From 191509ca1c39dcce9ef2bbc4c4000133341c06e6 Mon Sep 17 00:00:00 2001
From: Gareth Tribello <gareth.tribello@gmail.com>
Date: Wed, 22 Feb 2017 08:43:32 +0000
Subject: [PATCH] Fixed histogram on sphere option
---
.../rt-spherical-integral/Makefile | 1 +
.../rt-spherical-integral/colvar.reference | 6 +
.../rt-spherical-integral/config | 3 +
.../rt-spherical-integral/forces.reference | 1015 +++++++++++++++++
.../rt-spherical-integral/plumed.dat | 8 +
.../rt-spherical-integral/trajectory.xyz | 1015 +++++++++++++++++
src/analysis/Histogram.cpp | 92 +-
src/crystallization/BondOrientation.cpp | 119 ++
src/crystallization/VectorMean.cpp | 2 +-
src/crystallization/VectorSum.cpp | 3 +-
src/gridtools/GridVessel.h | 3 +-
src/gridtools/HistogramOnGrid.cpp | 14 +-
12 files changed, 2236 insertions(+), 45 deletions(-)
create mode 100644 regtest/crystallization/rt-spherical-integral/Makefile
create mode 100644 regtest/crystallization/rt-spherical-integral/colvar.reference
create mode 100644 regtest/crystallization/rt-spherical-integral/config
create mode 100644 regtest/crystallization/rt-spherical-integral/forces.reference
create mode 100644 regtest/crystallization/rt-spherical-integral/plumed.dat
create mode 100644 regtest/crystallization/rt-spherical-integral/trajectory.xyz
create mode 100644 src/crystallization/BondOrientation.cpp
diff --git a/regtest/crystallization/rt-spherical-integral/Makefile b/regtest/crystallization/rt-spherical-integral/Makefile
new file mode 100644
index 000000000..3703b27ce
--- /dev/null
+++ b/regtest/crystallization/rt-spherical-integral/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
diff --git a/regtest/crystallization/rt-spherical-integral/colvar.reference b/regtest/crystallization/rt-spherical-integral/colvar.reference
new file mode 100644
index 000000000..f8684e6a3
--- /dev/null
+++ b/regtest/crystallization/rt-spherical-integral/colvar.reference
@@ -0,0 +1,6 @@
+#! FIELDS time iv b.bias b.force2
+ 0.000000 1.0485 0.4455 8.9106
+ 1.000000 0.9842 0.2741 5.4827
+ 2.000000 1.0049 0.3249 6.4986
+ 3.000000 0.9474 0.1949 3.8973
+ 4.000000 0.9911 0.2907 5.8143
diff --git a/regtest/crystallization/rt-spherical-integral/config b/regtest/crystallization/rt-spherical-integral/config
new file mode 100644
index 000000000..31b0428ec
--- /dev/null
+++ b/regtest/crystallization/rt-spherical-integral/config
@@ -0,0 +1,3 @@
+type=driver
+# this is to test a different name
+arg="--plumed plumed.dat --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt %8.4f" # --debug-forces forces.num"
diff --git a/regtest/crystallization/rt-spherical-integral/forces.reference b/regtest/crystallization/rt-spherical-integral/forces.reference
new file mode 100644
index 000000000..1d0ff64ec
--- /dev/null
+++ b/regtest/crystallization/rt-spherical-integral/forces.reference
@@ -0,0 +1,1015 @@
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diff --git a/regtest/crystallization/rt-spherical-integral/plumed.dat b/regtest/crystallization/rt-spherical-integral/plumed.dat
new file mode 100644
index 000000000..128dd216b
--- /dev/null
+++ b/regtest/crystallization/rt-spherical-integral/plumed.dat
@@ -0,0 +1,8 @@
+b1: BOND_DIRECTION GROUP=1-5 SWITCH={RATIONAL D_0=2.0 R_0=0.5 D_MAX=5.0}
+
+h: HISTOGRAM VECTORS=b1 CONCENTRATION=10 GRID_BIN=100
+
+iv: INTEGRATE_GRID GRID=h
+
+b: RESTRAINT ARG=iv AT=0.75 KAPPA=10.0
+PRINT ARG=iv,b.* FILE=colvar FMT=%8.4f
diff --git a/regtest/crystallization/rt-spherical-integral/trajectory.xyz b/regtest/crystallization/rt-spherical-integral/trajectory.xyz
new file mode 100644
index 000000000..13fdd1145
--- /dev/null
+++ b/regtest/crystallization/rt-spherical-integral/trajectory.xyz
@@ -0,0 +1,1015 @@
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+Ar 5 5 5
+Ar 0.585477 0.110114 0.684869
+Ar 9.77116 3.83664 2.40794
+Ar 4.18684 8.20726 9.4046
+Ar 3.33783 8.9657 6.45655
+Ar 2.25867 1.53205 9.13491
+Ar 6.07855 2.26309 5.67751
+Ar 1.83592 6.33235 7.80252
+Ar 2.45704 5.39349 8.31407
+Ar 9.6476 7.29512 9.0851
+Ar 9.65072 9.63741 5.91994
+Ar 4.9685 5.53802 7.4905
+Ar 4.97498 4.42215 3.02191
+Ar 3.18246 7.53316 9.83366
+Ar 0.0564456 8.68118 4.52756
+Ar 3.45015 6.72995 0.199055
+Ar 4.07436 7.82501 4.95659
+Ar 5.55356 8.63532 3.74031
+Ar 8.66305 9.87988 1.10149
+Ar 5.79989 8.70389 6.19807
+Ar 9.0962 9.78863 7.57851
+Ar 1.7219 9.95458 6.64506
+Ar 2.31068 5.55694 5.49373
+Ar 5.55733 1.9875 3.98937
+Ar 4.9474 0.995039 3.62681
+Ar 3.73159 6.80556 1.09921
+Ar 5.52801 9.24063 7.2093
+Ar 0.250363 7.84688 2.58753
+Ar 7.90095 1.20215 4.6146
+Ar 0.0740833 5.11728 6.08319
+Ar 4.33937 1.86764 9.36867
+Ar 4.3229 4.94322 0.726531
+Ar 9.45025 0.38419 7.07826
+Ar 4.0198 0.790307 2.68303
+Ar 3.72159 8.70243 1.74004
+Ar 0.741926 9.55034 2.6045
+Ar 6.10995 9.87933 1.97273
+Ar 1.69951 3.6705 0.0135434
+Ar 0.975465 4.64788 6.92031
+Ar 6.46646 1.76885 9.04255
+Ar 2.46148 0.102676 5.67826
+Ar 5.12551 4.46475 8.9939
+Ar 9.13758 5.27377 6.30692
+Ar 0.648155 3.53456 5.41551
+Ar 9.61115 4.56171 8.58274
+Ar 8.47088 0.0661062 1.0468
+Ar 6.26861 6.57449 7.44073
+Ar 5.98648 4.85276 0.419553
+Ar 4.91754 9.03034 2.95524
+Ar 1.11 5.71734 1.3814
+Ar 7.75146 8.72537 7.31582
+Ar 8.2173 8.13283 8.42835
+Ar 5.87103 4.41705 7.36285
+Ar 9.59406 7.41339 6.86644
+Ar 8.44531 0.363607 1.13458
+Ar 4.12048 2.8767 8.66202
+Ar 6.61595 4.21433 0.190167
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+Ar 4.82227 7.90702 3.33424
+Ar 0.0198728 4.00283 5.56947
+Ar 4.28414 3.61125 4.26834
+Ar 4.84291 4.7602 4.7442
+Ar 0.814141 3.27089 3.80451
+Ar 9.43368 1.93755 4.33632
+Ar 5.91948 8.66953 8.8569
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+Ar 2.31509 9.70521 5.54465
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+Ar 4.99441 1.03751 7.4424
+Ar 7.81586 1.18925 7.74786
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+Ar 5.97392 3.70014 8.24905
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+Ar 2.08414 8.20126 8.5472
+Ar 8.71225 6.83691 7.88704
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+Ar 0.0157827 5.25929 2.88429
+Ar 0.632955 8.0814 4.11825
+Ar 5.01598 3.58241 9.48683
+Ar 6.2658 9.24671 9.49752
+Ar 5.29306 0.482018 1.27549
+Ar 1.34334 7.5973 7.88174
+Ar 6.84132 2.1142 3.40302
+Ar 8.03589 9.19091 1.63418
+Ar 0.873677 3.89043 6.50166
+Ar 2.08449 4.0845 8.1333
+Ar 0.499961 2.83645 2.26594
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+Ar 7.96486 5.35161 4.56202
+Ar 0.835465 1.66366 1.1062
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+Ar 9.00944 1.63399 2.39468
+Ar 8.10724 8.31387 1.1825
+Ar 7.40154 7.65349 2.18798
+Ar 5.80881 8.67864 1.94781
+Ar 4.47492 9.93644 1.79788
+Ar 8.01359 4.39 2.7289
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+Ar 6.64434 1.34455 7.78315
+Ar 9.5285 5.42773 3.83717
+Ar 3.79528 7.30003 1.58419
+Ar 8.66185 9.6574 1.92608
+Ar 3.86281 2.25192 8.08468
+Ar 5.4693 2.60563 2.80889
+Ar 2.73772 2.92202 0.463033
+Ar 9.32158 7.7224 0.34999
+Ar 3.39061 5.98839 6.82779
+Ar 5.58232 2.10435 7.73404
+Ar 9.11083 5.67101 2.63003
+Ar 0.590107 7.93451 5.35025
+Ar 7.92024 5.52079 7.95577
+Ar 8.834 3.01055 8.28432
+Ar 8.8867 8.8272 8.6824
+Ar 2.77907 7.78888 7.70617
+Ar 9.63608 3.52666 2.59576
+Ar 9.9523 8.32903 6.02341
+Ar 5.02671 3.86767 3.99013
+Ar 9.89527 9.85848 1.39968
+Ar 5.66065 8.60828 9.44422
+Ar 3.25281 9.9649 0.0565812
+Ar 9.22475 0.377142 8.63133
+Ar 6.98223 0.27845 9.91102
+Ar 0.954877 8.61968 0.9086
+Ar 4.66669 2.98862 9.7805
+Ar 3.2901 6.73037 7.29006
+Ar 9.43989 6.2528 0.73777
+Ar 5.2691 7.78675 1.9626
+Ar 2.37807 8.25969 0.664659
+Ar 5.7161 0.444766 5.19037
+Ar 1.77788 0.838111 6.12816
+Ar 3.77918 6.68077 3.73031
+Ar 7.05868 5.18765 8.83197
+Ar 5.07012 3.43673 1.10128
+Ar 5.46813 2.88451 9.94419
+Ar 9.86988 2.99554 6.02776
+Ar 2.1216 7.68248 9.39316
+Ar 9.15878 1.55022 4.47531
+Ar 4.50696 8.42133 7.25026
+Ar 2.39512 4.72938 6.73935
+Ar 9.49451 4.19622 5.86391
+Ar 6.70501 1.07076 6.31325
+Ar 7.49134 7.01545 8.59661
+Ar 2.83648 2.75877 6.57069
+Ar 0.226766 1.25274 4.87276
+Ar 2.96327 3.68784 1.49853
+Ar 8.14282 6.32737 4.09754
+Ar 4.63358 6.59755 5.0765
+Ar 4.76308 3.09981 8.49083
+Ar 2.2856 4.0852 9.92717
+Ar 8.72976 1.0972 0.622184
+Ar 4.05474 7.98644 8.01343
+Ar 6.0611 8.82793 0.971363
+Ar 5.21621 8.90506 7.42054
+Ar 0.85252 8.31187 7.55784
+Ar 5.08025 3.78838 1.26698
+Ar 4.28152 9.54903 0.467227
+Ar 1.27929 1.10995 4.96625
+Ar 7.85078 8.07968 5.21226
+Ar 2.03223 5.74007 3.43845
+Ar 6.12752 5.15792 9.0895
+Ar 6.31432 4.74453 1.28442
+Ar 0.14469 1.80883 1.00882
+Ar 3.38733 0.859129 9.3866
+Ar 1.8513 4.83748 3.57565
+Ar 4.9641 1.69709 2.92853
+Ar 4.69439 8.58465 2.24284
+Ar 8.52547 7.61727 3.499
+Ar 5.41058 5.62408 3.91523
+Ar 4.29181 2.48439 5.20293
+Ar 2.54077 2.77065 6.32843
+Ar 9.42594 1.73494 9.07766
+Ar 7.05099 6.06211 5.80371
+Ar 5.62884 3.99252 2.32817
+Ar 3.01044 6.47846 3.49305
+Ar 8.11484 6.03974 9.99273
+Ar 6.75007 8.43681 7.50192
+Ar 7.78899 9.57315 5.97498
+Ar 5.15115 5.30966 9.47706
+Ar 9.31936 0.443993 2.18826
+Ar 7.14071 3.97125 4.85273
+Ar 5.07424 2.67889 4.05894
+Ar 1.72002 8.30412 7.30678
+Ar 8.9812 7.09069 3.30219
+Ar 2.71071 8.90597 2.62741
+Ar 1.81835 1.03718 1.82565
+Ar 8.37568 0.125978 7.30861
+Ar 8.92944 7.10977 3.83388
+Ar 9.39118 7.58272 2.7392
+201
+10 10 10
+Ar 5 5 5
+Ar 3.87313 5.73295 3.63497
+Ar 1.26258 0.100799 4.12172
+Ar 1.10159 4.34212 8.03789
+Ar 1.68553 8.74191 5.25031
+Ar 3.13274 1.94513 1.85997
+Ar 7.03405 1.31265 1.73485
+Ar 4.08922 7.47022 2.06127
+Ar 3.58184 0.00244104 1.02653
+Ar 5.27005 3.80757 3.76106
+Ar 2.89607 4.28288 2.40539
+Ar 0.114875 0.702451 6.08648
+Ar 9.34867 3.02487 9.05185
+Ar 1.84465 2.99507 8.0757
+Ar 6.06855 4.20323 3.7223
+Ar 3.25266 7.48637 3.35445
+Ar 7.16833 8.19242 0.0718171
+Ar 9.08901 9.00553 5.94015
+Ar 0.189675 7.86545 4.61016
+Ar 6.39849 9.35537 5.73023
+Ar 0.697546 3.65579 2.9288
+Ar 9.39054 6.74899 0.240582
+Ar 5.49707 9.28968 1.65453
+Ar 3.27444 3.51501 6.81452
+Ar 6.29866 1.5525 2.79149
+Ar 4.64982 9.60691 3.2555
+Ar 8.15288 5.51547 8.54029
+Ar 6.94179 0.599838 1.47644
+Ar 5.37966 5.96036 5.79728
+Ar 9.8735 3.95466 5.96734
+Ar 4.16777 7.64724 7.08618
+Ar 6.04369 6.22166 7.43236
+Ar 3.97462 1.4452 9.53387
+Ar 2.57261 7.93528 8.18957
+Ar 2.63467 0.829112 4.88013
+Ar 8.1737 5.4002 1.11248
+Ar 5.12547 3.70872 2.44357
+Ar 3.82244 3.81637 1.79699
+Ar 9.31441 7.23388 9.79397
+Ar 5.2172 5.52303 5.55224
+Ar 1.51073 0.920974 8.80278
+Ar 6.54699 5.25457 3.63229
+Ar 0.975062 7.86054 2.08892
+Ar 9.40749 1.6041 0.0695826
+Ar 9.3944 1.76099 7.02375
+Ar 1.05714 7.26908 1.40206
+Ar 0.875512 4.73728 9.53985
+Ar 0.87403 9.82149 9.78365
+Ar 9.08002 7.92467 9.95481
+Ar 8.81729 2.21584 1.57518
+Ar 9.95981 4.57134 0.530516
+Ar 3.01772 8.74764 1.52663
+Ar 1.4901 4.09918 4.85936
+Ar 2.14934 4.01285 4.04616
+Ar 3.94403 7.37757 4.88059
+Ar 2.71207 1.79254 7.2659
+Ar 7.72304 1.19616 3.9264
+Ar 1.46436 1.41616 1.41128
+Ar 6.25419 4.08813 9.26625
+Ar 5.47793 7.64297 5.31423
+Ar 1.24938 8.28795 5.64537
+Ar 5.906 2.20219 2.22719
+Ar 7.99586 6.40725 6.67558
+Ar 7.90695 2.08468 7.22678
+Ar 2.38571 6.54578 4.94976
+Ar 0.543483 4.32665 7.95794
+Ar 9.07555 2.81133 9.97924
+Ar 1.23925 7.99383 2.2824
+Ar 2.93181 4.88769 7.48209
+Ar 6.57922 7.03311 5.44743
+Ar 5.12078 4.9839 4.35566
+Ar 0.802694 0.877835 3.76606
+Ar 8.24957 0.516574 2.06065
+Ar 8.90722 3.65429 7.58976
+Ar 0.790915 2.90278 7.03097
+Ar 1.48872 0.835137 6.15335
+Ar 0.880791 3.45231 2.98357
+Ar 0.616992 9.78219 9.32629
+Ar 6.93267 7.37385 2.29875
+Ar 7.83518 5.78737 8.30345
+Ar 3.45898 5.08621 3.93421
+Ar 3.18839 7.21309 0.34932
+Ar 7.35437 4.84111 4.51841
+Ar 4.74387 0.259729 5.26859
+Ar 3.91218 1.96141 5.39494
+Ar 6.36433 5.35012 9.44947
+Ar 5.57066 6.1013 4.57543
+Ar 3.71078 7.13575 0.554679
+Ar 7.13267 8.751 8.08733
+Ar 8.4745 0.95792 9.7614
+Ar 6.51654 3.49025 0.550051
+Ar 4.51249 1.40634 6.39581
+Ar 4.61514 6.63256 3.35415
+Ar 6.44425 8.54386 6.58629
+Ar 3.85636 3.77078 5.43398
+Ar 9.44688 3.70312 8.32443
+Ar 3.20095 8.29598 0.518127
+Ar 8.66746 3.93658 2.16028
+Ar 4.47321 1.24615 3.99721
+Ar 3.23632 2.8568 4.22255
+Ar 0.305042 6.84601 0.845912
+Ar 4.30951 9.89081 4.81353
+Ar 5.91209 4.46826 8.08957
+Ar 2.89971 5.44071 2.08941
+Ar 9.1212 0.0409497 8.2423
+Ar 8.0862 4.81407 9.99059
+Ar 8.70323 5.10685 0.842173
+Ar 3.37046 7.37802 2.33168
+Ar 0.57017 2.84092 7.35925
+Ar 1.86622 5.56774 7.07927
+Ar 5.84218 9.5658 2.48035
+Ar 7.12449 1.24036 6.78823
+Ar 7.54274 0.831074 7.85693
+Ar 3.43707 6.7934 6.59203
+Ar 4.49628 8.96041 7.62218
+Ar 5.13876 7.08872 0.0466171
+Ar 0.329645 0.343775 7.82165
+Ar 5.90956 2.02453 6.30304
+Ar 5.60079 2.5502 1.13809
+Ar 0.648723 3.07937 4.9558
+Ar 6.55088 0.616576 2.78534
+Ar 1.88598 7.69475 5.67168
+Ar 6.47486 3.03928 1.09507
+Ar 4.7741 8.22263 7.81637
+Ar 4.67219 5.55962 0.577062
+Ar 2.12326 5.69258 5.24466
+Ar 1.13544 3.34053 4.33406
+Ar 4.29996 9.34654 7.28091
+Ar 8.37924 9.93932 0.116003
+Ar 3.85205 1.44965 4.19509
+Ar 7.23612 7.55002 3.13938
+Ar 6.55743 0.648518 9.64876
+Ar 5.7365 3.36003 2.04684
+Ar 5.40897 8.60198 3.3941
+Ar 8.8512 2.10176 4.25653
+Ar 8.37896 5.1477 7.42059
+Ar 2.43862 5.87741 1.59926
+Ar 0.857514 2.23809 5.65975
+Ar 5.20599 7.00215 5.14985
+Ar 2.245 1.74703 2.32142
+Ar 8.19193 1.72719 8.80939
+Ar 1.92166 7.2765 6.12871
+Ar 9.60594 7.0251 0.783787
+Ar 7.49085 8.79009 5.01202
+Ar 5.12531 1.03312 3.61994
+Ar 6.68699 8.23934 8.65404
+Ar 5.85407 9.37865 6.91885
+Ar 8.28803 6.91793 9.71231
+Ar 0.154994 4.99089 1.81561
+Ar 7.47213 4.11338 3.59508
+Ar 4.94654 6.47822 9.44509
+Ar 5.0936 8.16921 9.92238
+Ar 1.06304 6.57717 2.5574
+Ar 6.40198 8.14627 4.44098
+Ar 4.90826 3.16757 7.38135
+Ar 8.95555 6.00488 4.08592
+Ar 3.95336 4.17199 8.71278
+Ar 5.47846 6.40654 4.7525
+Ar 7.36347 7.83685 3.85437
+Ar 8.27623 8.65346 8.70981
+Ar 1.6617 8.19874 6.1984
+Ar 4.50241 2.00458 0.971449
+Ar 7.76135 5.04448 2.63619
+Ar 8.71161 6.07659 9.21288
+Ar 6.76582 3.08604 7.01563
+Ar 9.21579 9.78598 2.96539
+Ar 0.855888 4.90513 0.457679
+Ar 8.2507 9.56063 5.59129
+Ar 2.08136 1.42156 2.19529
+Ar 7.70847 6.17798 3.27745
+Ar 0.754502 0.909584 7.37261
+Ar 9.43419 0.423678 0.760008
+Ar 5.435 6.11527 9.33427
+Ar 8.02994 9.2571 4.03267
+Ar 0.606574 4.6945 0.383465
+Ar 9.35323 9.74732 3.19666
+Ar 6.36671 5.22578 9.74157
+Ar 5.95597 1.91401 8.77683
+Ar 1.40332 5.56064 7.74702
+Ar 6.30169 2.42405 1.04518
+Ar 2.34835 8.69722 4.20179
+Ar 0.670357 6.6892 5.34706
+Ar 8.63881 2.45052 5.89593
+Ar 1.26038 3.14406 2.16308
+Ar 1.58515 1.54755 9.59656
+Ar 7.05547 1.25183 9.5881
+Ar 3.01513 5.25619 0.776404
+Ar 2.64111 9.14238 6.04527
+Ar 6.33888 7.62816 6.48992
+Ar 5.49963 2.2152 0.907294
+Ar 7.72449 5.53304 3.83241
+Ar 4.46581 6.90197 1.34986
+Ar 7.2834 2.1483 6.41683
+Ar 9.77827 3.36416 1.43895
+Ar 3.87117 2.67413 4.07172
+Ar 6.46873 9.92897 6.25149
+Ar 0.268344 0.0617421 7.69979
+Ar 8.13526 9.23425 0.117487
+Ar 9.51619 8.66444 3.31978
+Ar 2.70354 8.34826 9.27735
+Ar 3.98257 4.97261 4.6757
diff --git a/src/analysis/Histogram.cpp b/src/analysis/Histogram.cpp
index 53c09e374..8a6f6067e 100644
--- a/src/analysis/Histogram.cpp
+++ b/src/analysis/Histogram.cpp
@@ -161,7 +161,7 @@ DUMPGRID GRID=hh FILE=histo STRIDE=100000
class Histogram : public gridtools::ActionWithGrid {
private:
double ww;
- bool in_apply;
+ bool in_apply, mvectors;
KernelFunctions* kernel;
std::vector<double> forcesToApply, finalForces;
std::vector<vesselbase::ActionWithVessel*> myvessels;
@@ -186,6 +186,7 @@ PLUMED_REGISTER_ACTION(Histogram,"HISTOGRAM")
void Histogram::registerKeywords( Keywords& keys ){
gridtools::ActionWithGrid::registerKeywords( keys ); keys.use("ARG");
keys.add("optional","DATA","input data from action with vessel and compute histogram");
+ keys.add("optional","VECTORS","input three dimsnional vectors for computing histogram");
keys.add("compulsory","GRID_MIN","the lower bounds for the grid");
keys.add("compulsory","GRID_MAX","the upper bounds for the grid");
keys.add("optional","GRID_BIN","the number of bins for the grid");
@@ -198,46 +199,58 @@ Action(ao),
ActionWithGrid(ao),
ww(0.0),
in_apply(false),
+mvectors(false),
kernel(NULL)
{
// Read in arguments
- std::vector<std::string> mlab; parseVector("DATA",mlab);
- if( mlab.size()>0 ){
- for(unsigned i=0;i<mlab.size();++i){
- ActionWithVessel* myv = plumed.getActionSet().selectWithLabel<ActionWithVessel*>( mlab[i] );
- if( !myv ) error("action labelled " + mlab[i] + " does not exist or is not an ActionWithVessel");
- myvessels.push_back( myv ); stashes.push_back( myv->buildDataStashes( NULL ) );
- // log.printf(" for all base quantities calculated by %s \n",myvessel->getLabel().c_str() );
- // Add the dependency
- addDependency( myv );
- }
- unsigned nvals = myvessels[0]->getFullNumberOfTasks();
- for(unsigned i=1;i<mlab.size();++i){
- if( nvals!=myvessels[i]->getFullNumberOfTasks() ) error("mismatched number of quantities calculated by actions input to histogram");
- }
- log.printf(" for all base quantities calculated by %s ", myvessels[0]->getLabel().c_str() );
- for(unsigned i=1;i<mlab.size();++i) log.printf(", %s \n", myvessels[i]->getLabel().c_str() );
- log.printf("\n");
+ std::string vlab; parse("VECTORS",vlab);
+ if( vlab.length()>0 ){
+ ActionWithVessel* myv = plumed.getActionSet().selectWithLabel<ActionWithVessel*>( vlab );
+ if( !myv ) error("action labelled " + vlab + " does not exist or is not an ActionWithVessel");
+ myvessels.push_back( myv ); stashes.push_back( myv->buildDataStashes( NULL ) );
+ addDependency( myv ); mvectors=true;
+ if( myv->getNumberOfQuantities()!=5 ) error("can only compute histograms for three dimensional vectors");
+ log.printf(" for vector quantities calculated by %s \n", vlab.c_str() );
} else {
- std::vector<Value*> arg; parseArgumentList("ARG",arg);
- if(!arg.empty()){
- log.printf(" with arguments");
- for(unsigned i=0;i<arg.size();i++) log.printf(" %s",arg[i]->getName().c_str());
+ std::vector<std::string> mlab; parseVector("DATA",mlab);
+ if( mlab.size()>0 ){
+ for(unsigned i=0;i<mlab.size();++i){
+ ActionWithVessel* myv = plumed.getActionSet().selectWithLabel<ActionWithVessel*>( mlab[i] );
+ if( !myv ) error("action labelled " + mlab[i] + " does not exist or is not an ActionWithVessel");
+ myvessels.push_back( myv ); stashes.push_back( myv->buildDataStashes( NULL ) );
+ // log.printf(" for all base quantities calculated by %s \n",myvessel->getLabel().c_str() );
+ // Add the dependency
+ addDependency( myv );
+ }
+ unsigned nvals = myvessels[0]->getFullNumberOfTasks();
+ for(unsigned i=1;i<mlab.size();++i){
+ if( nvals!=myvessels[i]->getFullNumberOfTasks() ) error("mismatched number of quantities calculated by actions input to histogram");
+ }
+ log.printf(" for all base quantities calculated by %s ", myvessels[0]->getLabel().c_str() );
+ for(unsigned i=1;i<mlab.size();++i) log.printf(", %s \n", myvessels[i]->getLabel().c_str() );
log.printf("\n");
- // Retrieve the bias acting and make sure we request this also
- std::vector<Value*> bias( ActionWithArguments::getArguments() );
- for(unsigned i=0;i<bias.size();++i) arg.push_back( bias[i] );
- requestArguments(arg);
+ } else {
+ std::vector<Value*> arg; parseArgumentList("ARG",arg);
+ if(!arg.empty()){
+ log.printf(" with arguments");
+ for(unsigned i=0;i<arg.size();i++) log.printf(" %s",arg[i]->getName().c_str());
+ log.printf("\n");
+ // Retrieve the bias acting and make sure we request this also
+ std::vector<Value*> bias( ActionWithArguments::getArguments() );
+ for(unsigned i=0;i<bias.size();++i) arg.push_back( bias[i] );
+ requestArguments(arg);
+ }
}
}
// Read stuff for grid
unsigned narg = getNumberOfArguments();
if( myvessels.size()>0 ) narg=myvessels.size();
-
// Input of name and labels
std::string vstring="COMPONENTS=" + getLabel();
- if( myvessels.size()>0 ){
+ if( mvectors ){
+ vstring += " COORDINATES=x,y,z PBC=F,F,F";
+ } else if( myvessels.size()>0 ){
vstring += " COORDINATES=" + myvessels[0]->getLabel();
for(unsigned i=1;i<myvessels.size();++i) vstring +="," + myvessels[i]->getLabel();
// Input for PBC
@@ -261,6 +274,7 @@ kernel(NULL)
// And create the grid
createGrid( "histogram", vstring );
if( mygrid->getType()=="flat" ){
+ if( mvectors ) error("computing histogram for three dimensional vectors but grid is not of fibonacci type - use CONCENTRATION");
std::vector<std::string> gmin( narg ), gmax( narg );
parseVector("GRID_MIN",gmin); parseVector("GRID_MAX",gmax);
std::vector<unsigned> nbin; parseVector("GRID_BIN",nbin);
@@ -286,7 +300,7 @@ kernel(NULL)
myhist->addOneKernelEachTimeOnly();
setAveragingAction( mygrid, myhist->noDiscreteKernels() );
}
- checkRead();
+ checkRead();
}
void Histogram::turnOnDerivatives(){
@@ -317,7 +331,8 @@ unsigned Histogram::getNumberOfDerivatives(){
}
unsigned Histogram::getNumberOfQuantities() const {
- if( myvessels.size()>0 ) return myvessels.size()+2;
+ if( mvectors ) return myvessels[0]->getNumberOfQuantities();
+ else if( myvessels.size()>0 ) return myvessels.size()+2;
return 2;
}
@@ -365,7 +380,21 @@ void Histogram::finishAveraging(){
}
void Histogram::compute( const unsigned& current, MultiValue& myvals ) const {
- if( myvessels.size()>0 ){
+ if( mvectors ){
+ std::vector<double> cvals( myvessels[0]->getNumberOfQuantities() );
+ stashes[0]->retrieveSequentialValue( current, true, cvals );
+ for(unsigned i=2;i<myvessels[0]->getNumberOfQuantities();++i) myvals.setValue( i-1, cvals[i] );
+ myvals.setValue( 0, cvals[0] ); myvals.setValue( myvessels[0]->getNumberOfQuantities() - 1, ww );
+ if( in_apply ){
+ MultiValue tmpval( myvessels[0]->getNumberOfQuantities(), myvessels[0]->getNumberOfDerivatives() );
+ stashes[0]->retrieveDerivatives( stashes[0]->getTrueIndex(current), true, tmpval );
+ for(unsigned j=0;j<tmpval.getNumberActive();++j){
+ unsigned jder=tmpval.getActiveIndex(j); myvals.addDerivative( 0, jder, tmpval.getDerivative(0, jder) );
+ for(unsigned i=2;i<myvessels[0]->getNumberOfQuantities();++i) myvals.addDerivative( i-1, jder, tmpval.getDerivative(i, jder) );
+ }
+ myvals.updateDynamicList();
+ }
+ } else if( myvessels.size()>0 ){
std::vector<double> cvals( myvessels[0]->getNumberOfQuantities() );
stashes[0]->retrieveSequentialValue( current, false, cvals );
unsigned derbase; double totweight=cvals[0], tnorm = cvals[0]; myvals.setValue( 1, cvals[1] );
@@ -415,6 +444,7 @@ void Histogram::compute( const unsigned& current, MultiValue& myvals ) const {
// Evaluate the histogram at the relevant grid point and set the values
double vvh = kernel->evaluate( vv, der ,true); myvals.setValue( 1, vvh );
} else {
+ plumed_merror("normalisation of vectors does not work with arguments and spherical grids");
// Evalulate dot product
double dot=0; for(unsigned j=0;j<getNumberOfArguments();++j){ dot+=val[j]*getArgument(j); der[j]=val[j]; }
// Von misses distribution for concentration parameter
diff --git a/src/crystallization/BondOrientation.cpp b/src/crystallization/BondOrientation.cpp
new file mode 100644
index 000000000..efac59c44
--- /dev/null
+++ b/src/crystallization/BondOrientation.cpp
@@ -0,0 +1,119 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ Copyright (c) 2013-2016 The plumed team
+ (see the PEOPLE file at the root of the distribution for a list of names)
+
+ See http://www.plumed.org for more information.
+
+ This file is part of plumed, version 2.
+
+ plumed is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ plumed is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with plumed. If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#include "tools/SwitchingFunction.h"
+#include "core/ActionRegister.h"
+#include "VectorMultiColvar.h"
+
+namespace PLMD {
+namespace crystallization {
+
+class BondOrientation : public VectorMultiColvar {
+private:
+ double rcut2;
+ SwitchingFunction switchingFunction;
+public:
+ static void registerKeywords( Keywords& keys );
+ explicit BondOrientation( const ActionOptions& ao );
+ double calculateWeight( const unsigned& current, const double& weight, multicolvar::AtomValuePack& myatoms ) const ;
+ void calculateVector( multicolvar::AtomValuePack& myatoms ) const ;
+};
+
+PLUMED_REGISTER_ACTION(BondOrientation,"BOND_DIRECTION")
+
+void BondOrientation::registerKeywords( Keywords& keys ){
+ VectorMultiColvar::registerKeywords( keys );
+ keys.use("ATOMS");
+ keys.add("atoms-1","GROUP","Calculate the distance between each distinct pair of atoms in the group");
+ keys.add("atoms-2","GROUPA","Calculate the distances between all the atoms in GROUPA and all "
+ "the atoms in GROUPB. This must be used in conjuction with GROUPB.");
+ keys.add("atoms-2","GROUPB","Calculate the distances between all the atoms in GROUPA and all the atoms "
+ "in GROUPB. This must be used in conjuction with GROUPA.");
+ keys.add("compulsory","NN","12","The n parameter of the switching function ");
+ keys.add("compulsory","MM","0","The m parameter of the switching function; 0 implies 2*NN");
+ keys.add("compulsory","D_0","0.0","The d_0 parameter of the switching function");
+ keys.add("compulsory","R_0","The r_0 parameter of the switching function");
+ keys.add("optional","SWITCH","This keyword is used if you want to employ an alternative to the continuous swiching function defined above. "
+ "The following provides information on the \\ref switchingfunction that are available. "
+ "When this keyword is present you no longer need the NN, MM, D_0 and R_0 keywords.");
+ keys.use("VMEAN"); keys.use("VSUM");
+}
+
+BondOrientation::BondOrientation( const ActionOptions& ao ):
+Action(ao),
+VectorMultiColvar(ao)
+{
+ // Read atoms
+ weightHasDerivatives=true;
+ std::vector<AtomNumber> all_atoms;
+ readTwoGroups( "GROUP", "GROUPA", "GROUPB", all_atoms );
+ int natoms=2; readAtoms( natoms, all_atoms );
+ // Read in the switching function
+ std::string sw, errors; parse("SWITCH",sw);
+ if(sw.length()>0){
+ switchingFunction.set(sw,errors);
+ } else {
+ double r_0=-1.0, d_0; int nn, mm;
+ parse("NN",nn); parse("MM",mm);
+ parse("R_0",r_0); parse("D_0",d_0);
+ if( r_0<0.0 ) error("you must set a value for R_0");
+ switchingFunction.set(nn,mm,r_0,d_0);
+ }
+ log.printf(" orientation of those bonds with lengths are less than %s\n",( switchingFunction.description() ).c_str() );
+ // Set the link cell cutoff
+ setLinkCellCutoff( switchingFunction.get_dmax() );
+ double rcut = switchingFunction.get_dmax(); rcut2 = rcut*rcut;
+ // Set the dimensionality of the vectors
+ setVectorDimensionality(3);
+}
+
+double BondOrientation::calculateWeight( const unsigned& current, const double& weight, multicolvar::AtomValuePack& myatoms ) const {
+ Vector distance=getSeparation( myatoms.getPosition(0), myatoms.getPosition(1) ); double distm=distance.modulo2();
+ if( distm>rcut2 ) return 0.0;
+ double df, ww=switchingFunction.calculateSqr( distm, df );
+ // Derivatives of weights
+ addAtomDerivatives( 0, 0, -df*weight*distance, myatoms );
+ addAtomDerivatives( 0, 1, df*weight*distance, myatoms );
+ myatoms.addBoxDerivatives( 0, (-df)*weight*Tensor(distance,distance) );
+ return ww;
+}
+
+void BondOrientation::calculateVector( multicolvar::AtomValuePack& myatoms ) const {
+ Vector distance=getSeparation( myatoms.getPosition(0), myatoms.getPosition(1) );
+
+ addAtomDerivatives( 2, 0, Vector(-1.0,0,0), myatoms );
+ addAtomDerivatives( 2, 1, Vector(+1.0,0,0), myatoms );
+ myatoms.addBoxDerivatives( 2, Tensor(distance,Vector(-1.0,0,0)) );
+ myatoms.addValue( 2, distance[0] );
+
+ addAtomDerivatives( 3, 0, Vector(0,-1.0,0), myatoms );
+ addAtomDerivatives( 3, 1, Vector(0,+1.0,0), myatoms );
+ myatoms.addBoxDerivatives( 3, Tensor(distance,Vector(0,-1.0,0)) );
+ myatoms.addValue( 3, distance[1] );
+
+ addAtomDerivatives( 4 , 0, Vector(0,0,-1.0), myatoms );
+ addAtomDerivatives( 4 , 1, Vector(0,0,+1.0), myatoms );
+ myatoms.addBoxDerivatives( 4, Tensor(distance,Vector(0,0,-1.0)) );
+ myatoms.addValue( 4, distance[2] );
+}
+
+}
+}
diff --git a/src/crystallization/VectorMean.cpp b/src/crystallization/VectorMean.cpp
index f4775acd4..9fae24b4c 100644
--- a/src/crystallization/VectorMean.cpp
+++ b/src/crystallization/VectorMean.cpp
@@ -103,7 +103,7 @@ void VectorMean::finish( const std::vector<double>& buffer ){
Value* fval=getFinalValue(); double tw = 1.0 / sqrt(sum);
for(unsigned icomp=0;icomp<ncomp;++icomp){
- double tmp = buffer[(icomp+1)*(1+nder)] / ww;
+ double tmp = buffer[bufstart + (icomp+1)*(1+nder)] / ww;
unsigned bstart = bufstart + (1+icomp)*(nder+1) + 1;
for(unsigned jder=0;jder<nder;++jder) fval->addDerivative( jder, (tw*tmp/ww)*( buffer[bstart + jder] - tmp*buffer[bufstart + 1 + jder] ) );
}
diff --git a/src/crystallization/VectorSum.cpp b/src/crystallization/VectorSum.cpp
index 0b8fc359a..a9c81445b 100644
--- a/src/crystallization/VectorSum.cpp
+++ b/src/crystallization/VectorSum.cpp
@@ -79,7 +79,6 @@ void VectorSum::calculate( const unsigned& current, MultiValue& myvals, std::vec
double weight=myvals.get(0);
plumed_dbg_assert( weight>=getTolerance() );
- buffer[bufstart] += weight;
for(unsigned i=0;i<ncomp;++i) buffer[bufstart + i*(1+nder)] += weight*myvals.get(2+i);
if( !getAction()->derivativesAreRequired() ) return;
@@ -105,7 +104,7 @@ void VectorSum::finish( const std::vector<double>& buffer ){
Value* fval=getFinalValue();
for(unsigned icomp=0;icomp<ncomp;++icomp){
- double tmp = buffer[icomp*(1+nder)];
+ double tmp = buffer[bufstart + icomp*(1+nder)];
unsigned bstart = bufstart + icomp*(nder+1) + 1;
for(unsigned jder=0;jder<nder;++jder) fval->addDerivative( jder, tw*tmp*buffer[bstart + jder] );
}
diff --git a/src/gridtools/GridVessel.h b/src/gridtools/GridVessel.h
index 2e2c08a2c..18f467ca7 100644
--- a/src/gridtools/GridVessel.h
+++ b/src/gridtools/GridVessel.h
@@ -204,8 +204,7 @@ double GridVessel::getCellVolume() const {
double myvol=1.0; for(unsigned i=0;i<dimension;++i) myvol *= dx[i];
return myvol;
} else {
- plumed_merror("cell volume for surface grid not worked out yet");
- return 0.0;
+ return 4*pi / static_cast<double>( getNumberOfPoints() );
}
}
diff --git a/src/gridtools/HistogramOnGrid.cpp b/src/gridtools/HistogramOnGrid.cpp
index e47c5380f..8adb3b13e 100644
--- a/src/gridtools/HistogramOnGrid.cpp
+++ b/src/gridtools/HistogramOnGrid.cpp
@@ -112,11 +112,6 @@ void HistogramOnGrid::calculate( const unsigned& current, MultiValue& myvals, st
unsigned num_neigh; std::vector<unsigned> neighbors;
std::vector<double> der( dimension );
KernelFunctions* kernel=getKernelAndNeighbors( point, num_neigh, neighbors );
- // If no kernel normalize the vector so von misses distribution is calculated correctly
- if( !kernel ){
- double norm=0; for(unsigned j=0;j<dimension;++j) norm += point[j]*point[j];
- norm=sqrt( norm ); for(unsigned j=0;j<dimension;++j) point[j] = point[j] / norm;
- }
if( !kernel && getType()=="flat" ){
plumed_dbg_assert( num_neigh==1 );
@@ -131,8 +126,8 @@ void HistogramOnGrid::calculate( const unsigned& current, MultiValue& myvals, st
unsigned ineigh=neighbors[i];
if( inactive( ineigh ) ) continue ;
getGridPointCoordinates( ineigh, xx );
- for(unsigned j=0;j<dimension;++j) vv[j]->set(xx[j]);
if( kernel ){
+ for(unsigned j=0;j<dimension;++j) vv[j]->set(xx[j]);
newval = kernel->evaluate( vv, der, true );
} else {
// Evalulate dot product
@@ -149,14 +144,15 @@ void HistogramOnGrid::calculate( const unsigned& current, MultiValue& myvals, st
}
}
if( wasForced() ){
+ // Minus sign for kernel here as we are taking derivative with respect to position of center of
+ // kernel NOT derivative wrt to grid point
+ double pref = 1; if( kernel ) pref = -1;
unsigned nder = getAction()->getNumberOfDerivatives();
unsigned gridbuf = getNumberOfBufferPoints()*getNumberOfQuantities();
for(unsigned j=0;j<dimension;++j){
for(unsigned k=0;k<myvals.getNumberActive();++k){
- // Minus sign here as we are taking derivative with respect to position of center of kernel NOT derivative wrt to
- // grid point
unsigned kder=myvals.getActiveIndex(k);
- buffer[ bufstart + gridbuf + kder ] -= intforce[j]*myvals.getDerivative( j+1, kder );
+ buffer[ bufstart + gridbuf + kder ] += pref*intforce[j]*myvals.getDerivative( j+1, kder );
}
}
// Accumulate the sum of all the weights
--
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