From 22c8a6ec8354619fa9e85c8d9d72899ae4d6aee3 Mon Sep 17 00:00:00 2001
From: Gareth Tribello <gareth.tribello@gmail.com>
Date: Sat, 7 Apr 2012 16:04:16 +0200
Subject: [PATCH] Added infrastructure for field cvs. In field cv formalism
the bias is an overlap integral between the current field and some reference
field ( this can be a sum of fields visited at previous times ala
metadynamics ). To test the derivatives of the field I changed
calculateNumericalDerivatives this routine can now be passed an
ActionWithValue so that you can differentiate objects where something other
than a value is passed between Actions. Currently only histogram style field
cvs are implemented. Wrote documentation for FIELD keyword and for MOMENT
keyword. Also rethought numbered keywords and so changed the keywords class
a little bit Changed number of decimal places in tests so that they worked on
other computers. Also made test 23 much less expensive Fixed a very
persisent bug in field cvs - horay!!!
---
developer-doc/usingDoxygen.txt | 2 +-
regtest/rt22/colvar1.reference | 10 +-
regtest/rt22/colvar2.reference | 10 +-
regtest/rt22/derivatives1.reference | 3090 +++++++++++++--------------
regtest/rt22/derivatives2.reference | 390 ++--
regtest/rt22/plumed.dat | 8 +-
regtest/rt23/colvar1.reference | 10 +-
regtest/rt23/colvar2.reference | 10 +-
regtest/rt23/derivatives1.reference | 1890 +++-------------
regtest/rt23/derivatives2.reference | 1755 ++-------------
regtest/rt23/plumed.dat | 16 +-
regtest/rt24/Makefile | 1 +
regtest/rt24/config | 3 +
regtest/rt24/derivatives.reference | 151 ++
regtest/rt24/field.1.reference | 208 ++
regtest/rt24/plumed.dat | 6 +
regtest/rt24/trajectory.xyz | 550 +++++
regtest/rt25/derivatives.reference | 390 ++--
regtest/rt25/plumed.dat | 2 +-
src/Action.cpp | 14 +-
src/Action.h | 13 +-
src/ActionAtomistic.cpp | 16 +-
src/ActionAtomistic.h | 4 +-
src/ActionWithArguments.cpp | 14 +-
src/ActionWithArguments.h | 4 +-
src/ActionWithDistribution.cpp | 324 +--
src/ActionWithDistribution.h | 101 +-
src/ActionWithField.cpp | 147 ++
src/ActionWithField.h | 46 +
src/BiasFieldMetadynamics.cpp | 92 +
src/BiasMovingRestraint.cpp | 5 +-
src/ColvarAngle.cpp | 2 +-
src/CubicInterpolation.cpp | 10 +
src/CubicInterpolation.h | 2 +
src/DistributionFunctions.h | 1 +
src/DistributionMoment.cpp | 7 +
src/Field.cpp | 232 ++
src/Field.h | 141 ++
src/GenericDumpField.cpp | 114 +
src/GenericWholeMolecules.cpp | 3 +-
src/Keywords.cpp | 98 +-
src/Keywords.h | 21 +-
src/MultiColvar.cpp | 135 +-
src/MultiColvar.h | 15 +-
src/MultiColvarDistance.cpp | 1 +
user-doc/bibliography.bib | 14 +
46 files changed, 4565 insertions(+), 5513 deletions(-)
create mode 120000 regtest/rt24/Makefile
create mode 100644 regtest/rt24/config
create mode 100644 regtest/rt24/derivatives.reference
create mode 100644 regtest/rt24/field.1.reference
create mode 100644 regtest/rt24/plumed.dat
create mode 100644 regtest/rt24/trajectory.xyz
create mode 100644 src/ActionWithField.cpp
create mode 100644 src/ActionWithField.h
create mode 100644 src/BiasFieldMetadynamics.cpp
create mode 100644 src/Field.cpp
create mode 100644 src/Field.h
create mode 100644 src/GenericDumpField.cpp
diff --git a/developer-doc/usingDoxygen.txt b/developer-doc/usingDoxygen.txt
index f115a9c3c..b5a4928a9 100644
--- a/developer-doc/usingDoxygen.txt
+++ b/developer-doc/usingDoxygen.txt
@@ -63,7 +63,7 @@ the keywords for your new method. These keywords will have one of 5 attributes:
</tr> <tr>
<td> <b> atoms </b> </td> <td> If you are reading a list of atoms after the keyword then you should use this keyword </td>
</tr> <tr>
-<td> <b> numbered </b> </td> <td> If you need to read in a list of similar keywords such as keyword0, keyword1, keyword2... then you must use this option </td>
+<td> <b> numbered </b> </td> <td> If you need to read in a list of similar keywords such as keyword0, keyword1, keyword2... then you must use this option. These keywords will be assumed to be optional. However, you can set them to be atoms or whatever by using reset_style(keyword,newstyle). </td>
</tr> <tr>
<td> <b> nohtml </b> </td> <td> Specifies that the manual information should only appear in the log file on a crash and not in the html version manual. This is used for when there is a special methods for generating the documentation for the keyword in the manual. </td>
</tr>
diff --git a/regtest/rt22/colvar1.reference b/regtest/rt22/colvar1.reference
index 16e703e53..773092c29 100644
--- a/regtest/rt22/colvar1.reference
+++ b/regtest/rt22/colvar1.reference
@@ -1,6 +1,6 @@
#! FIELDS time d1.densityForXin0&0.5
- 0.000000 42.78380
- 0.050000 42.77599
- 0.100000 42.75937
- 0.150000 42.75709
- 0.200000 42.74141
+ 0.000000 42.7838
+ 0.050000 42.7760
+ 0.100000 42.7594
+ 0.150000 42.7571
+ 0.200000 42.7414
diff --git a/regtest/rt22/colvar2.reference b/regtest/rt22/colvar2.reference
index a5dce8b7a..50e1aa8b4 100644
--- a/regtest/rt22/colvar2.reference
+++ b/regtest/rt22/colvar2.reference
@@ -1,6 +1,6 @@
#! FIELDS time c1.averageForYin0&0.5
- 0.000000 1.20277
- 0.050000 1.20462
- 0.100000 1.21685
- 0.150000 1.20687
- 0.200000 1.14994
+ 0.000000 1.2028
+ 0.050000 1.2046
+ 0.100000 1.2169
+ 0.150000 1.2069
+ 0.200000 1.1499
diff --git a/regtest/rt22/derivatives1.reference b/regtest/rt22/derivatives1.reference
index 7ee426347..6a255c3ac 100644
--- a/regtest/rt22/derivatives1.reference
+++ b/regtest/rt22/derivatives1.reference
@@ -1,1546 +1,1546 @@
#! FIELDS time parameter d1.densityForXin0&0.5 d1n.densityForXin0&0.5
- 0.000000 0 0.20051 0.20051
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- 0.000000 2 0.00000 0.00000
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+ 0.200000 0 0.2040 0.2040
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+ 0.200000 10 0.0000 0.0000
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+ 0.200000 16 0.0000 0.0000
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+ 0.200000 25 0.0000 0.0000
+ 0.200000 26 0.0000 0.0000
+ 0.200000 27 0.1371 0.1371
+ 0.200000 28 0.0000 0.0000
+ 0.200000 29 0.0000 0.0000
+ 0.200000 30 0.0387 0.0387
+ 0.200000 31 0.0000 0.0000
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+ 0.200000 33 0.1863 0.1863
+ 0.200000 34 0.0000 0.0000
+ 0.200000 35 0.0000 0.0000
+ 0.200000 36 0.1776 0.1776
+ 0.200000 37 0.0000 0.0000
+ 0.200000 38 0.0000 0.0000
+ 0.200000 39 0.0924 0.0924
+ 0.200000 40 0.0000 0.0000
+ 0.200000 41 0.0000 0.0000
+ 0.200000 42 0.0645 0.0645
+ 0.200000 43 0.0000 0.0000
+ 0.200000 44 0.0000 0.0000
+ 0.200000 45 0.1906 0.1906
+ 0.200000 46 0.0000 0.0000
+ 0.200000 47 0.0000 0.0000
+ 0.200000 48 0.2103 0.2103
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+ 0.200000 51 0.0903 0.0903
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+ 0.200000 53 0.0000 0.0000
+ 0.200000 54 0.0877 0.0877
+ 0.200000 55 0.0000 0.0000
+ 0.200000 56 0.0000 0.0000
+ 0.200000 57 0.1998 0.1998
+ 0.200000 58 0.0000 0.0000
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+ 0.200000 60 0.1821 0.1821
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+ 0.200000 63 0.0663 0.0663
+ 0.200000 64 0.0000 0.0000
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+ 0.200000 69 0.1940 0.1940
+ 0.200000 70 0.0000 0.0000
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+ 0.200000 72 0.1798 0.1798
+ 0.200000 73 0.0000 0.0000
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+ 0.200000 78 0.0978 0.0978
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+ 0.200000 87 0.0728 0.0728
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+ 0.200000 93 0.1967 0.1967
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+ 0.200000 99 0.0817 0.0817
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+ 0.200000 102 0.0814 0.0814
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+ 0.200000 104 0.0000 0.0000
+ 0.200000 105 0.1997 0.1997
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+ 0.200000 108 -0.0627 -0.0627
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+ 0.200000 111 -0.1878 -0.1878
+ 0.200000 112 0.0000 0.0000
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+ 0.200000 114 -0.2086 -0.2086
+ 0.200000 115 0.0000 0.0000
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+ 0.200000 117 -0.1346 -0.1346
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+ 0.200000 120 -0.0828 -0.0828
+ 0.200000 121 0.0000 0.0000
+ 0.200000 122 0.0000 0.0000
+ 0.200000 123 -0.1900 -0.1900
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+ 0.200000 125 0.0000 0.0000
+ 0.200000 126 -0.1970 -0.1970
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+ 0.200000 128 0.0000 0.0000
+ 0.200000 129 -0.1234 -0.1234
+ 0.200000 130 0.0000 0.0000
+ 0.200000 131 0.0000 0.0000
+ 0.200000 132 -0.1095 -0.1095
+ 0.200000 133 0.0000 0.0000
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+ 0.200000 135 -0.2084 -0.2084
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+ 0.200000 137 0.0000 0.0000
+ 0.200000 138 -0.2008 -0.2008
+ 0.200000 139 0.0000 0.0000
+ 0.200000 140 0.0000 0.0000
+ 0.200000 141 -0.0765 -0.0765
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+ 0.200000 144 -0.0917 -0.0917
+ 0.200000 145 0.0000 0.0000
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+ 0.200000 147 -0.2090 -0.2090
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+ 0.200000 156 -0.1028 -0.1028
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+ 0.200000 165 -0.0999 -0.0999
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+ 0.200000 172 0.0000 0.0000
+ 0.200000 173 0.0000 0.0000
+ 0.200000 174 -0.1962 -0.1962
+ 0.200000 175 0.0000 0.0000
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+ 0.200000 177 -0.0805 -0.0805
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+ 0.200000 180 -0.0714 -0.0714
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+ 0.200000 182 0.0000 0.0000
+ 0.200000 183 -0.2002 -0.2002
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+ 0.200000 186 -0.2074 -0.2074
+ 0.200000 187 0.0000 0.0000
+ 0.200000 188 0.0000 0.0000
+ 0.200000 189 -0.0873 -0.0873
+ 0.200000 190 0.0000 0.0000
+ 0.200000 191 0.0000 0.0000
+ 0.200000 192 -0.0467 -0.0467
+ 0.200000 193 0.0000 0.0000
+ 0.200000 194 0.0000 0.0000
+ 0.200000 195 -0.2065 -0.2065
+ 0.200000 196 0.0000 0.0000
+ 0.200000 197 0.0000 0.0000
+ 0.200000 198 -0.1744 -0.1744
+ 0.200000 199 0.0000 0.0000
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+ 0.200000 204 -0.0991 -0.0991
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+ 0.200000 206 0.0000 0.0000
+ 0.200000 207 -0.1994 -0.1994
+ 0.200000 208 0.0000 0.0000
+ 0.200000 209 0.0000 0.0000
+ 0.200000 210 -0.2033 -0.2033
+ 0.200000 211 0.0000 0.0000
+ 0.200000 212 0.0000 0.0000
+ 0.200000 213 -0.0661 -0.0661
+ 0.200000 214 0.0000 0.0000
+ 0.200000 215 0.0000 0.0000
+ 0.200000 216 -0.2009 -0.2009
+ 0.200000 217 0.0000 0.0000
+ 0.200000 218 0.0000 0.0000
+ 0.200000 219 -0.1385 -0.1385
+ 0.200000 220 0.0000 0.0000
+ 0.200000 221 0.0000 0.0000
+ 0.200000 222 -0.1309 -0.1309
+ 0.200000 223 0.0000 0.0000
+ 0.200000 224 0.0000 0.0000
+ 0.200000 225 -0.1945 -0.1945
+ 0.200000 226 0.0000 0.0000
+ 0.200000 227 0.0000 0.0000
+ 0.200000 228 -0.2049 -0.2049
+ 0.200000 229 0.0000 0.0000
+ 0.200000 230 0.0000 0.0000
+ 0.200000 231 -0.1318 -0.1318
+ 0.200000 232 0.0000 0.0000
+ 0.200000 233 0.0000 0.0000
+ 0.200000 234 -0.1433 -0.1433
+ 0.200000 235 0.0000 0.0000
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+ 0.200000 237 -0.2140 -0.2140
+ 0.200000 238 0.0000 0.0000
+ 0.200000 239 0.0000 0.0000
+ 0.200000 240 -0.2022 -0.2022
+ 0.200000 241 0.0000 0.0000
+ 0.200000 242 0.0000 0.0000
+ 0.200000 243 -0.1319 -0.1319
+ 0.200000 244 0.0000 0.0000
+ 0.200000 245 0.0000 0.0000
+ 0.200000 246 -0.1282 -0.1282
+ 0.200000 247 0.0000 0.0000
+ 0.200000 248 0.0000 0.0000
+ 0.200000 249 -0.2019 -0.2019
+ 0.200000 250 0.0000 0.0000
+ 0.200000 251 0.0000 0.0000
+ 0.200000 252 -0.2021 -0.2021
+ 0.200000 253 0.0000 0.0000
+ 0.200000 254 0.0000 0.0000
+ 0.200000 255 -0.1353 -0.1353
+ 0.200000 256 0.0000 0.0000
+ 0.200000 257 0.0000 0.0000
+ 0.200000 258 -0.1263 -0.1263
+ 0.200000 259 0.0000 0.0000
+ 0.200000 260 0.0000 0.0000
+ 0.200000 261 -0.2018 -0.2018
+ 0.200000 262 0.0000 0.0000
+ 0.200000 263 0.0000 0.0000
+ 0.200000 264 -0.2000 -0.2000
+ 0.200000 265 0.0000 0.0000
+ 0.200000 266 0.0000 0.0000
+ 0.200000 267 -0.1380 -0.1380
+ 0.200000 268 0.0000 0.0000
+ 0.200000 269 0.0000 0.0000
+ 0.200000 270 -0.1394 -0.1394
+ 0.200000 271 0.0000 0.0000
+ 0.200000 272 0.0000 0.0000
+ 0.200000 273 -0.2027 -0.2027
+ 0.200000 274 0.0000 0.0000
+ 0.200000 275 0.0000 0.0000
+ 0.200000 276 -0.2077 -0.2077
+ 0.200000 277 0.0000 0.0000
+ 0.200000 278 0.0000 0.0000
+ 0.200000 279 -0.1349 -0.1349
+ 0.200000 280 0.0000 0.0000
+ 0.200000 281 0.0000 0.0000
+ 0.200000 282 -0.1362 -0.1362
+ 0.200000 283 0.0000 0.0000
+ 0.200000 284 0.0000 0.0000
+ 0.200000 285 -0.2073 -0.2073
+ 0.200000 286 0.0000 0.0000
+ 0.200000 287 0.0000 0.0000
+ 0.200000 288 -0.2020 -0.2020
+ 0.200000 289 0.0000 0.0000
+ 0.200000 290 0.0000 0.0000
+ 0.200000 291 -0.1248 -0.1248
+ 0.200000 292 0.0000 0.0000
+ 0.200000 293 0.0000 0.0000
+ 0.200000 294 -0.1429 -0.1429
+ 0.200000 295 0.0000 0.0000
+ 0.200000 296 0.0000 0.0000
+ 0.200000 297 -0.2069 -0.2069
+ 0.200000 298 0.0000 0.0000
+ 0.200000 299 0.0000 0.0000
+ 0.200000 300 0.0000 0.0000
+ 0.200000 301 0.0000 0.0000
+ 0.200000 302 0.0000 0.0000
+ 0.200000 303 0.0000 0.0000
+ 0.200000 304 0.0000 0.0000
+ 0.200000 305 0.0000 0.0000
+ 0.200000 306 0.0000 0.0000
+ 0.200000 307 0.0000 0.0000
+ 0.200000 308 0.0000 0.0000
diff --git a/regtest/rt22/derivatives2.reference b/regtest/rt22/derivatives2.reference
index 7fc41a7fa..75c1febb2 100644
--- a/regtest/rt22/derivatives2.reference
+++ b/regtest/rt22/derivatives2.reference
@@ -1,196 +1,196 @@
#! FIELDS time parameter c1.averageForYin0&0.5 c1n.averageForYin0&0.5
- 0.000000 0 0.32997 0.32997
- 0.000000 1 0.26051 0.26051
- 0.000000 2 0.11018 0.11018
- 0.000000 3 -0.31683 -0.31683
- 0.000000 4 0.43332 0.43332
- 0.000000 5 0.02233 0.02233
- 0.000000 6 -0.39241 -0.39241
- 0.000000 7 -0.41101 -0.41101
- 0.000000 8 0.29341 0.29341
- 0.000000 9 0.53208 0.53208
- 0.000000 10 -0.45103 -0.45103
- 0.000000 11 0.00418 0.00418
- 0.000000 12 0.37492 0.37492
- 0.000000 13 0.48295 0.48295
- 0.000000 14 0.00993 0.00993
- 0.000000 15 -0.35195 -0.35195
- 0.000000 16 0.30035 0.30035
- 0.000000 17 -0.20528 -0.20528
- 0.000000 18 -0.51512 -0.51512
- 0.000000 19 -0.46633 -0.46633
- 0.000000 20 -0.04610 -0.04610
- 0.000000 21 0.33835 0.33835
- 0.000000 22 -0.45197 -0.45197
- 0.000000 23 -0.20602 -0.20602
- 0.000000 24 0.19281 0.19281
- 0.000000 25 0.08587 0.08587
- 0.000000 26 -0.14794 -0.14794
- 0.000000 27 -0.19182 -0.19182
- 0.000000 28 0.07283 0.07283
- 0.000000 29 0.16531 0.16531
- 0.000000 30 1.52170 1.52170
- 0.000000 31 0.00825 0.00824
- 0.000000 32 -0.18838 -0.18839
- 0.000000 33 0.00825 0.00825
- 0.000000 34 1.48433 1.48433
- 0.000000 35 -0.03733 -0.03732
- 0.000000 36 -0.18838 0.29215
- 0.000000 37 -0.03733 -0.75155
- 0.000000 38 2.41192 2.41192
- 0.050000 0 0.31002 0.31002
- 0.050000 1 0.24472 0.24472
- 0.050000 2 0.08968 0.08968
- 0.050000 3 -0.30319 -0.30319
- 0.050000 4 0.41152 0.41152
- 0.050000 5 0.03059 0.03059
- 0.050000 6 -0.40544 -0.40544
- 0.050000 7 -0.38164 -0.38164
- 0.050000 8 0.32367 0.32367
- 0.050000 9 0.51810 0.51810
- 0.050000 10 -0.45606 -0.45605
- 0.050000 11 -0.00085 -0.00085
- 0.050000 12 0.38791 0.38791
- 0.050000 13 0.48775 0.48775
- 0.050000 14 0.01830 0.01830
- 0.050000 15 -0.35806 -0.35806
- 0.050000 16 0.30984 0.30984
- 0.050000 17 -0.24293 -0.24293
- 0.050000 18 -0.48351 -0.48351
- 0.050000 19 -0.47840 -0.47840
- 0.050000 20 -0.05595 -0.05595
- 0.050000 21 0.33000 0.33000
- 0.050000 22 -0.44889 -0.44889
- 0.050000 23 -0.17428 -0.17428
- 0.050000 24 0.18641 0.18641
- 0.050000 25 0.08062 0.08062
- 0.050000 26 -0.15279 -0.15279
- 0.050000 27 -0.18224 -0.18224
- 0.050000 28 0.05785 0.05785
- 0.050000 29 0.16456 0.16456
- 0.050000 30 1.54417 1.54417
- 0.050000 31 0.00915 0.00915
- 0.050000 32 -0.18896 -0.18896
- 0.050000 33 0.00915 0.00915
- 0.050000 34 1.42736 1.42736
- 0.050000 35 -0.07372 -0.07372
- 0.050000 36 -0.18896 0.27093
- 0.050000 37 -0.07372 -0.70064
- 0.050000 38 2.38255 2.38255
- 0.100000 0 0.29613 0.29613
- 0.100000 1 0.26067 0.26067
- 0.100000 2 0.09590 0.09590
- 0.100000 3 -0.30410 -0.30410
- 0.100000 4 0.39866 0.39867
- 0.100000 5 0.05801 0.05801
- 0.100000 6 -0.38862 -0.38862
- 0.100000 7 -0.36685 -0.36685
- 0.100000 8 0.31495 0.31495
- 0.100000 9 0.48491 0.48491
- 0.100000 10 -0.47230 -0.47230
- 0.100000 11 0.03641 0.03641
- 0.100000 12 0.40737 0.40737
- 0.100000 13 0.54916 0.54915
- 0.100000 14 0.01147 0.01147
- 0.100000 15 -0.35013 -0.35013
- 0.100000 16 0.29352 0.29352
- 0.100000 17 -0.29043 -0.29043
- 0.100000 18 -0.47506 -0.47506
- 0.100000 19 -0.51172 -0.51173
- 0.100000 20 -0.05901 -0.05901
- 0.100000 21 0.33620 0.33620
- 0.100000 22 -0.41875 -0.41875
- 0.100000 23 -0.21299 -0.21299
- 0.100000 24 0.17066 0.17066
- 0.100000 25 0.04043 0.04043
- 0.100000 26 -0.11197 -0.11197
- 0.100000 27 -0.17737 -0.17737
- 0.100000 28 0.05180 0.05180
- 0.100000 29 0.15767 0.15767
- 0.100000 30 1.58855 1.58855
- 0.100000 31 0.01296 0.01297
- 0.100000 32 -0.16631 -0.16631
- 0.100000 33 0.01296 0.01296
- 0.100000 34 1.34539 1.34539
- 0.100000 35 -0.06269 -0.06269
- 0.100000 36 -0.16631 0.26924
- 0.100000 37 -0.06269 -0.64138
- 0.100000 38 2.40100 2.40100
- 0.150000 0 0.26899 0.26900
- 0.150000 1 0.27406 0.27406
- 0.150000 2 0.10245 0.10245
- 0.150000 3 -0.29931 -0.29931
- 0.150000 4 0.40316 0.40316
- 0.150000 5 0.09051 0.09051
- 0.150000 6 -0.34487 -0.34487
- 0.150000 7 -0.33101 -0.33101
- 0.150000 8 0.29621 0.29621
- 0.150000 9 0.43377 0.43377
- 0.150000 10 -0.46692 -0.46692
- 0.150000 11 0.07721 0.07721
- 0.150000 12 0.41137 0.41137
- 0.150000 13 0.55341 0.55341
- 0.150000 14 0.00787 0.00787
- 0.150000 15 -0.33175 -0.33175
- 0.150000 16 0.25530 0.25530
- 0.150000 17 -0.32181 -0.32181
- 0.150000 18 -0.45369 -0.45369
- 0.150000 19 -0.52957 -0.52957
- 0.150000 20 -0.07008 -0.07008
- 0.150000 21 0.32118 0.32118
- 0.150000 22 -0.39423 -0.39423
- 0.150000 23 -0.24879 -0.24879
- 0.150000 24 0.15556 0.15556
- 0.150000 25 0.01372 0.01372
- 0.150000 26 -0.07718 -0.07718
- 0.150000 27 -0.16125 -0.16125
- 0.150000 28 0.04967 0.04967
- 0.150000 29 0.14361 0.14361
- 0.150000 30 1.57593 1.57593
- 0.150000 31 0.00140 0.00140
- 0.150000 32 -0.14317 -0.14317
- 0.150000 33 0.00140 0.00140
- 0.150000 34 1.23115 1.23115
- 0.150000 35 -0.02869 -0.02869
- 0.150000 36 -0.14317 0.23439
- 0.150000 37 -0.02869 -0.56633
- 0.150000 38 2.38011 2.38011
- 0.200000 0 0.24456 0.24456
- 0.200000 1 0.30225 0.30225
- 0.200000 2 0.10675 0.10675
- 0.200000 3 -0.27962 -0.27962
- 0.200000 4 0.40471 0.40471
- 0.200000 5 0.08791 0.08791
- 0.200000 6 -0.30969 -0.30970
- 0.200000 7 -0.29486 -0.29486
- 0.200000 8 0.28600 0.28600
- 0.200000 9 0.38960 0.38960
- 0.200000 10 -0.45736 -0.45736
- 0.200000 11 0.07117 0.07117
- 0.200000 12 0.38927 0.38927
- 0.200000 13 0.52110 0.52110
- 0.200000 14 0.01828 0.01828
- 0.200000 15 -0.33162 -0.33162
- 0.200000 16 0.22884 0.22884
- 0.200000 17 -0.32839 -0.32839
- 0.200000 18 -0.40913 -0.40913
- 0.200000 19 -0.52221 -0.52221
- 0.200000 20 -0.05924 -0.05924
- 0.200000 21 0.30555 0.30554
- 0.200000 22 -0.38550 -0.38550
- 0.200000 23 -0.25856 -0.25856
- 0.200000 24 0.14477 0.14477
- 0.200000 25 0.01449 0.01449
- 0.200000 26 -0.05091 -0.05091
- 0.200000 27 -0.14368 -0.14369
- 0.200000 28 0.05035 0.05035
- 0.200000 29 0.12699 0.12699
- 0.200000 30 1.50819 1.50819
- 0.200000 31 -0.00764 -0.00766
- 0.200000 32 -0.12301 -0.12300
- 0.200000 33 -0.00764 -0.00764
- 0.200000 34 1.19154 1.19154
- 0.200000 35 0.00584 0.00584
- 0.200000 36 -0.12301 0.18916
- 0.200000 37 0.00584 -0.48461
- 0.200000 38 2.27687 2.27687
+ 0.000000 0 0.3300 0.3300
+ 0.000000 1 0.2605 0.2605
+ 0.000000 2 0.1102 0.1102
+ 0.000000 3 -0.3168 -0.3168
+ 0.000000 4 0.4333 0.4333
+ 0.000000 5 0.0223 0.0223
+ 0.000000 6 -0.3924 -0.3924
+ 0.000000 7 -0.4110 -0.4110
+ 0.000000 8 0.2934 0.2934
+ 0.000000 9 0.5321 0.5321
+ 0.000000 10 -0.4510 -0.4510
+ 0.000000 11 0.0042 0.0042
+ 0.000000 12 0.3749 0.3749
+ 0.000000 13 0.4829 0.4829
+ 0.000000 14 0.0099 0.0099
+ 0.000000 15 -0.3519 -0.3519
+ 0.000000 16 0.3003 0.3003
+ 0.000000 17 -0.2053 -0.2053
+ 0.000000 18 -0.5151 -0.5151
+ 0.000000 19 -0.4663 -0.4663
+ 0.000000 20 -0.0461 -0.0461
+ 0.000000 21 0.3383 0.3383
+ 0.000000 22 -0.4520 -0.4520
+ 0.000000 23 -0.2060 -0.2060
+ 0.000000 24 0.1928 0.1928
+ 0.000000 25 0.0859 0.0859
+ 0.000000 26 -0.1479 -0.1479
+ 0.000000 27 -0.1918 -0.1918
+ 0.000000 28 0.0728 0.0728
+ 0.000000 29 0.1653 0.1653
+ 0.000000 30 1.5217 1.5217
+ 0.000000 31 0.0082 0.0082
+ 0.000000 32 -0.1884 -0.1884
+ 0.000000 33 0.0082 0.0082
+ 0.000000 34 1.4843 1.4843
+ 0.000000 35 -0.0373 -0.0373
+ 0.000000 36 -0.1884 0.2921
+ 0.000000 37 -0.0373 -0.7516
+ 0.000000 38 2.4119 2.4119
+ 0.050000 0 0.3100 0.3100
+ 0.050000 1 0.2447 0.2447
+ 0.050000 2 0.0897 0.0897
+ 0.050000 3 -0.3032 -0.3032
+ 0.050000 4 0.4115 0.4115
+ 0.050000 5 0.0306 0.0306
+ 0.050000 6 -0.4054 -0.4054
+ 0.050000 7 -0.3816 -0.3816
+ 0.050000 8 0.3237 0.3237
+ 0.050000 9 0.5181 0.5181
+ 0.050000 10 -0.4561 -0.4561
+ 0.050000 11 -0.0009 -0.0009
+ 0.050000 12 0.3879 0.3879
+ 0.050000 13 0.4877 0.4877
+ 0.050000 14 0.0183 0.0183
+ 0.050000 15 -0.3581 -0.3581
+ 0.050000 16 0.3098 0.3098
+ 0.050000 17 -0.2429 -0.2429
+ 0.050000 18 -0.4835 -0.4835
+ 0.050000 19 -0.4784 -0.4784
+ 0.050000 20 -0.0559 -0.0559
+ 0.050000 21 0.3300 0.3300
+ 0.050000 22 -0.4489 -0.4489
+ 0.050000 23 -0.1743 -0.1743
+ 0.050000 24 0.1864 0.1864
+ 0.050000 25 0.0806 0.0806
+ 0.050000 26 -0.1528 -0.1528
+ 0.050000 27 -0.1822 -0.1822
+ 0.050000 28 0.0578 0.0578
+ 0.050000 29 0.1646 0.1646
+ 0.050000 30 1.5442 1.5442
+ 0.050000 31 0.0091 0.0092
+ 0.050000 32 -0.1890 -0.1890
+ 0.050000 33 0.0091 0.0091
+ 0.050000 34 1.4274 1.4274
+ 0.050000 35 -0.0737 -0.0737
+ 0.050000 36 -0.1890 0.2709
+ 0.050000 37 -0.0737 -0.7006
+ 0.050000 38 2.3825 2.3825
+ 0.100000 0 0.2961 0.2961
+ 0.100000 1 0.2607 0.2607
+ 0.100000 2 0.0959 0.0959
+ 0.100000 3 -0.3041 -0.3041
+ 0.100000 4 0.3987 0.3987
+ 0.100000 5 0.0580 0.0580
+ 0.100000 6 -0.3886 -0.3886
+ 0.100000 7 -0.3669 -0.3669
+ 0.100000 8 0.3150 0.3149
+ 0.100000 9 0.4849 0.4849
+ 0.100000 10 -0.4723 -0.4723
+ 0.100000 11 0.0364 0.0364
+ 0.100000 12 0.4074 0.4074
+ 0.100000 13 0.5492 0.5492
+ 0.100000 14 0.0115 0.0115
+ 0.100000 15 -0.3501 -0.3501
+ 0.100000 16 0.2935 0.2935
+ 0.100000 17 -0.2904 -0.2904
+ 0.100000 18 -0.4751 -0.4751
+ 0.100000 19 -0.5117 -0.5117
+ 0.100000 20 -0.0590 -0.0590
+ 0.100000 21 0.3362 0.3362
+ 0.100000 22 -0.4187 -0.4187
+ 0.100000 23 -0.2130 -0.2130
+ 0.100000 24 0.1707 0.1707
+ 0.100000 25 0.0404 0.0404
+ 0.100000 26 -0.1120 -0.1120
+ 0.100000 27 -0.1774 -0.1774
+ 0.100000 28 0.0518 0.0518
+ 0.100000 29 0.1577 0.1577
+ 0.100000 30 1.5886 1.5886
+ 0.100000 31 0.0130 0.0130
+ 0.100000 32 -0.1663 -0.1663
+ 0.100000 33 0.0130 0.0130
+ 0.100000 34 1.3454 1.3454
+ 0.100000 35 -0.0627 -0.0627
+ 0.100000 36 -0.1663 0.2692
+ 0.100000 37 -0.0627 -0.6414
+ 0.100000 38 2.4010 2.4010
+ 0.150000 0 0.2690 0.2690
+ 0.150000 1 0.2741 0.2741
+ 0.150000 2 0.1024 0.1024
+ 0.150000 3 -0.2993 -0.2993
+ 0.150000 4 0.4032 0.4032
+ 0.150000 5 0.0905 0.0905
+ 0.150000 6 -0.3449 -0.3449
+ 0.150000 7 -0.3310 -0.3310
+ 0.150000 8 0.2962 0.2962
+ 0.150000 9 0.4338 0.4338
+ 0.150000 10 -0.4669 -0.4669
+ 0.150000 11 0.0772 0.0772
+ 0.150000 12 0.4114 0.4114
+ 0.150000 13 0.5534 0.5534
+ 0.150000 14 0.0079 0.0079
+ 0.150000 15 -0.3318 -0.3318
+ 0.150000 16 0.2553 0.2553
+ 0.150000 17 -0.3218 -0.3218
+ 0.150000 18 -0.4537 -0.4537
+ 0.150000 19 -0.5296 -0.5296
+ 0.150000 20 -0.0701 -0.0701
+ 0.150000 21 0.3212 0.3212
+ 0.150000 22 -0.3942 -0.3942
+ 0.150000 23 -0.2488 -0.2488
+ 0.150000 24 0.1556 0.1556
+ 0.150000 25 0.0137 0.0137
+ 0.150000 26 -0.0772 -0.0772
+ 0.150000 27 -0.1613 -0.1613
+ 0.150000 28 0.0497 0.0497
+ 0.150000 29 0.1436 0.1436
+ 0.150000 30 1.5759 1.5759
+ 0.150000 31 0.0014 0.0014
+ 0.150000 32 -0.1432 -0.1432
+ 0.150000 33 0.0014 0.0014
+ 0.150000 34 1.2312 1.2312
+ 0.150000 35 -0.0287 -0.0287
+ 0.150000 36 -0.1432 0.2344
+ 0.150000 37 -0.0287 -0.5663
+ 0.150000 38 2.3801 2.3801
+ 0.200000 0 0.2446 0.2446
+ 0.200000 1 0.3022 0.3022
+ 0.200000 2 0.1068 0.1068
+ 0.200000 3 -0.2796 -0.2796
+ 0.200000 4 0.4047 0.4047
+ 0.200000 5 0.0879 0.0879
+ 0.200000 6 -0.3097 -0.3097
+ 0.200000 7 -0.2949 -0.2949
+ 0.200000 8 0.2860 0.2860
+ 0.200000 9 0.3896 0.3896
+ 0.200000 10 -0.4574 -0.4574
+ 0.200000 11 0.0712 0.0712
+ 0.200000 12 0.3893 0.3893
+ 0.200000 13 0.5211 0.5211
+ 0.200000 14 0.0183 0.0183
+ 0.200000 15 -0.3316 -0.3316
+ 0.200000 16 0.2288 0.2288
+ 0.200000 17 -0.3284 -0.3284
+ 0.200000 18 -0.4091 -0.4091
+ 0.200000 19 -0.5222 -0.5222
+ 0.200000 20 -0.0592 -0.0592
+ 0.200000 21 0.3055 0.3055
+ 0.200000 22 -0.3855 -0.3855
+ 0.200000 23 -0.2586 -0.2586
+ 0.200000 24 0.1448 0.1448
+ 0.200000 25 0.0145 0.0145
+ 0.200000 26 -0.0509 -0.0509
+ 0.200000 27 -0.1437 -0.1437
+ 0.200000 28 0.0504 0.0504
+ 0.200000 29 0.1270 0.1270
+ 0.200000 30 1.5082 1.5082
+ 0.200000 31 -0.0076 -0.0077
+ 0.200000 32 -0.1230 -0.1230
+ 0.200000 33 -0.0076 -0.0076
+ 0.200000 34 1.1915 1.1915
+ 0.200000 35 0.0058 0.0058
+ 0.200000 36 -0.1230 0.1892
+ 0.200000 37 0.0058 -0.4846
+ 0.200000 38 2.2769 2.2769
diff --git a/regtest/rt22/plumed.dat b/regtest/rt22/plumed.dat
index 66b157240..4070fea14 100644
--- a/regtest/rt22/plumed.dat
+++ b/regtest/rt22/plumed.dat
@@ -1,9 +1,9 @@
DENSITY SPECIES=1-100 SUBCELL=(XLOWER=0.0 XUPPER=0.5 XSMEAR=0.6) LABEL=d1
DENSITY SPECIES=1-100 SUBCELL=(XLOWER=0.0 XUPPER=0.5 XSMEAR=0.6) NUMERICAL_DERIVATIVES LABEL=d1n
-PRINT ARG=d1.* FILE=colvar1 FMT=%8.5f
-DUMPDERIVATIVES ARG=d1.*,d1n.* FILE=derivatives1 FMT=%8.5f
+PRINT ARG=d1.* FILE=colvar1 FMT=%8.4f
+DUMPDERIVATIVES ARG=d1.*,d1n.* FILE=derivatives1 FMT=%8.4f
COORDINATIONNUMBER SPECIES=1-10 SWITCH=(SPLINE R_0=1.0) SUBCELL=(YLOWER=0.0 YUPPER=0.5 YSMEAR=0.1) LABEL=c1
COORDINATIONNUMBER SPECIES=1-10 SWITCH=(SPLINE R_0=1.0) SUBCELL=(YLOWER=0.0 YUPPER=0.5 YSMEAR=0.1) NUMERICAL_DERIVATIVES LABEL=c1n
-PRINT ARG=c1.* FILE=colvar2 FMT=%8.5f
-DUMPDERIVATIVES ARG=c1.*,c1n.* FILE=derivatives2 FMT=%8.5f
+PRINT ARG=c1.* FILE=colvar2 FMT=%8.4f
+DUMPDERIVATIVES ARG=c1.*,c1n.* FILE=derivatives2 FMT=%8.4f
diff --git a/regtest/rt23/colvar1.reference b/regtest/rt23/colvar1.reference
index 07b30e6fb..fd839f03b 100644
--- a/regtest/rt23/colvar1.reference
+++ b/regtest/rt23/colvar1.reference
@@ -1,6 +1,6 @@
#! FIELDS time d1.gradient
- 0.000000 568.93092
- 0.050000 533.40518
- 0.100000 503.32957
- 0.150000 487.12517
- 0.200000 476.74393
+ 0.000000 85.4991
+ 0.050000 83.8139
+ 0.100000 78.8883
+ 0.150000 73.9544
+ 0.200000 70.7225
diff --git a/regtest/rt23/colvar2.reference b/regtest/rt23/colvar2.reference
index d318a3bfc..e328ec2a7 100644
--- a/regtest/rt23/colvar2.reference
+++ b/regtest/rt23/colvar2.reference
@@ -1,6 +1,6 @@
#! FIELDS time c1.xgradient
- 0.000000 0.13347
- 0.050000 0.16157
- 0.100000 0.15456
- 0.150000 0.15440
- 0.200000 0.17695
+ 0.000000 0.0869
+ 0.050000 0.1188
+ 0.100000 0.0878
+ 0.150000 0.0752
+ 0.200000 0.1032
diff --git a/regtest/rt23/derivatives1.reference b/regtest/rt23/derivatives1.reference
index e537abba5..a7fa9f45d 100644
--- a/regtest/rt23/derivatives1.reference
+++ b/regtest/rt23/derivatives1.reference
@@ -1,1546 +1,346 @@
#! FIELDS time parameter d1.gradient d1n.gradient
- 0.000000 0 22.96772 22.96773
- 0.000000 1 20.20660 20.20660
- 0.000000 2 20.67703 20.67703
- 0.000000 3 -33.05842 -33.05842
- 0.000000 4 20.23349 20.23349
- 0.000000 5 -31.76646 -31.76646
- 0.000000 6 -30.37437 -30.37437
- 0.000000 7 -29.57483 -29.57482
- 0.000000 8 20.28890 20.28890
- 0.000000 9 22.29566 22.29566
- 0.000000 10 -31.48823 -31.48824
- 0.000000 11 -28.04952 -28.04951
- 0.000000 12 22.91705 22.91705
- 0.000000 13 19.58638 19.58638
- 0.000000 14 23.92418 23.92419
- 0.000000 15 -31.63279 -31.63279
- 0.000000 16 19.66249 19.66249
- 0.000000 17 -5.30370 -5.30370
- 0.000000 18 -31.38433 -31.38433
- 0.000000 19 -29.26720 -29.26720
- 0.000000 20 20.31925 20.31926
- 0.000000 21 22.97399 22.97399
- 0.000000 22 -27.67342 -27.67342
- 0.000000 23 -3.79027 -3.79026
- 0.000000 24 22.13978 22.13978
- 0.000000 25 20.05454 20.05454
- 0.000000 26 -10.84176 -10.84177
- 0.000000 27 -27.37622 -27.37621
- 0.000000 28 20.07996 20.07996
- 0.000000 29 -4.04088 -4.04088
- 0.000000 30 -31.79723 -31.79723
- 0.000000 31 -30.70438 -30.70438
- 0.000000 32 -10.20896 -10.20896
- 0.000000 33 22.97248 22.97248
- 0.000000 34 -31.15038 -31.15038
- 0.000000 35 1.57059 1.57059
- 0.000000 36 22.06035 22.06036
- 0.000000 37 21.47925 21.47925
- 0.000000 38 20.56482 20.56482
- 0.000000 39 -27.39333 -27.39333
- 0.000000 40 14.81156 14.81155
- 0.000000 41 -29.18387 -29.18386
- 0.000000 42 -31.44751 -31.44751
- 0.000000 43 10.68751 10.68751
- 0.000000 44 20.55948 20.55949
- 0.000000 45 22.32470 22.32471
- 0.000000 46 10.44420 10.44420
- 0.000000 47 -28.78718 -28.78717
- 0.000000 48 22.96859 22.96859
- 0.000000 49 17.52907 17.52907
- 0.000000 50 10.63693 10.63694
- 0.000000 51 -25.41561 -25.41561
- 0.000000 52 24.53519 24.53519
- 0.000000 53 -5.56942 -5.56941
- 0.000000 54 -31.15538 -31.15538
- 0.000000 55 10.96265 10.96265
- 0.000000 56 10.11300 10.11301
- 0.000000 57 20.93628 20.93629
- 0.000000 58 11.77857 11.77857
- 0.000000 59 -2.93625 -2.93624
- 0.000000 60 18.79590 18.79590
- 0.000000 61 17.33116 17.33116
- 0.000000 62 -11.91580 -11.91579
- 0.000000 63 -33.11396 -33.11396
- 0.000000 64 14.59142 14.59142
- 0.000000 65 -1.85018 -1.85018
- 0.000000 66 -30.59329 -30.59328
- 0.000000 67 11.68601 11.68600
- 0.000000 68 -16.06371 -16.06371
- 0.000000 69 21.78602 21.78602
- 0.000000 70 8.54619 8.54620
- 0.000000 71 23.83976 23.83977
- 0.000000 72 20.65550 20.65550
- 0.000000 73 -15.82389 -15.82389
- 0.000000 74 20.71948 20.71948
- 0.000000 75 -30.60112 -30.60112
- 0.000000 76 -16.01062 -16.01063
- 0.000000 77 -29.97817 -29.97816
- 0.000000 78 -32.12858 -32.12858
- 0.000000 79 12.04202 12.04202
- 0.000000 80 20.40238 20.40238
- 0.000000 81 22.79234 22.79234
- 0.000000 82 -15.84916 -15.84917
- 0.000000 83 -33.51912 -33.51911
- 0.000000 84 22.06156 22.06156
- 0.000000 85 -17.58104 -17.58104
- 0.000000 86 24.93337 24.93338
- 0.000000 87 -27.26150 -27.26151
- 0.000000 88 -17.31785 -17.31785
- 0.000000 89 -4.36304 -4.36304
- 0.000000 90 -31.31276 -31.31276
- 0.000000 91 -5.90648 -5.90648
- 0.000000 92 22.30155 22.30156
- 0.000000 93 22.42626 22.42627
- 0.000000 94 8.26122 8.26122
- 0.000000 95 -4.84410 -4.84409
- 0.000000 96 23.00198 23.00198
- 0.000000 97 -13.24380 -13.24380
- 0.000000 98 -14.59082 -14.59082
- 0.000000 99 -31.27553 -31.27553
- 0.000000 100 -16.89918 -16.89918
- 0.000000 101 6.82924 6.82924
- 0.000000 102 -30.48054 -30.48054
- 0.000000 103 5.74240 5.74240
- 0.000000 104 -3.18116 -3.18115
- 0.000000 105 22.99623 22.99624
- 0.000000 106 9.01696 9.01696
- 0.000000 107 12.62699 12.62699
- 0.000000 108 27.13546 27.13546
- 0.000000 109 19.64555 19.64555
- 0.000000 110 20.72250 20.72250
- 0.000000 111 7.09732 7.09733
- 0.000000 112 19.81397 19.81397
- 0.000000 113 -36.08701 -36.08701
- 0.000000 114 9.35853 9.35854
- 0.000000 115 -28.74104 -28.74104
- 0.000000 116 20.56221 20.56222
- 0.000000 117 8.52190 8.52190
- 0.000000 118 -26.65020 -26.65020
- 0.000000 119 -30.06345 -30.06345
- 0.000000 120 13.56403 13.56403
- 0.000000 121 20.10695 20.10696
- 0.000000 122 13.91646 13.91647
- 0.000000 123 5.40568 5.40569
- 0.000000 124 20.19785 20.19785
- 0.000000 125 -5.69136 -5.69136
- 0.000000 126 8.47359 8.47359
- 0.000000 127 -29.02402 -29.02402
- 0.000000 128 22.16411 22.16412
- 0.000000 129 10.86619 10.86619
- 0.000000 130 -29.53575 -29.53574
- 0.000000 131 -2.03407 -2.03407
- 0.000000 132 6.44584 6.44584
- 0.000000 133 20.23333 20.23333
- 0.000000 134 -14.96924 -14.96924
- 0.000000 135 7.85899 7.85899
- 0.000000 136 19.68530 19.68530
- 0.000000 137 -8.61905 -8.61906
- 0.000000 138 7.40474 7.40475
- 0.000000 139 -29.03341 -29.03341
- 0.000000 140 -16.42702 -16.42701
- 0.000000 141 20.85463 20.85463
- 0.000000 142 -32.00093 -32.00093
- 0.000000 143 0.49939 0.49939
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+ 0.050000 5 -9.4949 -9.4949
+ 0.050000 6 -16.6640 -16.6640
+ 0.050000 7 -7.7347 -7.7347
+ 0.050000 8 5.3455 5.3455
+ 0.050000 9 14.9870 14.9870
+ 0.050000 10 -7.7421 -7.7421
+ 0.050000 11 -7.7293 -7.7293
+ 0.050000 12 15.0841 15.0841
+ 0.050000 13 8.0299 8.0299
+ 0.050000 14 8.5993 8.5993
+ 0.050000 15 -17.6155 -17.6155
+ 0.050000 16 8.2056 8.2056
+ 0.050000 17 -0.5827 -0.5827
+ 0.050000 18 -18.2261 -18.2261
+ 0.050000 19 -7.6778 -7.6778
+ 0.050000 20 7.5253 7.5253
+ 0.050000 21 14.9170 14.9170
+ 0.050000 22 -7.4742 -7.4742
+ 0.050000 23 -0.4820 -0.4820
+ 0.050000 24 12.1533 12.1533
+ 0.050000 25 9.0085 9.0085
+ 0.050000 26 -2.2019 -2.2019
+ 0.050000 27 -10.3334 -10.3334
+ 0.050000 28 9.2574 9.2574
+ 0.050000 29 -1.9137 -1.9137
+ 0.050000 30 -18.8913 -18.8913
+ 0.050000 31 -7.7512 -7.7512
+ 0.050000 32 -2.1982 -2.1982
+ 0.050000 33 14.9046 14.9046
+ 0.050000 34 -7.7181 -7.7181
+ 0.050000 35 -0.1584 -0.1584
+ 0.050000 36 14.5536 14.5536
+ 0.050000 37 1.6946 1.6946
+ 0.050000 38 5.7223 5.7223
+ 0.050000 39 -11.0735 -11.0735
+ 0.050000 40 1.0160 1.0160
+ 0.050000 41 -8.1785 -8.1785
+ 0.050000 42 -18.3995 -18.3995
+ 0.050000 43 5.6669 5.6669
+ 0.050000 44 5.5262 5.5262
+ 0.050000 45 14.7472 14.7472
+ 0.050000 46 5.5463 5.5463
+ 0.050000 47 -8.1384 -8.1384
+ 0.050000 48 14.4026 14.4026
+ 0.050000 49 1.4379 1.4379
+ 0.050000 50 2.4977 2.4977
+ 0.050000 51 -8.4401 -8.4401
+ 0.050000 52 1.9899 1.9899
+ 0.050000 53 -0.6744 -0.6744
+ 0.050000 54 -17.4076 -17.4076
+ 0.050000 55 5.4507 5.4508
+ 0.050000 56 2.5087 2.5087
+ 0.050000 57 13.9372 13.9372
+ 0.050000 58 3.8810 3.8810
+ 0.050000 59 -0.4553 -0.4553
+ 0.050000 60 0.0000 0.0000
+ 0.050000 61 0.0000 0.0000
+ 0.050000 62 0.0000 0.0000
+ 0.050000 63 0.0000 0.0000
+ 0.050000 64 0.0000 0.0000
+ 0.050000 65 0.0000 0.0000
+ 0.050000 66 0.0000 0.0000
+ 0.050000 67 0.0000 0.0000
+ 0.050000 68 0.0000 -0.0000
+ 0.100000 0 13.6808 13.6808
+ 0.100000 1 9.7065 9.7065
+ 0.100000 2 5.2078 5.2078
+ 0.100000 3 -18.9230 -18.9230
+ 0.100000 4 9.7864 9.7864
+ 0.100000 5 -9.3717 -9.3717
+ 0.100000 6 -15.2642 -15.2642
+ 0.100000 7 -8.1972 -8.1972
+ 0.100000 8 4.8787 4.8787
+ 0.100000 9 14.2735 14.2735
+ 0.100000 10 -8.2078 -8.2078
+ 0.100000 11 -6.8309 -6.8309
+ 0.100000 12 14.2823 14.2823
+ 0.100000 13 6.4522 6.4522
+ 0.100000 14 8.0642 8.0642
+ 0.100000 15 -15.4486 -15.4486
+ 0.100000 16 7.6799 7.6799
+ 0.100000 17 -0.4697 -0.4697
+ 0.100000 18 -16.6116 -16.6116
+ 0.100000 19 -8.1176 -8.1176
+ 0.100000 20 7.2643 7.2643
+ 0.100000 21 13.5146 13.5146
+ 0.100000 22 -7.8982 -7.8982
+ 0.100000 23 -0.4301 -0.4301
+ 0.100000 24 9.3016 9.3016
+ 0.100000 25 9.8123 9.8123
+ 0.100000 26 -2.1187 -2.1187
+ 0.100000 27 -5.9974 -5.9974
+ 0.100000 28 9.9126 9.9126
+ 0.100000 29 -1.5749 -1.5749
+ 0.100000 30 -17.7876 -17.7876
+ 0.100000 31 -8.1679 -8.1679
+ 0.100000 32 -2.1719 -2.1719
+ 0.100000 33 14.2583 14.2583
+ 0.100000 34 -8.0693 -8.0693
+ 0.100000 35 -1.1874 -1.1874
+ 0.100000 36 13.1645 13.1645
+ 0.100000 37 2.0441 2.0441
+ 0.100000 38 5.1337 5.1337
+ 0.100000 39 -9.3381 -9.3381
+ 0.100000 40 1.7607 1.7607
+ 0.100000 41 -7.6791 -7.6791
+ 0.100000 42 -17.1028 -17.1028
+ 0.100000 43 3.5145 3.5145
+ 0.100000 44 4.8048 4.8048
+ 0.100000 45 13.8154 13.8154
+ 0.100000 46 3.1458 3.1458
+ 0.100000 47 -7.0775 -7.0775
+ 0.100000 48 12.1334 12.1334
+ 0.100000 49 2.0087 2.0087
+ 0.100000 50 2.4380 2.4380
+ 0.100000 51 -8.1374 -8.1374
+ 0.100000 52 1.8615 1.8615
+ 0.100000 53 -0.6023 -0.6023
+ 0.100000 54 -14.7386 -14.7386
+ 0.100000 55 3.4661 3.4661
+ 0.100000 56 1.8801 1.8801
+ 0.100000 57 13.8239 13.8239
+ 0.100000 58 2.3562 2.3562
+ 0.100000 59 -0.4828 -0.4828
+ 0.100000 60 0.0000 0.0000
+ 0.100000 61 0.0000 0.0000
+ 0.100000 62 0.0000 0.0000
+ 0.100000 63 0.0000 0.0000
+ 0.100000 64 0.0000 0.0000
+ 0.100000 65 0.0000 0.0000
+ 0.100000 66 0.0000 0.0000
+ 0.100000 67 0.0000 0.0000
+ 0.100000 68 0.0000 -0.0000
+ 0.150000 0 12.7798 12.7798
+ 0.150000 1 9.7131 9.7131
+ 0.150000 2 4.7800 4.7800
+ 0.150000 3 -14.8569 -14.8569
+ 0.150000 4 9.6495 9.6495
+ 0.150000 5 -8.7216 -8.7216
+ 0.150000 6 -12.8826 -12.8826
+ 0.150000 7 -9.7428 -9.7428
+ 0.150000 8 4.5853 4.5853
+ 0.150000 9 13.1940 13.1940
+ 0.150000 10 -9.7791 -9.7791
+ 0.150000 11 -5.6227 -5.6227
+ 0.150000 12 13.5098 13.5098
+ 0.150000 13 4.3321 4.3321
+ 0.150000 14 7.0487 7.0487
+ 0.150000 15 -12.3210 -12.3210
+ 0.150000 16 6.8379 6.8379
+ 0.150000 17 1.1669 1.1669
+ 0.150000 18 -13.4999 -13.4999
+ 0.150000 19 -9.2276 -9.2276
+ 0.150000 20 6.5908 6.5908
+ 0.150000 21 12.0812 12.0812
+ 0.150000 22 -8.6936 -8.6936
+ 0.150000 23 1.1572 1.1572
+ 0.150000 24 6.7019 6.7019
+ 0.150000 25 10.0911 10.0911
+ 0.150000 26 -2.2231 -2.2231
+ 0.150000 27 -3.3669 -3.3669
+ 0.150000 28 10.0677 10.0677
+ 0.150000 29 -0.7409 -0.7409
+ 0.150000 30 -14.7813 -14.7813
+ 0.150000 31 -9.9096 -9.9096
+ 0.150000 32 -2.4709 -2.4709
+ 0.150000 33 12.6381 12.6381
+ 0.150000 34 -10.1337 -10.1337
+ 0.150000 35 -1.8282 -1.8282
+ 0.150000 36 10.8586 10.8586
+ 0.150000 37 3.4158 3.4158
+ 0.150000 38 4.4767 4.4767
+ 0.150000 39 -8.3890 -8.3890
+ 0.150000 40 3.2791 3.2791
+ 0.150000 41 -7.2960 -7.2960
+ 0.150000 42 -13.6326 -13.6326
+ 0.150000 43 1.2494 1.2494
+ 0.150000 44 4.4655 4.4655
+ 0.150000 45 12.8525 12.8525
+ 0.150000 46 0.8248 0.8248
+ 0.150000 47 -6.0962 -6.0962
+ 0.150000 48 9.9795 9.9795
+ 0.150000 49 3.4359 3.4359
+ 0.150000 50 2.6755 2.6755
+ 0.150000 51 -8.4643 -8.4643
+ 0.150000 52 2.2568 2.2568
+ 0.150000 53 0.8633 0.8633
+ 0.150000 54 -11.1483 -11.1483
+ 0.150000 55 1.3221 1.3221
+ 0.150000 56 0.9799 0.9799
+ 0.150000 57 13.4291 13.4291
+ 0.150000 58 0.7274 0.7274
+ 0.150000 59 0.6366 0.6366
+ 0.150000 60 0.0000 0.0000
+ 0.150000 61 0.0000 0.0000
+ 0.150000 62 0.0000 0.0000
+ 0.150000 63 0.0000 0.0000
+ 0.150000 64 0.0000 0.0000
+ 0.150000 65 0.0000 0.0000
+ 0.150000 66 0.0000 0.0000
+ 0.150000 67 0.0000 0.0000
+ 0.150000 68 0.0000 0.0000
+ 0.200000 0 12.4674 12.4674
+ 0.200000 1 9.1943 9.1943
+ 0.200000 2 4.9446 4.9446
+ 0.200000 3 -11.8412 -11.8412
+ 0.200000 4 9.1455 9.1455
+ 0.200000 5 -7.2875 -7.2875
+ 0.200000 6 -10.2954 -10.2954
+ 0.200000 7 -9.7151 -9.7151
+ 0.200000 8 4.8992 4.8992
+ 0.200000 9 12.4609 12.4609
+ 0.200000 10 -9.8753 -9.8753
+ 0.200000 11 -4.8578 -4.8578
+ 0.200000 12 13.1483 13.1483
+ 0.200000 13 3.6284 3.6284
+ 0.200000 14 5.4303 5.4303
+ 0.200000 15 -9.5647 -9.5647
+ 0.200000 16 5.1485 5.1485
+ 0.200000 17 2.0649 2.0649
+ 0.200000 18 -10.3018 -10.3018
+ 0.200000 19 -9.2700 -9.2700
+ 0.200000 20 5.5876 5.5876
+ 0.200000 21 11.5241 11.5241
+ 0.200000 22 -8.8854 -8.8854
+ 0.200000 23 2.0514 2.0514
+ 0.200000 24 5.6953 5.6953
+ 0.200000 25 9.5884 9.5884
+ 0.200000 26 -2.2315 -2.2315
+ 0.200000 27 -2.6731 -2.6731
+ 0.200000 28 9.5816 9.5816
+ 0.200000 29 -0.1341 -0.1341
+ 0.200000 30 -11.5958 -11.5958
+ 0.200000 31 -9.2897 -9.2897
+ 0.200000 32 -2.4445 -2.4445
+ 0.200000 33 10.6175 10.6175
+ 0.200000 34 -10.0477 -10.0477
+ 0.200000 35 -2.2740 -2.2740
+ 0.200000 36 7.5593 7.5592
+ 0.200000 37 3.3894 3.3894
+ 0.200000 38 4.8854 4.8854
+ 0.200000 39 -7.9307 -7.9307
+ 0.200000 40 3.5029 3.5029
+ 0.200000 41 -6.9099 -6.9099
+ 0.200000 42 -10.3936 -10.3936
+ 0.200000 43 -0.1503 -0.1503
+ 0.200000 44 5.0281 5.0281
+ 0.200000 45 11.8759 11.8759
+ 0.200000 46 -0.7203 -0.7203
+ 0.200000 47 -5.8079 -5.8079
+ 0.200000 48 8.9561 8.9561
+ 0.200000 49 3.0604 3.0604
+ 0.200000 50 3.7155 3.7155
+ 0.200000 51 -8.1385 -8.1385
+ 0.200000 52 0.7073 0.7073
+ 0.200000 53 1.6522 1.6522
+ 0.200000 54 -8.4031 -8.4031
+ 0.200000 55 0.1036 0.1036
+ 0.200000 56 0.6263 0.6263
+ 0.200000 57 13.1350 13.1350
+ 0.200000 58 -0.2911 -0.2911
+ 0.200000 59 1.3774 1.3774
+ 0.200000 60 0.0000 0.0000
+ 0.200000 61 0.0000 0.0000
+ 0.200000 62 0.0000 0.0000
+ 0.200000 63 0.0000 0.0000
+ 0.200000 64 0.0000 0.0000
+ 0.200000 65 0.0000 0.0000
+ 0.200000 66 0.0000 0.0000
+ 0.200000 67 0.0000 0.0000
+ 0.200000 68 0.0000 0.0000
diff --git a/regtest/rt23/derivatives2.reference b/regtest/rt23/derivatives2.reference
index 3cf39c2b0..85d1d4351 100644
--- a/regtest/rt23/derivatives2.reference
+++ b/regtest/rt23/derivatives2.reference
@@ -1,1546 +1,211 @@
#! FIELDS time parameter c1.xgradient c1n.xgradient
- 0.000000 0 0.16486 0.16486
- 0.000000 1 -0.00105 -0.00105
- 0.000000 2 -0.01655 -0.01655
- 0.000000 3 0.03791 0.03791
- 0.000000 4 -0.01037 -0.01037
- 0.000000 5 0.00131 0.00131
- 0.000000 6 0.02340 0.02340
- 0.000000 7 0.00939 0.00939
- 0.000000 8 0.01250 0.01250
- 0.000000 9 0.15689 0.15689
- 0.000000 10 0.01144 0.01144
- 0.000000 11 -0.00197 -0.00197
- 0.000000 12 0.15163 0.15163
- 0.000000 13 -0.00526 -0.00526
- 0.000000 14 0.01014 0.01014
- 0.000000 15 0.04362 0.04362
- 0.000000 16 -0.00068 -0.00068
- 0.000000 17 -0.02035 -0.02035
- 0.000000 18 0.02197 0.02197
- 0.000000 19 -0.00434 -0.00434
- 0.000000 20 0.01611 0.01611
- 0.000000 21 0.18947 0.18947
- 0.000000 22 -0.00376 -0.00376
- 0.000000 23 -0.02341 -0.02341
- 0.000000 24 0.15168 0.15168
- 0.000000 25 -0.04592 -0.04592
- 0.000000 26 0.00485 0.00485
- 0.000000 27 0.04117 0.04117
- 0.000000 28 -0.00811 -0.00811
- 0.000000 29 0.02726 0.02726
- 0.000000 30 0.03278 0.03278
- 0.000000 31 0.03067 0.03067
- 0.000000 32 -0.01188 -0.01188
- 0.000000 33 0.20620 0.20620
- 0.000000 34 -0.03621 -0.03621
- 0.000000 35 0.02416 0.02416
- 0.000000 36 0.20187 0.20187
- 0.000000 37 -0.01973 -0.01973
- 0.000000 38 0.03702 0.03702
- 0.000000 39 0.01550 0.01550
- 0.000000 40 -0.00629 -0.00629
- 0.000000 41 -0.03243 -0.03243
- 0.000000 42 0.04007 0.04007
- 0.000000 43 0.01308 0.01308
- 0.000000 44 -0.00398 -0.00398
- 0.000000 45 0.20427 0.20427
- 0.000000 46 -0.01231 -0.01231
- 0.000000 47 0.00593 0.00593
- 0.000000 48 0.18452 0.18452
- 0.000000 49 -0.01946 -0.01946
- 0.000000 50 -0.01105 -0.01105
- 0.000000 51 0.02773 0.02773
- 0.000000 52 -0.01447 -0.01447
- 0.000000 53 -0.00400 -0.00400
- 0.000000 54 0.03295 0.03295
- 0.000000 55 0.02453 0.02453
- 0.000000 56 0.03302 0.03302
- 0.000000 57 0.16800 0.16800
- 0.000000 58 0.03616 0.03616
- 0.000000 59 -0.00271 -0.00271
- 0.000000 60 0.21156 0.21156
- 0.000000 61 0.00895 0.00895
- 0.000000 62 -0.01354 -0.01354
- 0.000000 63 0.03286 0.03286
- 0.000000 64 0.01586 0.01586
- 0.000000 65 -0.00622 -0.00622
- 0.000000 66 0.01770 0.01770
- 0.000000 67 0.01377 0.01377
- 0.000000 68 0.02685 0.02685
- 0.000000 69 0.19950 0.19950
- 0.000000 70 0.04616 0.04616
- 0.000000 71 -0.01566 -0.01566
- 0.000000 72 0.17156 0.17156
- 0.000000 73 0.02261 0.02261
- 0.000000 74 -0.02226 -0.02226
- 0.000000 75 0.03580 0.03580
- 0.000000 76 -0.00991 -0.00991
- 0.000000 77 -0.01059 -0.01059
- 0.000000 78 0.05334 0.05334
- 0.000000 79 -0.00602 -0.00603
- 0.000000 80 -0.01041 -0.01041
- 0.000000 81 0.15646 0.15646
- 0.000000 82 -0.00886 -0.00886
- 0.000000 83 0.01801 0.01801
- 0.000000 84 0.15461 0.15461
- 0.000000 85 0.01965 0.01965
- 0.000000 86 0.03660 0.03660
- 0.000000 87 0.03206 0.03206
- 0.000000 88 -0.01708 -0.01708
- 0.000000 89 -0.00577 -0.00577
- 0.000000 90 0.03792 0.03792
- 0.000000 91 0.00724 0.00724
- 0.000000 92 -0.00501 -0.00501
- 0.000000 93 0.10896 0.10896
- 0.000000 94 -0.03084 -0.03084
- 0.000000 95 0.00516 0.00516
- 0.000000 96 0.11721 0.11721
- 0.000000 97 0.02425 0.02425
- 0.000000 98 -0.00242 -0.00242
- 0.000000 99 0.03876 0.03876
- 0.000000 100 -0.02782 -0.02782
- 0.000000 101 0.00835 0.00835
- 0.000000 102 0.04265 0.04265
- 0.000000 103 -0.01812 -0.01812
- 0.000000 104 -0.02175 -0.02175
- 0.000000 105 0.10630 0.10630
- 0.000000 106 -0.01997 -0.01997
- 0.000000 107 -0.01087 -0.01087
- 0.000000 108 -0.11218 -0.11218
- 0.000000 109 -0.01576 -0.01576
- 0.000000 110 0.01112 0.01112
- 0.000000 111 -0.04992 -0.04992
- 0.000000 112 0.00578 0.00578
- 0.000000 113 -0.01698 -0.01698
- 0.000000 114 -0.05042 -0.05042
- 0.000000 115 -0.00450 -0.00450
- 0.000000 116 0.00513 0.00513
- 0.000000 117 -0.09525 -0.09525
- 0.000000 118 -0.01158 -0.01158
- 0.000000 119 -0.00317 -0.00317
- 0.000000 120 -0.11718 -0.11718
- 0.000000 121 -0.00264 -0.00264
- 0.000000 122 0.00506 0.00506
- 0.000000 123 -0.04301 -0.04301
- 0.000000 124 -0.00655 -0.00655
- 0.000000 125 0.00796 0.00796
- 0.000000 126 -0.04734 -0.04734
- 0.000000 127 0.00576 0.00576
- 0.000000 128 -0.00009 -0.00009
- 0.000000 129 -0.10472 -0.10472
- 0.000000 130 -0.00364 -0.00364
- 0.000000 131 0.00191 0.00191
- 0.000000 132 -0.09481 -0.09481
- 0.000000 133 -0.00541 -0.00541
- 0.000000 134 0.00024 0.00024
- 0.000000 135 -0.04869 -0.04869
- 0.000000 136 -0.01119 -0.01119
- 0.000000 137 0.00134 0.00134
- 0.000000 138 -0.04994 -0.04994
- 0.000000 139 -0.00326 -0.00326
- 0.000000 140 -0.00826 -0.00826
- 0.000000 141 -0.10479 -0.10479
- 0.000000 142 0.01998 0.01998
- 0.000000 143 -0.00097 -0.00097
- 0.000000 144 -0.10816 -0.10816
- 0.000000 145 0.00693 0.00693
- 0.000000 146 -0.00954 -0.00954
- 0.000000 147 -0.05204 -0.05204
- 0.000000 148 -0.00097 -0.00097
- 0.000000 149 -0.00036 -0.00036
- 0.000000 150 -0.05355 -0.05355
- 0.000000 151 0.00001 0.00001
- 0.000000 152 0.00515 0.00515
- 0.000000 153 -0.10179 -0.10179
- 0.000000 154 0.00542 0.00542
- 0.000000 155 -0.01493 -0.01493
- 0.000000 156 -0.09382 -0.09382
- 0.000000 157 0.00760 0.00760
- 0.000000 158 0.00934 0.00934
- 0.000000 159 -0.05521 -0.05521
- 0.000000 160 -0.00006 -0.00006
- 0.000000 161 0.00339 0.00339
- 0.000000 162 -0.05360 -0.05360
- 0.000000 163 0.00513 0.00513
- 0.000000 164 -0.00183 -0.00183
- 0.000000 165 -0.10453 -0.10453
- 0.000000 166 0.00661 0.00661
- 0.000000 167 -0.00495 -0.00495
- 0.000000 168 -0.10568 -0.10568
- 0.000000 169 0.00491 0.00491
- 0.000000 170 0.01017 0.01017
- 0.000000 171 -0.05594 -0.05594
- 0.000000 172 -0.00508 -0.00508
- 0.000000 173 0.00674 0.00674
- 0.000000 174 -0.04700 -0.04700
- 0.000000 175 0.01812 0.01812
- 0.000000 176 -0.01495 -0.01495
- 0.000000 177 -0.12806 -0.12806
- 0.000000 178 0.00832 0.00832
- 0.000000 179 -0.00010 -0.00010
- 0.000000 180 -0.11843 -0.11843
- 0.000000 181 -0.00676 -0.00676
- 0.000000 182 -0.00819 -0.00819
- 0.000000 183 -0.05234 -0.05234
- 0.000000 184 -0.00027 -0.00027
- 0.000000 185 0.00273 0.00273
- 0.000000 186 -0.05262 -0.05262
- 0.000000 187 0.00150 0.00150
- 0.000000 188 -0.00762 -0.00762
- 0.000000 189 -0.11387 -0.11387
- 0.000000 190 0.00747 0.00747
- 0.000000 191 -0.00855 -0.00855
- 0.000000 192 -0.11254 -0.11254
- 0.000000 193 -0.00873 -0.00873
- 0.000000 194 0.00520 0.00520
- 0.000000 195 -0.03996 -0.03996
- 0.000000 196 0.00927 0.00927
- 0.000000 197 0.01579 0.01579
- 0.000000 198 -0.03895 -0.03895
- 0.000000 199 -0.01056 -0.01056
- 0.000000 200 0.01311 0.01311
- 0.000000 201 -0.11069 -0.11069
- 0.000000 202 0.00646 0.00646
- 0.000000 203 -0.00106 -0.00106
- 0.000000 204 -0.10900 -0.10900
- 0.000000 205 -0.00532 -0.00532
- 0.000000 206 0.00868 0.00868
- 0.000000 207 -0.04090 -0.04090
- 0.000000 208 0.01559 0.01559
- 0.000000 209 -0.01102 -0.01102
- 0.000000 210 -0.03276 -0.03276
- 0.000000 211 -0.01340 -0.01340
- 0.000000 212 -0.00110 -0.00110
- 0.000000 213 -0.10607 -0.10607
- 0.000000 214 -0.00547 -0.00547
- 0.000000 215 0.00306 0.00306
- 0.000000 216 -0.06844 -0.06844
- 0.000000 217 -0.00299 -0.00299
- 0.000000 218 0.00034 0.00034
- 0.000000 219 -0.02682 -0.02682
- 0.000000 220 -0.00715 -0.00715
- 0.000000 221 0.06674 0.06674
- 0.000000 222 -0.09935 -0.09935
- 0.000000 223 -0.01861 -0.01861
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+ 0.150000 18 0.0558 0.0558
+ 0.150000 19 0.0412 0.0412
+ 0.150000 20 0.0180 0.0180
+ 0.150000 21 -0.0650 -0.0650
+ 0.150000 22 -0.0480 -0.0480
+ 0.150000 23 -0.0226 -0.0226
+ 0.150000 24 0.0154 0.0154
+ 0.150000 25 0.0079 0.0079
+ 0.150000 26 0.0172 0.0172
+ 0.150000 27 0.2578 0.2578
+ 0.150000 28 0.2139 0.2139
+ 0.150000 29 -0.0123 -0.0123
+ 0.150000 30 0.0571 0.0571
+ 0.150000 31 -0.0114 -0.0114
+ 0.150000 32 0.0075 0.0075
+ 0.150000 33 0.3221 0.3221
+ 0.150000 34 0.2828 -0.8210
+ 0.150000 35 -0.0467 -0.0203
+ 0.150000 36 0.2828 0.2767
+ 0.150000 37 0.2541 0.2541
+ 0.150000 38 0.0112 0.0137
+ 0.150000 39 -0.0467 0.3232
+ 0.150000 40 0.0112 -0.0022
+ 0.150000 41 0.0409 0.0409
+ 0.200000 0 0.0204 0.0204
+ 0.200000 1 0.0004 0.0004
+ 0.200000 2 -0.0358 -0.0358
+ 0.200000 3 -0.0508 -0.0508
+ 0.200000 4 0.0078 0.0078
+ 0.200000 5 0.0329 0.0329
+ 0.200000 6 -0.4789 -0.4789
+ 0.200000 7 -0.4432 -0.4432
+ 0.200000 8 0.0321 0.0321
+ 0.200000 9 0.0565 0.0565
+ 0.200000 10 0.0439 0.0439
+ 0.200000 11 -0.0168 -0.0168
+ 0.200000 12 0.0358 0.0358
+ 0.200000 13 0.0624 0.0624
+ 0.200000 14 0.0027 0.0027
+ 0.200000 15 -0.0952 -0.0952
+ 0.200000 16 -0.0474 -0.0474
+ 0.200000 17 -0.0143 -0.0143
+ 0.200000 18 0.0583 0.0583
+ 0.200000 19 0.0284 0.0284
+ 0.200000 20 0.0179 0.0179
+ 0.200000 21 -0.0569 -0.0569
+ 0.200000 22 -0.0378 -0.0378
+ 0.200000 23 -0.0186 -0.0186
+ 0.200000 24 0.0628 0.0628
+ 0.200000 25 0.0509 0.0509
+ 0.200000 26 0.0239 0.0239
+ 0.200000 27 0.3710 0.3710
+ 0.200000 28 0.3475 0.3475
+ 0.200000 29 -0.0322 -0.0322
+ 0.200000 30 -0.0036 -0.0036
+ 0.200000 31 -0.0129 -0.0129
+ 0.200000 32 0.0081 0.0081
+ 0.200000 33 0.4881 0.4881
+ 0.200000 34 0.4289 -1.5647
+ 0.200000 35 -0.0037 0.0820
+ 0.200000 36 0.4289 0.4203
+ 0.200000 37 0.3385 0.3385
+ 0.200000 38 0.0134 0.0195
+ 0.200000 39 -0.0037 0.1226
+ 0.200000 40 0.0134 0.0211
+ 0.200000 41 -0.0173 -0.0173
diff --git a/regtest/rt23/plumed.dat b/regtest/rt23/plumed.dat
index eba6ca401..fda60d6b2 100644
--- a/regtest/rt23/plumed.dat
+++ b/regtest/rt23/plumed.dat
@@ -1,9 +1,9 @@
-DENSITY SPECIES=1-100 GRADIENT=(XBINS=10 YBINS=10 ZBINS=10) LABEL=d1
-DENSITY SPECIES=1-100 GRADIENT=(XBINS=10 YBINS=10 ZBINS=10) NUMERICAL_DERIVATIVES LABEL=d1n
-PRINT ARG=d1.* FILE=colvar1 FMT=%8.5f
-DUMPDERIVATIVES ARG=d1.*,d1n.* FILE=derivatives1 FMT=%8.5f
-COORDINATIONNUMBER SPECIES=1-100 SWITCH=(SPLINE R_0=1.0) GRADIENT=(XBINS=10) LABEL=c1
-COORDINATIONNUMBER SPECIES=1-100 SWITCH=(SPLINE R_0=1.0) GRADIENT=(XBINS=10) NUMERICAL_DERIVATIVES LABEL=c1n
-PRINT ARG=c1.* FILE=colvar2 FMT=%8.5f
-DUMPDERIVATIVES ARG=c1.*,c1n.* FILE=derivatives2 FMT=%8.5f
+DENSITY SPECIES=1-20 GRADIENT=(XBINS=10 YBINS=10 ZBINS=10) LABEL=d1
+DENSITY SPECIES=1-20 GRADIENT=(XBINS=10 YBINS=10 ZBINS=10) NUMERICAL_DERIVATIVES LABEL=d1n
+PRINT ARG=d1.* FILE=colvar1 FMT=%8.4f
+DUMPDERIVATIVES ARG=d1.*,d1n.* FILE=derivatives1 FMT=%8.4f
+COORDINATIONNUMBER SPECIES=1,10,20,30,40,50,60,70,80,90,100 SWITCH=(SPLINE R_0=1.0) GRADIENT=(XBINS=10) LABEL=c1
+COORDINATIONNUMBER SPECIES=1,10,20,30,40,50,60,70,80,90,100 SWITCH=(SPLINE R_0=1.0) GRADIENT=(XBINS=10) NUMERICAL_DERIVATIVES LABEL=c1n
+PRINT ARG=c1.* FILE=colvar2 FMT=%8.4f
+DUMPDERIVATIVES ARG=c1.*,c1n.* FILE=derivatives2 FMT=%8.4f
diff --git a/regtest/rt24/Makefile b/regtest/rt24/Makefile
new file mode 120000
index 000000000..a19fbb5e9
--- /dev/null
+++ b/regtest/rt24/Makefile
@@ -0,0 +1 @@
+../scripts/test.make
\ No newline at end of file
diff --git a/regtest/rt24/config b/regtest/rt24/config
new file mode 100644
index 000000000..e441f5aec
--- /dev/null
+++ b/regtest/rt24/config
@@ -0,0 +1,3 @@
+type=driver
+# this is to test a different name
+arg="--plumed plumed.dat --timestep 0.005 trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f"
diff --git a/regtest/rt24/derivatives.reference b/regtest/rt24/derivatives.reference
new file mode 100644
index 000000000..30414af34
--- /dev/null
+++ b/regtest/rt24/derivatives.reference
@@ -0,0 +1,151 @@
+#! FIELDS time parameter m1.bias m1num.bias
+ 0.000000 0 0.0000 0.0000
+ 0.000000 1 0.0000 0.0000
+ 0.000000 2 0.0000 0.0000
+ 0.000000 3 0.0000 0.0000
+ 0.000000 4 0.0000 0.0000
+ 0.000000 5 0.0000 0.0000
+ 0.000000 6 0.0000 0.0000
+ 0.000000 7 0.0000 0.0000
+ 0.000000 8 0.0000 0.0000
+ 0.000000 9 0.0000 0.0000
+ 0.000000 10 0.0000 0.0000
+ 0.000000 11 0.0000 0.0000
+ 0.000000 12 0.0000 0.0000
+ 0.000000 13 0.0000 0.0000
+ 0.000000 14 0.0000 0.0000
+ 0.000000 15 0.0000 0.0000
+ 0.000000 16 0.0000 0.0000
+ 0.000000 17 0.0000 0.0000
+ 0.000000 18 0.0000 0.0000
+ 0.000000 19 0.0000 0.0000
+ 0.000000 20 0.0000 0.0000
+ 0.000000 21 0.0000 0.0000
+ 0.000000 22 0.0000 0.0000
+ 0.000000 23 0.0000 0.0000
+ 0.000000 24 0.0000 0.0000
+ 0.000000 25 0.0000 0.0000
+ 0.000000 26 0.0000 0.0000
+ 0.000000 27 0.0000 0.0000
+ 0.000000 28 0.0000 0.0000
+ 0.000000 29 0.0000 0.0000
+ 0.005000 0 10.2851 10.2851
+ 0.005000 1 3.0644 3.0644
+ 0.005000 2 7.6475 7.6475
+ 0.005000 3 -14.2740 -14.2740
+ 0.005000 4 2.2358 2.2358
+ 0.005000 5 -2.3071 -2.3071
+ 0.005000 6 4.3466 4.3466
+ 0.005000 7 -0.7113 -0.7113
+ 0.005000 8 -8.9860 -8.9860
+ 0.005000 9 0.6726 0.6726
+ 0.005000 10 -3.0367 -3.0367
+ 0.005000 11 7.9387 7.9387
+ 0.005000 12 2.6543 2.6543
+ 0.005000 13 -5.4347 -5.4347
+ 0.005000 14 3.0186 3.0186
+ 0.005000 15 -4.1893 -4.1893
+ 0.005000 16 -4.6599 -4.6599
+ 0.005000 17 0.2499 0.2498
+ 0.005000 18 0.5047 0.5048
+ 0.005000 19 8.5424 8.5424
+ 0.005000 20 -7.5615 -7.5615
+ 0.005000 21 13.9228 13.9229
+ 0.005000 22 -4.8061 -4.8062
+ 0.005000 23 16.3786 16.3789
+ 0.005000 24 -4.8061 -4.8061
+ 0.005000 25 -2.8429 -2.8429
+ 0.005000 26 6.4878 6.4878
+ 0.005000 27 16.3786 16.3786
+ 0.005000 28 6.4878 6.4878
+ 0.005000 29 3.6041 3.6041
+ 0.010000 0 10.6844 10.6844
+ 0.010000 1 0.1318 0.1319
+ 0.010000 2 4.8392 4.8392
+ 0.010000 3 -16.1652 -16.1652
+ 0.010000 4 -0.6701 -0.6701
+ 0.010000 5 -3.8376 -3.8376
+ 0.010000 6 2.6083 2.6083
+ 0.010000 7 -1.0743 -1.0743
+ 0.010000 8 -7.3085 -7.3085
+ 0.010000 9 4.7365 4.7365
+ 0.010000 10 3.9390 3.9390
+ 0.010000 11 7.8995 7.8995
+ 0.010000 12 3.1824 3.1824
+ 0.010000 13 -11.3427 -11.3427
+ 0.010000 14 6.4737 6.4737
+ 0.010000 15 -5.4269 -5.4269
+ 0.010000 16 -5.1043 -5.1043
+ 0.010000 17 0.1428 0.1428
+ 0.010000 18 0.3805 0.3805
+ 0.010000 19 14.1205 14.1206
+ 0.010000 20 -8.2090 -8.2089
+ 0.010000 21 19.6252 19.6252
+ 0.010000 22 -6.6606 -6.6607
+ 0.010000 23 17.9477 17.9476
+ 0.010000 24 -6.6606 -6.6607
+ 0.010000 25 -11.7381 -11.7381
+ 0.010000 26 4.9252 4.9251
+ 0.010000 27 17.9477 17.9477
+ 0.010000 28 4.9252 4.9250
+ 0.010000 29 0.9625 0.9625
+ 0.015000 0 9.0453 9.0453
+ 0.015000 1 -1.8840 -1.8840
+ 0.015000 2 -0.1185 -0.1185
+ 0.015000 3 -13.7203 -13.7202
+ 0.015000 4 -3.4546 -3.4545
+ 0.015000 5 -4.0316 -4.0316
+ 0.015000 6 -2.4838 -2.4839
+ 0.015000 7 -2.8091 -2.8091
+ 0.015000 8 -2.6763 -2.6763
+ 0.015000 9 9.3645 9.3645
+ 0.015000 10 7.9811 7.9811
+ 0.015000 11 7.3547 7.3548
+ 0.015000 12 4.4296 4.4297
+ 0.015000 13 -12.6854 -12.6854
+ 0.015000 14 8.0004 8.0004
+ 0.015000 15 -6.4792 -6.4792
+ 0.015000 16 -4.0503 -4.0504
+ 0.015000 17 -1.4081 -1.4081
+ 0.015000 18 -0.1562 -0.1562
+ 0.015000 19 16.9023 16.9023
+ 0.015000 20 -7.1206 -7.1206
+ 0.015000 21 24.3911 24.3910
+ 0.015000 22 -5.5502 -5.5502
+ 0.015000 23 15.0739 15.0737
+ 0.015000 24 -5.5502 -5.5504
+ 0.015000 25 -14.2845 -14.2845
+ 0.015000 26 0.2478 0.2480
+ 0.015000 27 15.0739 15.0738
+ 0.015000 28 0.2478 0.2477
+ 0.015000 29 0.8776 0.8775
+ 0.020000 0 9.5651 9.5651
+ 0.020000 1 -2.8507 -2.8507
+ 0.020000 2 -1.9504 -1.9504
+ 0.020000 3 -11.8501 -11.8501
+ 0.020000 4 -4.5546 -4.5547
+ 0.020000 5 -3.4492 -3.4493
+ 0.020000 6 -7.5274 -7.5274
+ 0.020000 7 -4.0642 -4.0642
+ 0.020000 8 1.6517 1.6517
+ 0.020000 9 11.8037 11.8037
+ 0.020000 10 9.9740 9.9740
+ 0.020000 11 5.8625 5.8625
+ 0.020000 12 5.8885 5.8885
+ 0.020000 13 -11.4466 -11.4466
+ 0.020000 14 7.6905 7.6905
+ 0.020000 15 -6.6977 -6.6977
+ 0.020000 16 -2.7627 -2.7627
+ 0.020000 17 -3.1920 -3.1920
+ 0.020000 18 -1.1821 -1.1821
+ 0.020000 19 15.7048 15.7048
+ 0.020000 20 -6.6130 -6.6130
+ 0.020000 21 29.4117 29.4117
+ 0.020000 22 -2.8105 -2.8103
+ 0.020000 23 11.8000 11.8002
+ 0.020000 24 -2.8105 -2.8104
+ 0.020000 25 -14.2707 -14.2707
+ 0.020000 26 -2.0961 -2.0962
+ 0.020000 27 11.8000 11.8000
+ 0.020000 28 -2.0961 -2.0962
+ 0.020000 29 5.2297 5.2297
diff --git a/regtest/rt24/field.1.reference b/regtest/rt24/field.1.reference
new file mode 100644
index 000000000..aa0ba7969
--- /dev/null
+++ b/regtest/rt24/field.1.reference
@@ -0,0 +1,208 @@
+#! DEFINITE INTEGRAL 1.000000
+#! DERIVATIVE 0
+#! NVAR 1
+#! BIN 201
+#! MIN 0.500000000
+#! MAX 3.012500000
+#! PBC 0
+ 0.500000000 0.000000004
+ 0.512500000 0.000000357
+ 0.525000000 0.000000713
+ 0.537500000 0.000001075
+ 0.550000000 0.000001446
+ 0.562500000 0.000001829
+ 0.575000000 0.000002228
+ 0.587500000 0.000002645
+ 0.600000000 0.000003083
+ 0.612500000 0.000003545
+ 0.625000000 0.000004035
+ 0.637500000 0.000044714
+ 0.650000000 0.000130299
+ 0.662500000 0.000216694
+ 0.675000000 0.000304427
+ 0.687500000 0.000394028
+ 0.700000000 0.000486024
+ 0.712500000 0.000580944
+ 0.725000000 0.000679316
+ 0.737500000 0.000781668
+ 0.750000000 0.000888529
+ 0.762500000 0.001000426
+ 0.775000000 0.005271400
+ 0.787500000 0.009796172
+ 0.800000000 0.014362706
+ 0.812500000 0.018989575
+ 0.825000000 0.023695352
+ 0.837500000 0.028498610
+ 0.850000000 0.033417924
+ 0.862500000 0.038471865
+ 0.875000000 0.043679007
+ 0.887500000 0.049057924
+ 0.900000000 0.075655078
+ 0.912500000 0.131419709
+ 0.925000000 0.187559080
+ 0.937500000 0.244195383
+ 0.950000000 0.301450809
+ 0.962500000 0.359447550
+ 0.975000000 0.418307796
+ 0.987500000 0.478153738
+ 1.000000000 0.539107569
+ 1.012500000 0.601291478
+ 1.025000000 0.664827658
+ 1.037500000 0.790182143
+ 1.050000000 0.924092873
+ 1.062500000 1.059421995
+ 1.075000000 1.196133127
+ 1.087500000 1.334189889
+ 1.100000000 1.473555901
+ 1.112500000 1.614194780
+ 1.125000000 1.756070147
+ 1.137500000 1.899145621
+ 1.150000000 2.043384820
+ 1.162500000 2.115443998
+ 1.175000000 2.062823777
+ 1.187500000 2.010910641
+ 1.200000000 1.959414268
+ 1.212500000 1.908044334
+ 1.225000000 1.856510519
+ 1.237500000 1.804522500
+ 1.250000000 1.751789955
+ 1.262500000 1.698022562
+ 1.275000000 1.642929998
+ 1.287500000 1.586221942
+ 1.300000000 1.483133696
+ 1.312500000 1.369857501
+ 1.325000000 1.254870787
+ 1.337500000 1.138304460
+ 1.350000000 1.020289421
+ 1.362500000 0.900956575
+ 1.375000000 0.780436824
+ 1.387500000 0.658861071
+ 1.400000000 0.536360221
+ 1.412500000 0.413065175
+ 1.425000000 0.331838273
+ 1.437500000 0.342651735
+ 1.450000000 0.353019494
+ 1.462500000 0.363038851
+ 1.475000000 0.372807103
+ 1.487500000 0.382421548
+ 1.500000000 0.391979486
+ 1.512500000 0.401578216
+ 1.525000000 0.411315034
+ 1.537500000 0.421287241
+ 1.550000000 0.431592135
+ 1.562500000 0.437498760
+ 1.575000000 0.442508770
+ 1.587500000 0.447826106
+ 1.600000000 0.453370774
+ 1.612500000 0.459062784
+ 1.625000000 0.464822144
+ 1.637500000 0.470568860
+ 1.650000000 0.476222941
+ 1.662500000 0.481704396
+ 1.675000000 0.486933230
+ 1.687500000 0.483367208
+ 1.700000000 0.455729666
+ 1.712500000 0.427738579
+ 1.725000000 0.399424036
+ 1.737500000 0.370816126
+ 1.750000000 0.341944940
+ 1.762500000 0.312840567
+ 1.775000000 0.283533096
+ 1.787500000 0.254052616
+ 1.800000000 0.224429218
+ 1.812500000 0.194692990
+ 1.825000000 0.200003929
+ 1.837500000 0.217816711
+ 1.850000000 0.235626575
+ 1.862500000 0.253474918
+ 1.875000000 0.271403141
+ 1.887500000 0.289452640
+ 1.900000000 0.307664817
+ 1.912500000 0.326081068
+ 1.925000000 0.344742793
+ 1.937500000 0.363691390
+ 1.950000000 0.380515852
+ 1.962500000 0.388485100
+ 1.975000000 0.396745673
+ 1.987500000 0.405240050
+ 2.000000000 0.413910712
+ 2.012500000 0.422700138
+ 2.025000000 0.431550808
+ 2.037500000 0.440405203
+ 2.050000000 0.449205801
+ 2.062500000 0.457895083
+ 2.075000000 0.466415528
+ 2.087500000 0.448837100
+ 2.100000000 0.419066251
+ 2.112500000 0.389036635
+ 2.125000000 0.358739797
+ 2.137500000 0.328167277
+ 2.150000000 0.297310617
+ 2.162500000 0.266161360
+ 2.175000000 0.234711048
+ 2.187500000 0.202951223
+ 2.200000000 0.170873427
+ 2.212500000 0.141976457
+ 2.225000000 0.131460573
+ 2.237500000 0.120649734
+ 2.250000000 0.109577273
+ 2.262500000 0.098276525
+ 2.275000000 0.086780822
+ 2.287500000 0.075123498
+ 2.300000000 0.063337887
+ 2.312500000 0.051457321
+ 2.325000000 0.039515135
+ 2.337500000 0.027544661
+ 2.350000000 0.031015234
+ 2.362500000 0.043524876
+ 2.375000000 0.056096571
+ 2.387500000 0.068757733
+ 2.400000000 0.081535773
+ 2.412500000 0.094458106
+ 2.425000000 0.107552143
+ 2.437500000 0.120845299
+ 2.450000000 0.134364985
+ 2.462500000 0.148138615
+ 2.475000000 0.162607746
+ 2.487500000 0.180893518
+ 2.500000000 0.199454268
+ 2.512500000 0.218262031
+ 2.525000000 0.237288844
+ 2.537500000 0.256506744
+ 2.550000000 0.275887768
+ 2.562500000 0.295403951
+ 2.575000000 0.315027330
+ 2.587500000 0.334729943
+ 2.600000000 0.354483824
+ 2.612500000 0.352471697
+ 2.625000000 0.334606535
+ 2.637500000 0.316704297
+ 2.650000000 0.298734199
+ 2.662500000 0.280665456
+ 2.675000000 0.262467283
+ 2.687500000 0.244108896
+ 2.700000000 0.225559509
+ 2.712500000 0.206788338
+ 2.725000000 0.187764597
+ 2.737500000 0.168776896
+ 2.750000000 0.155234740
+ 2.762500000 0.141405278
+ 2.775000000 0.127312462
+ 2.787500000 0.112980244
+ 2.800000000 0.098432576
+ 2.812500000 0.083693409
+ 2.825000000 0.068786697
+ 2.837500000 0.053736390
+ 2.850000000 0.038566440
+ 2.862500000 0.023300800
+ 2.875000000 0.015360623
+ 2.887500000 0.014020545
+ 2.900000000 0.012628587
+ 2.912500000 0.011190324
+ 2.925000000 0.009711333
+ 2.937500000 0.008197192
+ 2.950000000 0.006653477
+ 2.962500000 0.005085765
+ 2.975000000 0.003499633
+ 2.987500000 0.001900657
+ 3.000000000 0.000294415
diff --git a/regtest/rt24/plumed.dat b/regtest/rt24/plumed.dat
new file mode 100644
index 000000000..c4854792e
--- /dev/null
+++ b/regtest/rt24/plumed.dat
@@ -0,0 +1,6 @@
+DISTANCES GROUP=1-7 FIELD=(MIN=0.5 MAX=3.0 NSPLINE=20 SIGMA=0.1) LABEL=f1
+DUMPFIELD FIELD=f1 NGRID=200 STRIDE=50 FILE_BASE=field
+FIELD_METAD FIELD=f1 NGRID=400 STRIDE=1 PACE=10 HEIGHT=40.0 LABEL=m1
+FIELD_METAD FIELD=f1 NGRID=400 STRIDE=1 PACE=10 HEIGHT=40.0 NUMERICAL_DERIVATIVES LABEL=m1num
+PRINT ARG=m1.bias STRIDE=1 FILE=colvar FMT=%8.4f
+DUMPDERIVATIVES ARG=m1.*,m1num.* STRIDE=1 FILE=derivatives FMT=%8.4f
diff --git a/regtest/rt24/trajectory.xyz b/regtest/rt24/trajectory.xyz
new file mode 100644
index 000000000..f3c9dd586
--- /dev/null
+++ b/regtest/rt24/trajectory.xyz
@@ -0,0 +1,550 @@
+ 108
+ 5.03880000000000 5.03880000000000 5.03880000000000
+ Ar -3.442612640030015E-002 -3.038146094065802E-003 8.961853877526049E-003
+ Ar 0.912465016333831 -1.524861115033656E-002 0.844060122693179
+ Ar 0.832342813262219 0.848949986466364 4.278373810313130E-002
+ Ar 3.527583123517383E-002 0.896047934140808 0.795328840291565
+ Ar -1.888111290252139E-003 4.453056230294513E-002 1.62162507464617
+ Ar 0.860851777160665 4.089630217237031E-002 2.48983344757901
+ Ar 0.854675871454438 0.842986941975215 1.66825869975346
+ Ar -1.030990630180061E-002 0.815049429651274 2.52945420325888
+ Ar -8.659954805468062E-002 1.618984616300863E-002 3.35333175349348
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diff --git a/regtest/rt25/derivatives.reference b/regtest/rt25/derivatives.reference
index d81ff6b28..b16103964 100644
--- a/regtest/rt25/derivatives.reference
+++ b/regtest/rt25/derivatives.reference
@@ -1,196 +1,196 @@
#! FIELDS time parameter c1.moment_3 c1num.moment_3
- 0.000000 0 -0.02075 -0.02075
- 0.000000 1 -0.01695 -0.01695
- 0.000000 2 -0.01943 -0.01943
- 0.000000 3 0.01779 0.01779
- 0.000000 4 -0.01955 -0.01955
- 0.000000 5 0.01238 0.01238
- 0.000000 6 0.01862 0.01862
- 0.000000 7 0.02529 0.02529
- 0.000000 8 -0.02268 -0.02268
- 0.000000 9 -0.00330 -0.00330
- 0.000000 10 0.00163 0.00163
- 0.000000 11 0.01840 0.01840
- 0.000000 12 -0.00246 -0.00246
- 0.000000 13 0.00479 0.00479
- 0.000000 14 -0.00684 -0.00684
- 0.000000 15 0.01331 0.01331
- 0.000000 16 -0.01926 -0.01926
- 0.000000 17 0.01903 0.01903
- 0.000000 18 -0.00784 -0.00784
- 0.000000 19 0.00115 0.00115
- 0.000000 20 -0.01019 -0.01019
- 0.000000 21 -0.02217 -0.02217
- 0.000000 22 0.00944 0.00944
- 0.000000 23 0.02363 0.02363
- 0.000000 24 0.03388 0.03388
- 0.000000 25 0.01162 0.01162
- 0.000000 26 0.00402 0.00402
- 0.000000 27 -0.02707 -0.02707
- 0.000000 28 0.00184 0.00184
- 0.000000 29 -0.01832 -0.01832
- 0.000000 30 -0.01332 -0.01332
- 0.000000 31 0.01143 0.01143
- 0.000000 32 0.01344 0.01343
- 0.000000 33 0.01143 0.01143
- 0.000000 34 -0.03159 -0.03159
- 0.000000 35 -0.00805 -0.00805
- 0.000000 36 0.01344 0.02755
- 0.000000 37 -0.00805 -0.01805
- 0.000000 38 0.00449 0.00449
- 0.005000 0 -0.02229 -0.02229
- 0.005000 1 -0.01564 -0.01564
- 0.005000 2 -0.01905 -0.01905
- 0.005000 3 0.02347 0.02347
- 0.005000 4 -0.02829 -0.02829
- 0.005000 5 0.01096 0.01096
- 0.005000 6 0.01598 0.01598
- 0.005000 7 0.03010 0.03010
- 0.005000 8 -0.02402 -0.02402
- 0.005000 9 -0.00260 -0.00260
- 0.005000 10 -0.00128 -0.00128
- 0.005000 11 0.01919 0.01919
- 0.005000 12 -0.00335 -0.00335
- 0.005000 13 0.00738 0.00738
- 0.005000 14 -0.00862 -0.00862
- 0.005000 15 0.01727 0.01727
- 0.005000 16 -0.02229 -0.02229
- 0.005000 17 0.02044 0.02044
- 0.005000 18 -0.00934 -0.00934
- 0.005000 19 0.00566 0.00566
- 0.005000 20 -0.00927 -0.00927
- 0.005000 21 -0.02910 -0.02910
- 0.005000 22 0.00736 0.00736
- 0.005000 23 0.03100 0.03100
- 0.005000 24 0.03791 0.03791
- 0.005000 25 0.01520 0.01520
- 0.005000 26 0.00114 0.00114
- 0.005000 27 -0.02795 -0.02795
- 0.005000 28 0.00180 0.00180
- 0.005000 29 -0.02178 -0.02178
- 0.005000 30 -0.01869 -0.01869
- 0.005000 31 0.01705 0.01705
- 0.005000 32 0.01534 0.01534
- 0.005000 33 0.01705 0.01705
- 0.005000 34 -0.03493 -0.03493
- 0.005000 35 -0.01393 -0.01393
- 0.005000 36 0.01534 0.02356
- 0.005000 37 -0.01393 -0.02055
- 0.005000 38 0.00255 0.00255
- 0.010000 0 -0.04346 -0.04346
- 0.010000 1 -0.02771 -0.02771
- 0.010000 2 -0.01177 -0.01177
- 0.010000 3 0.02203 0.02203
- 0.010000 4 -0.03996 -0.03996
- 0.010000 5 0.02423 0.02423
- 0.010000 6 0.02824 0.02824
- 0.010000 7 0.05051 0.05051
- 0.010000 8 -0.02918 -0.02918
- 0.010000 9 -0.01147 -0.01147
- 0.010000 10 -0.00945 -0.00945
- 0.010000 11 0.04875 0.04875
- 0.010000 12 0.03658 0.03658
- 0.010000 13 0.04816 0.04816
- 0.010000 14 -0.01290 -0.01290
- 0.010000 15 0.01584 0.01584
- 0.010000 16 -0.02621 -0.02621
- 0.010000 17 0.01387 0.01387
- 0.010000 18 -0.03215 -0.03215
- 0.010000 19 -0.00700 -0.00700
- 0.010000 20 -0.00795 -0.00795
- 0.010000 21 -0.03884 -0.03884
- 0.010000 22 -0.00154 -0.00154
- 0.010000 23 0.02270 0.02270
- 0.010000 24 0.04587 0.04587
- 0.010000 25 0.01975 0.01975
- 0.010000 26 -0.00065 -0.00065
- 0.010000 27 -0.02263 -0.02263
- 0.010000 28 -0.00655 -0.00655
- 0.010000 29 -0.04709 -0.04709
- 0.010000 30 -0.01249 -0.01249
- 0.010000 31 0.03377 0.03377
- 0.010000 32 0.02746 0.02746
- 0.010000 33 0.03377 0.03377
- 0.010000 34 -0.03203 -0.03203
- 0.010000 35 -0.02882 -0.02882
- 0.010000 36 0.02746 -0.01832
- 0.010000 37 -0.02882 0.00369
- 0.010000 38 0.01573 0.01573
- 0.015000 0 -0.05933 -0.05933
- 0.015000 1 -0.04027 -0.04027
- 0.015000 2 -0.00244 -0.00244
- 0.015000 3 0.01901 0.01901
- 0.015000 4 -0.04115 -0.04115
- 0.015000 5 0.03419 0.03419
- 0.015000 6 0.03489 0.03489
- 0.015000 7 0.05626 0.05626
- 0.015000 8 -0.02956 -0.02956
- 0.015000 9 -0.01655 -0.01655
- 0.015000 10 -0.00691 -0.00691
- 0.015000 11 0.08431 0.08431
- 0.015000 12 0.08708 0.08708
- 0.015000 13 0.09002 0.09002
- 0.015000 14 -0.01294 -0.01294
- 0.015000 15 0.01293 0.01293
- 0.015000 16 -0.02175 -0.02175
- 0.015000 17 -0.00204 -0.00204
- 0.015000 18 -0.07196 -0.07196
- 0.015000 19 -0.03209 -0.03209
- 0.015000 20 -0.00269 -0.00269
- 0.015000 21 -0.03969 -0.03969
- 0.015000 22 -0.00916 -0.00916
- 0.015000 23 -0.00367 -0.00367
- 0.015000 24 0.04456 0.04456
- 0.015000 25 0.01846 0.01846
- 0.015000 26 0.00060 0.00060
- 0.015000 27 -0.01094 -0.01094
- 0.015000 28 -0.01340 -0.01340
- 0.015000 29 -0.06577 -0.06577
- 0.015000 30 0.01259 0.01259
- 0.015000 31 0.05240 0.05240
- 0.015000 32 0.03641 0.03641
- 0.015000 33 0.05240 0.05240
- 0.015000 34 -0.02355 -0.02355
- 0.015000 35 -0.04299 -0.04299
- 0.015000 36 0.03641 -0.06550
- 0.015000 37 -0.04299 0.02063
- 0.015000 38 0.03742 0.03742
- 0.020000 0 -0.04692 -0.04692
- 0.020000 1 -0.03696 -0.03696
- 0.020000 2 -0.00027 -0.00027
- 0.020000 3 0.01756 0.01756
- 0.020000 4 -0.02842 -0.02842
- 0.020000 5 0.02850 0.02850
- 0.020000 6 0.02546 0.02546
- 0.020000 7 0.03906 0.03906
- 0.020000 8 -0.02074 -0.02074
- 0.020000 9 -0.01337 -0.01337
- 0.020000 10 0.01109 0.01109
- 0.020000 11 0.06544 0.06544
- 0.020000 12 0.07374 0.07374
- 0.020000 13 0.06873 0.06873
- 0.020000 14 -0.00626 -0.00626
- 0.020000 15 0.01081 0.01081
- 0.020000 16 -0.01364 -0.01364
- 0.020000 17 -0.00791 -0.00791
- 0.020000 18 -0.06574 -0.06574
- 0.020000 19 -0.03588 -0.03588
- 0.020000 20 0.00296 0.00296
- 0.020000 21 -0.03070 -0.03070
- 0.020000 22 -0.00802 -0.00802
- 0.020000 23 -0.00495 -0.00495
- 0.020000 24 0.03777 0.03777
- 0.020000 25 0.01647 0.01647
- 0.020000 26 0.00301 0.00301
- 0.020000 27 -0.00861 -0.00861
- 0.020000 28 -0.01243 -0.01243
- 0.020000 29 -0.05977 -0.05977
- 0.020000 30 0.01666 0.01666
- 0.020000 31 0.05059 0.05059
- 0.020000 32 0.02948 0.02948
- 0.020000 33 0.05059 0.05059
- 0.020000 34 -0.01826 -0.01826
- 0.020000 35 -0.03973 -0.03973
- 0.020000 36 0.02948 -0.06181
- 0.020000 37 -0.03973 0.01551
- 0.020000 38 0.02872 0.02872
+ 0.000000 0 -0.0208 -0.0208
+ 0.000000 1 -0.0169 -0.0169
+ 0.000000 2 -0.0194 -0.0194
+ 0.000000 3 0.0178 0.0178
+ 0.000000 4 -0.0196 -0.0196
+ 0.000000 5 0.0124 0.0124
+ 0.000000 6 0.0186 0.0186
+ 0.000000 7 0.0253 0.0253
+ 0.000000 8 -0.0227 -0.0227
+ 0.000000 9 -0.0033 -0.0033
+ 0.000000 10 0.0016 0.0016
+ 0.000000 11 0.0184 0.0184
+ 0.000000 12 -0.0025 -0.0025
+ 0.000000 13 0.0048 0.0048
+ 0.000000 14 -0.0068 -0.0068
+ 0.000000 15 0.0133 0.0133
+ 0.000000 16 -0.0193 -0.0193
+ 0.000000 17 0.0190 0.0190
+ 0.000000 18 -0.0078 -0.0078
+ 0.000000 19 0.0012 0.0012
+ 0.000000 20 -0.0102 -0.0102
+ 0.000000 21 -0.0222 -0.0222
+ 0.000000 22 0.0094 0.0094
+ 0.000000 23 0.0236 0.0236
+ 0.000000 24 0.0339 0.0339
+ 0.000000 25 0.0116 0.0116
+ 0.000000 26 0.0040 0.0040
+ 0.000000 27 -0.0271 -0.0271
+ 0.000000 28 0.0018 0.0018
+ 0.000000 29 -0.0183 -0.0183
+ 0.000000 30 -0.0133 -0.0133
+ 0.000000 31 0.0114 0.0114
+ 0.000000 32 0.0134 0.0134
+ 0.000000 33 0.0114 0.0114
+ 0.000000 34 -0.0316 -0.0316
+ 0.000000 35 -0.0081 -0.0081
+ 0.000000 36 0.0134 0.0276
+ 0.000000 37 -0.0081 -0.0180
+ 0.000000 38 0.0045 0.0045
+ 0.005000 0 -0.0223 -0.0223
+ 0.005000 1 -0.0156 -0.0156
+ 0.005000 2 -0.0191 -0.0191
+ 0.005000 3 0.0235 0.0235
+ 0.005000 4 -0.0283 -0.0283
+ 0.005000 5 0.0110 0.0110
+ 0.005000 6 0.0160 0.0160
+ 0.005000 7 0.0301 0.0301
+ 0.005000 8 -0.0240 -0.0240
+ 0.005000 9 -0.0026 -0.0026
+ 0.005000 10 -0.0013 -0.0013
+ 0.005000 11 0.0192 0.0192
+ 0.005000 12 -0.0034 -0.0034
+ 0.005000 13 0.0074 0.0074
+ 0.005000 14 -0.0086 -0.0086
+ 0.005000 15 0.0173 0.0173
+ 0.005000 16 -0.0223 -0.0223
+ 0.005000 17 0.0204 0.0204
+ 0.005000 18 -0.0093 -0.0093
+ 0.005000 19 0.0057 0.0057
+ 0.005000 20 -0.0093 -0.0093
+ 0.005000 21 -0.0291 -0.0291
+ 0.005000 22 0.0074 0.0074
+ 0.005000 23 0.0310 0.0310
+ 0.005000 24 0.0379 0.0379
+ 0.005000 25 0.0152 0.0152
+ 0.005000 26 0.0011 0.0011
+ 0.005000 27 -0.0279 -0.0279
+ 0.005000 28 0.0018 0.0018
+ 0.005000 29 -0.0218 -0.0218
+ 0.005000 30 -0.0187 -0.0187
+ 0.005000 31 0.0171 0.0171
+ 0.005000 32 0.0153 0.0153
+ 0.005000 33 0.0171 0.0171
+ 0.005000 34 -0.0349 -0.0349
+ 0.005000 35 -0.0139 -0.0139
+ 0.005000 36 0.0153 0.0236
+ 0.005000 37 -0.0139 -0.0206
+ 0.005000 38 0.0026 0.0026
+ 0.010000 0 -0.0435 -0.0435
+ 0.010000 1 -0.0277 -0.0277
+ 0.010000 2 -0.0118 -0.0118
+ 0.010000 3 0.0220 0.0220
+ 0.010000 4 -0.0400 -0.0400
+ 0.010000 5 0.0242 0.0242
+ 0.010000 6 0.0282 0.0282
+ 0.010000 7 0.0505 0.0505
+ 0.010000 8 -0.0292 -0.0292
+ 0.010000 9 -0.0115 -0.0115
+ 0.010000 10 -0.0095 -0.0095
+ 0.010000 11 0.0488 0.0488
+ 0.010000 12 0.0366 0.0366
+ 0.010000 13 0.0482 0.0482
+ 0.010000 14 -0.0129 -0.0129
+ 0.010000 15 0.0158 0.0158
+ 0.010000 16 -0.0262 -0.0262
+ 0.010000 17 0.0139 0.0139
+ 0.010000 18 -0.0322 -0.0322
+ 0.010000 19 -0.0070 -0.0070
+ 0.010000 20 -0.0079 -0.0079
+ 0.010000 21 -0.0388 -0.0388
+ 0.010000 22 -0.0015 -0.0015
+ 0.010000 23 0.0227 0.0227
+ 0.010000 24 0.0459 0.0459
+ 0.010000 25 0.0197 0.0197
+ 0.010000 26 -0.0007 -0.0007
+ 0.010000 27 -0.0226 -0.0226
+ 0.010000 28 -0.0065 -0.0065
+ 0.010000 29 -0.0471 -0.0471
+ 0.010000 30 -0.0125 -0.0125
+ 0.010000 31 0.0338 0.0338
+ 0.010000 32 0.0275 0.0275
+ 0.010000 33 0.0338 0.0338
+ 0.010000 34 -0.0320 -0.0320
+ 0.010000 35 -0.0288 -0.0288
+ 0.010000 36 0.0275 -0.0183
+ 0.010000 37 -0.0288 0.0037
+ 0.010000 38 0.0157 0.0157
+ 0.015000 0 -0.0593 -0.0593
+ 0.015000 1 -0.0403 -0.0403
+ 0.015000 2 -0.0024 -0.0024
+ 0.015000 3 0.0190 0.0190
+ 0.015000 4 -0.0411 -0.0411
+ 0.015000 5 0.0342 0.0342
+ 0.015000 6 0.0349 0.0349
+ 0.015000 7 0.0563 0.0563
+ 0.015000 8 -0.0296 -0.0296
+ 0.015000 9 -0.0165 -0.0165
+ 0.015000 10 -0.0069 -0.0069
+ 0.015000 11 0.0843 0.0843
+ 0.015000 12 0.0871 0.0871
+ 0.015000 13 0.0900 0.0900
+ 0.015000 14 -0.0129 -0.0129
+ 0.015000 15 0.0129 0.0129
+ 0.015000 16 -0.0218 -0.0218
+ 0.015000 17 -0.0020 -0.0020
+ 0.015000 18 -0.0720 -0.0720
+ 0.015000 19 -0.0321 -0.0321
+ 0.015000 20 -0.0027 -0.0027
+ 0.015000 21 -0.0397 -0.0397
+ 0.015000 22 -0.0092 -0.0092
+ 0.015000 23 -0.0037 -0.0037
+ 0.015000 24 0.0446 0.0446
+ 0.015000 25 0.0185 0.0185
+ 0.015000 26 0.0006 0.0006
+ 0.015000 27 -0.0109 -0.0109
+ 0.015000 28 -0.0134 -0.0134
+ 0.015000 29 -0.0658 -0.0658
+ 0.015000 30 0.0126 0.0126
+ 0.015000 31 0.0524 0.0524
+ 0.015000 32 0.0364 0.0364
+ 0.015000 33 0.0524 0.0524
+ 0.015000 34 -0.0236 -0.0236
+ 0.015000 35 -0.0430 -0.0430
+ 0.015000 36 0.0364 -0.0655
+ 0.015000 37 -0.0430 0.0206
+ 0.015000 38 0.0374 0.0374
+ 0.020000 0 -0.0469 -0.0469
+ 0.020000 1 -0.0370 -0.0370
+ 0.020000 2 -0.0003 -0.0003
+ 0.020000 3 0.0176 0.0176
+ 0.020000 4 -0.0284 -0.0284
+ 0.020000 5 0.0285 0.0285
+ 0.020000 6 0.0255 0.0255
+ 0.020000 7 0.0391 0.0391
+ 0.020000 8 -0.0207 -0.0207
+ 0.020000 9 -0.0134 -0.0134
+ 0.020000 10 0.0111 0.0111
+ 0.020000 11 0.0654 0.0654
+ 0.020000 12 0.0737 0.0737
+ 0.020000 13 0.0687 0.0687
+ 0.020000 14 -0.0063 -0.0063
+ 0.020000 15 0.0108 0.0108
+ 0.020000 16 -0.0136 -0.0136
+ 0.020000 17 -0.0079 -0.0079
+ 0.020000 18 -0.0657 -0.0657
+ 0.020000 19 -0.0359 -0.0359
+ 0.020000 20 0.0030 0.0030
+ 0.020000 21 -0.0307 -0.0307
+ 0.020000 22 -0.0080 -0.0080
+ 0.020000 23 -0.0050 -0.0050
+ 0.020000 24 0.0378 0.0378
+ 0.020000 25 0.0165 0.0165
+ 0.020000 26 0.0030 0.0030
+ 0.020000 27 -0.0086 -0.0086
+ 0.020000 28 -0.0124 -0.0124
+ 0.020000 29 -0.0598 -0.0598
+ 0.020000 30 0.0167 0.0167
+ 0.020000 31 0.0506 0.0506
+ 0.020000 32 0.0295 0.0295
+ 0.020000 33 0.0506 0.0506
+ 0.020000 34 -0.0183 -0.0183
+ 0.020000 35 -0.0397 -0.0397
+ 0.020000 36 0.0295 -0.0618
+ 0.020000 37 -0.0397 0.0155
+ 0.020000 38 0.0287 0.0287
diff --git a/regtest/rt25/plumed.dat b/regtest/rt25/plumed.dat
index db0c807be..a6d318fc6 100644
--- a/regtest/rt25/plumed.dat
+++ b/regtest/rt25/plumed.dat
@@ -1,3 +1,3 @@
COORDINATIONNUMBER SPECIES=1-10 SWITCH=(SPLINE R_0=1.0) MOMENT=3 LABEL=c1
COORDINATIONNUMBER SPECIES=1-10 SWITCH=(SPLINE R_0=1.0) MOMENT=3 NUMERICAL_DERIVATIVES LABEL=c1num
-DUMPDERIVATIVES ARG=c1.*,c1num.* STRIDE=1 FILE=derivatives FMT=%8.5f
+DUMPDERIVATIVES ARG=c1.*,c1num.* STRIDE=1 FILE=derivatives FMT=%8.4f
diff --git a/src/Action.cpp b/src/Action.cpp
index 8f82ad335..23cd3ab9d 100644
--- a/src/Action.cpp
+++ b/src/Action.cpp
@@ -1,4 +1,5 @@
#include "Action.h"
+#include "ActionWithValue.h"
#include "PlumedMain.h"
#include "Log.h"
#include "PlumedException.h"
@@ -144,11 +145,12 @@ void Action::checkRead(){
std::string msg="cannot understand the following words from the input line : ";
for(unsigned i=0;i<line.size();i++) msg = msg + line[i] + ", ";
error(msg);
-// log.printf("ERROR READING INPUT FILE\n");
-// log.printf("I CANNOT UNDERSTAND THE FOLLOWING WORDS:\n");
-// for(unsigned i=0;i<line.size();i++) log.printf(" %s\n",line[i].c_str());
-// log.printf("STOP!!\n");
-// exit(1);
+ }
+ // Check numerical derivatives
+ if( checkNumericalDerivatives() ){
+ ActionWithValue* aa=dynamic_cast<ActionWithValue*>(this);
+ plumed_assert(aa);
+ if( aa->getNumberOfComponents()==0 ) error("cannot calculate numerical derivatives for this action");
}
}
@@ -170,7 +172,7 @@ void Action::exit(int c){
plumed.exit(c);
}
-void Action::calculateNumericalDerivatives(){
+void Action::calculateNumericalDerivatives( ActionWithValue* a ){
plumed_merror("if you get here it means that you are trying to use numerical derivatives for a class that does not implement them");
}
diff --git a/src/Action.h b/src/Action.h
index 889b0d5fa..fa82f5632 100644
--- a/src/Action.h
+++ b/src/Action.h
@@ -4,6 +4,7 @@
#include <string>
#include <set>
#include "Keywords.h"
+#include "Value.h"
#include "Tools.h"
#include "Log.h"
@@ -196,7 +197,9 @@ public:
virtual bool checkNeedsGradients()const{return false;}
/// Perform calculation using numerical derivatives
- virtual void calculateNumericalDerivatives();
+/// N.B. only pass an ActionWithValue to this routine if you know exactly what you
+/// are doing.
+ virtual void calculateNumericalDerivatives( ActionWithValue* a=NULL );
FILE *fopen(const char *path, const char *mode);
int fclose(FILE*fp);
@@ -246,8 +249,7 @@ template<class T>
bool Action::parseNumbered(const std::string&key, const int no, T&t){
// Check keyword has been registered
plumed_massert(keywords.exists(key),"keyword " + key + " has not been registered");
- plumed_massert( ( keywords.style(key,"nohtml") || keywords.style(key,"numbered") ),
- "keyword " + key + " has not been registered so you can read in numbered versions");
+ if( !keywords.numbered(key) ) error("numbered keywords are not allowed for " + key );
// Now try to read the keyword
bool found; std::string def;
@@ -299,14 +301,13 @@ void Action::parseVector(const std::string&key,std::vector<T>&t){
template<class T>
bool Action::parseNumberedVector(const std::string&key, const int no, std::vector<T>&t){
plumed_massert(keywords.exists(key),"keyword " + key + " has not been registered");
- plumed_massert( ( keywords.style(key,"nohtml") || keywords.style(key,"numbered") || keywords.style(key,"atoms") ),
- "keyword " + key + " has not been registered so you can read in numbered versions");
+ if( !keywords.numbered(key) ) error("numbered keywords are not allowed for " + key );
unsigned size=t.size(); bool skipcheck=false;
if(size==0) skipcheck=true;
std::string num; Tools::convert(no,num);
bool found=Tools::parseVector(line,key+num,t);
- if( keywords.style(key,"numbered") ){
+ if( keywords.style(key,"compulsory") ){
if (!skipcheck && found && t.size()!=size ) error("vector read in for keyword " + key + num + " has the wrong size");
} else if ( !found ){
t.resize(0);
diff --git a/src/ActionAtomistic.cpp b/src/ActionAtomistic.cpp
index eea5e5a1b..269ba48a3 100644
--- a/src/ActionAtomistic.cpp
+++ b/src/ActionAtomistic.cpp
@@ -6,6 +6,7 @@
#include "ActionWithValue.h"
#include "Colvar.h"
#include "ActionWithVirtualAtom.h"
+#include "ActionWithField.h"
#include "PlumedException.h"
#include "Atoms.h"
@@ -54,9 +55,12 @@ Vector ActionAtomistic::pbcDistance(const Vector &v1,const Vector &v2)const{
return pbc.distance(v1,v2);
}
-void ActionAtomistic::calculateNumericalDerivatives(){
- ActionWithValue*a=dynamic_cast<ActionWithValue*>(this);
- plumed_massert(a,"only Actions with a value can be differentiated");
+void ActionAtomistic::calculateNumericalDerivatives( ActionWithValue* a ){
+ if(!a){
+ a=dynamic_cast<ActionWithValue*>(this);
+ plumed_massert(a,"only Actions with a value can be differentiated");
+ }
+
const int nval=a->getNumberOfComponents();
const int natoms=getNumberOfAtoms();
std::vector<Vector> value(nval*natoms);
@@ -67,7 +71,7 @@ void ActionAtomistic::calculateNumericalDerivatives(){
for(int i=0;i<natoms;i++) for(int k=0;k<3;k++){
savedPositions[i][k]=positions[i][k];
positions[i][k]=positions[i][k]+delta;
- calculate();
+ a->calculate();
positions[i][k]=savedPositions[i][k];
for(unsigned j=0;j<nval;j++){
value[j*natoms+i][k]=a->getOutputQuantity(j);
@@ -79,14 +83,14 @@ void ActionAtomistic::calculateNumericalDerivatives(){
box(i,k)=box(i,k)+delta;
pbc.setBox(box);
for(int j=0;j<natoms;j++) positions[j]=pbc.scaledToReal(positions[j]);
- calculate();
+ a->calculate();
box(i,k)=arg0;
pbc.setBox(box);
for(int j=0;j<natoms;j++) positions[j]=savedPositions[j];
for(unsigned j=0;j<nval;j++) valuebox[j](i,k)=a->getOutputQuantity(j);
}
- calculate();
+ a->calculate();
a->clearDerivatives();
for(unsigned j=0;j<nval;j++){
Value* v=a->copyOutput(j);
diff --git a/src/ActionAtomistic.h b/src/ActionAtomistic.h
index 79d4a1b3e..e2c6a1c86 100644
--- a/src/ActionAtomistic.h
+++ b/src/ActionAtomistic.h
@@ -88,7 +88,9 @@ public:
void clearOutputForces();
- void calculateNumericalDerivatives();
+/// N.B. only pass an ActionWithValue to this routine if you know exactly what you
+/// are doing. The default will be correct for the vast majority of cases
+ void calculateNumericalDerivatives( ActionWithValue* a=NULL );
void retrieveAtoms();
void applyForces();
diff --git a/src/ActionWithArguments.cpp b/src/ActionWithArguments.cpp
index 48da48e23..fb7461109 100644
--- a/src/ActionWithArguments.cpp
+++ b/src/ActionWithArguments.cpp
@@ -1,6 +1,7 @@
#include "ActionWithArguments.h"
#include "ActionWithValue.h"
#include "PlumedMain.h"
+#include "ActionWithField.h"
#include "ActionSet.h"
using namespace std;
@@ -101,22 +102,25 @@ ActionWithArguments::ActionWithArguments(const ActionOptions&ao):
}
}
-void ActionWithArguments::calculateNumericalDerivatives(){
- ActionWithValue*a=dynamic_cast<ActionWithValue*>(this);
- plumed_massert(a,"cannot compute numerical derivatives for an action without values");
+void ActionWithArguments::calculateNumericalDerivatives( ActionWithValue* a ){
+ if(!a){
+ a=dynamic_cast<ActionWithValue*>(this);
+ plumed_massert(a,"cannot compute numerical derivatives for an action without values");
+ }
+
const int nval=a->getNumberOfComponents();
const int npar=arguments.size();
std::vector<double> value (nval*npar);
for(int i=0;i<npar;i++){
double arg0=arguments[i]->get();
arguments[i]->set(arg0+sqrt(epsilon));
- calculate();
+ a->calculate();
arguments[i]->set(arg0);
for(unsigned j=0;j<nval;j++){
value[i*nval+j]=a->getOutputQuantity(j);
}
}
- calculate();
+ a->calculate();
a->clearDerivatives();
std::vector<double> value0(nval);
for(unsigned j=0;j<nval;j++){
diff --git a/src/ActionWithArguments.h b/src/ActionWithArguments.h
index 00173fddc..4ce52ef4a 100644
--- a/src/ActionWithArguments.h
+++ b/src/ActionWithArguments.h
@@ -47,7 +47,9 @@ public:
/// Registers the list of keywords
static void registerKeywords( Keywords& keys );
/// Calculate the numerical derivatives
- void calculateNumericalDerivatives();
+/// N.B. only pass an ActionWithValue to this routine if you know exactly what you
+/// are doing. The default will be correct for the vast majority of cases
+ void calculateNumericalDerivatives( ActionWithValue* a=NULL );
void lockRequests();
void unlockRequests();
/// Returns an array of pointers to the arguments
diff --git a/src/ActionWithDistribution.cpp b/src/ActionWithDistribution.cpp
index c9de00126..d602c28e4 100644
--- a/src/ActionWithDistribution.cpp
+++ b/src/ActionWithDistribution.cpp
@@ -23,7 +23,7 @@ ActionWithDistribution::ActionWithDistribution(const ActionOptions&ao):
lastUpdate(0),
reduceAtNextStep(false),
tolerance(0),
- f_interpolator(NULL)
+ myfield(NULL)
{
if( keywords.exists("SERIAL") ) parseFlag("SERIAL",serial);
else serial=true;
@@ -40,12 +40,8 @@ ActionWithDistribution::ActionWithDistribution(const ActionOptions&ao):
}
ActionWithDistribution::~ActionWithDistribution(){
- delete f_interpolator;
- if( !use_field ){
- for(unsigned i=0;i<functions.size();++i) delete functions[i];
- } else {
- for(unsigned i=0;i<df_interpolators.size();++i) delete df_interpolators[i];
- }
+ delete myfield;
+ for(unsigned i=0;i<functions.size();++i) delete functions[i];
}
void ActionWithDistribution::addDistributionFunction( std::string name, DistributionFunction* fun ){
@@ -97,68 +93,24 @@ void ActionWithDistribution::requestDistribution(){
prepareForNeighborListUpdate(); reduceAtNextStep=true;
}
-void ActionWithDistribution::setupField( unsigned ldim ){
+void ActionWithDistribution::setupField( unsigned ldim, const std::string ftype ){
plumed_massert( keywords.exists("FIELD"), "you have chosen to use fields but have not written documentation for the FIELD keyword");
plumed_massert( ldim<=2 , "fields don't work with more than two dimensions" );
std::string fieldin;
parse("FIELD",fieldin);
- if( fieldin.size()==0 ) return ;
- all_values=false; use_field=true;
- std::vector<std::string> data=Tools::getWords(fieldin);
-
- std::vector<unsigned> nspline; std::vector<double> min,max; double sigma;
- bool found_s=Tools::parseVector( data,"NSPLINE", nspline );
- if(!found_s) field_error("did not find NPLINE keyword");
- if(nspline.size()!=ldim){
- std::string ll,ww;
- Tools::convert(ldim,ll);
- Tools::convert(nspline.size(),ww);
- field_error("found " + ww + " values for NSPLINE when expecting only " + ll);
- }
- bool found_min=Tools::parseVector( data, "MIN", min );
- if(!found_min) field_error("did not find MIN keyword");
- if(min.size()!=ldim){
- std::string ll,ww;
- Tools::convert(ldim,ll);
- Tools::convert(min.size(),ww);
- field_error("found " + ww + " values for MIN when expecting only " + ll);
- }
- bool found_max=Tools::parseVector( data, "MAX", max );
- if(!found_max) field_error("did not find MAX keyword");
- if(max.size()!=ldim){
- std::string ll,ww;
- Tools::convert(ldim,ll);
- Tools::convert(max.size(),ww);
- field_error("found " + ww + " values for MAX when expecting only " + ll);
- }
- bool found_sigma=Tools::parse( data, "SIGMA", sigma );
- if(!found_sigma) field_error("did not find SIGMA keyword");
-
- if( data.size()!=0 ){
- std::string err="found the following rogue keywords : ";
- for(unsigned i=0;i<data.size();++i) err=err + data[i] + ", ";
- field_error(err);
+ if( fieldin.size()==0 ) return;
+ all_values=false; use_field=true; std::string freport;
+ myfield = new Field(); myfield->read( fieldin, getNumberOfFunctionsInDistribution(), ldim, ftype, freport );
+ if( !myfield->check() ){
+ log.printf("ERROR for keyword FIELD in action %s with label %s : %s \n \n", getName().c_str(), getLabel().c_str(), ( myfield->errorMessage() ).c_str() );
+ myfield->printKeywords( log );
+ plumed_merror("ERROR for keyword FIELD in action " + getName() + " with label " + getLabel() + " : " + myfield->errorMessage() );
+ exit(1);
}
+ log.printf(" %s\n", freport.c_str() );
// Setup the field stuff in derived class
- derivedFieldSetup( sigma );
-
- // Setup the field
- unsigned np=1; for(unsigned i=0;i<nspline.size();++i) np*=nspline[i];
- ActionWithValue*a=dynamic_cast<ActionWithValue*>(this);
- plumed_massert(a,"can only do fields on ActionsWithValue");
- myfield.setup( getNumberOfFunctionsInDistribution(), np, a->getNumberOfComponents(), ldim );
-
- // Setup the interpolators
- if( ldim==1 ){
- f_interpolator=new InterpolateCubic( nspline, min, max );
- for(unsigned i=0;i<a->getNumberOfComponents();++i) df_interpolators.push_back( new InterpolateCubic( nspline, min, max ) );
- } else if( ldim==2 ) {
- f_interpolator=new InterpolateBicubic( nspline, min, max );
- for(unsigned i=0;i<a->getNumberOfComponents();++i) df_interpolators.push_back( new InterpolateBicubic( nspline, min, max ) );
- } else {
- plumed_assert(0);
- }
+ derivedFieldSetup( myfield->get_sigma() );
}
void ActionWithDistribution::prepare(){
@@ -167,16 +119,14 @@ void ActionWithDistribution::prepare(){
// Setup the functions by declaring enough space to hold the derivatives
for(unsigned i=0;i<functions.size();++i) functions[i]->setNumberOfDerivatives( final_values[0]->getNumberOfDerivatives() );
// Setup the buffers for mpi gather
- if(!serial){
- if( use_field ){
- std::vector<unsigned> cv_sizes( getNumberOfFunctionsInDistribution() );
- for(unsigned i=0;i<getNumberOfFunctionsInDistribution();++i){ cv_sizes[i]=getThisFunctionsNumberOfDerivatives(i); }
- myfield.resizeBaseQuantityBuffers( cv_sizes );
- } else {
- unsigned bufsize=0;
- for(unsigned i=0;i<functions.size();++i) bufsize+=functions[i]->requiredBufferSpace();
- buffer.resize( bufsize );
- }
+ if( use_field ){
+ std::vector<unsigned> cv_sizes( getNumberOfFunctionsInDistribution() );
+ for(unsigned i=0;i<getNumberOfFunctionsInDistribution();++i){ cv_sizes[i]=getThisFunctionsNumberOfDerivatives(i); }
+ myfield->resizeBaseQuantityBuffers( cv_sizes ); myfield->resizeDerivatives( getNumberOfFieldDerivatives() );
+ } else {
+ unsigned bufsize=0;
+ for(unsigned i=0;i<functions.size();++i) bufsize+=functions[i]->requiredBufferSpace();
+ buffer.resize( bufsize );
}
reduceAtNextStep=false;
}
@@ -187,16 +137,14 @@ void ActionWithDistribution::prepare(){
// Setup the functions by declaring enough space to hold the derivatives
for(unsigned i=0;i<functions.size();++i) functions[i]->setNumberOfDerivatives( final_values[0]->getNumberOfDerivatives() );
// Setup the buffers for mpi gather
- if(!serial){
- if( use_field ){
- std::vector<unsigned> cv_sizes( getNumberOfFunctionsInDistribution() );
- for(unsigned i=0;i<getNumberOfFunctionsInDistribution();++i){ cv_sizes[i]=getThisFunctionsNumberOfDerivatives(i); }
- myfield.resizeBaseQuantityBuffers( cv_sizes );
- } else {
- unsigned bufsize=0;
- for(unsigned i=0;i<functions.size();++i) bufsize+=functions[i]->requiredBufferSpace();
- buffer.resize( bufsize );
- }
+ if( use_field ){
+ std::vector<unsigned> cv_sizes( getNumberOfFunctionsInDistribution() );
+ for(unsigned i=0;i<getNumberOfFunctionsInDistribution();++i){ cv_sizes[i]=getThisFunctionsNumberOfDerivatives(i); }
+ myfield->resizeBaseQuantityBuffers( cv_sizes ); myfield->resizeDerivatives( getNumberOfFieldDerivatives() );
+ } else {
+ unsigned bufsize=0;
+ for(unsigned i=0;i<functions.size();++i) bufsize+=functions[i]->requiredBufferSpace();
+ buffer.resize( bufsize );
}
reduceAtNextStep=true;
lastUpdate=getStep();
@@ -205,90 +153,6 @@ void ActionWithDistribution::prepare(){
void ActionWithDistribution::calculate(){
plumed_massert( read, "you must have a call to requestDistribution somewhere" );
-
- if( use_field ) calculateField();
- else calculateFunctions();
-}
-
-void ActionWithDistribution::calculateField(){
- unsigned stride=comm.Get_size();
- unsigned rank=comm.Get_rank();
- if(serial){ stride=1; rank=0; }
-
- // Set everything in the field to zero
- myfield.clear();
- unsigned kk; std::vector<Value> aux; Value* tmpvalue=new Value();
- // A loop over the functions in the distribution
- for(unsigned i=rank;i<members.getNumberActive();i+=stride){
- // Retrieve the function we are calculating from the dynamic list
- kk=members[i];
- // Make sure we have enough derivatives in this value
- unsigned nder=getThisFunctionsNumberOfDerivatives(kk);
- if( tmpvalue->getNumberOfDerivatives()!=nder ){ tmpvalue->resizeDerivatives(nder); }
-
- // Calculate the value of this particular function
- calculateThisFunction( kk, tmpvalue, aux );
- // Transfer the value to the field buffers
- myfield.setBaseQuantity( kk, tmpvalue );
-
- // Skip if we are not calculating this particular value
- if( reduceAtNextStep && !tmpvalue->valueHasBeenSet() ){ members.deactivate(kk); deactivate(kk); }
-
- // Reset everything ready for next step
- tmpvalue->clearDerivatives();
- }
- if(!serial){ myfield.gatherBaseQuantities( comm ); }
- // Set the output values for this quantity (we use these to chain rule forces)
- for(unsigned i=0;i<myfield.get_NdX();++i){
- unsigned nder=getThisFunctionsNumberOfDerivatives(i);
- if( tmpvalue->getNumberOfDerivatives()!=nder ){ tmpvalue->resizeDerivatives(nder); }
- myfield.extractBaseQuantity( i, tmpvalue );
- setFieldOutputValue( i, tmpvalue );
- }
-
- std::vector<double> thisp( myfield.get_Ndx() ); bool keep;
- Value tmpstress; tmpstress.resizeDerivatives( myfield.get_Ndx() );
- std::vector<Value> tmpder; tmpder.resize( myfield.get_NdX() );
- for(unsigned i=0;i<myfield.get_NdX();++i) tmpder[i].resizeDerivatives( myfield.get_Ndx() );
-
- // Now loop over the spline points
- unsigned ik=0;
- for(unsigned i=0;i<f_interpolator->getNumberOfSplinePoints();++i){
- f_interpolator->getSplinePoint(i,thisp);
- // Calculate the contributions of all the active colvars
- if( updateFreq>0 ){ keep=false; } else { keep=true; }
- for(unsigned j=0;j<members.getNumberActive();++j){
- if( (ik++)%stride!=rank ) continue; // Ensures we parallelize the double loop over nodes
-
- kk=members[j];
- unsigned nder=getThisFunctionsNumberOfDerivatives(j);
- if( tmpvalue->getNumberOfDerivatives()!=nder ){ tmpvalue->resizeDerivatives(nder); }
- myfield.extractBaseQuantity( i, tmpvalue );
- // Calculate the field at point i that arises because of the jth component of the field
- calculateFieldContribution( j, thisp, tmpvalue, tmpstress, tmpder );
- if( tmpstress.get()>tolerance ){
- myfield.addStress( i, tmpstress ); keep=true;
- for(unsigned k=0;k<myfield.get_NdX();++k) myfield.addDerivative( i, k, tmpder[k] );
- }
- // Reset all the tempory values we have used to do this calculation
- tmpvalue->clearDerivatives(); tmpstress.clearDerivatives();
- for(unsigned k=0;k<myfield.get_NdX();++k) tmpder[k].clearDerivatives();
- }
- // If the contribution of this quantity is very small at neighbour list time ignore it
- // untill next neighbour list time
- if( reduceAtNextStep && !keep ){ members.deactivate(kk); deactivate(kk); }
- }
- // Update the dynamic list
- if(reduceAtNextStep){ members.mpi_gatherActiveMembers( comm ); }
- // Accumulate the field
- if(!serial) myfield.gatherField( comm );
-
- // And set up the interpololators
-
- delete tmpvalue;
-}
-
-void ActionWithDistribution::calculateFunctions(){
unsigned stride=comm.Get_size();
unsigned rank=comm.Get_rank();
if(serial){ stride=1; rank=0; }
@@ -296,6 +160,7 @@ void ActionWithDistribution::calculateFunctions(){
std::vector<Value> aux;
// Reset everything
for(unsigned j=0;j<functions.size();++j) functions[j]->reset();
+ if( myfield ) myfield->clear();
// Create a value to store stuff in
Value* tmpvalue=new Value();
@@ -316,21 +181,24 @@ void ActionWithDistribution::calculateFunctions(){
calculateThisFunction( kk, tmpvalue, aux );
// Skip if we are not calculating this particular value
- if( reduceAtNextStep && !tmpvalue->valueHasBeenSet() ){ members.deactivate(kk); deactivate(kk); continue; }
+ if( reduceAtNextStep && !tmpvalue->valueHasBeenSet() ){ members.deactivate(kk); deactivateValue(kk); continue; }
// Now incorporate the derivative of the function into the derivatives for the min etc
if( updateFreq>0 ){ keep=false; } else { keep=true; }
for(unsigned j=0;j<functions.size();++j){
- functions[j]->calculate( tmpvalue, aux );
+ functions[j]->clear(); functions[j]->calculate( tmpvalue, aux );
if( functions[j]->sizableContribution( tolerance ) ){
keep=true; functions[j]->mergeDerivatives( kk, *this );
}
- }
+ }
+ // Transfer the value to the field buffers
+ if( myfield ){ keep=true; myfield->setBaseQuantity( kk, tmpvalue ); }
+
tmpvalue->clearDerivatives();
for(unsigned i=0;i<aux.size();++i) aux[i].clearDerivatives();
// If the contribution of this quantity is very small at neighbour list time ignore it
// untill next neighbour list time
- if( reduceAtNextStep && !keep ){ members.deactivate(kk); deactivate(kk); }
+ if( reduceAtNextStep && !keep ){ members.deactivate(kk); deactivateValue(kk); }
}
// Update the dynamic list
if(reduceAtNextStep){ members.mpi_gatherActiveMembers( comm ); }
@@ -344,80 +212,60 @@ void ActionWithDistribution::calculateFunctions(){
bufsize=0;
for(unsigned i=0;i<functions.size();++i) functions[i]->retrieveDataFromBuffers( bufsize, buffer );
plumed_assert( bufsize==buffer.size() );
+
+ if( myfield ) myfield->gatherBaseQuantities( comm );
}
- // Delete the tmpvalues
- delete tmpvalue;
// Set the final value of the function
for(unsigned j=0;j<final_values.size();++j) functions[j]->finish( final_values[j] );
-}
-
-void ActionWithDistribution::retrieveDomain( const unsigned nn, double& min, double& max ){
- plumed_massert(0, "If your function is periodic you need to add a retrieveDomain function so that ActionWithDistribution can retrieve the domain");
-}
-void ActionWithDistribution::field_error( const std::string msg ){
- Keywords field_keys;
- field_keys.add("compulsory","NPSPLINE","the number of points in each direction at which to calculate the value of the field");
- field_keys.add("compulsory","MIN","the minimum value at which the value of the field should be calculated in each direction");
- field_keys.add("compulsory","MAX","the maximum value at which the value of the field should be calculated in each direction");
- field_keys.add("compulsory","SIGMA","the value of the sigma parameter in the field");
-
- log.printf("ERROR for keyword FIELD in action %s with label %s : %s \n \n",getName().c_str(), getLabel().c_str(), msg.c_str() );
- field_keys.print( log );
- plumed_merror("ERROR for keyword FIELD in action " + getName() + " with label " + getLabel() + " : " + msg );
- exit(1);
-}
-
-void ActionWithDistribution::FieldClass::setup( const unsigned nfunc, const unsigned np, const unsigned D, const unsigned d ){
-// Set everything for base quantities
- baseq_nder.resize(nfunc); baseq_starts.resize(nfunc);
-// Set everything for grid
- npoints=np; ndX=D; ndx=d; nper=(ndX+1)*(ndx+1); grid_buffer.resize( npoints*nper );
-}
-
-void ActionWithDistribution::FieldClass::clear(){
- baseq_buffer.assign( baseq_buffer.size(), 0.0 );
- grid_buffer.assign( grid_buffer.size(), 0.0 );
-}
-
-void ActionWithDistribution::FieldClass::resizeBaseQuantityBuffers( const std::vector<unsigned>& cv_sizes ){
- plumed_assert( cv_sizes.size()==baseq_nder.size() && cv_sizes.size()==baseq_starts.size() );
- unsigned nn=0;
- for(unsigned i=0;i<cv_sizes.size();++i){
- baseq_starts[i]=nn; baseq_nder[i]=cv_sizes[i]; nn+=cv_sizes[i]+1;
+ if( myfield ){
+ std::vector<double> thisp( myfield->get_Ndx() ); bool keep;
+ Value tmpstress; tmpstress.resizeDerivatives( myfield->get_Ndx() );
+ std::vector<Value> tmpder; tmpder.resize( myfield->get_NdX() );
+ for(unsigned i=0;i<myfield->get_NdX();++i){
+ tmpder[i].set(0); // This is really important don't delete it
+ tmpder[i].resizeDerivatives( myfield->get_Ndx() );
+ }
+
+ // Now loop over the spline points
+ unsigned ik=0;
+ for(unsigned i=0;i<myfield->getNumberOfSplinePoints();++i){
+ myfield->getSplinePoint(i,thisp);
+ // Calculate the contributions of all the active colvars
+ if( updateFreq>0 ){ keep=false; } else { keep=true; }
+ for(unsigned j=0;j<members.getNumberActive();++j){
+ if( (ik++)%stride!=rank ) continue; // Ensures we parallelize the double loop over nodes
+
+ kk=members[j];
+ unsigned nder=getThisFunctionsNumberOfDerivatives(j);
+ if( tmpvalue->getNumberOfDerivatives()!=nder ){ tmpvalue->resizeDerivatives(nder); }
+ myfield->extractBaseQuantity( kk, tmpvalue );
+ // Calculate the field at point i that arises because of the jth component of the field
+ calculateFieldContribution( kk, thisp, tmpvalue, tmpstress, tmpder );
+ if( tmpstress.get()>tolerance ){
+ myfield->addStress( i, tmpstress ); keep=true;
+ for(unsigned k=0;k<myfield->get_NdX();++k) myfield->addDerivative( i, k, tmpder[k] );
+ }
+ // Reset all the tempory values we have used to do this calculation
+ tmpvalue->clearDerivatives(); tmpstress.clearDerivatives();
+ for(unsigned k=0;k<myfield->get_NdX();++k){ tmpder[k].set(0); tmpder[k].clearDerivatives(); }
+ }
+ // If the contribution of this quantity is very small at neighbour list time ignore it
+ // untill next neighbour list time
+ if( reduceAtNextStep && !keep ){ members.deactivate(kk); deactivateValue(kk); }
+ }
+ // Update the dynamic list
+ if(reduceAtNextStep){ members.mpi_gatherActiveMembers( comm ); }
+ // Accumulate the field
+ if(!serial) myfield->gatherField( comm );
+ // setup the interpolation tables
+ myfield->set_tables();
}
- baseq_buffer.resize(nn); // And resize the buffers
-}
-
-void ActionWithDistribution::FieldClass::setBaseQuantity( const unsigned nn, Value* val ){
- plumed_assert( nn<baseq_nder.size() );
- plumed_assert( val->getNumberOfDerivatives()==baseq_nder[nn] );
-
- unsigned kk=baseq_starts[nn];
- baseq_buffer[kk]=val->get(); kk++;
- for(unsigned i=0;i<val->getNumberOfDerivatives();++i){ baseq_buffer[kk]=val->getDerivative(i); kk++; }
- if( (nn+1)==baseq_starts.size() ){ plumed_assert( kk==baseq_buffer.size() ); }
- else{ plumed_assert( kk==baseq_starts[nn+1] ); }
-}
-
-void ActionWithDistribution::FieldClass::gatherBaseQuantities( PlumedCommunicator& comm ){
- comm.Sum( &baseq_buffer[0],baseq_buffer.size() );
-}
-
-void ActionWithDistribution::FieldClass::extractBaseQuantity( const unsigned nn, Value* val ){
- plumed_assert( nn<baseq_nder.size() );
- if( baseq_nder[nn]!=val->getNumberOfDerivatives() ) val->resizeDerivatives(baseq_nder[nn]);
-
- val->clearDerivatives();
- unsigned kk=baseq_starts[nn];
- val->set( baseq_buffer[kk] ); kk++;
- for(unsigned i=0;i<val->getNumberOfDerivatives();++i){ val->addDerivative( i, baseq_buffer[kk] ); kk++; }
- if( (nn+1)==baseq_starts.size() ){ plumed_assert( kk==baseq_buffer.size() ); }
- else{ plumed_assert( kk==baseq_starts[nn+1] ); }
+ // Delete the tmpvalues
+ delete tmpvalue;
}
-void ActionWithDistribution::FieldClass::gatherField( PlumedCommunicator& comm ){
- comm.Sum( &grid_buffer[0],grid_buffer.size() );
+void ActionWithDistribution::retrieveDomain( const unsigned nn, double& min, double& max ){
+ plumed_massert(0, "If your function is periodic you need to add a retrieveDomain function so that ActionWithDistribution can retrieve the domain");
}
-
diff --git a/src/ActionWithDistribution.h b/src/ActionWithDistribution.h
index 7cd2900a7..ef005142e 100644
--- a/src/ActionWithDistribution.h
+++ b/src/ActionWithDistribution.h
@@ -4,9 +4,9 @@
#include "ActionWithValue.h"
#include "ActionAtomistic.h"
#include "Value.h"
+#include "Field.h"
#include "PlumedException.h"
#include "DistributionFunctions.h"
-#include "CubicInterpolation.h"
#include "DynamicList.h"
#include <vector>
@@ -36,68 +36,17 @@ private:
std::vector<DistributionFunction*> functions;
/// The list of quantities that should be calculated
DynamicList<unsigned> members;
-// ---- STUFF FOR FIELDS ------ //
-
- // A class for storing the field
- class FieldClass {
- private:
- /// Total number of points
- unsigned npoints;
- /// Number of high dimensionality vectors
- unsigned ndX;
- /// Number of low dimensionality vectors
- unsigned ndx;
- /// Number of doubles for each point in the grid
- unsigned nper;
- /// The sizes of all the base quantities
- std::vector<unsigned> baseq_nder;
- /// The start in baseq_buffer for each function
- std::vector<unsigned> baseq_starts;
- /// Storage space for the input data
- std::vector<double> baseq_buffer;
- /// Storage space for the grid
- std::vector<double> grid_buffer;
- public:
- /// Setup the field
- void setup( const unsigned nfunc, const unsigned np, const unsigned D, const unsigned d );
- /// Set everything for the field equal to zero
- void clear();
- /// Set the sizes of all the base quantity buffers
- void resizeBaseQuantityBuffers( const std::vector<unsigned>& cv_sizes );
- /// Set the derivatives for one of the base quantities
- void setBaseQuantity( const unsigned nn, Value* val );
- /// Gather the values and derivatives for all the base quantities
- void gatherBaseQuantities( PlumedCommunicator& comm );
- /// Extract one of the base quantities
- void extractBaseQuantity( const unsigned nn, Value* val );
- /// Get number of high dimensional derivatives
- unsigned get_NdX() const ;
- /// Get number of low dimensional derivatives
- unsigned get_Ndx() const ;
- /// Add some stress
- void addStress( const unsigned ii, const Value& x);
- /// Add some derivative
- void addDerivative( const unsigned ii, const unsigned nn, const Value& dx );
- /// Complete the field calculation by doing mpi_sum
- void gatherField( PlumedCommunicator& comm );
- };
/// This holds everything for the field
- FieldClass myfield;
-/// This holds the interpolator for the field
- CInterpolation* f_interpolator;
-// This holds the interpolators for the derivatives of the field
- std::vector<CInterpolation*> df_interpolators;
+ Field* myfield;
/// Calculate if this is a function of the distribution
void calculateFunctions();
-/// Calculate the field if this is a field
- void calculateField();
-/// Errors for input in field
- void field_error( const std::string msg );
+/// Setup stuff for the derivatives of the field
+ void setNumberOfFieldDerivatives( const unsigned D );
protected:
/// Add a distribution function to the list (this routine must be called after construction of ActionWithValue)
void addDistributionFunction( std::string name, DistributionFunction* fun );
/// Setup a field cv
- void setupField( unsigned ldim );
+ void setupField( unsigned ldim, const std::string ftype );
/// Complete the setup of this object (this routine must be called after construction of ActionWithValue)
void requestDistribution();
/// Find out if we are running the calculation without mpi
@@ -126,7 +75,7 @@ public:
/// than just calculating everything and seeing whats big.
virtual void completeNeighborListUpdate(){};
/// Ensure that nothing gets done for your deactivated colvars
- virtual void deactivate( const unsigned j )=0;
+ virtual void deactivateValue( const unsigned j )=0;
/// Merge the derivatives
virtual void mergeDerivatives( const unsigned j, Value* value_in, Value* value_out )=0;
/// Are the base quantities periodic
@@ -143,12 +92,19 @@ public:
/// Setup the values for this field cv and set the value of SIGMA
virtual void derivedFieldSetup( const double sig )=0;
-/// Set the kkth output of the field
- virtual void setFieldOutputValue( const unsigned& kk, Value* tmpvalue )=0;
+/// Get the number of derivatives of the field
+ virtual unsigned getNumberOfFieldDerivatives()=0;
/// Calculate the contribution of a particular value to the field
virtual void calculateFieldContribution( const unsigned& j, const std::vector<double>& hisp, Value* tmpvalue, Value& tmpstress, std::vector<Value>& tmpder )=0;
+/// Return a pointer to the field
+ Field* getField();
};
+inline
+Field* ActionWithDistribution::getField() {
+ return myfield;
+}
+
inline
bool ActionWithDistribution::getSerial() const {
return serial;
@@ -169,33 +125,6 @@ int ActionWithDistribution::getUpdateFreq() const {
return updateFreq;
}
-inline
-unsigned ActionWithDistribution::FieldClass::get_NdX() const {
- return ndX;
}
-
-inline
-unsigned ActionWithDistribution::FieldClass::get_Ndx() const {
- return ndx;
-}
-
-inline
-void ActionWithDistribution::FieldClass::addStress( const unsigned ii, const Value& x){
- plumed_assert( x.getNumberOfDerivatives()==ndx ); plumed_assert( ii<npoints );
- grid_buffer[ii*nper]+=x.get();
- for(unsigned k=0;k<ndx;++k) grid_buffer[ ii*nper + k + 1 ]+=x.getDerivative(k);
-}
-
-inline
-void ActionWithDistribution::FieldClass::addDerivative( const unsigned ii, const unsigned nn, const Value& dx ){
- plumed_assert( dx.getNumberOfDerivatives()==ndx );
- plumed_assert( ii<npoints && nn<ndX );
- grid_buffer[ ii*nper + (nn+1)*(1+ndx) ]+=dx.get();
- for(unsigned k=0;k<ndx;++k) grid_buffer[ ii*nper + (nn+1)*(1+ndx) + k + 1 ]+=dx.getDerivative(k);
-}
-
-
-}
-
#endif
diff --git a/src/ActionWithField.cpp b/src/ActionWithField.cpp
new file mode 100644
index 000000000..9e66c16dd
--- /dev/null
+++ b/src/ActionWithField.cpp
@@ -0,0 +1,147 @@
+#include "ActionWithField.h"
+#include "PlumedMain.h"
+#include "ActionSet.h"
+
+using namespace std;
+using namespace PLMD;
+
+void ActionWithField::registerKeywords(Keywords& keys){
+ Action::registerKeywords(keys);
+ ActionWithValue::registerKeywords(keys);
+ ActionPilot::registerKeywords(keys);
+ keys.add("compulsory","STRIDE","1","the frequency with which to output the field");
+ keys.add("compulsory","FIELD","the input for this action is the field calculated during one of the other actions.");
+ keys.add("compulsory","NGRID","number of grid points to use in each direction");
+ keys.addFlag("SERIAL", false, "do the calculation in serial");
+}
+
+ActionWithField::ActionWithField(const ActionOptions&ao):
+ Action(ao),
+ ActionWithValue(ao),
+ ActionPilot(ao),
+ serial(false)
+{
+ if( checkNumericalDerivatives() ) warning("cannot parallelize field with numerical derivatives over actions");
+ parseFlag("SERIAL",serial);
+ if(serial) log.printf(" doing calculation in serial\n");
+
+ // Find the field we are using
+ std::string ll; parse("FIELD",ll);
+ ActionWithDistribution* field=plumed.getActionSet().selectWithLabel<ActionWithDistribution*>(ll);
+ addDependency(field);
+ if(!field) error("cannot find action named " + ll);
+ myfield=field->getField();
+ if(!myfield) error("action " + ll + " calculates a colvar and not a field");
+ apply_action=dynamic_cast<Action*>( field );
+
+ // Read how we descritize the integrals
+ std::vector<unsigned> ngrid( myfield->get_Ndx() ); parseVector("NGRID",ngrid);
+ log.printf(" using field %s and descritizing %d dimensional integrals over ",ll.c_str(), ngrid.size() );
+ for(unsigned i=0;i<ngrid.size();++i) log.printf("%d ",ngrid[i]);
+ log.printf("points\n");
+
+ // Create the grid where we store the bias
+ std::vector<double> min, max;
+ myfield->retrieveBoundaries( min, max );
+ plumed_assert( min.size()==ngrid.size() && max.size()==ngrid.size() );
+ std::vector<bool> pbc(min.size(), false );
+ bias=new Grid( min, max, ngrid, pbc, false, false );
+ buffer.resize( bias->getSize() + 2 );
+
+ // Setup the blocks for parallelizing the grid calculations
+ unsigned stride=comm.Get_size();
+ if(serial) stride=1;
+
+ blocks.resize( stride+1 );
+ unsigned nn=std::floor( bias->getSize() / stride );
+ unsigned nrem=bias->getSize() - nn*stride;
+
+ blocks[0]=0;
+ for(unsigned i=1;i<blocks.size();++i){
+ for(unsigned j=0;j<i;++j) blocks[i]+=blocks[j];
+ if( i<=nrem ) blocks[i]+=nn + 1;
+ else blocks[i]+=nn;
+ }
+ plumed_assert( blocks[blocks.size()-1]==bias->getSize() );
+
+ // Add something for the bias and set up the forces
+ addComponentWithDerivatives("bias");
+ getPntrToComponent("bias")->resizeDerivatives( 1 );
+}
+
+void ActionWithField::clearBias(){
+ std::vector<unsigned> ngrid; ngrid=bias->getNbin();
+ delete bias;
+ std::vector<double> min, max; myfield->retrieveBoundaries( min, max );
+ plumed_assert( min.size()==ngrid.size() && max.size()==ngrid.size() );
+ std::vector<bool> pbc(min.size(), false );
+ bias=new Grid( min, max, ngrid, pbc, false, false );
+}
+
+void ActionWithField::calculate(){
+ unsigned rank=comm.Get_rank();
+ if(serial) rank=0;
+
+ unsigned nder=myfield->get_NdX();
+ if( derivatives.size()!=nder ){
+ derivatives.resize( nder );
+ getPntrToComponent("bias")->resizeDerivatives( nder );
+ }
+
+ // This calculates the current field if we are doing numerical derivatives
+ if( checkNumericalDerivatives() ) apply_action->calculate();
+
+ // The loop for the bias
+ buffer.assign( buffer.size(), 0.0 );
+ std::vector<double> pp( myfield->get_Ndx() );
+ for(unsigned i=blocks[rank];i<blocks[rank+1];++i){
+ bias->getPoint( i, pp );
+ buffer[i+2]=myfield->calculateField( pp );
+ buffer[0]+=buffer[i+2];
+ buffer[1]+=buffer[i+2]*bias->getValue( i );
+ }
+ buffer[0]*=bias->getBinVolume();
+ buffer[1]*=bias->getBinVolume() / buffer[0];
+ if(!serial) comm.Sum( &buffer[0], buffer.size() );
+ getPntrToComponent("bias")->set(buffer[1]);
+
+ if( checkNumericalDerivatives() ) return ;
+
+ // The loop for the derivatives
+ derivatives.assign( derivatives.size(), 0.0 );
+ std::vector<double> tmpforce( derivatives.size() );
+ for(unsigned i=blocks[rank];i<blocks[rank+1];++i){
+ bias->getPoint( i, pp );
+ myfield->calculateFieldDerivatives( pp, tmpforce );
+ for(unsigned j=0;j<derivatives.size();++j){
+ derivatives[j] += tmpforce[j] * ( bias->getValue( i ) - buffer[1] );
+ }
+ }
+ for(unsigned j=0;j<derivatives.size();++j) derivatives[j]*=bias->getBinVolume() / buffer[0];
+ if(!serial) comm.Sum( &derivatives[0], derivatives.size() );
+ Value* bb=getPntrToComponent("bias");
+ for(unsigned j=0;j<derivatives.size();++j) bb->addDerivative( j, derivatives[j] );
+}
+
+void ActionWithField::calculateNumericalDerivatives( ActionWithValue* a ){
+ apply_action->calculateNumericalDerivatives( this );
+}
+
+void ActionWithField::addFieldToBias( const double& hh ){
+ for(unsigned i=0;i<bias->getSize();++i){
+ bias->addValue( i, hh*buffer[i+2]/buffer[0] );
+ }
+}
+
+void ActionWithField::apply(){
+ if(onStep()){
+ for(unsigned j=0;j<derivatives.size();++j) derivatives[j]*=-1.0*getStride();
+ myfield->addForces( derivatives );
+ }
+}
+
+ActionWithField::~ActionWithField(){
+ delete bias;
+}
+
+
diff --git a/src/ActionWithField.h b/src/ActionWithField.h
new file mode 100644
index 000000000..84f7f21ee
--- /dev/null
+++ b/src/ActionWithField.h
@@ -0,0 +1,46 @@
+#ifndef __PLUMED_ActionWithField_h
+#define __PLUMED_ActionWithField_h
+
+#include "Action.h"
+#include "ActionPilot.h"
+#include "ActionWithValue.h"
+#include "PlumedException.h"
+#include "ActionWithDistribution.h"
+#include "Grid.h"
+#include "Field.h"
+
+namespace PLMD{
+
+class ActionWithField :
+ public ActionWithValue,
+ public ActionPilot
+ {
+private:
+ bool serial;
+ Action* apply_action;
+ Field* myfield;
+ Grid* bias;
+ std::vector<double> buffer;
+ std::vector<unsigned> blocks;
+ std::vector<double> derivatives;
+protected:
+ Grid* getPntrToBias();
+ void clearBias();
+ void addFieldToBias( const double& hh );
+public:
+ static void registerKeywords(Keywords& keys);
+ ActionWithField(const ActionOptions&ao);
+ ~ActionWithField();
+ void calculate();
+ void calculateNumericalDerivatives( ActionWithValue* a=NULL );
+ void apply();
+};
+
+inline
+Grid* ActionWithField::getPntrToBias(){
+ return bias;
+}
+
+}
+
+#endif
diff --git a/src/BiasFieldMetadynamics.cpp b/src/BiasFieldMetadynamics.cpp
new file mode 100644
index 000000000..6d3037cc9
--- /dev/null
+++ b/src/BiasFieldMetadynamics.cpp
@@ -0,0 +1,92 @@
+#include "ActionPilot.h"
+#include "ActionRegister.h"
+#include "ActionWithValue.h"
+#include "ActionWithField.h"
+#include "PlumedMain.h"
+#include "Atoms.h"
+
+namespace PLMD {
+
+//+PLUMEDOC BIAS FIELD_METAD
+/**
+Field metadynamics is a method for enhancing sampling, which, much like conventional
+metadynamcis, generates a bias based on the history of visited configurations. However,
+unlike metadynamics, for which the instantaneous state of the system is represented using
+a vector of collective variables, the instantaneous state of the system is represented
+using a continueous probability distribution \f$\psi(X,z)\f$ that is calcualted based on
+the instantaneous atomic positions.
+
+This means that the bias at any given time is calculated as an overlap integral \cite field-cvs namely:
+
+\f[
+V(X,t) = \int \textrm{d}z \psi(X(t),z) \sum_{t'=0}^t \psi(X(t'),z)
+\f]
+
+\par Examples
+The following input is performing field metadynamics using the histogram
+of distances between the atoms in the specified group to describe the instantaneous
+state fo the system
+\verbatim
+DISTANCES GROUP=1-7 FIELD=(MIN=0.5 MAX=3.0 NSPLINE=20 SIGMA=0.1) LABEL=f1
+FIELD_METAD FIELD=f1 NGRID=400 STRIDE=1 PACE=10 HEIGHT=40.0 LABEL=m1
+\endverbatim
+(See also \ref DISTANCES)
+
+*/
+//+ENDPLUMEDOC
+
+class BiasFieldMetadynamics : public ActionWithField {
+private:
+ unsigned freq;
+ double hw;
+ double biasf;
+ double temp;
+ bool welltemp;
+public:
+ BiasFieldMetadynamics(const ActionOptions&);
+ static void registerKeywords(Keywords& keys);
+ void update();
+};
+
+PLUMED_REGISTER_ACTION(BiasFieldMetadynamics,"FIELD_METAD")
+
+void BiasFieldMetadynamics::registerKeywords(Keywords& keys){
+ ActionWithField::registerKeywords(keys);
+ keys.add("compulsory","PACE","the frequency with which to add hills");
+ keys.add("compulsory","HEIGHT","the heights of the hills");
+ keys.add("optional","BIASFACTOR","use well tempered metadynamics and use this biasfactor. Please note you must also specify temp");
+ keys.add("optional","TEMP","the system temperature - this is only needed if you are doing well-tempered metadynamics");
+}
+
+BiasFieldMetadynamics::BiasFieldMetadynamics(const ActionOptions& ao):
+Action(ao),
+ActionWithField(ao),
+freq(0),
+hw(0),
+biasf(1.0),
+temp(0.0),
+welltemp(false)
+{
+ parse("PACE",freq);
+ parse("HEIGHT",hw);
+ parse("BIASFACTOR",biasf);
+ if( biasf<1.0 ) error("Bias factor has not been set properly it must be greater than 1");
+ parse("TEMP",temp);
+ if( biasf>1.0 && temp<0.0 ) error("You must set the temperature using TEMP when you do well tempered metadynamics");
+ checkRead();
+ if( biasf>1.0 ) welltemp=true;
+}
+
+void BiasFieldMetadynamics::update(){
+ if( getStep()%freq==0 ){
+ double this_ww;
+ if(welltemp){
+ this_ww = hw*exp(-getPntrToComponent("bias")->get()/(plumed.getAtoms().getKBoltzmann()*temp*(biasf-1.0)));
+ } else {
+ this_ww=hw;
+ }
+ addFieldToBias( this_ww );
+ }
+}
+
+}
diff --git a/src/BiasMovingRestraint.cpp b/src/BiasMovingRestraint.cpp
index 4ec1acea4..6f577d6f2 100644
--- a/src/BiasMovingRestraint.cpp
+++ b/src/BiasMovingRestraint.cpp
@@ -94,9 +94,12 @@ void BiasMovingRestraint::registerKeywords( Keywords& keys ){
Bias::registerKeywords(keys);
keys.use("ARG");
keys.add("compulsory","VERSE","B","Tells plumed whether the restraint is only acting for CV larger (U) or smaller (L) than the restraint or whether it is acting on both sides (B)");
- keys.add("numbered","STEP","This keyword appears multiple times as STEPx with x=0,1,2,...,n. Each value given represents the MD step at which the restraint parameters take the values KAPPAx and ATx.");
+ keys.add("numbered","STEP","This keyword appears multiple times as STEPx with x=0,1,2,...,n. Each value given represents the MD step at which the restraint parameters take the values KAPPAx and ATx.");
+ keys.reset_style("STEP","compulsory");
keys.add("numbered","AT","ATx is equal to the position of the restraint at time STEPx. For intermediate times this parameter is linearly interpolated. If no ATx is specified for STEPx then the values of AT are kept constant during the interval of time between STEPx-1 and STEPx.");
+ keys.reset_style("AT","compulsory");
keys.add("numbered","KAPPA","KAPPAx is equal to the value of the force constants at time STEPx. For intermediate times this parameter is linearly interpolated. If no ATx is specified for STEPx then the values of KAPPAx are kept constant during the interval of time between STEPx-1 and STEPx.");
+ keys.reset_style("KAPPA","compulsory");
}
BiasMovingRestraint::BiasMovingRestraint(const ActionOptions&ao):
diff --git a/src/ColvarAngle.cpp b/src/ColvarAngle.cpp
index 1ebc5f12f..ae3d231d3 100644
--- a/src/ColvarAngle.cpp
+++ b/src/ColvarAngle.cpp
@@ -60,7 +60,6 @@ pbc(true)
parseFlag("NOPBC",nopbc);
pbc=!nopbc;
parseFlag("PBC",pbc);
- checkRead();
if(atoms.size()==3){
log.printf(" between atoms %d %d %d\n",atoms[0].serial(),atoms[1].serial(),atoms[2].serial());
@@ -76,6 +75,7 @@ pbc(true)
addValueWithDerivatives(); setNotPeriodic();
requestAtoms(atoms);
+ checkRead();
}
// calculator
diff --git a/src/CubicInterpolation.cpp b/src/CubicInterpolation.cpp
index 8a31de0db..e8280afb1 100644
--- a/src/CubicInterpolation.cpp
+++ b/src/CubicInterpolation.cpp
@@ -27,6 +27,15 @@ bold(0)
lb.resize( np.size() ); ub.resize( np.size() );
}
+CInterpolation::~CInterpolation(){
+ splinepoints.resize(0,0); lb.resize(0); ub.resize(0); np.resize(0); stride.resize(0);
+}
+
+void CInterpolation::getNumbersOfPoints( std::vector<unsigned>& nspline ) const {
+ nspline.resize( np.size() );
+ for(unsigned i=0;i<np.size();++i) nspline[i]=np[i];
+}
+
unsigned CInterpolation::findBox( const std::vector<double>& pos ){
plumed_massert( pos.size()==np.size(), "position size does not match the size of the grid");
@@ -194,6 +203,7 @@ double InterpolateBicubic::get_fdf( const std::vector<double>& pos ){
c3=cbase; c2=c3-1; c1=c2-1; c0=c1-1; cbase=c0-1;
f= t*f + ( ( (*c3)*u + (*c2) )*u + (*c1) )*u + (*c0);
}
+ delete cbase; delete c3; delete c2; delete c1; delete c0;
return f;
}
diff --git a/src/CubicInterpolation.h b/src/CubicInterpolation.h
index a5fae4b52..6d6b6e177 100644
--- a/src/CubicInterpolation.h
+++ b/src/CubicInterpolation.h
@@ -21,7 +21,9 @@ protected:
double getCrossTermDenominator( const unsigned i, const unsigned j ) const ;
public:
CInterpolation( const std::vector<unsigned>& dd, const std::vector<double>& fmin, const std::vector<double>& fmax );
+ virtual ~CInterpolation();
unsigned getNumberOfSplinePoints() const ;
+ void getNumbersOfPoints( std::vector<unsigned>& nspline ) const ;
void getSplinePoint( const unsigned nn, std::vector<double>& pp ) const ;
void getGridBoundaries( std::vector<double>& gmin, std::vector<double>& gmax ) const ;
virtual void set_table( const std::vector<Value>& ff )=0;
diff --git a/src/DistributionFunctions.h b/src/DistributionFunctions.h
index c7f0a333c..b2a81ac21 100644
--- a/src/DistributionFunctions.h
+++ b/src/DistributionFunctions.h
@@ -224,6 +224,7 @@ private:
unsigned nval;
unsigned power;
public:
+ static std::string documentation();
static void generateParameters(const unsigned& number, const unsigned& nder, std::string& params );
moment( const std::string& parameters );
void calculate( Value* value_in, std::vector<Value>& aux );
diff --git a/src/DistributionMoment.cpp b/src/DistributionMoment.cpp
index 49f5d95eb..ffb5f8c2a 100644
--- a/src/DistributionMoment.cpp
+++ b/src/DistributionMoment.cpp
@@ -2,6 +2,13 @@
namespace PLMD {
+std::string moment::documentation(){
+ std::ostringstream ostr;
+ ostr<<"The \\f$m\\f$th moment of a distribution is calculated using \\f$\\frac{1}{N} \\sum_{i=1}^N ( s_i - \\overline{s} )^m \\f$, where \\f$\\overline{s}\\f$ is ";
+ ostr<<"the average for the distribution. The moment keyword takes a single integer as input; namely, the value of \\f$m\\f$.";
+ return ostr.str();
+}
+
void moment::generateParameters(const unsigned& number, const unsigned& nder, std::string& params ){
std::ostringstream ostr;
ostr<<"NUMBER="<<nder<<" POWER="<<number;
diff --git a/src/Field.cpp b/src/Field.cpp
new file mode 100644
index 000000000..1b7ca6163
--- /dev/null
+++ b/src/Field.cpp
@@ -0,0 +1,232 @@
+#include "Field.h"
+
+using namespace PLMD;
+
+std::string Field::documentation(){
+ std::ostringstream ostr;
+ ostr<<"Fields provide an alternative to collective variables \\cite field-cvs in which the instantaneous state of the system ";
+ ostr<<"is represented by a function calculated on on a 1 or 2 D grid rather than by a vector of collective variables. ";
+ ostr<<"Within this scheme biasing methods such as metadynamics (\\ref FIELD_METAD) can be re-formulated in terms of overlap integrals. ";
+ ostr<<"Alternatively one can simply output the instaneous value of the FIELD using \\ref DUMPFIELD. ";
+ ostr<<"To make calculations involving fields efficient we calculate the value of the field at a small number of grid points and then use either ";
+ ostr<<"cubic or bicubic interpolation to interpolate the function onto a finer grid for the eventual integration. The input for a field looks ";
+ ostr<<"something like FIELD=(MIN=\\f$r_0\\f$ MAX=\\f$x_1\\f$ NSPLINE=\\f$n\\f$ SIGMA=\\f$\\sigma\\f$) where \\f$r_0\\f$ is the lower limit for the ";
+ ostr<<"integrals, \\f$x_1\\f$ is the upper limit for the integrals, \\f$n\\f$ is the number of points at which the function should be explicitally ";
+ ostr<<"calculated and \\f$\\sigma\\f$ is the value of the \\f$\\sigma\\f$ parameter in the equation above.";
+ return ostr.str();
+}
+
+Field::~Field(){
+ delete f_interpolator;
+ for(unsigned i=0;i<df_interpolators.size();++i) delete df_interpolators[i];
+}
+
+void Field::read( const std::string& input, const unsigned nfunc, const unsigned d, const std::string ftype, std::string& report ){
+ if( ftype=="identity") fstyle=identity;
+ else if( ftype=="gaussian") fstyle=gaussian;
+ else error("type " + ftype + " is not implemented in field");
+
+ std::vector<std::string> data=Tools::getWords(input);
+ std::vector<unsigned> nspline; std::vector<double> min,max;
+ bool found_s=Tools::parseVector( data,"NSPLINE", nspline );
+ if(!found_s) error("did not find NPLINE keyword");
+ if(nspline.size()!=d){
+ std::string ll,ww;
+ Tools::convert(d,ll);
+ Tools::convert(nspline.size(),ww);
+ error("found " + ww + " values for NSPLINE when expecting only " + ll);
+ }
+ bool found_min=Tools::parseVector( data, "MIN", min );
+ if(!found_min) error("did not find MIN keyword");
+ if(min.size()!=d){
+ std::string ll,ww;
+ Tools::convert(d,ll);
+ Tools::convert(min.size(),ww);
+ error("found " + ww + " values for MIN when expecting only " + ll);
+ }
+ bool found_max=Tools::parseVector( data, "MAX", max );
+ if(!found_max) error("did not find MAX keyword");
+ if(max.size()!=d){
+ std::string ll,ww;
+ Tools::convert(d,ll);
+ Tools::convert(max.size(),ww);
+ error("found " + ww + " values for MAX when expecting only " + ll);
+ }
+ bool found_sigma=Tools::parse( data, "SIGMA", sigma );
+ if(!found_sigma) error("did not find SIGMA keyword");
+
+ if( data.size()!=0 ){
+ std::string err="found the following rogue keywords : ";
+ for(unsigned i=0;i<data.size();++i) err=err + data[i] + ", ";
+ error(err);
+ }
+ std::ostringstream ostr;
+ ostr<<"generating "<<d<<" dimensional field min : ";
+ for(unsigned i=0;i<min.size();++i) ostr<<min[i]<<" ";
+ ostr<<"max : ";
+ for(unsigned i=0;i<max.size();++i) ostr<<max[i]<<" ";
+ ostr<<"nspline : ";
+ for(unsigned i=0;i<nspline.size();++i) ostr<<nspline[i];
+ report=ostr.str();
+
+// Set everything for base quantities
+ baseq_nder.resize(nfunc); baseq_starts.resize(nfunc);
+// Set everything for grid
+ unsigned np=1; for(unsigned i=0;i<nspline.size();++i) np*=nspline[i];
+ npoints=np; ndx=d;
+
+ // Setup the interpolators
+ if( ndx==1 ) f_interpolator=new InterpolateCubic( nspline, min, max );
+ else if( ndx==2 ) f_interpolator=new InterpolateBicubic( nspline, min, max );
+ else plumed_assert(0);
+}
+
+void Field::resizeDerivatives( const unsigned D ){
+ ndX=D; nper=(ndX+1)*(ndx+1); grid_buffer.resize( npoints*nper );
+
+ for(unsigned i=0;i<df_interpolators.size();++i) delete df_interpolators[i];
+ df_interpolators.resize(0);
+ std::vector<unsigned> nspline(ndx); std::vector<double> min(ndx), max(ndx);
+ f_interpolator->getNumbersOfPoints( nspline );
+ f_interpolator->getSplinePoint( 0, min );
+ f_interpolator->getSplinePoint( f_interpolator->getNumberOfSplinePoints()-1, max );
+ if( ndx==1 ){
+ for(unsigned i=0;i<D;++i) df_interpolators.push_back( new InterpolateCubic( nspline, min, max ) );
+ } else if( ndx==2 ){
+ for(unsigned i=0;i<D;++i) df_interpolators.push_back( new InterpolateBicubic( nspline, min, max ) );
+ } else {
+ plumed_assert(0);
+ }
+ forces.resize(D);
+}
+
+void Field::retrieveBoundaries( std::vector<double>& min, std::vector<double>& max ){
+ min.resize(ndx); f_interpolator->getSplinePoint( 0, min );
+ max.resize(ndx); f_interpolator->getSplinePoint( f_interpolator->getNumberOfSplinePoints()-1, max );
+}
+
+void Field::clear(){
+ wasforced=false;
+ baseq_buffer.assign( baseq_buffer.size(), 0.0 );
+ grid_buffer.assign( grid_buffer.size(), 0.0 );
+}
+
+void Field::resizeBaseQuantityBuffers( const std::vector<unsigned>& cv_sizes ){
+ plumed_assert( cv_sizes.size()==baseq_nder.size() && cv_sizes.size()==baseq_starts.size() );
+ unsigned nn=0;
+ for(unsigned i=0;i<cv_sizes.size();++i){
+ baseq_starts[i]=nn; baseq_nder[i]=cv_sizes[i]; nn+=cv_sizes[i]+1;
+ }
+ baseq_buffer.resize(nn); // And resize the buffers
+}
+
+void Field::setBaseQuantity( const unsigned nn, Value* val ){
+ plumed_assert( nn<baseq_nder.size() );
+ plumed_assert( val->getNumberOfDerivatives()==baseq_nder[nn] );
+
+ unsigned kk=baseq_starts[nn];
+ baseq_buffer[kk]=val->get(); kk++;
+ for(unsigned i=0;i<val->getNumberOfDerivatives();++i){ baseq_buffer[kk]=val->getDerivative(i); kk++; }
+ if( (nn+1)==baseq_starts.size() ){ plumed_assert( kk==baseq_buffer.size() ); }
+ else{ plumed_assert( kk==baseq_starts[nn+1] ); }
+}
+
+void Field::gatherBaseQuantities( PlumedCommunicator& comm ){
+ comm.Sum( &baseq_buffer[0],baseq_buffer.size() );
+}
+
+void Field::getSplinePoint( const unsigned nn, std::vector<double>& pp ) const {
+ f_interpolator->getSplinePoint( nn, pp );
+}
+
+void Field::extractBaseQuantity( const unsigned nn, Value* val ){
+ plumed_assert( nn<baseq_nder.size() );
+ if( baseq_nder[nn]!=val->getNumberOfDerivatives() ) val->resizeDerivatives(baseq_nder[nn]);
+
+ val->clearDerivatives();
+ unsigned kk=baseq_starts[nn];
+ val->set( baseq_buffer[kk] ); kk++;
+ for(unsigned i=0;i<val->getNumberOfDerivatives();++i){ val->addDerivative( i, baseq_buffer[kk] ); kk++; }
+ if( (nn+1)==baseq_starts.size() ){ plumed_assert( kk==baseq_buffer.size() ); }
+ else{ plumed_assert( kk==baseq_starts[nn+1] ); }
+}
+
+double Field::calculateField( const std::vector<double>& pp ) const {
+ if( fstyle==identity ){
+ return f_interpolator->get_fdf(pp);
+ } else if( fstyle==gaussian ) {
+ double tmp=f_interpolator->get_fdf(pp);
+ return exp( -tmp/(2*sigma*sigma) );
+ }
+ plumed_massert(0, "no field calculate style defined");
+ return 0;
+}
+
+void Field::calculateFieldDerivatives( const std::vector<double>& pp, std::vector<double>& der ) const {
+ plumed_assert( der.size()==df_interpolators.size() );
+ if( fstyle==identity ){
+ for(unsigned i=0;i<der.size();++i) der[i]=df_interpolators[i]->get_fdf(pp);
+ } else if( fstyle==gaussian ) {
+ double tmp=f_interpolator->get_fdf(pp); double pref=-exp( -tmp/(2*sigma*sigma) ) / ( 2*sigma*sigma );
+ for(unsigned i=0;i<der.size();++i) der[i]=pref*df_interpolators[i]->get_fdf(pp);
+ }
+}
+
+void Field::gatherField( PlumedCommunicator& comm ){
+ comm.Sum( &grid_buffer[0],grid_buffer.size() );
+}
+
+void Field::set_tables(){
+ std::vector<Value> vv(npoints);
+ for(unsigned i=0;i<npoints;++i){
+ vv[i].set( grid_buffer[i*nper] );
+ vv[i].resizeDerivatives( ndx );
+ for(unsigned j=0;j<ndx;++j) vv[i].addDerivative( j, grid_buffer[ i*nper + j + 1 ] );
+ }
+ f_interpolator->set_table( vv );
+
+ unsigned kk;
+ for(unsigned n=0;n<df_interpolators.size();++n){
+ for(unsigned i=0;i<npoints;++i){
+ vv[i].clearDerivatives();
+ kk=i*nper + (n+1)*(1+ndx); vv[i].set( grid_buffer[kk] ); kk++;
+ for(unsigned j=0;j<ndx;++j){ vv[i].addDerivative( j, grid_buffer[kk] ); kk++; }
+ }
+ df_interpolators[n]->set_table( vv );
+ }
+}
+
+bool Field::applyForces( std::vector<double>& outforces ) const {
+ plumed_assert( outforces.size()==forces.size() );
+ for(unsigned i=0;i<forces.size();++i) outforces[i]=forces[i];
+ return wasforced;
+}
+
+void Field::addForces( std::vector<double>& inforces ){
+ plumed_assert( inforces.size()==forces.size() );
+ wasforced=true;
+ for(unsigned i=0;i<forces.size();++i) forces[i]=inforces[i];
+}
+
+
+void Field::error( const std::string msg){
+ errormsg=msg;
+}
+
+std::string Field::errorMessage() const {
+ return errormsg;
+}
+
+bool Field::check() const {
+ if( errormsg.size()!=0 ) return false;
+ return true;
+}
+
+void Field::printKeywords( Log& log ){
+ Keywords field_keys;
+ field_keys.add("compulsory","NPSPLINE","the number of points in each direction at which to calculate the value of the field");
+ field_keys.add("compulsory","MIN","the minimum value at which the value of the field should be calculated in each direction");
+ field_keys.add("compulsory","MAX","the maximum value at which the value of the field should be calculated in each direction");
+ field_keys.add("compulsory","SIGMA","the value of the sigma parameter in the field");
+ field_keys.print( log );
+}
diff --git a/src/Field.h b/src/Field.h
new file mode 100644
index 000000000..3e5592542
--- /dev/null
+++ b/src/Field.h
@@ -0,0 +1,141 @@
+#ifndef __PLUMED_Field_h
+#define __PLUMED_Field_h
+
+#include "PlumedException.h"
+#include "PlumedCommunicator.h"
+#include "Keywords.h"
+#include "Field.h"
+#include "Tools.h"
+#include "Value.h"
+#include "CubicInterpolation.h"
+
+namespace PLMD{
+
+// A class for storing the field
+class Field {
+private:
+/// The type of field this is
+ enum {identity,gaussian} fstyle;
+/// Total number of points
+ unsigned npoints;
+/// Number of high dimensionality vectors
+ unsigned ndX;
+/// Number of low dimensionality vectors
+ unsigned ndx;
+/// Number of doubles for each point in the grid
+ unsigned nper;
+/// The value of sigma
+ double sigma;
+/// The sizes of all the base quantities
+ std::vector<unsigned> baseq_nder;
+/// The start in baseq_buffer for each function
+ std::vector<unsigned> baseq_starts;
+/// Storage space for the input data
+ std::vector<double> baseq_buffer;
+/// Storage space for the grid
+ std::vector<double> grid_buffer;
+/// The error message
+ std::string errormsg;
+/// The interpolator for the field
+ CInterpolation* f_interpolator;
+/// The interpolator for the derivatives
+ std::vector<CInterpolation*> df_interpolators;
+/// Everything to pass forces like Values
+ bool wasforced;
+ std::vector<double> forces;
+public:
+ ~Field();
+/// Write the documentation for the field
+ static std::string documentation();
+/// Write out the keywords for this action
+ static void printKeywords( Log& log );
+/// Read in the stuff for the field
+ void read( const std::string& input, const unsigned nfunc, const unsigned d, const std::string ftype, std::string& report );
+/// Store an error message if something goes wrong during readin
+ void error( const std::string msg );
+/// Return the value of the error message
+ std::string errorMessage() const ;
+/// Check if there was a problem on readin
+ bool check() const ;
+/// Set the number of high dimensional coordinates
+ void resizeDerivatives( const unsigned D );
+/// Get the upper and lower boundaries of the grid
+ void retrieveBoundaries( std::vector<double>& min, std::vector<double>& max );
+/// Set up to recalculate everything in the field
+ void clear();
+/// Set the sizes of all the base quantity buffers
+ void resizeBaseQuantityBuffers( const std::vector<unsigned>& cv_sizes );
+/// Set the derivatives for one of the base quantities
+ void setBaseQuantity( const unsigned nn, Value* val );
+/// Gather the values and derivatives for all the base quantities
+ void gatherBaseQuantities( PlumedCommunicator& comm );
+/// Extract one of the base quantities
+ void extractBaseQuantity( const unsigned nn, Value* val );
+/// Get number of high dimensional derivatives
+ unsigned get_NdX() const ;
+/// Get number of low dimensional derivatives
+ unsigned get_Ndx() const ;
+/// Get the value of sigma
+ double get_sigma() const ;
+/// Get the number of spline points
+ unsigned getNumberOfSplinePoints() const ;
+/// Get the coordinates of one of the spline points
+ void getSplinePoint( const unsigned nn, std::vector<double>& pp ) const ;
+/// Add some stress
+ void addStress( const unsigned ii, const Value& x);
+/// Add some derivative
+ void addDerivative( const unsigned ii, const unsigned nn, const Value& dx );
+/// Complete the field calculation by doing mpi_sum
+ void gatherField( PlumedCommunicator& comm );
+/// Setup the interpolation tables
+ void set_tables();
+/// Calculate the value of the field at a particular point in space
+ double calculateField( const std::vector<double>& pp ) const ;
+/// Calcualte the derivatives of the field at a particular point in space
+ void calculateFieldDerivatives( const std::vector<double>& pp, std::vector<double>& tmpforce ) const ;
+/// Add some forces to this field
+ void addForces( std::vector<double>& inforces );
+/// Apply the forces from this field
+ bool applyForces( std::vector<double>& outforces ) const ;
+};
+
+inline
+unsigned Field::get_NdX() const {
+ return ndX;
+}
+
+inline
+unsigned Field::get_Ndx() const {
+ return ndx;
+}
+
+inline
+double Field::get_sigma() const {
+ return sigma;
+}
+
+inline
+unsigned Field::getNumberOfSplinePoints() const {
+ return f_interpolator->getNumberOfSplinePoints();
+}
+
+inline
+void Field::addStress( const unsigned ii, const Value& x){
+ plumed_assert( x.getNumberOfDerivatives()==ndx ); plumed_assert( ii<npoints );
+ unsigned kk=ii*nper;
+ grid_buffer[kk]+=x.get(); kk++;
+ for(unsigned k=0;k<ndx;++k){ grid_buffer[kk]+=x.getDerivative(k); kk++; }
+}
+
+inline
+void Field::addDerivative( const unsigned ii, const unsigned nn, const Value& dx ){
+ plumed_assert( dx.getNumberOfDerivatives()==ndx );
+ plumed_assert( ii<npoints && nn<ndX );
+ unsigned kk=ii*nper + (nn+1)*(1+ndx);
+ grid_buffer[kk]+=dx.get(); kk++;
+ for(unsigned k=0;k<ndx;++k){ grid_buffer[kk]+=dx.getDerivative(k); kk++;}
+}
+
+}
+
+#endif
diff --git a/src/GenericDumpField.cpp b/src/GenericDumpField.cpp
new file mode 100644
index 000000000..6a0e6beba
--- /dev/null
+++ b/src/GenericDumpField.cpp
@@ -0,0 +1,114 @@
+#include "ActionPilot.h"
+#include "ActionRegister.h"
+#include "ActionWithDistribution.h"
+#include "PlumedMain.h"
+#include "ActionSet.h"
+#include "Field.h"
+#include "Grid.h"
+
+namespace PLMD {
+
+//+PLUMEDOC ANALYSIS DUMPFIELD
+/**
+Print out the instantaneous of a field that would be used to represent the instantaneous
+state of the system in a method such as \ref FIELD_METAD
+
+\par Examples
+The following input writes out the histogram of distances between the atoms in the
+specified group every 10 steps to file called field.1, field.2...
+\verbatim
+DISTANCES GROUP=1-7 FIELD=(MIN=0.5 MAX=3.0 NSPLINE=20 SIGMA=0.1) LABEL=f1
+DUMPFIELD FIELD=f1 NGRID=200 STRIDE=50 FILE_BASE=field
+\endverbatim
+(See also \ref DISTANCES)
+
+*/
+//+ENDPLUMEDOC
+
+class GenericDumpField :
+public ActionPilot
+{
+private:
+ int fnum;
+ Field* myfield;
+ std::vector<unsigned> ngrid;
+ std::string fbase;
+public:
+ GenericDumpField(const ActionOptions&);
+ static void registerKeywords(Keywords& keys);
+ void calculate(){};
+ void apply(){};
+ void update();
+ bool retrieveForces( std::vector<double>& force ){ return false; }
+};
+
+PLUMED_REGISTER_ACTION(GenericDumpField,"DUMPFIELD")
+
+void GenericDumpField::registerKeywords(Keywords& keys){
+ Action::registerKeywords(keys);
+ ActionPilot::registerKeywords(keys);
+ keys.add("compulsory","FIELD","the field we are writing out");
+ keys.add("compulsory","STRIDE","the frequency with which to output the field");
+ keys.add("compulsory","FILE_BASE","field","the base name to use to output the field");
+ keys.add("compulsory","NGRID","number of grid points to use in each direction");
+}
+
+GenericDumpField::GenericDumpField(const ActionOptions& ao):
+Action(ao),
+ActionPilot(ao)
+{
+
+ // Find the field we are using
+ std::string ll; parse("FIELD",ll);
+ ActionWithDistribution* field=plumed.getActionSet().selectWithLabel<ActionWithDistribution*>(ll);
+ if(!field) error("cannot find action named " + ll);
+ myfield=field->getField();
+ if(!myfield) error("action " + ll + " calculates a colvar and not a field");
+ addDependency(field);
+
+ ngrid.resize( myfield->get_Ndx() );
+ parseVector("NGRID",ngrid);
+
+ parse("FILE_BASE",fbase);
+ log.printf(" printing field on files named %s\n",fbase.c_str() );
+ log.printf(" printing %d dimensional field %s on a grid with dimensions ",ngrid.size(), ll.c_str() );
+ for(unsigned i=0;i<ngrid.size();++i) log.printf("%d ",ngrid[i]);
+ log.printf("\n");
+ fnum=1;
+ checkRead();
+}
+
+void GenericDumpField::update(){
+ std::vector<double> min, max; myfield->retrieveBoundaries( min, max );
+ plumed_assert( min.size()==ngrid.size() && max.size()==ngrid.size() );
+ std::vector<bool> pbc(min.size(), false );
+ Grid gg( min, max, ngrid, pbc, false, false );
+
+ // Check field is properly normalized
+ double norm=0; std::vector<double> pp( myfield->get_Ndx() );
+ for(unsigned i=0;i<gg.getSize();++i){
+ gg.getPoint( i, pp ); gg.setValue( i, myfield->calculateField( pp ) );
+ norm+=gg.getValue(i);
+ }
+ norm*=gg.getBinVolume();
+
+ double norm2=0.0;
+ for(unsigned i=0;i<gg.getSize();++i){
+ gg.getPoint( i, pp ); gg.setValue( i, gg.getValue(i)/norm );
+ norm2+=gg.getValue(i);
+ }
+ norm2*=gg.getBinVolume();
+
+ if(comm.Get_rank()==0){
+ std::string num, fname;
+ Tools::convert( fnum, num );
+ fname = fbase + "." + num;
+ FILE* gfile=fopen( fname.c_str(), "w" );
+ fprintf(gfile,"#! DEFINITE INTEGRAL %f\n",norm2);
+ gg.writeToFile( gfile );
+ fclose(gfile);
+ }
+ fnum++;
+}
+
+}
diff --git a/src/GenericWholeMolecules.cpp b/src/GenericWholeMolecules.cpp
index 525f8cc8c..fa2f4db6e 100644
--- a/src/GenericWholeMolecules.cpp
+++ b/src/GenericWholeMolecules.cpp
@@ -63,7 +63,8 @@ PLUMED_REGISTER_ACTION(GenericWholeMolecules,"WHOLEMOLECULES")
void GenericWholeMolecules::registerKeywords( Keywords& keys ){
ActionAtomistic::registerKeywords( keys );
keys.add("compulsory","STRIDE","1","the frequency with which molecules are reassembled. Unless you are completely certain about what you are doing leave this set equal to 1!");
- keys.add("atoms","ENTITY","the atoms that make up a molecule that you wish to align. To specify multiple molecules use a list of ENTITY keywords: ENTITY1, ENTITY2,...");
+ keys.add("numbered","ENTITY","the atoms that make up a molecule that you wish to align. To specify multiple molecules use a list of ENTITY keywords: ENTITY1, ENTITY2,...");
+ keys.reset_style("ENTITY","atoms");
}
inline
diff --git a/src/Keywords.cpp b/src/Keywords.cpp
index ba9fe13c7..796407e86 100644
--- a/src/Keywords.cpp
+++ b/src/Keywords.cpp
@@ -12,8 +12,6 @@ KeyType::KeyType( const std::string& type ){
style=optional;
} else if( type=="atoms" ){
style=atoms;
- } else if( type=="numbered" ){
- style=numbered;
} else if( type=="nohtml" ){
style=nohtml;
} else if( type=="hidden" ){
@@ -26,23 +24,58 @@ KeyType::KeyType( const std::string& type ){
void Keywords::reserve( const std::string t, const std::string k, const std::string d ){
plumed_assert( !exists(k) ); plumed_assert( t!="flag"); // Cannot reserve flags at the moment - if you need it let me know
plumed_assert( !reserved(k) );
- reserved_types.push_back( KeyType(t) ); reserved_keys.push_back(k); reserved_documentation.push_back(d);
+ std::string fd;
+ if( t=="numbered" ){
+ fd=d + " You can use multiple instances of this keyword i.e. " + k +"1, " + k + "2, " + k + "3...";
+ reserved_allowmultiple.push_back(true);
+ reserved_types.push_back( KeyType("optional") );
+ } else {
+ fd=d;
+ reserved_allowmultiple.push_back(false);
+ reserved_types.push_back( KeyType(t) );
+ }
+ reserved_keys.push_back(k); reserved_documentation.push_back(fd);
}
void Keywords::use( const std::string k ){
plumed_assert( reserved(k) );
for(unsigned i=0;i<reserved_keys.size();++i){
if(reserved_keys[i]==k){
- types.push_back( reserved_types[i] ); keys.push_back( reserved_keys[i] ); documentation.push_back( reserved_documentation[i] );
+ types.push_back( reserved_types[i] ); keys.push_back( reserved_keys[i] );
+ documentation.push_back( reserved_documentation[i] );
+ allowmultiple.push_back( reserved_allowmultiple[i] );
}
}
}
+void Keywords::reset_style( const std::string k, const std::string style ){
+ if( exists(k) ){
+ for(unsigned i=0;i<keys.size();++i){
+ if( keys[i]==k ){ types[i]=KeyType(style); }
+ }
+ } else if ( reserved(k) ){
+ for(unsigned i=0;i<reserved_keys.size();++i){
+ if( reserved_keys[i]==k ){ reserved_types[i]=KeyType(style); }
+ }
+ } else {
+ plumed_assert(0);
+ }
+}
+
void Keywords::add( const std::string t, const std::string k, const std::string d ){
plumed_assert( !exists(k) ); plumed_assert( t!="flag"); // Use addFlag to add flags
plumed_assert( !reserved(k) );
- types.push_back( KeyType(t) ); keys.push_back(k); documentation.push_back(d);
- //defaults.push_back(false);
+ std::string fd;
+ if( t=="numbered" ){
+ fd=d + " You can use multiple instances of this keyword i.e. " + k +"1, " + k + "2, " + k + "3...";
+ allowmultiple.push_back(true);
+ types.push_back( KeyType("optional") );
+ } else {
+ fd=d;
+ allowmultiple.push_back(false);
+ types.push_back( KeyType(t) );
+ }
+ keys.push_back(k); documentation.push_back(fd);
}
void Keywords::add( const std::string t, const std::string k, const std::string def, const std::string d ){
@@ -50,6 +83,7 @@ void Keywords::add( const std::string t, const std::string k, const std::string
plumed_assert( !reserved(k) );
types.push_back( KeyType(t) ); keys.push_back(k);
documentation.push_back( "( default=" + def + " ) " + d );
+ allowmultiple.push_back(false);
numdefs.insert( std::pair<std::string,std::string>(k,def) );
}
@@ -57,7 +91,10 @@ void Keywords::addFlag( const std::string k, const bool def, const std::string d
plumed_assert( !exists(k) ); std::string defstr, flag="flag";
plumed_assert( !reserved(k) );
if( def ) { defstr="( default=on ) "; } else { defstr="( default=off ) "; }
- types.push_back( KeyType(flag) ); keys.push_back(k); documentation.push_back( defstr + d ); //defaults.push_back(def);
+ types.push_back( KeyType(flag) );
+ keys.push_back(k);
+ documentation.push_back( defstr + d ); //defaults.push_back(def);
+ allowmultiple.push_back(false);
booldefs.insert( std::pair<std::string,bool>(k,def) );
}
@@ -69,16 +106,28 @@ void Keywords::remove( const std::string k ){
if(j<keys.size()){
types.erase(types.begin()+j);
keys.erase(keys.begin()+j);
+ allowmultiple.erase(allowmultiple.begin()+j);
documentation.erase(documentation.begin()+j);
- //defaults.erase(defaults.begin()+j);
found=true;
} else break;
}
plumed_massert(found,"You are trying to forbid " + k + " a keyword that isn't there"); // You have tried to forbid a keyword that isn't there
}
+bool Keywords::numbered( const std::string k ) const {
+ unsigned j=0;
+ while(true){
+ for(j=0;j<keys.size();j++) if(keys[j]==k) break;
+ if( j<keys.size() ){
+ return allowmultiple[j];
+ } else break;
+ }
+ plumed_massert(0,"Did not find keyword " + k );
+ return false;
+}
+
void Keywords::clear() {
- types.clear(); keys.clear(); documentation.clear(); //defaults.clear();
+ types.clear(); keys.clear(); documentation.clear(); allowmultiple.clear(); //defaults.clear();
}
bool Keywords::style( const std::string k, const std::string t ) const {
@@ -104,11 +153,6 @@ bool Keywords::style( const std::string k, const std::string t ) const {
if( keys[i]==k ) return types[i].isAtomList();
}
plumed_assert(false);
- } else if( t=="numbered" ){
- for(unsigned i=0;i<keys.size();++i){
- if( keys[i]==k ) return types[i].isNumbered();
- }
- plumed_assert(false);
} else if( t=="nohtml" ){
for(unsigned i=0;i<keys.size();++i){
if( keys[i]==k ) return types[i].isNoHTML();
@@ -129,13 +173,14 @@ bool Keywords::style( const std::string k, const std::string t ) const {
unsigned Keywords::size() const {
plumed_assert( keys.size()==documentation.size() );
plumed_assert( keys.size()==types.size() );
-// plumed_assert( keys.size()==defaults.size() );
+ plumed_assert( keys.size()==allowmultiple.size() );
return keys.size();
}
bool Keywords::exists( const std::string k ) const {
plumed_massert( keys.size()==documentation.size(), "documentation doesn't match keys" );
plumed_massert( keys.size()==types.size(), "types doesn't match keys" );
+ plumed_assert( keys.size()==allowmultiple.size() );
for(unsigned i=0;i<keys.size();++i){
if( keys[i]==k ) return true;
@@ -146,6 +191,7 @@ bool Keywords::exists( const std::string k ) const {
bool Keywords::reserved( const std::string k ) const {
plumed_massert( reserved_keys.size()==reserved_documentation.size(), "documentation doesn't match keys" );
plumed_massert( reserved_keys.size()==reserved_types.size(), "types doesn't match keys" );
+ plumed_massert( reserved_keys.size()==reserved_allowmultiple.size(),"allowmultiple doesn't match keys" );
for(unsigned i=0;i<reserved_keys.size();++i){
if( reserved_keys[i]==k ) return true;
@@ -179,18 +225,6 @@ void Keywords::print_html() const {
std::cout<<"</table>\n\n";
}
nkeys=0;
- for(unsigned i=0;i<keys.size();++i){
- if ( types[i].isNumbered() ) nkeys++;
- }
- if( nkeys>0 ){
- std::cout<<"\\par Numbered keywords\n\n";
- std::cout<<" <table align=center frame=void width=95%% cellpadding=5%%> \n";
- for(unsigned i=0;i<keys.size();++i){
- if ( types[i].isNumbered() ) print_html_item( i );
- }
- std::cout<<"</table>\n\n";
- }
- nkeys=0;
for(unsigned i=0;i<keys.size();++i){
if ( types[i].isFlag() ) nkeys++;
}
@@ -238,16 +272,6 @@ void Keywords::print( Log& log ) const {
if ( types[i].isCompulsory() ) printKeyword( i, log ); //log.printKeyword( keys[i], documentation[i] );
}
}
- // This is a special option specifically for steered MD
- nkeys=0;
- for(unsigned i=0;i<keys.size();++i){
- if ( types[i].isNumbered() ) nkeys++;
- }
- if( nkeys>0 ){
- for(unsigned i=0;i<keys.size();++i){
- if ( types[i].isNumbered() ) printKeyword( i, log ); //log.printKeyword( keys[i], documentation[i] );
- }
- }
nkeys=0;
for(unsigned i=0;i<keys.size();++i){
if ( types[i].isFlag() ) nkeys++;
diff --git a/src/Keywords.h b/src/Keywords.h
index 504057d5e..ceb435895 100644
--- a/src/Keywords.h
+++ b/src/Keywords.h
@@ -14,14 +14,13 @@ namespace PLMD{
class KeyType{
friend class Keyword;
private:
- enum {compulsory,flag,optional,atoms,numbered,nohtml,hidden} style;
+ enum {compulsory,flag,optional,atoms,nohtml,hidden} style;
public:
KeyType( const std::string& type );
bool isCompulsory() const { return (style==compulsory); }
bool isFlag() const { return (style==flag); }
bool isOptional() const { return (style==optional); }
bool isAtomList() const { return (style==atoms); }
- bool isNumbered() const { return (style==numbered); }
bool isNoHTML() const { return (style==nohtml); }
bool isHidden() const { return (style==hidden); }
};
@@ -34,12 +33,16 @@ private:
std::vector<KeyType> reserved_types;
/// The names of the keyword
std::vector<std::string> reserved_keys;
+/// The allowance of stuff like key1, key2 etc
+ std::vector<bool> reserved_allowmultiple;
/// The documentation for the keywords
std::vector<std::string> reserved_documentation;
/// Whether the keyword is compulsory, optional...
std::vector<KeyType> types;
/// The names of the keyword
std::vector<std::string> keys;
+/// Do we allow stuff like key1, key2 etc
+ std::vector<bool> allowmultiple;
/// The documentation for the keywords
std::vector<std::string> documentation;
/// The default values for the flags (are they on or of)
@@ -58,6 +61,8 @@ private:
void clear();
/// Return the number of defined keywords
unsigned size() const;
+/// Check if numbered keywords are allowed for this action
+ bool numbered( const std::string k ) const ;
public:
/// Print the documentation to the log file (used by PLMD::Action::error)
void print( Log& log ) const ;
@@ -73,24 +78,16 @@ public:
void addFlag( const std::string k, const bool def, const std::string d );
/// Remove the keyword with name k
void remove( const std::string k );
-// /// Clear all the keywords
-// void clear();
-// /// Return the number of defined keywords
-// unsigned size() const;
/// Check if there is a keyword with name k
bool exists( const std::string k ) const ;
/// Check the keyword k has been reserved
bool reserved( const std::string k ) const ;
/// Check if the keyword with name k has style t
bool style( const std::string k, const std::string t ) const ;
-// /// Print the documentation to the log file (used by PLMD::Action::error)
-// void print( Log& log ) const ;
/// Print an html version of the documentation
void print_html() const ;
-// /// find out whether flag key is on or off by default.
-// bool getLogicalDefault( std::string key, bool& def ) const ;
-// /// Get the value of the default for the keyword named key
-// bool getDefaultValue( std::string key, std::string& def ) const ;
+/// Change the style of a keyword
+ void reset_style( const std::string k, const std::string style );
};
}
diff --git a/src/MultiColvar.cpp b/src/MultiColvar.cpp
index 63d93e36e..ad3662d4f 100644
--- a/src/MultiColvar.cpp
+++ b/src/MultiColvar.cpp
@@ -13,11 +13,12 @@ void MultiColvar::registerKeywords( Keywords& keys ){
ActionAtomistic::registerKeywords( keys );
keys.addFlag("PBC",true,"use the periodic boundary conditions when calculating distances");
keys.addFlag("NOPBC",false,"ignore the periodic boundary conditions when calculating distances");
- keys.reserve("atoms","ATOMS","the atoms involved in each of the collective variables you wish to calculate. "
+ keys.reserve("numbered","ATOMS","the atoms involved in each of the collective variables you wish to calculate. "
"Keywords like ATOMS1, ATOMS2, ATOMS3,... should be listed and one CV will be "
"calculated for each ATOM keyword you specify (all ATOM keywords should "
"define the same number of atoms). The eventual number of quantities calculated by this "
"action will depend on what functions of the distribution you choose to calculate.");
+ keys.reset_style("ATOMS","atoms");
keys.reserve("atoms","GROUP","this keyword is used for colvars that are calculated from a pair of atoms. "
"One colvar is calculated for each distinct pair of atoms in the group.");
keys.reserve("atoms","GROUPA","this keyword is used for colvars that are calculated from a pair of atoms and must appaer with the keyword GROUPB. "
@@ -32,7 +33,11 @@ void MultiColvar::registerKeywords( Keywords& keys ){
"of the atoms specifies using SPECIESB is within the specified cutoff");
keys.reserve("atoms","SPECIESB","this keyword is used for colvars such as the coordination number. It must appear with SPECIESA. For a full explanation see "
"the documentation for that keyword");
- keys.add("optional","FIELD","create a field cv from these collective variables.");
+ keys.reserve("optional","FIELD","create a field cv from these collective variables. From a distribution of collective variables we calculate a 1D-field using "
+ " \\f$\\psi(z)=\\frac{\\sum_i G(z-s_i,\\sigma)}{\\int \\textrm{d}z \\sum_i G(z-s_i,\\sigma)}\\f$ where \\f$ G(z-s_i,\\sigma)\\f$ "
+ " is a normalized Gaussian function with standard deviation \\f$\\sigma\\f$ centered at the value of the \\f$i\\f$th collective variable"
+ " \\f$s_i$\\f$. In other words we use a histogram calculated from the values of all the constituent collective variables. "
+ + Field::documentation() );
keys.add("optional","MIN","calculate the minimum value and store it in a value called min. " + min::documentation() );
// keys.add("optional","MAX", "take the maximum value from these variables");
keys.addFlag("AVERAGE",false,"take the average value of these variables and store it in value called average.");
@@ -40,7 +45,8 @@ void MultiColvar::registerKeywords( Keywords& keys ){
keys.add("optional","MORE_THAN", "take the number of variables more than the specified target and store it in a value called gt<target>. " + more_than::documentation() );
keys.add("optional","HISTOGRAM", "create a discretized histogram of the distribution of collective variables. " + HistogramBead::histodocs() );
keys.add("numbered", "WITHIN", "calculate the number variabels that are within a certain range and store it in a value called between<lowerbound>&<upperbound>. " + within::documentation() );
- keys.add("numbered","MOMENT","calculate the ith moment of the distribution of collective variables.");
+ keys.add("numbered","MOMENT","calculate the mth moment of the distribution of collective variables. " + moment::documentation() +
+ " To calculate multiple moments use repeated instances of the moment keyword MOMENT1, MOMENT2, MOMENT3... ");
keys.reserve("numbered", "SUBCELL", "calculate the average value of the CV within a portion of the box and store it in a value called subcell. " + cvdens::documentation() );
keys.reserve("numbered", "GRADIENT", "calcualte the gradient of a CV across the box and store it in value called gradient. " + gradient::documentation() );
ActionWithDistribution::registerKeywords( keys );
@@ -188,7 +194,7 @@ void MultiColvar::readAtoms( int& natoms ){
}
}
- if( !usingDistributionFunctions() ) setupField(1); // Setup the field if we are not using any of the above
+ if( !usingDistributionFunctions() ) setupField(1, "identity"); // Setup the field if we are not using any of the above
requestDistribution(); // And setup the ActionWithDistribution
requestAtoms(); // Request the atoms in ActionAtomistic and set up the value sizes
}
@@ -202,7 +208,7 @@ void MultiColvar::readAtomsKeyword( int& natoms ){
if( t.size()==0 ) break;
log.printf(" Colvar %d is calculated from atoms : ", i);
- for(unsigned i=0;i<t.size();++i) log.printf("%d ",t[i].serial() );
+ for(unsigned j=0;j<t.size();++j) log.printf("%d ",t[j].serial() );
log.printf("\n");
if( i==1 && natoms<0 ) natoms=t.size();
@@ -439,11 +445,52 @@ void MultiColvar::calculateThisFunction( const unsigned& j, Value* value_in, std
}
void MultiColvar::calculateFieldContribution( const unsigned& j, const std::vector<double>& at, Value* value_in, Value& stress, std::vector<Value>& der ){
- plumed_assert(at.size()==1 && der.size()==1 );
-
- double dd, ss; dd=at[0]-value_in->get(); ss=fnorm*exp( -dd*dd/ fsigma2 );
- stress.set( ss ); stress.addDerivative( 0, ( dd / fsigma2 )*ss );
- der[0].set( -( dd / fsigma2 )*ss ); der[0].addDerivative( 0, ss*( ( dd*dd/fsigma4 ) + 1 ) );
+ plumed_assert( at.size()==1 && j<colvar_atoms.size() );
+ plumed_assert( stress.getNumberOfDerivatives()==1 && der[j].getNumberOfDerivatives()==1 );
+
+ double dd, ss, du; dd=at[0]-value_in->get();
+ ss=fnorm*exp( -(dd*dd)/(2*fsigma2) ); du=dd/fsigma2;
+ stress.set( ss ); stress.addDerivative( 0, -du*ss );
+ value_in->chainRule( du*ss );
+ int thisatom; unsigned innat=colvar_atoms[j].getNumberActive();
+ for(unsigned i=0;i<innat;++i){
+ thisatom=linkIndex( i, colvar_atoms[j], all_atoms );
+ plumed_assert( thisatom>=0 );
+ der[3*thisatom+0].add( value_in->getDerivative(3*i+0) );
+ der[3*thisatom+1].add( value_in->getDerivative(3*i+1) );
+ der[3*thisatom+2].add( value_in->getDerivative(3*i+2) );
+ }
+ // Easy to merge the virial
+ unsigned outnat=getNumberOfAtoms();
+ der[3*outnat+0].add( value_in->getDerivative(3*innat+0) );
+ der[3*outnat+1].add( value_in->getDerivative(3*innat+1) );
+ der[3*outnat+2].add( value_in->getDerivative(3*innat+2) );
+ der[3*outnat+3].add( value_in->getDerivative(3*innat+3) );
+ der[3*outnat+4].add( value_in->getDerivative(3*innat+4) );
+ der[3*outnat+5].add( value_in->getDerivative(3*innat+5) );
+ der[3*outnat+6].add( value_in->getDerivative(3*innat+6) );
+ der[3*outnat+7].add( value_in->getDerivative(3*innat+7) );
+ der[3*outnat+8].add( value_in->getDerivative(3*innat+8) );
+
+ value_in->chainRule( 1./(fsigma2*du) - du );
+ for(unsigned i=0;i<innat;++i){
+ thisatom=linkIndex( i, colvar_atoms[j], all_atoms );
+ plumed_assert( thisatom>=0 );
+ der[3*thisatom+0].addDerivative( 0, value_in->getDerivative(3*i+0) );
+ der[3*thisatom+1].addDerivative( 0, value_in->getDerivative(3*i+1) );
+ der[3*thisatom+2].addDerivative( 0, value_in->getDerivative(3*i+2) );
+ }
+ // Easy to merge the virial
+ der[3*outnat+0].addDerivative( 0, value_in->getDerivative(3*innat+0) );
+ der[3*outnat+1].addDerivative( 0, value_in->getDerivative(3*innat+1) );
+ der[3*outnat+2].addDerivative( 0, value_in->getDerivative(3*innat+2) );
+ der[3*outnat+3].addDerivative( 0, value_in->getDerivative(3*innat+3) );
+ der[3*outnat+4].addDerivative( 0, value_in->getDerivative(3*innat+4) );
+ der[3*outnat+5].addDerivative( 0, value_in->getDerivative(3*innat+5) );
+ der[3*outnat+6].addDerivative( 0, value_in->getDerivative(3*innat+6) );
+ der[3*outnat+7].addDerivative( 0, value_in->getDerivative(3*innat+7) );
+ der[3*outnat+8].addDerivative( 0, value_in->getDerivative(3*innat+8) );
+// der[j].set( du*ss ); der[j].addDerivative( 0, ss*( 1./fsigma2 - du*du ) );
}
void MultiColvar::mergeDerivatives( const unsigned j, Value* value_in, Value* value_out ){
@@ -473,21 +520,8 @@ void MultiColvar::mergeDerivatives( const unsigned j, Value* value_in, Value* va
void MultiColvar::derivedFieldSetup( const double sigma ){
const double pi=3.141592653589793238462643383279502884197169399375105820974944592307;
log.printf(" generating field cv from histogram in which each component CV is represented by a Gaussian of width %f\n",sigma);
- fsigma2=2*sigma*sigma;
- fsigma4=fsigma2*fsigma2;
- fnorm = 1.0 / ( sqrt(2*pi)*sigma );
- for(unsigned i=0;i<getNumberOfFunctionsInDistribution();++i){
- std::string ss; Tools::convert(i+1,ss);
- addComponentWithDerivatives("fval"+ss);
- }
-}
-
-void MultiColvar::setFieldOutputValue( const unsigned& j, Value* value_in ){
- plumed_assert( value_in->getNumberOfDerivatives()==getPntrToComponent(j)->getNumberOfDerivatives() );
- Value* value_out=getPntrToComponent(j);
- for(unsigned i=0;i<value_in->getNumberOfDerivatives();++i){ value_out->addDerivative( i, value_in->getDerivative(i) ); }
- // And store the value
- value_out->set( value_in->get() );
+ fsigma2=sigma*sigma;
+ fnorm = 1.0 / ( sqrt(2*pi)*sigma );
}
Vector MultiColvar::getSeparation( const Vector& vec1, const Vector& vec2 ) const {
@@ -506,31 +540,16 @@ void MultiColvar::apply(){
}
v.clear();
- unsigned nat=getNumberOfAtoms(); std::vector<double> forces; unsigned nder;
- if( usingDistributionFunctions() ) forces.resize(3*getNumberOfAtoms()+9);
+ unsigned nat=getNumberOfAtoms();
+ std::vector<double> forces(3*getNumberOfAtoms()+9);
- unsigned vstart=3*nat-9; unsigned thisatom;
+ unsigned vstart=3*getNumberOfAtoms();
for(int i=0;i<getNumberOfComponents();++i){
-
- if( !usingDistributionFunctions() ){
- nder=getThisFunctionsNumberOfDerivatives(i);
- if (forces.size()!=nder ) forces.resize(nder);
- if( getPntrToComponent(i)->applyForce( forces ) ){
- for(unsigned j=0;j<forces.size();++j){
- thisatom=linkIndex( i, colvar_atoms[j], all_atoms );
- plumed_assert( thisatom>=0 );
- f[thisatom][0]+=forces[3*j+0];
- f[thisatom][1]+=forces[3*j+1];
- f[thisatom][2]+=forces[3*j+2];
- }
- vstart=nder-9;
- }
- } else if( getPntrToComponent(i)->applyForce( forces ) ){
- for(unsigned j=0;j<nat;++j){
- f[j][0]+=forces[3*j+0];
- f[j][1]+=forces[3*j+1];
- f[j][2]+=forces[3*j+2];
- }
+ if( getPntrToComponent(i)->applyForce( forces ) ){
+ for(unsigned j=0;j<nat;++j){
+ f[j][0]+=forces[3*j+0];
+ f[j][1]+=forces[3*j+1];
+ f[j][2]+=forces[3*j+2];
}
v(0,0)+=forces[vstart+0];
v(0,1)+=forces[vstart+1];
@@ -541,6 +560,26 @@ void MultiColvar::apply(){
v(2,0)+=forces[vstart+6];
v(2,1)+=forces[vstart+7];
v(2,2)+=forces[vstart+8];
+ }
+ }
+
+ if( getField() ){
+ if( getField()->applyForces( forces ) ){
+ for(unsigned j=0;j<nat;++j){
+ f[j][0]+=forces[3*j+0];
+ f[j][1]+=forces[3*j+1];
+ f[j][2]+=forces[3*j+2];
+ }
+ v(0,0)+=forces[vstart+0];
+ v(0,1)+=forces[vstart+1];
+ v(0,2)+=forces[vstart+2];
+ v(1,0)+=forces[vstart+3];
+ v(1,1)+=forces[vstart+4];
+ v(1,2)+=forces[vstart+5];
+ v(2,0)+=forces[vstart+6];
+ v(2,1)+=forces[vstart+7];
+ v(2,2)+=forces[vstart+8];
+ }
}
}
diff --git a/src/MultiColvar.h b/src/MultiColvar.h
index e4142ee19..e4f925db9 100644
--- a/src/MultiColvar.h
+++ b/src/MultiColvar.h
@@ -164,7 +164,7 @@ private:
bool setperiods;
bool needsCentralAtomPosition;
/// Constants for fields
- double fsigma2, fsigma4, fnorm;
+ double fsigma2, fnorm;
/// The list of all the atoms involved in the colvar
DynamicList<AtomNumber> all_atoms;
/// The lists of the atoms involved in each of the individual colvars
@@ -216,7 +216,7 @@ public:
/// Merge the derivatives
void mergeDerivatives( const unsigned j, Value* value_in, Value* value_out );
/// Turn of atom requests when this colvar is deactivated cos its small
- void deactivate( const unsigned j );
+ void deactivateValue( const unsigned j );
/// Calcualte the colvar
void calculateThisFunction( const unsigned& j, Value* value_in, std::vector<Value>& aux );
/// And a virtual function which actually computes the colvar
@@ -225,8 +225,8 @@ public:
virtual void getCentralAtom( const std::vector<Vector>& pos, Vector& cpos, std::vector<Tensor>& deriv );
/// Setup everything that needs to be setup for field cvs
void derivedFieldSetup( const double sigma );
-/// Set the output values for the field (important if we to apply forces on fields)
- void setFieldOutputValue( const unsigned& j, Value* value_in );
+/// Returns the number of coordinates of the field
+ unsigned getNumberOfFieldDerivatives();
/// Calculate the contribution to the field at the point thisp
void calculateFieldContribution( const unsigned& j, const std::vector<double>& thisp, Value* tmpvalue, Value& tmpstress, std::vector<Value>& tmpder );
};
@@ -237,7 +237,12 @@ unsigned MultiColvar::getNumberOfFunctionsInDistribution(){
}
inline
-void MultiColvar::deactivate( const unsigned j ){
+unsigned MultiColvar::getNumberOfFieldDerivatives(){
+ return 3*getNumberOfAtoms()+9;
+}
+
+inline
+void MultiColvar::deactivateValue( const unsigned j ){
colvar_atoms[j].deactivateAll();
}
diff --git a/src/MultiColvarDistance.cpp b/src/MultiColvarDistance.cpp
index 271324c68..c23c43293 100644
--- a/src/MultiColvarDistance.cpp
+++ b/src/MultiColvarDistance.cpp
@@ -61,6 +61,7 @@ void MultiColvarDistance::registerKeywords( Keywords& keys ){
ActionWithDistribution::autoParallelize( keys );
keys.add("optional","NL_CUTOFF","The cutoff for the neighbor list");
keys.use("ATOMS"); keys.use("GROUP"); keys.use("GROUPA"); keys.use("GROUPB");
+ keys.use("FIELD");
}
MultiColvarDistance::MultiColvarDistance(const ActionOptions&ao):
diff --git a/user-doc/bibliography.bib b/user-doc/bibliography.bib
index 28b04e4b8..1ec08e92e 100644
--- a/user-doc/bibliography.bib
+++ b/user-doc/bibliography.bib
@@ -29,6 +29,20 @@
journal = {Proc. Natl. Acad. Sci. USA}
}
+@article{field-cvs,
+author = {Tribello, Gareth A. and Ceriotti, Michele and Parrinello, Michele},
+title = {Using sketch-map coordinates to analyze and bias molecular dynamics simulations},
+volume = {109},
+number = {14},
+pages = {5196-5201},
+year = {2012},
+doi = {10.1073/pnas.1201152109},
+abstract ={When examining complex problems, such as the folding of proteins, coarse grained descriptions of the system drive our investigation and help us to rationalize the results. Oftentimes collective variables (CVs), derived through some chemical intuition about the process of interest, serve this purpose. Because finding these CVs is the most difficult part of any investigation, we recently developed a dimensionality reduction algorithm, sketch-map, that can be used to build a low-dimensional map of a phase space of high-dimensionality. In this paper we discuss how these machine-generated CVs can be used to accelerate the exploration of phase space and to reconstruct free-energy landscapes. To do so, we develop a formalism in which high-dimensional configurations are no longer represented by low-dimensional position vectors. Instead, for each configuration we calculate a probability distribution, which has a domain that encompasses the entirety of the low-dimensional space. To construct a biasing potential, we exploit an analogy with metadynamics and use the trajectory to adaptively construct a repulsive, history-dependent bias from the distributions that correspond to the previously visited configurations. This potential forces the system to explore more of phase space by making it desirable to adopt configurations whose distributions do not overlap with the bias. We apply this algorithm to a small model protein and succeed in reproducing the free-energy surface that we obtain from a parallel tempering calculation.},
+URL = {http://www.pnas.org/content/109/14/5196.abstract},
+eprint = {http://www.pnas.org/content/109/14/5196.full.pdf+html},
+journal = {Proceedings of the National Academy of Sciences}
+}
+
@article{camilloni_protG,
Author = {Carlo Camilloni and Davide Provasi and Guido Tiana and Ricardo A. Broglia},
Journal = {Proteins},
--
GitLab