From dad09a02c350276a01066b188cad32400aeecf93 Mon Sep 17 00:00:00 2001
From: Gareth Tribello <gareth.tribello@gmail.com>
Date: Sun, 26 Apr 2015 14:28:44 +0100
Subject: [PATCH] Added regtest for multirmsd
Changes were also needed as this feature was broken as a consequence
of changes in no-buffer branch. Change to dynamic list deletes
a check that is active when you compile with -DNDEBUG that is not really needed
---
regtest/basic/rt-multirmsd/COLVAR.reference | 6 +
regtest/basic/rt-multirmsd/Makefile | 1 +
regtest/basic/rt-multirmsd/config | 4 +
regtest/basic/rt-multirmsd/deriv.reference | 271 ++++++++++++++++++++
regtest/basic/rt-multirmsd/plumed.dat | 21 ++
regtest/basic/rt-multirmsd/test0.pdb | 17 ++
regtest/basic/rt-multirmsd/test1.pdb | 17 ++
regtest/basic/rt-multirmsd/test2.pdb | 16 ++
src/colvar/MultiRMSD.cpp | 1 -
src/reference/MultiDomainRMSD.cpp | 21 +-
src/reference/ReferenceValuePack.cpp | 2 +-
src/tools/DynamicList.h | 3 -
src/tools/PDB.cpp | 7 +-
13 files changed, 368 insertions(+), 19 deletions(-)
create mode 100644 regtest/basic/rt-multirmsd/COLVAR.reference
create mode 100644 regtest/basic/rt-multirmsd/Makefile
create mode 100644 regtest/basic/rt-multirmsd/config
create mode 100644 regtest/basic/rt-multirmsd/deriv.reference
create mode 100644 regtest/basic/rt-multirmsd/plumed.dat
create mode 100644 regtest/basic/rt-multirmsd/test0.pdb
create mode 100644 regtest/basic/rt-multirmsd/test1.pdb
create mode 100644 regtest/basic/rt-multirmsd/test2.pdb
diff --git a/regtest/basic/rt-multirmsd/COLVAR.reference b/regtest/basic/rt-multirmsd/COLVAR.reference
new file mode 100644
index 000000000..d78fe5a91
--- /dev/null
+++ b/regtest/basic/rt-multirmsd/COLVAR.reference
@@ -0,0 +1,6 @@
+#! FIELDS time rmsd0 rmsds1 drmsd1
+ 0.000000 1.823 1.852 2.257
+ 0.050000 1.835 1.863 2.254
+ 0.100000 1.837 1.874 2.254
+ 0.150000 1.838 1.888 2.270
+ 0.200000 1.838 1.898 2.293
diff --git a/regtest/basic/rt-multirmsd/Makefile b/regtest/basic/rt-multirmsd/Makefile
new file mode 100644
index 000000000..3703b27ce
--- /dev/null
+++ b/regtest/basic/rt-multirmsd/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
diff --git a/regtest/basic/rt-multirmsd/config b/regtest/basic/rt-multirmsd/config
new file mode 100644
index 000000000..4804b7f2a
--- /dev/null
+++ b/regtest/basic/rt-multirmsd/config
@@ -0,0 +1,4 @@
+type=driver
+# this is to test a different name
+arg="--plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f"
+extra_files="../../trajectories/trajectory.xyz"
diff --git a/regtest/basic/rt-multirmsd/deriv.reference b/regtest/basic/rt-multirmsd/deriv.reference
new file mode 100644
index 000000000..175a5fef5
--- /dev/null
+++ b/regtest/basic/rt-multirmsd/deriv.reference
@@ -0,0 +1,271 @@
+#! FIELDS time parameter rmsd0 rmsds1 drmsd1
+ 0.000000 0 0.0241 0.0690 0.0714
+ 0.000000 1 -0.0212 -0.0468 -0.0636
+ 0.000000 2 -0.0997 -0.0748 -0.1659
+ 0.000000 3 -0.0275 -0.1153 -0.0579
+ 0.000000 4 0.0388 0.0804 0.0692
+ 0.000000 5 -0.1152 -0.1129 -0.0478
+ 0.000000 6 0.0298 0.0463 0.0593
+ 0.000000 7 -0.0281 -0.0337 -0.0605
+ 0.000000 8 0.0342 0.1877 0.0917
+ 0.000000 9 0.0324 0.0242 0.0634
+ 0.000000 10 0.0256 -0.0197 0.0576
+ 0.000000 11 -0.0386 -0.0584 -0.0417
+ 0.000000 12 -0.0471 -0.0094 -0.0687
+ 0.000000 13 0.0287 -0.0196 0.0537
+ 0.000000 14 0.0286 -0.0146 0.0973
+ 0.000000 15 -0.0435 -0.0191 -0.0675
+ 0.000000 16 -0.0226 -0.0722 -0.0563
+ 0.000000 17 0.0622 0.0310 0.0663
+ 0.000000 18 0.0318 0.0155 0.0297
+ 0.000000 19 -0.0212 -0.0734 -0.0507
+ 0.000000 20 0.1286 0.0695 0.0346
+ 0.000000 21 -0.0242 -0.0148 -0.0441
+ 0.000000 22 -0.0570 -0.0355 -0.0699
+ 0.000000 23 0.1321 0.0723 0.0284
+ 0.000000 24 0.0226 0.0245 0.0280
+ 0.000000 25 0.0020 0.0091 0.0054
+ 0.000000 26 -0.1093 -0.0822 0.0337
+ 0.000000 27 -0.0184 -0.0218 -0.0410
+ 0.000000 28 0.0424 0.0456 0.0810
+ 0.000000 29 -0.1152 -0.0829 0.0351
+ 0.000000 30 0.0117 0.0175 0.0239
+ 0.000000 31 -0.0175 0.0128 -0.0066
+ 0.000000 32 0.0006 -0.0013 -0.0192
+ 0.000000 33 0.0263 0.0132 0.0361
+ 0.000000 34 0.0376 0.0559 0.0256
+ 0.000000 35 -0.0589 -0.0375 -0.0977
+ 0.000000 36 -0.0251 -0.0243 -0.0378
+ 0.000000 37 0.0347 0.0561 0.0283
+ 0.000000 38 -0.0002 0.0010 -0.0164
+ 0.000000 39 -0.0178 -0.0218 -0.0331
+ 0.000000 40 -0.0203 0.0171 -0.0065
+ 0.000000 41 0.0463 0.0299 -0.0415
+ 0.000000 42 0.0249 0.0163 0.0382
+ 0.000000 43 -0.0218 0.0237 -0.0067
+ 0.000000 44 0.1046 0.0732 0.0430
+ 0.000000 45 -0.1710 -0.1869 -0.2966
+ 0.000000 46 0.0311 0.0414 0.0722
+ 0.000000 47 0.0459 -0.0597 0.1272
+ 0.000000 48 0.0311 0.1260 0.0722
+ 0.000000 49 -0.2232 -0.5119 -0.6806
+ 0.000000 50 0.3591 0.3565 -0.0881
+ 0.000000 51 0.0459 -0.0398 0.1272
+ 0.000000 52 0.3591 0.3672 -0.0881
+ 0.000000 53 -1.5345 -1.0892 -1.6681
+ 0.050000 0 0.0288 0.0753 0.0809
+ 0.050000 1 -0.0210 -0.0496 -0.0641
+ 0.050000 2 -0.0995 -0.0725 -0.0422
+ 0.050000 3 -0.0265 -0.1180 -0.0575
+ 0.050000 4 0.0398 0.0798 0.0718
+ 0.050000 5 -0.1164 -0.1153 -0.0519
+ 0.050000 6 0.0298 0.0427 0.0601
+ 0.050000 7 -0.0251 -0.0302 -0.0554
+ 0.050000 8 0.0337 0.1878 0.0913
+ 0.050000 9 0.0343 0.0252 0.0677
+ 0.050000 10 0.0245 -0.0201 0.0556
+ 0.050000 11 -0.0392 -0.0590 -0.0433
+ 0.050000 12 -0.0483 -0.0104 -0.0727
+ 0.050000 13 0.0252 -0.0213 0.0470
+ 0.050000 14 0.0286 -0.0146 0.0998
+ 0.050000 15 -0.0474 -0.0223 -0.0785
+ 0.050000 16 -0.0215 -0.0712 -0.0549
+ 0.050000 17 0.0631 0.0310 -0.0537
+ 0.050000 18 0.0293 0.0131 0.0242
+ 0.050000 19 -0.0219 -0.0734 -0.0524
+ 0.050000 20 0.1297 0.0695 0.0353
+ 0.050000 21 -0.0239 -0.0148 -0.0445
+ 0.050000 22 -0.0553 -0.0334 -0.0666
+ 0.050000 23 0.1308 0.0716 0.0275
+ 0.050000 24 0.0196 0.0227 0.0239
+ 0.050000 25 0.0021 0.0096 0.0063
+ 0.050000 26 -0.1103 -0.0833 0.0300
+ 0.050000 27 -0.0173 -0.0204 -0.0391
+ 0.050000 28 0.0414 0.0454 0.0806
+ 0.050000 29 -0.1172 -0.0838 0.0316
+ 0.050000 30 0.0071 0.0150 0.0184
+ 0.050000 31 -0.0212 0.0105 -0.0117
+ 0.050000 32 -0.0014 -0.0029 -0.0227
+ 0.050000 33 0.0253 0.0136 0.0361
+ 0.050000 34 0.0367 0.0552 0.0244
+ 0.050000 35 -0.0548 -0.0347 -0.0921
+ 0.050000 36 -0.0242 -0.0226 -0.0356
+ 0.050000 37 0.0360 0.0569 0.0306
+ 0.050000 38 0.0022 0.0030 -0.0123
+ 0.050000 39 -0.0131 -0.0175 -0.0255
+ 0.050000 40 -0.0202 0.0170 -0.0070
+ 0.050000 41 0.0463 0.0302 -0.0407
+ 0.050000 42 0.0265 0.0186 0.0421
+ 0.050000 43 -0.0195 0.0248 -0.0042
+ 0.050000 44 0.1043 0.0730 0.0434
+ 0.050000 45 -0.1747 -0.1912 -0.3127
+ 0.050000 46 0.0287 0.0303 0.0667
+ 0.050000 47 0.0538 -0.0580 0.0109
+ 0.050000 48 0.0287 0.1181 0.0667
+ 0.050000 49 -0.2165 -0.5115 -0.6699
+ 0.050000 50 0.3507 0.3443 -0.0836
+ 0.050000 51 0.0538 -0.0363 0.0109
+ 0.050000 52 0.3507 0.3538 -0.0836
+ 0.050000 53 -1.5506 -1.0987 -1.6614
+ 0.100000 0 0.0340 0.0849 0.0923
+ 0.100000 1 -0.0194 -0.0474 -0.0602
+ 0.100000 2 -0.0985 -0.0694 -0.0390
+ 0.100000 3 -0.0284 -0.1266 -0.0628
+ 0.100000 4 0.0386 0.0724 0.0685
+ 0.100000 5 -0.1168 -0.1176 -0.0542
+ 0.100000 6 0.0307 0.0417 0.0624
+ 0.100000 7 -0.0215 -0.0250 -0.0489
+ 0.100000 8 0.0341 0.1870 0.0918
+ 0.100000 9 0.0377 0.0262 0.0731
+ 0.100000 10 0.0240 -0.0202 0.0541
+ 0.100000 11 -0.0400 -0.0593 -0.0459
+ 0.100000 12 -0.0502 -0.0121 -0.0781
+ 0.100000 13 0.0233 -0.0218 0.0444
+ 0.100000 14 0.0266 -0.0155 0.0967
+ 0.100000 15 -0.0502 -0.0249 -0.0869
+ 0.100000 16 -0.0229 -0.0715 -0.0579
+ 0.100000 17 0.0651 0.0320 -0.0493
+ 0.100000 18 0.0264 0.0104 0.0178
+ 0.100000 19 -0.0221 -0.0733 -0.0499
+ 0.100000 20 0.1296 0.0688 0.0345
+ 0.100000 21 -0.0207 -0.0117 -0.0391
+ 0.100000 22 -0.0534 -0.0318 -0.0636
+ 0.100000 23 0.1321 0.0721 0.0291
+ 0.100000 24 0.0182 0.0225 0.0230
+ 0.100000 25 0.0031 0.0106 0.0080
+ 0.100000 26 -0.1100 -0.0827 0.0300
+ 0.100000 27 -0.0172 -0.0195 -0.0381
+ 0.100000 28 0.0419 0.0456 0.0225
+ 0.100000 29 -0.1185 -0.0842 0.0293
+ 0.100000 30 0.0074 0.0159 0.0198
+ 0.100000 31 -0.0241 0.0088 -0.0154
+ 0.100000 32 -0.0025 -0.0036 -0.0242
+ 0.100000 33 0.0240 0.0133 0.0350
+ 0.100000 34 0.0340 0.0534 0.0757
+ 0.100000 35 -0.0537 -0.0337 -0.0903
+ 0.100000 36 -0.0271 -0.0238 -0.0392
+ 0.100000 37 0.0343 0.0557 0.0283
+ 0.100000 38 0.0048 0.0049 -0.0079
+ 0.100000 39 -0.0105 -0.0151 -0.0213
+ 0.100000 40 -0.0203 0.0169 -0.0073
+ 0.100000 41 0.0456 0.0297 -0.0413
+ 0.100000 42 0.0260 0.0188 0.0420
+ 0.100000 43 -0.0154 0.0276 0.0018
+ 0.100000 44 0.1023 0.0715 0.0409
+ 0.100000 45 -0.1864 -0.2119 -0.3427
+ 0.100000 46 0.0305 0.0229 0.0187
+ 0.100000 47 0.0609 -0.0585 0.0159
+ 0.100000 48 0.0305 0.1119 0.0187
+ 0.100000 49 -0.2039 -0.4988 -0.6507
+ 0.100000 50 0.3441 0.3297 0.1343
+ 0.100000 51 0.0609 -0.0352 0.0159
+ 0.100000 52 0.3441 0.3396 0.1343
+ 0.100000 53 -1.5538 -1.0985 -1.6526
+ 0.150000 0 0.0387 0.0939 0.1025
+ 0.150000 1 -0.0179 -0.0441 -0.0553
+ 0.150000 2 -0.0965 -0.0648 -0.1572
+ 0.150000 3 -0.0306 -0.1354 -0.0683
+ 0.150000 4 0.0375 0.0644 0.0640
+ 0.150000 5 -0.1176 -0.1223 -0.0572
+ 0.150000 6 0.0319 0.0415 0.0650
+ 0.150000 7 -0.0182 -0.0203 -0.0430
+ 0.150000 8 0.0356 0.1871 0.0936
+ 0.150000 9 0.0415 0.0276 0.0787
+ 0.150000 10 0.0235 -0.0200 0.0513
+ 0.150000 11 -0.0419 -0.0600 -0.0508
+ 0.150000 12 -0.0516 -0.0133 -0.0827
+ 0.150000 13 0.0233 -0.0207 0.0452
+ 0.150000 14 0.0254 -0.0155 0.0944
+ 0.150000 15 -0.0531 -0.0273 -0.0951
+ 0.150000 16 -0.0250 -0.0717 -0.0623
+ 0.150000 17 0.0661 0.0324 0.0772
+ 0.150000 18 0.0232 0.0077 0.0115
+ 0.150000 19 -0.0233 -0.0735 -0.0512
+ 0.150000 20 0.1289 0.0678 0.0329
+ 0.150000 21 -0.0177 -0.0084 -0.0329
+ 0.150000 22 -0.0531 -0.0317 -0.0631
+ 0.150000 23 0.1331 0.0723 0.0301
+ 0.150000 24 0.0183 0.0236 0.0247
+ 0.150000 25 0.0049 0.0115 0.0103
+ 0.150000 26 -0.1086 -0.0808 0.0327
+ 0.150000 27 -0.0173 -0.0188 -0.0370
+ 0.150000 28 0.0423 0.0455 0.0229
+ 0.150000 29 -0.1185 -0.0837 0.0287
+ 0.150000 30 0.0100 0.0182 0.0242
+ 0.150000 31 -0.0259 0.0078 -0.0175
+ 0.150000 32 -0.0027 -0.0032 -0.0234
+ 0.150000 33 0.0232 0.0130 0.0340
+ 0.150000 34 0.0325 0.0522 0.0734
+ 0.150000 35 -0.0546 -0.0339 -0.0911
+ 0.150000 36 -0.0301 -0.0252 -0.0427
+ 0.150000 37 0.0314 0.0535 0.0243
+ 0.150000 38 0.0070 0.0063 -0.0045
+ 0.150000 39 -0.0112 -0.0152 -0.0219
+ 0.150000 40 -0.0194 0.0175 -0.0054
+ 0.150000 41 0.0449 0.0290 -0.0422
+ 0.150000 42 0.0248 0.0180 0.0401
+ 0.150000 43 -0.0127 0.0295 0.0063
+ 0.150000 44 0.0993 0.0694 0.0369
+ 0.150000 45 -0.2038 -0.2394 -0.3816
+ 0.150000 46 0.0311 0.0157 0.0143
+ 0.150000 47 0.0745 -0.0579 0.1885
+ 0.150000 48 0.0311 0.1050 0.0143
+ 0.150000 49 -0.1971 -0.4861 -0.6372
+ 0.150000 50 0.3474 0.3224 0.1391
+ 0.150000 51 0.0745 -0.0341 0.1885
+ 0.150000 52 0.3474 0.3319 0.1391
+ 0.150000 53 -1.5432 -1.0925 -1.6450
+ 0.200000 0 0.0413 0.0982 0.1068
+ 0.200000 1 -0.0182 -0.0461 -0.0553
+ 0.200000 2 -0.0956 -0.0625 -0.1535
+ 0.200000 3 -0.0323 -0.1411 -0.0724
+ 0.200000 4 0.0379 0.0619 0.0632
+ 0.200000 5 -0.1191 -0.1267 -0.0605
+ 0.200000 6 0.0332 0.0429 0.0670
+ 0.200000 7 -0.0154 -0.0159 -0.0380
+ 0.200000 8 0.0373 0.1892 0.0960
+ 0.200000 9 0.0434 0.0282 0.0809
+ 0.200000 10 0.0241 -0.0185 0.0511
+ 0.200000 11 -0.0441 -0.0609 -0.0549
+ 0.200000 12 -0.0520 -0.0138 -0.0840
+ 0.200000 13 0.0250 -0.0183 0.0478
+ 0.200000 14 0.0263 -0.0147 0.0959
+ 0.200000 15 -0.0539 -0.0283 -0.0983
+ 0.200000 16 -0.0281 -0.0723 -0.0689
+ 0.200000 17 0.0663 0.0322 0.0770
+ 0.200000 18 0.0202 0.0053 0.0058
+ 0.200000 19 -0.0252 -0.0734 -0.0507
+ 0.200000 20 0.1290 0.0671 0.0316
+ 0.200000 21 -0.0156 -0.0058 -0.0281
+ 0.200000 22 -0.0532 -0.0327 -0.0643
+ 0.200000 23 0.1335 0.0726 0.0307
+ 0.200000 24 0.0203 0.0257 0.0287
+ 0.200000 25 0.0056 0.0114 0.0109
+ 0.200000 26 -0.1061 -0.0780 -0.0132
+ 0.200000 27 -0.0165 -0.0176 -0.0345
+ 0.200000 28 0.0437 0.0456 0.0242
+ 0.200000 29 -0.1168 -0.0823 0.0304
+ 0.200000 30 0.0131 0.0207 0.0291
+ 0.200000 31 -0.0270 0.0068 -0.0187
+ 0.200000 32 -0.0031 -0.0030 -0.0231
+ 0.200000 33 0.0224 0.0126 0.0328
+ 0.200000 34 0.0319 0.0515 0.0724
+ 0.200000 35 -0.0553 -0.0342 -0.0914
+ 0.200000 36 -0.0333 -0.0270 -0.0464
+ 0.200000 37 0.0289 0.0515 0.0208
+ 0.200000 38 0.0075 0.0062 -0.0045
+ 0.200000 39 -0.0148 -0.0174 -0.0264
+ 0.200000 40 -0.0181 0.0183 -0.0028
+ 0.200000 41 0.0448 0.0286 0.0084
+ 0.200000 42 0.0244 0.0176 0.0391
+ 0.200000 43 -0.0119 0.0301 0.0083
+ 0.200000 44 0.0955 0.0666 0.0311
+ 0.200000 45 -0.2170 -0.2603 -0.4071
+ 0.200000 46 0.0322 0.0147 0.0117
+ 0.200000 47 0.0892 -0.0560 0.2214
+ 0.200000 48 0.0322 0.1039 0.0117
+ 0.200000 49 -0.2016 -0.4799 -0.6402
+ 0.200000 50 0.3564 0.3212 0.1430
+ 0.200000 51 0.0892 -0.0326 0.2214
+ 0.200000 52 0.3564 0.3288 0.1430
+ 0.200000 53 -1.5257 -1.0834 -1.6404
diff --git a/regtest/basic/rt-multirmsd/plumed.dat b/regtest/basic/rt-multirmsd/plumed.dat
new file mode 100644
index 000000000..3b8dc02bd
--- /dev/null
+++ b/regtest/basic/rt-multirmsd/plumed.dat
@@ -0,0 +1,21 @@
+rmsd0: MULTI-RMSD TYPE=MULTI-OPTIMAL REFERENCE=test0.pdb
+rmsds1: MULTI-RMSD TYPE=MULTI-SIMPLE REFERENCE=test1.pdb
+drmsd1: MULTI-RMSD TYPE=MULTI-DRMSD REFERENCE=test2.pdb
+
+PRINT ...
+ STRIDE=1
+ ARG=*
+ FILE=COLVAR FMT=%6.3f
+... PRINT
+
+DUMPDERIVATIVES ARG=rmsd0,rmsds1,drmsd1 FILE=deriv FMT=%8.4f
+
+#rmsd0n: MULTI-RMSD TYPE=MULTI-OPTIMAL REFERENCE=test0.pdb NUMERICAL_DERIVATIVES
+#rmsds1n: MULTI-RMSD TYPE=MULTI-SIMPLE REFERENCE=test1.pdb NUMERICAL_DERIVATIVES
+#drmsd1n: MULTI-RMSD TYPE=MULTI-DRMSD REFERENCE=test2.pdb NUMERICAL_DERIVATIVES
+#
+#DUMPDERIVATIVES ARG=rmsd0,rmsd0n,rmsds1,rmsds1n,drmsd1,drmsd1n FILE=deriv2 FMT=%8.4f
+
+ENDPLUMED
+
+text here should be ignored
diff --git a/regtest/basic/rt-multirmsd/test0.pdb b/regtest/basic/rt-multirmsd/test0.pdb
new file mode 100644
index 000000000..c99361e98
--- /dev/null
+++ b/regtest/basic/rt-multirmsd/test0.pdb
@@ -0,0 +1,17 @@
+ATOM 2 O ALA 2 -0.926 -2.447 -0.497 1.00 1.00 DIA O
+ATOM 4 HNT ALA 2 0.533 -0.396 1.184 1.00 1.00 DIA H
+ATOM 6 HT1 ALA 2 -0.216 -2.590 1.371 1.00 1.00 DIA H
+ATOM 7 HT2 ALA 2 -0.309 -1.255 2.315 1.00 1.00 DIA H
+ATOM 8 HT3 ALA 2 -1.480 -1.560 1.212 1.00 1.00 DIA H
+ATOM 9 CAY ALA 2 -0.096 2.144 -0.669 1.00 1.00 DIA C
+ATOM 10 HY1 ALA 2 0.871 2.385 -0.588 1.00 1.00 DIA H
+TER
+ATOM 12 HY3 ALA 2 -0.520 2.679 -1.400 1.00 1.00 DIA H
+ATOM 14 OY ALA 2 -1.139 0.931 -0.973 1.00 1.00 DIA O
+ATOM 16 HN ALA 2 1.713 1.021 -0.873 1.00 1.00 DIA H
+ATOM 18 HA ALA 2 0.099 -0.774 -2.218 1.00 1.00 DIA H
+ATOM 19 CB ALA 2 2.063 -1.223 -1.276 1.00 1.00 DIA C
+ATOM 20 HB1 ALA 2 2.670 -0.716 -2.057 1.00 1.00 DIA H
+ATOM 21 HB2 ALA 2 2.556 -1.051 -0.295 1.00 1.00 DIA H
+ATOM 22 HB3 ALA 2 2.070 -2.314 -1.490 1.00 1.00 DIA H
+TER
diff --git a/regtest/basic/rt-multirmsd/test1.pdb b/regtest/basic/rt-multirmsd/test1.pdb
new file mode 100644
index 000000000..1c044b6a5
--- /dev/null
+++ b/regtest/basic/rt-multirmsd/test1.pdb
@@ -0,0 +1,17 @@
+ATOM 2 O ALA 2 -0.926 -2.447 -0.497 1.00 1.01 DIA O
+ATOM 4 HNT ALA 2 0.533 -0.396 1.184 1.00 1.00 DIA H
+ATOM 6 HT1 ALA 2 -0.216 -2.590 1.371 1.00 1.00 DIA H
+TER
+ATOM 7 HT2 ALA 2 -0.309 -1.255 2.315 1.00 1.00 DIA H
+ATOM 8 HT3 ALA 2 -1.480 -1.560 1.212 1.00 1.00 DIA H
+ATOM 9 CAY ALA 2 -0.096 2.144 -0.669 1.00 1.00 DIA C
+ATOM 10 HY1 ALA 2 0.871 2.385 -0.588 1.00 1.00 DIA H
+ATOM 12 HY3 ALA 2 -0.520 2.679 -1.400 1.00 1.00 DIA H
+ATOM 14 OY ALA 2 -1.139 0.931 -0.973 1.00 1.00 DIA O
+ATOM 16 HN ALA 2 1.713 1.021 -0.873 1.00 1.00 DIA H
+ATOM 18 HA ALA 2 0.099 -0.774 -2.218 1.00 1.00 DIA H
+ATOM 19 CB ALA 2 2.063 -1.223 -1.276 1.00 0.99 DIA C
+ATOM 20 HB1 ALA 2 2.670 -0.716 -2.057 1.00 1.00 DIA H
+ATOM 21 HB2 ALA 2 2.556 -1.051 -0.295 1.00 1.00 DIA H
+ATOM 22 HB3 ALA 2 2.070 -2.314 -1.490 1.00 1.00 DIA H
+TER
diff --git a/regtest/basic/rt-multirmsd/test2.pdb b/regtest/basic/rt-multirmsd/test2.pdb
new file mode 100644
index 000000000..c47e6f503
--- /dev/null
+++ b/regtest/basic/rt-multirmsd/test2.pdb
@@ -0,0 +1,16 @@
+ATOM 2 O ALA 2 -0.926 -2.447 -0.497 1.00 1.00 DIA O
+ATOM 4 HNT ALA 2 0.533 -0.396 1.184 1.00 1.00 DIA H
+ATOM 6 HT1 ALA 2 -0.216 -2.590 1.371 1.00 1.00 DIA H
+ATOM 7 HT2 ALA 2 -0.309 -1.255 2.315 1.00 1.00 DIA H
+ATOM 8 HT3 ALA 2 -1.480 -1.560 1.212 1.00 1.00 DIA H
+ATOM 9 CAY ALA 2 -0.096 2.144 -0.669 1.00 1.00 DIA C
+TER
+ATOM 10 HY1 ALA 2 0.871 2.385 -0.588 1.00 1.00 DIA H
+ATOM 12 HY3 ALA 2 -0.520 2.679 -1.400 1.00 1.00 DIA H
+ATOM 14 OY ALA 2 -1.139 0.931 -0.973 1.00 1.00 DIA O
+ATOM 16 HN ALA 2 1.713 1.021 -0.873 1.00 1.00 DIA H
+ATOM 18 HA ALA 2 0.099 -0.774 -2.218 1.00 1.00 DIA H
+ATOM 19 CB ALA 2 2.063 -1.223 -1.276 1.00 1.00 DIA C
+ATOM 20 HB1 ALA 2 2.670 -0.716 -2.057 1.00 1.00 DIA H
+ATOM 21 HB2 ALA 2 2.556 -1.051 -0.295 1.00 1.00 DIA H
+ATOM 22 HB3 ALA 2 2.070 -2.314 -1.490 1.00 1.00 DIA H
diff --git a/src/colvar/MultiRMSD.cpp b/src/colvar/MultiRMSD.cpp
index a52aa688e..ecd428f2c 100644
--- a/src/colvar/MultiRMSD.cpp
+++ b/src/colvar/MultiRMSD.cpp
@@ -149,7 +149,6 @@ PLUMED_COLVAR_INIT(ao),squared(false),myvals(1,0), mypack(0,0,myvals)
std::vector<AtomNumber> atoms;
rmsd->getAtomRequests( atoms );
-// rmsd->setNumberOfAtoms( atoms.size() );
requestAtoms( atoms );
myvals.resize( 1, 3*atoms.size()+9 );
diff --git a/src/reference/MultiDomainRMSD.cpp b/src/reference/MultiDomainRMSD.cpp
index 168f7eada..4908d7ce5 100644
--- a/src/reference/MultiDomainRMSD.cpp
+++ b/src/reference/MultiDomainRMSD.cpp
@@ -88,20 +88,19 @@ void MultiDomainRMSD::setReferenceAtoms( const std::vector<Vector>& conf, const
}
double MultiDomainRMSD::calculate( const std::vector<Vector>& pos, const Pbc& pbc, ReferenceValuePack& myder, const bool& squared ) const {
- //clearDerivatives();
- double totd=0.; Tensor tvirial; std::vector<Vector> mypos;
- MultiValue tvals( 1, myder.getNumberOfDerivatives() ); ReferenceValuePack tder( 0, 0, tvals );
+ double totd=0.; Tensor tvirial; std::vector<Vector> mypos; MultiValue tvals( 1, 3*pos.size()+9 );
+ ReferenceValuePack tder( 0, getNumberOfAtoms(), tvals ); tder.setValIndex(0);
+
for(unsigned i=0;i<domains.size();++i){
// Must extract appropriate positions here
- mypos.resize( blocks[i+1] - blocks[i] );
- unsigned n=0; tder.resize( 0, mypos.size() );
- if( pca ) domains[i]->setupPCAStorage( tder );
- for(unsigned j=blocks[i];j<blocks[i+1];++j){ tder.setAtomIndex(n,j); mypos[n]=pos[j]; n++; }
-
+ mypos.resize( blocks[i+1] - blocks[i] );
+ if( pca ) domains[i]->setupPCAStorage( tder );
+ unsigned n=0; for(unsigned j=blocks[i];j<blocks[i+1];++j){ tder.setAtomIndex(n,j); mypos[n]=pos[j]; n++; }
+ for(unsigned k=n;k<getNumberOfAtoms();++k) tder.setAtomIndex(k,pos.size()+1);
// This actually does the calculation
totd += weights[i]*domains[i]->calculate( mypos, pbc, tder, true );
// Now merge the derivative
- myder.copyScaledDerivatives( 1, weights[i], tvals );
+ myder.copyScaledDerivatives( 0, weights[i], tvals );
// If PCA copy PCA stuff
if(pca){
unsigned n=0;
@@ -118,7 +117,7 @@ double MultiDomainRMSD::calculate( const std::vector<Vector>& pos, const Pbc& pb
// Make sure virial status is set correctly in output derivative pack
// This is only done here so I do this by using class friendship
if( tder.virialWasSet() ) myder.boxWasSet=true;
- // And clear
+ // Clear the tempory derivatives ready for next loop
tder.clear();
}
if( !squared ){
@@ -185,7 +184,7 @@ double MultiDomainRMSD::projectAtomicDisplacementOnVector( const unsigned& iv, c
domains[i]->projectAtomicDisplacementOnVector( iv, tvecs, mypos, tder );
// And derivatives
- mypack.copyScaledDerivatives( 1, weights[i], tvals );
+ mypack.copyScaledDerivatives( 0, weights[i], tvals );
}
return totd;
diff --git a/src/reference/ReferenceValuePack.cpp b/src/reference/ReferenceValuePack.cpp
index bf4d3eb61..ec319149f 100644
--- a/src/reference/ReferenceValuePack.cpp
+++ b/src/reference/ReferenceValuePack.cpp
@@ -41,7 +41,7 @@ void ReferenceValuePack::updateDynamicLists(){
for(unsigned i=0;i<numberOfArgs;++i) myvals.putIndexInActiveArray( i );
for(unsigned i=0;i<atom_indices.size();++i){
unsigned nbase = numberOfArgs + 3*atom_indices[i];
- if( myvals.isActive( nbase ) ){
+ if( atom_indices[i]<atom_indices.size() && myvals.isActive( nbase ) ){
myvals.putIndexInActiveArray( nbase+0 ); myvals.putIndexInActiveArray( nbase+1 ); myvals.putIndexInActiveArray( nbase+2 );
}
}
diff --git a/src/tools/DynamicList.h b/src/tools/DynamicList.h
index dce74d156..482cc3b95 100644
--- a/src/tools/DynamicList.h
+++ b/src/tools/DynamicList.h
@@ -277,9 +277,6 @@ void DynamicList<T>::deactivateAll(){
allWereDeactivated=true; allWereActivated=false;
for(unsigned i=0;i<nactive;++i) onoff[ active[i] ]= 0;
nactive=0;
-#ifndef NDEBUG
- for(unsigned i=0;i<onoff.size();++i) plumed_dbg_assert( onoff[i]==0 );
-#endif
}
template <typename T>
diff --git a/src/tools/PDB.cpp b/src/tools/PDB.cpp
index 140980930..be5e34dfd 100644
--- a/src/tools/PDB.cpp
+++ b/src/tools/PDB.cpp
@@ -95,7 +95,7 @@ bool PDB::readFromFilepointer(FILE *fp,bool naturalUnits,double scale){
bool file_is_alive=false;
if(naturalUnits) scale=1.0;
string line;
- fpos_t pos;
+ fpos_t pos; bool between_ters=true;
while(Tools::getline(fp,line)){
//cerr<<line<<"\n";
fgetpos (fp,&pos);
@@ -112,7 +112,7 @@ bool PDB::readFromFilepointer(FILE *fp,bool naturalUnits,double scale){
string occ=line.substr(54,6);
string bet=line.substr(60,6);
Tools::trim(record);
- if(record=="TER"){ block_ends.push_back( positions.size() ); }
+ if(record=="TER"){ between_ters=false; block_ends.push_back( positions.size() ); }
if(record=="END"){ file_is_alive=true; break;}
if(record=="ENDMDL"){ file_is_alive=true; break;}
if(record=="REMARK"){
@@ -120,6 +120,7 @@ bool PDB::readFromFilepointer(FILE *fp,bool naturalUnits,double scale){
addRemark( v1 );
}
if(record=="ATOM" || record=="HETATM"){
+ between_ters=true;
AtomNumber a; unsigned resno;
double o,b;
Vector p;
@@ -145,7 +146,7 @@ bool PDB::readFromFilepointer(FILE *fp,bool naturalUnits,double scale){
residuenames.push_back(residuename);
}
}
- block_ends.push_back( positions.size() );
+ if( between_ters ) block_ends.push_back( positions.size() );
return file_is_alive;
}
--
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