diff --git a/regtest/analysis/rt-cube/Makefile b/regtest/analysis/rt-cube/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..3703b27cea227aa053fb6d1d73f861e4384dbcee
--- /dev/null
+++ b/regtest/analysis/rt-cube/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
diff --git a/regtest/analysis/rt-cube/config b/regtest/analysis/rt-cube/config
new file mode 100644
index 0000000000000000000000000000000000000000..f93ec1a97465724691bf162d4735f5ea3648bbb4
--- /dev/null
+++ b/regtest/analysis/rt-cube/config
@@ -0,0 +1,3 @@
+type=driver
+# this is to test a different name
+arg="--plumed plumed.dat --ixyz trajectory.xyz"
diff --git a/regtest/analysis/rt-cube/fesA1.cube.reference b/regtest/analysis/rt-cube/fesA1.cube.reference
new file mode 100644
index 0000000000000000000000000000000000000000..2fb4d61fefdcfbcf8e97547c53b704eb7d197e79
--- /dev/null
+++ b/regtest/analysis/rt-cube/fesA1.cube.reference
@@ -0,0 +1,207 @@
+PLUMED CUBE FILE
+OUTER LOOP: X, MIDDLE LOOP: Y, INNER LOOP: Z
+1 -1.650 -1.650 -1.650
+10 0.300 0.000 0.000
+10 0.000 0.300 0.000
+10 0.000 0.000 0.300
+1 0.000 0.000 0.000
+ 16.849 15.812 14.995 14.398 14.021 13.862
+ 13.921 14.197 14.690 15.399
+ 15.812 14.771 13.949 13.347 12.964 12.798
+ 12.850 13.119 13.603 14.302
+ 14.995 13.949 13.123 12.515 12.125 11.952
+ 11.996 12.256 12.731 13.419
+ 14.398 13.347 12.515 11.901 11.503 11.323
+ 11.358 11.608 12.072 12.750
+ 14.021 12.964 12.125 11.503 11.098 10.909
+ 10.935 11.174 11.627 12.293
+ 13.862 12.798 11.952 11.323 10.909 10.710
+ 10.725 10.954 11.395 12.048
+ 13.921 12.850 11.996 11.358 10.935 10.725
+ 10.730 10.946 11.375 12.015
+ 14.197 13.119 12.256 11.608 11.174 10.954
+ 10.946 11.150 11.566 12.192
+ 14.690 13.603 12.731 12.072 11.627 11.395
+ 11.375 11.566 11.968 12.581
+ 15.399 14.302 13.419 12.750 12.293 12.048
+ 12.015 12.192 12.581 13.179
+ 15.812 14.771 13.949 13.347 12.964 12.798
+ 12.850 13.119 13.603 14.302
+ 14.771 13.725 12.898 12.290 11.901 11.728
+ 11.772 12.032 12.506 13.195
+ 13.949 12.898 12.066 11.451 11.054 10.874
+ 10.909 11.159 11.623 12.301
+ 13.347 12.290 11.451 10.830 10.425 10.236
+ 10.261 10.501 10.954 11.620
+ 12.964 11.901 11.054 10.425 10.011 9.812
+ 9.827 10.056 10.497 11.150
+ 12.798 11.728 10.874 10.236 9.812 9.603
+ 9.607 9.824 10.252 10.892
+ 12.850 11.772 10.909 10.261 9.827 9.607
+ 9.599 9.803 10.219 10.845
+ 13.119 12.032 11.159 10.501 10.056 9.824
+ 9.803 9.994 10.396 11.009
+ 13.603 12.506 11.623 10.954 10.497 10.252
+ 10.219 10.396 10.785 11.383
+ 14.302 13.195 12.301 11.620 11.150 10.892
+ 10.845 11.009 11.383 11.968
+ 14.995 13.949 13.123 12.515 12.125 11.952
+ 11.996 12.256 12.731 13.419
+ 13.949 12.898 12.066 11.451 11.054 10.874
+ 10.909 11.159 11.623 12.301
+ 13.123 12.066 11.227 10.605 10.200 10.011
+ 10.037 10.276 10.730 11.395
+ 12.515 11.451 10.605 9.976 9.562 9.363
+ 9.379 9.607 10.048 10.701
+ 12.125 11.054 10.200 9.562 9.139 8.930
+ 8.934 9.150 9.579 10.219
+ 11.952 10.874 10.011 9.363 8.930 8.709
+ 8.701 8.905 9.321 9.947
+ 11.996 10.909 10.037 9.379 8.934 8.701
+ 8.681 8.872 9.274 9.887
+ 12.256 11.159 10.276 9.607 9.150 8.905
+ 8.872 9.049 9.438 10.036
+ 12.731 11.623 10.730 10.048 9.579 9.321
+ 9.274 9.438 9.812 10.396
+ 13.419 12.301 11.395 10.701 10.219 9.947
+ 9.887 10.036 10.396 10.967
+ 14.398 13.347 12.515 11.901 11.503 11.323
+ 11.358 11.608 12.072 12.750
+ 13.347 12.290 11.451 10.830 10.425 10.236
+ 10.261 10.501 10.954 11.620
+ 12.515 11.451 10.605 9.976 9.562 9.363
+ 9.379 9.607 10.048 10.701
+ 11.901 10.830 9.976 9.338 8.914 8.705
+ 8.709 8.926 9.354 9.994
+ 11.503 10.425 9.562 8.914 8.481 8.260
+ 8.252 8.456 8.872 9.498
+ 11.323 10.236 9.363 8.705 8.260 8.028
+ 8.007 8.198 8.600 9.213
+ 11.358 10.261 9.379 8.709 8.252 8.007
+ 7.974 8.151 8.540 9.138
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+ 8.151 8.315 8.689 9.274
+ 12.072 10.954 10.048 9.354 8.872 8.600
+ 8.540 8.689 9.049 9.620
+ 12.750 11.620 10.701 9.994 9.498 9.213
+ 9.138 9.274 9.620 10.178
+ 14.021 12.964 12.125 11.503 11.098 10.909
+ 10.935 11.174 11.627 12.293
+ 12.964 11.901 11.054 10.425 10.011 9.812
+ 9.827 10.056 10.497 11.150
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+ 8.934 9.150 9.579 10.219
+ 11.503 10.425 9.562 8.914 8.481 8.260
+ 8.252 8.456 8.872 9.498
+ 11.098 10.011 9.139 8.481 8.036 7.803
+ 7.783 7.974 8.376 8.989
+ 10.909 9.812 8.930 8.260 7.803 7.558
+ 7.525 7.703 8.091 8.689
+ 10.935 9.827 8.934 8.252 7.783 7.525
+ 7.478 7.642 8.016 8.600
+ 11.174 10.056 9.150 8.456 7.974 7.703
+ 7.642 7.791 8.152 8.722
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+ 8.016 8.152 8.498 9.055
+ 12.293 11.150 10.219 9.498 8.989 8.689
+ 8.600 8.722 9.055 9.599
+ 13.862 12.798 11.952 11.323 10.909 10.710
+ 10.725 10.954 11.395 12.048
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+ 9.607 9.824 10.252 10.892
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+ 8.701 8.905 9.321 9.947
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+ 8.007 8.198 8.600 9.213
+ 10.909 9.812 8.930 8.260 7.803 7.558
+ 7.525 7.703 8.091 8.689
+ 10.710 9.603 8.709 8.028 7.558 7.301
+ 7.254 7.417 7.791 8.376
+ 10.725 9.607 8.701 8.007 7.525 7.254
+ 7.193 7.342 7.703 8.273
+ 10.954 9.824 8.905 8.198 7.703 7.417
+ 7.342 7.478 7.824 8.382
+ 11.395 10.252 9.321 8.600 8.091 7.791
+ 7.703 7.824 8.157 8.701
+ 12.048 10.892 9.947 9.213 8.689 8.376
+ 8.273 8.382 8.701 9.233
+ 13.921 12.850 11.996 11.358 10.935 10.725
+ 10.730 10.946 11.375 12.015
+ 12.850 11.772 10.909 10.261 9.827 9.607
+ 9.599 9.803 10.219 10.845
+ 11.996 10.909 10.037 9.379 8.934 8.701
+ 8.681 8.872 9.274 9.887
+ 11.358 10.261 9.379 8.709 8.252 8.007
+ 7.974 8.151 8.540 9.138
+ 10.935 9.827 8.934 8.252 7.783 7.525
+ 7.478 7.642 8.016 8.600
+ 10.725 9.607 8.701 8.007 7.525 7.254
+ 7.193 7.342 7.703 8.273
+ 10.730 9.599 8.681 7.974 7.478 7.193
+ 7.118 7.254 7.600 8.157
+ 10.946 9.803 8.872 8.151 7.642 7.342
+ 7.254 7.375 7.708 8.252
+ 11.375 10.219 9.274 8.540 8.016 7.703
+ 7.600 7.708 8.028 8.559
+ 12.015 10.845 9.887 9.138 8.600 8.273
+ 8.157 8.252 8.559 9.079
+ 14.197 13.119 12.256 11.608 11.174 10.954
+ 10.946 11.150 11.566 12.192
+ 13.119 12.032 11.159 10.501 10.056 9.824
+ 9.803 9.994 10.396 11.009
+ 12.256 11.159 10.276 9.607 9.150 8.905
+ 8.872 9.049 9.438 10.036
+ 11.608 10.501 9.607 8.926 8.456 8.198
+ 8.151 8.315 8.689 9.274
+ 11.174 10.056 9.150 8.456 7.974 7.703
+ 7.642 7.791 8.152 8.722
+ 10.954 9.824 8.905 8.198 7.703 7.417
+ 7.342 7.478 7.824 8.382
+ 10.946 9.803 8.872 8.151 7.642 7.342
+ 7.254 7.375 7.708 8.252
+ 11.150 9.994 9.049 8.315 7.791 7.478
+ 7.375 7.484 7.803 8.335
+ 11.566 10.396 9.438 8.689 8.152 7.824
+ 7.708 7.803 8.110 8.630
+ 12.192 11.009 10.036 9.274 8.722 8.382
+ 8.252 8.335 8.630 9.139
+ 14.690 13.603 12.731 12.072 11.627 11.395
+ 11.375 11.566 11.968 12.581
+ 13.603 12.506 11.623 10.954 10.497 10.252
+ 10.219 10.396 10.785 11.383
+ 12.731 11.623 10.730 10.048 9.579 9.321
+ 9.274 9.438 9.812 10.396
+ 12.072 10.954 10.048 9.354 8.872 8.600
+ 8.540 8.689 9.049 9.620
+ 11.627 10.497 9.579 8.872 8.376 8.091
+ 8.016 8.152 8.498 9.055
+ 11.395 10.252 9.321 8.600 8.091 7.791
+ 7.703 7.824 8.157 8.701
+ 11.375 10.219 9.274 8.540 8.016 7.703
+ 7.600 7.708 8.028 8.559
+ 11.566 10.396 9.438 8.689 8.152 7.824
+ 7.708 7.803 8.110 8.630
+ 11.968 10.785 9.812 9.049 8.498 8.157
+ 8.028 8.110 8.406 8.914
+ 12.581 11.383 10.396 9.620 9.055 8.701
+ 8.559 8.630 8.914 9.412
+ 15.399 14.302 13.419 12.750 12.293 12.048
+ 12.015 12.192 12.581 13.179
+ 14.302 13.195 12.301 11.620 11.150 10.892
+ 10.845 11.009 11.383 11.968
+ 13.419 12.301 11.395 10.701 10.219 9.947
+ 9.887 10.036 10.396 10.967
+ 12.750 11.620 10.701 9.994 9.498 9.213
+ 9.138 9.274 9.620 10.178
+ 12.293 11.150 10.219 9.498 8.989 8.689
+ 8.600 8.722 9.055 9.599
+ 12.048 10.892 9.947 9.213 8.689 8.376
+ 8.273 8.382 8.701 9.233
+ 12.015 10.845 9.887 9.138 8.600 8.273
+ 8.157 8.252 8.559 9.079
+ 12.192 11.009 10.036 9.274 8.722 8.382
+ 8.252 8.335 8.630 9.139
+ 12.581 11.383 10.396 9.620 9.055 8.701
+ 8.559 8.630 8.914 9.412
+ 13.179 11.968 10.967 10.178 9.599 9.233
+ 9.079 9.139 9.412 9.901
diff --git a/regtest/analysis/rt-cube/fesA2.cube.reference b/regtest/analysis/rt-cube/fesA2.cube.reference
new file mode 100644
index 0000000000000000000000000000000000000000..e893cd16f76f1b972a04361530a571e6021ba59e
--- /dev/null
+++ b/regtest/analysis/rt-cube/fesA2.cube.reference
@@ -0,0 +1,207 @@
+PLUMED CUBE FILE
+OUTER LOOP: X, MIDDLE LOOP: Y, INNER LOOP: Z
+1 -1.650 -1.650 -1.650
+10 0.300 0.000 0.000
+10 0.000 0.300 0.000
+10 0.000 0.000 0.300
+1 0.000 0.000 0.000
+ 16.849 15.812 14.995 14.398 14.021 13.862
+ 13.921 14.197 14.690 15.399
+ 15.812 14.771 13.949 13.347 12.964 12.798
+ 12.850 13.119 13.603 14.302
+ 14.995 13.949 13.123 12.515 12.125 11.952
+ 11.996 12.256 12.731 13.419
+ 14.398 13.347 12.515 11.900 11.503 11.323
+ 11.358 11.608 12.072 12.750
+ 14.021 12.964 12.125 11.503 11.098 10.909
+ 10.935 11.174 11.627 12.293
+ 13.862 12.798 11.952 11.323 10.909 10.710
+ 10.725 10.954 11.395 12.048
+ 13.921 12.850 11.996 11.358 10.935 10.725
+ 10.730 10.946 11.375 12.015
+ 14.197 13.119 12.256 11.608 11.174 10.954
+ 10.946 11.150 11.566 12.192
+ 14.690 13.603 12.731 12.072 11.627 11.395
+ 11.375 11.566 11.968 12.580
+ 15.399 14.302 13.419 12.750 12.293 12.048
+ 12.015 12.192 12.580 13.179
+ 15.812 14.771 13.949 13.347 12.964 12.798
+ 12.850 13.119 13.603 14.302
+ 14.771 13.725 12.898 12.290 11.900 11.728
+ 11.772 12.032 12.506 13.195
+ 13.949 12.898 12.066 11.452 11.054 10.874
+ 10.909 11.159 11.623 12.301
+ 13.347 12.290 11.452 10.830 10.425 10.236
+ 10.261 10.501 10.954 11.620
+ 12.964 11.900 11.054 10.425 10.011 9.812
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+ 9.607 9.824 10.252 10.892
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+ 9.599 9.803 10.219 10.845
+ 13.119 12.032 11.159 10.501 10.056 9.824
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+ 10.219 10.396 10.785 11.383
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diff --git a/regtest/analysis/rt-cube/histoA1.cube.reference b/regtest/analysis/rt-cube/histoA1.cube.reference
new file mode 100644
index 0000000000000000000000000000000000000000..10c48d5b154ffecc6e9a966ae1b05d4272395448
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diff --git a/regtest/analysis/rt-cube/histoA2.cube.reference b/regtest/analysis/rt-cube/histoA2.cube.reference
new file mode 100644
index 0000000000000000000000000000000000000000..1fa84a79083ed3c49bc448ccdfbc67071c9b14ea
--- /dev/null
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+ 0.0052 0.0080 0.0114 0.0148 0.0177 0.0195
+ 0.0196 0.0182 0.0155 0.0121
+ 0.0073 0.0114 0.0162 0.0212 0.0255 0.0281
+ 0.0285 0.0266 0.0227 0.0179
+ 0.0095 0.0148 0.0212 0.0279 0.0337 0.0374
+ 0.0381 0.0357 0.0307 0.0243
+ 0.0113 0.0177 0.0255 0.0337 0.0409 0.0456
+ 0.0467 0.0440 0.0381 0.0303
+ 0.0124 0.0195 0.0281 0.0374 0.0456 0.0511
+ 0.0527 0.0499 0.0434 0.0347
+ 0.0124 0.0196 0.0285 0.0381 0.0467 0.0527
+ 0.0546 0.0520 0.0455 0.0366
+ 0.0114 0.0182 0.0266 0.0357 0.0440 0.0499
+ 0.0520 0.0498 0.0438 0.0354
+ 0.0097 0.0155 0.0227 0.0307 0.0381 0.0434
+ 0.0455 0.0438 0.0387 0.0314
+ 0.0075 0.0121 0.0179 0.0243 0.0303 0.0347
+ 0.0366 0.0354 0.0314 0.0256
+ 0.0028 0.0043 0.0061 0.0079 0.0095 0.0104
+ 0.0105 0.0097 0.0082 0.0065
+ 0.0043 0.0066 0.0095 0.0124 0.0149 0.0164
+ 0.0166 0.0155 0.0133 0.0104
+ 0.0061 0.0095 0.0135 0.0178 0.0215 0.0238
+ 0.0243 0.0227 0.0196 0.0155
+ 0.0079 0.0124 0.0178 0.0235 0.0285 0.0318
+ 0.0326 0.0307 0.0266 0.0211
+ 0.0095 0.0149 0.0215 0.0285 0.0348 0.0390
+ 0.0402 0.0381 0.0331 0.0265
+ 0.0104 0.0164 0.0238 0.0318 0.0390 0.0440
+ 0.0456 0.0434 0.0380 0.0305
+ 0.0105 0.0166 0.0243 0.0326 0.0402 0.0456
+ 0.0475 0.0455 0.0400 0.0323
+ 0.0097 0.0155 0.0227 0.0307 0.0381 0.0434
+ 0.0455 0.0438 0.0387 0.0314
+ 0.0082 0.0133 0.0196 0.0266 0.0331 0.0380
+ 0.0400 0.0387 0.0344 0.0280
+ 0.0065 0.0104 0.0155 0.0211 0.0265 0.0305
+ 0.0323 0.0314 0.0280 0.0230
+ 0.0021 0.0032 0.0046 0.0060 0.0072 0.0080
+ 0.0081 0.0075 0.0065 0.0051
+ 0.0032 0.0050 0.0072 0.0095 0.0114 0.0127
+ 0.0129 0.0121 0.0104 0.0082
+ 0.0046 0.0072 0.0104 0.0137 0.0166 0.0185
+ 0.0190 0.0179 0.0155 0.0123
+ 0.0060 0.0095 0.0137 0.0182 0.0222 0.0249
+ 0.0256 0.0243 0.0211 0.0169
+ 0.0072 0.0114 0.0166 0.0222 0.0272 0.0307
+ 0.0318 0.0303 0.0265 0.0213
+ 0.0080 0.0127 0.0185 0.0249 0.0307 0.0348
+ 0.0363 0.0347 0.0305 0.0247
+ 0.0081 0.0129 0.0190 0.0256 0.0318 0.0363
+ 0.0380 0.0366 0.0323 0.0263
+ 0.0075 0.0121 0.0179 0.0243 0.0303 0.0347
+ 0.0366 0.0354 0.0314 0.0256
+ 0.0065 0.0104 0.0155 0.0211 0.0265 0.0305
+ 0.0323 0.0314 0.0280 0.0230
+ 0.0051 0.0082 0.0123 0.0169 0.0213 0.0247
+ 0.0263 0.0256 0.0230 0.0189
diff --git a/regtest/analysis/rt-cube/plumed.dat b/regtest/analysis/rt-cube/plumed.dat
new file mode 100755
index 0000000000000000000000000000000000000000..f62456dd7877409758531206698dfab644d8bc45
--- /dev/null
+++ b/regtest/analysis/rt-cube/plumed.dat
@@ -0,0 +1,35 @@
+x1: DISTANCE ATOMS=1,2
+x2: DISTANCE ATOMS=1,2
+x3: DISTANCE ATOMS=1,2
+
+HISTOGRAM ...
+ ARG=x1,x2,x3
+ TEMP=300
+ GRID_MIN=0.0,0.0,0.0
+ GRID_MAX=3.0,3.0,3.0
+ GRID_BIN=10,10,10
+ BANDWIDTH=1.0,1.0,1.0
+ LABEL=hA1
+... HISTOGRAM
+
+PRINT_GRID GRID=hA1 STRIDE=1 FILE=histoA1
+PRINT_CUBE GRID=hA1 STRIDE=1 FILE=histoA1.cube FMT=%8.4f
+
+CONVERT_TO_FES GRID=hA1 TEMP=300 LABEL=fA1
+PRINT_CUBE GRID=fA1 STRIDE=1 FILE=fesA1.cube FMT=%8.3f
+
+HISTOGRAM ...
+ ARG=x1,x2,x3
+ TEMP=300
+ GRID_MIN=0.0,0.0,0.0
+ GRID_MAX=3.0,3.0,3.0
+ GRID_BIN=10,10,10
+ BANDWIDTH=1.0,1.0,1.0
+ NOMEMORY
+ LABEL=hA2
+... HISTOGRAM
+
+PRINT_CUBE GRID=hA2 STRIDE=2 FILE=histoA2.cube FMT=%8.4f
+
+CONVERT_TO_FES GRID=hA2 TEMP=300 LABEL=fA2
+PRINT_CUBE GRID=fA2 STRIDE=2 FILE=fesA2.cube FMT=%8.3f
diff --git a/regtest/analysis/rt-cube/trajectory.xyz b/regtest/analysis/rt-cube/trajectory.xyz
new file mode 100644
index 0000000000000000000000000000000000000000..c910ae5c6fda2241cfe5be857f9b8493db430ed3
--- /dev/null
+++ b/regtest/analysis/rt-cube/trajectory.xyz
@@ -0,0 +1,12 @@
+2
+0 0 0
+X 0 0 0
+X 0 0 1
+2
+0 0 0
+X 0 0 0
+X 0 0 1.5
+2
+0 0 0
+X 0 0 0
+X 0 0 2
diff --git a/regtest/analysis/rt-histo/Makefile b/regtest/analysis/rt-histo/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..3703b27cea227aa053fb6d1d73f861e4384dbcee
--- /dev/null
+++ b/regtest/analysis/rt-histo/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
diff --git a/regtest/analysis/rt-histo/analysis.0.fesA1.reference b/regtest/analysis/rt-histo/analysis.0.fesA1.reference
new file mode 100644
index 0000000000000000000000000000000000000000..27fd0bbb32936bfd4c5b4343044469c28b883453
--- /dev/null
+++ b/regtest/analysis/rt-histo/analysis.0.fesA1.reference
@@ -0,0 +1,107 @@
+#! FIELDS x fA1 dfA1_x
+#! SET normalisation 1.0000
+#! SET min_x 0.0
+#! SET max_x 3.0
+#! SET nbins_x 100
+#! SET periodic_x false
+ 0.0000 inf nan
+ 0.0300 inf nan
+ 0.0600 inf nan
+ 0.0900 inf nan
+ 0.1200 inf nan
+ 0.1500 inf nan
+ 0.1800 inf nan
+ 0.2100 inf nan
+ 0.2400 inf nan
+ 0.2700 inf nan
+ 0.3000 inf nan
+ 0.3300 inf nan
+ 0.3600 inf nan
+ 0.3900 inf nan
+ 0.4200 inf nan
+ 0.4500 inf nan
+ 0.4800 inf nan
+ 0.5100 inf nan
+ 0.5400 inf nan
+ 0.5700 inf nan
+ 0.6000 inf nan
+ 0.6300 inf nan
+ 0.6600 inf nan
+ 0.6900 inf nan
+ 0.7200 inf nan
+ 0.7500 inf nan
+ 0.7800 inf nan
+ 0.8100 inf nan
+ 0.8400 inf nan
+ 0.8700 inf nan
+ 0.9000 inf nan
+ 0.9300 inf nan
+ 0.9600 inf nan
+ 0.9900 inf nan
+ 1.0200 inf nan
+ 1.0500 inf nan
+ 1.0800 inf nan
+ 1.1100 inf nan
+ 1.1400 12.7120 -89.7962
+ 1.1700 10.1304 -82.3132
+ 1.2000 7.7732 -74.8302
+ 1.2300 5.6406 -67.3471
+ 1.2600 3.7324 -59.8641
+ 1.2900 2.0487 -52.3811
+ 1.3200 0.5895 -44.8981
+ 1.3500 -0.6452 -37.4151
+ 1.3800 -1.6554 -29.9321
+ 1.4100 -2.4411 -22.4490
+ 1.4400 -3.0023 -14.9660
+ 1.4700 -3.3390 -7.4830
+ 1.5000 -3.4513 0.0000
+ 1.5300 -3.3390 7.4830
+ 1.5600 -3.0023 14.9660
+ 1.5900 -2.4411 22.4490
+ 1.6200 -1.6554 29.9321
+ 1.6500 -0.6452 37.4151
+ 1.6800 0.5895 44.8981
+ 1.7100 2.0487 52.3811
+ 1.7400 3.7324 59.8641
+ 1.7700 5.6406 67.3471
+ 1.8000 7.7732 74.8302
+ 1.8300 10.1304 82.3132
+ 1.8600 12.7120 89.7962
+ 1.8900 inf nan
+ 1.9200 inf nan
+ 1.9500 inf nan
+ 1.9800 inf nan
+ 2.0100 inf nan
+ 2.0400 inf nan
+ 2.0700 inf nan
+ 2.1000 inf nan
+ 2.1300 inf nan
+ 2.1600 inf nan
+ 2.1900 inf nan
+ 2.2200 inf nan
+ 2.2500 inf nan
+ 2.2800 inf nan
+ 2.3100 inf nan
+ 2.3400 inf nan
+ 2.3700 inf nan
+ 2.4000 inf nan
+ 2.4300 inf nan
+ 2.4600 inf nan
+ 2.4900 inf nan
+ 2.5200 inf nan
+ 2.5500 inf nan
+ 2.5800 inf nan
+ 2.6100 inf nan
+ 2.6400 inf nan
+ 2.6700 inf nan
+ 2.7000 inf nan
+ 2.7300 inf nan
+ 2.7600 inf nan
+ 2.7900 inf nan
+ 2.8200 inf nan
+ 2.8500 inf nan
+ 2.8800 inf nan
+ 2.9100 inf nan
+ 2.9400 inf nan
+ 2.9700 inf nan
+ 3.0000 inf nan
diff --git a/regtest/analysis/rt-histo/analysis.0.histoA1.reference b/regtest/analysis/rt-histo/analysis.0.histoA1.reference
new file mode 100644
index 0000000000000000000000000000000000000000..88a4336bed9ff8e1e8a939c7e49a27b91a97e583
--- /dev/null
+++ b/regtest/analysis/rt-histo/analysis.0.histoA1.reference
@@ -0,0 +1,107 @@
+#! FIELDS x hA1 dhA1_x
+#! SET normalisation 1.0000
+#! SET min_x 0.0
+#! SET max_x 3.0
+#! SET nbins_x 100
+#! SET periodic_x false
+ 0.0000 0.0000 0.0000
+ 0.0300 0.0000 0.0000
+ 0.0600 0.0000 0.0000
+ 0.0900 0.0000 0.0000
+ 0.1200 0.0000 0.0000
+ 0.1500 0.0000 0.0000
+ 0.1800 0.0000 0.0000
+ 0.2100 0.0000 0.0000
+ 0.2400 0.0000 0.0000
+ 0.2700 0.0000 0.0000
+ 0.3000 0.0000 0.0000
+ 0.3300 0.0000 0.0000
+ 0.3600 0.0000 0.0000
+ 0.3900 0.0000 0.0000
+ 0.4200 0.0000 0.0000
+ 0.4500 0.0000 0.0000
+ 0.4800 0.0000 0.0000
+ 0.5100 0.0000 0.0000
+ 0.5400 0.0000 0.0000
+ 0.5700 0.0000 0.0000
+ 0.6000 0.0000 0.0000
+ 0.6300 0.0000 0.0000
+ 0.6600 0.0000 0.0000
+ 0.6900 0.0000 0.0000
+ 0.7200 0.0000 0.0000
+ 0.7500 0.0000 0.0000
+ 0.7800 0.0000 0.0000
+ 0.8100 0.0000 0.0000
+ 0.8400 0.0000 0.0000
+ 0.8700 0.0000 0.0000
+ 0.9000 0.0000 0.0000
+ 0.9300 0.0000 0.0000
+ 0.9600 0.0000 0.0000
+ 0.9900 0.0000 0.0000
+ 1.0200 0.0000 0.0000
+ 1.0500 0.0000 0.0000
+ 1.0800 0.0000 0.0000
+ 1.1100 0.0000 0.0000
+ 1.1400 0.0061 0.2203
+ 1.1700 0.0172 0.5684
+ 1.2000 0.0443 1.3296
+ 1.2300 0.1042 2.8137
+ 1.2600 0.2239 5.3747
+ 1.2900 0.4398 9.2366
+ 1.3200 0.7895 14.2110
+ 1.3500 1.2952 19.4276
+ 1.3800 1.9419 23.3023
+ 1.4100 2.6609 23.9477
+ 1.4400 3.3322 19.9935
+ 1.4700 3.8139 11.4416
+ 1.5000 3.9894 0.0000
+ 1.5300 3.8139 -11.4416
+ 1.5600 3.3322 -19.9935
+ 1.5900 2.6609 -23.9477
+ 1.6200 1.9419 -23.3023
+ 1.6500 1.2952 -19.4276
+ 1.6800 0.7895 -14.2110
+ 1.7100 0.4398 -9.2366
+ 1.7400 0.2239 -5.3747
+ 1.7700 0.1042 -2.8137
+ 1.8000 0.0443 -1.3296
+ 1.8300 0.0172 -0.5684
+ 1.8600 0.0061 -0.2203
+ 1.8900 0.0000 0.0000
+ 1.9200 0.0000 0.0000
+ 1.9500 0.0000 0.0000
+ 1.9800 0.0000 0.0000
+ 2.0100 0.0000 0.0000
+ 2.0400 0.0000 0.0000
+ 2.0700 0.0000 0.0000
+ 2.1000 0.0000 0.0000
+ 2.1300 0.0000 0.0000
+ 2.1600 0.0000 0.0000
+ 2.1900 0.0000 0.0000
+ 2.2200 0.0000 0.0000
+ 2.2500 0.0000 0.0000
+ 2.2800 0.0000 0.0000
+ 2.3100 0.0000 0.0000
+ 2.3400 0.0000 0.0000
+ 2.3700 0.0000 0.0000
+ 2.4000 0.0000 0.0000
+ 2.4300 0.0000 0.0000
+ 2.4600 0.0000 0.0000
+ 2.4900 0.0000 0.0000
+ 2.5200 0.0000 0.0000
+ 2.5500 0.0000 0.0000
+ 2.5800 0.0000 0.0000
+ 2.6100 0.0000 0.0000
+ 2.6400 0.0000 0.0000
+ 2.6700 0.0000 0.0000
+ 2.7000 0.0000 0.0000
+ 2.7300 0.0000 0.0000
+ 2.7600 0.0000 0.0000
+ 2.7900 0.0000 0.0000
+ 2.8200 0.0000 0.0000
+ 2.8500 0.0000 0.0000
+ 2.8800 0.0000 0.0000
+ 2.9100 0.0000 0.0000
+ 2.9400 0.0000 0.0000
+ 2.9700 0.0000 0.0000
+ 3.0000 0.0000 0.0000
diff --git a/regtest/analysis/rt-histo/analysis.0.histoA1n.reference b/regtest/analysis/rt-histo/analysis.0.histoA1n.reference
new file mode 100644
index 0000000000000000000000000000000000000000..0f957405022c2e5d960bc28e8bd3c1a68d1087af
--- /dev/null
+++ b/regtest/analysis/rt-histo/analysis.0.histoA1n.reference
@@ -0,0 +1,107 @@
+#! FIELDS x hA1n dhA1n_x
+#! SET normalisation 1.0000
+#! SET min_x 0.0
+#! SET max_x 3.0
+#! SET nbins_x 100
+#! SET periodic_x false
+ 0.0000 0.0000 0.0000
+ 0.0300 0.0000 0.0000
+ 0.0600 0.0000 0.0000
+ 0.0900 0.0000 0.0000
+ 0.1200 0.0000 0.0000
+ 0.1500 0.0000 0.0000
+ 0.1800 0.0000 0.0000
+ 0.2100 0.0000 0.0000
+ 0.2400 0.0000 0.0000
+ 0.2700 0.0000 0.0000
+ 0.3000 0.0000 0.0000
+ 0.3300 0.0000 0.0000
+ 0.3600 0.0000 0.0000
+ 0.3900 0.0000 0.0000
+ 0.4200 0.0000 0.0000
+ 0.4500 0.0000 0.0000
+ 0.4800 0.0000 0.0000
+ 0.5100 0.0000 0.0000
+ 0.5400 0.0000 0.0000
+ 0.5700 0.0000 0.0000
+ 0.6000 0.0000 0.0000
+ 0.6300 0.0000 0.0000
+ 0.6600 0.0000 0.0000
+ 0.6900 0.0000 0.0000
+ 0.7200 0.0000 0.0000
+ 0.7500 0.0000 0.0000
+ 0.7800 0.0000 0.0000
+ 0.8100 0.0000 0.0000
+ 0.8400 0.0000 0.0000
+ 0.8700 0.0000 0.0000
+ 0.9000 0.0000 0.0000
+ 0.9300 0.0000 0.0000
+ 0.9600 0.0000 0.0000
+ 0.9900 0.0000 0.0000
+ 1.0200 0.0000 0.0000
+ 1.0500 0.0000 0.0000
+ 1.0800 0.0000 0.0000
+ 1.1100 0.0000 0.0000
+ 1.1400 0.0061 0.2203
+ 1.1700 0.0172 0.5684
+ 1.2000 0.0443 1.3296
+ 1.2300 0.1042 2.8137
+ 1.2600 0.2239 5.3747
+ 1.2900 0.4398 9.2366
+ 1.3200 0.7895 14.2110
+ 1.3500 1.2952 19.4276
+ 1.3800 1.9419 23.3023
+ 1.4100 2.6609 23.9477
+ 1.4400 3.3322 19.9935
+ 1.4700 3.8139 11.4416
+ 1.5000 3.9894 0.0000
+ 1.5300 3.8139 -11.4416
+ 1.5600 3.3322 -19.9935
+ 1.5900 2.6609 -23.9477
+ 1.6200 1.9419 -23.3023
+ 1.6500 1.2952 -19.4276
+ 1.6800 0.7895 -14.2110
+ 1.7100 0.4398 -9.2366
+ 1.7400 0.2239 -5.3747
+ 1.7700 0.1042 -2.8137
+ 1.8000 0.0443 -1.3296
+ 1.8300 0.0172 -0.5684
+ 1.8600 0.0061 -0.2203
+ 1.8900 0.0000 0.0000
+ 1.9200 0.0000 0.0000
+ 1.9500 0.0000 0.0000
+ 1.9800 0.0000 0.0000
+ 2.0100 0.0000 0.0000
+ 2.0400 0.0000 0.0000
+ 2.0700 0.0000 0.0000
+ 2.1000 0.0000 0.0000
+ 2.1300 0.0000 0.0000
+ 2.1600 0.0000 0.0000
+ 2.1900 0.0000 0.0000
+ 2.2200 0.0000 0.0000
+ 2.2500 0.0000 0.0000
+ 2.2800 0.0000 0.0000
+ 2.3100 0.0000 0.0000
+ 2.3400 0.0000 0.0000
+ 2.3700 0.0000 0.0000
+ 2.4000 0.0000 0.0000
+ 2.4300 0.0000 0.0000
+ 2.4600 0.0000 0.0000
+ 2.4900 0.0000 0.0000
+ 2.5200 0.0000 0.0000
+ 2.5500 0.0000 0.0000
+ 2.5800 0.0000 0.0000
+ 2.6100 0.0000 0.0000
+ 2.6400 0.0000 0.0000
+ 2.6700 0.0000 0.0000
+ 2.7000 0.0000 0.0000
+ 2.7300 0.0000 0.0000
+ 2.7600 0.0000 0.0000
+ 2.7900 0.0000 0.0000
+ 2.8200 0.0000 0.0000
+ 2.8500 0.0000 0.0000
+ 2.8800 0.0000 0.0000
+ 2.9100 0.0000 0.0000
+ 2.9400 0.0000 0.0000
+ 2.9700 0.0000 0.0000
+ 3.0000 0.0000 0.0000
diff --git a/regtest/analysis/rt-histo/config b/regtest/analysis/rt-histo/config
new file mode 100644
index 0000000000000000000000000000000000000000..f93ec1a97465724691bf162d4735f5ea3648bbb4
--- /dev/null
+++ b/regtest/analysis/rt-histo/config
@@ -0,0 +1,3 @@
+type=driver
+# this is to test a different name
+arg="--plumed plumed.dat --ixyz trajectory.xyz"
diff --git a/regtest/analysis/rt-histo/fesA1.reference b/regtest/analysis/rt-histo/fesA1.reference
new file mode 100644
index 0000000000000000000000000000000000000000..8d48222eceef025b1c15e859c47dddc10dba73ff
--- /dev/null
+++ b/regtest/analysis/rt-histo/fesA1.reference
@@ -0,0 +1,107 @@
+#! FIELDS x fA1 dfA1_x
+#! SET normalisation 2.0000
+#! SET min_x 0.0
+#! SET max_x 3.0
+#! SET nbins_x 100
+#! SET periodic_x false
+ 0.0000 inf nan
+ 0.0300 inf nan
+ 0.0600 inf nan
+ 0.0900 inf nan
+ 0.1200 inf nan
+ 0.1500 inf nan
+ 0.1800 inf nan
+ 0.2100 inf nan
+ 0.2400 inf nan
+ 0.2700 inf nan
+ 0.3000 inf nan
+ 0.3300 inf nan
+ 0.3600 inf nan
+ 0.3900 inf nan
+ 0.4200 inf nan
+ 0.4500 inf nan
+ 0.4800 inf nan
+ 0.5100 inf nan
+ 0.5400 inf nan
+ 0.5700 inf nan
+ 0.6000 inf nan
+ 0.6300 inf nan
+ 0.6600 inf nan
+ 0.6900 inf nan
+ 0.7200 inf nan
+ 0.7500 inf nan
+ 0.7800 inf nan
+ 0.8100 inf nan
+ 0.8400 inf nan
+ 0.8700 inf nan
+ 0.9000 inf nan
+ 0.9300 inf nan
+ 0.9600 inf nan
+ 0.9900 inf nan
+ 1.0200 inf nan
+ 1.0500 inf nan
+ 1.0800 inf nan
+ 1.1100 inf nan
+ 1.1400 14.4487 -90.0824
+ 1.1700 11.8631 -82.4292
+ 1.2000 9.5032 -74.8639
+ 1.2300 7.3697 -67.3543
+ 1.2600 5.4619 -59.8764
+ 1.2900 3.7779 -52.3856
+ 1.3200 2.3185 -44.8981
+ 1.3500 1.0837 -37.4143
+ 1.3800 0.0735 -29.9314
+ 1.4100 -0.7122 -22.4487
+ 1.4400 -1.2733 -14.9663
+ 1.4700 -1.6101 -7.4830
+ 1.5000 -1.7223 0.0000
+ 1.5300 -1.6101 7.4830
+ 1.5600 -1.2733 14.9663
+ 1.5900 -0.7122 22.4487
+ 1.6200 0.0698 29.7442
+ 1.6500 1.0670 36.5796
+ 1.6800 2.2443 41.2424
+ 1.7100 3.4613 37.5174
+ 1.7400 4.2792 12.7801
+ 1.7700 4.0939 -23.8285
+ 1.8000 3.0696 -40.4271
+ 1.8300 1.8368 -40.1618
+ 1.8600 0.7120 -34.4135
+ 1.8900 -0.2133 -27.4377
+ 1.9200 -0.9242 -19.9547
+ 1.9500 -1.4105 -12.4717
+ 1.9800 -1.6725 -4.9887
+ 2.0100 -1.7099 2.4943
+ 2.0400 -1.5228 9.9774
+ 2.0700 -1.1112 17.4604
+ 2.1000 -0.4752 24.9434
+ 2.1300 0.3854 32.4264
+ 2.1600 1.4704 39.9094
+ 2.1900 2.7799 47.3924
+ 2.2200 4.3140 54.8754
+ 2.2500 6.0725 62.3585
+ 2.2800 8.0555 69.8415
+ 2.3100 10.2630 77.3245
+ 2.3400 12.6949 84.8075
+ 2.3700 inf nan
+ 2.4000 inf nan
+ 2.4300 inf nan
+ 2.4600 inf nan
+ 2.4900 inf nan
+ 2.5200 inf nan
+ 2.5500 inf nan
+ 2.5800 inf nan
+ 2.6100 inf nan
+ 2.6400 inf nan
+ 2.6700 inf nan
+ 2.7000 inf nan
+ 2.7300 inf nan
+ 2.7600 inf nan
+ 2.7900 inf nan
+ 2.8200 inf nan
+ 2.8500 inf nan
+ 2.8800 inf nan
+ 2.9100 inf nan
+ 2.9400 inf nan
+ 2.9700 inf nan
+ 3.0000 inf nan
diff --git a/regtest/analysis/rt-histo/fesA1u.reference b/regtest/analysis/rt-histo/fesA1u.reference
new file mode 100644
index 0000000000000000000000000000000000000000..3dface3c882b88c4102913840f32450ec37b2333
--- /dev/null
+++ b/regtest/analysis/rt-histo/fesA1u.reference
@@ -0,0 +1,107 @@
+#! FIELDS x fA1u dfA1u_x
+#! SET normalisation 2.0000
+#! SET min_x 0.0
+#! SET max_x 3.0
+#! SET nbins_x 100
+#! SET periodic_x false
+ 0.0000 inf nan
+ 0.0300 inf nan
+ 0.0600 inf nan
+ 0.0900 inf nan
+ 0.1200 inf nan
+ 0.1500 inf nan
+ 0.1800 inf nan
+ 0.2100 inf nan
+ 0.2400 inf nan
+ 0.2700 inf nan
+ 0.3000 inf nan
+ 0.3300 inf nan
+ 0.3600 inf nan
+ 0.3900 inf nan
+ 0.4200 inf nan
+ 0.4500 inf nan
+ 0.4800 inf nan
+ 0.5100 inf nan
+ 0.5400 inf nan
+ 0.5700 inf nan
+ 0.6000 inf nan
+ 0.6300 inf nan
+ 0.6600 inf nan
+ 0.6900 inf nan
+ 0.7200 inf nan
+ 0.7500 inf nan
+ 0.7800 inf nan
+ 0.8100 inf nan
+ 0.8400 inf nan
+ 0.8700 inf nan
+ 0.9000 inf nan
+ 0.9300 inf nan
+ 0.9600 inf nan
+ 0.9900 inf nan
+ 1.0200 inf nan
+ 1.0500 inf nan
+ 1.0800 inf nan
+ 1.1100 inf nan
+ 1.1400 12.7198 -90.0824
+ 1.1700 10.1341 -82.4292
+ 1.2000 7.7743 -74.8639
+ 1.2300 5.6408 -67.3543
+ 1.2600 3.7329 -59.8764
+ 1.2900 2.0489 -52.3856
+ 1.3200 0.5896 -44.8981
+ 1.3500 -0.6452 -37.4143
+ 1.3800 -1.6554 -29.9314
+ 1.4100 -2.4411 -22.4487
+ 1.4400 -3.0023 -14.9663
+ 1.4700 -3.3391 -7.4830
+ 1.5000 -3.4513 0.0000
+ 1.5300 -3.3391 7.4830
+ 1.5600 -3.0023 14.9663
+ 1.5900 -2.4411 22.4487
+ 1.6200 -1.6592 29.7442
+ 1.6500 -0.6619 36.5796
+ 1.6800 0.5153 41.2424
+ 1.7100 1.7323 37.5174
+ 1.7400 2.5502 12.7801
+ 1.7700 2.3649 -23.8285
+ 1.8000 1.3407 -40.4271
+ 1.8300 0.1078 -40.1618
+ 1.8600 -1.0170 -34.4135
+ 1.8900 -1.9422 -27.4377
+ 1.9200 -2.6531 -19.9547
+ 1.9500 -3.1395 -12.4717
+ 1.9800 -3.4014 -4.9887
+ 2.0100 -3.4388 2.4943
+ 2.0400 -3.2517 9.9774
+ 2.0700 -2.8402 17.4604
+ 2.1000 -2.2041 24.9434
+ 2.1300 -1.3436 32.4264
+ 2.1600 -0.2585 39.9094
+ 2.1900 1.0510 47.3924
+ 2.2200 2.5850 54.8754
+ 2.2500 4.3435 62.3585
+ 2.2800 6.3265 69.8415
+ 2.3100 8.5340 77.3245
+ 2.3400 10.9660 84.8075
+ 2.3700 inf nan
+ 2.4000 inf nan
+ 2.4300 inf nan
+ 2.4600 inf nan
+ 2.4900 inf nan
+ 2.5200 inf nan
+ 2.5500 inf nan
+ 2.5800 inf nan
+ 2.6100 inf nan
+ 2.6400 inf nan
+ 2.6700 inf nan
+ 2.7000 inf nan
+ 2.7300 inf nan
+ 2.7600 inf nan
+ 2.7900 inf nan
+ 2.8200 inf nan
+ 2.8500 inf nan
+ 2.8800 inf nan
+ 2.9100 inf nan
+ 2.9400 inf nan
+ 2.9700 inf nan
+ 3.0000 inf nan
diff --git a/regtest/analysis/rt-histo/fesA2.reference b/regtest/analysis/rt-histo/fesA2.reference
new file mode 100644
index 0000000000000000000000000000000000000000..a844cd83b428ed5dd82d1565e7b39a85fb026006
--- /dev/null
+++ b/regtest/analysis/rt-histo/fesA2.reference
@@ -0,0 +1,107 @@
+#! FIELDS x fA2 dfA2_x
+#! SET normalisation 2.0000
+#! SET min_x 0.0
+#! SET max_x 3.0
+#! SET nbins_x 100
+#! SET periodic_x false
+ 0.0000 inf nan
+ 0.0300 inf nan
+ 0.0600 inf nan
+ 0.0900 inf nan
+ 0.1200 inf nan
+ 0.1500 inf nan
+ 0.1800 inf nan
+ 0.2100 inf nan
+ 0.2400 inf nan
+ 0.2700 inf nan
+ 0.3000 inf nan
+ 0.3300 inf nan
+ 0.3600 inf nan
+ 0.3900 inf nan
+ 0.4200 inf nan
+ 0.4500 inf nan
+ 0.4800 inf nan
+ 0.5100 inf nan
+ 0.5400 inf nan
+ 0.5700 inf nan
+ 0.6000 inf nan
+ 0.6300 inf nan
+ 0.6600 inf nan
+ 0.6900 inf nan
+ 0.7200 inf nan
+ 0.7500 inf nan
+ 0.7800 inf nan
+ 0.8100 inf nan
+ 0.8400 inf nan
+ 0.8700 inf nan
+ 0.9000 inf nan
+ 0.9300 inf nan
+ 0.9600 inf nan
+ 0.9900 inf nan
+ 1.0200 inf nan
+ 1.0500 inf nan
+ 1.0800 inf nan
+ 1.1100 inf nan
+ 1.1400 14.4410 -89.7962
+ 1.1700 11.8593 -82.3132
+ 1.2000 9.5022 -74.8302
+ 1.2300 7.3695 -67.3471
+ 1.2600 5.4614 -59.8641
+ 1.2900 3.7777 -52.3811
+ 1.3200 2.3185 -44.8981
+ 1.3500 1.0838 -37.4151
+ 1.3800 0.0736 -29.9321
+ 1.4100 -0.7121 -22.4490
+ 1.4400 -1.2734 -14.9660
+ 1.4700 -1.6101 -7.4830
+ 1.5000 -1.7223 0.0000
+ 1.5300 -1.6101 7.4830
+ 1.5600 -1.2734 14.9660
+ 1.5900 -0.7121 22.4490
+ 1.6200 0.0698 29.7448
+ 1.6500 1.0670 36.5804
+ 1.6800 2.2443 41.2424
+ 1.7100 3.4611 37.5145
+ 1.7400 4.2788 12.7784
+ 1.7700 4.0938 -23.8282
+ 1.8000 3.0696 -40.4260
+ 1.8300 1.8367 -40.1606
+ 1.8600 0.7119 -34.4131
+ 1.8900 -0.2133 -27.4377
+ 1.9200 -0.9242 -19.9547
+ 1.9500 -1.4105 -12.4717
+ 1.9800 -1.6725 -4.9887
+ 2.0100 -1.7099 2.4943
+ 2.0400 -1.5228 9.9774
+ 2.0700 -1.1112 17.4604
+ 2.1000 -0.4752 24.9434
+ 2.1300 0.3854 32.4264
+ 2.1600 1.4704 39.9094
+ 2.1900 2.7799 47.3924
+ 2.2200 4.3140 54.8754
+ 2.2500 6.0725 62.3585
+ 2.2800 8.0555 69.8415
+ 2.3100 10.2630 77.3245
+ 2.3400 12.6949 84.8075
+ 2.3700 inf nan
+ 2.4000 inf nan
+ 2.4300 inf nan
+ 2.4600 inf nan
+ 2.4900 inf nan
+ 2.5200 inf nan
+ 2.5500 inf nan
+ 2.5800 inf nan
+ 2.6100 inf nan
+ 2.6400 inf nan
+ 2.6700 inf nan
+ 2.7000 inf nan
+ 2.7300 inf nan
+ 2.7600 inf nan
+ 2.7900 inf nan
+ 2.8200 inf nan
+ 2.8500 inf nan
+ 2.8800 inf nan
+ 2.9100 inf nan
+ 2.9400 inf nan
+ 2.9700 inf nan
+ 3.0000 inf nan
diff --git a/regtest/analysis/rt-histo/fesA2u.reference b/regtest/analysis/rt-histo/fesA2u.reference
new file mode 100644
index 0000000000000000000000000000000000000000..2916194d6a5cdb8f6e8980e9941136f78af70cf3
--- /dev/null
+++ b/regtest/analysis/rt-histo/fesA2u.reference
@@ -0,0 +1,107 @@
+#! FIELDS x fA2u dfA2u_x
+#! SET normalisation 2.0000
+#! SET min_x 0.0
+#! SET max_x 3.0
+#! SET nbins_x 100
+#! SET periodic_x false
+ 0.0000 inf nan
+ 0.0300 inf nan
+ 0.0600 inf nan
+ 0.0900 inf nan
+ 0.1200 inf nan
+ 0.1500 inf nan
+ 0.1800 inf nan
+ 0.2100 inf nan
+ 0.2400 inf nan
+ 0.2700 inf nan
+ 0.3000 inf nan
+ 0.3300 inf nan
+ 0.3600 inf nan
+ 0.3900 inf nan
+ 0.4200 inf nan
+ 0.4500 inf nan
+ 0.4800 inf nan
+ 0.5100 inf nan
+ 0.5400 inf nan
+ 0.5700 inf nan
+ 0.6000 inf nan
+ 0.6300 inf nan
+ 0.6600 inf nan
+ 0.6900 inf nan
+ 0.7200 inf nan
+ 0.7500 inf nan
+ 0.7800 inf nan
+ 0.8100 inf nan
+ 0.8400 inf nan
+ 0.8700 inf nan
+ 0.9000 inf nan
+ 0.9300 inf nan
+ 0.9600 inf nan
+ 0.9900 inf nan
+ 1.0200 inf nan
+ 1.0500 inf nan
+ 1.0800 inf nan
+ 1.1100 inf nan
+ 1.1400 12.7120 -89.7962
+ 1.1700 10.1304 -82.3132
+ 1.2000 7.7732 -74.8302
+ 1.2300 5.6406 -67.3471
+ 1.2600 3.7324 -59.8641
+ 1.2900 2.0487 -52.3811
+ 1.3200 0.5895 -44.8981
+ 1.3500 -0.6452 -37.4151
+ 1.3800 -1.6554 -29.9321
+ 1.4100 -2.4411 -22.4490
+ 1.4400 -3.0023 -14.9660
+ 1.4700 -3.3390 -7.4830
+ 1.5000 -3.4513 0.0000
+ 1.5300 -3.3390 7.4830
+ 1.5600 -3.0023 14.9660
+ 1.5900 -2.4411 22.4490
+ 1.6200 -1.6591 29.7448
+ 1.6500 -0.6619 36.5804
+ 1.6800 0.5153 41.2424
+ 1.7100 1.7321 37.5145
+ 1.7400 2.5499 12.7784
+ 1.7700 2.3649 -23.8282
+ 1.8000 1.3406 -40.4260
+ 1.8300 0.1078 -40.1606
+ 1.8600 -1.0170 -34.4131
+ 1.8900 -1.9422 -27.4377
+ 1.9200 -2.6531 -19.9547
+ 1.9500 -3.1395 -12.4717
+ 1.9800 -3.4014 -4.9887
+ 2.0100 -3.4388 2.4943
+ 2.0400 -3.2517 9.9774
+ 2.0700 -2.8402 17.4604
+ 2.1000 -2.2041 24.9434
+ 2.1300 -1.3436 32.4264
+ 2.1600 -0.2585 39.9094
+ 2.1900 1.0510 47.3924
+ 2.2200 2.5850 54.8754
+ 2.2500 4.3435 62.3585
+ 2.2800 6.3265 69.8415
+ 2.3100 8.5340 77.3245
+ 2.3400 10.9660 84.8075
+ 2.3700 inf nan
+ 2.4000 inf nan
+ 2.4300 inf nan
+ 2.4600 inf nan
+ 2.4900 inf nan
+ 2.5200 inf nan
+ 2.5500 inf nan
+ 2.5800 inf nan
+ 2.6100 inf nan
+ 2.6400 inf nan
+ 2.6700 inf nan
+ 2.7000 inf nan
+ 2.7300 inf nan
+ 2.7600 inf nan
+ 2.7900 inf nan
+ 2.8200 inf nan
+ 2.8500 inf nan
+ 2.8800 inf nan
+ 2.9100 inf nan
+ 2.9400 inf nan
+ 2.9700 inf nan
+ 3.0000 inf nan
diff --git a/regtest/analysis/rt-histo/fesA3.reference b/regtest/analysis/rt-histo/fesA3.reference
new file mode 100644
index 0000000000000000000000000000000000000000..644466e0d1bd20d9ccf59082a6c8b8d84612c758
--- /dev/null
+++ b/regtest/analysis/rt-histo/fesA3.reference
@@ -0,0 +1,107 @@
+#! FIELDS x fA3 dfA3_x
+#! SET normalisation 3.0000
+#! SET min_x 0.0
+#! SET max_x 3.0
+#! SET nbins_x 100
+#! SET periodic_x false
+ 0.0000 inf nan
+ 0.0300 inf nan
+ 0.0600 inf nan
+ 0.0900 inf nan
+ 0.1200 inf nan
+ 0.1500 inf nan
+ 0.1800 inf nan
+ 0.2100 inf nan
+ 0.2400 inf nan
+ 0.2700 inf nan
+ 0.3000 inf nan
+ 0.3300 inf nan
+ 0.3600 inf nan
+ 0.3900 inf nan
+ 0.4200 inf nan
+ 0.4500 inf nan
+ 0.4800 inf nan
+ 0.5100 inf nan
+ 0.5400 inf nan
+ 0.5700 inf nan
+ 0.6000 inf nan
+ 0.6300 16.3628 -92.2905
+ 0.6600 13.7063 -84.8075
+ 0.6900 11.2743 -77.3245
+ 0.7200 9.0668 -69.8415
+ 0.7500 7.0838 -62.3585
+ 0.7800 5.3253 -54.8754
+ 0.8100 3.7913 -47.3924
+ 0.8400 2.4818 -39.9094
+ 0.8700 1.3967 -32.4264
+ 0.9000 0.5362 -24.9434
+ 0.9300 -0.0999 -17.4604
+ 0.9600 -0.5114 -9.9774
+ 0.9900 -0.6985 -2.4943
+ 1.0200 -0.6611 4.9887
+ 1.0500 -0.3992 12.4717
+ 1.0800 0.0872 19.9547
+ 1.1100 0.7981 27.4377
+ 1.1400 1.7233 34.4131
+ 1.1700 2.8481 40.1606
+ 1.2000 4.0809 40.4260
+ 1.2300 5.1052 23.8282
+ 1.2600 5.2902 -12.7784
+ 1.2900 4.4724 -37.5145
+ 1.3200 3.2556 -41.2424
+ 1.3500 2.0784 -36.5804
+ 1.3800 1.0850 -29.9321
+ 1.4100 0.2992 -22.4490
+ 1.4400 -0.2620 -14.9660
+ 1.4700 -0.5987 -7.4830
+ 1.5000 -0.7110 0.0000
+ 1.5300 -0.5987 7.4830
+ 1.5600 -0.2620 14.9660
+ 1.5900 0.2992 22.4490
+ 1.6200 1.0812 29.7448
+ 1.6500 2.0784 36.5804
+ 1.6800 3.2556 41.2424
+ 1.7100 4.4724 37.5145
+ 1.7400 5.2902 12.7784
+ 1.7700 5.1052 -23.8282
+ 1.8000 4.0809 -40.4260
+ 1.8300 2.8481 -40.1606
+ 1.8600 1.7233 -34.4131
+ 1.8900 0.7981 -27.4377
+ 1.9200 0.0872 -19.9547
+ 1.9500 -0.3992 -12.4717
+ 1.9800 -0.6611 -4.9887
+ 2.0100 -0.6985 2.4943
+ 2.0400 -0.5114 9.9774
+ 2.0700 -0.0999 17.4604
+ 2.1000 0.5362 24.9434
+ 2.1300 1.3967 32.4264
+ 2.1600 2.4818 39.9094
+ 2.1900 3.7913 47.3924
+ 2.2200 5.3253 54.8754
+ 2.2500 7.0838 62.3585
+ 2.2800 9.0668 69.8415
+ 2.3100 11.2743 77.3245
+ 2.3400 13.7063 84.8075
+ 2.3700 inf nan
+ 2.4000 inf nan
+ 2.4300 inf nan
+ 2.4600 inf nan
+ 2.4900 inf nan
+ 2.5200 inf nan
+ 2.5500 inf nan
+ 2.5800 inf nan
+ 2.6100 inf nan
+ 2.6400 inf nan
+ 2.6700 inf nan
+ 2.7000 inf nan
+ 2.7300 inf nan
+ 2.7600 inf nan
+ 2.7900 inf nan
+ 2.8200 inf nan
+ 2.8500 inf nan
+ 2.8800 inf nan
+ 2.9100 inf nan
+ 2.9400 inf nan
+ 2.9700 inf nan
+ 3.0000 inf nan
diff --git a/regtest/analysis/rt-histo/histoA1.reference b/regtest/analysis/rt-histo/histoA1.reference
new file mode 100644
index 0000000000000000000000000000000000000000..e193cda0e6f5b7d08bfcd45d402731bf60a872e9
--- /dev/null
+++ b/regtest/analysis/rt-histo/histoA1.reference
@@ -0,0 +1,107 @@
+#! FIELDS x hA1 dhA1_x
+#! SET normalisation 2.0000
+#! SET min_x 0.0
+#! SET max_x 3.0
+#! SET nbins_x 100
+#! SET periodic_x false
+ 0.0000 0.0000 0.0000
+ 0.0300 0.0000 0.0000
+ 0.0600 0.0000 0.0000
+ 0.0900 0.0000 0.0000
+ 0.1200 0.0000 0.0000
+ 0.1500 0.0000 0.0000
+ 0.1800 0.0000 0.0000
+ 0.2100 0.0000 0.0000
+ 0.2400 0.0000 0.0000
+ 0.2700 0.0000 0.0000
+ 0.3000 0.0000 0.0000
+ 0.3300 0.0000 0.0000
+ 0.3600 0.0000 0.0000
+ 0.3900 0.0000 0.0000
+ 0.4200 0.0000 0.0000
+ 0.4500 0.0000 0.0000
+ 0.4800 0.0000 0.0000
+ 0.5100 0.0000 0.0000
+ 0.5400 0.0000 0.0000
+ 0.5700 0.0000 0.0000
+ 0.6000 0.0000 0.0000
+ 0.6300 0.0000 0.0000
+ 0.6600 0.0000 0.0000
+ 0.6900 0.0000 0.0000
+ 0.7200 0.0000 0.0000
+ 0.7500 0.0000 0.0000
+ 0.7800 0.0000 0.0000
+ 0.8100 0.0000 0.0000
+ 0.8400 0.0000 0.0000
+ 0.8700 0.0000 0.0000
+ 0.9000 0.0000 0.0000
+ 0.9300 0.0000 0.0000
+ 0.9600 0.0000 0.0000
+ 0.9900 0.0000 0.0000
+ 1.0200 0.0000 0.0000
+ 1.0500 0.0000 0.0000
+ 1.0800 0.0000 0.0000
+ 1.1100 0.0000 0.0000
+ 1.1400 0.0031 0.1101
+ 1.1700 0.0086 0.2842
+ 1.2000 0.0221 0.6648
+ 1.2300 0.0521 1.4068
+ 1.2600 0.1119 2.6873
+ 1.2900 0.2199 4.6183
+ 1.3200 0.3947 7.1055
+ 1.3500 0.6476 9.7138
+ 1.3800 0.9709 11.6511
+ 1.4100 1.3304 11.9739
+ 1.4400 1.6661 9.9968
+ 1.4700 1.9069 5.7208
+ 1.5000 1.9947 0.0000
+ 1.5300 1.9069 -5.7208
+ 1.5600 1.6661 -9.9968
+ 1.5900 1.3304 -11.9739
+ 1.6200 0.9724 -11.5957
+ 1.6500 0.6520 -9.5611
+ 1.6800 0.4067 -6.7240
+ 1.7100 0.2497 -3.7552
+ 1.7400 0.1799 -0.9216
+ 1.7700 0.1937 1.8508
+ 1.8000 0.2921 4.7343
+ 1.8300 0.4788 7.7100
+ 1.8600 0.7517 10.3708
+ 1.8900 1.0893 11.9819
+ 1.9200 1.4485 11.5877
+ 1.9500 1.7603 8.8016
+ 1.9800 1.9552 3.9104
+ 2.0100 1.9848 -1.9848
+ 2.0400 1.8414 -7.3654
+ 2.0700 1.5613 -10.9289
+ 2.1000 1.2099 -12.0985
+ 2.1300 0.8568 -11.1390
+ 2.1600 0.5546 -8.8737
+ 2.1900 0.3281 -6.2335
+ 2.2200 0.1774 -3.9022
+ 2.2500 0.0876 -2.1910
+ 2.2800 0.0396 -1.1082
+ 2.3100 0.0163 -0.5064
+ 2.3400 0.0062 -0.2095
+ 2.3700 0.0000 0.0000
+ 2.4000 0.0000 0.0000
+ 2.4300 0.0000 0.0000
+ 2.4600 0.0000 0.0000
+ 2.4900 0.0000 0.0000
+ 2.5200 0.0000 0.0000
+ 2.5500 0.0000 0.0000
+ 2.5800 0.0000 0.0000
+ 2.6100 0.0000 0.0000
+ 2.6400 0.0000 0.0000
+ 2.6700 0.0000 0.0000
+ 2.7000 0.0000 0.0000
+ 2.7300 0.0000 0.0000
+ 2.7600 0.0000 0.0000
+ 2.7900 0.0000 0.0000
+ 2.8200 0.0000 0.0000
+ 2.8500 0.0000 0.0000
+ 2.8800 0.0000 0.0000
+ 2.9100 0.0000 0.0000
+ 2.9400 0.0000 0.0000
+ 2.9700 0.0000 0.0000
+ 3.0000 0.0000 0.0000
diff --git a/regtest/analysis/rt-histo/histoA1n.reference b/regtest/analysis/rt-histo/histoA1n.reference
new file mode 100644
index 0000000000000000000000000000000000000000..9f4035e1e0a0a9a8a3032c1baf0b4a347125fbc7
--- /dev/null
+++ b/regtest/analysis/rt-histo/histoA1n.reference
@@ -0,0 +1,107 @@
+#! FIELDS x hA1n dhA1n_x
+#! SET normalisation 1.0000
+#! SET min_x 0.0
+#! SET max_x 3.0
+#! SET nbins_x 100
+#! SET periodic_x false
+ 0.0000 0.0000 0.0000
+ 0.0300 0.0000 0.0000
+ 0.0600 0.0000 0.0000
+ 0.0900 0.0000 0.0000
+ 0.1200 0.0000 0.0000
+ 0.1500 0.0000 0.0000
+ 0.1800 0.0000 0.0000
+ 0.2100 0.0000 0.0000
+ 0.2400 0.0000 0.0000
+ 0.2700 0.0000 0.0000
+ 0.3000 0.0000 0.0000
+ 0.3300 0.0000 0.0000
+ 0.3600 0.0000 0.0000
+ 0.3900 0.0000 0.0000
+ 0.4200 0.0000 0.0000
+ 0.4500 0.0000 0.0000
+ 0.4800 0.0000 0.0000
+ 0.5100 0.0000 0.0000
+ 0.5400 0.0000 0.0000
+ 0.5700 0.0000 0.0000
+ 0.6000 0.0000 0.0000
+ 0.6300 0.0000 0.0000
+ 0.6600 0.0000 0.0000
+ 0.6900 0.0000 0.0000
+ 0.7200 0.0000 0.0000
+ 0.7500 0.0000 0.0000
+ 0.7800 0.0000 0.0000
+ 0.8100 0.0000 0.0000
+ 0.8400 0.0000 0.0000
+ 0.8700 0.0000 0.0000
+ 0.9000 0.0000 0.0000
+ 0.9300 0.0000 0.0000
+ 0.9600 0.0000 0.0000
+ 0.9900 0.0000 0.0000
+ 1.0200 0.0000 0.0000
+ 1.0500 0.0000 0.0000
+ 1.0800 0.0000 0.0000
+ 1.1100 0.0000 0.0000
+ 1.1400 0.0000 0.0000
+ 1.1700 0.0000 0.0000
+ 1.2000 0.0000 0.0000
+ 1.2300 0.0000 0.0000
+ 1.2600 0.0000 0.0000
+ 1.2900 0.0000 0.0000
+ 1.3200 0.0000 0.0000
+ 1.3500 0.0000 0.0000
+ 1.3800 0.0000 0.0000
+ 1.4100 0.0000 0.0000
+ 1.4400 0.0000 0.0000
+ 1.4700 0.0000 0.0000
+ 1.5000 0.0000 0.0000
+ 1.5300 0.0000 0.0000
+ 1.5600 0.0000 0.0000
+ 1.5900 0.0000 0.0000
+ 1.6200 0.0029 0.1109
+ 1.6500 0.0087 0.3054
+ 1.6800 0.0238 0.7629
+ 1.7100 0.0595 1.7262
+ 1.7400 0.1358 3.5316
+ 1.7700 0.2833 6.5152
+ 1.8000 0.5399 10.7982
+ 1.8300 0.9405 15.9883
+ 1.8600 1.4973 20.9618
+ 1.8900 2.1785 23.9637
+ 1.9200 2.8969 23.1753
+ 1.9500 3.5207 17.6033
+ 1.9800 3.9104 7.8209
+ 2.0100 3.9695 -3.9695
+ 2.0400 3.6827 -14.7308
+ 2.0700 3.1225 -21.8578
+ 2.1000 2.4197 -24.1971
+ 2.1300 1.7137 -22.2779
+ 2.1600 1.1092 -17.7473
+ 2.1900 0.6562 -12.4670
+ 2.2200 0.3547 -7.8044
+ 2.2500 0.1753 -4.3821
+ 2.2800 0.0792 -2.2163
+ 2.3100 0.0327 -1.0127
+ 2.3400 0.0123 -0.4190
+ 2.3700 0.0000 0.0000
+ 2.4000 0.0000 0.0000
+ 2.4300 0.0000 0.0000
+ 2.4600 0.0000 0.0000
+ 2.4900 0.0000 0.0000
+ 2.5200 0.0000 0.0000
+ 2.5500 0.0000 0.0000
+ 2.5800 0.0000 0.0000
+ 2.6100 0.0000 0.0000
+ 2.6400 0.0000 0.0000
+ 2.6700 0.0000 0.0000
+ 2.7000 0.0000 0.0000
+ 2.7300 0.0000 0.0000
+ 2.7600 0.0000 0.0000
+ 2.7900 0.0000 0.0000
+ 2.8200 0.0000 0.0000
+ 2.8500 0.0000 0.0000
+ 2.8800 0.0000 0.0000
+ 2.9100 0.0000 0.0000
+ 2.9400 0.0000 0.0000
+ 2.9700 0.0000 0.0000
+ 3.0000 0.0000 0.0000
diff --git a/regtest/analysis/rt-histo/histoA1u.reference b/regtest/analysis/rt-histo/histoA1u.reference
new file mode 100644
index 0000000000000000000000000000000000000000..7f8ee59be84197978643b795775fe1db9eb6690c
--- /dev/null
+++ b/regtest/analysis/rt-histo/histoA1u.reference
@@ -0,0 +1,107 @@
+#! FIELDS x hA1u dhA1u_x
+#! SET normalisation 2.0000
+#! SET min_x 0.0
+#! SET max_x 3.0
+#! SET nbins_x 100
+#! SET periodic_x false
+ 0.0000 0.0000 0.0000
+ 0.0300 0.0000 0.0000
+ 0.0600 0.0000 0.0000
+ 0.0900 0.0000 0.0000
+ 0.1200 0.0000 0.0000
+ 0.1500 0.0000 0.0000
+ 0.1800 0.0000 0.0000
+ 0.2100 0.0000 0.0000
+ 0.2400 0.0000 0.0000
+ 0.2700 0.0000 0.0000
+ 0.3000 0.0000 0.0000
+ 0.3300 0.0000 0.0000
+ 0.3600 0.0000 0.0000
+ 0.3900 0.0000 0.0000
+ 0.4200 0.0000 0.0000
+ 0.4500 0.0000 0.0000
+ 0.4800 0.0000 0.0000
+ 0.5100 0.0000 0.0000
+ 0.5400 0.0000 0.0000
+ 0.5700 0.0000 0.0000
+ 0.6000 0.0000 0.0000
+ 0.6300 0.0000 0.0000
+ 0.6600 0.0000 0.0000
+ 0.6900 0.0000 0.0000
+ 0.7200 0.0000 0.0000
+ 0.7500 0.0000 0.0000
+ 0.7800 0.0000 0.0000
+ 0.8100 0.0000 0.0000
+ 0.8400 0.0000 0.0000
+ 0.8700 0.0000 0.0000
+ 0.9000 0.0000 0.0000
+ 0.9300 0.0000 0.0000
+ 0.9600 0.0000 0.0000
+ 0.9900 0.0000 0.0000
+ 1.0200 0.0000 0.0000
+ 1.0500 0.0000 0.0000
+ 1.0800 0.0000 0.0000
+ 1.1100 0.0000 0.0000
+ 1.1400 0.0061 0.2203
+ 1.1700 0.0172 0.5684
+ 1.2000 0.0443 1.3296
+ 1.2300 0.1042 2.8137
+ 1.2600 0.2239 5.3747
+ 1.2900 0.4398 9.2366
+ 1.3200 0.7895 14.2110
+ 1.3500 1.2952 19.4276
+ 1.3800 1.9419 23.3023
+ 1.4100 2.6609 23.9477
+ 1.4400 3.3322 19.9935
+ 1.4700 3.8139 11.4416
+ 1.5000 3.9894 0.0000
+ 1.5300 3.8139 -11.4416
+ 1.5600 3.3322 -19.9935
+ 1.5900 2.6609 -23.9477
+ 1.6200 1.9448 -23.1914
+ 1.6500 1.3039 -19.1222
+ 1.6800 0.8133 -13.4481
+ 1.7100 0.4993 -7.5104
+ 1.7400 0.3597 -1.8431
+ 1.7700 0.3875 3.7015
+ 1.8000 0.5842 9.4686
+ 1.8300 0.9577 15.4199
+ 1.8600 1.5034 20.7415
+ 1.8900 2.1785 23.9637
+ 1.9200 2.8969 23.1753
+ 1.9500 3.5207 17.6033
+ 1.9800 3.9104 7.8209
+ 2.0100 3.9695 -3.9695
+ 2.0400 3.6827 -14.7308
+ 2.0700 3.1225 -21.8578
+ 2.1000 2.4197 -24.1971
+ 2.1300 1.7137 -22.2779
+ 2.1600 1.1092 -17.7473
+ 2.1900 0.6562 -12.4670
+ 2.2200 0.3547 -7.8044
+ 2.2500 0.1753 -4.3821
+ 2.2800 0.0792 -2.2163
+ 2.3100 0.0327 -1.0127
+ 2.3400 0.0123 -0.4190
+ 2.3700 0.0000 0.0000
+ 2.4000 0.0000 0.0000
+ 2.4300 0.0000 0.0000
+ 2.4600 0.0000 0.0000
+ 2.4900 0.0000 0.0000
+ 2.5200 0.0000 0.0000
+ 2.5500 0.0000 0.0000
+ 2.5800 0.0000 0.0000
+ 2.6100 0.0000 0.0000
+ 2.6400 0.0000 0.0000
+ 2.6700 0.0000 0.0000
+ 2.7000 0.0000 0.0000
+ 2.7300 0.0000 0.0000
+ 2.7600 0.0000 0.0000
+ 2.7900 0.0000 0.0000
+ 2.8200 0.0000 0.0000
+ 2.8500 0.0000 0.0000
+ 2.8800 0.0000 0.0000
+ 2.9100 0.0000 0.0000
+ 2.9400 0.0000 0.0000
+ 2.9700 0.0000 0.0000
+ 3.0000 0.0000 0.0000
diff --git a/regtest/analysis/rt-histo/histoA2.reference b/regtest/analysis/rt-histo/histoA2.reference
new file mode 100644
index 0000000000000000000000000000000000000000..028e7757fa61cb28fa30e22cd2b5b68acf12315e
--- /dev/null
+++ b/regtest/analysis/rt-histo/histoA2.reference
@@ -0,0 +1,107 @@
+#! FIELDS x hA2 dhA2_x
+#! SET normalisation 2.0000
+#! SET min_x 0.0
+#! SET max_x 3.0
+#! SET nbins_x 100
+#! SET periodic_x false
+ 0.0000 0.0000 0.0000
+ 0.0300 0.0000 0.0000
+ 0.0600 0.0000 0.0000
+ 0.0900 0.0000 0.0000
+ 0.1200 0.0000 0.0000
+ 0.1500 0.0000 0.0000
+ 0.1800 0.0000 0.0000
+ 0.2100 0.0000 0.0000
+ 0.2400 0.0000 0.0000
+ 0.2700 0.0000 0.0000
+ 0.3000 0.0000 0.0000
+ 0.3300 0.0000 0.0000
+ 0.3600 0.0000 0.0000
+ 0.3900 0.0000 0.0000
+ 0.4200 0.0000 0.0000
+ 0.4500 0.0000 0.0000
+ 0.4800 0.0000 0.0000
+ 0.5100 0.0000 0.0000
+ 0.5400 0.0000 0.0000
+ 0.5700 0.0000 0.0000
+ 0.6000 0.0000 0.0000
+ 0.6300 0.0000 0.0000
+ 0.6600 0.0000 0.0000
+ 0.6900 0.0000 0.0000
+ 0.7200 0.0000 0.0000
+ 0.7500 0.0000 0.0000
+ 0.7800 0.0000 0.0000
+ 0.8100 0.0000 0.0000
+ 0.8400 0.0000 0.0000
+ 0.8700 0.0000 0.0000
+ 0.9000 0.0000 0.0000
+ 0.9300 0.0000 0.0000
+ 0.9600 0.0000 0.0000
+ 0.9900 0.0000 0.0000
+ 1.0200 0.0000 0.0000
+ 1.0500 0.0000 0.0000
+ 1.0800 0.0000 0.0000
+ 1.1100 0.0000 0.0000
+ 1.1400 0.0031 0.1101
+ 1.1700 0.0086 0.2842
+ 1.2000 0.0222 0.6648
+ 1.2300 0.0521 1.4068
+ 1.2600 0.1120 2.6873
+ 1.2900 0.2199 4.6183
+ 1.3200 0.3948 7.1055
+ 1.3500 0.6476 9.7138
+ 1.3800 0.9709 11.6512
+ 1.4100 1.3304 11.9738
+ 1.4400 1.6661 9.9967
+ 1.4700 1.9069 5.7208
+ 1.5000 1.9947 0.0000
+ 1.5300 1.9069 -5.7208
+ 1.5600 1.6661 -9.9967
+ 1.5900 1.3304 -11.9738
+ 1.6200 0.9724 -11.5957
+ 1.6500 0.6520 -9.5611
+ 1.6800 0.4067 -6.7241
+ 1.7100 0.2497 -3.7552
+ 1.7400 0.1799 -0.9216
+ 1.7700 0.1937 1.8508
+ 1.8000 0.2921 4.7343
+ 1.8300 0.4789 7.7099
+ 1.8600 0.7517 10.3708
+ 1.8900 1.0893 11.9819
+ 1.9200 1.4485 11.5877
+ 1.9500 1.7603 8.8016
+ 1.9800 1.9552 3.9104
+ 2.0100 1.9848 -1.9848
+ 2.0400 1.8414 -7.3654
+ 2.0700 1.5613 -10.9289
+ 2.1000 1.2099 -12.0985
+ 2.1300 0.8568 -11.1390
+ 2.1600 0.5546 -8.8737
+ 2.1900 0.3281 -6.2335
+ 2.2200 0.1774 -3.9022
+ 2.2500 0.0876 -2.1910
+ 2.2800 0.0396 -1.1082
+ 2.3100 0.0163 -0.5064
+ 2.3400 0.0062 -0.2095
+ 2.3700 0.0000 0.0000
+ 2.4000 0.0000 0.0000
+ 2.4300 0.0000 0.0000
+ 2.4600 0.0000 0.0000
+ 2.4900 0.0000 0.0000
+ 2.5200 0.0000 0.0000
+ 2.5500 0.0000 0.0000
+ 2.5800 0.0000 0.0000
+ 2.6100 0.0000 0.0000
+ 2.6400 0.0000 0.0000
+ 2.6700 0.0000 0.0000
+ 2.7000 0.0000 0.0000
+ 2.7300 0.0000 0.0000
+ 2.7600 0.0000 0.0000
+ 2.7900 0.0000 0.0000
+ 2.8200 0.0000 0.0000
+ 2.8500 0.0000 0.0000
+ 2.8800 0.0000 0.0000
+ 2.9100 0.0000 0.0000
+ 2.9400 0.0000 0.0000
+ 2.9700 0.0000 0.0000
+ 3.0000 0.0000 0.0000
diff --git a/regtest/analysis/rt-histo/histoA2u.reference b/regtest/analysis/rt-histo/histoA2u.reference
new file mode 100644
index 0000000000000000000000000000000000000000..1dd2347177ec2a3c25ae4adbaf0cc2dab7419489
--- /dev/null
+++ b/regtest/analysis/rt-histo/histoA2u.reference
@@ -0,0 +1,107 @@
+#! FIELDS x hA2u dhA2u_x
+#! SET normalisation 2.0000
+#! SET min_x 0.0
+#! SET max_x 3.0
+#! SET nbins_x 100
+#! SET periodic_x false
+ 0.0000 0.0000 0.0000
+ 0.0300 0.0000 0.0000
+ 0.0600 0.0000 0.0000
+ 0.0900 0.0000 0.0000
+ 0.1200 0.0000 0.0000
+ 0.1500 0.0000 0.0000
+ 0.1800 0.0000 0.0000
+ 0.2100 0.0000 0.0000
+ 0.2400 0.0000 0.0000
+ 0.2700 0.0000 0.0000
+ 0.3000 0.0000 0.0000
+ 0.3300 0.0000 0.0000
+ 0.3600 0.0000 0.0000
+ 0.3900 0.0000 0.0000
+ 0.4200 0.0000 0.0000
+ 0.4500 0.0000 0.0000
+ 0.4800 0.0000 0.0000
+ 0.5100 0.0000 0.0000
+ 0.5400 0.0000 0.0000
+ 0.5700 0.0000 0.0000
+ 0.6000 0.0000 0.0000
+ 0.6300 0.0000 0.0000
+ 0.6600 0.0000 0.0000
+ 0.6900 0.0000 0.0000
+ 0.7200 0.0000 0.0000
+ 0.7500 0.0000 0.0000
+ 0.7800 0.0000 0.0000
+ 0.8100 0.0000 0.0000
+ 0.8400 0.0000 0.0000
+ 0.8700 0.0000 0.0000
+ 0.9000 0.0000 0.0000
+ 0.9300 0.0000 0.0000
+ 0.9600 0.0000 0.0000
+ 0.9900 0.0000 0.0000
+ 1.0200 0.0000 0.0000
+ 1.0500 0.0000 0.0000
+ 1.0800 0.0000 0.0000
+ 1.1100 0.0000 0.0000
+ 1.1400 0.0061 0.2203
+ 1.1700 0.0172 0.5684
+ 1.2000 0.0443 1.3296
+ 1.2300 0.1042 2.8137
+ 1.2600 0.2239 5.3747
+ 1.2900 0.4398 9.2366
+ 1.3200 0.7895 14.2110
+ 1.3500 1.2952 19.4276
+ 1.3800 1.9419 23.3023
+ 1.4100 2.6609 23.9477
+ 1.4400 3.3322 19.9935
+ 1.4700 3.8139 11.4416
+ 1.5000 3.9894 0.0000
+ 1.5300 3.8139 -11.4416
+ 1.5600 3.3322 -19.9935
+ 1.5900 2.6609 -23.9477
+ 1.6200 1.9448 -23.1914
+ 1.6500 1.3039 -19.1222
+ 1.6800 0.8133 -13.4481
+ 1.7100 0.4994 -7.5103
+ 1.7400 0.3598 -1.8431
+ 1.7700 0.3875 3.7016
+ 1.8000 0.5842 9.4686
+ 1.8300 0.9577 15.4199
+ 1.8600 1.5034 20.7416
+ 1.8900 2.1785 23.9637
+ 1.9200 2.8969 23.1753
+ 1.9500 3.5207 17.6033
+ 1.9800 3.9104 7.8209
+ 2.0100 3.9695 -3.9695
+ 2.0400 3.6827 -14.7308
+ 2.0700 3.1225 -21.8578
+ 2.1000 2.4197 -24.1971
+ 2.1300 1.7137 -22.2779
+ 2.1600 1.1092 -17.7473
+ 2.1900 0.6562 -12.4670
+ 2.2200 0.3547 -7.8044
+ 2.2500 0.1753 -4.3821
+ 2.2800 0.0792 -2.2163
+ 2.3100 0.0327 -1.0127
+ 2.3400 0.0123 -0.4190
+ 2.3700 0.0000 0.0000
+ 2.4000 0.0000 0.0000
+ 2.4300 0.0000 0.0000
+ 2.4600 0.0000 0.0000
+ 2.4900 0.0000 0.0000
+ 2.5200 0.0000 0.0000
+ 2.5500 0.0000 0.0000
+ 2.5800 0.0000 0.0000
+ 2.6100 0.0000 0.0000
+ 2.6400 0.0000 0.0000
+ 2.6700 0.0000 0.0000
+ 2.7000 0.0000 0.0000
+ 2.7300 0.0000 0.0000
+ 2.7600 0.0000 0.0000
+ 2.7900 0.0000 0.0000
+ 2.8200 0.0000 0.0000
+ 2.8500 0.0000 0.0000
+ 2.8800 0.0000 0.0000
+ 2.9100 0.0000 0.0000
+ 2.9400 0.0000 0.0000
+ 2.9700 0.0000 0.0000
+ 3.0000 0.0000 0.0000
diff --git a/regtest/analysis/rt-histo/histoA3.reference b/regtest/analysis/rt-histo/histoA3.reference
new file mode 100644
index 0000000000000000000000000000000000000000..4e8c24c835b878bc037001e37fe35491b723b3aa
--- /dev/null
+++ b/regtest/analysis/rt-histo/histoA3.reference
@@ -0,0 +1,107 @@
+#! FIELDS x hA3 dhA3_x
+#! SET normalisation 3.0000
+#! SET min_x 0.0
+#! SET max_x 3.0
+#! SET nbins_x 100
+#! SET periodic_x false
+ 0.0000 0.0000 0.0000
+ 0.0300 0.0000 0.0000
+ 0.0600 0.0000 0.0000
+ 0.0900 0.0000 0.0000
+ 0.1200 0.0000 0.0000
+ 0.1500 0.0000 0.0000
+ 0.1800 0.0000 0.0000
+ 0.2100 0.0000 0.0000
+ 0.2400 0.0000 0.0000
+ 0.2700 0.0000 0.0000
+ 0.3000 0.0000 0.0000
+ 0.3300 0.0000 0.0000
+ 0.3600 0.0000 0.0000
+ 0.3900 0.0000 0.0000
+ 0.4200 0.0000 0.0000
+ 0.4500 0.0000 0.0000
+ 0.4800 0.0000 0.0000
+ 0.5100 0.0000 0.0000
+ 0.5400 0.0000 0.0000
+ 0.5700 0.0000 0.0000
+ 0.6000 0.0000 0.0000
+ 0.6300 0.0014 0.0524
+ 0.6600 0.0041 0.1397
+ 0.6900 0.0109 0.3376
+ 0.7200 0.0264 0.7388
+ 0.7500 0.0584 1.4607
+ 0.7800 0.1182 2.6015
+ 0.8100 0.2187 4.1557
+ 0.8400 0.3697 5.9158
+ 0.8700 0.5712 7.4260
+ 0.9000 0.8066 8.0657
+ 0.9300 1.0408 7.2859
+ 0.9600 1.2276 4.9103
+ 0.9900 1.3232 1.3232
+ 1.0200 1.3035 -2.6070
+ 1.0500 1.1736 -5.8678
+ 1.0800 0.9656 -7.7251
+ 1.1100 0.7262 -7.9879
+ 1.1400 0.5011 -6.9139
+ 1.1700 0.3192 -5.1400
+ 1.2000 0.1947 -3.1562
+ 1.2300 0.1292 -1.2339
+ 1.2600 0.1199 0.6144
+ 1.2900 0.1665 2.5034
+ 1.3200 0.2711 4.4827
+ 1.3500 0.4346 6.3741
+ 1.3800 0.6473 7.7674
+ 1.4100 0.8870 7.9826
+ 1.4400 1.1107 6.6645
+ 1.4700 1.2713 3.8139
+ 1.5000 1.3298 0.0000
+ 1.5300 1.2713 -3.8139
+ 1.5600 1.1107 -6.6645
+ 1.5900 0.8870 -7.9826
+ 1.6200 0.6483 -7.7305
+ 1.6500 0.4346 -6.3741
+ 1.6800 0.2711 -4.4827
+ 1.7100 0.1665 -2.5034
+ 1.7400 0.1199 -0.6144
+ 1.7700 0.1292 1.2339
+ 1.8000 0.1947 3.1562
+ 1.8300 0.3192 5.1400
+ 1.8600 0.5011 6.9139
+ 1.8900 0.7262 7.9879
+ 1.9200 0.9656 7.7251
+ 1.9500 1.1736 5.8678
+ 1.9800 1.3035 2.6070
+ 2.0100 1.3232 -1.3232
+ 2.0400 1.2276 -4.9103
+ 2.0700 1.0408 -7.2859
+ 2.1000 0.8066 -8.0657
+ 2.1300 0.5712 -7.4260
+ 2.1600 0.3697 -5.9158
+ 2.1900 0.2187 -4.1557
+ 2.2200 0.1182 -2.6015
+ 2.2500 0.0584 -1.4607
+ 2.2800 0.0264 -0.7388
+ 2.3100 0.0109 -0.3376
+ 2.3400 0.0041 -0.1397
+ 2.3700 0.0000 0.0000
+ 2.4000 0.0000 0.0000
+ 2.4300 0.0000 0.0000
+ 2.4600 0.0000 0.0000
+ 2.4900 0.0000 0.0000
+ 2.5200 0.0000 0.0000
+ 2.5500 0.0000 0.0000
+ 2.5800 0.0000 0.0000
+ 2.6100 0.0000 0.0000
+ 2.6400 0.0000 0.0000
+ 2.6700 0.0000 0.0000
+ 2.7000 0.0000 0.0000
+ 2.7300 0.0000 0.0000
+ 2.7600 0.0000 0.0000
+ 2.7900 0.0000 0.0000
+ 2.8200 0.0000 0.0000
+ 2.8500 0.0000 0.0000
+ 2.8800 0.0000 0.0000
+ 2.9100 0.0000 0.0000
+ 2.9400 0.0000 0.0000
+ 2.9700 0.0000 0.0000
+ 3.0000 0.0000 0.0000
diff --git a/regtest/analysis/rt-histo/plumed.dat b/regtest/analysis/rt-histo/plumed.dat
new file mode 100755
index 0000000000000000000000000000000000000000..d1b86eef2d2d6f90b74d7f33394682aa6e39a224
--- /dev/null
+++ b/regtest/analysis/rt-histo/plumed.dat
@@ -0,0 +1,86 @@
+x: DISTANCE ATOMS=1,2
+
+HISTOGRAM ...
+ ARG=x
+ TEMP=300
+ GRID_MIN=0.0
+ GRID_MAX=3.0
+ GRID_BIN=100
+ BANDWIDTH=0.1
+ LABEL=hA1
+... HISTOGRAM
+
+HISTOGRAM ...
+ ARG=x
+ TEMP=300
+ GRID_MIN=0.0
+ GRID_MAX=3.0
+ GRID_BIN=100
+ BANDWIDTH=0.1
+ LABEL=hA2
+... HISTOGRAM
+
+HISTOGRAM ...
+ ARG=x
+ TEMP=300
+ GRID_MIN=0.0
+ GRID_MAX=3.0
+ GRID_BIN=100
+ BANDWIDTH=0.1
+ LABEL=hA3
+... HISTOGRAM
+
+HISTOGRAM ...
+ ARG=x
+ TEMP=300
+ GRID_MIN=0.0
+ GRID_MAX=3.0
+ GRID_BIN=100
+ BANDWIDTH=0.1
+ NOMEMORY
+ LABEL=hA1n
+... HISTOGRAM
+
+PRINT_GRID GRID=hA1 FILE=histoA1 STRIDE=1 FMT=%8.4f
+PRINT_GRID GRID=hA1n FILE=histoA1n STRIDE=1 FMT=%8.4f
+PRINT_GRID GRID=hA2 FILE=histoA2 STRIDE=2 FMT=%8.4f
+PRINT_GRID GRID=hA3 FILE=histoA3 USE_ALL_DATA FMT=%8.4f
+
+HISTOGRAM ...
+ ARG=x
+ TEMP=300
+ GRID_MIN=0.0
+ GRID_MAX=3.0
+ GRID_BIN=100
+ BANDWIDTH=0.1
+ UNORMALIZED
+ LABEL=hA1u
+... HISTOGRAM
+
+HISTOGRAM ...
+ ARG=x
+ TEMP=300
+ GRID_MIN=0.0
+ GRID_MAX=3.0
+ GRID_BIN=100
+ BANDWIDTH=0.1
+ UNORMALIZED
+ LABEL=hA2u
+... HISTOGRAM
+
+PRINT_GRID GRID=hA1u FILE=histoA1u STRIDE=1 FMT=%8.4f
+PRINT_GRID GRID=hA2u FILE=histoA2u STRIDE=2 FMT=%8.4f
+
+CONVERT_TO_FES GRID=hA1 TEMP=300 LABEL=fA1
+CONVERT_TO_FES GRID=hA2 TEMP=300 LABEL=fA2
+CONVERT_TO_FES GRID=hA3 TEMP=300 LABEL=fA3
+
+PRINT_GRID GRID=fA1 FILE=fesA1 STRIDE=1 FMT=%8.4f
+PRINT_GRID GRID=fA2 FILE=fesA2 STRIDE=2 FMT=%8.4f
+PRINT_GRID GRID=fA3 FILE=fesA3 USE_ALL_DATA FMT=%8.4f
+
+CONVERT_TO_FES GRID=hA1u TEMP=300 LABEL=fA1u
+CONVERT_TO_FES GRID=hA2u TEMP=300 LABEL=fA2u
+
+PRINT_GRID GRID=fA1u FILE=fesA1u STRIDE=1 FMT=%8.4f
+PRINT_GRID GRID=fA2u FILE=fesA2u STRIDE=2 FMT=%8.4f
diff --git a/regtest/analysis/rt-histo/trajectory.xyz b/regtest/analysis/rt-histo/trajectory.xyz
new file mode 100644
index 0000000000000000000000000000000000000000..c910ae5c6fda2241cfe5be857f9b8493db430ed3
--- /dev/null
+++ b/regtest/analysis/rt-histo/trajectory.xyz
@@ -0,0 +1,12 @@
+2
+0 0 0
+X 0 0 0
+X 0 0 1
+2
+0 0 0
+X 0 0 0
+X 0 0 1.5
+2
+0 0 0
+X 0 0 0
+X 0 0 2
diff --git a/regtest/analysis/rt0/histoA.reference b/regtest/analysis/rt0/histoA.reference
index 11425019a9f1aa584941f61388daf5301c3fbaac..a9c66815b9bdb363075a5c1aa7825ca422297301 100644
--- a/regtest/analysis/rt0/histoA.reference
+++ b/regtest/analysis/rt0/histoA.reference
@@ -1,106 +1,107 @@
-#! FIELDS x probs
+#! FIELDS x hA dhA_x
+#! SET normalisation 2.0000
#! SET min_x 0.0
#! SET max_x 3.0
-#! SET nbins_x 101
+#! SET nbins_x 100
#! SET periodic_x false
- 0.0000 0.0000
- 0.0300 0.0000
- 0.0600 0.0000
- 0.0900 0.0000
- 0.1200 0.0000
- 0.1500 0.0000
- 0.1800 0.0000
- 0.2100 0.0000
- 0.2400 0.0000
- 0.2700 0.0000
- 0.3000 0.0000
- 0.3300 0.0000
- 0.3600 0.0000
- 0.3900 0.0000
- 0.4200 0.0000
- 0.4500 0.0000
- 0.4800 0.0000
- 0.5100 0.0000
- 0.5400 0.0000
- 0.5700 0.0000
- 0.6000 0.0000
- 0.6300 0.0000
- 0.6600 0.0000
- 0.6900 0.0000
- 0.7200 0.0000
- 0.7500 0.0000
- 0.7800 0.0000
- 0.8100 0.0000
- 0.8400 0.0000
- 0.8700 0.0000
- 0.9000 0.0000
- 0.9300 0.0000
- 0.9600 0.0000
- 0.9900 0.0000
- 1.0200 0.0000
- 1.0500 0.0000
- 1.0800 0.0000
- 1.1100 0.0000
- 1.1400 0.0031
- 1.1700 0.0086
- 1.2000 0.0221
- 1.2300 0.0521
- 1.2600 0.1119
- 1.2900 0.2199
- 1.3200 0.3947
- 1.3500 0.6476
- 1.3800 0.9709
- 1.4100 1.3304
- 1.4400 1.6661
- 1.4700 1.9069
- 1.5000 1.9947
- 1.5300 1.9069
- 1.5600 1.6661
- 1.5900 1.3304
- 1.6200 0.9724
- 1.6500 0.6520
- 1.6800 0.4067
- 1.7100 0.2497
- 1.7400 0.1799
- 1.7700 0.1937
- 1.8000 0.2921
- 1.8300 0.4788
- 1.8600 0.7517
- 1.8900 1.0893
- 1.9200 1.4485
- 1.9500 1.7603
- 1.9800 1.9552
- 2.0100 1.9848
- 2.0400 1.8414
- 2.0700 1.5613
- 2.1000 1.2099
- 2.1300 0.8568
- 2.1600 0.5546
- 2.1900 0.3281
- 2.2200 0.1774
- 2.2500 0.0876
- 2.2800 0.0396
- 2.3100 0.0163
- 2.3400 0.0062
- 2.3700 0.0000
- 2.4000 0.0000
- 2.4300 0.0000
- 2.4600 0.0000
- 2.4900 0.0000
- 2.5200 0.0000
- 2.5500 0.0000
- 2.5800 0.0000
- 2.6100 0.0000
- 2.6400 0.0000
- 2.6700 0.0000
- 2.7000 0.0000
- 2.7300 0.0000
- 2.7600 0.0000
- 2.7900 0.0000
- 2.8200 0.0000
- 2.8500 0.0000
- 2.8800 0.0000
- 2.9100 0.0000
- 2.9400 0.0000
- 2.9700 0.0000
- 3.0000 0.0000
+ 0.0000 0.0000 0.0000
+ 0.0300 0.0000 0.0000
+ 0.0600 0.0000 0.0000
+ 0.0900 0.0000 0.0000
+ 0.1200 0.0000 0.0000
+ 0.1500 0.0000 0.0000
+ 0.1800 0.0000 0.0000
+ 0.2100 0.0000 0.0000
+ 0.2400 0.0000 0.0000
+ 0.2700 0.0000 0.0000
+ 0.3000 0.0000 0.0000
+ 0.3300 0.0000 0.0000
+ 0.3600 0.0000 0.0000
+ 0.3900 0.0000 0.0000
+ 0.4200 0.0000 0.0000
+ 0.4500 0.0000 0.0000
+ 0.4800 0.0000 0.0000
+ 0.5100 0.0000 0.0000
+ 0.5400 0.0000 0.0000
+ 0.5700 0.0000 0.0000
+ 0.6000 0.0000 0.0000
+ 0.6300 0.0000 0.0000
+ 0.6600 0.0000 0.0000
+ 0.6900 0.0000 0.0000
+ 0.7200 0.0000 0.0000
+ 0.7500 0.0000 0.0000
+ 0.7800 0.0000 0.0000
+ 0.8100 0.0000 0.0000
+ 0.8400 0.0000 0.0000
+ 0.8700 0.0000 0.0000
+ 0.9000 0.0000 0.0000
+ 0.9300 0.0000 0.0000
+ 0.9600 0.0000 0.0000
+ 0.9900 0.0000 0.0000
+ 1.0200 0.0000 0.0000
+ 1.0500 0.0000 0.0000
+ 1.0800 0.0000 0.0000
+ 1.1100 0.0000 0.0000
+ 1.1400 0.0031 0.1101
+ 1.1700 0.0086 0.2842
+ 1.2000 0.0221 0.6648
+ 1.2300 0.0521 1.4068
+ 1.2600 0.1119 2.6873
+ 1.2900 0.2199 4.6183
+ 1.3200 0.3947 7.1055
+ 1.3500 0.6476 9.7138
+ 1.3800 0.9709 11.6511
+ 1.4100 1.3304 11.9739
+ 1.4400 1.6661 9.9968
+ 1.4700 1.9069 5.7208
+ 1.5000 1.9947 0.0000
+ 1.5300 1.9069 -5.7208
+ 1.5600 1.6661 -9.9968
+ 1.5900 1.3304 -11.9739
+ 1.6200 0.9724 -11.5957
+ 1.6500 0.6520 -9.5611
+ 1.6800 0.4067 -6.7240
+ 1.7100 0.2497 -3.7552
+ 1.7400 0.1799 -0.9216
+ 1.7700 0.1937 1.8508
+ 1.8000 0.2921 4.7343
+ 1.8300 0.4788 7.7100
+ 1.8600 0.7517 10.3708
+ 1.8900 1.0893 11.9819
+ 1.9200 1.4485 11.5877
+ 1.9500 1.7603 8.8016
+ 1.9800 1.9552 3.9104
+ 2.0100 1.9848 -1.9848
+ 2.0400 1.8414 -7.3654
+ 2.0700 1.5613 -10.9289
+ 2.1000 1.2099 -12.0985
+ 2.1300 0.8568 -11.1390
+ 2.1600 0.5546 -8.8737
+ 2.1900 0.3281 -6.2335
+ 2.2200 0.1774 -3.9022
+ 2.2500 0.0876 -2.1910
+ 2.2800 0.0396 -1.1082
+ 2.3100 0.0163 -0.5064
+ 2.3400 0.0062 -0.2095
+ 2.3700 0.0000 0.0000
+ 2.4000 0.0000 0.0000
+ 2.4300 0.0000 0.0000
+ 2.4600 0.0000 0.0000
+ 2.4900 0.0000 0.0000
+ 2.5200 0.0000 0.0000
+ 2.5500 0.0000 0.0000
+ 2.5800 0.0000 0.0000
+ 2.6100 0.0000 0.0000
+ 2.6400 0.0000 0.0000
+ 2.6700 0.0000 0.0000
+ 2.7000 0.0000 0.0000
+ 2.7300 0.0000 0.0000
+ 2.7600 0.0000 0.0000
+ 2.7900 0.0000 0.0000
+ 2.8200 0.0000 0.0000
+ 2.8500 0.0000 0.0000
+ 2.8800 0.0000 0.0000
+ 2.9100 0.0000 0.0000
+ 2.9400 0.0000 0.0000
+ 2.9700 0.0000 0.0000
+ 3.0000 0.0000 0.0000
diff --git a/regtest/analysis/rt0/histoB.reference b/regtest/analysis/rt0/histoB.reference
index 0facce1f608dbfad4d6f637ce120bf88ab7d1794..292e70eff32ddd97ae7e58bacfc7148fd21583d3 100644
--- a/regtest/analysis/rt0/histoB.reference
+++ b/regtest/analysis/rt0/histoB.reference
@@ -1,106 +1,107 @@
-#! FIELDS x probs
+#! FIELDS x hB dhB_x
+#! SET normalisation 2.2220
#! SET min_x 0.0
#! SET max_x 3.0
-#! SET nbins_x 101
+#! SET nbins_x 100
#! SET periodic_x false
- 0.0000 0.0000
- 0.0300 0.0000
- 0.0600 0.0000
- 0.0900 0.0000
- 0.1200 0.0000
- 0.1500 0.0000
- 0.1800 0.0000
- 0.2100 0.0000
- 0.2400 0.0000
- 0.2700 0.0000
- 0.3000 0.0000
- 0.3300 0.0000
- 0.3600 0.0000
- 0.3900 0.0000
- 0.4200 0.0000
- 0.4500 0.0000
- 0.4800 0.0000
- 0.5100 0.0000
- 0.5400 0.0000
- 0.5700 0.0000
- 0.6000 0.0000
- 0.6300 0.0000
- 0.6600 0.0000
- 0.6900 0.0000
- 0.7200 0.0000
- 0.7500 0.0000
- 0.7800 0.0000
- 0.8100 0.0000
- 0.8400 0.0000
- 0.8700 0.0000
- 0.9000 0.0000
- 0.9300 0.0000
- 0.9600 0.0000
- 0.9900 0.0000
- 1.0200 0.0000
- 1.0500 0.0000
- 1.0800 0.0000
- 1.1100 0.0000
- 1.1400 0.0027
- 1.1700 0.0077
- 1.2000 0.0199
- 1.2300 0.0469
- 1.2600 0.1008
- 1.2900 0.1979
- 1.3200 0.3553
- 1.3500 0.5829
- 1.3800 0.8740
- 1.4100 1.1975
- 1.4400 1.4997
- 1.4700 1.7165
- 1.5000 1.7954
- 1.5300 1.7165
- 1.5600 1.4997
- 1.5900 1.1975
- 1.6200 0.8756
- 1.6500 0.5877
- 1.6800 0.3684
- 1.7100 0.2307
- 1.7400 0.1755
- 1.7700 0.2027
- 1.8000 0.3169
- 1.8300 0.5250
- 1.8600 0.8262
- 1.8900 1.1981
- 1.9200 1.5931
- 1.9500 1.9362
- 1.9800 2.1505
- 2.0100 2.1830
- 2.0400 2.0253
- 2.0700 1.7172
- 2.1000 1.3307
- 2.1300 0.9424
- 2.1600 0.6100
- 2.1900 0.3609
- 2.2200 0.1951
- 2.2500 0.0964
- 2.2800 0.0435
- 2.3100 0.0180
- 2.3400 0.0068
- 2.3700 0.0000
- 2.4000 0.0000
- 2.4300 0.0000
- 2.4600 0.0000
- 2.4900 0.0000
- 2.5200 0.0000
- 2.5500 0.0000
- 2.5800 0.0000
- 2.6100 0.0000
- 2.6400 0.0000
- 2.6700 0.0000
- 2.7000 0.0000
- 2.7300 0.0000
- 2.7600 0.0000
- 2.7900 0.0000
- 2.8200 0.0000
- 2.8500 0.0000
- 2.8800 0.0000
- 2.9100 0.0000
- 2.9400 0.0000
- 2.9700 0.0000
- 3.0000 0.0000
+ 0.0000 0.0000 0.0000
+ 0.0300 0.0000 0.0000
+ 0.0600 0.0000 0.0000
+ 0.0900 0.0000 0.0000
+ 0.1200 0.0000 0.0000
+ 0.1500 0.0000 0.0000
+ 0.1800 0.0000 0.0000
+ 0.2100 0.0000 0.0000
+ 0.2400 0.0000 0.0000
+ 0.2700 0.0000 0.0000
+ 0.3000 0.0000 0.0000
+ 0.3300 0.0000 0.0000
+ 0.3600 0.0000 0.0000
+ 0.3900 0.0000 0.0000
+ 0.4200 0.0000 0.0000
+ 0.4500 0.0000 0.0000
+ 0.4800 0.0000 0.0000
+ 0.5100 0.0000 0.0000
+ 0.5400 0.0000 0.0000
+ 0.5700 0.0000 0.0000
+ 0.6000 0.0000 0.0000
+ 0.6300 0.0000 0.0000
+ 0.6600 0.0000 0.0000
+ 0.6900 0.0000 0.0000
+ 0.7200 0.0000 0.0000
+ 0.7500 0.0000 0.0000
+ 0.7800 0.0000 0.0000
+ 0.8100 0.0000 0.0000
+ 0.8400 0.0000 0.0000
+ 0.8700 0.0000 0.0000
+ 0.9000 0.0000 0.0000
+ 0.9300 0.0000 0.0000
+ 0.9600 0.0000 0.0000
+ 0.9900 0.0000 0.0000
+ 1.0200 0.0000 0.0000
+ 1.0500 0.0000 0.0000
+ 1.0800 0.0000 0.0000
+ 1.1100 0.0000 0.0000
+ 1.1400 0.0027 0.0991
+ 1.1700 0.0077 0.2558
+ 1.2000 0.0199 0.5984
+ 1.2300 0.0469 1.2663
+ 1.2600 0.1008 2.4189
+ 1.2900 0.1979 4.1570
+ 1.3200 0.3553 6.3957
+ 1.3500 0.5829 8.7435
+ 1.3800 0.8740 10.4873
+ 1.4100 1.1975 10.7777
+ 1.4400 1.4997 8.9981
+ 1.4700 1.7165 5.1493
+ 1.5000 1.7954 0.0000
+ 1.5300 1.7165 -5.1493
+ 1.5600 1.4997 -8.9981
+ 1.5900 1.1975 -10.7777
+ 1.6200 0.8756 -10.4263
+ 1.6500 0.5877 -8.5755
+ 1.6800 0.3684 -5.9762
+ 1.7100 0.2307 -3.2076
+ 1.7400 0.1755 -0.4767
+ 1.7700 0.2027 2.3167
+ 1.8000 0.3169 5.3400
+ 1.8300 0.5250 8.5369
+ 1.8600 0.8262 11.4287
+ 1.8900 1.1981 13.1788
+ 1.9200 1.5931 12.7452
+ 1.9500 1.9362 9.6809
+ 1.9800 2.1505 4.3011
+ 2.0100 2.1830 -2.1830
+ 2.0400 2.0253 -8.1012
+ 2.0700 1.7172 -12.0206
+ 2.1000 1.3307 -13.3071
+ 2.1300 0.9424 -12.2517
+ 2.1600 0.6100 -9.7601
+ 2.1900 0.3609 -6.8562
+ 2.2200 0.1951 -4.2920
+ 2.2500 0.0964 -2.4099
+ 2.2800 0.0435 -1.2189
+ 2.3100 0.0180 -0.5569
+ 2.3400 0.0068 -0.2304
+ 2.3700 0.0000 0.0000
+ 2.4000 0.0000 0.0000
+ 2.4300 0.0000 0.0000
+ 2.4600 0.0000 0.0000
+ 2.4900 0.0000 0.0000
+ 2.5200 0.0000 0.0000
+ 2.5500 0.0000 0.0000
+ 2.5800 0.0000 0.0000
+ 2.6100 0.0000 0.0000
+ 2.6400 0.0000 0.0000
+ 2.6700 0.0000 0.0000
+ 2.7000 0.0000 0.0000
+ 2.7300 0.0000 0.0000
+ 2.7600 0.0000 0.0000
+ 2.7900 0.0000 0.0000
+ 2.8200 0.0000 0.0000
+ 2.8500 0.0000 0.0000
+ 2.8800 0.0000 0.0000
+ 2.9100 0.0000 0.0000
+ 2.9400 0.0000 0.0000
+ 2.9700 0.0000 0.0000
+ 3.0000 0.0000 0.0000
diff --git a/regtest/analysis/rt0/histoD.reference b/regtest/analysis/rt0/histoD.reference
index 7a451957c6d1e1f59d1bd0a90188f404090e6059..c2827416c9d5a8a190f694c7894805489a1bc6d2 100644
--- a/regtest/analysis/rt0/histoD.reference
+++ b/regtest/analysis/rt0/histoD.reference
@@ -1,7 +1,8 @@
-#! FIELDS x probs
+#! FIELDS x hD
+#! SET normalisation 5.5474
#! SET min_x 0.0
#! SET max_x 3.0
-#! SET nbins_x 101
+#! SET nbins_x 100
#! SET periodic_x false
0.0000 0.0000
0.0300 0.0000
diff --git a/regtest/analysis/rt0/histoD1.reference b/regtest/analysis/rt0/histoD1.reference
index c21f52ccfd3c72e262aa1a21ea6f5e5b69d1fb9d..7a6242f4ed92381dca7a3ff17e8db8ac6929560d 100644
--- a/regtest/analysis/rt0/histoD1.reference
+++ b/regtest/analysis/rt0/histoD1.reference
@@ -1,7 +1,8 @@
-#! FIELDS x probs
+#! FIELDS x hD1
+#! SET normalisation 1.4932
#! SET min_x 0.0
#! SET max_x 3.0
-#! SET nbins_x 101
+#! SET nbins_x 100
#! SET periodic_x false
0.0000 0.0000
0.0300 0.0000
diff --git a/regtest/analysis/rt0/histoD2.reference b/regtest/analysis/rt0/histoD2.reference
index c30dbc322bd8396ac3bd9b1de94c8bee39a7f259..fbdf557840a378a257ea4a6d4ba3c4cc9be52118 100644
--- a/regtest/analysis/rt0/histoD2.reference
+++ b/regtest/analysis/rt0/histoD2.reference
@@ -1,7 +1,8 @@
-#! FIELDS x probs
+#! FIELDS x hD2
+#! SET normalisation 1.8246
#! SET min_x 0.0
#! SET max_x 3.0
-#! SET nbins_x 101
+#! SET nbins_x 100
#! SET periodic_x false
0.0000 0.0000
0.0300 0.0000
diff --git a/regtest/analysis/rt0/histoE.reference b/regtest/analysis/rt0/histoE.reference
index d4e388b3a0edd623cdc5f0eb3d7044a5d825829d..b36b2558f2211d383cbb60cddb29fe689871f6d6 100644
--- a/regtest/analysis/rt0/histoE.reference
+++ b/regtest/analysis/rt0/histoE.reference
@@ -1,7 +1,8 @@
-#! FIELDS x probs
+#! FIELDS x fE
+#! SET normalisation 3.0547
#! SET min_x 0.0
#! SET max_x 3.0
-#! SET nbins_x 101
+#! SET nbins_x 100
#! SET periodic_x false
0.0000 inf
0.0300 inf
diff --git a/regtest/analysis/rt0/plumed.dat b/regtest/analysis/rt0/plumed.dat
index 22ba7aca7f82bca2173987a7de2e8ed4e983eade..b5ff3b6cde0b363efc2fcc1b5c19d27aae080357 100755
--- a/regtest/analysis/rt0/plumed.dat
+++ b/regtest/analysis/rt0/plumed.dat
@@ -46,10 +46,11 @@ HISTOGRAM ...
GRID_BIN=100
KERNEL=DISCRETE
REWEIGHT_BIAS
+ UNORMALIZED
LABEL=hD
... HISTOGRAM
-PRINT_GRID GRID=hD FILE=histoD FMT=%8.4f UNNORMALIZED USE_ALL_DATA
+PRINT_GRID GRID=hD FILE=histoD FMT=%8.4f USE_ALL_DATA
HISTOGRAM ...
ARG=x
@@ -59,10 +60,11 @@ HISTOGRAM ...
GRID_BIN=100
KERNEL=DISCRETE
REWEIGHT_BIAS
+ UNORMALIZED
LABEL=hE
... HISTOGRAM
-fE: CONVERT_TO_FES GRID=hE TEMP=10000 UNNORMALIZED
+fE: CONVERT_TO_FES GRID=hE TEMP=10000
PRINT_GRID GRID=fE FMT=%8.4f USE_ALL_DATA FILE=histoE
HISTOGRAM ...
@@ -75,10 +77,11 @@ HISTOGRAM ...
REWEIGHT_BIAS
UPDATE_FROM=0
UPDATE_UNTIL=1
+ UNORMALIZED
LABEL=hD1
... HISTOGRAM
-PRINT_GRID GRID=hD1 FILE=histoD1 FMT=%8.4f UNNORMALIZED USE_ALL_DATA
+PRINT_GRID GRID=hD1 FILE=histoD1 FMT=%8.4f USE_ALL_DATA
HISTOGRAM ...
ARG=x
@@ -90,10 +93,11 @@ HISTOGRAM ...
REWEIGHT_BIAS
UPDATE_FROM=1
UPDATE_UNTIL=2
+ UNORMALIZED
LABEL=hD2
... HISTOGRAM
-PRINT_GRID GRID=hD2 FILE=histoD2 FMT=%8.4f UNNORMALIZED USE_ALL_DATA
+PRINT_GRID GRID=hD2 FILE=histoD2 FMT=%8.4f USE_ALL_DATA
diff --git a/src/analysis/Analysis.cpp b/src/analysis/Analysis.cpp
index d4b1f573e7be0d6a619195d89c1d14f9b82ee2eb..fb539218ce322ae201f0e0a7c06a5e5fb8849bfc 100644
--- a/src/analysis/Analysis.cpp
+++ b/src/analysis/Analysis.cpp
@@ -89,7 +89,7 @@ ActionPilot(ao),
ActionAtomistic(ao),
ActionWithArguments(ao),
ActionWithVessel(ao),
-single_run(false),
+single_run(true),
nomemory(true),
write_chq(false),
reusing_data(false),
@@ -176,7 +176,6 @@ argument_names(getNumberOfArguments())
if(simtemp==0) error("The MD engine does not pass the temperature to plumed so you have to specify it using TEMP");
}
- single_run=true;
if( keywords.exists("USE_ALL_DATA") ){
parseFlag("USE_ALL_DATA",single_run);
if( !single_run ){
@@ -219,8 +218,8 @@ argument_names(getNumberOfArguments())
}
void Analysis::setAnalysisStride( const bool& use_all, const unsigned& astride ){
- if( freq>0 && astride!=freq ) error("frequency for output does not match frequency for run");
- else if( freq>0 || use_all ) return;
+ if( freq>0 && astride!=freq ) error("each histogram can only be output with one stride");
+ else if( use_all ) return;
freq=astride; single_run=false;
if( astride%getStride()!= 0 ) error("Frequncy of running is not a multiple of the stride");
@@ -407,7 +406,7 @@ void Analysis::runAnalysis(){
norm=mydatastash->retrieveNorm();
}
// This ensures everything is set up to run the calculation
- setAnalysisStride( single_run, freq );
+ if( single_run ) setAnalysisStride( single_run, freq );
// And run the analysis
performAnalysis(); idata=0;
// Update total normalization constant
diff --git a/src/analysis/Histogram.cpp b/src/analysis/Histogram.cpp
index 73fde2065fadce288298156a25d0b2d46ec22c32..72a4f66da67dbc5a1ecbc07c8c744b80cb198aef 100644
--- a/src/analysis/Histogram.cpp
+++ b/src/analysis/Histogram.cpp
@@ -145,7 +145,7 @@ void Histogram::registerKeywords( Keywords& keys ){
keys.add("compulsory","KERNEL","gaussian","the kernel function you are using. Use discrete/DISCRETE if you want to accumulate a discrete histogram. \
More details on the kernels available in plumed can be found in \\ref kernelfunctions.");
keys.add("optional","BANDWIDTH","the bandwdith for kernel density estimation");
- keys.addFlag("UNNORMALIZED",false,"Set to TRUE if you don't want histogram to be normalized or free energy to be shifted.");
+ keys.addFlag("UNORMALIZED",false,"Set to TRUE if you don't want histogram to be normalized or free energy to be shifted.");
keys.use("NOMEMORY");
}
@@ -168,7 +168,12 @@ unnormalized(false)
if( getPeriodicityInformation(i, dmin, dmax) ) vstring+=",T";
else vstring+=",F";
}
- vstring += " STORE_NORMED COMPONENTS=" + getLabel();
+ bool unorm=false; parseFlag("UNORMALIZED",unorm);
+ if( unorm ){
+ log.printf(" working with unormalised grid \n");
+ vstring += " UNORMALIZED";
+ }
+ vstring += " COMPONENTS=" + getLabel();
vstring += " COORDINATES=" + getPntrToArgument(0)->getName();
for(unsigned i=1;i<getNumberOfArguments();++i) vstring += "," + getPntrToArgument(i)->getName();
if( !usingMemory() ) vstring += " NOMEMORY";
@@ -190,9 +195,13 @@ unnormalized(false)
}
void Histogram::setAnalysisStride( const bool& use_all, const unsigned& astride ){
- if( getFullNumberOfTasks()>0 && getFullNumberOfTasks()==getNumberOfDataPoints() ) return;
- Analysis::setAnalysisStride( use_all, astride ); plumed_assert( getFullNumberOfTasks()==0 );
+ Analysis::setAnalysisStride( use_all, astride );
+ if( getNumberOfDataPoints()==getFullNumberOfTasks() ) return ;
+ plumed_assert( getFullNumberOfTasks()==0 );
for(unsigned i=0;i<getNumberOfDataPoints();++i) addTaskToList( i );
+ deactivateAllTasks();
+ for(unsigned i=0;i<getNumberOfDataPoints();++i) taskFlags[i]=1;
+ lockContributors();
}
unsigned Histogram::getNumberOfQuantities() const {
@@ -209,7 +218,7 @@ void Histogram::performTask( const unsigned& task_index, const unsigned& current
void Histogram::performAnalysis(){
if( mygrid->wasreset() ) mygrid->clear();
- runAllTasks(); mygrid->setNorm( getNormalization() );
+ mygrid->setNorm( getNormalization() ); runAllTasks();
}
}
diff --git a/src/gridtools/ActionWithInputGrid.cpp b/src/gridtools/ActionWithInputGrid.cpp
index d29153c4c7278cc2d00e177f57fb23c289c645f0..a4b363727ccb3e1a508d0ccc6bf35d3b507f0042 100644
--- a/src/gridtools/ActionWithInputGrid.cpp
+++ b/src/gridtools/ActionWithInputGrid.cpp
@@ -33,24 +33,23 @@ void ActionWithInputGrid::registerKeywords( Keywords& keys ){
keys.add("compulsory","GRID","the action that creates the input grid you would like to use");
keys.add("optional","STRIDE","the frequency with which to output the grid");
keys.addFlag("USE_ALL_DATA",false,"use the data from the entire trajectory to perform the analysis");
- keys.addFlag("UNNORMALIZED",false,"output an unormalised grid");
}
ActionWithInputGrid::ActionWithInputGrid(const ActionOptions&ao):
Action(ao),
ActionPilot(ao),
ActionWithVessel(ao),
-norm(0.0),
+single_run(true),
mygrid(NULL)
{
std::string mlab; parse("GRID",mlab);
- vesselbase::ActionWithVessel* mves= plumed.getActionSet().selectWithLabel<vesselbase::ActionWithVessel*>(mlab);
+ mves= plumed.getActionSet().selectWithLabel<vesselbase::ActionWithVessel*>(mlab);
if(!mves) error("action labelled " + mlab + " does not exist or does not have vessels");
addDependency(mves);
ActionPilot* ap=dynamic_cast<ActionPilot*>( mves );
if( ap ){
- if( getStride()!=ap->getStride() ) error("mismatch between strides in " + ap->getLabel() + " and " + getLabel() );
+ if( getStride()%ap->getStride()!=0 ) error("mismatch between strides in " + ap->getLabel() + " and " + getLabel() );
}
log.printf(" using grid calculated by action %s \n",mves->getLabel().c_str() );
@@ -60,29 +59,29 @@ mygrid(NULL)
}
if( !mygrid ) error("input action does not calculate a grid");
- parseFlag("UNNORMALIZED",unormalised);
- if( unormalised ){
- log.printf(" working with unormalised grid \n");
- mygrid->switchOffNormalisation();
- }
-
if( keywords.exists("USE_ALL_DATA") ){
parseFlag("USE_ALL_DATA",single_run);
if( !single_run ){
mves->setAnalysisStride( false, getStride() );
log.printf(" outputting every %u steps \n", getStride() );
- } else log.printf(" outputting at end of calculation\n");
+ } else {
+ log.printf(" outputting at end of calculation\n");
+ }
}
}
void ActionWithInputGrid::setAnalysisStride( const bool& use_all, const unsigned& astride ){
single_run=use_all;
- if( !single_run ) setStride( astride );
+ if( !single_run ){
+ setStride( astride ); mves->setAnalysisStride( false, getStride() );
+ }
}
void ActionWithInputGrid::update(){
- if( unormalised ) norm = 1.0;
- else norm=1.0/mygrid->getNorm();
+ // Don't analyse the first frame in the trajectory
+ if( single_run || getStep()==0 ) return;
+ // Now check that all stuff for restarting is done correctly
+ if( !mygrid->foundprint ) error("an additional PRINT_GRID action is required before this action so grid is restarted correctly");
if( checkAllActive() ){
for(unsigned i=0;i<mygrid->getNumberOfPoints();++i){
@@ -94,11 +93,13 @@ void ActionWithInputGrid::update(){
void ActionWithInputGrid::runFinalJobs(){
if( !single_run ) return ;
- if( unormalised ) norm = 1.0;
- else norm=1.0/mygrid->getNorm();
performOperationsWithGrid( false );
}
+void ActionWithInputGrid::invertTask( const std::vector<double>& indata, std::vector<double>& outdata ){
+ plumed_merror("Shouldn't appear here");
+}
+
}
}
diff --git a/src/gridtools/ActionWithInputGrid.h b/src/gridtools/ActionWithInputGrid.h
index 0246be6ae0acd477ed3cf3c0556dfce242783b19..83ff5fd024267963da3a25ef44963e5617235ff8 100644
--- a/src/gridtools/ActionWithInputGrid.h
+++ b/src/gridtools/ActionWithInputGrid.h
@@ -32,14 +32,13 @@ class ActionWithInputGrid :
public ActionPilot,
public vesselbase::ActionWithVessel
{
+friend class GridFunction;
private:
- double norm;
- bool unormalised;
+ vesselbase::ActionWithVessel* mves;
protected:
bool single_run;
GridVessel* mygrid;
- double getGridElement( const std::vector<unsigned>& pp, const unsigned& ind ) const ;
- double getGridElement( const unsigned& ind, const unsigned& jind ) const ;
+ double getGridElementAndDerivatives( const std::vector<double>& x, std::vector<double>& der ) const ;
public:
static void registerKeywords( Keywords& keys );
explicit ActionWithInputGrid(const ActionOptions&ao);
@@ -50,18 +49,10 @@ public:
virtual bool checkAllActive() const { return true; }
virtual void performOperationsWithGrid( const bool& from_update )=0;
void setAnalysisStride( const bool& use_all, const unsigned& astride );
+ virtual bool isGridPrint() const { return false; }
+ virtual void invertTask( const std::vector<double>& indata, std::vector<double>& outdata );
};
-inline
-double ActionWithInputGrid::getGridElement( const std::vector<unsigned>& pp, const unsigned& ind ) const {
- return norm*mygrid->getGridElement( pp, ind );
-}
-
-inline
-double ActionWithInputGrid::getGridElement( const unsigned& ind, const unsigned& jind ) const {
- return norm*mygrid->getGridElement( ind, jind );
-}
-
}
}
#endif
diff --git a/src/gridtools/AverageOnGrid.cpp b/src/gridtools/AverageOnGrid.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..51f6acb71329a1816b02bbf04a24410703583f04
--- /dev/null
+++ b/src/gridtools/AverageOnGrid.cpp
@@ -0,0 +1,61 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ 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 "AverageOnGrid.h"
+
+namespace PLMD {
+namespace gridtools {
+
+void AverageOnGrid::registerKeywords( Keywords& keys ){
+ HistogramOnGrid::registerKeywords( keys );
+}
+
+AverageOnGrid::AverageOnGrid( const vesselbase::VesselOptions& da ):
+HistogramOnGrid(da)
+{
+ plumed_assert( nper==(dimension+1) );
+ arg_names.push_back( "density" );
+ if( !discrete ){
+ for(unsigned i=0;i<dimension;++i) arg_names.push_back( "ddensity_" + arg_names[i] );
+ nper = 2*(dimension+1);
+ } else {
+ nper = 2;
+ }
+}
+
+void AverageOnGrid::accumulate( const unsigned& ipoint, const double& weight, const double& dens, const std::vector<double>& der, std::vector<double>& buffer ) const {
+ buffer[bufstart+nper*ipoint] += weight*dens; buffer[bufstart+nper*ipoint+1+dimension] += dens;
+ if( der.size()>0 ){
+ for(unsigned j=0;j<dimension;++j) buffer[bufstart+nper*ipoint+ 1 + j] += weight*der[j];
+ for(unsigned j=0;j<dimension;++j) buffer[bufstart+nper*ipoint + 1 + dimension + 1 + j] += der[j];
+ }
+}
+
+double AverageOnGrid::getGridElement( const unsigned& ipoint, const unsigned& jelement ) const {
+ if( unormalised ) return data[nper*ipoint + jelement];
+ if( jelement==0 ) return data[nper*ipoint] / data[nper*ipoint + 1 + dimension];
+ double rdenom = 1.0;
+ if( fabs(data[nper*ipoint+1+dimension])>epsilon ) rdenom = 1. / data[nper*ipoint + 1 + dimension];
+ return rdenom*data[nper*ipoint+1+jelement] - rdenom*rdenom*data[nper*ipoint]*data[nper*ipoint+1+dimension+1+jelement];
+}
+
+}
+}
diff --git a/src/gridtools/AverageOnGrid.h b/src/gridtools/AverageOnGrid.h
new file mode 100644
index 0000000000000000000000000000000000000000..2506b78fafa331a04c5448d632d277fa0c1049c2
--- /dev/null
+++ b/src/gridtools/AverageOnGrid.h
@@ -0,0 +1,40 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ 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/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#ifndef __PLUMED_gridtools_AverageOnGrid_h
+#define __PLUMED_gridtools_AverageOnGrid_h
+
+#include "HistogramOnGrid.h"
+
+namespace PLMD {
+namespace gridtools {
+
+class AverageOnGrid : public HistogramOnGrid {
+public:
+ static void registerKeywords( Keywords& keys );
+ explicit AverageOnGrid( const vesselbase::VesselOptions& da );
+ void accumulate( const unsigned& ipoint, const double& weight, const double& dens, const std::vector<double>& der, std::vector<double>& buffer ) const ;
+ double getGridElement( const unsigned& ipoint, const unsigned& jelement ) const ;
+};
+
+}
+}
+#endif
diff --git a/src/gridtools/ConvertToFES.cpp b/src/gridtools/ConvertToFES.cpp
index 0d7ce6d8ba6b8f189e0bce2ee3c60f8246a3ba03..1ec285003915f05ee7b5b6f8602593d0a6b88199 100644
--- a/src/gridtools/ConvertToFES.cpp
+++ b/src/gridtools/ConvertToFES.cpp
@@ -39,6 +39,7 @@ public:
unsigned getNumberOfDerivatives(){ return 0; }
unsigned getNumberOfQuantities() const ;
void performTask( const unsigned& task_index, const unsigned& current, MultiValue& myvals ) const ;
+ void invertTask( const std::vector<double>& indata, std::vector<double>& outdata );
bool isPeriodic(){ return false; }
};
@@ -70,9 +71,14 @@ ActionWithInputGrid(ao)
simtemp=0.; parse("TEMP",simtemp);
if(simtemp>0) simtemp*=plumed.getAtoms().getKBoltzmann();
else simtemp=plumed.getAtoms().getKbT();
+ if( simtemp==0 ) error("TEMP not set - use keyword TEMP");
// Now create task list
for(unsigned i=0;i<mygrid->getNumberOfPoints();++i) addTaskToList(i);
+ // And activate all tasks
+ deactivateAllTasks();
+ for(unsigned i=0;i<mygrid->getNumberOfPoints();++i) taskFlags[i]=1;
+ lockContributors();
}
unsigned ConvertToFES::getNumberOfQuantities() const {
@@ -81,19 +87,22 @@ unsigned ConvertToFES::getNumberOfQuantities() const {
}
void ConvertToFES::performOperationsWithGrid( const bool& from_update ){
- outgrid->clear(); runAllTasks(); outgrid->reset();
+ outgrid->clear(); outgrid->setNorm( mygrid->getNorm() );
+ runAllTasks(); outgrid->reset();
}
void ConvertToFES::performTask( const unsigned& task_index, const unsigned& current, MultiValue& myvals ) const {
- double val=getGridElement(current, 0);
+ double val=mygrid->getGridElement(current, 0);
myvals.setValue( 0, 1.0 ); myvals.setValue(1, -simtemp*std::log(val) );
if( !mygrid->noDerivatives() ){
- for(unsigned i=0;i<mygrid->getDimension();++i) myvals.setValue( 2+i, -(simtemp/val)*getGridElement(current,i+1) );
+ for(unsigned i=0;i<mygrid->getDimension();++i) myvals.setValue( 2+i, -(simtemp/val)*mygrid->getGridElement(current,i+1) );
}
}
-
-
+void ConvertToFES::invertTask( const std::vector<double>& indata, std::vector<double>& outdata ){
+ outdata[0] = exp( -indata[0]/simtemp );
+ for(unsigned i=0;i<mygrid->getDimension();++i) outdata[1+i] = -(indata[0]/simtemp)*indata[1+i];
+}
}
}
diff --git a/src/gridtools/FindContour.cpp b/src/gridtools/FindContour.cpp
index 2aff20ad28ad57a0f19f6ee3ab31e0c6b018cdf2..8e9e107352594775401358496f55f74b868d38b0 100644
--- a/src/gridtools/FindContour.cpp
+++ b/src/gridtools/FindContour.cpp
@@ -138,7 +138,7 @@ outgrid(NULL)
Keywords keys; GridFunction::registerKeywords( keys );
vesselbase::VesselOptions dar( da, keys );
outgrid = new GridFunction(dar); addVessel( outgrid );
- if( mygrid->noDerivatives() ) outgrid->setNoDerivatives();
+ outgrid->setNoDerivatives();
}
// START OF BIT TO IMPROVE
@@ -228,7 +228,7 @@ void FindContour::performOperationsWithGrid( const bool& from_update ){
if( cycle ) continue;
// Get the value of a point on the grid
- double val1=getGridElement( i, mycomp*(mygrid->getDimension()+1) ) - contour;
+ double val1=mygrid->getGridElement( i, mycomp*(mygrid->getDimension()+1) ) - contour;
bool edge=false;
for(unsigned j=0;j<mygrid->getDimension();++j){
@@ -237,7 +237,7 @@ void FindContour::performOperationsWithGrid( const bool& from_update ){
if( !mygrid->isPeriodic(j) && (ind[j]+1)==nbin[j] ) continue;
else if( (ind[j]+1)==nbin[j] ){ edge=true; ind[j]=0; }
else ind[j]+=1;
- double val2=getGridElement(ind,mycomp*(mygrid->getDimension()+1)) - contour;
+ double val2=mygrid->getGridElement(ind,mycomp*(mygrid->getDimension()+1)) - contour;
if( val1*val2<0 ){
// Use initial point location as first guess for search
contour_points[npoints].resize( mygrid->getDimension() );
diff --git a/src/gridtools/GridFunction.cpp b/src/gridtools/GridFunction.cpp
index b4b5a1bd2d9338da9d4ba5af3fe01cc8300c24c5..1e719474bccf4502a8dbb89ae4843e268d9c0b05 100644
--- a/src/gridtools/GridFunction.cpp
+++ b/src/gridtools/GridFunction.cpp
@@ -20,6 +20,7 @@
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
#include "GridFunction.h"
+#include "ActionWithInputGrid.h"
namespace PLMD {
namespace gridtools {
@@ -44,5 +45,16 @@ void GridFunction::finish( const std::vector<double>& buffer ){
for(unsigned i=0;i<data.size();++i) data[i]+=buffer[bufstart + i];
}
+void GridFunction::incorporateRestartDataIntoGrid( const double& old_norm, std::vector<double>& indata ){
+ ActionWithInputGrid* myfunc = dynamic_cast<ActionWithInputGrid*>( getAction() );
+ std::vector<double> pin( nper ), pout( nper );
+ for(unsigned i=0;i<getNumberOfPoints();++i){
+ for(unsigned j=0;j<nper;++j) pin[j]=indata[i*nper+j];
+ myfunc->invertTask( pin, pout );
+ for(unsigned j=0;j<nper;++j) indata[i*nper+j]=pout[j];
+ }
+ (myfunc->mygrid)->incorporateRestartDataIntoGrid( old_norm, indata );
+}
+
}
}
diff --git a/src/gridtools/GridFunction.h b/src/gridtools/GridFunction.h
index 202edf836417ec800c8e9ffaa44e760c19821bb3..308d60cc3b0348c1b8867c5ade9b78e768d7bfbd 100644
--- a/src/gridtools/GridFunction.h
+++ b/src/gridtools/GridFunction.h
@@ -34,6 +34,7 @@ public:
void calculate( const unsigned& current, MultiValue& myvals, std::vector<double>& buffer, std::vector<unsigned>& der_list ) const ;
void finish( const std::vector<double>& );
bool applyForce( std::vector<double>& forces ){ return false; }
+ void incorporateRestartDataIntoGrid( const double& old_norm, std::vector<double>& indata );
};
}
diff --git a/src/gridtools/GridVessel.cpp b/src/gridtools/GridVessel.cpp
index d90fe8650c5605d3fd0b8ecda553a052fad0d557..091c0feed7286b9bd8328af755290bab57ff5d3b 100644
--- a/src/gridtools/GridVessel.cpp
+++ b/src/gridtools/GridVessel.cpp
@@ -32,6 +32,7 @@ void GridVessel::registerKeywords( Keywords& keys ){
keys.add("compulsory","COORDINATES","the names of the coordinates of the grid");
keys.add("compulsory","PBC","is the grid periodic in each direction or not");
keys.addFlag("NOMEMORY",false,"should the data in the grid be deleted after print/analysis");
+ keys.addFlag("UNORMALIZED",false,"don't normalise grid");
}
GridVessel::GridVessel( const vesselbase::VesselOptions& da ):
@@ -40,14 +41,15 @@ noderiv(false),
wascleared(true),
bounds_set(false),
cube_units(1.0),
-naccumulate_grids(1)
+norm(1)
{
std::vector<std::string> compnames; parseVector("COMPONENTS",compnames);
std::vector<std::string> coordnames; parseVector("COORDINATES",coordnames);
dimension=coordnames.size();
std::vector<std::string> spbc( dimension ); parseVector("PBC",spbc);
str_min.resize( dimension); str_max.resize( dimension );
- parseFlag("NOMEMORY",nomemory);
+ parseFlag("NOMEMORY",nomemory); parseFlag("UNORMALIZED",unormalised);
+ foundprint=nomemory;
unsigned n=0; nper=compnames.size()*( 1 + coordnames.size() );
arg_names.resize( coordnames.size() + compnames.size()*( 1 + coordnames.size() ) );
@@ -121,7 +123,7 @@ std::string GridVessel::description(){
void GridVessel::resize(){
plumed_massert( nper>0, "Number of datapoints at each grid point has not been set");
- resizeBuffer( naccumulate_grids*npoints*nper );
+ resizeBuffer( npoints*nper );
if( data.size()!=npoints*nper ){
data.resize( npoints*nper, 0 );
active.resize( npoints, true );
@@ -281,7 +283,7 @@ void GridVessel::getNeighbors( const std::vector<unsigned>& indices, const std::
void GridVessel::reset(){
if( !nomemory ) return ;
- wascleared=true;
+ wascleared=true;
}
void GridVessel::clear(){
diff --git a/src/gridtools/GridVessel.h b/src/gridtools/GridVessel.h
index e3e3fc82a2e8ad3c0ffd6c9c2d45b0b396c04716..58ee3dfc603b7201f52b373687fa3697a0b8ed52 100644
--- a/src/gridtools/GridVessel.h
+++ b/src/gridtools/GridVessel.h
@@ -31,6 +31,8 @@ namespace PLMD {
namespace gridtools {
class GridVessel : public vesselbase::Vessel {
+friend class ActionWithInputGrid;
+friend class PrintGrid;
private:
/// Do we have derivatives
bool noderiv;
@@ -42,8 +44,8 @@ private:
unsigned npoints;
/// Units for Gaussian Cube file
double cube_units;
-/// The names of the various columns in the grid file
- std::vector<std::string> arg_names;
+/// This flag is used to check if the user has created a valid input
+ bool foundprint;
/// The minimum and maximum of the grid stored as doubles
std::vector<double> min, max;
/// The numerical distance between adjacent grid points
@@ -53,13 +55,17 @@ private:
/// The grid point that was requested last by getGridPointCoordinates
unsigned currentGridPoint;
protected:
+/// The names of the various columns in the grid file
+ std::vector<std::string> arg_names;
+/// The normalisation constant to use
+ double norm;
/// Are we deleting the data after print
bool nomemory;
+/// Are we outputting unormalised data
+ bool unormalised;
/// The number of pieces of information we are storing for each
/// point in the grid
unsigned nper;
-/// Number of grids we are accumulating
- unsigned naccumulate_grids;
/// Is this direction periodic
std::vector<bool> pbc;
/// The minimum and maximum in the grid stored as strings
@@ -127,7 +133,7 @@ public:
/// Return the volume of one of the grid cells
double getCellVolume() const ;
/// Get the value of the ith grid element
- double getGridElement( const unsigned&, const unsigned& ) const ;
+ virtual double getGridElement( const unsigned&, const unsigned& ) const ;
/// Get the set of points neighouring a particular location in space
void getNeighbors( const std::vector<double>& pp, const std::vector<unsigned>& nneigh,
unsigned& num_neighbours, std::vector<unsigned>& neighbors ) const ;
@@ -148,8 +154,6 @@ public:
void setCubeUnits( const double& units );
/// This ensures that Gaussian cube files are in correct units
double getCubeUnits() const ;
-/// This gives the normalisation of histograms
- virtual double getNorm() const ;
virtual void switchOffNormalisation(){}
/// Return a string containing the input to the grid so we can clone it
std::string getInputString() const ;
@@ -163,6 +167,11 @@ public:
void activateThesePoints( const std::vector<bool>& to_activate );
/// Is this point active
bool inactive( const unsigned& ip ) const ;
+///
+ virtual void incorporateRestartDataIntoGrid( const double& old_norm, std::vector<double>& indata ) = 0;
+/// Functions for dealing with normalisation constant
+ void setNorm( const double& snorm );
+ double getNorm() const ;
};
inline
@@ -212,11 +221,6 @@ double GridVessel::getGridExtent( const unsigned& i ) const {
return max[i] - min[i];
}
-inline
-double GridVessel::getNorm() const {
- return 1.0;
-}
-
inline
bool GridVessel::noDerivatives() const {
return noderiv;
@@ -233,6 +237,16 @@ bool GridVessel::inactive( const unsigned& ip ) const {
return !active[ip];
}
+inline
+void GridVessel::setNorm( const double& snorm ){
+ norm=snorm;
+}
+
+inline
+double GridVessel::getNorm() const {
+ return norm;
+}
+
}
}
#endif
diff --git a/src/gridtools/HistogramOnGrid.cpp b/src/gridtools/HistogramOnGrid.cpp
index b50527175086d7418f810db85546889809275bd5..1f4473ca44233d2cb94a88438fc1d698c8bde5b7 100644
--- a/src/gridtools/HistogramOnGrid.cpp
+++ b/src/gridtools/HistogramOnGrid.cpp
@@ -30,20 +30,16 @@ void HistogramOnGrid::registerKeywords( Keywords& keys ){
keys.add("compulsory","KERNEL","the type of kernel to use");
keys.add("compulsory","BANDWIDTH","the bandwidths");
keys.addFlag("AVERAGE",false,"are we computed a weighted average over the grid");
- keys.addFlag("STORE_NORMED",false,"are we to store the data normalised");
}
HistogramOnGrid::HistogramOnGrid( const vesselbase::VesselOptions& da ):
GridVessel(da),
-norm(0),
-store_normed(false),
bandwidths(dimension),
discrete(false)
{
- naccumulate_grids=2;
parseFlag("AVERAGE",average);
- parseFlag("STORE_NORMED",store_normed); parse("KERNEL",kerneltype);
+ parse("KERNEL",kerneltype);
if( kerneltype=="discrete" || kerneltype=="DISCRETE" ){
discrete=true; setNoDerivatives();
} else {
@@ -51,10 +47,6 @@ discrete(false)
}
}
-void HistogramOnGrid::switchOffNormalisation(){
- store_normed=false;
-}
-
void HistogramOnGrid::setBounds( const std::vector<std::string>& smin, const std::vector<std::string>& smax,
const std::vector<unsigned>& nbins, const std::vector<double>& spacing ){
GridVessel::setBounds( smin, smax, nbins, spacing );
@@ -73,12 +65,11 @@ void HistogramOnGrid::calculate( const unsigned& current, MultiValue& myvals, st
// Create a kernel function at the point of interest
std::vector<double> point( dimension ); double weight=myvals.get(0)*myvals.get( 1+dimension );
for(unsigned i=0;i<dimension;++i) point[i]=myvals.get( 1+i );
-
+
if( discrete ){
for(unsigned i=0;i<dimension;++i) point[i] += 0.5*dx[i];
- unsigned ipoint = getIndex( point );
- buffer[bufstart + nper*ipoint] += weight;
- buffer[bufstart+nper*(nper+ipoint)] += 1.0;
+ unsigned ipoint = getIndex( point ); std::vector<double> fake_der;
+ accumulate( ipoint, weight, 1.0, fake_der, buffer );
} else {
KernelFunctions kernel( point, bandwidths, kerneltype, false, 1.0, true );
@@ -99,41 +90,31 @@ void HistogramOnGrid::calculate( const unsigned& current, MultiValue& myvals, st
getGridPointCoordinates( ineigh, xx );
for(unsigned j=0;j<dimension;++j) vv[j]->set(xx[j]);
newval = kernel.evaluate( vv, der, true );
- buffer[bufstart+nper*ineigh] += weight*newval;
- for(unsigned j=0;j<dimension;++j) buffer[bufstart+nper*ineigh + 1 + j] += weight*der[j];
- buffer[bufstart+ntot+nper*ineigh] += newval;
- for(unsigned j=0;j<dimension;++j) buffer[bufstart+ntot+nper*ineigh + 1 + j] += newval;
+ accumulate( ineigh, weight, newval, der, buffer );
}
for(unsigned i=0;i<dimension;++i) delete vv[i];
}
return;
}
+void HistogramOnGrid::accumulate( const unsigned& ipoint, const double& weight, const double& dens, const std::vector<double>& der, std::vector<double>& buffer ) const {
+ buffer[bufstart+nper*ipoint] += weight*dens;
+ if( der.size()>0 ) for(unsigned j=0;j<dimension;++j) buffer[bufstart+nper*ipoint + 1 + j] += weight*der[j];
+}
+
+double HistogramOnGrid::getGridElement( const unsigned& ipoint, const unsigned& jelement ) const {
+ if( unormalised ) return GridVessel::getGridElement( ipoint, jelement );
+ return GridVessel::getGridElement( ipoint, jelement ) / norm;
+}
+
void HistogramOnGrid::finish( const std::vector<double>& buffer ){
- if( average ){
- unsigned ntot=nper*getNumberOfPoints();
- for(unsigned i=0;i<getNumberOfPoints();++i){
- double rdenom;
- if( fabs(buffer[bufstart+ntot+nper*i])>epsilon ) rdenom = 1. / buffer[bufstart+ntot+nper*i];
- else rdenom = 1.0;
- data[i*nper] = rdenom * buffer[bufstart+nper*i];
- for(unsigned j=0;j<dimension;++j){
- data[i*nper + 1 + j] += rdenom*buffer[bufstart+nper*i+1+j] - rdenom*rdenom*buffer[bufstart+nper*i]*buffer[bufstart+ntot+nper*i+1+j];
- }
- }
- } else {
- for(unsigned i=0;i<data.size();++i) data[i]+=buffer[bufstart + i];
- }
+ for(unsigned i=0;i<data.size();++i) data[i]+=buffer[bufstart + i];
}
-void HistogramOnGrid::clear(){
- if( !nomemory && !store_normed ) return ;
- if( nomemory ){
- norm = 0.; GridVessel::clear(); return;
- }
- if( norm>0 && store_normed ){
- for(unsigned i=0;i<data.size();++i) data[i] /= norm;
- }
+void HistogramOnGrid::incorporateRestartDataIntoGrid( const double& old_norm, std::vector<double>& indata ){
+ plumed_assert( data.size()==indata.size() );
+ if( unormalised ) for(unsigned i=0;i<data.size();++i) data[i] = old_norm*data[i] + indata[i];
+ else for(unsigned i=0;i<data.size();++i) data[i] += indata[i];
}
}
diff --git a/src/gridtools/HistogramOnGrid.h b/src/gridtools/HistogramOnGrid.h
index a3fa8d913de83bfe2fe5f211a5a434a0ef35e436..af66f50249203d84da9ff20eefbc5d8288d6f633 100644
--- a/src/gridtools/HistogramOnGrid.h
+++ b/src/gridtools/HistogramOnGrid.h
@@ -29,43 +29,25 @@ namespace gridtools {
class HistogramOnGrid : public GridVessel {
private:
- double norm;
bool average;
- bool store_normed;
std::string kerneltype;
std::vector<double> bandwidths;
- bool discrete;
std::vector<unsigned> nneigh;
+protected:
+ bool discrete;
public:
static void registerKeywords( Keywords& keys );
explicit HistogramOnGrid( const vesselbase::VesselOptions& da );
void setBounds( const std::vector<std::string>& smin, const std::vector<std::string>& smax,
const std::vector<unsigned>& nbins, const std::vector<double>& spacing );
void calculate( const unsigned& current, MultiValue& myvals, std::vector<double>& buffer, std::vector<unsigned>& der_list ) const ;
- void finish( const std::vector<double>& );
+ virtual void accumulate( const unsigned& ipoint, const double& weight, const double& dens, const std::vector<double>& der, std::vector<double>& buffer ) const ;
+ virtual void finish( const std::vector<double>& );
+ virtual double getGridElement( const unsigned& ipoint, const unsigned& jelement ) const ;
bool applyForce( std::vector<double>& forces ){ return false; }
- void addToNorm( const double& anorm );
- void setNorm( const double& snorm );
- double getNorm() const ;
- void switchOffNormalisation();
- void clear();
+ void incorporateRestartDataIntoGrid( const double& old_norm, std::vector<double>& indata );
};
-inline
-void HistogramOnGrid::addToNorm( const double& anorm ){
- norm+=anorm;
-}
-
-inline
-void HistogramOnGrid::setNorm( const double& snorm ){
- norm=snorm;
-}
-
-inline
-double HistogramOnGrid::getNorm() const {
- return norm;
-}
-
}
}
#endif
diff --git a/src/gridtools/PrintCube.cpp b/src/gridtools/PrintCube.cpp
index 09b216818b265f55dd943ff46257f948eb279c75..c268c970b03a0265dbe9315ba4f4f531e4ac829f 100644
--- a/src/gridtools/PrintCube.cpp
+++ b/src/gridtools/PrintCube.cpp
@@ -72,16 +72,17 @@ void PrintCube::performOperationsWithGrid( const bool& from_update ){
ofile.printf("PLUMED CUBE FILE\n");
ofile.printf("OUTER LOOP: X, MIDDLE LOOP: Y, INNER LOOP: Z\n");
// Number of atoms followed by position of origin (origin set so that center of grid is in center of cell)
- ofile.printf("%d %f %f %f\n",1,-0.5*lunit*mygrid->getGridExtent(0),-0.5*lunit*mygrid->getGridExtent(1),-0.5*lunit*mygrid->getGridExtent(2));
- ofile.printf("%u %f %f %f\n",mygrid->getNbin()[0],lunit*mygrid->getGridSpacing()[0],0.0,0.0); // Number of bins in each direction followed by
- ofile.printf("%u %f %f %f\n",mygrid->getNbin()[1],0.0,lunit*mygrid->getGridSpacing()[1],0.0); // shape of voxel
- ofile.printf("%u %f %f %f\n",mygrid->getNbin()[2],0.0,0.0,lunit*mygrid->getGridSpacing()[2]);
- ofile.printf("%u %f %f %f\n",1,0.0,0.0,0.0); // Fake atom otherwise VMD doesn't work
+ std::string ostr = "%d" + fmt + fmt + fmt + "\n";
+ ofile.printf(ostr.c_str(),1,-0.5*lunit*mygrid->getGridExtent(0),-0.5*lunit*mygrid->getGridExtent(1),-0.5*lunit*mygrid->getGridExtent(2));
+ ofile.printf(ostr.c_str(),mygrid->getNbin()[0],lunit*mygrid->getGridSpacing()[0],0.0,0.0); // Number of bins in each direction followed by
+ ofile.printf(ostr.c_str(),mygrid->getNbin()[1],0.0,lunit*mygrid->getGridSpacing()[1],0.0); // shape of voxel
+ ofile.printf(ostr.c_str(),mygrid->getNbin()[2],0.0,0.0,lunit*mygrid->getGridSpacing()[2]);
+ ofile.printf(ostr.c_str(),1,0.0,0.0,0.0); // Fake atom otherwise VMD doesn't work
std::vector<unsigned> pp(3); std::vector<unsigned> nbin( mygrid->getNbin() );
for(pp[0]=0;pp[0]<nbin[0];++pp[0]){
for(pp[1]=0;pp[1]<nbin[1];++pp[1]){
for(pp[2]=0;pp[2]<nbin[2];++pp[2]){
- ofile.printf("%f ",getGridElement( pp, 0 ) );
+ ofile.printf(fmt.c_str(),mygrid->getGridElement( pp, 0 ) );
if(pp[2]%6==5) ofile.printf("\n");
}
ofile.printf("\n");
diff --git a/src/gridtools/PrintGrid.cpp b/src/gridtools/PrintGrid.cpp
index 5be56b1a6e51272323cc10fabbb3029e808de288..861e45879a0fe3b6c517845acdbd3a0b95dc96ac 100644
--- a/src/gridtools/PrintGrid.cpp
+++ b/src/gridtools/PrintGrid.cpp
@@ -21,6 +21,7 @@
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
#include "ActionWithInputGrid.h"
#include "core/ActionRegister.h"
+#include "tools/IFile.h"
#include "tools/OFile.h"
namespace PLMD {
@@ -36,6 +37,8 @@ public:
unsigned getNumberOfDerivatives(){ return 0; }
void performTask( const unsigned& , const unsigned& , MultiValue& ) const {}
bool isPeriodic(){ return false; }
+ bool isGridPrint() const { return true; }
+ void readGridFile( IFile& ifile );
};
PLUMED_REGISTER_ACTION(PrintGrid,"PRINT_GRID")
@@ -51,6 +54,8 @@ Action(ao),
ActionWithInputGrid(ao),
fmt("%f")
{
+ // This ensures that restarting of grids works with NOMEMORY
+ mygrid->foundprint=true;
parse("FMT",fmt); fmt=" "+fmt; parse("FILE",filename);
if(filename.length()==0) error("name out output file was not specified");
log.printf(" outputting grid to file named %s with format %s \n",filename.c_str(), fmt.c_str() );
@@ -60,8 +65,19 @@ fmt("%f")
void PrintGrid::performOperationsWithGrid( const bool& from_update ){
if( !from_update && !single_run ) return ;
+
+ // Read in the old grid and ensure that it is considered
+ if( from_update && !mygrid->nomemory ){
+ IFile oldf; oldf.link(*this);
+ if( oldf.FileExist(filename) ){
+ oldf.open(filename);
+ readGridFile( oldf );
+ oldf.close();
+ }
+ }
+
OFile ofile; ofile.link(*this);
- if( from_update ) ofile.setBackupString("analysis");
+ if ( from_update ) ofile.setBackupString("analysis");
ofile.open( filename );
ofile.addConstantField("normalisation");
@@ -72,13 +88,12 @@ void PrintGrid::performOperationsWithGrid( const bool& from_update ){
ofile.addConstantField("periodic_" + mygrid->getComponentName(i) );
}
- double norm = mygrid->getNorm();
std::vector<double> xx( mygrid->getDimension() );
std::vector<unsigned> ind( mygrid->getDimension() );
for(unsigned i=0;i<mygrid->getNumberOfPoints();++i){
mygrid->getIndices( i, ind );
if(i>0 && mygrid->getDimension()==2 && ind[mygrid->getDimension()-2]==0) ofile.printf("\n");
- ofile.fmtField(fmt); ofile.printField("normalisation", norm );
+ ofile.fmtField(fmt); ofile.printField("normalisation", mygrid->norm );
for(unsigned j=0;j<mygrid->getDimension();++j){
ofile.printField("min_" + mygrid->getComponentName(j), mygrid->getMin()[j] );
ofile.printField("max_" + mygrid->getComponentName(j), mygrid->getMax()[j] );
@@ -90,7 +105,7 @@ void PrintGrid::performOperationsWithGrid( const bool& from_update ){
mygrid->getGridPointCoordinates(i, xx );
for(unsigned j=0;j<mygrid->getDimension();++j){ ofile.fmtField(fmt); ofile.printField(mygrid->getComponentName(j),xx[j]); }
for(unsigned j=0;j<mygrid->getNumberOfQuantities();++j){
- ofile.fmtField(fmt); ofile.printField(mygrid->getComponentName(mygrid->getDimension()+j), getGridElement( i, j ) );
+ ofile.fmtField(fmt); ofile.printField(mygrid->arg_names[mygrid->dimension+j], mygrid->getGridElement( i, j ) );
}
ofile.printField();
}
@@ -100,5 +115,49 @@ void PrintGrid::performOperationsWithGrid( const bool& from_update ){
if( from_update ) mygrid->reset();
}
+void PrintGrid::readGridFile( IFile& ifile ){
+ // First check that everything in the file is as expected
+ std::string min; int nb; std::vector<std::string> fieldnames; ifile.scanFieldList( fieldnames );
+ for(unsigned i=0;i<mygrid->dimension;++i){
+ ifile.scanField("min_" + mygrid->arg_names[i], min );
+ if( min!=mygrid->str_min[i] ) error("minimum of grid in restart file does not match stored minimum");
+ ifile.scanField("max_" + mygrid->arg_names[i], min );
+ if( min!=mygrid->str_max[i] ) error("maximum of grid in restart file does not match stored minimum");
+ ifile.scanField("periodic_" + mygrid->arg_names[i], min );
+ if( mygrid->pbc[i] && min!="true" ) error("periodicity of grid in restart file does not match stored periodicity");
+ else if( mygrid->pbc[i] && min!="false" ) error("periodicity of grid in restart file does not match stored periodicity");
+ ifile.scanField("nbins_" + mygrid->arg_names[i], nb );
+ if( mygrid->pbc[i] && nb!=mygrid->nbin[i] ) error("number of bins in restart file does not match stored number of bins");
+ else if( !mygrid->pbc[i] && (nb+1)!=mygrid->nbin[i] ) error("number of bins in restart file does not match stored number of bins");
+ bool found_field=false;
+ for(unsigned j=0;j<fieldnames.size();++j){
+ if( fieldnames[j]==mygrid->arg_names[i] ){ found_field=true; break; }
+ }
+ if( !found_field ) error("missing field " + mygrid->arg_names[i] + " in restart file");
+ }
+ // Check if all the fields we need are there
+ for(unsigned i=0;i<mygrid->arg_names.size();++i){
+ if( !ifile.FieldExist( mygrid->arg_names[i] ) ) error("an expected field is missing from the input grid");
+ }
+ // Now we read in the grid
+ unsigned np=0; std::vector<double> indata( mygrid->npoints*mygrid->nper ); double f, old_norm;
+ while( ifile.scanField(mygrid->arg_names[0],f) ){
+ // Read in coordinates
+ for(unsigned i=1;i<mygrid->dimension;++i) ifile.scanField(mygrid->arg_names[i],f);
+ // Read header
+ ifile.scanField("normalisation", old_norm );
+ for(unsigned i=0;i<mygrid->dimension;++i){
+ ifile.scanField("min_" + mygrid->arg_names[i], min );
+ ifile.scanField("max_" + mygrid->arg_names[i], min );
+ ifile.scanField("periodic_" + mygrid->arg_names[i], min );
+ ifile.scanField("nbins_" + mygrid->arg_names[i], nb );
+ }
+ // Now read data of interest
+ for(unsigned i=mygrid->dimension;i<mygrid->arg_names.size();++i){ ifile.scanField(mygrid->arg_names[i],indata[np]); np++; }
+ ifile.scanField();
+ }
+ mygrid->incorporateRestartDataIntoGrid( old_norm, indata );
+}
+
}
}
diff --git a/src/multicolvar/MultiColvarDensity.cpp b/src/multicolvar/MultiColvarDensity.cpp
index 502dba9388173bfa257c5368f739cb74129b7eec..91a6839d81052052072b98077c706658219417ea 100644
--- a/src/multicolvar/MultiColvarDensity.cpp
+++ b/src/multicolvar/MultiColvarDensity.cpp
@@ -318,7 +318,7 @@ void MultiColvarDensity::update(){
lockContributors();
// Now perform All Tasks
origin = getPosition(0);
- runAllTasks(); mygrid->addToNorm( 1.0 );
+ runAllTasks();
}
void MultiColvarDensity::performTask( const unsigned& tindex, const unsigned& current, MultiValue& myvals ) const {