From 8378e6fd7c15f4b96241f7b33ac816e2e4a6150c Mon Sep 17 00:00:00 2001
From: Gareth Tribello <gt@eider.phy.qub.ac.uk>
Date: Thu, 2 Jul 2015 15:06:15 +0100
Subject: [PATCH] Added functionality to OutputPDBFile so that projections can
be written out
---
regtest/.gitignore | 1 +
.../dimred/rt-mds/analysis.0.embed.reference | 700 ++++++++++++++++++
regtest/dimred/rt-mds/embed.reference | 700 ++++++++++++++++++
regtest/dimred/rt-mds/plumed.dat | 2 +-
src/analysis/AnalysisBase.h | 15 +-
src/analysis/AnalysisWithDataCollection.cpp | 9 +-
src/analysis/AnalysisWithDataCollection.h | 6 +-
src/analysis/EuclideanDissimilarityMatrix.cpp | 3 +-
src/analysis/LandmarkSelectionBase.h | 6 +-
src/analysis/OutputColvarFile.cpp | 5 +-
src/analysis/OutputPDBFile.cpp | 12 +-
src/analysis/ReadDissimilarityMatrix.cpp | 10 +-
src/dimred/DimensionalityReductionBase.cpp | 24 +-
src/dimred/DimensionalityReductionBase.h | 3 +-
src/dimred/ProjectNonLandmarkPoints.cpp | 11 +-
src/reference/ReferenceArguments.cpp | 5 +-
src/reference/ReferenceArguments.h | 2 +-
src/reference/ReferenceConfiguration.cpp | 9 +-
src/reference/ReferenceConfiguration.h | 2 +-
19 files changed, 1475 insertions(+), 50 deletions(-)
create mode 100644 regtest/dimred/rt-mds/analysis.0.embed.reference
create mode 100644 regtest/dimred/rt-mds/embed.reference
diff --git a/regtest/.gitignore b/regtest/.gitignore
index 0e31cccc7..7b428d215 100644
--- a/regtest/.gitignore
+++ b/regtest/.gitignore
@@ -7,6 +7,7 @@
!/analysis
!/basic
!/crystallization
+!/dimred
!/mapping
!/multicolvar
!/secondarystructure
diff --git a/regtest/dimred/rt-mds/analysis.0.embed.reference b/regtest/dimred/rt-mds/analysis.0.embed.reference
new file mode 100644
index 000000000..bfcd2c1e8
--- /dev/null
+++ b/regtest/dimred/rt-mds/analysis.0.embed.reference
@@ -0,0 +1,700 @@
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=650626174834469268094976.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0873 mds.2=0.0013
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7551 c1.moment-3=1.3322
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=3443064697932843889721344.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0535 mds.2=0.0044
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7434 c1.moment-3=1.3003
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=4334990767809816147525632.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0150 mds.2=0.0044
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7333 c1.moment-3=1.2632
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1642551053927491148185600.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0136 mds.2=0.0019
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7283 c1.moment-3=1.2349
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=565077236443374117978112.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0308 mds.2=-0.0012
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7268 c1.moment-3=1.2175
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=506902826865531421720576.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0355 mds.2=-0.0018
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7262 c1.moment-3=1.2128
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=3497441683667193365004288.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0090 mds.2=-0.0015
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7327 c1.moment-3=1.2385
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=5816989471131786348068864.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0145 mds.2=0.0004
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7371 c1.moment-3=1.2616
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=5197629206541778607407104.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0191 mds.2=0.0022
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7366 c1.moment-3=1.2666
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=22568578815140474208124928.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0278 mds.2=0.0015
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7394 c1.moment-3=1.2748
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=8891751619370481308663808.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0091 mds.2=-0.0004
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7365 c1.moment-3=1.2562
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=145469732262582499147776.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0359 mds.2=-0.0012
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7255 c1.moment-3=1.2126
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=67243488566443176361984.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0540 mds.2=0.0004
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7193 c1.moment-3=1.1955
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=991674944473569693794304.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0322 mds.2=-0.0034
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7286 c1.moment-3=1.2156
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=433704577708501378269184.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0205 mds.2=-0.0150
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7429 c1.moment-3=1.2239
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=58924815689464923815936.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0282 mds.2=-0.0289
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7542 c1.moment-3=1.2128
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=28876419368888716754944.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0530 mds.2=-0.0358
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7544 c1.moment-3=1.1871
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=29493206461009996283904.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0769 mds.2=-0.0312
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7438 c1.moment-3=1.1652
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=15523379316519734345728.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0893 mds.2=-0.0259
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7355 c1.moment-3=1.1546
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=6036949107489532542976.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0697 mds.2=-0.0246
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7393 c1.moment-3=1.1739
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=6805982676529049501696.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0301 mds.2=-0.0196
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7448 c1.moment-3=1.2133
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=224283114659648425164800.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0093 mds.2=-0.0072
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7430 c1.moment-3=1.2547
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1937631236154971427700736.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0274 mds.2=0.0009
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7400 c1.moment-3=1.2742
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=8943884514170369755578368.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0301 mds.2=0.0016
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7400 c1.moment-3=1.2770
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1818542782073875176882176.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0265 mds.2=-0.0033
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7438 c1.moment-3=1.2723
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=356284804122361993363456.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0433 mds.2=-0.0053
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7501 c1.moment-3=1.2879
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=740928158795493248335872.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0514 mds.2=-0.0019
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7489 c1.moment-3=1.2967
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=3971376819483128291655680.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0222 mds.2=0.0031
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7365 c1.moment-3=1.2698
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=3616045831357711704391680.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0129 mds.2=0.0061
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7245 c1.moment-3=1.2366
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=866118050097568367509504.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0322 mds.2=0.0084
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7172 c1.moment-3=1.2186
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=473876430918082860417024.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0355 mds.2=0.0080
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7168 c1.moment-3=1.2153
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=549108949631639043964928.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0337 mds.2=0.0067
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7185 c1.moment-3=1.2168
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=714866179522068016529408.0000
+REMARK PROPERTIES=mds.1,mds.2
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+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7211 c1.moment-3=1.2191
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1514315762407424940572672.0000
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+REMARK mds.1=-0.0253 mds.2=0.0016
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7255 c1.moment-3=1.2235
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1741401785128748918505472.0000
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+REMARK mds.1=-0.0132 mds.2=-0.0021
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+REMARK c1.moment-2=0.7323 c1.moment-3=1.2343
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=3707685932716769910194176.0000
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+REMARK mds.1=0.0040 mds.2=-0.0031
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7377 c1.moment-3=1.2506
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=5279612145243834875379712.0000
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+REMARK mds.1=0.0107 mds.2=0.0011
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+REMARK c1.moment-2=0.7354 c1.moment-3=1.2582
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=14648991633879816569094144.0000
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+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
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+REMARK ARG=c1.moment-2,c1.moment-3
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+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=77977698769596315733065728.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0650 mds.2=0.0039
+REMARK ARG=c1.moment-2,c1.moment-3
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+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=5438198764112726743580672.0000
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+REMARK c1.moment-2=0.7421 c1.moment-3=1.2882
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1122421932113435130068992.0000
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+REMARK mds.1=0.0074 mds.2=0.0033
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7325 c1.moment-3=1.2555
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1623375579255821794541568.0000
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+REMARK mds.1=-0.0185 mds.2=0.0059
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7232 c1.moment-3=1.2312
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=824284132438079344476160.0000
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+REMARK mds.1=-0.0413 mds.2=0.0073
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7158 c1.moment-3=1.2096
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
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+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
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+REMARK ARG=c1.moment-2,c1.moment-3
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+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=255645304728742904463360.0000
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+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7243 c1.moment-3=1.2104
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=80831060875928311693312.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0584 mds.2=-0.0008
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7192 c1.moment-3=1.1910
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=410072896508362208837632.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0584 mds.2=0.0023
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7162 c1.moment-3=1.1918
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=473315368593257205334016.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0553 mds.2=0.0090
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7105 c1.moment-3=1.1965
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=49342818148888732499968.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0772 mds.2=0.0146
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.6995 c1.moment-3=1.1768
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=71439214621479799881728.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0757 mds.2=0.0157
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.6988 c1.moment-3=1.1785
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=372382770456105985245184.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0644 mds.2=0.0144
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7030 c1.moment-3=1.1891
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=396750501333421147553792.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0816 mds.2=0.0141
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.6988 c1.moment-3=1.1724
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=194367523462455551328256.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.1045 mds.2=0.0148
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.6922 c1.moment-3=1.1504
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=265390023546441746612224.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0867 mds.2=0.0111
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7004 c1.moment-3=1.1667
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=417842650383208029356032.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0365 mds.2=0.0014
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7228 c1.moment-3=1.2126
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=130034479906962406375424.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0113 mds.2=-0.0067
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7431 c1.moment-3=1.2567
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=453748863537616517070848.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0272 mds.2=-0.0074
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7479 c1.moment-3=1.2718
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=2549987501327281773608960.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0381 mds.2=-0.0012
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7448 c1.moment-3=1.2840
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=3357671899518696282914816.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0548 mds.2=0.0021
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7459 c1.moment-3=1.3010
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=2973694890310422329556992.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0470 mds.2=0.0012
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7447 c1.moment-3=1.2933
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=288602953154320790454272.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0227 mds.2=-0.0019
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7414 c1.moment-3=1.2690
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1760887739729704734687232.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0132 mds.2=-0.0022
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7392 c1.moment-3=1.2597
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1526973208100442807992320.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0040 mds.2=0.0004
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7343 c1.moment-3=1.2515
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=375263178685270183641088.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0045 mds.2=0.0008
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7317 c1.moment-3=1.2434
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=232661556808622295482368.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0145 mds.2=0.0006
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7293 c1.moment-3=1.2337
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=507064184978749788258304.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0116 mds.2=0.0025
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7282 c1.moment-3=1.2370
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1128952088522002253479936.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0031 mds.2=0.0044
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7286 c1.moment-3=1.2457
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1197960641606570746052608.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0148 mds.2=0.0086
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7216 c1.moment-3=1.2355
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=625774095016588059082752.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0318 mds.2=0.0109
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7149 c1.moment-3=1.2196
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=364912544013506169536512.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0166 mds.2=0.0078
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7218 c1.moment-3=1.2336
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1649391353916835862937600.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0154 mds.2=0.0036
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7342 c1.moment-3=1.2633
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=11346816644974575838298112.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0451 mds.2=0.0018
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7437 c1.moment-3=1.2915
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=20791509453694539808112640.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0364 mds.2=0.0021
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7411 c1.moment-3=1.2832
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1867515982473692874539008.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0125 mds.2=0.0036
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7335 c1.moment-3=1.2606
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=11344083134102028704284672.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0330 mds.2=0.0045
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7379 c1.moment-3=1.2806
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=120911330589421810499977216.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0605 mds.2=0.0048
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7448 c1.moment-3=1.3072
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=40351160276202809800523776.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0417 mds.2=0.0041
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7406 c1.moment-3=1.2889
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=9235968903630373689229312.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0115 mds.2=0.0011
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7356 c1.moment-3=1.2590
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=15198595282354971818852352.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0257 mds.2=-0.0018
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7421 c1.moment-3=1.2719
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=14695620601365390340128768.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0451 mds.2=-0.0029
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7483 c1.moment-3=1.2904
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=3504618985646781185916928.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0387 mds.2=-0.0032
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7469 c1.moment-3=1.2841
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1958037545372794977517568.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0254 mds.2=-0.0017
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7420 c1.moment-3=1.2716
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=7729740074168141073088512.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0311 mds.2=-0.0001
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7418 c1.moment-3=1.2775
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=26429041345273132897796096.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0448 mds.2=0.0006
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7448 c1.moment-3=1.2909
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=37403428414373558822633472.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0499 mds.2=0.0020
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7448 c1.moment-3=1.2962
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=69071824065210548899282944.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0543 mds.2=0.0037
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7443 c1.moment-3=1.3009
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=28746486049325375245254656.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0486 mds.2=0.0054
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7412 c1.moment-3=1.2959
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=5138199027537960106983424.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0459 mds.2=0.0051
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7407 c1.moment-3=1.2932
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=20730130763570579884736512.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0715 mds.2=-0.0001
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7524 c1.moment-3=1.3166
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=10053248420830524810985472.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0764 mds.2=-0.0063
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7596 c1.moment-3=1.3196
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=2341097486254890020765696.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0603 mds.2=-0.0119
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7609 c1.moment-3=1.3027
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1801241546807460694589440.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0378 mds.2=-0.0153
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7583 c1.moment-3=1.2800
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=2623886374903733202976768.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0214 mds.2=-0.0124
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7512 c1.moment-3=1.2649
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1540127025264497029808128.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0063 mds.2=-0.0091
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7441 c1.moment-3=1.2513
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=761250478060893041065984.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0095 mds.2=-0.0016
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7327 c1.moment-3=1.2380
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=815550859201229044580352.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0259 mds.2=0.0036
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7234 c1.moment-3=1.2235
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1031052805964853080489984.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0234 mds.2=0.0061
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7217 c1.moment-3=1.2265
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=828970472636431535702016.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0012 mds.2=0.0060
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7282 c1.moment-3=1.2502
+END
diff --git a/regtest/dimred/rt-mds/embed.reference b/regtest/dimred/rt-mds/embed.reference
new file mode 100644
index 000000000..8ecbcfdae
--- /dev/null
+++ b/regtest/dimred/rt-mds/embed.reference
@@ -0,0 +1,700 @@
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0008
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0594 mds.2=0.0053
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7340 c1.moment-3=1.2672
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0012
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0683 mds.2=0.0034
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7371 c1.moment-3=1.2758
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0004
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0705 mds.2=0.0006
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7401 c1.moment-3=1.2777
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0010
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0729 mds.2=-0.0019
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7428 c1.moment-3=1.2796
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0022
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0874 mds.2=-0.0069
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7497 c1.moment-3=1.2934
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0019
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0961 mds.2=-0.0095
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7533 c1.moment-3=1.3018
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0023
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0867 mds.2=-0.0062
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7489 c1.moment-3=1.2928
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0030
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0719 mds.2=-0.0008
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7417 c1.moment-3=1.2788
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0118
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0575 mds.2=0.0031
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7360 c1.moment-3=1.2651
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0063
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0552 mds.2=0.0034
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7354 c1.moment-3=1.2628
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0022
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0682 mds.2=-0.0002
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7405 c1.moment-3=1.2753
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0029
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0781 mds.2=-0.0024
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7440 c1.moment-3=1.2847
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0010
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0785 mds.2=-0.0025
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7441 c1.moment-3=1.2852
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0004
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0763 mds.2=-0.0027
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7441 c1.moment-3=1.2829
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0013
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0755 mds.2=-0.0041
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7454 c1.moment-3=1.2820
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0069
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0792 mds.2=-0.0069
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7486 c1.moment-3=1.2853
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0096
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0778 mds.2=-0.0062
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7477 c1.moment-3=1.2840
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0076
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0727 mds.2=-0.0025
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7434 c1.moment-3=1.2795
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0143
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0726 mds.2=0.0014
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7396 c1.moment-3=1.2798
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0302
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0756 mds.2=0.0030
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7384 c1.moment-3=1.2830
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0171
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0821 mds.2=0.0017
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7405 c1.moment-3=1.2893
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0013
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0816 mds.2=0.0001
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7420 c1.moment-3=1.2886
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0167
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0774 mds.2=0.0008
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7407 c1.moment-3=1.2845
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0234
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0766 mds.2=0.0008
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7407 c1.moment-3=1.2837
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0171
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0838 mds.2=-0.0005
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7429 c1.moment-3=1.2906
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0265
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0931 mds.2=-0.0016
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7452 c1.moment-3=1.2997
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0521
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0936 mds.2=-0.0010
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7446 c1.moment-3=1.3004
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0504
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0923 mds.2=-0.0009
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7443 c1.moment-3=1.2990
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0443
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0906 mds.2=-0.0008
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7440 c1.moment-3=1.2974
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0270
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0706 mds.2=0.0025
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7382 c1.moment-3=1.2780
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0120
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0664 mds.2=0.0050
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7352 c1.moment-3=1.2741
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0517
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0901 mds.2=0.0019
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7412 c1.moment-3=1.2972
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0821
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.1059 mds.2=-0.0015
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7467 c1.moment-3=1.3125
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0206
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0917 mds.2=0.0006
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7428 c1.moment-3=1.2986
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0206
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0876 mds.2=0.0021
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7407 c1.moment-3=1.2948
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0207
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.1008 mds.2=-0.0001
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7446 c1.moment-3=1.3076
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0270
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0955 mds.2=-0.0014
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7452 c1.moment-3=1.3022
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0171
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0858 mds.2=-0.0018
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7444 c1.moment-3=1.2925
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0345
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0894 mds.2=-0.0005
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7436 c1.moment-3=1.2963
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0819
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0922 mds.2=0.0014
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7420 c1.moment-3=1.2992
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.1159
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0917 mds.2=0.0010
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7423 c1.moment-3=1.2987
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0266
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0925 mds.2=-0.0043
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7477 c1.moment-3=1.2989
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0072
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0967 mds.2=-0.0102
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7541 c1.moment-3=1.3023
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0358
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.1073 mds.2=-0.0096
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7548 c1.moment-3=1.3129
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0264
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.1065 mds.2=-0.0047
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7499 c1.moment-3=1.3126
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0087
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0935 mds.2=-0.0003
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7439 c1.moment-3=1.3003
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0055
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0668 mds.2=0.0049
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7353 c1.moment-3=1.2745
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0047
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0411 mds.2=0.0087
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7284 c1.moment-3=1.2494
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0049
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0264 mds.2=0.0110
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7242 c1.moment-3=1.2352
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0014
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0254 mds.2=0.0125
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7226 c1.moment-3=1.2344
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0015
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0503 mds.2=0.0085
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7297 c1.moment-3=1.2586
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0025
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0855 mds.2=0.0007
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7419 c1.moment-3=1.2925
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0045
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0975 mds.2=-0.0028
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7469 c1.moment-3=1.3039
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0336
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0983 mds.2=-0.0035
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7477 c1.moment-3=1.3047
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0570
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0997 mds.2=-0.0044
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7487 c1.moment-3=1.3059
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0021
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0877 mds.2=-0.0021
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7449 c1.moment-3=1.2944
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0002
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0501 mds.2=0.0053
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7328 c1.moment-3=1.2580
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0004
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0104 mds.2=0.0140
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7192 c1.moment-3=1.2197
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0009
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0199 mds.2=0.0221
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7074 c1.moment-3=1.1907
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0004
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0416 mds.2=0.0277
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.6990 c1.moment-3=1.1698
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0688 mds.2=0.0338
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.6895 c1.moment-3=1.1436
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0858 mds.2=0.0354
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.6858 c1.moment-3=1.1269
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0897 mds.2=0.0313
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.6894 c1.moment-3=1.1226
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0920 mds.2=0.0254
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.6950 c1.moment-3=1.1195
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.1168 mds.2=0.0227
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.6945 c1.moment-3=1.0946
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0001
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.1447 mds.2=0.0227
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.6910 c1.moment-3=1.0669
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0004
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.1636 mds.2=0.0221
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.6892 c1.moment-3=1.0481
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0011
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.1461 mds.2=0.0182
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.6953 c1.moment-3=1.0650
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0004
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.1212 mds.2=0.0139
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7027 c1.moment-3=1.0891
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0005
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0775 mds.2=0.0056
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7164 c1.moment-3=1.1314
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0004
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0008 mds.2=-0.0041
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7358 c1.moment-3=1.2063
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0007
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0469 mds.2=-0.0038
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7415 c1.moment-3=1.2537
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0074
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0771 mds.2=-0.0004
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7419 c1.moment-3=1.2840
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0384
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0917 mds.2=0.0005
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7428 c1.moment-3=1.2986
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0153
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0656 mds.2=0.0042
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7359 c1.moment-3=1.2732
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0016
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0034 mds.2=0.0115
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7200 c1.moment-3=1.2057
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0006
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0901 mds.2=0.0141
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7064 c1.moment-3=1.1200
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0005
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.1784 mds.2=0.0069
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7024 c1.moment-3=1.0315
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0002
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.2253 mds.2=-0.0077
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7109 c1.moment-3=0.9832
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0001
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.2372 mds.2=-0.0248
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7264 c1.moment-3=0.9692
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.2415 mds.2=-0.0448
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7456 c1.moment-3=0.9624
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.2562 mds.2=-0.0539
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7529 c1.moment-3=0.9466
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.2901 mds.2=-0.0433
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7381 c1.moment-3=0.9144
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.3173 mds.2=-0.0215
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7130 c1.moment-3=0.8902
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.3117 mds.2=0.0096
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.6829 c1.moment-3=0.8996
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.2787 mds.2=0.0317
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.6651 c1.moment-3=0.9352
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.2319 mds.2=0.0372
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.6656 c1.moment-3=0.9823
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.1897 mds.2=0.0305
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.6776 c1.moment-3=1.0233
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0001
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.1592 mds.2=0.0142
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.6975 c1.moment-3=1.0515
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.1211 mds.2=-0.0049
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7213 c1.moment-3=1.0868
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0960 mds.2=-0.0150
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7345 c1.moment-3=1.1105
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0001
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0842 mds.2=-0.0162
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7372 c1.moment-3=1.1221
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0001
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0813 mds.2=-0.0187
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7401 c1.moment-3=1.1246
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0823 mds.2=-0.0193
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7406 c1.moment-3=1.1235
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0773 mds.2=-0.0179
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7398 c1.moment-3=1.1287
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0621 mds.2=-0.0202
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7440 c1.moment-3=1.1435
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0449 mds.2=-0.0215
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7475 c1.moment-3=1.1604
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0269 mds.2=-0.0307
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7589 c1.moment-3=1.1770
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0000
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0075 mds.2=-0.0368
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7673 c1.moment-3=1.1955
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=0.0002
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0266 mds.2=-0.0342
+REMARK ARG=c1.moment-2,c1.moment-3
+REMARK c1.moment-2=0.7690 c1.moment-3=1.2297
+END
diff --git a/regtest/dimred/rt-mds/plumed.dat b/regtest/dimred/rt-mds/plumed.dat
index 61954ad8f..1c63ced77 100755
--- a/regtest/dimred/rt-mds/plumed.dat
+++ b/regtest/dimred/rt-mds/plumed.dat
@@ -26,4 +26,4 @@ CLASSICAL_MDS ...
... CLASSICAL_MDS
OUTPUT_ANALYSIS_DATA_TO_COLVAR USE_OUTPUT_DATA_FROM=mds FILE=list_embed FMT=%8.4f
-# OUTPUT_ANALYSIS_DATA_TO_PDB USE_OUTPUT_DATA_FROM=mds FILE=embed FMT=%8.4f
+OUTPUT_ANALYSIS_DATA_TO_PDB USE_OUTPUT_DATA_FROM=mds FILE=embed FMT=%8.4f
diff --git a/src/analysis/AnalysisBase.h b/src/analysis/AnalysisBase.h
index cfa1a613a..62c00a725 100644
--- a/src/analysis/AnalysisBase.h
+++ b/src/analysis/AnalysisBase.h
@@ -80,8 +80,10 @@ public:
virtual std::string getBaseDataLabel() const ;
/// Get the ith data point
virtual void getDataPoint( const unsigned& idata, std::vector<double>& point, double& weight ) const ;
-/// Get a reference configuration
- virtual ReferenceConfiguration* getReferenceConfiguration( const unsigned& idata );
+/// Get a reference configuration (in dimensionality reduction this returns the projection)
+ virtual ReferenceConfiguration* getReferenceConfiguration( const unsigned& idata, bool& isprojection );
+/// Get the input configuration (in dimensionality reduction this returns the high dimensional configuration)
+ virtual ReferenceConfiguration* getInputReferenceConfiguration( const unsigned& idata );
/// This actually performs the analysis
virtual void performAnalysis()=0;
/// These overwrite things from inherited classes (this is a bit of a fudge)
@@ -156,8 +158,13 @@ void AnalysisBase::getDataPoint( const unsigned& idata, std::vector<double>& poi
}
inline
-ReferenceConfiguration* AnalysisBase::getReferenceConfiguration( const unsigned& idata ){
- return mydata->getReferenceConfiguration( idata );
+ReferenceConfiguration* AnalysisBase::getReferenceConfiguration( const unsigned& idata, bool& isprojection ){
+ return mydata->getReferenceConfiguration( idata, isprojection );
+}
+
+inline
+ReferenceConfiguration* AnalysisBase::getInputReferenceConfiguration( const unsigned& idata ){
+ return mydata->getInputReferenceConfiguration( idata );
}
}
diff --git a/src/analysis/AnalysisWithDataCollection.cpp b/src/analysis/AnalysisWithDataCollection.cpp
index e19409dbd..100e6d302 100644
--- a/src/analysis/AnalysisWithDataCollection.cpp
+++ b/src/analysis/AnalysisWithDataCollection.cpp
@@ -227,9 +227,14 @@ void AnalysisWithDataCollection::getDataPoint( const unsigned& idat, std::vector
}
}
-ReferenceConfiguration* AnalysisWithDataCollection::getReferenceConfiguration( const unsigned& idat ){
+ReferenceConfiguration* AnalysisWithDataCollection::getReferenceConfiguration( const unsigned& idat, bool& isprojection ){
+ if( !mydata ){ plumed_dbg_assert( idat<data.size() ); isprojection=false; return data[idat]; }
+ return AnalysisBase::getReferenceConfiguration( idat, isprojection );
+}
+
+ReferenceConfiguration* AnalysisWithDataCollection::getInputReferenceConfiguration( const unsigned& idat ){
if( !mydata ){ plumed_dbg_assert( idat<data.size() ); return data[idat]; }
- return AnalysisBase::getReferenceConfiguration( idat );
+ return AnalysisBase::getInputReferenceConfiguration( idat );
}
void AnalysisWithDataCollection::update(){
diff --git a/src/analysis/AnalysisWithDataCollection.h b/src/analysis/AnalysisWithDataCollection.h
index 2d4dd9bc6..2a54464db 100644
--- a/src/analysis/AnalysisWithDataCollection.h
+++ b/src/analysis/AnalysisWithDataCollection.h
@@ -87,8 +87,10 @@ public:
std::string getBaseDataLabel() const ;
/// Get the ith data point
virtual void getDataPoint( const unsigned& idata, std::vector<double>& point, double& weight ) const ;
-/// Get a reference configuration
- virtual ReferenceConfiguration* getReferenceConfiguration( const unsigned& idat );
+/// Get a reference configuration (in dimensionality reduction this returns the projection)
+ virtual ReferenceConfiguration* getReferenceConfiguration( const unsigned& idat, bool& isprojection );
+/// Get the underlying reference configuration (in dimensionality reduction this return the high dimensional point)
+ ReferenceConfiguration* getInputReferenceConfiguration( const unsigned& idat );
/// This ensures that the energy is stored if we are reweighting
void prepare();
/// This stores the data and calls the analysis to be performed
diff --git a/src/analysis/EuclideanDissimilarityMatrix.cpp b/src/analysis/EuclideanDissimilarityMatrix.cpp
index 468b81efb..bbe1545d7 100644
--- a/src/analysis/EuclideanDissimilarityMatrix.cpp
+++ b/src/analysis/EuclideanDissimilarityMatrix.cpp
@@ -63,7 +63,8 @@ double EuclideanDissimilarityMatrix::getDissimilarity( const unsigned& iframe, c
plumed_dbg_assert( iframe<dissimilarities.nrows() && jframe<dissimilarities.ncols() );
if( dissimilarities(iframe,jframe)>0. ){ return dissimilarities(iframe,jframe); }
if( iframe!=jframe ){
- dissimilarities(iframe,jframe) = dissimilarities(jframe,iframe) = distance( getPbc(), getArguments(), getReferenceConfiguration(iframe), getReferenceConfiguration(jframe), true );
+ bool ignore;
+ dissimilarities(iframe,jframe) = dissimilarities(jframe,iframe) = distance( getPbc(), getArguments(), getReferenceConfiguration(iframe,ignore), getReferenceConfiguration(jframe,ignore), true );
return dissimilarities(iframe,jframe);
}
return 0.0;
diff --git a/src/analysis/LandmarkSelectionBase.h b/src/analysis/LandmarkSelectionBase.h
index ce9723c1f..2a54eb53b 100644
--- a/src/analysis/LandmarkSelectionBase.h
+++ b/src/analysis/LandmarkSelectionBase.h
@@ -52,7 +52,7 @@ public:
/// Get the ith data point
void getDataPoint( const unsigned& idata, std::vector<double>& point, double& weight ) const ;
/// Get a reference configuration
- ReferenceConfiguration* getReferenceConfiguration( const unsigned& idat );
+ ReferenceConfiguration* getReferenceConfiguration( const unsigned& idat, bool& isprojection );
/// Select landmark configurations
void performAnalysis();
virtual void selectLandmarks()=0;
@@ -83,8 +83,8 @@ void LandmarkSelectionBase::getDataPoint( const unsigned& idata, std::vector<dou
}
inline
-ReferenceConfiguration* LandmarkSelectionBase::getReferenceConfiguration( const unsigned& idat ){
- return AnalysisWithDataCollection::getReferenceConfiguration( landmark_indices[idat] );
+ReferenceConfiguration* LandmarkSelectionBase::getReferenceConfiguration( const unsigned& idat, bool& isprojection ){
+ return AnalysisWithDataCollection::getReferenceConfiguration( landmark_indices[idat], isprojection );
}
inline
diff --git a/src/analysis/OutputColvarFile.cpp b/src/analysis/OutputColvarFile.cpp
index d858320c2..754426519 100644
--- a/src/analysis/OutputColvarFile.cpp
+++ b/src/analysis/OutputColvarFile.cpp
@@ -82,12 +82,13 @@ void OutputColvarFile::performAnalysis(){
gfile.open( filename.c_str() );
// Can't print out all landmark data if we have reference atom positions
- ReferenceAtoms* myat=dynamic_cast<ReferenceAtoms*>( getReferenceConfiguration(0) );
+ bool ignore;
+ ReferenceAtoms* myat=dynamic_cast<ReferenceAtoms*>( getReferenceConfiguration(0,ignore) );
plumed_assert( !myat );
// Print embedding coordinates
for(unsigned i=0;i<getNumberOfDataPoints();++i){
- ReferenceArguments* myref=dynamic_cast<ReferenceArguments*>( getReferenceConfiguration(i) );
+ ReferenceArguments* myref=dynamic_cast<ReferenceArguments*>( getReferenceConfiguration(i,ignore) );
plumed_assert( myref );
for(unsigned j=0;j<myref->getReferenceArguments().size();++j){
gfile.printField( myref->getArgumentNames()[j], myref->getReferenceArgument(j) );
diff --git a/src/analysis/OutputPDBFile.cpp b/src/analysis/OutputPDBFile.cpp
index 23548dc2f..dbcf8d2ed 100644
--- a/src/analysis/OutputPDBFile.cpp
+++ b/src/analysis/OutputPDBFile.cpp
@@ -70,12 +70,18 @@ fmt("%f")
void OutputPDBFile::performAnalysis(){
// Output the embedding in plumed pdb format
OFile afile; afile.link(*this); afile.setBackupString("analysis"); std::size_t psign=fmt.find("%");
- afile.open( filename.c_str() ); std::string descr="REMARK WEIGHT=%-" + fmt.substr(psign+1) + "\n";
+ afile.open( filename.c_str() ); bool isprojection; std::string descr="REMARK WEIGHT=%-" + fmt.substr(psign+1) + "\n";
for(unsigned j=0;j<getNumberOfDataPoints();++j){
afile.printf("DESCRIPTION: analysis data from calculation done at time %f \n",getLabel().c_str(),getTime() );
afile.printf(descr.c_str(),getWeight(j) );
- if( plumed.getAtoms().usingNaturalUnits() ) getReferenceConfiguration(j)->print( 1.0, afile, fmt );
- else getReferenceConfiguration(j)->print( plumed.getAtoms().getUnits().getLength()/0.1, afile, fmt );
+ ReferenceConfiguration* myref = getReferenceConfiguration(j,isprojection);
+ if( plumed.getAtoms().usingNaturalUnits() ) myref->print( 1.0, afile, fmt, isprojection );
+ else myref->print( plumed.getAtoms().getUnits().getLength()/0.1, afile, fmt, isprojection );
+ // This ensures the high dimensional position is projected if we are working with dimensionality reduction
+ if( isprojection ){
+ if( plumed.getAtoms().usingNaturalUnits() ) getInputReferenceConfiguration(j)->print( 1.0, afile, fmt, false );
+ else getInputReferenceConfiguration(j)->print( plumed.getAtoms().getUnits().getLength()/0.1, afile, fmt, false );
+ }
}
afile.close();
}
diff --git a/src/analysis/ReadDissimilarityMatrix.cpp b/src/analysis/ReadDissimilarityMatrix.cpp
index 935a7de8f..dfc4dcb6c 100644
--- a/src/analysis/ReadDissimilarityMatrix.cpp
+++ b/src/analysis/ReadDissimilarityMatrix.cpp
@@ -39,7 +39,8 @@ public:
ReadDissimilarityMatrix( const ActionOptions& ao );
unsigned getNumberOfDataPoints() const { return nnodes; }
/// This gives an error as if we read in the matrix we dont have the coordinates
- ReferenceConfiguration* getReferenceConfiguration( const unsigned& idata );
+ ReferenceConfiguration* getReferenceConfiguration( const unsigned& idata, bool& isprojection );
+ ReferenceConfiguration* getInputReferenceConfiguration( const unsigned& idata );
/// This gives an error as if we read in the matrix we dont have the coordinates
void getDataPoint( const unsigned& idata, std::vector<double>& point, double& weight ) const ;
/// Tell everyone we have dissimilarities
@@ -114,7 +115,12 @@ double ReadDissimilarityMatrix::getDissimilarity( const unsigned& iframe, const
return dissimilarities( iframe, jframe );
}
-ReferenceConfiguration* ReadDissimilarityMatrix::getReferenceConfiguration( const unsigned& idata ){
+ReferenceConfiguration* ReadDissimilarityMatrix::getReferenceConfiguration( const unsigned& idata, bool& isprojection ){
+ plumed_merror("cannot get reference configurations from read in dissimilarity matrix");
+ return NULL;
+}
+
+ReferenceConfiguration* ReadDissimilarityMatrix::getInputReferenceConfiguration( const unsigned& idata ){
plumed_merror("cannot get reference configurations from read in dissimilarity matrix");
return NULL;
}
diff --git a/src/dimred/DimensionalityReductionBase.cpp b/src/dimred/DimensionalityReductionBase.cpp
index f930cd75f..505bbe4bb 100644
--- a/src/dimred/DimensionalityReductionBase.cpp
+++ b/src/dimred/DimensionalityReductionBase.cpp
@@ -64,40 +64,28 @@ DimensionalityReductionBase::~DimensionalityReductionBase(){
delete myref;
}
-ReferenceConfiguration* DimensionalityReductionBase::getReferenceConfiguration( const unsigned& idata ){
- std::vector<double> pp(nlow); for(unsigned i=0;i<nlow;++i) pp[i]=projections(idata,i);
- std::vector<double> empty( pp.size() );
+ReferenceConfiguration* DimensionalityReductionBase::getReferenceConfiguration( const unsigned& idat, bool& isprojection ){
+ std::vector<double> pp(nlow); for(unsigned i=0;i<nlow;++i) pp[i]=projections(idat,i);
+ std::vector<double> empty( pp.size() ); isprojection=true;
myref->setReferenceConfig( std::vector<Vector>(), pp, empty );
return myref;
}
-// double DimensionalityReductionBase::getInputDissimilarity( const unsigned& idata, const unsigned& jdata ){
-// if( dimredbase && use_dimred_dissims ) return dimredbase->getOutputDissimilarity( idata, jdata );
-// if( dimredbase ) return dimredbase->getInputDissimilarity( idata, jdata );
-// return getDissimilarity( idata, jdata );
-// }
+ReferenceConfiguration* DimensionalityReductionBase::getInputReferenceConfiguration( const unsigned& idat ){
+ return mydata->getInputReferenceConfiguration( idat );
+}
void DimensionalityReductionBase::getDataPoint( const unsigned& idata, std::vector<double>& point, double& weight ) const {
if( point.size()!=nlow ) point.resize( nlow );
weight = getWeight(idata); for(unsigned i=0;i<nlow;++i) point[i]=projections(idata,i);
}
-// double DimensionalityReductionBase::getOutputDissimilarity( const unsigned& idata, const unsigned& jdata ){
-// double dissim=0; for(unsigned i=0;i<nlow;++i){ double tmp=projections(idata,i)-projections(jdata,i); dissim+=tmp*tmp; }
-// return dissim;
-// }
-
void DimensionalityReductionBase::performAnalysis(){
// Resize the tempory array (this is used for out of sample)
dtargets.resize( getNumberOfDataPoints() );
// Resize the projections array
projections.resize( getNumberOfDataPoints(), nlow );
-// // Retrieve the weights from the previous calculation
-// std::vector<double> lweights( getNumberOfDataPoints() );
-// for(unsigned i=0;i<getNumberOfDataPoints();++i) lweights[i]=getWeight(i);
-// setOutputWeights( lweights );
-
// Retreive the projections from the previous calculation
if( dimredbase ){
std::vector<double> newp( nlow ); double w;
diff --git a/src/dimred/DimensionalityReductionBase.h b/src/dimred/DimensionalityReductionBase.h
index 8543dfc87..66725aa80 100644
--- a/src/dimred/DimensionalityReductionBase.h
+++ b/src/dimred/DimensionalityReductionBase.h
@@ -51,7 +51,8 @@ public:
/// Get the ith data point (this returns the projection)
void getDataPoint( const unsigned& idata, std::vector<double>& point, double& weight ) const ;
/// Get a reference configuration (this returns the projection)
- ReferenceConfiguration* getReferenceConfiguration( const unsigned& idata );
+ ReferenceConfiguration* getReferenceConfiguration( const unsigned& idata, bool& isprojection );
+ ReferenceConfiguration* getInputReferenceConfiguration( const unsigned& idata );
/// Actually perform the analysis
void performAnalysis();
/// Calculate the projections of points
diff --git a/src/dimred/ProjectNonLandmarkPoints.cpp b/src/dimred/ProjectNonLandmarkPoints.cpp
index 5b039c47d..5b4a2cf96 100644
--- a/src/dimred/ProjectNonLandmarkPoints.cpp
+++ b/src/dimred/ProjectNonLandmarkPoints.cpp
@@ -51,7 +51,8 @@ public:
/// Get the ith data point (this returns the projection)
void getDataPoint( const unsigned& idata, std::vector<double>& point );
/// Get a reference configuration (this returns the projection)
- ReferenceConfiguration* getReferenceConfiguration( const unsigned& idata );
+ ReferenceConfiguration* getReferenceConfiguration( const unsigned& idata, bool& isprojection );
+ ReferenceConfiguration* getInputReferenceConfiguration( const unsigned& idata );
/// This does nothing -- projections are calculated when getDataPoint and getReferenceConfiguration are called
void performAnalysis(){}
/// This just calls calculate stress in the underlying projection object
@@ -109,12 +110,16 @@ void ProjectNonLandmarkPoints::generateProjection( const unsigned& idata, std::v
myminimiser.minimise( cgtol, point, &ProjectNonLandmarkPoints::calculateStress );
}
-ReferenceConfiguration* ProjectNonLandmarkPoints::getReferenceConfiguration( const unsigned& idata ){
+ReferenceConfiguration* ProjectNonLandmarkPoints::getReferenceConfiguration( const unsigned& idata, bool& isprojection ){
std::vector<double> pp(nlow); std::vector<double> empty( pp.size() ); generateProjection( idata, pp );
- myref->setReferenceConfig( std::vector<Vector>(), pp, empty );
+ myref->setReferenceConfig( std::vector<Vector>(), pp, empty ); isprojection=true;
return myref;
}
+ReferenceConfiguration* ProjectNonLandmarkPoints::getInputReferenceConfiguration( const unsigned& idata ){
+ return mydata->getInputReferenceConfiguration( idata );
+}
+
void ProjectNonLandmarkPoints::getDataPoint( const unsigned& idata, std::vector<double>& point ){
if( point.size()!=nlow ) point.resize( nlow );
generateProjection( idata, point );
diff --git a/src/reference/ReferenceArguments.cpp b/src/reference/ReferenceArguments.cpp
index 3a9f137e2..50cb45786 100644
--- a/src/reference/ReferenceArguments.cpp
+++ b/src/reference/ReferenceArguments.cpp
@@ -120,8 +120,9 @@ void ReferenceArguments::getArgumentRequests( std::vector<std::string>& argout,
}
}
-void ReferenceArguments::printArguments( OFile& ofile, const std::string& fmt ) const {
- ofile.printf("REMARK ARG=%s", arg_names[0].c_str() );
+void ReferenceArguments::printArguments( OFile& ofile, const std::string& fmt, const bool& isproperty ) const {
+ if( isproperty ) ofile.printf("REMARK PROPERTIES=%s", arg_names[0].c_str() );
+ else ofile.printf("REMARK ARG=%s", arg_names[0].c_str() );
for(unsigned i=1;i<arg_names.size();++i) ofile.printf(",%s", arg_names[i].c_str() );
ofile.printf("\n");
ofile.printf("REMARK ");
diff --git a/src/reference/ReferenceArguments.h b/src/reference/ReferenceArguments.h
index 8e17ad41d..d1fc4db14 100644
--- a/src/reference/ReferenceArguments.h
+++ b/src/reference/ReferenceArguments.h
@@ -80,7 +80,7 @@ public:
/// Get the value of the ith reference argument
double getReferenceArgument( const unsigned& i ) const ;
/// Print the arguments out
- void printArguments( OFile& ofile, const std::string& fmt ) const ;
+ void printArguments( OFile& ofile, const std::string& fmt, const bool& isproperty ) const ;
/// Return all the reference arguments
const std::vector<double>& getReferenceArguments();
const std::vector<double>& getReferenceMetric();
diff --git a/src/reference/ReferenceConfiguration.cpp b/src/reference/ReferenceConfiguration.cpp
index 530013ef2..b20e9b9bc 100644
--- a/src/reference/ReferenceConfiguration.cpp
+++ b/src/reference/ReferenceConfiguration.cpp
@@ -158,15 +158,16 @@ double ReferenceConfiguration::calculate( const std::vector<Vector>& pos, const
void ReferenceConfiguration::print( const double& lunits, OFile& ofile, const double& time, const double& weight, const double& old_norm ){
ofile.printf("REMARK TIME=%f LOG_WEIGHT=%f OLD_NORM=%f\n",time, weight, old_norm );
- print( lunits, ofile, "%f" ); // HARD CODED FORMAT HERE AS THIS IS FOR CHECKPOINT FILE
+ print( lunits, ofile, "%f", false ); // HARD CODED FORMAT HERE AS THIS IS FOR CHECKPOINT FILE
}
-void ReferenceConfiguration::print( const double& lunits, OFile& ofile, const std::string& fmt ){
+void ReferenceConfiguration::print( const double& lunits, OFile& ofile, const std::string& fmt, const bool& isproperty ){
ReferenceArguments* args=dynamic_cast<ReferenceArguments*>(this);
- if(args) args->printArguments( ofile, fmt );
+ if(args) args->printArguments( ofile, fmt, isproperty );
ReferenceAtoms* atoms=dynamic_cast<ReferenceAtoms*>(this);
+ if( atoms && isproperty ) plumed_merror("a set of atoms is not a list of properties");
if(atoms) atoms->printAtoms( lunits, ofile );
- ofile.printf("END\n");
+ if( !isproperty ) ofile.printf("END\n");
}
double distance( const Pbc& pbc, const std::vector<Value*> & vals, ReferenceConfiguration* ref1, ReferenceConfiguration* ref2, const bool& squared ){
diff --git a/src/reference/ReferenceConfiguration.h b/src/reference/ReferenceConfiguration.h
index 6864a19ef..a94a010df 100644
--- a/src/reference/ReferenceConfiguration.h
+++ b/src/reference/ReferenceConfiguration.h
@@ -143,7 +143,7 @@ public:
void setReferenceConfig( const std::vector<Vector>& pos, const std::vector<double>& arg, const std::vector<double>& metric );
/// Print a pdb file containing the reference configuration
void print( const double& lunits, OFile& ofile, const double& time, const double& weight, const double& old_norm );
- void print( const double& lunits, OFile& ofile, const std::string& fmt );
+ void print( const double& lunits, OFile& ofile, const std::string& fmt, const bool& isproperty );
/// Get one of the referene arguments
virtual double getReferenceArgument( const unsigned& i ) const { plumed_error(); return 0.0; }
/// These are overwritten in ReferenceArguments and ReferenceAtoms but are required here
--
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