diff --git a/regtest/analysis/rt-calc-dissims/Makefile b/regtest/analysis/rt-calc-dissims/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..3703b27cea227aa053fb6d1d73f861e4384dbcee
--- /dev/null
+++ b/regtest/analysis/rt-calc-dissims/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
diff --git a/regtest/analysis/rt-calc-dissims/analysis.0.mymatrix3.dat.reference b/regtest/analysis/rt-calc-dissims/analysis.0.mymatrix3.dat.reference
new file mode 100644
index 0000000000000000000000000000000000000000..964f0140e8c2167fe941708048cc98c5a18bf19e
--- /dev/null
+++ b/regtest/analysis/rt-calc-dissims/analysis.0.mymatrix3.dat.reference
@@ -0,0 +1,6 @@
+ 0.0000 1.0000 4.0000 9.0000 16.0000 25.0000
+ 1.0000 0.0000 1.0000 4.0000 9.0000 16.0000
+ 4.0000 1.0000 0.0000 1.0000 4.0000 9.0000
+ 9.0000 4.0000 1.0000 0.0000 1.0000 4.0000
+ 16.0000 9.0000 4.0000 1.0000 0.0000 1.0000
+ 25.0000 16.0000 9.0000 4.0000 1.0000 0.0000
diff --git a/regtest/analysis/rt-calc-dissims/colv_in b/regtest/analysis/rt-calc-dissims/colv_in
new file mode 100644
index 0000000000000000000000000000000000000000..bbcb4dd1b881d802ba5739da0aecf12848617971
--- /dev/null
+++ b/regtest/analysis/rt-calc-dissims/colv_in
@@ -0,0 +1,14 @@
+#! FIELDS time data
+0 0
+1 0
+2 1
+3 2
+4 3
+5 4
+6 5
+7 6
+8 7
+9 8
+10 9
+11 10
+12 11
diff --git a/regtest/analysis/rt-calc-dissims/config b/regtest/analysis/rt-calc-dissims/config
new file mode 100644
index 0000000000000000000000000000000000000000..73d164c9563b29348f4ad678148013dc849d7154
--- /dev/null
+++ b/regtest/analysis/rt-calc-dissims/config
@@ -0,0 +1,3 @@
+type=driver
+arg="--noatoms --plumed plumed.dat"
+
diff --git a/regtest/analysis/rt-calc-dissims/mymatrix.dat.reference b/regtest/analysis/rt-calc-dissims/mymatrix.dat.reference
new file mode 100644
index 0000000000000000000000000000000000000000..e7c6219200c2527789efe28e8e248687c0686c60
--- /dev/null
+++ b/regtest/analysis/rt-calc-dissims/mymatrix.dat.reference
@@ -0,0 +1,13 @@
+ 0.0000 0.0000 1.0000 4.0000 9.0000 16.0000 25.0000 36.0000 49.0000 64.0000 81.0000 100.0000 121.0000
+ 0.0000 0.0000 1.0000 4.0000 9.0000 16.0000 25.0000 36.0000 49.0000 64.0000 81.0000 100.0000 121.0000
+ 1.0000 1.0000 0.0000 1.0000 4.0000 9.0000 16.0000 25.0000 36.0000 49.0000 64.0000 81.0000 100.0000
+ 4.0000 4.0000 1.0000 0.0000 1.0000 4.0000 9.0000 16.0000 25.0000 36.0000 49.0000 64.0000 81.0000
+ 9.0000 9.0000 4.0000 1.0000 0.0000 1.0000 4.0000 9.0000 16.0000 25.0000 36.0000 49.0000 64.0000
+ 16.0000 16.0000 9.0000 4.0000 1.0000 0.0000 1.0000 4.0000 9.0000 16.0000 25.0000 36.0000 49.0000
+ 25.0000 25.0000 16.0000 9.0000 4.0000 1.0000 0.0000 1.0000 4.0000 9.0000 16.0000 25.0000 36.0000
+ 36.0000 36.0000 25.0000 16.0000 9.0000 4.0000 1.0000 0.0000 1.0000 4.0000 9.0000 16.0000 25.0000
+ 49.0000 49.0000 36.0000 25.0000 16.0000 9.0000 4.0000 1.0000 0.0000 1.0000 4.0000 9.0000 16.0000
+ 64.0000 64.0000 49.0000 36.0000 25.0000 16.0000 9.0000 4.0000 1.0000 0.0000 1.0000 4.0000 9.0000
+ 81.0000 81.0000 64.0000 49.0000 36.0000 25.0000 16.0000 9.0000 4.0000 1.0000 0.0000 1.0000 4.0000
+ 100.0000 100.0000 81.0000 64.0000 49.0000 36.0000 25.0000 16.0000 9.0000 4.0000 1.0000 0.0000 1.0000
+ 121.0000 121.0000 100.0000 81.0000 64.0000 49.0000 36.0000 25.0000 16.0000 9.0000 4.0000 1.0000 0.0000
diff --git a/regtest/analysis/rt-calc-dissims/mymatrix2.dat.reference b/regtest/analysis/rt-calc-dissims/mymatrix2.dat.reference
new file mode 100644
index 0000000000000000000000000000000000000000..5ed581592c5380c3d7e69b9b450150c554650b00
--- /dev/null
+++ b/regtest/analysis/rt-calc-dissims/mymatrix2.dat.reference
@@ -0,0 +1,5 @@
+ 0.0000 1.0000 9.0000 25.0000 49.0000
+ 1.0000 0.0000 4.0000 16.0000 36.0000
+ 9.0000 4.0000 0.0000 4.0000 16.0000
+ 25.0000 16.0000 4.0000 0.0000 4.0000
+ 49.0000 36.0000 16.0000 4.0000 0.0000
diff --git a/regtest/analysis/rt-calc-dissims/mymatrix3.dat.reference b/regtest/analysis/rt-calc-dissims/mymatrix3.dat.reference
new file mode 100644
index 0000000000000000000000000000000000000000..964f0140e8c2167fe941708048cc98c5a18bf19e
--- /dev/null
+++ b/regtest/analysis/rt-calc-dissims/mymatrix3.dat.reference
@@ -0,0 +1,6 @@
+ 0.0000 1.0000 4.0000 9.0000 16.0000 25.0000
+ 1.0000 0.0000 1.0000 4.0000 9.0000 16.0000
+ 4.0000 1.0000 0.0000 1.0000 4.0000 9.0000
+ 9.0000 4.0000 1.0000 0.0000 1.0000 4.0000
+ 16.0000 9.0000 4.0000 1.0000 0.0000 1.0000
+ 25.0000 16.0000 9.0000 4.0000 1.0000 0.0000
diff --git a/regtest/analysis/rt-calc-dissims/output-fps.pdb.reference b/regtest/analysis/rt-calc-dissims/output-fps.pdb.reference
new file mode 100644
index 0000000000000000000000000000000000000000..02b2c082ddda04b9c65f1060bebaf720978f5b29
--- /dev/null
+++ b/regtest/analysis/rt-calc-dissims/output-fps.pdb.reference
@@ -0,0 +1,15 @@
+DESCRIPTION: analysis data from calculation done at time 12.000000
+REMARK WEIGHT=6.000000
+REMARK ARG=d1
+REMARK d1=7.000000
+END
+DESCRIPTION: analysis data from calculation done at time 12.000000
+REMARK WEIGHT=5.000000
+REMARK ARG=d1
+REMARK d1=0.000000
+END
+DESCRIPTION: analysis data from calculation done at time 12.000000
+REMARK WEIGHT=2.000000
+REMARK ARG=d1
+REMARK d1=11.000000
+END
diff --git a/regtest/analysis/rt-calc-dissims/output-stride.pdb.reference b/regtest/analysis/rt-calc-dissims/output-stride.pdb.reference
new file mode 100644
index 0000000000000000000000000000000000000000..607e10619a20af49b374f51db634e9af605f4751
--- /dev/null
+++ b/regtest/analysis/rt-calc-dissims/output-stride.pdb.reference
@@ -0,0 +1,25 @@
+DESCRIPTION: analysis data from calculation done at time 12.000000
+REMARK WEIGHT=2.000000
+REMARK ARG=d1
+REMARK d1=0.000000
+END
+DESCRIPTION: analysis data from calculation done at time 12.000000
+REMARK WEIGHT=2.000000
+REMARK ARG=d1
+REMARK d1=1.000000
+END
+DESCRIPTION: analysis data from calculation done at time 12.000000
+REMARK WEIGHT=2.000000
+REMARK ARG=d1
+REMARK d1=3.000000
+END
+DESCRIPTION: analysis data from calculation done at time 12.000000
+REMARK WEIGHT=2.000000
+REMARK ARG=d1
+REMARK d1=5.000000
+END
+DESCRIPTION: analysis data from calculation done at time 12.000000
+REMARK WEIGHT=5.000000
+REMARK ARG=d1
+REMARK d1=7.000000
+END
diff --git a/regtest/analysis/rt-calc-dissims/plumed.dat b/regtest/analysis/rt-calc-dissims/plumed.dat
new file mode 100644
index 0000000000000000000000000000000000000000..e1f37516f336443365ad7af34836819be4030afd
--- /dev/null
+++ b/regtest/analysis/rt-calc-dissims/plumed.dat
@@ -0,0 +1,15 @@
+d1: READ FILE=colv_in VALUES=data
+
+ss1: EUCLIDEAN_DISSIMILARITIES STRIDE=1 USE_ALL_DATA ARG=d1
+PRINT_DISSIMILARITY_MATRIX USE_OUTPUT_DATA_FROM=ss1 FILE=mymatrix.dat FMT=%8.4f
+
+ll1: LANDMARK_SELECT_STRIDE ARG=d1 USE_OUTPUT_DATA_FROM=ss1 NLANDMARKS=5
+ss2: EUCLIDEAN_DISSIMILARITIES USE_OUTPUT_DATA_FROM=ll1
+OUTPUT_ANALYSIS_DATA_TO_PDB USE_OUTPUT_DATA_FROM=ll1 FILE=output-stride.pdb
+PRINT_DISSIMILARITY_MATRIX USE_OUTPUT_DATA_FROM=ll1 FILE=mymatrix2.dat FMT=%8.4f
+
+ll2: LANDMARK_SELECT_FPS USE_OUTPUT_DATA_FROM=ss1 NLANDMARKS=3
+OUTPUT_ANALYSIS_DATA_TO_PDB USE_OUTPUT_DATA_FROM=ll2 FILE=output-fps.pdb
+
+ss3: EUCLIDEAN_DISSIMILARITIES STRIDE=1 RUN=6 ARG=d1
+oo: PRINT_DISSIMILARITY_MATRIX USE_OUTPUT_DATA_FROM=ss3 FILE=mymatrix3.dat FMT=%8.4f
diff --git a/regtest/analysis/rt-read-dissims/Makefile b/regtest/analysis/rt-read-dissims/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..3703b27cea227aa053fb6d1d73f861e4384dbcee
--- /dev/null
+++ b/regtest/analysis/rt-read-dissims/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
diff --git a/regtest/analysis/rt-read-dissims/config b/regtest/analysis/rt-read-dissims/config
new file mode 100644
index 0000000000000000000000000000000000000000..73d164c9563b29348f4ad678148013dc849d7154
--- /dev/null
+++ b/regtest/analysis/rt-read-dissims/config
@@ -0,0 +1,3 @@
+type=driver
+arg="--noatoms --plumed plumed.dat"
+
diff --git a/regtest/analysis/rt-read-dissims/mymatrix.dat b/regtest/analysis/rt-read-dissims/mymatrix.dat
new file mode 100644
index 0000000000000000000000000000000000000000..f2292edb988d895bd4362621c2b1373fd50bc248
--- /dev/null
+++ b/regtest/analysis/rt-read-dissims/mymatrix.dat
@@ -0,0 +1,13 @@
+ 0.0000 1.0000 1.0000 4.0000 9.0000 16.0000 25.0000 36.0000 49.0000 64.0000 81.0000 100.0000 121.0000
+ 1.0000 0.0000 1.0000 4.0000 9.0000 16.0000 25.0000 36.0000 49.0000 64.0000 81.0000 100.0000 121.0000
+ 1.0000 1.0000 0.0000 1.0000 4.0000 9.0000 16.0000 25.0000 36.0000 49.0000 64.0000 81.0000 100.0000
+ 4.0000 4.0000 1.0000 0.0000 1.0000 4.0000 9.0000 16.0000 25.0000 36.0000 49.0000 64.0000 81.0000
+ 9.0000 9.0000 4.0000 1.0000 0.0000 1.0000 4.0000 9.0000 16.0000 25.0000 36.0000 49.0000 64.0000
+ 16.0000 16.0000 9.0000 4.0000 1.0000 0.0000 1.0000 4.0000 9.0000 16.0000 25.0000 36.0000 49.0000
+ 25.0000 25.0000 16.0000 9.0000 4.0000 1.0000 0.0000 1.0000 4.0000 9.0000 16.0000 25.0000 36.0000
+ 36.0000 36.0000 25.0000 16.0000 9.0000 4.0000 1.0000 0.0000 1.0000 4.0000 9.0000 16.0000 25.0000
+ 49.0000 49.0000 36.0000 25.0000 16.0000 9.0000 4.0000 1.0000 0.0000 1.0000 4.0000 9.0000 16.0000
+ 64.0000 64.0000 49.0000 36.0000 25.0000 16.0000 9.0000 4.0000 1.0000 0.0000 1.0000 4.0000 9.0000
+ 81.0000 81.0000 64.0000 49.0000 36.0000 25.0000 16.0000 9.0000 4.0000 1.0000 0.0000 1.0000 4.0000
+ 100.0000 100.0000 81.0000 64.0000 49.0000 36.0000 25.0000 16.0000 9.0000 4.0000 1.0000 0.0000 1.0000
+ 121.0000 121.0000 100.0000 81.0000 64.0000 49.0000 36.0000 25.0000 16.0000 9.0000 4.0000 1.0000 0.0000
diff --git a/regtest/analysis/rt-read-dissims/mymatrix_out.dat.reference b/regtest/analysis/rt-read-dissims/mymatrix_out.dat.reference
new file mode 100644
index 0000000000000000000000000000000000000000..f2292edb988d895bd4362621c2b1373fd50bc248
--- /dev/null
+++ b/regtest/analysis/rt-read-dissims/mymatrix_out.dat.reference
@@ -0,0 +1,13 @@
+ 0.0000 1.0000 1.0000 4.0000 9.0000 16.0000 25.0000 36.0000 49.0000 64.0000 81.0000 100.0000 121.0000
+ 1.0000 0.0000 1.0000 4.0000 9.0000 16.0000 25.0000 36.0000 49.0000 64.0000 81.0000 100.0000 121.0000
+ 1.0000 1.0000 0.0000 1.0000 4.0000 9.0000 16.0000 25.0000 36.0000 49.0000 64.0000 81.0000 100.0000
+ 4.0000 4.0000 1.0000 0.0000 1.0000 4.0000 9.0000 16.0000 25.0000 36.0000 49.0000 64.0000 81.0000
+ 9.0000 9.0000 4.0000 1.0000 0.0000 1.0000 4.0000 9.0000 16.0000 25.0000 36.0000 49.0000 64.0000
+ 16.0000 16.0000 9.0000 4.0000 1.0000 0.0000 1.0000 4.0000 9.0000 16.0000 25.0000 36.0000 49.0000
+ 25.0000 25.0000 16.0000 9.0000 4.0000 1.0000 0.0000 1.0000 4.0000 9.0000 16.0000 25.0000 36.0000
+ 36.0000 36.0000 25.0000 16.0000 9.0000 4.0000 1.0000 0.0000 1.0000 4.0000 9.0000 16.0000 25.0000
+ 49.0000 49.0000 36.0000 25.0000 16.0000 9.0000 4.0000 1.0000 0.0000 1.0000 4.0000 9.0000 16.0000
+ 64.0000 64.0000 49.0000 36.0000 25.0000 16.0000 9.0000 4.0000 1.0000 0.0000 1.0000 4.0000 9.0000
+ 81.0000 81.0000 64.0000 49.0000 36.0000 25.0000 16.0000 9.0000 4.0000 1.0000 0.0000 1.0000 4.0000
+ 100.0000 100.0000 81.0000 64.0000 49.0000 36.0000 25.0000 16.0000 9.0000 4.0000 1.0000 0.0000 1.0000
+ 121.0000 121.0000 100.0000 81.0000 64.0000 49.0000 36.0000 25.0000 16.0000 9.0000 4.0000 1.0000 0.0000
diff --git a/regtest/analysis/rt-read-dissims/mymatrix_stride.dat.reference b/regtest/analysis/rt-read-dissims/mymatrix_stride.dat.reference
new file mode 100644
index 0000000000000000000000000000000000000000..5ed581592c5380c3d7e69b9b450150c554650b00
--- /dev/null
+++ b/regtest/analysis/rt-read-dissims/mymatrix_stride.dat.reference
@@ -0,0 +1,5 @@
+ 0.0000 1.0000 9.0000 25.0000 49.0000
+ 1.0000 0.0000 4.0000 16.0000 36.0000
+ 9.0000 4.0000 0.0000 4.0000 16.0000
+ 25.0000 16.0000 4.0000 0.0000 4.0000
+ 49.0000 36.0000 16.0000 4.0000 0.0000
diff --git a/regtest/analysis/rt-read-dissims/plumed.dat b/regtest/analysis/rt-read-dissims/plumed.dat
new file mode 100644
index 0000000000000000000000000000000000000000..f28f96fdc9a406d7f629976fc051e6c1142cb8b8
--- /dev/null
+++ b/regtest/analysis/rt-read-dissims/plumed.dat
@@ -0,0 +1,5 @@
+r1: READ_DISSIMILARITY_MATRIX FILE=mymatrix.dat
+PRINT_DISSIMILARITY_MATRIX USE_OUTPUT_DATA_FROM=r1 FILE=mymatrix_out.dat FMT=%8.4f
+
+l1: LANDMARK_SELECT_STRIDE USE_OUTPUT_DATA_FROM=r1 NLANDMARKS=5
+PRINT_DISSIMILARITY_MATRIX USE_OUTPUT_DATA_FROM=l1 FILE=mymatrix_stride.dat FMT=%8.4f
diff --git a/regtest/analysis/rt-store-print/Makefile b/regtest/analysis/rt-store-print/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..3703b27cea227aa053fb6d1d73f861e4384dbcee
--- /dev/null
+++ b/regtest/analysis/rt-store-print/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
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
new file mode 100644
index 0000000000000000000000000000000000000000..bf99439cf74b2563e4e1d30e92e3c20d14199c82
--- /dev/null
+++ b/regtest/analysis/rt-store-print/analysis.0.output-half.pdb.reference
@@ -0,0 +1,7 @@
+#! FIELDS d1
+0.000000
+1.000000
+2.000000
+3.000000
+4.000000
+5.000000
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
new file mode 100644
index 0000000000000000000000000000000000000000..59f916c90079db43135ad0b155387f1faac29313
--- /dev/null
+++ b/regtest/analysis/rt-store-print/analysis.0.output-stride2.pdb.reference
@@ -0,0 +1,4 @@
+#! FIELDS d1
+0.000000
+2.000000
+4.000000
diff --git a/regtest/analysis/rt-store-print/colv_in b/regtest/analysis/rt-store-print/colv_in
new file mode 100644
index 0000000000000000000000000000000000000000..bbcb4dd1b881d802ba5739da0aecf12848617971
--- /dev/null
+++ b/regtest/analysis/rt-store-print/colv_in
@@ -0,0 +1,14 @@
+#! FIELDS time data
+0 0
+1 0
+2 1
+3 2
+4 3
+5 4
+6 5
+7 6
+8 7
+9 8
+10 9
+11 10
+12 11
diff --git a/regtest/analysis/rt-store-print/config b/regtest/analysis/rt-store-print/config
new file mode 100644
index 0000000000000000000000000000000000000000..73d164c9563b29348f4ad678148013dc849d7154
--- /dev/null
+++ b/regtest/analysis/rt-store-print/config
@@ -0,0 +1,3 @@
+type=driver
+arg="--noatoms --plumed plumed.dat"
+
diff --git a/regtest/analysis/rt-store-print/output-all.pdb.reference b/regtest/analysis/rt-store-print/output-all.pdb.reference
new file mode 100644
index 0000000000000000000000000000000000000000..28cf6f1a23b24dfc22ed57587cdf10b36ca69a0a
--- /dev/null
+++ b/regtest/analysis/rt-store-print/output-all.pdb.reference
@@ -0,0 +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
diff --git a/regtest/analysis/rt-store-print/output-half.pdb.reference b/regtest/analysis/rt-store-print/output-half.pdb.reference
new file mode 100644
index 0000000000000000000000000000000000000000..894fea15fcb0ad0949d484b0e12e2a981f26c41c
--- /dev/null
+++ b/regtest/analysis/rt-store-print/output-half.pdb.reference
@@ -0,0 +1,7 @@
+#! FIELDS d1
+6.000000
+7.000000
+8.000000
+9.000000
+10.000000
+11.000000
diff --git a/regtest/analysis/rt-store-print/output-reuse.pdb.reference b/regtest/analysis/rt-store-print/output-reuse.pdb.reference
new file mode 100644
index 0000000000000000000000000000000000000000..28cf6f1a23b24dfc22ed57587cdf10b36ca69a0a
--- /dev/null
+++ b/regtest/analysis/rt-store-print/output-reuse.pdb.reference
@@ -0,0 +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
diff --git a/regtest/analysis/rt-store-print/output-stride.pdb.reference b/regtest/analysis/rt-store-print/output-stride.pdb.reference
new file mode 100644
index 0000000000000000000000000000000000000000..9af0c7c91dc443faf6ef5ab71aed39e67ced3cb5
--- /dev/null
+++ b/regtest/analysis/rt-store-print/output-stride.pdb.reference
@@ -0,0 +1,6 @@
+#! FIELDS d1
+0.000000
+1.000000
+3.000000
+5.000000
+7.000000
diff --git a/regtest/analysis/rt-store-print/output-stride2.pdb.reference b/regtest/analysis/rt-store-print/output-stride2.pdb.reference
new file mode 100644
index 0000000000000000000000000000000000000000..4e9c140cda4f2303e8b1e90804a8e55a3c90b5f0
--- /dev/null
+++ b/regtest/analysis/rt-store-print/output-stride2.pdb.reference
@@ -0,0 +1,4 @@
+#! FIELDS d1
+6.000000
+8.000000
+10.000000
diff --git a/regtest/analysis/rt-store-print/plumed.dat b/regtest/analysis/rt-store-print/plumed.dat
new file mode 100644
index 0000000000000000000000000000000000000000..89c6f78faa26f503a317300c4bd553b1c4c185a1
--- /dev/null
+++ b/regtest/analysis/rt-store-print/plumed.dat
@@ -0,0 +1,11 @@
+d1: READ FILE=colv_in VALUES=data
+
+ss1: OUTPUT_ANALYSIS_DATA_TO_COLVAR STRIDE=1 RUN=6 ARG=d1 FILE=output-half.pdb
+ss2: OUTPUT_ANALYSIS_DATA_TO_COLVAR STRIDE=1 USE_ALL_DATA ARG=d1 FILE=output-all.pdb
+ss3: OUTPUT_ANALYSIS_DATA_TO_COLVAR REUSE_INPUT_DATA_FROM=ss2 FILE=output-reuse.pdb
+
+ll1: LANDMARK_SELECT_STRIDE ARG=d1 REUSE_INPUT_DATA_FROM=ss3 NLANDMARKS=5 NOVORONOI
+OUTPUT_ANALYSIS_DATA_TO_COLVAR USE_OUTPUT_DATA_FROM=ll1 FILE=output-stride.pdb
+
+ll2: LANDMARK_SELECT_STRIDE ARG=d1 REUSE_INPUT_DATA_FROM=ss1 NLANDMARKS=3 NOVORONOI
+OUTPUT_ANALYSIS_DATA_TO_COLVAR USE_OUTPUT_DATA_FROM=ll2 FILE=output-stride2.pdb
diff --git a/src/analysis/EuclideanDissimilarityMatrix.cpp b/src/analysis/EuclideanDissimilarityMatrix.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..468b81efbc43ac0b4160b7c66fa9bd239d061b63
--- /dev/null
+++ b/src/analysis/EuclideanDissimilarityMatrix.cpp
@@ -0,0 +1,73 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Copyright (c) 2013,2014 The plumed team
+ (see the PEOPLE file at the root of the distribution for a list of names)
+
+ See http://www.plumed-code.org for more information.
+
+ This file is part of plumed, version 2.
+
+ plumed is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ plumed is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with plumed. If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#include "AnalysisWithDataCollection.h"
+#include "core/ActionRegister.h"
+#include "reference/ReferenceConfiguration.h"
+
+namespace PLMD {
+namespace analysis {
+
+class EuclideanDissimilarityMatrix : public AnalysisWithDataCollection {
+private:
+ Matrix<double> dissimilarities;
+public:
+ static void registerKeywords( Keywords& keys );
+ EuclideanDissimilarityMatrix( const ActionOptions& ao );
+/// Do the analysis
+ void performAnalysis();
+/// This ensures that classes that use this data know that dissimilarities were set
+ bool dissimilaritiesWereSet() const { return true; }
+/// Get the squared dissimilarity between two reference configurations
+ double getDissimilarity( const unsigned& i, const unsigned& j );
+/// This is just to deal with ActionWithVessel
+ void performTask( const unsigned& , const unsigned& , MultiValue& ) const { plumed_error(); }
+};
+
+PLUMED_REGISTER_ACTION(EuclideanDissimilarityMatrix,"EUCLIDEAN_DISSIMILARITIES")
+
+void EuclideanDissimilarityMatrix::registerKeywords( Keywords& keys ){
+ AnalysisWithDataCollection::registerKeywords( keys );
+}
+
+EuclideanDissimilarityMatrix::EuclideanDissimilarityMatrix( const ActionOptions& ao ):
+Action(ao),
+AnalysisWithDataCollection(ao)
+{
+}
+
+void EuclideanDissimilarityMatrix::performAnalysis(){
+ // Resize dissimilarities matrix and set all elements to zero
+ dissimilarities.resize( getNumberOfDataPoints(), getNumberOfDataPoints() ); dissimilarities=0;
+}
+
+double EuclideanDissimilarityMatrix::getDissimilarity( const unsigned& iframe, const unsigned& jframe ){
+ 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 );
+ return dissimilarities(iframe,jframe);
+ }
+ return 0.0;
+}
+
+}
+}
diff --git a/src/analysis/FarthestPointSampling.cpp b/src/analysis/FarthestPointSampling.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..7b2465af78d240c46648a35d4385d143209791ec
--- /dev/null
+++ b/src/analysis/FarthestPointSampling.cpp
@@ -0,0 +1,82 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Copyright (c) 2012-2014 The plumed team
+ (see the PEOPLE file at the root of the distribution for a list of names)
+
+ See http://www.plumed-code.org for more information.
+
+ This file is part of plumed, version 2.
+
+ plumed is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ plumed is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with plumed. If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#include "LandmarkSelectionBase.h"
+#include "core/ActionRegister.h"
+#include "tools/Random.h"
+
+namespace PLMD {
+namespace analysis {
+
+class FarthestPointSampling : public LandmarkSelectionBase {
+private:
+ unsigned seed;
+public:
+ static void registerKeywords( Keywords& keys );
+ FarthestPointSampling( const ActionOptions& ao );
+ void selectLandmarks();
+};
+
+PLUMED_REGISTER_ACTION(FarthestPointSampling,"LANDMARK_SELECT_FPS")
+
+void FarthestPointSampling::registerKeywords( Keywords& keys ){
+ LandmarkSelectionBase::registerKeywords(keys);
+ keys.add("compulsory","SEED","1234","a random number seed");
+}
+
+FarthestPointSampling::FarthestPointSampling( const ActionOptions& ao ):
+Action(ao),
+LandmarkSelectionBase(ao)
+{
+ if( !dissimilaritiesWereSet() ) error("dissimilarities have not been calcualted in input action");
+ parse("SEED",seed);
+}
+
+void FarthestPointSampling::selectLandmarks(){
+ std::vector<unsigned> landmarks( getNumberOfDataPoints() );
+
+ // Select first point at random
+ Random random; random.setSeed(-seed); double rand=random.RandU01();
+ landmarks[0] = std::floor( mydata->getNumberOfDataPoints()*rand );
+ selectFrame( landmarks[0] );
+
+ // Now find distance to all other points (N.B. We can use squared distances here for speed)
+ Matrix<double> distances( getNumberOfDataPoints(), mydata->getNumberOfDataPoints() );
+ for(unsigned i=0;i<mydata->getNumberOfDataPoints();++i) distances(0,i) = mydata->getDissimilarity( landmarks[0], i );
+
+ // Now find all other landmarks
+ for(unsigned i=1;i<getNumberOfDataPoints();++i){
+ // Find point that has the largest minimum distance from the landmarks selected thus far
+ double maxd=0;
+ for(unsigned j=0;j<mydata->getNumberOfDataPoints();++j){
+ double mind=distances(0,j);
+ for(unsigned k=1;k<i;++k){
+ if( distances(k,j)<mind ){ mind=distances(k,j); }
+ }
+ if( mind>maxd ){ maxd=mind; landmarks[i]=j; }
+ }
+ selectFrame( landmarks[i] );
+ for(unsigned k=0;k<mydata->getNumberOfDataPoints();++k) distances(i,k) = mydata->getDissimilarity( landmarks[i], k );
+ }
+}
+
+}
+}
diff --git a/src/analysis/LandmarkSelectionBase.cpp b/src/analysis/LandmarkSelectionBase.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..d694abf17995b366cf84dbbf84e3a7d9af9f31e2
--- /dev/null
+++ b/src/analysis/LandmarkSelectionBase.cpp
@@ -0,0 +1,76 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Copyright (c) 2012-2015 The plumed team
+ (see the PEOPLE file at the root of the distribution for a list of names)
+
+ See http://www.plumed-code.org for more information.
+
+ This file is part of plumed, version 2.
+
+ plumed is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ plumed is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with plumed. If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#include "LandmarkSelectionBase.h"
+
+namespace PLMD {
+namespace analysis {
+
+void LandmarkSelectionBase::registerKeywords( Keywords& keys ){
+ AnalysisWithDataCollection::registerKeywords( keys );
+ keys.add("compulsory","NLANDMARKS","the number of landmarks that you would like to select");
+ keys.addFlag("NOVORONOI",false,"do not do a Voronoi analysis of the data to determine weights of final points");
+ keys.addFlag("IGNORE_WEIGHTS",false,"ignore the weights in the underlying analysis object");
+}
+
+LandmarkSelectionBase::LandmarkSelectionBase( const ActionOptions& ao ):
+Action(ao),
+AnalysisWithDataCollection(ao)
+{
+ parse("NLANDMARKS",nlandmarks);
+ log.printf(" selecting %d landmark points \n",nlandmarks);
+ lweights.resize( nlandmarks );
+
+ parseFlag("NOVORONOI",novoronoi);
+ if( !novoronoi && !dissimilaritiesWereSet() ) error("cannot calculate voronoi weights without dissimilarity mesaure");
+
+ if( !novoronoi ) log.printf(" ascribing weights to landmarks using voronoi analysis\n");
+ else log.printf(" ascribing weights of original points to landmark\n");
+}
+
+void LandmarkSelectionBase::selectFrame( const unsigned& iframe ){
+ landmark_indices.push_back( iframe );
+}
+
+void LandmarkSelectionBase::performAnalysis(){
+ landmark_indices.resize(0); selectLandmarks();
+ plumed_dbg_assert( nlandmarks==getNumberOfDataPoints() );
+
+ if( !novoronoi ){
+ lweights.assign(lweights.size(),0.0);
+ unsigned rank=comm.Get_rank(), size=comm.Get_size();
+ for(unsigned i=rank;i<mydata->getNumberOfDataPoints();i+=size){
+ unsigned closest=0;
+ double mindist=mydata->getDissimilarity( i, landmark_indices[0] );
+ for(unsigned j=1;j<nlandmarks;++j){
+ double dist=mydata->getDissimilarity( i, landmark_indices[j] );
+ if( dist<mindist ){ mindist=dist; closest=j; }
+ }
+ lweights[closest] += mydata->getWeight(i);
+ }
+ comm.Sum( &lweights[0], lweights.size() );
+ } else {
+ for(unsigned i=0;i<nlandmarks;++i) lweights[i]=getWeight( landmark_indices[i] );
+ }
+}
+
+}
+}
diff --git a/src/analysis/LandmarkSelectionBase.h b/src/analysis/LandmarkSelectionBase.h
new file mode 100644
index 0000000000000000000000000000000000000000..ce9723c1fb023f5dbad07a97273ecec4b5dc0b1e
--- /dev/null
+++ b/src/analysis/LandmarkSelectionBase.h
@@ -0,0 +1,97 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Copyright (c) 2013,2014 The plumed team
+ (see the PEOPLE file at the root of the distribution for a list of names)
+
+ See http://www.plumed-code.org for more information.
+
+ This file is part of plumed, version 2.
+
+ plumed is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ plumed is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with plumed. If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#ifndef __PLUMED_analysis_LandmarkSelectionBase_h
+#define __PLUMED_analysis_LandmarkSelectionBase_h
+
+#include "AnalysisWithDataCollection.h"
+
+namespace PLMD {
+namespace analysis {
+
+class LandmarkSelectionBase : public AnalysisWithDataCollection {
+private:
+/// The number of landmarks we are selecting
+ unsigned nlandmarks;
+/// The weights of the landmark points
+ std::vector<double> lweights;
+/// The indices of the landmarks in the original data set
+ std::vector<unsigned> landmark_indices;
+/// How do we treat weights
+ bool novoronoi, noweights;
+protected:
+/// Transfer frame i in the underlying action to the object we are going to analyze
+ void selectFrame( const unsigned& );
+public:
+ static void registerKeywords( Keywords& keys );
+ LandmarkSelectionBase( const ActionOptions& ao );
+/// Return the number of data points
+ unsigned getNumberOfDataPoints() const ;
+/// Return the index of the data point in the base class
+ unsigned getDataPointIndexInBase( const unsigned& idata ) const ;
+/// Get the weight
+ double getWeight( const unsigned& idata ) const ;
+/// 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 );
+/// Select landmark configurations
+ void performAnalysis();
+ virtual void selectLandmarks()=0;
+/// Get the squared dissimilarity between two reference configurations
+ double getDissimilarity( const unsigned& i, const unsigned& j );
+/// This does nothing - it just ensures the final class is not abstract
+ void performTask( const unsigned& , const unsigned& , MultiValue& ) const { plumed_error(); }
+};
+
+inline
+unsigned LandmarkSelectionBase::getNumberOfDataPoints() const {
+ return nlandmarks;
+}
+
+inline
+unsigned LandmarkSelectionBase::getDataPointIndexInBase( const unsigned& idata ) const {
+ return AnalysisWithDataCollection::getDataPointIndexInBase( landmark_indices[idata] );
+}
+
+inline
+double LandmarkSelectionBase::getWeight( const unsigned& idata ) const {
+ return lweights[idata];
+}
+
+inline
+void LandmarkSelectionBase::getDataPoint( const unsigned& idata, std::vector<double>& point, double& weight ) const {
+ AnalysisWithDataCollection::getDataPoint( landmark_indices[idata], point, weight );
+}
+
+inline
+ReferenceConfiguration* LandmarkSelectionBase::getReferenceConfiguration( const unsigned& idat ){
+ return AnalysisWithDataCollection::getReferenceConfiguration( landmark_indices[idat] );
+}
+
+inline
+double LandmarkSelectionBase::getDissimilarity( const unsigned& i, const unsigned& j ){
+ return AnalysisBase::getDissimilarity( landmark_indices[i], landmark_indices[j] );
+}
+
+}
+}
+#endif
diff --git a/src/analysis/OutputColvarFile.cpp b/src/analysis/OutputColvarFile.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..d858320c226f8a0fe5be87c7280649f2b11274ed
--- /dev/null
+++ b/src/analysis/OutputColvarFile.cpp
@@ -0,0 +1,101 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Copyright (c) 2012 The plumed team
+ (see the PEOPLE file at the root of the distribution for a list of names)
+
+ See http://www.plumed-code.org for more information.
+
+ This file is part of plumed, version 2.0.
+
+ plumed is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ plumed is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with plumed. If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#include "AnalysisWithDataCollection.h"
+#include "reference/ReferenceAtoms.h"
+#include "reference/ReferenceArguments.h"
+#include "core/ActionRegister.h"
+#include "core/PlumedMain.h"
+#include "core/Atoms.h"
+
+namespace PLMD {
+namespace analysis {
+
+//+PLUMEDOC ANALYSIS OUTPUT_ANALYSIS_DATA_TO_COLVAR
+/*
+This can be used to output the data that has been stored in an Analysis object.
+
+The most useful application of this method is to output all projections of all the
+points that were stored in an analysis object that performs some form of dimensionality
+reduction. If you use the USE_DIMRED_DATA_FROM option below projections of all the
+stored points will be output to a file. The positions of these projections will be calculated
+using that dimensionality reduction algorithms out-of-sample extension algorithm.
+
+\par Examples
+
+*/
+//+ENDPLUMEDOC
+
+class OutputColvarFile : public AnalysisWithDataCollection {
+private:
+ std::string fmt;
+ std::string filename;
+public:
+ static void registerKeywords( Keywords& keys );
+ OutputColvarFile( const ActionOptions& );
+ void performTask( const unsigned& , const unsigned& , MultiValue& ) const { plumed_error(); }
+ void performAnalysis();
+};
+
+PLUMED_REGISTER_ACTION(OutputColvarFile,"OUTPUT_ANALYSIS_DATA_TO_COLVAR")
+
+void OutputColvarFile::registerKeywords( Keywords& keys ){
+ AnalysisWithDataCollection::registerKeywords( keys );
+ keys.add("compulsory","FILE","the name of the file to output to");
+ keys.add("optional","FMT","the format to output the data using");
+}
+
+OutputColvarFile::OutputColvarFile( const ActionOptions& ao ):
+Action(ao),
+AnalysisWithDataCollection(ao),
+fmt("%f")
+{
+ parse("FILE",filename); parse("FMT",fmt);
+ if( !getRestart() ){ OFile ofile; ofile.link(*this); ofile.setBackupString("analysis"); ofile.backupAllFiles(filename); }
+ log.printf(" printing data to file named %s \n",filename.c_str() );
+}
+
+void OutputColvarFile::performAnalysis(){
+
+ // Output the embedding as long lists of data
+ OFile gfile; gfile.link(*this);
+ gfile.setBackupString("analysis");
+ gfile.fmtField(fmt+" ");
+ 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) );
+ plumed_assert( !myat );
+
+ // Print embedding coordinates
+ for(unsigned i=0;i<getNumberOfDataPoints();++i){
+ ReferenceArguments* myref=dynamic_cast<ReferenceArguments*>( getReferenceConfiguration(i) );
+ plumed_assert( myref );
+ for(unsigned j=0;j<myref->getReferenceArguments().size();++j){
+ gfile.printField( myref->getArgumentNames()[j], myref->getReferenceArgument(j) );
+ }
+ gfile.printField();
+ }
+ gfile.close();
+}
+
+}
+}
diff --git a/src/analysis/OutputPDBFile.cpp b/src/analysis/OutputPDBFile.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..23548dc2f3b1e16edd58c492988be4d9d864a461
--- /dev/null
+++ b/src/analysis/OutputPDBFile.cpp
@@ -0,0 +1,84 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Copyright (c) 2012 The plumed team
+ (see the PEOPLE file at the root of the distribution for a list of names)
+
+ See http://www.plumed-code.org for more information.
+
+ This file is part of plumed, version 2.0.
+
+ plumed is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ plumed is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with plumed. If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#include "AnalysisWithDataCollection.h"
+#include "reference/ReferenceAtoms.h"
+#include "reference/ReferenceArguments.h"
+#include "core/ActionRegister.h"
+#include "core/PlumedMain.h"
+#include "core/Atoms.h"
+
+namespace PLMD {
+namespace analysis {
+
+//+PLUMEDOC ANALYSIS OUTPUT_ANALYSIS_DATA_TO_PDB
+/*
+This can be used to output the data that has been stored in an Analysis object.
+
+\par Examples
+
+*/
+//+ENDPLUMEDOC
+
+class OutputPDBFile : public AnalysisWithDataCollection {
+private:
+ std::string fmt;
+ std::string filename;
+public:
+ static void registerKeywords( Keywords& keys );
+ OutputPDBFile( const ActionOptions& );
+ void performTask( const unsigned& , const unsigned& , MultiValue& ) const { plumed_error(); }
+ void performAnalysis();
+};
+
+PLUMED_REGISTER_ACTION(OutputPDBFile,"OUTPUT_ANALYSIS_DATA_TO_PDB")
+
+void OutputPDBFile::registerKeywords( Keywords& keys ){
+ AnalysisWithDataCollection::registerKeywords( keys );
+ keys.add("compulsory","FILE","the name of the file to output to");
+ keys.add("optional","FMT","the format to use in the output file");
+}
+
+OutputPDBFile::OutputPDBFile( const ActionOptions& ao ):
+Action(ao),
+AnalysisWithDataCollection(ao),
+fmt("%f")
+{
+ parse("FILE",filename); parse("FMT",fmt);
+ if( !getRestart() ){ OFile ofile; ofile.link(*this); ofile.setBackupString("analysis"); ofile.backupAllFiles(filename); }
+ log.printf(" printing data to file named %s \n",filename.c_str() );
+}
+
+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";
+ 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 );
+ }
+ afile.close();
+}
+
+}
+}
diff --git a/src/analysis/PrintDissimilarityMatrix.cpp b/src/analysis/PrintDissimilarityMatrix.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..1b76c3bb66dc0339dabe1727ea5b196acce04673
--- /dev/null
+++ b/src/analysis/PrintDissimilarityMatrix.cpp
@@ -0,0 +1,71 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Copyright (c) 2013,2014 The plumed team
+ (see the PEOPLE file at the root of the distribution for a list of names)
+
+ See http://www.plumed-code.org for more information.
+
+ This file is part of plumed, version 2.
+
+ plumed is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ plumed is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with plumed. If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#include "tools/OFile.h"
+#include "AnalysisBase.h"
+#include "core/ActionRegister.h"
+
+namespace PLMD {
+namespace analysis {
+
+class PrintDissimilarityMatrix : public AnalysisBase {
+private:
+ std::string fmt;
+ std::string fname;
+public:
+ static void registerKeywords( Keywords& keys );
+ PrintDissimilarityMatrix( const ActionOptions& ao );
+ void performAnalysis();
+ void performTask( const unsigned& , const unsigned& , MultiValue& ) const { plumed_error(); }
+};
+
+PLUMED_REGISTER_ACTION(PrintDissimilarityMatrix,"PRINT_DISSIMILARITY_MATRIX")
+
+void PrintDissimilarityMatrix::registerKeywords( Keywords& keys ){
+ AnalysisBase::registerKeywords( keys );
+ keys.add("compulsory","FILE","name of file on which to output the data");
+ keys.add("optional","FMT","the format to use for the output of numbers");
+}
+
+PrintDissimilarityMatrix::PrintDissimilarityMatrix( const ActionOptions& ao ):
+Action(ao),
+AnalysisBase(ao),
+fmt("%f")
+{
+ if( !dissimilaritiesWereSet() ) error("dissimilarities have not been set in base classes");
+
+ parse("FILE",fname); parse("FMT",fmt);
+ if( !getRestart() ){ OFile ofile; ofile.link(*this); ofile.setBackupString("analysis"); ofile.backupAllFiles(fname); }
+ log.printf(" printing to file named %s with formt %s \n",fname.c_str(), fmt.c_str() );
+}
+
+void PrintDissimilarityMatrix::performAnalysis(){
+ std::string ofmt=" "+fmt;
+ OFile ofile; ofile.setBackupString("analysis"); ofile.open(fname);
+ for(unsigned i=0;i<getNumberOfDataPoints();++i){
+ for(unsigned j=0;j<getNumberOfDataPoints();++j) ofile.printf(ofmt.c_str(), mydata->getDissimilarity( i,j ) );
+ ofile.printf("\n");
+ }
+ ofile.close();
+}
+
+}
+}
diff --git a/src/analysis/ReadDissimilarityMatrix.cpp b/src/analysis/ReadDissimilarityMatrix.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..935a7de8fb6db0fdf0abe7d6301684aa3b0e99f9
--- /dev/null
+++ b/src/analysis/ReadDissimilarityMatrix.cpp
@@ -0,0 +1,131 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Copyright (c) 2013,2014 The plumed team
+ (see the PEOPLE file at the root of the distribution for a list of names)
+
+ See http://www.plumed-code.org for more information.
+
+ This file is part of plumed, version 2.
+
+ plumed is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ plumed is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with plumed. If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#include "AnalysisBase.h"
+#include "core/PlumedMain.h"
+#include "core/ActionSet.h"
+#include "core/ActionRegister.h"
+#include "tools/IFile.h"
+
+namespace PLMD {
+namespace analysis {
+
+class ReadDissimilarityMatrix : public AnalysisBase {
+private:
+ unsigned nnodes;
+ std::string fname, wfile;
+ Matrix<double> dissimilarities;
+ std::vector<double> weights;
+public:
+ static void registerKeywords( Keywords& keys );
+ 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 );
+/// 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
+ bool dissimilaritiesWereSet() const { return true; }
+/// Get the dissimilarity between two data points
+ double getDissimilarity( const unsigned& , const unsigned& );
+/// Get the weight from the input file
+ double getWeight( const unsigned& idata ) const ;
+/// Just tell plumed to stop
+ void update();
+/// Read in the dissimilarity matrix
+ void performAnalysis();
+/// Overwrite virtual function in base class
+ void performTask( const unsigned& , const unsigned& , MultiValue& ) const { plumed_error(); }
+};
+
+PLUMED_REGISTER_ACTION(ReadDissimilarityMatrix,"READ_DISSIMILARITY_MATRIX")
+
+void ReadDissimilarityMatrix::registerKeywords( Keywords& keys ){
+ AnalysisBase::registerKeywords( keys ); keys.remove("USE_OUTPUT_DATA_FROM");
+ keys.add("compulsory","FILE","an input file containing the matrix of dissimilarities");
+ keys.add("optional","WFILE","input file containing weights of points");
+}
+
+ReadDissimilarityMatrix::ReadDissimilarityMatrix( const ActionOptions& ao ):
+Action(ao),
+AnalysisBase(ao),
+nnodes(1)
+{
+ if( plumed.getActionSet().size()!=0 ) error("read dissimilarity matrix command must be at top of input file");
+
+ parse("FILE",fname);
+ log.printf(" reading dissimilarity matrix from file %s \n",fname.c_str() );
+ parse("WFILE",wfile);
+ if( wfile.length()>0 ) log.printf(" reading weights of nodes from file named %s \n",wfile.c_str() );
+ else log.printf(" setting weights of all nodes equal to one\n");
+
+ // We have to set the information on how often we are reading data from the trajectory and how
+ // often we are running here so that the code behaves
+ use_all_data=true; freq=1; setStride(1);
+}
+
+void ReadDissimilarityMatrix::update(){ plumed.stop(); }
+
+void ReadDissimilarityMatrix::performAnalysis(){
+ IFile mfile; mfile.open(fname);
+ // Read in first line
+ std::vector<std::string> words; Tools::getParsedLine( mfile, words );
+ nnodes=words.size(); dissimilarities.resize( nnodes, nnodes );
+ for(unsigned j=0;j<nnodes;++j) Tools::convert( words[j], dissimilarities(0,j) );
+
+ for(unsigned i=1;i<nnodes;++i){
+ Tools::getParsedLine( mfile, words );
+ if( words.size()!=nnodes ) error("bad formatting in matrix file");
+ for(unsigned j=0;j<nnodes;++j) Tools::convert( words[j], dissimilarities(i,j) );
+ }
+ mfile.close();
+
+ weights.resize( nnodes );
+ if( wfile.length()>0 ){
+ IFile wfilef; wfilef.open(wfile);
+ for(unsigned i=0;i<nnodes;++i){
+ Tools::getParsedLine( wfilef, words ); Tools::convert( words[0], weights[i] );
+ }
+ wfilef.close();
+ } else {
+ weights.assign(weights.size(),1.0);
+ }
+}
+
+double ReadDissimilarityMatrix::getDissimilarity( const unsigned& iframe, const unsigned& jframe ){
+ return dissimilarities( iframe, jframe );
+}
+
+ReferenceConfiguration* ReadDissimilarityMatrix::getReferenceConfiguration( const unsigned& idata ){
+ plumed_merror("cannot get reference configurations from read in dissimilarity matrix");
+ return NULL;
+}
+
+void ReadDissimilarityMatrix::getDataPoint( const unsigned& idata, std::vector<double>& point, double& weight ) const {
+ plumed_merror("cannot get data points from read in dissmimilarity matrix");
+}
+
+double ReadDissimilarityMatrix::getWeight( const unsigned& idata ) const {
+ plumed_assert( idata<nnodes ); return weights[idata];
+}
+
+}
+}
diff --git a/src/analysis/SelectWithStride.cpp b/src/analysis/SelectWithStride.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..12a2ef97077b3cbc6bb68e3fbff6634b11a5091b
--- /dev/null
+++ b/src/analysis/SelectWithStride.cpp
@@ -0,0 +1,53 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Copyright (c) 2012-2014 The plumed team
+ (see the PEOPLE file at the root of the distribution for a list of names)
+
+ See http://www.plumed-code.org for more information.
+
+ This file is part of plumed, version 2.
+
+ plumed is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ plumed is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with plumed. If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#include "LandmarkSelectionBase.h"
+#include "core/ActionRegister.h"
+
+namespace PLMD {
+namespace analysis {
+
+class SelectWithStride : public LandmarkSelectionBase {
+public:
+ static void registerKeywords( Keywords& keys );
+ SelectWithStride( const ActionOptions& ao );
+ void selectLandmarks();
+};
+
+PLUMED_REGISTER_ACTION(SelectWithStride,"LANDMARK_SELECT_STRIDE")
+
+void SelectWithStride::registerKeywords( Keywords& keys ){
+ LandmarkSelectionBase::registerKeywords( keys );
+}
+
+SelectWithStride::SelectWithStride( const ActionOptions& ao ):
+Action(ao),
+LandmarkSelectionBase(ao)
+{
+}
+
+void SelectWithStride::selectLandmarks(){
+ unsigned stride = std::floor( mydata->getNumberOfDataPoints() / getNumberOfDataPoints() ), max=stride*getNumberOfDataPoints();
+ for(unsigned i=0;i<max;i+=stride) selectFrame( i );
+}
+
+}
+}