0022
- 0.0040 0.0004
- -0.0045 0.0008
- -0.0145 0.0006
- -0.0116 0.0025
- -0.0031 0.0044
- -0.0148 0.0086
- -0.0318 0.0109
- -0.0166 0.0078
- 0.0154 0.0036
- 0.0451 0.0018
- 0.0364 0.0021
- 0.0125 0.0036
- 0.0330 0.0045
- 0.0605 0.0048
- 0.0417 0.0041
- 0.0115 0.0011
- 0.0257 -0.0018
- 0.0451 -0.0029
- 0.0387 -0.0032
- 0.0254 -0.0017
- 0.0311 -0.0001
- 0.0448 0.0006
- 0.0499 0.0020
- 0.0543 0.0037
- 0.0486 0.0054
- 0.0459 0.0051
- 0.0715 -0.0001
- 0.0764 -0.0063
- 0.0603 -0.0119
- 0.0378 -0.0153
- 0.0214 -0.0124
- 0.0063 -0.0091
- -0.0095 -0.0016
- -0.0259 0.0036
- -0.0234 0.0061
- 0.0012 0.0060
+#! FIELDS mds.1 mds.2 weight
+ 0.0873 0.0013 1.0000
+ 0.0535 0.0044 1.0000
+ 0.0150 0.0044 1.0000
+ -0.0136 0.0019 1.0000
+ -0.0308 -0.0012 1.0000
+ -0.0355 -0.0018 1.0000
+ -0.0090 -0.0015 1.0000
+ 0.0145 0.0004 1.0000
+ 0.0191 0.0022 1.0000
+ 0.0278 0.0015 1.0000
+ 0.0091 -0.0004 1.0000
+ -0.0359 -0.0012 1.0000
+ -0.0540 0.0004 1.0000
+ -0.0322 -0.0034 1.0000
+ -0.0205 -0.0150 1.0000
+ -0.0282 -0.0289 1.0000
+ -0.0530 -0.0358 1.0000
+ -0.0769 -0.0312 1.0000
+ -0.0893 -0.0259 1.0000
+ -0.0697 -0.0246 1.0000
+ -0.0302 -0.0196 1.0000
+ 0.0093 -0.0072 1.0000
+ 0.0274 0.0009 1.0000
+ 0.0301 0.0016 1.0000
+ 0.0265 -0.0033 1.0000
+ 0.0433 -0.0053 1.0000
+ 0.0514 -0.0019 1.0000
+ 0.0222 0.0031 1.0000
+ -0.0129 0.0061 1.0000
+ -0.0322 0.0084 1.0000
+ -0.0355 0.0080 1.0000
+ -0.0337 0.0067 1.0000
+ -0.0308 0.0047 1.0000
+ -0.0253 0.0016 1.0000
+ -0.0132 -0.0021 1.0000
+ 0.0040 -0.0031 1.0000
+ 0.0107 0.0011 1.0000
+ 0.0299 0.0060 1.0000
+ 0.0540 0.0070 1.0000
+ 0.0650 0.0039 1.0000
+ 0.0415 0.0025 1.0000
+ 0.0074 0.0033 1.0000
+ -0.0185 0.0059 1.0000
+ -0.0413 0.0073 1.0000
+ -0.0548 0.0074 1.0000
+ -0.0385 0.0041 1.0000
+ -0.0383 -0.0006 1.0000
+ -0.0584 -0.0008 1.0000
+ -0.0584 0.0023 1.0000
+ -0.0553 0.0090 1.0000
+ -0.0772 0.0146 1.0000
+ -0.0757 0.0157 1.0000
+ -0.0644 0.0144 1.0000
+ -0.0816 0.0141 1.0000
+ -0.1045 0.0148 1.0000
+ -0.0867 0.0111 1.0000
+ -0.0365 0.0014 1.0000
+ 0.0113 -0.0067 1.0000
+ 0.0272 -0.0074 1.0000
+ 0.0381 -0.0012 1.0000
+ 0.0548 0.0021 1.0000
+ 0.0470 0.0012 1.0000
+ 0.0227 -0.0019 1.0000
+ 0.0132 -0.0022 1.0000
+ 0.0040 0.0004 1.0000
+ -0.0045 0.0008 1.0000
+ -0.0145 0.0006 1.0000
+ -0.0116 0.0025 1.0000
+ -0.0031 0.0044 1.0000
+ -0.0148 0.0086 1.0000
+ -0.0318 0.0109 1.0000
+ -0.0166 0.0078 1.0000
+ 0.0154 0.0036 1.0000
+ 0.0451 0.0018 1.0000
+ 0.0364 0.0021 1.0000
+ 0.0125 0.0036 1.0000
+ 0.0330 0.0045 1.0000
+ 0.0605 0.0048 1.0000
+ 0.0417 0.0041 1.0000
+ 0.0115 0.0011 1.0000
+ 0.0257 -0.0018 1.0000
+ 0.0451 -0.0029 1.0000
+ 0.0387 -0.0032 1.0000
+ 0.0254 -0.0017 1.0000
+ 0.0311 -0.0001 1.0000
+ 0.0448 0.0006 1.0000
+ 0.0499 0.0020 1.0000
+ 0.0543 0.0037 1.0000
+ 0.0486 0.0054 1.0000
+ 0.0459 0.0051 1.0000
+ 0.0715 -0.0001 1.0000
+ 0.0764 -0.0063 1.0000
+ 0.0603 -0.0119 1.0000
+ 0.0378 -0.0153 1.0000
+ 0.0214 -0.0124 1.0000
+ 0.0063 -0.0091 1.0000
+ -0.0095 -0.0016 1.0000
+ -0.0259 0.0036 1.0000
+ -0.0234 0.0061 1.0000
+ 0.0012 0.0060 1.0000
diff --git a/regtest/dimred/rt-mds2/list_embed.reference b/regtest/dimred/rt-mds2/list_embed.reference
index b24c465dfceac9021d1e5b3dec7800870f408522..583254a00b55764b6973300fb6bd335e41e3e26c 100644
--- a/regtest/dimred/rt-mds2/list_embed.reference
+++ b/regtest/dimred/rt-mds2/list_embed.reference
@@ -1,101 +1,101 @@
-#! FIELDS mds.1 mds.2
- 0.0594 0.0053
- 0.0683 0.0034
- 0.0705 0.0006
- 0.0729 -0.0019
- 0.0874 -0.0069
- 0.0961 -0.0095
- 0.0867 -0.0062
- 0.0719 -0.0008
- 0.0575 0.0031
- 0.0552 0.0034
- 0.0682 -0.0002
- 0.0781 -0.0024
- 0.0785 -0.0025
- 0.0763 -0.0027
- 0.0755 -0.0041
- 0.0792 -0.0069
- 0.0778 -0.0062
- 0.0727 -0.0025
- 0.0726 0.0014
- 0.0756 0.0030
- 0.0821 0.0017
- 0.0816 0.0001
- 0.0774 0.0008
- 0.0766 0.0008
- 0.0838 -0.0005
- 0.0931 -0.0016
- 0.0936 -0.0010
- 0.0923 -0.0009
- 0.0906 -0.0008
- 0.0706 0.0025
- 0.0664 0.0050
- 0.0901 0.0019
- 0.1059 -0.0015
- 0.0917 0.0006
- 0.0876 0.0021
- 0.1008 -0.0001
- 0.0955 -0.0014
- 0.0858 -0.0018
- 0.0894 -0.0005
- 0.0922 0.0014
- 0.0917 0.0010
- 0.0925 -0.0043
- 0.0967 -0.0102
- 0.1073 -0.0096
- 0.1065 -0.0047
- 0.0935 -0.0003
- 0.0668 0.0049
- 0.0410 0.0086
- 0.0264 0.0110
- 0.0254 0.0125
- 0.0503 0.0085
- 0.0855 0.0007
- 0.0975 -0.0028
- 0.0983 -0.0035
- 0.0997 -0.0044
- 0.0877 -0.0021
- 0.0501 0.0053
- 0.0104 0.0140
- -0.0199 0.0221
- -0.0416 0.0277
- -0.0688 0.0338
- -0.0858 0.0354
- -0.0897 0.0313
- -0.0920 0.0254
- -0.1168 0.0227
- -0.1447 0.0227
- -0.1636 0.0221
- -0.1461 0.0182
- -0.1212 0.0139
- -0.0775 0.0056
- -0.0008 -0.0041
- 0.0469 -0.0038
- 0.0771 -0.0004
- 0.0917 0.0005
- 0.0656 0.0042
- -0.0034 0.0115
- -0.0901 0.0141
- -0.1784 0.0069
- -0.2253 -0.0077
- -0.2372 -0.0248
- -0.2415 -0.0448
- -0.2562 -0.0539
- -0.2901 -0.0433
- -0.3173 -0.0215
- -0.3117 0.0096
- -0.2787 0.0317
- -0.2319 0.0372
- -0.1897 0.0305
- -0.1592 0.0142
- -0.1212 -0.0049
- -0.0960 -0.0150
- -0.0842 -0.0162
- -0.0813 -0.0187
- -0.0823 -0.0193
- -0.0773 -0.0179
- -0.0621 -0.0202
- -0.0449 -0.0215
- -0.0269 -0.0307
- -0.0075 -0.0368
- 0.0266 -0.0342
+#! FIELDS mds.1 mds.2 weight
+ 0.0594 0.0053 1.0000
+ 0.0683 0.0034 1.0000
+ 0.0705 0.0006 1.0000
+ 0.0729 -0.0019 1.0000
+ 0.0874 -0.0069 1.0000
+ 0.0961 -0.0095 1.0000
+ 0.0867 -0.0062 1.0000
+ 0.0719 -0.0008 1.0000
+ 0.0575 0.0031 1.0000
+ 0.0552 0.0034 1.0000
+ 0.0682 -0.0002 1.0000
+ 0.0781 -0.0024 1.0000
+ 0.0785 -0.0025 1.0000
+ 0.0763 -0.0027 1.0000
+ 0.0755 -0.0041 1.0000
+ 0.0792 -0.0069 1.0000
+ 0.0778 -0.0062 1.0000
+ 0.0727 -0.0025 1.0000
+ 0.0726 0.0014 1.0000
+ 0.0756 0.0030 1.0000
+ 0.0821 0.0017 1.0000
+ 0.0816 0.0001 1.0000
+ 0.0774 0.0008 1.0000
+ 0.0766 0.0008 1.0000
+ 0.0838 -0.0005 1.0000
+ 0.0931 -0.0016 1.0000
+ 0.0936 -0.0010 1.0000
+ 0.0923 -0.0009 1.0000
+ 0.0906 -0.0008 1.0000
+ 0.0706 0.0025 1.0000
+ 0.0664 0.0050 1.0000
+ 0.0901 0.0019 1.0000
+ 0.1059 -0.0015 1.0000
+ 0.0917 0.0006 1.0000
+ 0.0876 0.0021 1.0000
+ 0.1008 -0.0001 1.0000
+ 0.0955 -0.0014 1.0000
+ 0.0858 -0.0018 1.0000
+ 0.0894 -0.0005 1.0000
+ 0.0922 0.0014 1.0000
+ 0.0917 0.0010 1.0000
+ 0.0925 -0.0043 1.0000
+ 0.0967 -0.0102 1.0000
+ 0.1073 -0.0096 1.0000
+ 0.1065 -0.0047 1.0000
+ 0.0935 -0.0003 1.0000
+ 0.0668 0.0049 1.0000
+ 0.0410 0.0086 1.0000
+ 0.0264 0.0110 1.0000
+ 0.0254 0.0125 1.0000
+ 0.0503 0.0085 1.0000
+ 0.0855 0.0007 1.0000
+ 0.0975 -0.0028 1.0000
+ 0.0983 -0.0035 1.0000
+ 0.0997 -0.0044 1.0000
+ 0.0877 -0.0021 1.0000
+ 0.0501 0.0053 1.0000
+ 0.0104 0.0140 1.0000
+ -0.0199 0.0221 1.0000
+ -0.0416 0.0277 1.0000
+ -0.0688 0.0338 1.0000
+ -0.0858 0.0354 1.0000
+ -0.0897 0.0313 1.0000
+ -0.0920 0.0254 1.0000
+ -0.1168 0.0227 1.0000
+ -0.1447 0.0227 1.0000
+ -0.1636 0.0221 1.0000
+ -0.1461 0.0182 1.0000
+ -0.1212 0.0139 1.0000
+ -0.0775 0.0056 1.0000
+ -0.0008 -0.0041 1.0000
+ 0.0469 -0.0038 1.0000
+ 0.0771 -0.0004 1.0000
+ 0.0917 0.0005 1.0000
+ 0.0656 0.0042 1.0000
+ -0.0034 0.0115 1.0000
+ -0.0901 0.0141 1.0000
+ -0.1784 0.0069 1.0000
+ -0.2253 -0.0077 1.0000
+ -0.2372 -0.0248 1.0000
+ -0.2415 -0.0448 1.0000
+ -0.2562 -0.0539 1.0000
+ -0.2901 -0.0433 1.0000
+ -0.3173 -0.0215 1.0000
+ -0.3117 0.0096 1.0000
+ -0.2787 0.0317 1.0000
+ -0.2319 0.0372 1.0000
+ -0.1897 0.0305 1.0000
+ -0.1592 0.0142 1.0000
+ -0.1212 -0.0049 1.0000
+ -0.0960 -0.0150 1.0000
+ -0.0842 -0.0162 1.0000
+ -0.0813 -0.0187 1.0000
+ -0.0823 -0.0193 1.0000
+ -0.0773 -0.0179 1.0000
+ -0.0621 -0.0202 1.0000
+ -0.0449 -0.0215 1.0000
+ -0.0269 -0.0307 1.0000
+ -0.0075 -0.0368 1.0000
+ 0.0266 -0.0342 1.0000
diff --git a/src/analysis/AnalysisBase.h b/src/analysis/AnalysisBase.h
index 3b3b35f9e8a80f145c995363fc1e2e22e282031c..eb068cc4037479c90ad7da2a1924f778fd3e60be 100644
--- a/src/analysis/AnalysisBase.h
+++ b/src/analysis/AnalysisBase.h
@@ -81,6 +81,8 @@ public:
virtual double getDissimilarity( const unsigned& i, const unsigned& j );
/// This returns the label of the object that contains the base data
virtual std::string getBaseDataLabel() const ;
+/// Overwrite getArguments so we get arguments from underlying class
+ virtual const std::vector<Value*> & getArguments() const ;
/// Get the ith data point
virtual void getDataPoint( const unsigned& idata, std::vector<double>& point, double& weight ) const ;
/// Get a reference configuration (in dimensionality reduction this returns the projection)
@@ -153,6 +155,11 @@ double AnalysisBase::getDissimilarity( const unsigned& i, const unsigned& j ){
return mydata->getDissimilarity( i, j );
}
+inline
+const std::vector<Value*> & AnalysisBase::getArguments() const {
+ return mydata->getArguments();
+}
+
inline
std::string AnalysisBase::getBaseDataLabel() const {
return mydata->getBaseDataLabel();
diff --git a/src/analysis/AnalysisWithDataCollection.h b/src/analysis/AnalysisWithDataCollection.h
index 6bde3447f9e544464a0adcfa14de6f09624ea681..3cef4221001edea557ec5920c5745d2b705e6e35 100644
--- a/src/analysis/AnalysisWithDataCollection.h
+++ b/src/analysis/AnalysisWithDataCollection.h
@@ -100,6 +100,8 @@ public:
virtual void getDataPoint( const unsigned& idata, std::vector<double>& point, double& weight ) const ;
/// Get a reference configuration (in dimensionality reduction this returns the projection)
virtual ReferenceConfiguration* getReferenceConfiguration( const unsigned& idat, const bool& calcdist );
+/// Now we can get the arguments from the right place
+ const std::vector<Value*> & getArguments() const ;
/// This ensures that the energy is stored if we are reweighting
void prepare();
/// This stores the data and calls the analysis to be performed
@@ -158,6 +160,12 @@ inline
unsigned AnalysisWithDataCollection::getNumberOfArguments() const {
unsigned nargs=ActionWithArguments::getNumberOfArguments();
return nargs - biases.size();
+}
+
+inline
+const std::vector<Value*> & AnalysisWithDataCollection::getArguments() const {
+ if( !mydata ) return ActionWithArguments::getArguments();
+ return AnalysisBase::getArguments();
}
}
diff --git a/src/analysis/LandmarkSelectionBase.cpp b/src/analysis/LandmarkSelectionBase.cpp
index cff31bf575ee5ab8c4ae6b8b85b3cff53702370f..0892e8bce202c0ceb56440059271f91c4324c0b3 100644
--- a/src/analysis/LandmarkSelectionBase.cpp
+++ b/src/analysis/LandmarkSelectionBase.cpp
@@ -60,7 +60,7 @@ void LandmarkSelectionBase::performAnalysis(){
std::vector<unsigned> tmpass( mydata->getNumberOfDataPoints() );
voronoiAnalysis( landmark_indices, lweights, tmpass );
} else {
- for(unsigned i=0;i<nlandmarks;++i) lweights[i]=getWeight( landmark_indices[i] );
+ for(unsigned i=0;i<nlandmarks;++i) lweights[i]=mydata->getWeight( landmark_indices[i] );
}
}
diff --git a/src/analysis/OutputColvarFile.cpp b/src/analysis/OutputColvarFile.cpp
index c295779818103b6dbf2a06512255f18c310e980c..a77700c767a13a3c8d780cae08b25ecc79330ba1 100644
--- a/src/analysis/OutputColvarFile.cpp
+++ b/src/analysis/OutputColvarFile.cpp
@@ -89,7 +89,10 @@ void OutputColvarFile::performAnalysis(){
gfile.open( filename.c_str() );
ReferenceConfiguration* myp = getReferenceConfiguration(0,false);
- if( myp->getNumberOfProperties()==0 ) plumed_assert( !dynamic_cast<ReferenceAtoms*>( myp ) );
+ if( myp->getNumberOfProperties()==0 ){
+ plumed_assert( !dynamic_cast<ReferenceAtoms*>( myp ) );
+ for(unsigned j=0;j<myp->getReferenceArguments().size();++j) gfile.setupPrintValue( getArguments()[j] );
+ }
// Print embedding coordinates
for(unsigned i=0;i<getNumberOfDataPoints();++i){
@@ -101,9 +104,10 @@ void OutputColvarFile::performAnalysis(){
ReferenceArguments* myref=dynamic_cast<ReferenceArguments*>( mypoint );
plumed_assert( myref );
for(unsigned j=0;j<myref->getReferenceArguments().size();++j){
- gfile.printField( myref->getArgumentNames()[j], myref->getReferenceArgument(j) );
+ gfile.printField( getArguments()[j], myref->getReferenceArgument(j) );
}
}
+ gfile.printField( "weight", getWeight(i) );
gfile.printField();
}
gfile.close();
diff --git a/src/core/ActionWithArguments.h b/src/core/ActionWithArguments.h
index feef08a6da5f054e6c3d043e1ec1ebffb81d07cd..b7a7ad5705608c27c1cf93b00d098ecad829b428 100644
--- a/src/core/ActionWithArguments.h
+++ b/src/core/ActionWithArguments.h
@@ -78,7 +78,7 @@ public:
void lockRequests();
void unlockRequests();
/// Returns an array of pointers to the arguments
- const std::vector<Value*> & getArguments() const ;
+ virtual const std::vector<Value*> & getArguments() const ;
/// Convert a list of argument names into a list of pointers to the values
void interpretArgumentList(const std::vector<std::string>& c, std::vector<Value*>&arg);
};