diff --git a/regtest/crystallization/rt-q6-subset/config b/regtest/crystallization/rt-q6-subset/config
index e07432072a91405171ff68d3c3d22a09fde3346c..5a728e15c66e0706504e44ff7ae4b5eb22a08492 100644
--- a/regtest/crystallization/rt-q6-subset/config
+++ b/regtest/crystallization/rt-q6-subset/config
@@ -1,3 +1,3 @@
type=driver
# this is to test a different name
-arg="--plumed plumed.dat --ixyz 64.xyz"
+arg="--plumed plumed.dat --ixyz 64.xyz --dump-forces forces --dump-forces-fmt=%8.4f" # --debug-forces forces.num"
diff --git a/regtest/crystallization/rt-q6-subset/deriv3.reference b/regtest/crystallization/rt-q6-subset/deriv3.reference
index 9f41d77a42ff704de192e37490ea99b8ee8f0561..ddb88fd1cc3a3ef15c20b49d440e1afad4677739 100644
--- a/regtest/crystallization/rt-q6-subset/deriv3.reference
+++ b/regtest/crystallization/rt-q6-subset/deriv3.reference
@@ -14,381 +14,780 @@
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+ 0.000000 533 0.0010
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+ 0.000000 544 0.0006
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+ 0.000000 567 0.0003
+ 0.000000 568 0.0013
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+ 0.000000 577 0.0045
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+ 0.000000 579 -0.0088
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+ 0.000000 582 -0.0231
+ 0.000000 583 -0.0070
+ 0.000000 584 0.0063
+ 0.000000 585 -0.0088
+ 0.000000 586 0.0039
+ 0.000000 587 -0.0083
+ 0.000000 588 0.0010
+ 0.000000 589 0.0005
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+ 0.000000 780 0.0000
+ 0.000000 781 0.0000
+ 0.000000 782 0.0000
+ 0.000000 783 -0.0231
+ 0.000000 784 -0.1953
+ 0.000000 785 0.0762
+ 0.000000 786 -0.1953
+ 0.000000 787 0.0424
+ 0.000000 788 -0.1586
+ 0.000000 789 0.0762
+ 0.000000 790 -0.1586
+ 0.000000 791 -0.0484
diff --git a/regtest/crystallization/rt-q6-subset/forces.reference b/regtest/crystallization/rt-q6-subset/forces.reference
new file mode 100644
index 0000000000000000000000000000000000000000..bced07e02c2940b858aa44d093384f8d3ccd220a
--- /dev/null
+++ b/regtest/crystallization/rt-q6-subset/forces.reference
@@ -0,0 +1,66 @@
+64
+ -0.0122 0.0224 -0.0256
+X -0.0148 -0.0029 0.0010
+X -0.0141 0.0035 -0.0314
+X 0.0215 -0.0139 -0.0436
+X -0.0043 0.0038 0.0117
+X 0.0064 0.0164 0.0080
+X -0.0076 -0.0132 0.0037
+X 0.0029 -0.0016 0.0002
+X 0.0086 0.0114 -0.0099
+X -0.0014 0.0006 0.0003
+X -0.0007 -0.0034 0.0008
+X -0.0075 0.0014 0.0084
+X -0.0034 0.0024 0.0030
+X 0.0018 -0.0002 0.0039
+X -0.0001 0.0086 0.0079
+X 0.0023 -0.0016 -0.0000
+X -0.0025 0.0019 0.0002
+X 0.0053 -0.0063 -0.0007
+X -0.0009 -0.0028 -0.0004
+X -0.0006 -0.0106 0.0090
+X 0.0019 0.0085 -0.0023
+X -0.0046 0.0059 -0.0012
+X 0.0001 0.0033 -0.0009
+X 0.0026 0.0031 -0.0064
+X 0.0033 0.0047 -0.0078
+X 0.0043 0.0076 0.0081
+X 0.0019 0.0011 0.0001
+X 0.0082 -0.0058 0.0037
+X 0.0026 -0.0007 0.0000
+X -0.0032 0.0090 -0.0071
+X -0.0029 -0.0026 0.0086
+X 0.0080 -0.0046 0.0001
+X -0.0041 -0.0007 -0.0031
+X 0.0012 0.0017 -0.0065
+X 0.0007 0.0041 -0.0003
+X -0.0079 -0.0051 -0.0063
+X 0.0067 -0.0063 0.0172
+X -0.0014 0.0044 0.0020
+X 0.0009 -0.0075 0.0013
+X 0.0027 -0.0172 -0.0197
+X 0.0184 -0.0021 0.0159
+X -0.0097 0.0104 0.0092
+X -0.0012 -0.0029 0.0027
+X 0.0012 0.0015 -0.0036
+X -0.0199 -0.0096 0.0064
+X 0.0004 0.0008 0.0011
+X 0.0059 0.0033 0.0004
+X 0.0009 0.0012 -0.0004
+X 0.0011 -0.0012 -0.0010
+X -0.0040 0.0003 -0.0042
+X -0.0089 -0.0077 0.0021
+X -0.0021 0.0013 0.0029
+X 0.0058 -0.0067 0.0070
+X 0.0190 -0.0070 0.0060
+X -0.0059 0.0008 -0.0014
+X 0.0080 0.0003 -0.0108
+X -0.0072 -0.0051 0.0247
+X 0.0002 0.0006 -0.0013
+X 0.0012 0.0165 0.0000
+X 0.0013 0.0014 0.0011
+X 0.0014 0.0040 0.0018
+X -0.0035 0.0026 -0.0095
+X -0.0115 -0.0008 0.0056
+X -0.0037 0.0020 -0.0044
+X 0.0005 0.0003 -0.0020
diff --git a/regtest/crystallization/rt-q6-subset/plumed.dat b/regtest/crystallization/rt-q6-subset/plumed.dat
index f158902207a5ba1fe99ec385b24a6bbd7adb0e06..0c8cab700879b2c466b4de063b1e9cf0f112e3fc 100644
--- a/regtest/crystallization/rt-q6-subset/plumed.dat
+++ b/regtest/crystallization/rt-q6-subset/plumed.dat
@@ -5,3 +5,5 @@ LOCAL_Q6 SPECIESA=q6a SPECIESB=q6a,q6b SWITCH={RATIONAL D_0=3.0 R_0=1.5} MEAN LO
PRINT ARG=w6.* FILE=colv3
DUMPDERIVATIVES ARG=w6.* FILE=deriv3 FMT=%8.4f
+r: RESTRAINT ARG=w6.* AT=0.0 KAPPA=100.
+
diff --git a/regtest/crystallization/rt-urea/Makefile b/regtest/crystallization/rt-urea/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..3703b27cea227aa053fb6d1d73f861e4384dbcee
--- /dev/null
+++ b/regtest/crystallization/rt-urea/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
diff --git a/regtest/crystallization/rt-urea/colvar.reference b/regtest/crystallization/rt-urea/colvar.reference
new file mode 100644
index 0000000000000000000000000000000000000000..80aad3418a74bd7fa2b83b070acd8c520c799906
--- /dev/null
+++ b/regtest/crystallization/rt-urea/colvar.reference
@@ -0,0 +1,4 @@
+#! FIELDS time smac.morethan cc1.morethan cc2
+ 0.000000 25.3134 13.0006 300.0000
+ 1.000000 28.8656 16.3745 300.0000
+ 2.000000 33.0560 16.3061 300.0000
diff --git a/regtest/crystallization/rt-urea/config b/regtest/crystallization/rt-urea/config
new file mode 100644
index 0000000000000000000000000000000000000000..67334ce385c4d77b45c4b0128543c5f97cf4a076
--- /dev/null
+++ b/regtest/crystallization/rt-urea/config
@@ -0,0 +1,3 @@
+type=driver
+# this is to test a different name
+arg="--ixyz traj.xyz --box 26.699,26.717,28.643"
diff --git a/regtest/crystallization/rt-urea/plumed.dat b/regtest/crystallization/rt-urea/plumed.dat
new file mode 100644
index 0000000000000000000000000000000000000000..de1ded8a7544508f250d2e230a582567766457d3
--- /dev/null
+++ b/regtest/crystallization/rt-urea/plumed.dat
@@ -0,0 +1,315 @@
+MOLECULES ...
+MOL1=1,2,1
+MOL2=5,6,5
+MOL3=9,10,9
+MOL4=13,14,13
+MOL5=17,18,17
+MOL6=21,22,21
+MOL7=25,26,25
+MOL8=29,30,29
+MOL9=33,34,33
+MOL10=37,38,37
+MOL11=41,42,41
+MOL12=45,46,45
+MOL13=49,50,49
+MOL14=53,54,53
+MOL15=57,58,57
+MOL16=61,62,61
+MOL17=65,66,65
+MOL18=69,70,69
+MOL19=73,74,73
+MOL20=77,78,77
+MOL21=81,82,81
+MOL22=85,86,85
+MOL23=89,90,89
+MOL24=93,94,93
+MOL25=97,98,97
+MOL26=101,102,101
+MOL27=105,106,105
+MOL28=109,110,109
+MOL29=113,114,113
+MOL30=117,118,117
+MOL31=121,122,121
+MOL32=125,126,125
+MOL33=129,130,129
+MOL34=133,134,133
+MOL35=137,138,137
+MOL36=141,142,141
+MOL37=145,146,145
+MOL38=149,150,149
+MOL39=153,154,153
+MOL40=157,158,157
+MOL41=161,162,161
+MOL42=165,166,165
+MOL43=169,170,169
+MOL44=173,174,173
+MOL45=177,178,177
+MOL46=181,182,181
+MOL47=185,186,185
+MOL48=189,190,189
+MOL49=193,194,193
+MOL50=197,198,197
+MOL51=201,202,201
+MOL52=205,206,205
+MOL53=209,210,209
+MOL54=213,214,213
+MOL55=217,218,217
+MOL56=221,222,221
+MOL57=225,226,225
+MOL58=229,230,229
+MOL59=233,234,233
+MOL60=237,238,237
+MOL61=241,242,241
+MOL62=245,246,245
+MOL63=249,250,249
+MOL64=253,254,253
+MOL65=257,258,257
+MOL66=261,262,261
+MOL67=265,266,265
+MOL68=269,270,269
+MOL69=273,274,273
+MOL70=277,278,277
+MOL71=281,282,281
+MOL72=285,286,285
+MOL73=289,290,289
+MOL74=293,294,293
+MOL75=297,298,297
+MOL76=301,302,301
+MOL77=305,306,305
+MOL78=309,310,309
+MOL79=313,314,313
+MOL80=317,318,317
+MOL81=321,322,321
+MOL82=325,326,325
+MOL83=329,330,329
+MOL84=333,334,333
+MOL85=337,338,337
+MOL86=341,342,341
+MOL87=345,346,345
+MOL88=349,350,349
+MOL89=353,354,353
+MOL90=357,358,357
+MOL91=361,362,361
+MOL92=365,366,365
+MOL93=369,370,369
+MOL94=373,374,373
+MOL95=377,378,377
+MOL96=381,382,381
+MOL97=385,386,385
+MOL98=389,390,389
+MOL99=393,394,393
+MOL100=397,398,397
+MOL101=401,402,401
+MOL102=405,406,405
+MOL103=409,410,409
+MOL104=413,414,413
+MOL105=417,418,417
+MOL106=421,422,421
+MOL107=425,426,425
+MOL108=429,430,429
+MOL109=433,434,433
+MOL110=437,438,437
+MOL111=441,442,441
+MOL112=445,446,445
+MOL113=449,450,449
+MOL114=453,454,453
+MOL115=457,458,457
+MOL116=461,462,461
+MOL117=465,466,465
+MOL118=469,470,469
+MOL119=473,474,473
+MOL120=477,478,477
+MOL121=481,482,481
+MOL122=485,486,485
+MOL123=489,490,489
+MOL124=493,494,493
+MOL125=497,498,497
+MOL126=501,502,501
+MOL127=505,506,505
+MOL128=509,510,509
+MOL129=513,514,513
+MOL130=517,518,517
+MOL131=521,522,521
+MOL132=525,526,525
+MOL133=529,530,529
+MOL134=533,534,533
+MOL135=537,538,537
+MOL136=541,542,541
+MOL137=545,546,545
+MOL138=549,550,549
+MOL139=553,554,553
+MOL140=557,558,557
+MOL141=561,562,561
+MOL142=565,566,565
+MOL143=569,570,569
+MOL144=573,574,573
+MOL145=577,578,577
+MOL146=581,582,581
+MOL147=585,586,585
+MOL148=589,590,589
+MOL149=593,594,593
+MOL150=597,598,597
+MOL151=601,602,601
+MOL152=605,606,605
+MOL153=609,610,609
+MOL154=613,614,613
+MOL155=617,618,617
+MOL156=621,622,621
+MOL157=625,626,625
+MOL158=629,630,629
+MOL159=633,634,633
+MOL160=637,638,637
+MOL161=641,642,641
+MOL162=645,646,645
+MOL163=649,650,649
+MOL164=653,654,653
+MOL165=657,658,657
+MOL166=661,662,661
+MOL167=665,666,665
+MOL168=669,670,669
+MOL169=673,674,673
+MOL170=677,678,677
+MOL171=681,682,681
+MOL172=685,686,685
+MOL173=689,690,689
+MOL174=693,694,693
+MOL175=697,698,697
+MOL176=701,702,701
+MOL177=705,706,705
+MOL178=709,710,709
+MOL179=713,714,713
+MOL180=717,718,717
+MOL181=721,722,721
+MOL182=725,726,725
+MOL183=729,730,729
+MOL184=733,734,733
+MOL185=737,738,737
+MOL186=741,742,741
+MOL187=745,746,745
+MOL188=749,750,749
+MOL189=753,754,753
+MOL190=757,758,757
+MOL191=761,762,761
+MOL192=765,766,765
+MOL193=769,770,769
+MOL194=773,774,773
+MOL195=777,778,777
+MOL196=781,782,781
+MOL197=785,786,785
+MOL198=789,790,789
+MOL199=793,794,793
+MOL200=797,798,797
+MOL201=801,802,801
+MOL202=805,806,805
+MOL203=809,810,809
+MOL204=813,814,813
+MOL205=817,818,817
+MOL206=821,822,821
+MOL207=825,826,825
+MOL208=829,830,829
+MOL209=833,834,833
+MOL210=837,838,837
+MOL211=841,842,841
+MOL212=845,846,845
+MOL213=849,850,849
+MOL214=853,854,853
+MOL215=857,858,857
+MOL216=861,862,861
+MOL217=865,866,865
+MOL218=869,870,869
+MOL219=873,874,873
+MOL220=877,878,877
+MOL221=881,882,881
+MOL222=885,886,885
+MOL223=889,890,889
+MOL224=893,894,893
+MOL225=897,898,897
+MOL226=901,902,901
+MOL227=905,906,905
+MOL228=909,910,909
+MOL229=913,914,913
+MOL230=917,918,917
+MOL231=921,922,921
+MOL232=925,926,925
+MOL233=929,930,929
+MOL234=933,934,933
+MOL235=937,938,937
+MOL236=941,942,941
+MOL237=945,946,945
+MOL238=949,950,949
+MOL239=953,954,953
+MOL240=957,958,957
+MOL241=961,962,961
+MOL242=965,966,965
+MOL243=969,970,969
+MOL244=973,974,973
+MOL245=977,978,977
+MOL246=981,982,981
+MOL247=985,986,985
+MOL248=989,990,989
+MOL249=993,994,993
+MOL250=997,998,997
+MOL251=1001,1002,1001
+MOL252=1005,1006,1005
+MOL253=1009,1010,1009
+MOL254=1013,1014,1013
+MOL255=1017,1018,1017
+MOL256=1021,1022,1021
+MOL257=1025,1026,1025
+MOL258=1029,1030,1029
+MOL259=1033,1034,1033
+MOL260=1037,1038,1037
+MOL261=1041,1042,1041
+MOL262=1045,1046,1045
+MOL263=1049,1050,1049
+MOL264=1053,1054,1053
+MOL265=1057,1058,1057
+MOL266=1061,1062,1061
+MOL267=1065,1066,1065
+MOL268=1069,1070,1069
+MOL269=1073,1074,1073
+MOL270=1077,1078,1077
+MOL271=1081,1082,1081
+MOL272=1085,1086,1085
+MOL273=1089,1090,1089
+MOL274=1093,1094,1093
+MOL275=1097,1098,1097
+MOL276=1101,1102,1101
+MOL277=1105,1106,1105
+MOL278=1109,1110,1109
+MOL279=1113,1114,1113
+MOL280=1117,1118,1117
+MOL281=1121,1122,1121
+MOL282=1125,1126,1125
+MOL283=1129,1130,1129
+MOL284=1133,1134,1133
+MOL285=1137,1138,1137
+MOL286=1141,1142,1141
+MOL287=1145,1146,1145
+MOL288=1149,1150,1149
+MOL289=1153,1154,1153
+MOL290=1157,1158,1157
+MOL291=1161,1162,1161
+MOL292=1165,1166,1165
+MOL293=1169,1170,1169
+MOL294=1173,1174,1173
+MOL295=1177,1178,1177
+MOL296=1181,1182,1181
+MOL297=1185,1186,1185
+MOL298=1189,1190,1189
+MOL299=1193,1194,1193
+MOL300=1197,1198,1197
+LABEL=m1
+... MOLECULES
+
+smac: SMAC SPECIES=m1 SWITCH={RATIONAL D_0=5.99 R_0=0.1 D_MAX=6.0} KERNEL1={TRIANGULAR CENTER=0 SIGMA=1.0} KERNEL2={TRIANGULAR CENTER=pi SIGMA=0.6} SWITCH_COORD={RATIONAL R_0=0.001} MORE_THAN={GAUSSIAN D_0=0.41 R_0=0.5 D_MAX=0.42}
+ff: MFILTER_MORE DATA=smac SWITCH={GAUSSIAN D_0=0.41 R_0=0.5 D_MAX=0.42}
+c1: CONTACT_MATRIX ATOMS=ff SWITCH={RATIONAL D_0=5.99 R_0=0.1 D_MAX=6.0}
+dfs: DFSCLUSTERING MATRIX=c1
+cc1: CLUSTER_PROPERTIES CLUSTERS=dfs CLUSTER=1 MORE_THAN={GAUSSIAN D_0=0.41 R_0=0.5 D_MAX=0.42}
+
+smacm: SMAC_MATRIX ATOMS=m1 SWITCH={RATIONAL D_0=5.99 R_0=0.1 D_MAX=6.0} KERNEL1={TRIANGULAR CENTER=0 SIGMA=1.0} KERNEL2={TRIANGULAR CENTER=pi SIGMA=0.6}
+dfs1: DFSCLUSTERING MATRIX=smacm
+cc2: CLUSTER_NATOMS CLUSTERS=dfs1 CLUSTER=1
+
+PRINT ARG=smac.*,cc1.*,cc2 FILE=colvar FMT=%8.4f
diff --git a/regtest/crystallization/rt-urea/traj.xyz b/regtest/crystallization/rt-urea/traj.xyz
new file mode 100644
index 0000000000000000000000000000000000000000..bb133931a69523e5594d84b1072a118b3fa9fd56
--- /dev/null
+++ b/regtest/crystallization/rt-urea/traj.xyz
@@ -0,0 +1,3606 @@
+1200
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diff --git a/regtest/multicolvar/rt-two-filter/Makefile b/regtest/multicolvar/rt-two-filter/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..3703b27cea227aa053fb6d1d73f861e4384dbcee
--- /dev/null
+++ b/regtest/multicolvar/rt-two-filter/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
diff --git a/regtest/multicolvar/rt-two-filter/colv.reference b/regtest/multicolvar/rt-two-filter/colv.reference
new file mode 100644
index 0000000000000000000000000000000000000000..b28db1691648b70a4fdacd931a81d46c3d8a7755
--- /dev/null
+++ b/regtest/multicolvar/rt-two-filter/colv.reference
@@ -0,0 +1,2 @@
+#! FIELDS time c2.morethan
+ 0.000000 24.263966
diff --git a/regtest/multicolvar/rt-two-filter/config b/regtest/multicolvar/rt-two-filter/config
new file mode 100644
index 0000000000000000000000000000000000000000..2980bbcf664ee5e01ecef35cdea181e8d4b03336
--- /dev/null
+++ b/regtest/multicolvar/rt-two-filter/config
@@ -0,0 +1,3 @@
+type=driver
+# this is to test a different name
+arg="--plumed plumed.dat --ixyz gas-one.xyz --dump-forces forces --dump-forces-fmt=%8.4f" #--debug-forces forces.num"
diff --git a/regtest/multicolvar/rt-two-filter/forces.reference b/regtest/multicolvar/rt-two-filter/forces.reference
new file mode 100644
index 0000000000000000000000000000000000000000..30e6f61e540430e96f21e22df093b790623622b2
--- /dev/null
+++ b/regtest/multicolvar/rt-two-filter/forces.reference
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new file mode 100644
index 0000000000000000000000000000000000000000..efb861494cc81783ae44682f976495da64dcd484
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diff --git a/regtest/multicolvar/rt-two-filter/log b/regtest/multicolvar/rt-two-filter/log
new file mode 100644
index 0000000000000000000000000000000000000000..9d2ae50d38fd3e30dcc127445ae56d6d7d60ccf1
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diff --git a/regtest/multicolvar/rt-two-filter/plumed.dat b/regtest/multicolvar/rt-two-filter/plumed.dat
new file mode 100644
index 0000000000000000000000000000000000000000..3012e984e8652cdae2fed95c88918389b0e6e33e
--- /dev/null
+++ b/regtest/multicolvar/rt-two-filter/plumed.dat
@@ -0,0 +1,7 @@
+c1: COORDINATIONNUMBER SPECIES=1-150 SWITCH={EXP D_0=4.0 R_0=0.5 D_MAX=6.0}
+cf: MFILTER_MORE DATA=c1 SWITCH={RATIONAL D_0=2.0 R_0=0.1} LOWMEM
+
+c2: COORDINATIONNUMBER SPECIES=cf SWITCH={EXP D_0=4.0 R_0=0.5 D_MAX=6.0} MORE_THAN={RATIONAL D_0=2.0 R_0=0.1}
+
+PRINT ARG=c2.* FILE=colv
+r: RESTRAINT ARG=c2.* AT=24.0 KAPPA=0.5
diff --git a/src/adjmat/AdjacencyMatrixBase.cpp b/src/adjmat/AdjacencyMatrixBase.cpp
index 36318cd041ed17901b21d847b8d4f59e2aaf6b77..92a8039f2ead431bdbd8bcb104415cf8c9efd764 100644
--- a/src/adjmat/AdjacencyMatrixBase.cpp
+++ b/src/adjmat/AdjacencyMatrixBase.cpp
@@ -174,7 +174,7 @@ void AdjacencyMatrixBase::readMaxThreeSpeciesMatrix( const std::string& key0, co
// }
void AdjacencyMatrixBase::addOrientationDerivatives( const unsigned& ival, const unsigned& iatom, const std::vector<double>& der, multicolvar::AtomValuePack& myatoms ) const {
- unsigned jatom=myatoms.getIndex(iatom); plumed_dbg_assert( jatom<colvar_label.size() );
+ unsigned jatom=myatoms.getIndex(iatom); plumed_dbg_assert( jatom<atom_lab.size() );
MultiValue myder(0,0); unsigned mmc=atom_lab[ival].first - 1; plumed_assert( !mybasemulticolvars[mmc]->weightWithDerivatives() );
plumed_dbg_assert( mybasedata[mmc]->storedValueIsActive( atom_lab[ival].second ) );
if( myder.getNumberOfValues()!=mybasemulticolvars[mmc]->getNumberOfQuantities() ||
diff --git a/src/adjmat/AdjacencyMatrixBase.h b/src/adjmat/AdjacencyMatrixBase.h
index bc5597d321dff659e25a2c04db95e37721a69ffb..4c8c0b9f041fe9ef523871ba5b4f0c21fa05e783 100644
--- a/src/adjmat/AdjacencyMatrixBase.h
+++ b/src/adjmat/AdjacencyMatrixBase.h
@@ -111,7 +111,7 @@ AtomNumber AdjacencyMatrixBase::getAbsoluteIndexOfCentralAtom( const unsigned& i
inline
void AdjacencyMatrixBase::getOrientationVector( const unsigned& ind, const bool& normed, std::vector<double>& orient ) const {
- plumed_dbg_assert( atom_lab[iatom].first>0 ); unsigned mmc=atom_lab[ind].first - 1;
+ plumed_dbg_assert( atom_lab[ind].first>0 ); unsigned mmc=atom_lab[ind].first - 1;
plumed_assert( !mybasemulticolvars[mmc]->weightWithDerivatives() ); plumed_dbg_assert( mybasedata[mmc]->storedValueIsActive( atom_lab[ind].second ) );
mybasedata[mmc]->retrieveValueWithIndex( atom_lab[ind].second, normed, orient );
}
diff --git a/src/adjmat/MatrixSummationBase.cpp b/src/adjmat/MatrixSummationBase.cpp
index b686584e24a5e0a5cd6aeb4da13db8d3014d068e..c7011484a6de14c1506762c4eed569d49970c642 100644
--- a/src/adjmat/MatrixSummationBase.cpp
+++ b/src/adjmat/MatrixSummationBase.cpp
@@ -85,10 +85,11 @@ void MatrixSummationBase::addConnectionDerivatives( const unsigned& i, const uns
unsigned vi, myelem = mymatrix->getStoreIndexFromMatrixIndices( i, j );
mymatrix->retrieveValueWithIndex( myelem, false, vals );
+ double df, val = (mymatrix->function)->transformStoredValues( vals, vi, df );
mymatrix->retrieveDerivatives( myelem, false, myvals );
for(unsigned jd=0;jd<myvals.getNumberActive();++jd){
unsigned ider=myvals.getActiveIndex(jd);
- myvout.addDerivative( 1, ider, myvals.getDerivative( vi, ider ) );
+ myvout.addDerivative( 1, ider, df*myvals.getDerivative( vi, ider ) );
}
}
diff --git a/src/crystallization/CubicHarmonicBase.cpp b/src/crystallization/CubicHarmonicBase.cpp
index 905c7e8b42aa08c62a4a2a5f8add512d17f41ebb..7f92c58d4aa2e7d4e1011149beec362544c9c750 100644
--- a/src/crystallization/CubicHarmonicBase.cpp
+++ b/src/crystallization/CubicHarmonicBase.cpp
@@ -91,7 +91,7 @@ MultiColvarBase(ao)
}
double CubicHarmonicBase::compute( const unsigned& tindex, multicolvar::AtomValuePack& myatoms ) const {
- double value=0, norm=0, dfunc; Vector rotatedis;
+ double dfunc; Vector rotatedis;
// Calculate the coordination number
Vector myder, rotateder, fder; unsigned nat=myatoms.getNumberOfAtoms();
@@ -106,8 +106,6 @@ double CubicHarmonicBase::compute( const unsigned& tindex, multicolvar::AtomValu
(d2+=distance[2]*distance[2])<rcut2) {
sw = switchingFunction.calculateSqr( d2, dfunc );
-
- norm += sw;
rotatedis[0]=rotationmatrix[0][0]*distance[0]
+rotationmatrix[0][1]*distance[1]
@@ -130,25 +128,16 @@ double CubicHarmonicBase::compute( const unsigned& tindex, multicolvar::AtomValu
myder[2]=rotationmatrix[0][2]*rotateder[0]
+rotationmatrix[1][2]*rotateder[1]
+rotationmatrix[2][2]*rotateder[2];
-
- value += sw*tmp;
fder = (+dfunc)*tmp*distance + sw*myder;
- addAtomDerivatives( 1, 0, -fder, myatoms );
- addAtomDerivatives( 1, i, +fder, myatoms);
- myatoms.addBoxDerivatives( 1, Tensor(distance,-fder) );
- addAtomDerivatives( -1, 0, (-dfunc)*distance, myatoms);
- addAtomDerivatives( -1, i, (+dfunc)*distance, myatoms);
- myatoms.addTemporyBoxDerivatives( (-dfunc)*Tensor(distance,distance) );
+ accumulateSymmetryFunction( 1, i, sw*tmp, fder, Tensor(distance,-fder), myatoms );
+ accumulateSymmetryFunction( -1, i, sw, (+dfunc)*distance, (-dfunc)*Tensor(distance,distance), myatoms );
}
}
-
- myatoms.setValue(1, value);
// values -> der of... value [0], weight[1], x coord [2], y, z... [more magic]
- updateActiveAtoms( myatoms ); myatoms.getUnderlyingMultiValue().quotientRule( 1, norm, 1 );
-
- return value / norm; // this is equivalent to getting an "atomic" CV
+ updateActiveAtoms( myatoms ); myatoms.getUnderlyingMultiValue().quotientRule( 1, 1 );
+ return myatoms.getValue(1); // this is equivalent to getting an "atomic" CV
}
}
diff --git a/src/crystallization/InterMolecularTorsions.cpp b/src/crystallization/InterMolecularTorsions.cpp
index 8eb278c507546bba35d21c4b81e8c206f73bd49b..448220e97bb4013527728a2d5670ea14cf2666d4 100644
--- a/src/crystallization/InterMolecularTorsions.cpp
+++ b/src/crystallization/InterMolecularTorsions.cpp
@@ -140,10 +140,10 @@ double InterMolecularTorsions::compute( const unsigned& tindex, AtomValuePack& m
// And accumulate derivatives
if( !doNotCalculateDerivatives() ){
- MultiValue& myder0=getVectorDerivatives( myatoms.getIndex(0), true );
- mergeVectorDerivatives( 1, 2, orient1.size(), myatoms.getIndex(0), orient0, myder0, myatoms );
- MultiValue& myder1=getVectorDerivatives( myatoms.getIndex(1), true );
- mergeVectorDerivatives( 1, 2, orient0.size(), myatoms.getIndex(1), orient1, myder1, myatoms );
+ MultiValue& myder0=getInputDerivatives( 0, true, myatoms );
+ mergeInputDerivatives( 1, 2, orient1.size(), 0, orient0, myder0, myatoms );
+ MultiValue& myder1=getInputDerivatives( 1, true, myatoms );
+ mergeInputDerivatives( 1, 2, orient0.size(), 1, orient1, myder1, myatoms );
addAtomDerivatives( 1, 0, -dconn, myatoms ); addAtomDerivatives( 1, 1, dconn, myatoms );
myatoms.addBoxDerivatives( 1, -Tensor( dconn, conn ) );
}
diff --git a/src/crystallization/OrientationSphere.cpp b/src/crystallization/OrientationSphere.cpp
index fe2eededdf1840b2e1716f24ba6e9a743f8bfacc..596ef89e7d37e98aa0cf7ea276a8f898a9dfd187 100644
--- a/src/crystallization/OrientationSphere.cpp
+++ b/src/crystallization/OrientationSphere.cpp
@@ -74,7 +74,7 @@ double OrientationSphere::compute( const unsigned& tindex, multicolvar::AtomValu
getVectorForTask( myatoms.getIndex(0), true, catom_orient );
multicolvar::CatomPack atom0;
- MultiValue& myder0=getVectorDerivatives( myatoms.getIndex(0), true );
+ MultiValue& myder0=getInputDerivatives( 0, true, myatoms );
if( !doNotCalculateDerivatives() ) atom0=getCentralAtomPackFromInput( myatoms.getIndex(0) );
for(unsigned i=1;i<myatoms.getNumberOfAtoms();++i){
@@ -91,9 +91,9 @@ double OrientationSphere::compute( const unsigned& tindex, multicolvar::AtomValu
if( !doNotCalculateDerivatives() ){
for(unsigned k=2;k<catom_orient.size();++k){ this_der[k]*=sw; catom_der[k]*=sw; }
- MultiValue& myder1=getVectorDerivatives( myatoms.getIndex(i), true );
- mergeVectorDerivatives( 1, 2, this_orient.size(), myatoms.getIndex(0), catom_der, myder0, myatoms );
- mergeVectorDerivatives( 1, 2, catom_der.size(), myatoms.getIndex(i), this_der, myder1, myatoms );
+ MultiValue& myder1=getInputDerivatives( i, true, myatoms );
+ mergeInputDerivatives( 1, 2, this_orient.size(), 0, catom_der, myder0, myatoms );
+ mergeInputDerivatives( 1, 2, catom_der.size(), i, this_der, myder1, myatoms );
myatoms.addComDerivatives( 1, f_dot*(-dfunc)*distance - sw*ddistance, atom0 );
addAtomDerivatives( 1, i, f_dot*(dfunc)*distance + sw*ddistance, myatoms );
myatoms.addBoxDerivatives( 1, (-dfunc)*f_dot*Tensor(distance,distance) - sw*Tensor( ddistance, distance ) );
diff --git a/src/crystallization/Steinhardt.cpp b/src/crystallization/Steinhardt.cpp
index 73854c46baf76877ff2573bd18e9ca03e5e1ca52..19cff612ea92df77449b86c3ebc5419553865a74 100644
--- a/src/crystallization/Steinhardt.cpp
+++ b/src/crystallization/Steinhardt.cpp
@@ -73,8 +73,8 @@ void Steinhardt::calculateVector( multicolvar::AtomValuePack& myatoms ) const {
// The square root of -1
std::complex<double> ii( 0.0, 1.0 ), dp_x, dp_y, dp_z;
- unsigned ncomp=2*tmom+1;
- double sw, poly_ass, d2, dlen, nbond=0.0; std::complex<double> powered;
+ unsigned ncomp=2*tmom+1;
+ double sw, poly_ass, d2, dlen; std::complex<double> powered;
for(unsigned i=1;i<myatoms.getNumberOfAtoms();++i){
Vector& distance=myatoms.getPosition(i); // getSeparation( myatoms.getPosition(0), myatoms.getPosition(i) );
if ( (d2=distance[0]*distance[0])<rcut2 &&
@@ -82,15 +82,8 @@ void Steinhardt::calculateVector( multicolvar::AtomValuePack& myatoms ) const {
(d2+=distance[2]*distance[2])<rcut2) {
dlen = sqrt(d2);
sw = switchingFunction.calculate( dlen, dfunc );
-
- nbond += sw; // Accumulate total number of bonds
+ accumulateSymmetryFunction( -1, i, sw, (+dfunc)*distance, (-dfunc)*Tensor( distance,distance ), myatoms );
double dlen3 = d2*dlen;
-
- // Store derivatives of weight
- addAtomDerivatives( -1, 0, (-dfunc)*distance, myatoms );
- addAtomDerivatives( -1, i, (+dfunc)*distance, myatoms );
- myatoms.addTemporyBoxDerivatives( (-dfunc)*Tensor( distance,distance ) );
-
// Do stuff for m=0
poly_ass=deriv_poly( 0, distance[2]/dlen, dpoly_ass );
// Derivatives of z/r wrt x, y, z
@@ -98,11 +91,7 @@ void Steinhardt::calculateVector( multicolvar::AtomValuePack& myatoms ) const {
// Derivative wrt to the vector connecting the two atoms
myrealvec = (+sw)*dpoly_ass*dz + poly_ass*(+dfunc)*distance;
// Accumulate the derivatives
- addAtomDerivatives( 2 + tmom, 0, -myrealvec, myatoms );
- addAtomDerivatives( 2 + tmom, i, myrealvec, myatoms);
- myatoms.addBoxDerivatives( 2 + tmom, Tensor( -myrealvec,distance ) );
- // And store the vector function
- myatoms.addValue( 2 + tmom, sw*poly_ass );
+ accumulateSymmetryFunction( 2 + tmom, i, sw*poly_ass, myrealvec, Tensor( -myrealvec,distance ), myatoms );
// The complex number of which we have to take powers
std::complex<double> com1( distance[0]/dlen ,distance[1]/dlen );
@@ -134,36 +123,24 @@ void Steinhardt::calculateVector( multicolvar::AtomValuePack& myatoms ) const {
myimagvec = (+sw)*dpoly_ass*imag_z*dz + (+dfunc)*distance*itq6 + (+sw)*poly_ass*imag_dz;
// Real part
- myatoms.addValue( 2+tmom+m, sw*tq6 );
- addAtomDerivatives( 2+tmom+m, 0, -myrealvec, myatoms );
- addAtomDerivatives( 2+tmom+m, i, myrealvec, myatoms );
- myatoms.addBoxDerivatives( 2+tmom+m, Tensor( -myrealvec,distance ) );
+ accumulateSymmetryFunction( 2 + tmom + m, i, sw*tq6, myrealvec, Tensor( -myrealvec,distance ), myatoms );
// Imaginary part
- myatoms.addValue( 2+ncomp+tmom+m, sw*itq6 );
- addAtomDerivatives( 2+ncomp+tmom+m, 0, -myimagvec, myatoms );
- addAtomDerivatives( 2+ncomp+tmom+m, i, myimagvec, myatoms );
- myatoms.addBoxDerivatives( 2+ncomp+tmom+m, Tensor( -myimagvec,distance ) );
+ accumulateSymmetryFunction( 2+ncomp+tmom+m, i, sw*itq6, myimagvec, Tensor( -myimagvec,distance ), myatoms );
// Store -m part of vector
double pref=pow(-1.0,m);
// -m part of vector is just +m part multiplied by (-1.0)**m and multiplied by complex
// conjugate of Legendre polynomial
// Real part
- myatoms.addValue( 2+tmom-m, pref*sw*tq6 );
- addAtomDerivatives( 2+tmom-m, 0, -pref*myrealvec, myatoms );
- addAtomDerivatives( 2+tmom-m, i, pref*myrealvec, myatoms );
- myatoms.addBoxDerivatives( 2+tmom-m, pref*Tensor( -myrealvec,distance ) );
+ accumulateSymmetryFunction( 2+tmom-m, i, pref*sw*tq6, pref*myrealvec, pref*Tensor( -myrealvec,distance ), myatoms );
// Imaginary part
- myatoms.addValue( 2+ncomp+tmom-m, -pref*sw*itq6 );
- addAtomDerivatives( 2+ncomp+tmom-m, 0, pref*myimagvec, myatoms );
- addAtomDerivatives( 2+ncomp+tmom-m, i, -pref*myimagvec, myatoms );
- myatoms.addBoxDerivatives( 2+ncomp+tmom-m, pref*Tensor( myimagvec,distance ) );
+ accumulateSymmetryFunction( 2+ncomp+tmom-m, i, -pref*sw*itq6, -pref*myimagvec, pref*Tensor( myimagvec,distance ), myatoms );
}
}
}
// Normalize
updateActiveAtoms( myatoms );
- for(unsigned i=0;i<getNumberOfComponentsInVector();++i) myatoms.getUnderlyingMultiValue().quotientRule( 2+i, nbond, 2+i );
+ for(unsigned i=0;i<getNumberOfComponentsInVector();++i) myatoms.getUnderlyingMultiValue().quotientRule( 2+i, 2+i );
}
double Steinhardt::deriv_poly( const unsigned& m, const double& val, double& df ) const {
diff --git a/src/multicolvar/CenterOfMultiColvar.cpp b/src/multicolvar/CenterOfMultiColvar.cpp
index 2c3604752cf19e2b7dcca7ecb4f149cbc32d0f5d..784b89bacd0cdaf2ee72bd02dc8644f70e2922ac 100644
--- a/src/multicolvar/CenterOfMultiColvar.cpp
+++ b/src/multicolvar/CenterOfMultiColvar.cpp
@@ -113,7 +113,7 @@ CenterOfMultiColvar::CenterOfMultiColvar(const ActionOptions&ao):
}
// We need the derivatives
mycolv->turnOnDerivatives(); addDependency(mycolv);
- mystash = mycolv->buildDataStashes( false, 0.0, NULL );
+ mystash = mycolv->buildDataStashes( NULL );
log.printf(" building center of mass based on weights calculated in multicolvar action named %s \n",mycolv->getLabel().c_str() );
}
diff --git a/src/multicolvar/CoordinationNumbers.cpp b/src/multicolvar/CoordinationNumbers.cpp
index fb54cac9024652ef66f851a44e444873304540e4..67ee34374fd41101f482d2ca16ce59a37db58901 100644
--- a/src/multicolvar/CoordinationNumbers.cpp
+++ b/src/multicolvar/CoordinationNumbers.cpp
@@ -121,26 +121,20 @@ MultiColvarBase(ao)
}
double CoordinationNumbers::compute( const unsigned& tindex, AtomValuePack& myatoms ) const {
- double value=0, dfunc;
-
// Calculate the coordination number
- double d2, sw;
+ double dfunc, d2, sw;
for(unsigned i=1;i<myatoms.getNumberOfAtoms();++i){
- Vector& distance=myatoms.getPosition(i); // getSeparation( myatoms.getPosition(0), myatoms.getPosition(i) );
+ Vector& distance=myatoms.getPosition(i);
if ( (d2=distance[0]*distance[0])<rcut2 &&
(d2+=distance[1]*distance[1])<rcut2 &&
(d2+=distance[2]*distance[2])<rcut2) {
sw = switchingFunction.calculateSqr( d2, dfunc );
-
- value += sw;
- addAtomDerivatives( 1, 0, (-dfunc)*distance, myatoms );
- addAtomDerivatives( 1, i, (dfunc)*distance, myatoms );
- myatoms.addBoxDerivatives( 1, (-dfunc)*Tensor(distance,distance) );
+ accumulateSymmetryFunction( 1, i, sw, (dfunc)*distance, (-dfunc)*Tensor(distance,distance), myatoms );
}
}
- return value;
+ return myatoms.getValue(1);
}
}
diff --git a/src/multicolvar/LocalAverage.cpp b/src/multicolvar/LocalAverage.cpp
index 282b90530781447d62cb5a5ca928125541d07277..462b71fc7f6ea323082313354beb38839d950644 100644
--- a/src/multicolvar/LocalAverage.cpp
+++ b/src/multicolvar/LocalAverage.cpp
@@ -144,33 +144,41 @@ unsigned LocalAverage::getNumberOfQuantities() const {
}
double LocalAverage::compute( const unsigned& tindex, AtomValuePack& myatoms ) const {
- double d2, sw, dfunc, nbond=1; CatomPack atom0, atom1;
+ double d2, sw, dfunc; CatomPack atom0, atom1; MultiValue& myvals = myatoms.getUnderlyingMultiValue();
std::vector<double> values( getBaseMultiColvar(0)->getNumberOfQuantities() );
getVectorForTask( myatoms.getIndex(0), false, values );
+ myvals.addTemporyValue( values[0] );
if( values.size()>2 ){
- for(unsigned j=2;j<values.size();++j) myatoms.addValue( j, values[j] );
+ for(unsigned j=2;j<values.size();++j) myatoms.addValue( j, values[0]*values[j] );
} else {
- myatoms.addValue( 1, values[1] );
+ myatoms.addValue( 1, values[0]*values[1] );
}
if( !doNotCalculateDerivatives() ){
atom0=getCentralAtomPackFromInput( myatoms.getIndex(0) );
- MultiValue& myder=getVectorDerivatives( myatoms.getIndex(0), false );
+ MultiValue& myder=getInputDerivatives( 0, false, myatoms );
if( values.size()>2 ){
for(unsigned j=0;j<myder.getNumberActive();++j){
unsigned jder=myder.getActiveIndex(j);
- for(unsigned k=2;k<values.size();++k) myatoms.addDerivative( k, jder, myder.getDerivative(k,jder) );
+ for(unsigned k=2;k<values.size();++k){
+ myatoms.addDerivative( k, jder, values[0]*myder.getDerivative(k,jder) );
+ myatoms.addDerivative( k, jder, values[k]*myder.getDerivative(0,jder) );
+ }
}
} else {
for(unsigned j=0;j<myder.getNumberActive();++j){
unsigned jder=myder.getActiveIndex(j);
- myatoms.addDerivative( 1, jder, myder.getDerivative(1,jder) );
+ myatoms.addDerivative( 1, jder, values[0]*myder.getDerivative(1,jder) );
+ myatoms.addDerivative( 1, jder, values[1]*myder.getDerivative(0,jder) );
}
}
+ for(unsigned j=0;j<myder.getNumberActive();++j){
+ unsigned jder=myder.getActiveIndex(j); myvals.addTemporyDerivative( jder, myder.getDerivative(0, jder) );
+ }
myder.clearAll();
}
-
+
for(unsigned i=1;i<myatoms.getNumberOfAtoms();++i){
Vector& distance=myatoms.getPosition(i); // getSeparation( myatoms.getPosition(0), myatoms.getPosition(i) );
if ( (d2=distance[0]*distance[0])<rcut2 &&
@@ -181,39 +189,46 @@ double LocalAverage::compute( const unsigned& tindex, AtomValuePack& myatoms ) c
getVectorForTask( myatoms.getIndex(i), false, values );
if( values.size()>2 ){
- for(unsigned j=2;j<values.size();++j) myatoms.addValue( j, sw*values[j] );
+ for(unsigned j=2;j<values.size();++j) myatoms.addValue( j, sw*values[0]*values[j] );
} else {
- myatoms.addValue( 1, sw*values[1] );
+ myatoms.addValue( 1, sw*values[0]*values[1] );
}
- nbond += sw;
+ myvals.addTemporyValue(sw);
if( !doNotCalculateDerivatives() ){
Tensor vir(distance,distance);
- MultiValue& myder=getVectorDerivatives( myatoms.getIndex(i), false );
+ MultiValue& myder=getInputDerivatives( i, false, myatoms );
atom1=getCentralAtomPackFromInput( myatoms.getIndex(i) );
if( values.size()>2 ){
for(unsigned j=0;j<myder.getNumberActive();++j){
unsigned jder=myder.getActiveIndex(j);
- for(unsigned k=2;k<values.size();++k) myatoms.addDerivative( k, jder, sw*myder.getDerivative(k,jder) );
+ for(unsigned k=2;k<values.size();++k){
+ myatoms.addDerivative( k, jder, sw*values[0]*myder.getDerivative(k,jder) );
+ myatoms.addDerivative( k, jder, sw*values[k]*myder.getDerivative(0,jder) );
+ }
}
for(unsigned k=2;k<values.size();++k){
- myatoms.addComDerivatives( k, (-dfunc)*values[k]*distance, atom0 );
- myatoms.addComDerivatives( k, (+dfunc)*values[k]*distance, atom1 );
- myatoms.addBoxDerivatives( k, (-dfunc)*values[k]*vir );
+ myatoms.addComDerivatives( k, (-dfunc)*values[0]*values[k]*distance, atom0 );
+ myatoms.addComDerivatives( k, (+dfunc)*values[0]*values[k]*distance, atom1 );
+ myatoms.addBoxDerivatives( k, (-dfunc)*values[0]*values[k]*vir );
}
} else {
for(unsigned j=0;j<myder.getNumberActive();++j){
unsigned jder=myder.getActiveIndex(j);
- myatoms.addDerivative( 1, jder, sw*myder.getDerivative(1,jder) );
+ myatoms.addDerivative( 1, jder, sw*values[0]*myder.getDerivative(1,jder) );
+ myatoms.addDerivative( 1, jder, sw*values[1]*myder.getDerivative(0,jder) );
}
- myatoms.addComDerivatives( 1, (-dfunc)*values[1]*distance, atom0 );
- myatoms.addComDerivatives( 1, (+dfunc)*values[1]*distance, atom1 );
- myatoms.addBoxDerivatives( 1, (-dfunc)*values[1]*vir );
+ myatoms.addComDerivatives( 1, (-dfunc)*values[0]*values[1]*distance, atom0 );
+ myatoms.addComDerivatives( 1, (+dfunc)*values[0]*values[1]*distance, atom1 );
+ myatoms.addBoxDerivatives( 1, (-dfunc)*values[0]*values[1]*vir );
}
// And the bit we use to average the vector
- myatoms.addComDerivatives( -1, (-dfunc)*distance, atom0 );
- myatoms.addComDerivatives( -1, (+dfunc)*distance, atom1 );
- myatoms.addTemporyBoxDerivatives( (-dfunc)*vir );
+ myatoms.addComDerivatives( -1, (-dfunc)*values[0]*distance, atom0 );
+ myatoms.addComDerivatives( -1, (+dfunc)*values[0]*distance, atom1 );
+ for(unsigned j=0;j<myder.getNumberActive();++j){
+ unsigned jder=myder.getActiveIndex(j); myvals.addTemporyDerivative( jder, sw*myder.getDerivative(0, jder) );
+ }
+ myatoms.addTemporyBoxDerivatives( (-dfunc)*values[0]*vir );
myder.clearAll();
}
}
@@ -223,9 +238,8 @@ double LocalAverage::compute( const unsigned& tindex, AtomValuePack& myatoms ) c
updateActiveAtoms( myatoms );
if( values.size()>2){
double norm=0;
- MultiValue& myvals=myatoms.getUnderlyingMultiValue();
for(unsigned i=2;i<values.size();++i){
- myvals.quotientRule( i, nbond, i );
+ myvals.quotientRule( i, i );
// Calculate length of vector
norm+=myvals.get(i)*myvals.get(i);
}
@@ -237,7 +251,7 @@ double LocalAverage::compute( const unsigned& tindex, AtomValuePack& myatoms ) c
}
}
} else {
- myatoms.getUnderlyingMultiValue().quotientRule( 1, nbond, 1 );
+ myvals.quotientRule( 1, 1 );
}
return myatoms.getValue(1);
diff --git a/src/multicolvar/MultiColvarBase.cpp b/src/multicolvar/MultiColvarBase.cpp
index 673d33cbe5631ed19e1606786f2a6258649d00af..57ae7903f92cf655abb80ff1d85e9d0869752421 100644
--- a/src/multicolvar/MultiColvarBase.cpp
+++ b/src/multicolvar/MultiColvarBase.cpp
@@ -23,7 +23,6 @@
#include "BridgedMultiColvarFunction.h"
#include "ActionVolume.h"
#include "MultiColvarFilter.h"
-#include "MultiColvarFunction.h"
#include "vesselbase/Vessel.h"
#include "vesselbase/BridgeVessel.h"
#include "core/PlumedMain.h"
@@ -134,6 +133,7 @@ bool MultiColvarBase::parseMultiColvarAtomList(const std::string& key, const int
for(unsigned i=0;i<tt.size();++i){ t.push_back( tt[i] ); log.printf("%d ",tt[i].serial() ); }
log.printf("\n");
} else if( found_mcolv==mlabs.size() ){
+ if( checkNumericalDerivatives() ) error("cannot use NUMERICAL_DERIVATIVES keyword with dynamic groups as input");
log.printf(" keyword %s takes dynamic groups of atoms constructed from multicolvars labelled : ", key.c_str() );
for(unsigned i=0;i<mlabs.size();++i) log.printf("%s ",mlabs[i].c_str() );
log.printf("\n");
@@ -389,8 +389,7 @@ void MultiColvarBase::setupMultiColvarBase( const std::vector<AtomNumber>& atoms
}
}
}
- MultiColvarFunction* myfunc = dynamic_cast<MultiColvarFunction*>( this );
- if( myfunc ){ for(unsigned i=0;i<mybasedata.size();++i) mybasedata[i]->resizeTemporyMultiValues(2); }
+ if( mybasemulticolvars.size()>0 ){ for(unsigned i=0;i<mybasedata.size();++i) mybasedata[i]->resizeTemporyMultiValues(2); }
// Copy lists of atoms involved from base multicolvars
std::vector<AtomNumber> tmp_atoms;
@@ -713,15 +712,104 @@ void MultiColvarBase::retrieveAtoms(){
if( !atomsWereRetrieved ){ ActionAtomistic::retrieveAtoms(); atomsWereRetrieved=true; }
}
+void MultiColvarBase::mergeInputDerivatives( const unsigned& ival, const unsigned& start, const unsigned& end,
+ const unsigned& jatom, const std::vector<double>& der,
+ MultiValue& myder, AtomValuePack& myatoms ) const {
+ MultiValue& myvals=myatoms.getUnderlyingMultiValue();
+ plumed_dbg_assert( ival<myatoms.getUnderlyingMultiValue().getNumberOfValues() );
+ plumed_dbg_assert( start<myder.getNumberOfValues() && end<=myder.getNumberOfValues() );
+ plumed_dbg_assert( der.size()==myder.getNumberOfValues() && jatom<myatoms.getNumberOfAtoms() );
+ // Convert input atom to local index
+ unsigned katom = myatoms.getIndex( jatom ); plumed_dbg_assert( atom_lab[katom].first>0 );
+ // Find base colvar
+ unsigned mmc=atom_lab[katom].first - 1; plumed_dbg_assert( mybasemulticolvars[mmc]->taskIsCurrentlyActive( atom_lab[katom].second ) );
+ // Get start of indices for this atom
+ unsigned basen=0; for(unsigned i=0;i<mmc;++i) basen+=mybasemulticolvars[i]->getNumberOfDerivatives() - 9;
+ plumed_dbg_assert( basen%3==0 ); // Check the number of atoms is consistent with input derivatives
+
+ unsigned virbas = myvals.getNumberOfDerivatives()-9;
+ for(unsigned j=0;j<myder.getNumberActive();++j){
+ unsigned jder=myder.getActiveIndex(j);
+ if( jder<mybasemulticolvars[mmc]->getNumberOfDerivatives()-9 ){
+ unsigned kder=basen+jder;
+ for(unsigned icomp=start;icomp<end;++icomp){
+ myvals.addDerivative( ival, kder, der[icomp]*myder.getDerivative( icomp, jder ) );
+ }
+ } else {
+ unsigned kder=virbas + (jder - mybasemulticolvars[mmc]->getNumberOfDerivatives() + 9);
+ for(unsigned icomp=start;icomp<end;++icomp){
+ myvals.addDerivative( ival, kder, der[icomp]*myder.getDerivative( icomp, jder ) );
+ }
+ }
+ }
+}
+
+void MultiColvarBase::addComDerivatives( const int& ival, const unsigned& iatom, const Vector& der, multicolvar::AtomValuePack& myatoms ) const {
+ plumed_dbg_assert( ival<static_cast<int>(myatoms.getUnderlyingMultiValue().getNumberOfValues()) && iatom<myatoms.getNumberOfAtoms() );
+ // Convert input atom to local index
+ unsigned katom = myatoms.getIndex( iatom ); plumed_dbg_assert( atom_lab[katom].first>0 );
+ // Find base colvar
+ unsigned mmc = atom_lab[katom].first - 1; plumed_dbg_assert( mybasemulticolvars[mmc]->taskIsCurrentlyActive( atom_lab[katom].second ) );
+ // Get start of indices for this atom
+ unsigned basen=0; for(unsigned i=0;i<mmc;++i) basen+=(mybasemulticolvars[i]->getNumberOfDerivatives() - 9) / 3;
+ multicolvar::CatomPack atom0=mybasemulticolvars[mmc]->getCentralAtomPack( basen, atom_lab[katom].second );
+ myatoms.addComDerivatives( ival, der, atom0 );
+}
+
+MultiValue& MultiColvarBase::getInputDerivatives( const unsigned& iatom, const bool& normed, const multicolvar::AtomValuePack& myatoms ) const {
+ unsigned katom = myatoms.getIndex(iatom), mmc = atom_lab[katom].first - 1;
+ if( usespecies && !normed && iatom==0 ) return mybasedata[mmc]->getTemporyMultiValue(0);
+
+ unsigned oval=0; if( iatom>0 ) oval=1;
+ MultiValue& myder=mybasedata[mmc]->getTemporyMultiValue(oval);
+ if( myder.getNumberOfValues()!=mybasemulticolvars[mmc]->getNumberOfQuantities() ||
+ myder.getNumberOfDerivatives()!=mybasemulticolvars[mmc]->getNumberOfDerivatives() ){
+ myder.resize( mybasemulticolvars[mmc]->getNumberOfQuantities(), mybasemulticolvars[mmc]->getNumberOfDerivatives() );
+ }
+ mybasedata[mmc]->retrieveDerivatives( atom_lab[katom].second, normed, myder );
+ return myder;
+}
+
+void MultiColvarBase::accumulateSymmetryFunction( const int& ival, const unsigned& iatom, const double& val, const Vector& der, const Tensor& vir, multicolvar::AtomValuePack& myatoms ) const {
+ plumed_dbg_assert( usespecies ); unsigned katom=myatoms.getIndex(0), jatom=myatoms.getIndex(iatom);
+ double weight0=1.0; if( atom_lab[katom].first>0 ) weight0=mybasedata[atom_lab[katom].first-1]->retrieveWeightWithIndex( atom_lab[katom].second );
+ double weighti=1.0; if( atom_lab[jatom].first>0 ) weighti=mybasedata[atom_lab[jatom].first-1]->retrieveWeightWithIndex( atom_lab[jatom].second );
+ // Accumulate the value
+ if( ival<0 ) myatoms.getUnderlyingMultiValue().addTemporyValue( weight0*weighti*val );
+ else myatoms.addValue( ival, weight0*weighti*val );
+
+ // Return if we don't need derivatives
+ if( doNotCalculateDerivatives() ) return ;
+ // And virial
+ if( ival<0 ) myatoms.addTemporyBoxDerivatives( weight0*weighti*vir );
+ else myatoms.addBoxDerivatives( ival, weight0*weighti*vir );
+
+ // Add derivatives of central atom
+ if( atom_lab[katom].first>0 ){
+ addComDerivatives( ival, 0, -weight0*weighti*der, myatoms );
+ std::vector<double> tmpder( mybasemulticolvars[atom_lab[katom].first - 1]->getNumberOfQuantities(), 0. );
+ tmpder[0]=weighti*val; mergeInputDerivatives( ival, 0, 1, 0, tmpder, getInputDerivatives(0, false, myatoms), myatoms );
+ } else {
+ if( ival<0 ) myatoms.addTemporyAtomsDerivatives( 0, -der );
+ else myatoms.addAtomsDerivatives( ival, 0, -der );
+ }
+ // Add derivatives of atom in coordination sphere
+ if( atom_lab[jatom].first>0 ){
+ addComDerivatives( ival, iatom, weight0*weighti*der, myatoms );
+ std::vector<double> tmpder( mybasemulticolvars[atom_lab[katom].first - 1]->getNumberOfQuantities(), 0. );
+ tmpder[0]=weight0*val; mergeInputDerivatives( ival, 0, 1, iatom, tmpder, getInputDerivatives(iatom, false, myatoms), myatoms );
+ } else {
+ if( ival<0 ) myatoms.addTemporyAtomsDerivatives( iatom, der );
+ else myatoms.addAtomsDerivatives( ival, iatom, der );
+ }
+}
+
void MultiColvarBase::addAtomDerivatives( const int& ival, const unsigned& iatom, const Vector& der, multicolvar::AtomValuePack& myatoms ) const {
if( doNotCalculateDerivatives() ) return ;
unsigned jatom=myatoms.getIndex(iatom);
if( atom_lab[jatom].first>0 ){
- unsigned mmc=atom_lab[jatom].first-1;
- unsigned basen=0; for(unsigned i=0;i<mmc;++i) basen+=mybasemulticolvars[i]->getNumberOfAtoms();
- multicolvar::CatomPack atom0=mybasemulticolvars[mmc]->getCentralAtomPack( basen, atom_lab[jatom].second );
- myatoms.addComDerivatives( ival, der, atom0 );
+ addComDerivatives( ival, iatom, der, myatoms );
} else {
if( ival<0 ) myatoms.addTemporyAtomsDerivatives( iatom, der );
else myatoms.addAtomsDerivatives( ival, iatom, der );
@@ -782,7 +870,15 @@ void MultiColvarBase::performTask( const unsigned& task_index, const unsigned& c
}
double MultiColvarBase::doCalculation( const unsigned& taskIndex, AtomValuePack& myatoms ) const {
- if( mybasemulticolvars.size()>0 ) mybasedata[0]->resetTemporyMultiValues();
+ if( usespecies && mybasemulticolvars.size()>0 && atom_lab[myatoms.getIndex(0)].first>0 ){
+ unsigned mmc = atom_lab[0].first - 1;
+ MultiValue& myder=mybasedata[mmc]->getTemporyMultiValue(0);
+ if( myder.getNumberOfValues()!=mybasemulticolvars[mmc]->getNumberOfQuantities() ||
+ myder.getNumberOfDerivatives()!=mybasemulticolvars[mmc]->getNumberOfDerivatives() ){
+ myder.resize( mybasemulticolvars[mmc]->getNumberOfQuantities(), mybasemulticolvars[mmc]->getNumberOfDerivatives() );
+ }
+ mybasedata[mmc]->retrieveDerivatives( atom_lab[myatoms.getIndex(0)].second, false, myder );
+ }
double val=compute( taskIndex, myatoms ); updateActiveAtoms( myatoms );
return val;
}
diff --git a/src/multicolvar/MultiColvarBase.h b/src/multicolvar/MultiColvarBase.h
index 24b967dcd75ca2bb4323d7d459599d7fbc61099f..f5ae649d7477ea61d26abda733cc523e2345bd4d 100644
--- a/src/multicolvar/MultiColvarBase.h
+++ b/src/multicolvar/MultiColvarBase.h
@@ -72,6 +72,8 @@ private:
bool setup_completed;
/// Ensures that retrieving of atoms is only done once per calculation loop
bool atomsWereRetrieved;
+/// Add derivatives of center of mass position
+ void addComDerivatives( const int& ival, const unsigned& iatom, const Vector& der, multicolvar::AtomValuePack& myatoms ) const ;
protected:
/// This is used to keep track of what is calculated where
std::vector< std::pair<unsigned,unsigned> > atom_lab;
@@ -102,6 +104,13 @@ protected:
void setupMultiColvarBase( const std::vector<AtomNumber>& atoms );
/// Add some derivatives to a particular component of a particular atom
void addAtomDerivatives( const int& , const unsigned& , const Vector& , multicolvar::AtomValuePack& ) const ;
+/// Retrieve the input derivatives
+ MultiValue& getInputDerivatives( const unsigned& iatom, const bool& normed, const multicolvar::AtomValuePack& myatoms ) const ;
+/// Add derivative of the input value
+ void mergeInputDerivatives( const unsigned& ival, const unsigned& start, const unsigned& end, const unsigned& jatom,
+ const std::vector<double>& der, MultiValue& myder, AtomValuePack& myatoms ) const ;
+/// This is used to accumulate functions of the coordination sphere. Ensures weights are taken into account
+ void accumulateSymmetryFunction( const int& ival, const unsigned& iatom, const double& val, const Vector& der, const Tensor& vir, multicolvar::AtomValuePack& myatoms ) const ;
/// Set which atoms are to be used to calculate the central atom position
void setAtomsForCentralAtom( const std::vector<bool>& catom_ind );
/// Set the value of the cutoff for the link cells
diff --git a/src/multicolvar/MultiColvarFunction.cpp b/src/multicolvar/MultiColvarFunction.cpp
index 835438aa8a4d306c3f37cd5e3be45d5adb38aa11..d3e48361cb0627edcbf6e5cf287ec0249d3b99ff 100644
--- a/src/multicolvar/MultiColvarFunction.cpp
+++ b/src/multicolvar/MultiColvarFunction.cpp
@@ -65,51 +65,6 @@ void MultiColvarFunction::buildSets(){
mybasedata[0]->resizeTemporyMultiValues( mybasemulticolvars.size() );
}
-MultiValue& MultiColvarFunction::getVectorDerivatives( const unsigned& ind, const bool& normed ) const {
- plumed_dbg_assert( atom_lab[ind].first>0 ); unsigned mmc=atom_lab[ind].first-1;
- plumed_dbg_assert( mybasedata[mmc]->storedValueIsActive( atom_lab[ind].second ) );
- // Get a tempory multi value from the base class
- MultiValue& myder=mybasedata[0]->getTemporyMultiValue();
-
- if( myder.getNumberOfValues()!=mybasemulticolvars[mmc]->getNumberOfQuantities() ||
- myder.getNumberOfDerivatives()!=mybasemulticolvars[mmc]->getNumberOfDerivatives() ){
- myder.resize( mybasemulticolvars[mmc]->getNumberOfQuantities(), mybasemulticolvars[mmc]->getNumberOfDerivatives() );
- }
- mybasedata[mmc]->retrieveDerivatives( atom_lab[ind].second, normed, myder );
- return myder;
-}
-
-void MultiColvarFunction::mergeVectorDerivatives( const unsigned& ival, const unsigned& start, const unsigned& end,
- const unsigned& jatom, const std::vector<double>& der,
- MultiValue& myder, AtomValuePack& myatoms ) const {
- plumed_dbg_assert( ival<myatoms.getUnderlyingMultiValue().getNumberOfValues() );
- plumed_dbg_assert( start<myder.getNumberOfValues() && end<=myder.getNumberOfValues() );
- plumed_dbg_assert( der.size()==myder.getNumberOfValues() && jatom<getFullNumberOfBaseTasks() );
-
- unsigned mmc=atom_lab[jatom].first - 1; plumed_dbg_assert( mybasedata[mmc]->storedValueIsActive( atom_lab[ind].second ) );
-
- // Get start of indices for this atom
- unsigned basen=0; for(unsigned i=0;i<mmc;++i) basen+=3*mybasemulticolvars[i]->getNumberOfAtoms();
-
- MultiValue& myvals=myatoms.getUnderlyingMultiValue();
- // Now get the start of the virial
- unsigned virbas = myvals.getNumberOfDerivatives()-9;
- for(unsigned j=0;j<myder.getNumberActive();++j){
- unsigned jder=myder.getActiveIndex(j);
- if( jder<3*mybasemulticolvars[mmc]->getNumberOfAtoms() ){
- unsigned kder=basen+jder;
- for(unsigned icomp=start;icomp<end;++icomp){
- myvals.addDerivative( ival, kder, der[icomp]*myder.getDerivative( icomp, jder ) );
- }
- } else {
- unsigned kder=virbas + (jder - 3*mybasemulticolvars[mmc]->getNumberOfAtoms());
- for(unsigned icomp=start;icomp<end;++icomp){
- myvals.addDerivative( ival, kder, der[icomp]*myder.getDerivative( icomp, jder ) );
- }
- }
- }
-}
-
}
}
diff --git a/src/multicolvar/MultiColvarFunction.h b/src/multicolvar/MultiColvarFunction.h
index 8c85837dd766c271714d5b8abbb69308bed91aa6..1ec0be5c4dfcf72c63886e0e9bc898135363901c 100644
--- a/src/multicolvar/MultiColvarFunction.h
+++ b/src/multicolvar/MultiColvarFunction.h
@@ -40,12 +40,6 @@ protected:
CatomPack getCentralAtomPackFromInput( const unsigned& ind ) const ;
///
void getVectorForTask( const unsigned& ind, const bool& normed, std::vector<double>& orient0 ) const ;
-///
- MultiValue& getVectorDerivatives( const unsigned& ind, const bool& normed ) const ;
-///
- void mergeVectorDerivatives( const unsigned& ival, const unsigned& start, const unsigned& end,
- const unsigned& jatom, const std::vector<double>& der,
- MultiValue& myder, AtomValuePack& myatoms ) const ;
/// Build sets by taking one multicolvar from each base
void buildSets();
public:
diff --git a/src/multicolvar/NumberOfLinks.cpp b/src/multicolvar/NumberOfLinks.cpp
index dc4e237e691a3aa10c740ba0f7615d7d2ac0bbdf..83820b2dd1fe24eb9c2fb3621511a7eef92f7d21 100644
--- a/src/multicolvar/NumberOfLinks.cpp
+++ b/src/multicolvar/NumberOfLinks.cpp
@@ -161,10 +161,10 @@ double NumberOfLinks::compute( const unsigned& tindex, AtomValuePack& myatoms )
}
if( !doNotCalculateDerivatives() ){
- MultiValue& myder0=getVectorDerivatives( myatoms.getIndex(0), true );
- mergeVectorDerivatives( 1, 2, orient1.size(), myatoms.getIndex(0), orient1, myder0, myatoms );
- MultiValue& myder1=getVectorDerivatives( myatoms.getIndex(1), true );
- mergeVectorDerivatives( 1, 2, orient0.size(), myatoms.getIndex(1), orient0, myder1, myatoms );
+ MultiValue& myder0=getInputDerivatives( 0, true, myatoms );
+ mergeInputDerivatives( 1, 2, orient1.size(), 0, orient1, myder0, myatoms );
+ MultiValue& myder1=getInputDerivatives( 1, true, myatoms );
+ mergeInputDerivatives( 1, 2, orient0.size(), 1, orient0, myder1, myatoms );
}
return dot;
diff --git a/src/tools/MultiValue.cpp b/src/tools/MultiValue.cpp
index 16e60ea161f9e5d76692dd7515addc824cf54668..6cd34b8627f17ba6600e464419b6fd897a7a394f 100644
--- a/src/tools/MultiValue.cpp
+++ b/src/tools/MultiValue.cpp
@@ -56,7 +56,7 @@ void MultiValue::clear( const unsigned& ival ){
}
void MultiValue::clearTemporyDerivatives(){
- unsigned ndert=hasDerivatives.getNumberActive();
+ unsigned ndert=hasDerivatives.getNumberActive(); tmpval=0.;
for(unsigned i=0;i<ndert;++i) tmpder[ hasDerivatives[i] ]=0.;
}
@@ -98,14 +98,14 @@ void MultiValue::copyDerivatives( MultiValue& outvals ){
}
}
-void MultiValue::quotientRule( const unsigned& nder, const double& denom, const unsigned& oder ){
+void MultiValue::quotientRule( const unsigned& nder, const unsigned& oder ){
plumed_dbg_assert( nder<values.size() && oder<values.size() );
if( !hasDerivatives.updateComplete() ) hasDerivatives.updateActiveMembers();
unsigned ndert=hasDerivatives.getNumberActive(); double wpref;
unsigned obase=oder*nderivatives, nbase=nder*nderivatives;
- if( fabs(denom)>epsilon ){ wpref=1.0/denom; }
+ if( fabs(tmpval)>epsilon ){ wpref=1.0/tmpval; }
else{ wpref=1.0; }
double pref = values[nder]*wpref*wpref;
diff --git a/src/tools/MultiValue.h b/src/tools/MultiValue.h
index 911cc6170b8b46b91323d9b6833b883e51d7d031..62beff3aee33da0aad6b33f76ef33c24d13a6f98 100644
--- a/src/tools/MultiValue.h
+++ b/src/tools/MultiValue.h
@@ -38,6 +38,8 @@ private:
unsigned nderivatives;
/// Derivatives
std::vector<double> derivatives;
+/// Tempory value
+ double tmpval;
/// Tempory vector of derivatives (used for calculating quotients
std::vector<double> tmpder;
/// Logical to check if any derivatives were set
@@ -62,6 +64,8 @@ public:
void addValue( const unsigned&, const double& );
/// Add derivative
void addDerivative( const unsigned& , const unsigned& , const double& );
+/// Add to the tempory value
+ void addTemporyValue( const double& val );
/// Add tempory derivatives - this is used for calculating quotients
void addTemporyDerivative( const unsigned& jder, const double& der );
/// Set the value of the derivative
@@ -98,7 +102,7 @@ public:
///
void copyDerivatives( MultiValue& );
///
- void quotientRule( const unsigned& nder, const double& denom, const unsigned& oder );
+ void quotientRule( const unsigned& nder, const unsigned& oder );
};
inline
@@ -135,6 +139,11 @@ void MultiValue::addDerivative( const unsigned& ival, const unsigned& jder, cons
hasDerivatives.activate(jder); derivatives[nderivatives*ival+jder] += der;
}
+inline
+void MultiValue::addTemporyValue( const double& val ){
+ tmpval += val;
+}
+
inline
void MultiValue::addTemporyDerivative( const unsigned& jder, const double& der ){
plumed_dbg_assert( jder<nderivatives ); atLeastOneSet=true;
diff --git a/src/vesselbase/ActionWithVessel.cpp b/src/vesselbase/ActionWithVessel.cpp
index bf7400d71e3f77af1783fe424da3d8a3114e9670..a15e5550d520e2fa0b612f5e3c7c4784c46b0d40 100644
--- a/src/vesselbase/ActionWithVessel.cpp
+++ b/src/vesselbase/ActionWithVessel.cpp
@@ -349,7 +349,7 @@ void ActionWithVessel::calculateAllVessels( const unsigned& taskCode, MultiValue
// Calculate returns a bool that tells us if this particular
// quantity is contributing more than the tolerance
functions[j]->calculate( taskCode, functions[j]->transformDerivatives(taskCode, myvals, bvals), buffer, der_list );
- if( !actionIsBridged && bvals.getNumberActive()>0 ) bvals.clearAll();
+ if( !actionIsBridged ) bvals.clearAll();
}
return;
}
diff --git a/src/vesselbase/StoreDataVessel.cpp b/src/vesselbase/StoreDataVessel.cpp
index 35c62ea641dc0322520aaa84aa80a6038ee41393..0820257ce8112c5c3d0777a322a23233dbe5f166 100644
--- a/src/vesselbase/StoreDataVessel.cpp
+++ b/src/vesselbase/StoreDataVessel.cpp
@@ -209,15 +209,8 @@ void StoreDataVessel::resizeTemporyMultiValues( const unsigned& nvals ){
for(unsigned i=0;i<nvals;++i) my_tmp_vals.push_back( MultiValue(0,0) );
}
-void StoreDataVessel::resetTemporyMultiValues(){
- tmp_index=0;
-}
-
-MultiValue& StoreDataVessel::getTemporyMultiValue(){
- unsigned ival;
- if( tmp_index<my_tmp_vals.size() ) ival=tmp_index;
- else ival=my_tmp_vals.size()-1;
- tmp_index++; return my_tmp_vals[ival];
+MultiValue& StoreDataVessel::getTemporyMultiValue( const unsigned& ind ){
+ plumed_dbg_assert( ind<my_tmp_vals.size() ); return my_tmp_vals[ind];
}
}
diff --git a/src/vesselbase/StoreDataVessel.h b/src/vesselbase/StoreDataVessel.h
index 9425ac2ff19f1ff6f20af84ded204abbdac0dbf6..7c4df37b140f8f65c9b5059daf560978271221cb 100644
--- a/src/vesselbase/StoreDataVessel.h
+++ b/src/vesselbase/StoreDataVessel.h
@@ -127,10 +127,8 @@ public:
ActionWithVessel* getDataUser( const unsigned& );
/// Set the number of tempory multivalues we need
void resizeTemporyMultiValues( const unsigned& nvals );
-/// Reset the tempory multi values at the start of the calculation
- void resetTemporyMultiValues();
/// Return a tempory multi value - we do this so as to avoid vector resizing
- MultiValue& getTemporyMultiValue();
+ MultiValue& getTemporyMultiValue( const unsigned& ind );
};
inline