diff --git a/regtest/rt45/colvar.reference b/regtest/rt45/colvar.reference
index 0daf0292763b5ad0477174b539a18981ece0268f..d85f89e9e89eedced5c940eb1ec4636a56630d0f 100644
--- a/regtest/rt45/colvar.reference
+++ b/regtest/rt45/colvar.reference
@@ -1,6 +1,6 @@
#! FIELDS time a1.mean a2.mean a2.less_than a2.between-1 a2.between-2 a2.more_than
- 0.000000 1.66115 1.66608 3.40427 0.54041 3.28252 2.45980
- 0.050000 1.65922 1.66308 3.27471 0.53982 3.15893 2.36446
- 0.100000 1.65828 1.66185 3.31055 0.53871 3.21053 2.40988
- 0.150000 1.65822 1.66250 3.41233 0.54348 3.32747 2.47687
- 0.200000 1.65684 1.66061 3.54666 0.54361 3.45293 2.56758
+ 0.000000 1.66115 1.66663 3.40427 0.54041 3.28252 2.45980
+ 0.050000 1.65922 1.66505 3.27471 0.53982 3.15893 2.36446
+ 0.100000 1.65828 1.66517 3.31055 0.53871 3.21053 2.40988
+ 0.150000 1.65822 1.66434 3.41575 0.54217 3.32747 2.47687
+ 0.200000 1.65684 1.66316 3.54666 0.54361 3.45293 2.56758
diff --git a/regtest/rt45/derivatives.reference b/regtest/rt45/derivatives.reference
index 7c99b2399ce81284292416796bc57a90fef6150d..614d9189e3789b881f411da1be438c2f7862901a 100644
--- a/regtest/rt45/derivatives.reference
+++ b/regtest/rt45/derivatives.reference
@@ -1,55 +1,55 @@
#! FIELDS time parameter a2.mean a2.less_than a2.between-1 a2.between-2 a2.more_than
- 0.000000 0 0.04922 -0.46110 -0.01577 -0.51808 -0.23022
- 0.000000 1 -0.04451 0.56163 0.00969 0.51733 0.27370
- 0.000000 2 -0.01315 0.19881 0.00056 0.18379 0.10046
- 0.000000 3 -0.00845 -1.10676 -0.00376 -1.04351 -0.82825
- 0.000000 4 0.00224 0.01324 -0.00040 0.01076 0.00961
- 0.000000 5 -0.00294 -0.97720 -0.00536 -0.93271 -0.73033
- 0.000000 6 0.00309 -1.24820 -0.01017 -1.19507 -0.91128
- 0.000000 7 -0.00359 -1.21440 -0.00765 -1.16042 -0.90816
- 0.000000 8 -0.00772 -0.04097 0.00272 -0.02772 -0.04570
- 0.000000 9 -0.00171 -0.11203 0.00073 -0.09507 -0.07782
- 0.000000 10 0.00125 -1.39940 -0.01080 -1.34896 -1.01629
- 0.000000 11 0.01015 -1.23403 -0.01326 -1.20298 -0.88080
- 0.000000 12 0.00088 -0.00851 0.00016 -0.00562 -0.00375
- 0.000000 13 0.00007 -0.01044 0.00017 -0.00866 -0.00778
- 0.000000 14 0.00802 -0.36833 -0.00080 -0.33249 -0.24550
+ 0.000000 0 0.04928 -0.45829 -0.01577 -0.51808 -0.26441
+ 0.000000 1 -0.04458 0.56901 0.00969 0.51733 0.24915
+ 0.000000 2 -0.01318 0.18970 0.00056 0.18379 0.10368
+ 0.000000 3 -0.00828 -1.09164 -0.00376 -1.04351 -0.79815
+ 0.000000 4 0.00224 0.01305 -0.00040 0.01076 0.00923
+ 0.000000 5 -0.00278 -0.96386 -0.00536 -0.93271 -0.70379
+ 0.000000 6 0.00329 -1.22528 -0.01017 -1.19507 -0.88172
+ 0.000000 7 -0.00340 -1.19187 -0.00765 -1.16042 -0.87910
+ 0.000000 8 -0.00771 -0.04007 0.00272 -0.02772 -0.04455
+ 0.000000 9 -0.00170 -0.11056 0.00073 -0.09507 -0.07579
+ 0.000000 10 0.00147 -1.38045 -0.01080 -1.34896 -0.99015
+ 0.000000 11 0.01034 -1.21745 -0.01326 -1.20298 -0.85794
+ 0.000000 12 0.00088 -0.00849 0.00016 -0.00562 -0.00363
+ 0.000000 13 0.00007 -0.01040 0.00017 -0.00866 -0.00760
+ 0.000000 14 0.00808 -0.36724 -0.00080 -0.33249 -0.23923
0.000000 15 0.00000 0.00000 0.00000 0.00000 0.00000
0.000000 16 0.00000 0.00000 0.00000 0.00000 0.00000
0.000000 17 0.00000 0.00000 0.00000 0.00000 0.00000
- 0.000000 18 0.00080 -0.02886 -0.00007 -0.02451 -0.01862
- 0.000000 19 0.00053 -0.02730 -0.00014 -0.02382 -0.01846
- 0.000000 20 0.00127 -0.05353 -0.00025 -0.04649 -0.03551
+ 0.000000 18 0.00080 -0.02679 -0.00007 -0.02451 -0.01642
+ 0.000000 19 0.00053 -0.02533 -0.00014 -0.02382 -0.01637
+ 0.000000 20 0.00128 -0.04966 -0.00025 -0.04649 -0.03141
0.000000 21 0.00000 0.00000 0.00000 0.00000 0.00000
0.000000 22 0.00000 0.00000 0.00000 0.00000 0.00000
0.000000 23 0.00000 0.00000 0.00000 0.00000 0.00000
- 0.000000 24 0.00039 0.00736 -0.00011 0.00670 0.00652
- 0.000000 25 -0.00010 -0.00247 -0.00016 -0.00366 -0.00244
- 0.000000 26 -0.00499 0.26741 0.00055 0.24179 0.18114
- 0.000000 27 -0.02993 -1.37937 -0.00314 -1.33707 -1.10424
- 0.000000 28 0.00856 -0.03445 -0.00460 -0.05535 -0.01742
- 0.000000 29 0.02431 1.41464 0.00537 1.38121 1.12639
- 0.000000 30 0.00055 -0.02382 -0.00009 -0.02051 -0.01537
- 0.000000 31 0.00044 -0.02298 0.00008 -0.01894 -0.01621
- 0.000000 32 -0.00093 0.04521 0.00002 0.03784 0.03034
- 0.000000 33 -0.00060 -0.00423 0.00065 0.00284 0.00118
- 0.000000 34 -0.00756 -1.19942 -0.00304 -1.11223 -0.89186
- 0.000000 35 -0.00632 1.16619 0.00816 1.09618 0.83716
- 0.000000 36 0.00058 -0.01634 -0.00021 -0.01487 -0.00871
- 0.000000 37 0.00813 -0.32210 -0.00202 -0.29739 -0.21170
- 0.000000 38 -0.00019 -0.00242 0.00011 -0.00174 -0.00196
- 0.000000 39 0.00091 -0.02809 -0.00011 -0.02559 -0.01833
- 0.000000 40 0.00162 -0.05828 -0.00015 -0.05309 -0.03802
- 0.000000 41 0.00078 -0.02741 -0.00009 -0.02509 -0.01830
+ 0.000000 24 0.00038 0.00723 -0.00011 0.00670 0.00620
+ 0.000000 25 -0.00010 -0.00242 -0.00016 -0.00366 -0.00232
+ 0.000000 26 -0.00503 0.26323 0.00055 0.24179 0.17079
+ 0.000000 27 -0.02970 -1.36495 -0.00314 -1.33707 -1.08107
+ 0.000000 28 0.00856 -0.03415 -0.00460 -0.05535 -0.01693
+ 0.000000 29 0.02408 1.39988 0.00537 1.38121 1.10269
+ 0.000000 30 0.00055 -0.02086 -0.00009 -0.02051 -0.01267
+ 0.000000 31 0.00044 -0.02009 0.00008 -0.01894 -0.01358
+ 0.000000 32 -0.00094 0.03962 0.00002 0.03784 0.02524
+ 0.000000 33 -0.00060 -0.00421 0.00065 0.00284 0.00121
+ 0.000000 34 -0.00737 -1.17902 -0.00304 -1.11223 -0.86592
+ 0.000000 35 -0.00650 1.14667 0.00816 1.09618 0.81235
+ 0.000000 36 0.00058 -0.01629 -0.00021 -0.01487 -0.00827
+ 0.000000 37 0.00817 -0.32114 -0.00202 -0.29739 -0.20234
+ 0.000000 38 -0.00019 -0.00241 0.00011 -0.00174 -0.00188
+ 0.000000 39 0.00091 -0.02637 -0.00011 -0.02559 -0.01542
+ 0.000000 40 0.00162 -0.05469 -0.00015 -0.05309 -0.03192
+ 0.000000 41 0.00078 -0.02572 -0.00009 -0.02509 -0.01543
0.000000 42 0.00000 0.00000 0.00000 0.00000 0.00000
0.000000 43 0.00000 0.00000 0.00000 0.00000 0.00000
0.000000 44 0.00000 0.00000 0.00000 0.00000 0.00000
0.000000 45 0.00000 0.00000 0.00000 0.00000 0.00000
0.000000 46 0.00000 0.00000 0.00000 0.00000 0.00000
0.000000 47 0.00000 0.00000 0.00000 0.00000 0.00000
- 0.000000 48 0.00003 -0.00016 0.00000 0.00000 -0.00000
- 0.000000 49 0.00028 -0.01324 0.00000 0.00000 -0.00854
- 0.000000 50 0.00052 -0.01361 0.00000 0.00000 -0.00889
+ 0.000000 48 0.00003 -0.00016 0.00000 0.00000 0.00000
+ 0.000000 49 0.00028 -0.00434 0.00000 0.00000 0.00000
+ 0.000000 50 0.00052 -0.00434 0.00000 0.00000 0.00000
0.000000 51 0.00000 0.00000 0.00000 0.00000 0.00000
0.000000 52 0.00000 0.00000 0.00000 0.00000 0.00000
0.000000 53 0.00000 0.00000 0.00000 0.00000 0.00000
@@ -59,69 +59,69 @@
0.000000 57 0.00000 0.00000 0.00000 0.00000 0.00000
0.000000 58 0.00000 0.00000 0.00000 0.00000 0.00000
0.000000 59 0.00000 0.00000 0.00000 0.00000 0.00000
- 0.000000 60 0.00007 -0.00166 0.00003 0.00001 -0.00096
- 0.000000 61 0.00037 -0.01741 -0.00002 -0.00173 -0.01167
- 0.000000 62 -0.00049 0.01732 0.00005 0.00190 0.01136
- 0.000000 63 0.00067 -0.02476 -0.00026 -0.01871 -0.01601
- 0.000000 64 0.00100 -0.04378 -0.00046 -0.03349 -0.02900
- 0.000000 65 -0.00056 0.02151 0.00035 0.01724 0.01471
+ 0.000000 60 0.00007 -0.00103 0.00003 0.00001 -0.00031
+ 0.000000 61 0.00037 -0.01048 -0.00002 -0.00173 -0.00448
+ 0.000000 62 -0.00050 0.01040 0.00005 0.00190 0.00418
+ 0.000000 63 0.00067 -0.02301 -0.00026 -0.01871 -0.01221
+ 0.000000 64 0.00100 -0.04064 -0.00046 -0.03349 -0.02219
+ 0.000000 65 -0.00057 0.01997 0.00035 0.01724 0.01135
0.000000 66 0.00000 0.00000 0.00000 0.00000 0.00000
0.000000 67 0.00000 0.00000 0.00000 0.00000 0.00000
0.000000 68 0.00000 0.00000 0.00000 0.00000 0.00000
0.000000 69 0.00000 0.00000 0.00000 0.00000 0.00000
0.000000 70 0.00000 0.00000 0.00000 0.00000 0.00000
0.000000 71 0.00000 0.00000 0.00000 0.00000 0.00000
- 0.000000 72 0.00037 -0.01753 -0.00013 -0.01590 -0.00980
- 0.000000 73 -0.00392 0.24609 0.00159 0.23058 0.16880
- 0.000000 74 -0.00020 0.00231 -0.00008 0.00106 0.00095
- 0.000000 75 0.00062 -0.02615 -0.00023 -0.02168 -0.01775
- 0.000000 76 -0.00100 0.05098 0.00041 0.04217 0.03446
- 0.000000 77 0.00040 -0.02411 -0.00025 -0.02034 -0.01665
- 0.000000 78 -0.00971 -1.08938 -0.00790 -1.05682 -0.83871
- 0.000000 79 0.00917 1.03325 0.00537 0.98903 0.79318
- 0.000000 80 0.00609 0.06702 -0.00136 0.05775 0.05927
- 0.000000 81 0.00034 -0.08263 0.00125 -0.06541 -0.05517
- 0.000000 82 0.00532 1.36756 0.00868 1.33183 1.03831
- 0.000000 83 -0.02253 -1.51498 -0.00934 -1.49518 -1.18900
- 0.000000 84 -0.00002 -0.00111 0.00003 -0.00014 -0.00077
- 0.000000 85 -0.00066 0.02166 0.00010 0.00821 0.01474
- 0.000000 86 0.00045 -0.02044 -0.00020 -0.00845 -0.01351
+ 0.000000 72 0.00037 -0.01725 -0.00013 -0.01590 -0.00893
+ 0.000000 73 -0.00396 0.24206 0.00159 0.23058 0.15598
+ 0.000000 74 -0.00020 0.00229 -0.00008 0.00106 0.00086
+ 0.000000 75 0.00063 -0.02447 -0.00023 -0.02168 -0.01509
+ 0.000000 76 -0.00101 0.04769 0.00041 0.04217 0.02924
+ 0.000000 77 0.00041 -0.02255 -0.00025 -0.02034 -0.01417
+ 0.000000 78 -0.00954 -1.06928 -0.00790 -1.05682 -0.81656
+ 0.000000 79 0.00901 1.01419 0.00537 0.98903 0.77218
+ 0.000000 80 0.00608 0.06571 -0.00136 0.05775 0.05782
+ 0.000000 81 0.00036 -0.08143 0.00125 -0.06541 -0.05390
+ 0.000000 82 0.00510 1.34663 0.00868 1.33183 1.01602
+ 0.000000 83 -0.02229 -1.49144 -0.00934 -1.49518 -1.16394
+ 0.000000 84 -0.00002 -0.00068 0.00003 -0.00014 -0.00040
+ 0.000000 85 -0.00066 0.01258 0.00010 0.00821 0.00669
+ 0.000000 86 0.00045 -0.01181 -0.00020 -0.00845 -0.00587
0.000000 87 0.00000 0.00000 0.00000 0.00000 0.00000
0.000000 88 0.00000 0.00000 0.00000 0.00000 0.00000
0.000000 89 0.00000 0.00000 0.00000 0.00000 0.00000
- 0.000000 90 0.00092 -0.03357 0.00004 -0.02962 -0.02177
- 0.000000 91 -0.00061 0.02947 -0.00001 0.02680 0.01962
- 0.000000 92 0.00128 -0.06075 0.00001 -0.05499 -0.04134
+ 0.000000 90 0.00092 -0.03250 0.00004 -0.02962 -0.02065
+ 0.000000 91 -0.00061 0.02851 -0.00001 0.02680 0.01861
+ 0.000000 92 0.00129 -0.05878 0.00001 -0.05499 -0.03927
0.000000 93 0.00000 0.00000 0.00000 0.00000 0.00000
0.000000 94 0.00000 0.00000 0.00000 0.00000 0.00000
0.000000 95 0.00000 0.00000 0.00000 0.00000 0.00000
- 0.000000 96 -0.00005 -0.00015 -0.00003 -0.00021 -0.00017
- 0.000000 97 -0.00046 0.01701 0.00007 0.00359 0.01136
- 0.000000 98 -0.00026 0.01561 0.00011 0.00359 0.01074
- 0.000000 99 0.00051 -0.02493 -0.00028 -0.02103 -0.01655
- 0.000000 100 -0.00094 0.04723 0.00045 0.03964 0.03236
- 0.000000 101 -0.00045 0.02432 0.00026 0.02051 0.01660
- 0.000000 102 0.00050 -0.02071 -0.00016 -0.01825 -0.01377
- 0.000000 103 -0.00042 0.01995 -0.00004 0.01645 0.01373
- 0.000000 104 -0.00088 0.04195 0.00015 0.03623 0.02844
- 0.000000 105 -0.00266 -0.02530 0.00050 -0.01889 -0.01529
- 0.000000 106 0.00475 1.12986 0.00915 1.09713 0.85475
- 0.000000 107 0.01417 1.17417 0.00963 1.15018 0.90717
- 0.000000 108 0.00427 -0.36074 -0.00093 -0.33215 -0.25380
- 0.000000 109 -0.00024 0.01636 0.00000 0.01424 0.01085
- 0.000000 110 0.00014 0.00382 0.00017 0.00423 0.00191
+ 0.000000 96 -0.00005 -0.00007 -0.00003 -0.00021 -0.00010
+ 0.000000 97 -0.00046 0.00670 0.00007 0.00359 0.00199
+ 0.000000 98 -0.00026 0.00593 0.00011 0.00359 0.00193
+ 0.000000 99 0.00052 -0.02312 -0.00028 -0.02103 -0.01368
+ 0.000000 100 -0.00095 0.04375 0.00045 0.03964 0.02688
+ 0.000000 101 -0.00045 0.02254 0.00026 0.02051 0.01379
+ 0.000000 102 0.00050 -0.01896 -0.00016 -0.01825 -0.00819
+ 0.000000 103 -0.00042 0.01826 -0.00004 0.01645 0.00836
+ 0.000000 104 -0.00089 0.03839 0.00015 0.03623 0.01709
+ 0.000000 105 -0.00266 -0.02484 0.00050 -0.01889 -0.01476
+ 0.000000 106 0.00457 1.10797 0.00915 1.09713 0.82959
+ 0.000000 107 0.01398 1.15123 0.00963 1.15018 0.88080
+ 0.000000 108 0.00433 -0.35918 -0.00093 -0.33215 -0.24474
+ 0.000000 109 -0.00024 0.01629 0.00000 0.01424 0.01046
+ 0.000000 110 0.00014 0.00381 0.00017 0.00423 0.00182
0.000000 111 0.00000 0.00000 0.00000 0.00000 0.00000
0.000000 112 0.00000 0.00000 0.00000 0.00000 0.00000
0.000000 113 0.00000 0.00000 0.00000 0.00000 0.00000
- 0.000000 114 -0.00037 0.00681 0.00000 0.00000 0.00363
- 0.000000 115 0.00022 -0.00250 0.00000 0.00000 -0.00128
- 0.000000 116 0.00001 -0.00003 0.00000 0.00000 -0.00002
- 0.000000 117 0.00100 -0.04649 -0.00054 -0.03623 -0.03098
- 0.000000 118 0.00032 -0.02041 -0.00015 -0.01567 -0.01391
- 0.000000 119 0.00046 -0.02060 -0.00030 -0.01677 -0.01485
- 0.000000 120 -0.00019 -0.01062 -0.00006 -0.00174 -0.00839
- 0.000000 121 -0.00003 -0.00023 -0.00000 -0.00001 0.00003
- 0.000000 122 -0.00028 -0.01029 -0.00006 -0.00173 -0.00830
+ 0.000000 114 -0.00038 0.00467 0.00000 0.00000 0.00000
+ 0.000000 115 0.00022 -0.00175 0.00000 0.00000 0.00000
+ 0.000000 116 0.00001 -0.00002 0.00000 0.00000 0.00000
+ 0.000000 117 0.00101 -0.04089 -0.00054 -0.03623 -0.02374
+ 0.000000 118 0.00033 -0.01790 -0.00015 -0.01567 -0.01066
+ 0.000000 119 0.00046 -0.01806 -0.00030 -0.01677 -0.01157
+ 0.000000 120 -0.00019 -0.00198 -0.00006 -0.00174 -0.00207
+ 0.000000 121 -0.00003 -0.00016 -0.00000 -0.00001 0.00008
+ 0.000000 122 -0.00027 -0.00179 -0.00006 -0.00173 -0.00209
0.000000 123 0.00000 0.00000 0.00000 0.00000 0.00000
0.000000 124 0.00000 0.00000 0.00000 0.00000 0.00000
0.000000 125 0.00000 0.00000 0.00000 0.00000 0.00000
@@ -131,21 +131,21 @@
0.000000 129 0.00000 0.00000 0.00000 0.00000 0.00000
0.000000 130 0.00000 0.00000 0.00000 0.00000 0.00000
0.000000 131 0.00000 0.00000 0.00000 0.00000 0.00000
- 0.000000 132 0.00024 -0.01211 -0.00007 -0.00184 -0.00871
- 0.000000 133 -0.00009 0.00008 0.00000 0.00001 0.00012
- 0.000000 134 -0.00011 0.01100 0.00005 0.00163 0.00779
- 0.000000 135 -0.00018 0.00173 0.00000 0.00000 0.00051
- 0.000000 136 0.00001 -0.00003 0.00000 0.00000 -0.00001
- 0.000000 137 -0.00013 0.00057 0.00000 0.00000 0.00017
+ 0.000000 132 0.00024 -0.00249 -0.00007 -0.00184 -0.00244
+ 0.000000 133 -0.00009 0.00002 0.00000 0.00001 0.00009
+ 0.000000 134 -0.00011 0.00224 0.00005 0.00163 0.00209
+ 0.000000 135 -0.00018 0.00000 0.00000 0.00000 0.00000
+ 0.000000 136 0.00001 0.00000 0.00000 0.00000 0.00000
+ 0.000000 137 -0.00013 0.00000 0.00000 0.00000 0.00000
0.000000 138 0.00000 0.00000 0.00000 0.00000 0.00000
0.000000 139 0.00000 0.00000 0.00000 0.00000 0.00000
0.000000 140 0.00000 0.00000 0.00000 0.00000 0.00000
- 0.000000 141 0.00095 -0.04667 -0.00027 -0.03769 -0.03139
- 0.000000 142 0.00045 -0.02535 -0.00001 -0.01970 -0.01795
- 0.000000 143 -0.00048 0.02319 0.00031 0.01995 0.01561
- 0.000000 144 0.00026 -0.01275 0.00000 0.00000 -0.00927
- 0.000000 145 0.00006 -0.01263 0.00000 0.00000 -0.00917
- 0.000000 146 -0.00010 0.00013 0.00000 0.00000 0.00011
+ 0.000000 141 0.00095 -0.04332 -0.00027 -0.03769 -0.02461
+ 0.000000 142 0.00045 -0.02353 -0.00001 -0.01970 -0.01425
+ 0.000000 143 -0.00049 0.02152 0.00031 0.01995 0.01221
+ 0.000000 144 0.00027 -0.00570 0.00000 0.00000 0.00000
+ 0.000000 145 0.00006 -0.00565 0.00000 0.00000 0.00000
+ 0.000000 146 -0.00010 0.00005 0.00000 0.00000 0.00000
0.000000 147 0.00000 0.00000 0.00000 0.00000 0.00000
0.000000 148 0.00000 0.00000 0.00000 0.00000 0.00000
0.000000 149 0.00000 0.00000 0.00000 0.00000 0.00000
@@ -179,18 +179,18 @@
0.000000 177 0.00000 0.00000 0.00000 0.00000 0.00000
0.000000 178 0.00000 0.00000 0.00000 0.00000 0.00000
0.000000 179 0.00000 0.00000 0.00000 0.00000 0.00000
- 0.000000 180 0.00030 -0.01798 -0.00009 -0.00403 -0.01220
- 0.000000 181 -0.00033 0.01811 0.00002 0.00365 0.01287
- 0.000000 182 0.00012 0.00045 0.00000 0.00013 0.00050
+ 0.000000 180 0.00031 -0.00859 -0.00009 -0.00403 -0.00558
+ 0.000000 181 -0.00034 0.00860 0.00002 0.00365 0.00617
+ 0.000000 182 0.00012 0.00014 0.00000 0.00013 0.00028
0.000000 183 0.00000 0.00000 0.00000 0.00000 0.00000
0.000000 184 0.00000 0.00000 0.00000 0.00000 0.00000
0.000000 185 0.00000 0.00000 0.00000 0.00000 0.00000
- 0.000000 186 -0.00077 0.00570 0.00000 0.00000 0.00136
- 0.000000 187 -0.00025 0.00192 0.00000 0.00000 0.00046
- 0.000000 188 -0.00006 0.00005 0.00000 0.00000 0.00001
- 0.000000 189 0.00092 -0.05417 -0.00040 -0.04520 -0.03721
- 0.000000 190 -0.00046 0.02651 0.00019 0.02232 0.01856
- 0.000000 191 0.00038 -0.02568 -0.00021 -0.02145 -0.01735
+ 0.000000 186 -0.00077 0.00000 0.00000 0.00000 0.00000
+ 0.000000 187 -0.00025 0.00000 0.00000 0.00000 0.00000
+ 0.000000 188 -0.00006 0.00000 0.00000 0.00000 0.00000
+ 0.000000 189 0.00093 -0.05240 -0.00040 -0.04520 -0.03318
+ 0.000000 190 -0.00046 0.02563 0.00019 0.02232 0.01656
+ 0.000000 191 0.00039 -0.02485 -0.00021 -0.02145 -0.01545
0.000000 192 0.00000 0.00000 0.00000 0.00000 0.00000
0.000000 193 0.00000 0.00000 0.00000 0.00000 0.00000
0.000000 194 0.00000 0.00000 0.00000 0.00000 0.00000
@@ -212,54 +212,54 @@
0.000000 210 0.00000 0.00000 0.00000 0.00000 0.00000
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+ 0.200000 102 0.00022 -0.01145 0.00006 -0.00908 -0.00651
+ 0.200000 103 -0.00045 0.01129 0.00000 0.00937 0.00627
+ 0.200000 104 -0.00021 0.02110 -0.00004 0.01801 0.01318
+ 0.200000 105 0.00142 -0.03846 -0.00078 -0.03714 -0.02104
+ 0.200000 106 -0.00251 0.48510 -0.00176 0.43813 0.34765
+ 0.200000 107 0.00863 0.51861 -0.00252 0.47974 0.39943
+ 0.200000 108 0.00084 -0.26999 -0.00101 -0.26062 -0.19122
+ 0.200000 109 -0.00099 0.02190 0.00043 0.02076 0.01144
+ 0.200000 110 0.00074 0.03850 0.00068 0.04137 0.02955
+ 0.200000 111 -0.00039 0.00000 0.00000 0.00000 0.00000
+ 0.200000 112 -0.00004 0.00000 0.00000 0.00000 0.00000
+ 0.200000 113 -0.00009 0.00000 0.00000 0.00000 0.00000
+ 0.200000 114 -0.00137 0.01942 0.00025 0.01829 0.00357
+ 0.200000 115 0.00021 -0.00526 -0.00006 -0.00514 -0.00105
+ 0.200000 116 0.00010 -0.00016 -0.00006 -0.00066 0.00027
+ 0.200000 117 0.00040 -0.02001 -0.00049 -0.02030 -0.01074
+ 0.200000 118 -0.00013 -0.00571 -0.00013 -0.00634 -0.00391
+ 0.200000 119 0.00028 -0.00769 -0.00015 -0.00744 -0.00422
+ 0.200000 120 -0.00024 -0.00425 -0.00010 -0.00536 -0.00402
+ 0.200000 121 -0.00006 -0.00001 -0.00000 -0.00014 -0.00018
+ 0.200000 122 -0.00032 -0.00394 -0.00011 -0.00543 -0.00409
0.200000 123 0.00000 0.00000 0.00000 0.00000 0.00000
0.200000 124 0.00000 0.00000 0.00000 0.00000 0.00000
0.200000 125 0.00000 0.00000 0.00000 0.00000 0.00000
@@ -1367,21 +1367,21 @@
0.200000 129 0.00000 0.00000 0.00000 0.00000 0.00000
0.200000 130 0.00000 0.00000 0.00000 0.00000 0.00000
0.200000 131 0.00000 0.00000 0.00000 0.00000 0.00000
- 0.200000 132 -0.00022 -0.00836 -0.00009 -0.00374 -0.00748
- 0.200000 133 -0.00002 -0.00044 0.00002 -0.00003 -0.00029
- 0.200000 134 0.00027 0.00705 0.00010 0.00329 0.00628
- 0.200000 135 -0.00137 0.02003 0.00024 0.01172 0.00988
- 0.200000 136 -0.00019 0.00094 -0.00003 0.00010 -0.00001
- 0.200000 137 -0.00049 0.00746 0.00003 0.00395 0.00342
+ 0.200000 132 -0.00021 -0.00268 -0.00009 -0.00374 -0.00204
+ 0.200000 133 -0.00002 -0.00016 0.00002 -0.00003 -0.00002
+ 0.200000 134 0.00027 0.00221 0.00010 0.00329 0.00164
+ 0.200000 135 -0.00138 0.01678 0.00024 0.01172 0.00255
+ 0.200000 136 -0.00019 0.00085 -0.00003 0.00010 -0.00021
+ 0.200000 137 -0.00049 0.00626 0.00003 0.00395 0.00072
0.200000 138 0.00000 0.00000 0.00000 0.00000 0.00000
0.200000 139 0.00000 0.00000 0.00000 0.00000 0.00000
0.200000 140 0.00000 0.00000 0.00000 0.00000 0.00000
- 0.200000 141 0.00109 -0.04452 -0.00021 -0.03586 -0.02898
- 0.200000 142 0.00024 -0.02237 -0.00001 -0.01804 -0.01628
- 0.200000 143 -0.00033 0.02121 0.00031 0.01890 0.01408
- 0.200000 144 0.00042 -0.01318 -0.00013 -0.00658 -0.00837
- 0.200000 145 0.00008 -0.01131 -0.00014 -0.00603 -0.00773
- 0.200000 146 0.00003 0.00043 -0.00000 0.00021 0.00036
+ 0.200000 141 0.00112 -0.04027 -0.00021 -0.03586 -0.02512
+ 0.200000 142 0.00026 -0.02015 -0.00001 -0.01804 -0.01426
+ 0.200000 143 -0.00035 0.01913 0.00031 0.01890 0.01219
+ 0.200000 144 0.00043 -0.00788 -0.00013 -0.00658 -0.00394
+ 0.200000 145 0.00009 -0.00656 -0.00014 -0.00603 -0.00377
+ 0.200000 146 0.00003 0.00024 -0.00000 0.00021 0.00020
0.200000 147 0.00000 0.00000 0.00000 0.00000 0.00000
0.200000 148 0.00000 0.00000 0.00000 0.00000 0.00000
0.200000 149 0.00000 0.00000 0.00000 0.00000 0.00000
@@ -1415,18 +1415,18 @@
0.200000 177 0.00000 0.00000 0.00000 0.00000 0.00000
0.200000 178 0.00000 0.00000 0.00000 0.00000 0.00000
0.200000 179 0.00000 0.00000 0.00000 0.00000 0.00000
- 0.200000 180 -0.00076 -0.00952 -0.00004 -0.00370 -0.00976
- 0.200000 181 0.00067 0.00985 0.00007 0.00398 0.00967
- 0.200000 182 0.00016 0.00068 0.00002 0.00042 0.00067
+ 0.200000 180 -0.00075 -0.00417 -0.00004 -0.00370 -0.00494
+ 0.200000 181 0.00066 0.00434 0.00007 0.00398 0.00471
+ 0.200000 182 0.00016 0.00026 0.00002 0.00042 0.00030
0.200000 183 0.00000 0.00000 0.00000 0.00000 0.00000
0.200000 184 0.00000 0.00000 0.00000 0.00000 0.00000
0.200000 185 0.00000 0.00000 0.00000 0.00000 0.00000
- 0.200000 186 -0.00079 0.01727 0.00018 0.00845 0.00974
- 0.200000 187 -0.00051 0.00718 0.00004 0.00304 0.00355
- 0.200000 188 0.00004 0.00031 -0.00002 -0.00004 0.00013
- 0.200000 189 -0.00065 -0.03585 -0.00010 -0.03199 -0.02943
- 0.200000 190 0.00022 0.02052 0.00014 0.01865 0.01593
- 0.200000 191 -0.00027 -0.01368 -0.00003 -0.01192 -0.01089
+ 0.200000 186 -0.00080 0.01252 0.00018 0.00845 0.00483
+ 0.200000 187 -0.00051 0.00537 0.00004 0.00304 0.00168
+ 0.200000 188 0.00004 0.00027 -0.00002 -0.00004 0.00009
+ 0.200000 189 -0.00063 -0.03200 -0.00010 -0.03199 -0.02617
+ 0.200000 190 0.00021 0.01834 0.00014 0.01865 0.01408
+ 0.200000 191 -0.00026 -0.01223 -0.00003 -0.01192 -0.00967
0.200000 192 0.00000 0.00000 0.00000 0.00000 0.00000
0.200000 193 0.00000 0.00000 0.00000 0.00000 0.00000
0.200000 194 0.00000 0.00000 0.00000 0.00000 0.00000
@@ -1448,54 +1448,54 @@
0.200000 210 0.00000 0.00000 0.00000 0.00000 0.00000
0.200000 211 0.00000 0.00000 0.00000 0.00000 0.00000
0.200000 212 0.00000 0.00000 0.00000 0.00000 0.00000
- 0.200000 213 0.00000 -0.03458 0.00018 -0.02829 -0.02634
- 0.200000 214 -0.00018 0.02008 -0.00008 0.01574 0.01434
- 0.200000 215 0.00024 0.02004 0.00002 0.01770 0.01613
- 0.200000 216 -0.01649 0.53113 0.00314 0.47055 0.32949
- 0.200000 217 -0.00409 0.06068 0.00003 0.04688 0.02895
- 0.200000 218 0.00124 -0.00281 -0.00052 -0.00408 0.00114
- 0.200000 219 0.02932 1.54971 0.00451 1.50664 1.23037
- 0.200000 220 -0.00362 0.34863 -0.00651 0.26156 0.22201
- 0.200000 221 -0.00733 -1.67488 -0.01129 -1.62416 -1.24896
- 0.200000 222 -0.02935 1.78027 0.01276 1.67492 1.19319
- 0.200000 223 0.02497 -2.08528 -0.01639 -1.98115 -1.41808
- 0.200000 224 0.00642 0.10624 -0.00783 0.06355 0.10453
- 0.200000 225 -0.00516 0.12002 -0.00072 0.09283 0.06908
- 0.200000 226 0.00272 -0.07157 0.00021 -0.05755 -0.04253
- 0.200000 227 0.00359 -0.07051 0.00014 -0.05505 -0.03871
- 0.200000 228 -0.00058 0.02369 0.00026 0.01240 0.01564
- 0.200000 229 0.00003 0.00038 -0.00009 -0.00058 0.00001
- 0.200000 230 0.00089 -0.02405 -0.00030 -0.01268 -0.01455
- 0.200000 231 0.00001 0.00444 -0.00000 0.00207 0.00312
- 0.200000 232 -0.00013 0.00138 -0.00005 0.00013 0.00085
- 0.200000 233 0.00035 -0.01557 -0.00015 -0.00795 -0.01020
- 0.200000 234 -0.00061 0.02603 -0.00012 0.02190 0.01737
- 0.200000 235 0.00024 -0.02591 0.00021 -0.02096 -0.01723
- 0.200000 236 0.00160 -0.05733 0.00042 -0.04512 -0.03654
+ 0.200000 213 0.00002 -0.03097 0.00018 -0.02829 -0.01997
+ 0.200000 214 -0.00019 0.01808 -0.00008 0.01574 0.01082
+ 0.200000 215 0.00023 0.01789 0.00002 0.01770 0.01234
+ 0.200000 216 -0.01684 0.51638 0.00314 0.47055 0.31764
+ 0.200000 217 -0.00413 0.05915 0.00003 0.04688 0.02772
+ 0.200000 218 0.00124 -0.00279 -0.00052 -0.00408 0.00116
+ 0.200000 219 0.02820 1.52089 0.00451 1.50664 1.20844
+ 0.200000 220 -0.00384 0.34273 -0.00651 0.26156 0.21751
+ 0.200000 221 -0.00616 -1.64461 -0.01129 -1.62416 -1.22592
+ 0.200000 222 -0.03055 1.76051 0.01276 1.67492 1.16102
+ 0.200000 223 0.02638 -2.06201 -0.01639 -1.98115 -1.38020
+ 0.200000 224 0.00634 0.10483 -0.00783 0.06355 0.10224
+ 0.200000 225 -0.00523 0.11181 -0.00072 0.09283 0.06381
+ 0.200000 226 0.00276 -0.06660 0.00021 -0.05755 -0.03935
+ 0.200000 227 0.00363 -0.06580 0.00014 -0.05505 -0.03569
+ 0.200000 228 -0.00059 0.01840 0.00026 0.01240 0.00884
+ 0.200000 229 0.00003 0.00038 -0.00009 -0.00058 0.00002
+ 0.200000 230 0.00090 -0.01875 -0.00030 -0.01268 -0.00774
+ 0.200000 231 0.00001 0.00347 -0.00000 0.00207 0.00173
+ 0.200000 232 -0.00013 0.00116 -0.00005 0.00013 0.00053
+ 0.200000 233 0.00036 -0.01226 -0.00015 -0.00795 -0.00553
+ 0.200000 234 -0.00062 0.02294 -0.00012 0.02190 0.01217
+ 0.200000 235 0.00026 -0.02286 0.00021 -0.02096 -0.01211
+ 0.200000 236 0.00164 -0.05081 0.00042 -0.04512 -0.02557
0.200000 237 0.00000 0.00000 0.00000 0.00000 0.00000
0.200000 238 0.00000 0.00000 0.00000 0.00000 0.00000
0.200000 239 0.00000 0.00000 0.00000 0.00000 0.00000
- 0.200000 240 -0.00159 0.03065 0.00027 0.01986 0.01744
- 0.200000 241 0.00015 -0.00228 -0.00015 -0.00280 -0.00186
- 0.200000 242 -0.00168 0.03103 0.00039 0.02067 0.01694
- 0.200000 243 0.01155 1.65575 0.01692 1.66578 1.26612
- 0.200000 244 -0.01902 0.65131 0.00869 0.61834 0.40728
- 0.200000 245 0.00385 1.86672 0.02795 1.91504 1.39220
- 0.200000 246 -0.00099 0.02861 0.00012 0.02140 0.01663
- 0.200000 247 0.00192 -0.04245 -0.00029 -0.03230 -0.02407
- 0.200000 248 -0.00309 0.07238 0.00054 0.05473 0.04094
- 0.200000 249 -0.00261 0.05409 0.00009 0.04349 0.03002
- 0.200000 250 0.00160 -0.03456 -0.00020 -0.02930 -0.02005
- 0.200000 251 -0.00166 0.03234 0.00002 0.02578 0.01751
- 0.200000 252 -0.00162 0.02181 0.00022 0.01262 0.01117
- 0.200000 253 0.00146 -0.02369 -0.00023 -0.01374 -0.01230
- 0.200000 254 0.00022 -0.00028 -0.00009 -0.00056 0.00024
- 0.200000 255 -0.00142 0.03107 -0.00006 0.02279 0.01907
- 0.200000 256 0.00346 -0.07449 0.00013 -0.05446 -0.04292
- 0.200000 257 0.00166 -0.03051 -0.00004 -0.02229 -0.01709
- 0.200000 258 0.00014 0.00272 0.00000 0.00000 0.00214
- 0.200000 259 -0.00005 0.01099 0.00000 0.00000 0.00801
- 0.200000 260 -0.00006 -0.00034 0.00000 0.00000 -0.00030
+ 0.200000 240 -0.00161 0.02500 0.00027 0.01986 0.01125
+ 0.200000 241 0.00015 -0.00170 -0.00015 -0.00280 -0.00123
+ 0.200000 242 -0.00170 0.02536 0.00039 0.02067 0.01074
+ 0.200000 243 0.01037 1.63706 0.01692 1.66578 1.23931
+ 0.200000 244 -0.01945 0.64456 0.00869 0.61834 0.39759
+ 0.200000 245 0.00254 1.84588 0.02795 1.91504 1.36231
+ 0.200000 246 -0.00101 0.02686 0.00012 0.02140 0.01240
+ 0.200000 247 0.00195 -0.03985 -0.00029 -0.03230 -0.01783
+ 0.200000 248 -0.00314 0.06801 0.00054 0.05473 0.03043
+ 0.200000 249 -0.00264 0.04852 0.00009 0.04349 0.02274
+ 0.200000 250 0.00162 -0.03093 -0.00020 -0.02930 -0.01529
+ 0.200000 251 -0.00168 0.02900 0.00002 0.02578 0.01316
+ 0.200000 252 -0.00164 0.01918 0.00022 0.01262 0.00647
+ 0.200000 253 0.00148 -0.02081 -0.00023 -0.01374 -0.00716
+ 0.200000 254 0.00022 -0.00029 -0.00009 -0.00056 0.00023
+ 0.200000 255 -0.00144 0.02761 -0.00006 0.02279 0.01581
+ 0.200000 256 0.00351 -0.06621 0.00013 -0.05446 -0.03514
+ 0.200000 257 0.00168 -0.02722 -0.00004 -0.02229 -0.01399
+ 0.200000 258 0.00014 0.00054 0.00000 0.00000 0.00070
+ 0.200000 259 -0.00005 0.00258 0.00000 0.00000 0.00247
+ 0.200000 260 -0.00006 -0.00021 0.00000 0.00000 -0.00022
0.200000 261 0.00000 0.00000 0.00000 0.00000 0.00000
0.200000 262 0.00000 0.00000 0.00000 0.00000 0.00000
0.200000 263 0.00000 0.00000 0.00000 0.00000 0.00000
@@ -1514,33 +1514,33 @@
0.200000 276 0.00000 0.00000 0.00000 0.00000 0.00000
0.200000 277 0.00000 0.00000 0.00000 0.00000 0.00000
0.200000 278 0.00000 0.00000 0.00000 0.00000 0.00000
- 0.200000 279 -0.00155 0.03752 0.00000 0.03019 0.02209
- 0.200000 280 0.00437 -0.08978 0.00004 -0.07081 -0.04994
- 0.200000 281 -0.00201 0.03499 -0.00014 0.02642 0.01915
+ 0.200000 279 -0.00158 0.03361 0.00000 0.03019 0.01775
+ 0.200000 280 0.00443 -0.08059 0.00004 -0.07081 -0.03972
+ 0.200000 281 -0.00203 0.03146 -0.00014 0.02642 0.01522
0.200000 282 0.00000 0.00000 0.00000 0.00000 0.00000
0.200000 283 0.00000 0.00000 0.00000 0.00000 0.00000
0.200000 284 0.00000 0.00000 0.00000 0.00000 0.00000
0.200000 285 0.00000 0.00000 0.00000 0.00000 0.00000
0.200000 286 0.00000 0.00000 0.00000 0.00000 0.00000
0.200000 287 0.00000 0.00000 0.00000 0.00000 0.00000
- 0.200000 288 -0.00000 0.01204 0.00011 0.00808 0.00846
- 0.200000 289 -0.00039 0.01483 0.00015 0.00965 0.00990
+ 0.200000 288 -0.00001 0.00842 0.00011 0.00808 0.00387
+ 0.200000 289 -0.00040 0.01058 0.00015 0.00965 0.00451
0.200000 290 0.00003 0.00011 0.00007 0.00044 0.00002
- 0.200000 291 0.00023 0.01206 0.00004 0.01008 0.01016
- 0.200000 292 -0.00008 0.03874 0.00039 0.03220 0.02868
- 0.200000 293 0.00005 -0.01817 -0.00022 -0.01546 -0.01322
- 0.200000 294 0.00598 0.67021 0.00516 0.65427 0.51682
- 0.200000 295 -0.00208 0.90336 0.00741 0.86352 0.65472
- 0.200000 296 0.00157 -0.02110 0.00008 -0.01483 -0.00833
- 0.200000 297 -0.00093 0.04454 0.00011 0.03558 0.03018
- 0.200000 298 -0.00083 0.02357 -0.00006 0.01775 0.01437
- 0.200000 299 0.00080 -0.02740 -0.00030 -0.02301 -0.01706
- 0.200000 300 -0.01402 10.25735 0.05533 9.52719 7.48022
- 0.200000 301 -0.03566 -0.41522 0.00022 -0.47524 -0.44094
- 0.200000 302 -0.02243 -0.84979 0.00368 -0.78543 -0.68443
- 0.200000 303 -0.03566 -0.41522 0.00022 -0.47524 -0.44094
- 0.200000 304 -0.03424 10.72737 0.05796 9.90675 7.74952
- 0.200000 305 -0.00541 0.37723 0.00081 0.36334 0.25231
- 0.200000 306 -0.02243 -0.84979 0.00368 -0.78543 -0.68443
- 0.200000 307 -0.00541 0.37723 0.00081 0.36334 0.25231
- 0.200000 308 0.03276 11.09035 0.07029 10.50661 8.29729
+ 0.200000 291 0.00022 0.01131 0.00004 0.01008 0.00917
+ 0.200000 292 -0.00011 0.03647 0.00039 0.03220 0.02569
+ 0.200000 293 0.00006 -0.01709 -0.00022 -0.01546 -0.01181
+ 0.200000 294 0.00551 0.65019 0.00516 0.65427 0.49891
+ 0.200000 295 -0.00270 0.87706 0.00741 0.86352 0.63119
+ 0.200000 296 0.00158 -0.02060 0.00008 -0.01483 -0.00789
+ 0.200000 297 -0.00095 0.04042 0.00011 0.03558 0.02702
+ 0.200000 298 -0.00085 0.02142 -0.00006 0.01775 0.01273
+ 0.200000 299 0.00081 -0.02490 -0.00030 -0.02301 -0.01516
+ 0.200000 300 -0.02116 9.87490 0.05533 9.52719 7.03387
+ 0.200000 301 -0.03532 -0.40623 0.00022 -0.47524 -0.42742
+ 0.200000 302 -0.02181 -0.82447 0.00368 -0.78543 -0.67861
+ 0.200000 303 -0.03532 -0.40623 0.00022 -0.47524 -0.42742
+ 0.200000 304 -0.04169 10.33639 0.05796 9.90675 7.29087
+ 0.200000 305 -0.00566 0.37408 0.00081 0.36334 0.26082
+ 0.200000 306 -0.02181 -0.82447 0.00368 -0.78543 -0.67861
+ 0.200000 307 -0.00566 0.37408 0.00081 0.36334 0.26082
+ 0.200000 308 0.02495 10.73474 0.07029 10.50661 7.87493
diff --git a/src/multicolvar/ActionVolume.cpp b/src/multicolvar/ActionVolume.cpp
index 8d5f60d66d655ccb83a18d74e0253a78c32172da..deb291c6ccdb348abc69285afd7b53997b7a7921 100644
--- a/src/multicolvar/ActionVolume.cpp
+++ b/src/multicolvar/ActionVolume.cpp
@@ -32,18 +32,23 @@ void ActionVolume::registerKeywords( Keywords& keys ){
ActionWithValue::registerKeywords( keys );
ActionWithVessel::registerKeywords( keys );
keys.use("MEAN"); keys.use("LESS_THAN"); keys.use("MORE_THAN");
- keys.use("BETWEEN"); keys.use("HISTOGRAM"); keys.use("MIN");
+ keys.use("BETWEEN"); keys.use("HISTOGRAM");
keys.add("compulsory","ARG","the label of the action that calculates the multicolvar we are interested in");
keys.add("compulsory","SIGMA","the width of the function to be used for kernel density estimation");
keys.add("compulsory","KERNEL","gaussian","the type of kernel function to be used");
keys.addFlag("OUTSIDE",false,"calculate quantities for colvars that are on atoms outside the region of interest");
+ keys.use("NL_TOL");
+ keys.add("hidden","NL_STRIDE","the frequency with which the neighbor list should be updated. Between neighbour list update steps all quantities "
+ "that contributed less than TOL at the previous neighbor list update step are ignored.");
}
ActionVolume::ActionVolume(const ActionOptions&ao):
Action(ao),
ActionAtomistic(ao),
ActionWithValue(ao),
-ActionWithVessel(ao)
+ActionWithVessel(ao),
+updateFreq(0),
+lastUpdate(0)
{
std::string mlab; parse("ARG",mlab);
mycolv = plumed.getActionSet().selectWithLabel<multicolvar::MultiColvar*>(mlab);
@@ -60,17 +65,28 @@ ActionWithVessel(ao)
plumed_assert( vv ); vv->useNumericalDerivatives();
}
+ // Neighbor list readin
+ parse("NL_STRIDE",updateFreq);
+ if(updateFreq>0){
+ if( !mycolv->isDensity() && updateFreq%mycolv->updateFreq!=0 ){
+ error("update frequency must be a multiple of update frequency for base multicolvar");
+ }
+ log.printf(" Updating contributors every %d steps.\n",updateFreq);
+ } else {
+ log.printf(" Updating contributors every step.\n");
+ }
+
parseFlag("OUTSIDE",not_in); parse("SIGMA",sigma);
bead.isPeriodic( 0, 1.0 );
std::string kerneltype; parse("KERNEL",kerneltype);
bead.setKernelType( kerneltype );
-
+ weightHasDerivatives=true;
+
if( mycolv->isDensity() ){
std::string input;
addVessel( "SUM", input, -1 ); // -1 here means that this value will be named getLabel()
resizeFunctions();
} else {
- weightHasDerivatives=true;
readVesselKeywords();
}
}
@@ -81,7 +97,22 @@ void ActionVolume::doJobsRequiredBeforeTaskList(){
ActionWithVessel::doJobsRequiredBeforeTaskList();
}
-bool ActionVolume::performTask( const unsigned& j ){
+void ActionVolume::prepare(){
+ if( contributorsAreUnlocked ) lockContributors();
+ if( updateFreq>0 && (getStep()-lastUpdate)>=updateFreq ){
+ if( !mycolv->isDensity() ){
+ mycolv->taskList.activateAll();
+ for(unsigned i=0;i<mycolv->taskList.getNumberActive();++i) mycolv->colvar_atoms[i].activateAll();
+ mycolv->unlockContributors(); mycolv->resizeDynamicArrays();
+ plumed_dbg_assert( mycolv->getNumberOfVessels()==0 );
+ } else {
+ plumed_massert( mycolv->contributorsAreUnlocked, "contributors are not unlocked in base multicolvar" );
+ }
+ unlockContributors();
+ }
+}
+
+void ActionVolume::performTask( const unsigned& j ){
Vector catom_pos=mycolv->retrieveCentralAtomPos( derivativesOfFractionalCoordinates() );
double weight; Vector wdf;
@@ -89,9 +120,10 @@ bool ActionVolume::performTask( const unsigned& j ){
if( not_in ){ weight = 1.0 - weight; wdf *= -1.; }
if( mycolv->isDensity() ){
- setElementValue( 0, weight ); setElementValue( 1, 1.0 );
+ unsigned nder=getNumberOfDerivatives();
+ setElementValue( 1, weight ); setElementValue( 0, 1.0 );
for(unsigned i=0;i<mycolv->getNAtoms();++i){
- unsigned nx=3*mycolv->getAtomIndex( i );
+ unsigned nx=nder + 3*mycolv->getAtomIndex( i );
addElementDerivative( nx+0, mycolv->getCentralAtomDerivative(i, 0, wdf ) );
addElementDerivative( nx+1, mycolv->getCentralAtomDerivative(i, 1, wdf ) );
addElementDerivative( nx+2, mycolv->getCentralAtomDerivative(i, 2, wdf ) );
@@ -123,9 +155,6 @@ bool ActionVolume::performTask( const unsigned& j ){
addElementDerivative( nx+2, ww*mycolv->getCentralAtomDerivative(i, 2, wdf ) );
}
}
-
- // Only continue if the weight is greater than tolerance
- return ( weight>=getTolerance() );
}
void ActionVolume::calculateNumericalDerivatives(){
diff --git a/src/multicolvar/ActionVolume.h b/src/multicolvar/ActionVolume.h
index 069f2442512646f908a2653069a37bd4bd523257..c6d977107dd4f88c1c29b011ccbfac11d1c1bd7b 100644
--- a/src/multicolvar/ActionVolume.h
+++ b/src/multicolvar/ActionVolume.h
@@ -56,6 +56,9 @@ private:
MultiColvar* mycolv;
/// The vessel that bridges
vesselbase::BridgeVessel* myBridgeVessel;
+/// Everything for controlling the updating of neighbor lists
+ int updateFreq;
+ unsigned lastUpdate;
protected:
double getSigma() const ;
MultiColvar* getPntrToMultiColvar();
@@ -71,10 +74,12 @@ public:
unsigned getNumberOfFunctionsInAction();
/// Is the output quantity periodic
bool isPeriodic();
+/// Jobs to be done when the action is activated
+ void prepare();
/// Do jobs required before tasks are undertaken
void doJobsRequiredBeforeTaskList();
/// This calculates all the vessels and is called from within a bridge vessel
- bool performTask(const unsigned& i );
+ void performTask(const unsigned& i );
/// Routines that have to be defined so as not to have problems with virtual methods
void deactivate_task();
void calculate(){}
diff --git a/src/multicolvar/CoordinationNumbers.cpp b/src/multicolvar/CoordinationNumbers.cpp
index f3fe1b660368e848c18222ba39fb7b15e1f8caf1..7d85bae231f320c5a30e3f1bbf10c00459d22020 100644
--- a/src/multicolvar/CoordinationNumbers.cpp
+++ b/src/multicolvar/CoordinationNumbers.cpp
@@ -140,8 +140,8 @@ double CoordinationNumbers::compute( const unsigned& j ){
addAtomsDerivatives( 0, (-dfunc)*distance );
addAtomsDerivatives( i, (dfunc)*distance );
addBoxDerivatives( (-dfunc)*Tensor(distance,distance) );
- } else if( isTimeForNeighborListUpdate() ){
- removeAtomRequest( i );
+ } else {
+ removeAtomRequest( i, sw );
}
}
diff --git a/src/multicolvar/DHEnergy.cpp b/src/multicolvar/DHEnergy.cpp
index a514ac664b6bdc44183b81523d35835fb7ce6a53..ca90f21741d0807bdafca44fbce918dcd6de0a3f 100644
--- a/src/multicolvar/DHEnergy.cpp
+++ b/src/multicolvar/DHEnergy.cpp
@@ -94,9 +94,9 @@ bool DHEnergy::calculate(){
double invdistance = 1.0 / val;
double f=exp(-k*val)*invdistance*constant*mycolv->getCharge(0)*mycolv->getCharge(1)/epsilon;
double dval=-(k+invdistance)*f;
- bool addval=addValue(0,f);
- if(addval) getAction()->chainRuleForElementDerivatives( 0, 0, dval, this );
- return addval;
+ addValueIgnoringTolerance(0,f);
+ getAction()->chainRuleForElementDerivatives( 0, 0, dval, this );
+ return true;
}
void DHEnergy::finish(){
diff --git a/src/multicolvar/MultiColvar.cpp b/src/multicolvar/MultiColvar.cpp
index 1826bd78fe5567cd55ed59f20f2cefb88e861b28..17c9898bc8abdc3e9d8600d660bec184d029d76c 100644
--- a/src/multicolvar/MultiColvar.cpp
+++ b/src/multicolvar/MultiColvar.cpp
@@ -52,9 +52,10 @@ void MultiColvar::registerKeywords( Keywords& keys ){
keys.reserve("atoms-4","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.addFlag("VERBOSE",false,"write a more detailed output");
- keys.add("hidden","NL_STRIDE","the frequency with which the neighbor list should be updated. Between neighbour list update steps all quantities "
- "that contributed less than TOL at the previous neighbor list update step are ignored.");
ActionWithVessel::registerKeywords( keys );
+ keys.use("NL_TOL");
+ keys.add("hidden","NL_STRIDE","the frequency with which the neighbor list should be updated. Between neighbour list update steps all quantities "
+ "that contributed less than TOL at the previous neighbor list update step are ignored.");
}
MultiColvar::MultiColvar(const ActionOptions&ao):
@@ -67,7 +68,6 @@ readatoms(false),
verbose_output(false),
updateFreq(0),
lastUpdate(0),
-reduceAtNextStep(false),
posHasBeenSet(false),
centralAtomDerivativesAreInFractional(false)
{
@@ -345,15 +345,15 @@ void MultiColvar::resizeDynamicArrays(){
void MultiColvar::prepare(){
updatetime=false;
- if( reduceAtNextStep ){
+ if( contributorsAreUnlocked ){
taskList.mpi_gatherActiveMembers( comm );
mpi_gatherActiveMembers( comm, colvar_atoms );
- reduceAtNextStep=false; updatetime=true;
+ lockContributors(); updatetime=true;
}
if( updateFreq>0 && (getStep()-lastUpdate)>=updateFreq ){
taskList.activateAll();
for(unsigned i=0;i<taskList.getNumberActive();++i) colvar_atoms[i].activateAll();
- reduceAtNextStep=true; updatetime=true; lastUpdate=getStep();
+ unlockContributors(); updatetime=true; lastUpdate=getStep();
}
if(updatetime){
resizeDynamicArrays();
@@ -387,14 +387,17 @@ const std::vector<Vector>& MultiColvar::getPositions(){
return pos;
}
-bool MultiColvar::performTask( const unsigned& j ){
- atoms_with_derivatives.deactivateAll(); // Currently no atoms have derivatives
- if( colvar_atoms[current].getNumberActive()==0 ) return false; // Do nothing if there are no active atoms in the colvar
- posHasBeenSet=false; // This ensures we don't set the pos array more than once per step
+void MultiColvar::performTask( const unsigned& j ){
+ atoms_with_derivatives.deactivateAll(); // Currently no atoms have derivatives
+ if( colvar_atoms[current].getNumberActive()==0 ){ // Do nothing if there are no active atoms in the colvar
+ setElementValue(1,0.0);
+ return;
+ }
+ posHasBeenSet=false; // This ensures we don't set the pos array more than once per step
// Do a quick check on the size of this contribution
calculateWeight();
- if( getElementValue(1)<getTolerance() ) return false;
+ if( getElementValue(1)<getTolerance() ) return;
// Compute everything
double vv=compute( j );
@@ -402,7 +405,7 @@ bool MultiColvar::performTask( const unsigned& j ){
setElementValue( 0, vv );
// And finally gather the list of active atoms
atoms_with_derivatives.updateActiveMembers();
- return true;
+ return;
}
Vector MultiColvar::retrieveCentralAtomPos( const bool& frac ){
diff --git a/src/multicolvar/MultiColvar.h b/src/multicolvar/MultiColvar.h
index a76f3b61039731f464491096e4f3abf9322b631c..5e4fa15d6a110d64f43efa64232dcffb659b5d5f 100644
--- a/src/multicolvar/MultiColvar.h
+++ b/src/multicolvar/MultiColvar.h
@@ -56,7 +56,6 @@ private:
/// Everything for controlling the updating of neighbor lists
int updateFreq;
unsigned lastUpdate;
- bool reduceAtNextStep;
/// A flag that tells us the position has been set already
bool posHasBeenSet;
/// The list of all the atoms involved in the colvar
@@ -100,10 +99,8 @@ protected:
unsigned getAtomIndex( const unsigned& ) const ;
/// Get the separation between a pair of vectors
Vector getSeparation( const Vector& vec1, const Vector& vec2 ) const ;
-/// Find out if it is time to do neighbor list update
- bool isTimeForNeighborListUpdate() const ;
/// Update the list of atoms after the neighbor list step
- void removeAtomRequest( const unsigned& aa );
+ void removeAtomRequest( const unsigned& aa, const double& weight );
/// Do we use pbc to calculate this quantity
bool usesPbc() const ;
/// Add some derivatives for an atom
@@ -147,7 +144,7 @@ public:
/// Turn on atom requests when the colvar is activated
void activateValue( const unsigned j );
/// Calcualte the colvar
- bool performTask( const unsigned& j );
+ void performTask( const unsigned& j );
/// You can use this to screen contributions that are very small so we can avoid expensive (and pointless) calculations
virtual void calculateWeight();
/// And a virtual function which actually computes the colvar
@@ -203,20 +200,16 @@ unsigned MultiColvar::getNumberOfFunctionsInAction(){
inline
void MultiColvar::deactivate_task(){
- if( !reduceAtNextStep ) return; // Deactivating tasks only possible during neighbor list update
+ if( !contributorsAreUnlocked ) return; // Deactivating tasks only possible during neighbor list update
deactivateCurrentTask(); // Deactivate the colvar from the list
colvar_atoms[current].deactivateAll(); // Deactivate all atom requests for this colvar
}
inline
-bool MultiColvar::isTimeForNeighborListUpdate() const {
- return reduceAtNextStep;
-}
-
-inline
-void MultiColvar::removeAtomRequest( const unsigned& i ){
- plumed_massert(reduceAtNextStep,"found removeAtomRequest but not during neighbor list step");
- colvar_atoms[current].deactivate( getAtomIndex(i) );
+void MultiColvar::removeAtomRequest( const unsigned& i, const double& weight ){
+ if( !contributorsAreUnlocked ) return;
+ plumed_dbg_assert( weight<getTolerance() );
+ if( weight<getNLTolerance() ) colvar_atoms[current].deactivate( getAtomIndex(i) );
}
inline
@@ -232,7 +225,7 @@ unsigned MultiColvar::getNAtoms() const {
inline
unsigned MultiColvar::getAtomIndex( const unsigned& iatom ) const {
plumed_dbg_assert( iatom<colvar_atoms[current].getNumberActive() );
- return colvar_atoms[current][iatom];
+ return linkIndex( iatom, colvar_atoms[current], all_atoms );
}
inline
diff --git a/src/multicolvar/MultiColvarFunction.cpp b/src/multicolvar/MultiColvarFunction.cpp
index 2ca918b7ae0d32df379773484849f8fc00e4ce2c..ea4bf5b459f153f720aef342d0d1697ef280c62e 100644
--- a/src/multicolvar/MultiColvarFunction.cpp
+++ b/src/multicolvar/MultiColvarFunction.cpp
@@ -43,8 +43,7 @@ ActionWithValue(ao),
ActionWithVessel(ao),
usepbc(false),
updateFreq(0),
-lastUpdate(0),
-reduceAtNextStep(false)
+lastUpdate(0)
{
weightHasDerivatives=true; // In most cases the weight will have derivatives
@@ -80,15 +79,15 @@ void MultiColvarFunction::completeSetup(){
void MultiColvarFunction::prepare(){
bool updatetime=false;
- if( reduceAtNextStep ){
+ if( contributorsAreUnlocked ){
taskList.mpi_gatherActiveMembers( comm );
mpi_gatherActiveMembers( comm, colvar_atoms );
- reduceAtNextStep=false; updatetime=true;
+ lockContributors(); updatetime=true;
}
if( updateFreq>0 && (getStep()-lastUpdate)>=updateFreq ){
taskList.activateAll();
for(unsigned i=0;i<taskList.getNumberActive();++i) colvar_atoms[i].activateAll();
- reduceAtNextStep=true; updatetime=true; lastUpdate=getStep();
+ unlockContributors(); updatetime=true; lastUpdate=getStep();
}
if(updatetime) resizeFunctions();
}
@@ -113,10 +112,11 @@ void MultiColvarFunction::calculateNumericalDerivatives( ActionWithValue* a ){
mycolv->calculateNumericalDerivatives( this );
}
-bool MultiColvarFunction::performTask( const unsigned& j ){
+void MultiColvarFunction::performTask( const unsigned& j ){
// Compute a weight for this quantity
double weight=calculateWeight();
- if( weight<getTolerance() ) return false;
+ setElementValue( 1, weight );
+ if( weight<getTolerance() ) return;
// Now compute the quantity of interest
double val=compute();
@@ -129,8 +129,7 @@ bool MultiColvarFunction::performTask( const unsigned& j ){
setElementDerivative( i, weight*getElementDerivative(i) + val*getElementDerivative(nder+i) );
}
}
- setElementValue( 1, weight );
- return true;
+ return;
}
void MultiColvarFunction::apply(){
diff --git a/src/multicolvar/MultiColvarFunction.h b/src/multicolvar/MultiColvarFunction.h
index 3259aec3c55f1cdf29a743e371690494c53bed23..e9ed5927a32115288bb65d2c2ec76974280cbadd 100644
--- a/src/multicolvar/MultiColvarFunction.h
+++ b/src/multicolvar/MultiColvarFunction.h
@@ -41,7 +41,6 @@ private:
/// Everything for controlling the updating of neighbor lists
int updateFreq;
unsigned lastUpdate;
- bool reduceAtNextStep;
/// The lists of the atoms involved in each of the individual colvars
/// note these refer to the atoms in all_atoms
std::vector< DynamicList<unsigned> > colvar_atoms;
@@ -58,10 +57,8 @@ protected:
void addColvar( const std::vector<unsigned>& newatoms );
/// Finish off the setup of the VectorFunction
void completeSetup();
-/// Find out if it is time to do neighbor list update
- bool isTimeForNeighborListUpdate() const ;
/// Update the list of atoms after the neighbor list step
- void removeAtomRequest( const unsigned& aa );
+ void removeAtomRequest( const unsigned& aa, const double& weight );
/// Get the number of atoms in this particular colvar
unsigned getNAtoms() const;
/// Get the index of an atom
@@ -98,7 +95,7 @@ public:
/// Turn on atom requests when the colvar is activated
void activateValue( const unsigned j );
/// Perform the task
- bool performTask( const unsigned& j );
+ void performTask( const unsigned& j );
/// Calculate the weight
virtual double calculateWeight()=0;
/// Actually compute one of the colvars
@@ -127,7 +124,7 @@ unsigned MultiColvarFunction::getNumberOfDerivatives(){
inline
void MultiColvarFunction::deactivate_task(){
- if( !reduceAtNextStep ) return; // Deactivating tasks only possible during neighbor list update
+ if( !contributorsAreUnlocked ) return; // Deactivating tasks only possible during neighbor list update
deactivateCurrentTask(); // Deactivate the colvar from the list
colvar_atoms[current].deactivateAll(); // Deactivate all atom requests for this colvar
}
@@ -139,13 +136,9 @@ void MultiColvarFunction::activateValue( const unsigned j ){
}
inline
-bool MultiColvarFunction::isTimeForNeighborListUpdate() const {
- return reduceAtNextStep;
-}
-
-inline
-void MultiColvarFunction::removeAtomRequest( const unsigned& i ){
- plumed_massert(reduceAtNextStep,"found removeAtomRequest but not during neighbor list step");
+void MultiColvarFunction::removeAtomRequest( const unsigned& i, const double& weight ){
+ if( !contributorsAreUnlocked ) return;
+ plumed_dbg_assert( weight<getTolerance() );
colvar_atoms[current].deactivate(i);
}
diff --git a/src/vesselbase/ActionWithVessel.cpp b/src/vesselbase/ActionWithVessel.cpp
index 67890be96193ea7a4578d330dc408607899348d1..ba70fdc55aa377c96574819b82c04b687ba88ac4 100644
--- a/src/vesselbase/ActionWithVessel.cpp
+++ b/src/vesselbase/ActionWithVessel.cpp
@@ -31,7 +31,14 @@ namespace PLMD{
namespace vesselbase{
void ActionWithVessel::registerKeywords(Keywords& keys){
- keys.add("optional","TOL","when accumulating sums quantities that contribute less than this will be ignored.");
+ keys.add("optional","TOL","this keyword can be used to speed up your calculation. When accumulating sums in which the individual "
+ "terms are numbers inbetween zero and one it is assumed that terms less than a certain tolerance "
+ "make only a small contribution to the sum. They can thus be safely ignored as can the the derivatives "
+ "wrt these small quantities.");
+ keys.reserve("optional","NL_TOL","this keyword can be used to speed up your calculation. It must be used in conjuction with the TOL "
+ "keyword and the value for NL_TOL must be set less than the value for TOL. This keyword ensures that "
+ "quantities, which are much less than TOL and which will thus not added to the sums being accumulated "
+ "are not calculated at every step. They are only calculated when the neighbor list is updated.");
keys.addFlag("SERIAL",false,"do the calculation in serial. Do not parallelize");
keys.add( vesselRegister().getKeywords() );
}
@@ -40,14 +47,21 @@ ActionWithVessel::ActionWithVessel(const ActionOptions&ao):
Action(ao),
read(false),
serial(false),
+ contributorsAreUnlocked(false),
weightHasDerivatives(false)
{
if( keywords.exists("SERIAL") ) parseFlag("SERIAL",serial);
else serial=true;
if(serial)log.printf(" doing calculation in serial\n");
- tolerance=epsilon;
+ tolerance=nl_tolerance=epsilon;
if( keywords.exists("TOL") ) parse("TOL",tolerance);
- if( tolerance>epsilon) log.printf(" Ignoring contributions less than %lf\n",tolerance);
+ if( tolerance>epsilon){
+ if( keywords.exists("NL_TOL") ) parse("NL_TOL",nl_tolerance);
+ if( nl_tolerance>tolerance ) error("NL_TOL must be smaller than TOL");
+ log.printf(" Ignoring contributions less than %lf",tolerance);
+ if( nl_tolerance>epsilon ) log.printf(" and ignoring quantities less than %lf inbetween neighbor list update steps\n");
+ else log.printf("\n");
+ }
}
ActionWithVessel::~ActionWithVessel(){
@@ -127,6 +141,7 @@ void ActionWithVessel::resizeFunctions(){
}
void ActionWithVessel::deactivateCurrentTask(){
+ plumed_dbg_assert( contributorsAreUnlocked );
for(unsigned i=0;i<taskList.fullSize();++i){
if( taskList(i)==current ) taskList.deactivate(i);
}
@@ -154,7 +169,6 @@ void ActionWithVessel::runAllTasks(){
plumed_massert( read, "you must have a call to readVesselKeywords somewhere" );
unsigned stride=comm.Get_size();
unsigned rank=comm.Get_rank();
- unsigned nder=getNumberOfDerivatives();
if(serial){ stride=1; rank=0; }
// Make sure jobs are done
@@ -164,23 +178,25 @@ void ActionWithVessel::runAllTasks(){
// Store the task we are currently working on
current=taskList[i];
// Calculate the stuff in the loop for this action
- bool keep=performTask(i);
+ performTask(i);
+ // Weight should be between zero and one
+ plumed_dbg_assert( thisval[1]>=0 && thisval[1]<=1.0 );
// Check for conditions that allow us to just to skip the calculation
- // the condition is that the weight of the contribution is low
- if( !keep ){
- plumed_dbg_assert( thisval[1]<getTolerance() && !thisval_wasset[0] );
+ // the condition is that the weight of the contribution is low
+ // N.B. Here weights are assumed to be between zero and one
+ if( thisval[1]<tolerance ){
// Clear the derivatives
clearAfterTask();
- // Deactivate task
- deactivate_task();
+ // Deactivate task if it is less than the neighbor list tolerance
+ if( thisval[1]<nl_tolerance && contributorsAreUnlocked ) deactivate_task();
continue;
}
// Now calculate all the functions
// If the contribution of this quantity is very small at neighbour list time ignore it
// untill next neighbour list time
- if( !calculateAllVessels() ) deactivate_task();
+ if( !calculateAllVessels() && contributorsAreUnlocked ) deactivate_task();
}
finishComputations();
}
diff --git a/src/vesselbase/ActionWithVessel.h b/src/vesselbase/ActionWithVessel.h
index 0cc19c55b15bf4049e322a46e157a5208656427e..17f0bc0cda4f0c0838dd52c220b7b4fcfdf02e9c 100644
--- a/src/vesselbase/ActionWithVessel.h
+++ b/src/vesselbase/ActionWithVessel.h
@@ -53,8 +53,10 @@ private:
bool read;
/// Do all calculations in serial
bool serial;
-/// The tolerance on the accumulators for neighbour list
+/// The tolerance on the accumulators
double tolerance;
+/// Tolerance for quantities being put in neighbor lists
+ double nl_tolerance;
/// The value of the current element in the sum
std::vector<double> thisval;
/// A boolean that makes sure we don't accumulate very wrong derivatives
@@ -69,9 +71,9 @@ private:
std::vector<Vessel*> functions;
/// Tempory storage for forces
std::vector<double> tmpforces;
-/// Avoid hiding of base class virtual function
- using Action::deactivate;
protected:
+/// The terms in the series are locked
+ bool contributorsAreUnlocked;
/// Does the weight have derivatives
bool weightHasDerivatives;
/// The numerical index of the task we are curently performing
@@ -87,6 +89,8 @@ protected:
void readVesselKeywords();
/// Return the value of the tolerance
double getTolerance() const ;
+/// Return the value for the neighbor list tolerance
+ double getNLTolerance() const ;
/// Get the number of vessels
unsigned getNumberOfVessels() const;
/// Get a pointer to the ith vessel
@@ -110,6 +114,9 @@ protected:
void accumulateDerivative( const unsigned& ider, const double& df );
/// Clear tempory data that is calculated for each task
void clearAfterTask();
+/// Used to make sure we are calculating everything during neighbor list update step
+ void unlockContributors();
+ void lockContributors();
public:
static void registerKeywords(Keywords& keys);
ActionWithVessel(const ActionOptions&ao);
@@ -136,7 +143,7 @@ public:
/// Do any jobs that are required before the task list is undertaken
virtual void doJobsRequiredBeforeTaskList();
/// Calculate one of the functions in the distribution
- virtual bool performTask( const unsigned& j )=0;
+ virtual void performTask( const unsigned& j )=0;
/// Return a pointer to the field
Vessel* getVessel( const std::string& name );
/// Add some derivative of the quantity in the sum wrt to a numbered element
@@ -154,6 +161,11 @@ double ActionWithVessel::getTolerance() const {
return tolerance;
}
+inline
+double ActionWithVessel::getNLTolerance() const {
+ return nl_tolerance;
+}
+
inline
unsigned ActionWithVessel::getNumberOfVessels() const {
return functions.size();
@@ -217,6 +229,16 @@ void ActionWithVessel::accumulateDerivative( const unsigned& ider, const double&
buffer[current_buffer_start + current_buffer_stride*ider] += der;
}
+inline
+void ActionWithVessel::unlockContributors(){
+ plumed_dbg_assert( taskList.getNumberActive()==taskList.fullSize() );
+ contributorsAreUnlocked=true;
+}
+
+inline
+void ActionWithVessel::lockContributors(){
+ contributorsAreUnlocked=false;
+}
}
}
diff --git a/src/vesselbase/Between.cpp b/src/vesselbase/Between.cpp
index 5d30fb9f79bb0228d0eb7e3cb25c012ba155b0d0..6b7a0bc3e9bc825f7dd34b27d33b99fdceed80c2 100644
--- a/src/vesselbase/Between.cpp
+++ b/src/vesselbase/Between.cpp
@@ -82,23 +82,21 @@ std::string Between::function_description(){
bool Between::calculate(){
double weight=getAction()->getElementValue(1);
+ plumed_dbg_assert( weight>=getTolerance() );
double val=getAction()->getElementValue(0);
double dval, f = hist.calculate(val, dval);
- bool addval2, addval=addValue(1,weight);
+ addValueIgnoringTolerance(1,weight);
+ double contr=weight*f;
+ bool addval=addValueUsingTolerance(0,contr);
if( addval ){
- addval2=addValue(0,weight*f);
- if( addval2 ){
- getAction()->chainRuleForElementDerivatives( 0, 0, weight*dval, this );
- if(diffweight) getAction()->chainRuleForElementDerivatives( 0, 1, f, this );
- if(norm){
- if(diffweight) getAction()->chainRuleForElementDerivatives( 1, 1, 1.0, this );
- return addval;
- }
+ getAction()->chainRuleForElementDerivatives( 0, 0, weight*dval, this );
+ if(diffweight){
+ getAction()->chainRuleForElementDerivatives( 0, 1, f, this );
+ if(norm) getAction()->chainRuleForElementDerivatives( 1, 1, 1.0, this );
}
- return addval2;
}
- return addval;
+ return ( contr>getNLTolerance() );
}
void Between::finish(){
diff --git a/src/vesselbase/BridgeVessel.cpp b/src/vesselbase/BridgeVessel.cpp
index 05b318e38d7fbebd712daa0f99a75c6d951b6d0f..ffe7c02a4c4c87f59a00b9a73066ab2f2332a9d9 100644
--- a/src/vesselbase/BridgeVessel.cpp
+++ b/src/vesselbase/BridgeVessel.cpp
@@ -56,12 +56,13 @@ void BridgeVessel::prepare(){
bool BridgeVessel::calculate(){
unsigned j;
- bool res=myOutputAction->performTask(j);
- if( !res ){
+ myOutputAction->performTask(j);
+ if( myOutputAction->thisval[1]<myOutputAction->getTolerance() ){
myOutputAction->clearAfterTask();
- return false;
+ return ( !myOutputAction->contributorsAreUnlocked || myOutputAction->thisval[1]>=myOutputAction->getNLTolerance() );
}
- return myOutputAction->calculateAllVessels();
+ bool keep=myOutputAction->calculateAllVessels();
+ return ( !myOutputAction->contributorsAreUnlocked || keep );
}
void BridgeVessel::finish(){
diff --git a/src/vesselbase/FunctionVessel.h b/src/vesselbase/FunctionVessel.h
index 1e55406384666e8bbc0a102fc0a347e6da57da5b..7caaf93cc01036ad3f9d55f35f8e795fc7a1ee3e 100644
--- a/src/vesselbase/FunctionVessel.h
+++ b/src/vesselbase/FunctionVessel.h
@@ -47,8 +47,10 @@ private:
protected:
/// Are the derivatives differentiable
bool diffweight;
-/// Add some value to the accumulator
- bool addValue( const unsigned& jval, const double& val );
+/// Add some value to the accumulator if it is greater than tolerance
+ bool addValueUsingTolerance( const unsigned& jval, const double& val );
+/// Add some value to the accumulator and ignore the tolerance
+ void addValueIgnoringTolerance( const unsigned& jval, const double& val );
/// Set the final value
void setOutputValue( const double& val );
/// Get the nth value in the distribution
@@ -71,12 +73,17 @@ public:
};
inline
-bool FunctionVessel::addValue( const unsigned& jval, const double& val ){
+bool FunctionVessel::addValueUsingTolerance( const unsigned& jval, const double& val ){
if( fabs(val)<getTolerance() ) return false;
addToBufferElement( (nderivatives+1)*jval, val );
return true;
}
+inline
+void FunctionVessel::addValueIgnoringTolerance( const unsigned& jval, const double& val ){
+ addToBufferElement( (nderivatives+1)*jval, val );
+}
+
inline
double FunctionVessel::getFinalValue(const unsigned& j){
plumed_dbg_assert( j<getNumberOfTerms() );
diff --git a/src/vesselbase/LessThan.cpp b/src/vesselbase/LessThan.cpp
index 89d145d013025abba447761db84dbe55d09e8729..c9f0758abcf4a0ba5ba5c1174ecff5d32e3dae52 100644
--- a/src/vesselbase/LessThan.cpp
+++ b/src/vesselbase/LessThan.cpp
@@ -67,14 +67,17 @@ std::string LessThan::function_description(){
bool LessThan::calculate(){
double weight=getAction()->getElementValue(1);
- if( weight<getTolerance() ) return false;
+ plumed_dbg_assert( weight>=getTolerance() );
double val=getAction()->getElementValue(0);
double dval, f = sf.calculate(val, dval); dval*=val;
- bool addval=addValue(0,weight*f);
- if(addval) getAction()->chainRuleForElementDerivatives(0, 0, weight*dval, this);
- if(diffweight) getAction()->chainRuleForElementDerivatives(0, 1, f, this);
- return addval;
+ double contr=weight*f;
+ bool addval=addValueUsingTolerance(0,contr);
+ if(addval){
+ getAction()->chainRuleForElementDerivatives(0, 0, weight*dval, this);
+ if(diffweight) getAction()->chainRuleForElementDerivatives(0, 1, f, this);
+ }
+ return ( contr>getNLTolerance() );
}
void LessThan::finish(){
diff --git a/src/vesselbase/Mean.cpp b/src/vesselbase/Mean.cpp
index f4ad8b72be7c6b37a15391b36dec290f44304ad7..25e2e4bfb8a03a24b3f933aa958bb75387afeb88 100644
--- a/src/vesselbase/Mean.cpp
+++ b/src/vesselbase/Mean.cpp
@@ -59,15 +59,16 @@ std::string Mean::function_description(){
bool Mean::calculate(){
double weight=getAction()->getElementValue(1);
- bool addval=addValue( 1, weight );
- if( addval ){
- double colvar=getAction()->getElementValue(0);
- bool ignore=addValue( 0, weight*colvar );
- getAction()->chainRuleForElementDerivatives( 0, 0, weight, this );
- if(diffweight) getAction()->chainRuleForElementDerivatives( 0, 1, colvar, this );
- if(diffweight) getAction()->chainRuleForElementDerivatives( 1, 1, 1.0, this );
+ plumed_dbg_assert( weight>=getTolerance() );
+ addValueIgnoringTolerance( 1, weight );
+ double colvar=getAction()->getElementValue(0);
+ addValueIgnoringTolerance( 0, weight*colvar );
+ getAction()->chainRuleForElementDerivatives( 0, 0, weight, this );
+ if(diffweight){
+ getAction()->chainRuleForElementDerivatives( 0, 1, colvar, this );
+ getAction()->chainRuleForElementDerivatives( 1, 1, 1.0, this );
}
- return addval;
+ return true;
}
void Mean::finish(){
diff --git a/src/vesselbase/Min.cpp b/src/vesselbase/Min.cpp
index 45f2958c33dbc64589199843bd758ef9454db009..5d1d25a6389a42e0300050b34324cf71533fcdfe 100644
--- a/src/vesselbase/Min.cpp
+++ b/src/vesselbase/Min.cpp
@@ -59,6 +59,8 @@ df(2)
{
if( getAction()->isPeriodic() ) error("min is not a meaningful option for periodic variables");
parse("BETA",beta);
+
+ if( diffweight ) error("can't calculate min if weight is differentiable");
}
std::string Min::function_description(){
@@ -67,15 +69,11 @@ std::string Min::function_description(){
}
bool Min::calculate(){
- double weight=getAction()->getElementValue(1);
- if( weight<getTolerance() ) return false;
-
double val=getAction()->getElementValue(0);
double dval, f = exp(beta/val); dval=f/(val*val);
- bool addval=addValue(0,f);
- if(addval) getAction()->chainRuleForElementDerivatives( 0, 0, weight*dval, this );
- if(diffweight) getAction()->chainRuleForElementDerivatives(0, 1, f, this);
- return addval;
+ addValueIgnoringTolerance(0,f);
+ getAction()->chainRuleForElementDerivatives( 0, 0, dval, this );
+ return true;
}
void Min::finish(){
diff --git a/src/vesselbase/MoreThan.cpp b/src/vesselbase/MoreThan.cpp
index fda53a049bac01cbcc7910042e715dca8ba4e5a1..23de6046adef818b511f6d37a861a6daa71c4b7c 100644
--- a/src/vesselbase/MoreThan.cpp
+++ b/src/vesselbase/MoreThan.cpp
@@ -69,14 +69,17 @@ std::string MoreThan::function_description(){
bool MoreThan::calculate(){
double weight=getAction()->getElementValue(1);
- if( weight<getTolerance() ) return false;
+ plumed_dbg_assert( weight>=getTolerance() );
double val=getAction()->getElementValue(0);
double dval, f = 1.0 - sf.calculate(val, dval); dval*=-val;
- bool addval=addValue(0,weight*f);
- if(addval) getAction()->chainRuleForElementDerivatives( 0, 0, weight*dval, this );
- if(diffweight) getAction()->chainRuleForElementDerivatives(0, 1, f, this);
- return addval;
+ double contr=weight*f;
+ bool addval=addValueUsingTolerance(0,contr);
+ if(addval){
+ getAction()->chainRuleForElementDerivatives( 0, 0, weight*dval, this );
+ if(diffweight) getAction()->chainRuleForElementDerivatives(0, 1, f, this);
+ }
+ return ( contr>getNLTolerance() );
}
void MoreThan::finish(){
diff --git a/src/vesselbase/Sum.cpp b/src/vesselbase/Sum.cpp
index b3f8283cc094603fb2a27dd513cccb160a3bf320..600e7602385680a3d614543ce01c15b580df3e4f 100644
--- a/src/vesselbase/Sum.cpp
+++ b/src/vesselbase/Sum.cpp
@@ -59,13 +59,13 @@ std::string Sum::function_description(){
bool Sum::calculate(){
double weight=getAction()->getElementValue(1);
- if( weight<getTolerance() ) return false;
+ plumed_dbg_assert( weight>=getTolerance() );
double val=getAction()->getElementValue(0);
- bool addval=addValue(0,weight*val);
- if(addval) getAction()->chainRuleForElementDerivatives( 0, 0, weight, this );
+ addValueIgnoringTolerance(0,weight*val);
+ getAction()->chainRuleForElementDerivatives( 0, 0, weight, this );
if(diffweight) getAction()->chainRuleForElementDerivatives(0, 1, val, this);
- return addval;
+ return true;
}
void Sum::finish(){
diff --git a/src/vesselbase/Vessel.h b/src/vesselbase/Vessel.h
index 3902ae68896ca4dd01ef74fb6640c5a1fb400ed0..96a744f86680a84cc9049811130067a88206747e 100644
--- a/src/vesselbase/Vessel.h
+++ b/src/vesselbase/Vessel.h
@@ -120,6 +120,8 @@ protected:
ActionWithVessel* getAction();
/// Return the value of the tolerance
double getTolerance() const ;
+/// Return the value of the neighbor list tolerance
+ double getNLTolerance() const ;
/// Set the size of the data buffer
void resizeBuffer( const unsigned& n );
/// Set the value of the ith element in the buffer
@@ -227,6 +229,11 @@ double Vessel::getTolerance() const {
return action->tolerance;
}
+inline
+double Vessel::getNLTolerance() const {
+ return action->nl_tolerance;
+}
+
inline
ActionWithVessel* Vessel::getAction(){
return action;