diff --git a/.travis.yml b/.travis.yml
index 8f095c34f116562c3b32f98fae5909fa48496372..4f344159d14ac33676b9f2bd3eef67b3c3df6b2e 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -80,7 +80,7 @@ install:
# I use 1.71 since 1.72 seems to report a lot of false positive
- if test "$CPPCHECK" == yes ; then ./.travis/install.cppcheck $CPPCHECK_VERSION ; fi
# for plumedcheck I need latest gawk
- - if test "$CPPCHECK" == yes ; then ./.travis/install.gawk ; fi
+ - if test "$CPPCHECK" == yes ; then ./.travis/install.gawk 4.1.4 ; fi
# installation of these packages takes a lot of time
# we do it only when needed
- if test "$PLUMED_CXX" == "mpic++" -a "$TRAVIS_OS_NAME" == "linux" ; then sudo apt-get install -y libopenmpi-dev openmpi-bin ; fi
diff --git a/.travis/install.cppcheck b/.travis/install.cppcheck
index 25543080f983183abe83aa534786eea78af63679..b00de738de4a5682e13cb1dc4c9e447a28d2077e 100755
--- a/.travis/install.cppcheck
+++ b/.travis/install.cppcheck
@@ -3,6 +3,7 @@
set -e
set -x
+cd "$(mktemp -d)"
git clone https://github.com/danmar/cppcheck.git
cd cppcheck
@@ -15,12 +16,9 @@ else
version=$(git tag | tail -n 1)
fi
-
git checkout $version
make -j 4 install CFGDIR="$HOME/opt/share/cppcheck/" CXXFLAGS="-O2 -march=native -mtune=native -Wunreachable-code" PREFIX="$HOME/opt"
cd ../
cppcheck --version
-
-
diff --git a/.travis/install.doxygen b/.travis/install.doxygen
index 7a425f33da380f8acd1753b03fd8c83794d3e4a4..1f020a22e0a5d7e0aa9b17b68fac69811c4642e1 100755
--- a/.travis/install.doxygen
+++ b/.travis/install.doxygen
@@ -3,6 +3,8 @@
set -e
set -x
+cd "$(mktemp -d)"
+
git clone https://github.com/doxygen/doxygen.git
cd doxygen
diff --git a/.travis/install.gawk b/.travis/install.gawk
index a0a66370e1e15898f13584906b7848782649cd02..d7fdf6edf2ff42d8ce8ab37c6564d9a8e0064d45 100755
--- a/.travis/install.gawk
+++ b/.travis/install.gawk
@@ -3,12 +3,25 @@
set -e
set -x
-echo "installing latest gawk"
-wget http://git.savannah.gnu.org/cgit/gawk.git/snapshot/gawk-4.1.4.tar.gz
-tar xzf gawk-4.1.4.tar.gz
-cd gawk-4.1.4
+cd "$(mktemp -d)"
+
+version=4.1.4
+
+if [ -n "$1" ] ; then
+ version=$1
+fi
+
+echo "installing gawk $version"
+
+wget http://git.savannah.gnu.org/cgit/gawk.git/snapshot/gawk-$version.tar.gz
+
+tar xzf gawk-$version.tar.gz
+
+cd gawk-$version
+
./configure --prefix="$HOME/opt"
+
make -j 4
+
make install
-cd ../
diff --git a/.travis/install.xdrfile b/.travis/install.xdrfile
index 96fa78f40cbb085d90c908609fef081c615241c0..296a8eaf3d1bb363dd05987c077b16d2af7f36ee 100755
--- a/.travis/install.xdrfile
+++ b/.travis/install.xdrfile
@@ -3,16 +3,25 @@
set -e
set -x
+cd "$(mktemp -d)"
+
echo "installing xdrfile library"
# wget ftp://ftp.gromacs.org/pub/contrib/xdrfile-1.1.4.tar.gz
# xdrfile was removed from gromacs ftp
# as a workaround I added a copy to people.sissa.it/~bussi/plumed
# this complies with its license
+
wget people.sissa.it/~bussi/plumed/xdrfile-1.1.4.tar.gz
+
tar xzf xdrfile-1.1.4.tar.gz
+
cd xdrfile-1.1.4
+
./configure --enable-shared --prefix="$HOME/opt"
+
make
+
make install
+
cd ../
diff --git a/regtest/crystallization/rt-spherical-integral/config b/regtest/crystallization/rt-spherical-integral/config
index 31b0428ecb877af3773c67492e5ed02d76fbda18..86881dd730e4432aee2f654848b24a98396564b2 100644
--- a/regtest/crystallization/rt-spherical-integral/config
+++ b/regtest/crystallization/rt-spherical-integral/config
@@ -1,3 +1,4 @@
type=driver
+plumed_modules=crystallization
# 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/multicolvar/rt-dist-contour/deriv.reference b/regtest/multicolvar/rt-dist-contour/deriv.reference
index 148e921166fac9db5f0425d1aef6402679c141f1..531fbfce89dd19ab6d5085ec44ac370d4d2f0496 100644
--- a/regtest/multicolvar/rt-dist-contour/deriv.reference
+++ b/regtest/multicolvar/rt-dist-contour/deriv.reference
@@ -1,10 +1,10 @@
#! FIELDS time parameter dc.qdist
0.000000 0 0.0000
0.000000 1 0.0000
- 0.000000 2 2.7307
+ 0.000000 2 -2.7307
0.000000 3 0.0000
0.000000 4 0.0000
- 0.000000 5 -2.7307
+ 0.000000 5 2.7307
0.000000 6 0.0000
0.000000 7 0.0000
0.000000 8 0.0000
@@ -13,2044 +13,2044 @@
0.000000 11 0.0000
0.000000 12 0.0000
0.000000 13 0.0000
- 0.000000 14 3.7283
+ 0.000000 14 -3.7283
1.000000 0 -0.0099
1.000000 1 -0.0015
- 1.000000 2 2.8856
+ 1.000000 2 -2.8856
1.000000 3 0.0099
1.000000 4 0.0015
- 1.000000 5 -2.8856
+ 1.000000 5 2.8856
1.000000 6 -0.0000
1.000000 7 -0.0000
1.000000 8 -0.0143
1.000000 9 -0.0000
1.000000 10 -0.0000
1.000000 11 -0.0022
- 1.000000 12 0.0143
- 1.000000 13 0.0022
- 1.000000 14 4.1634
+ 1.000000 12 -0.0143
+ 1.000000 13 -0.0022
+ 1.000000 14 -4.1634
2.000000 0 -0.0191
2.000000 1 -0.0059
- 2.000000 2 3.0068
+ 2.000000 2 -3.0068
2.000000 3 0.0191
2.000000 4 0.0059
- 2.000000 5 -3.0068
+ 2.000000 5 3.0068
2.000000 6 -0.0002
2.000000 7 -0.0001
2.000000 8 -0.0287
2.000000 9 -0.0001
2.000000 10 -0.0000
2.000000 11 -0.0089
- 2.000000 12 0.0287
- 2.000000 13 0.0089
- 2.000000 14 4.5204
+ 2.000000 12 -0.0287
+ 2.000000 13 -0.0089
+ 2.000000 14 -4.5204
3.000000 0 -0.0270
3.000000 1 -0.0130
- 3.000000 2 3.0678
+ 3.000000 2 -3.0678
3.000000 3 0.0270
3.000000 4 0.0130
- 3.000000 5 -3.0678
+ 3.000000 5 3.0678
3.000000 6 -0.0004
3.000000 7 -0.0002
3.000000 8 -0.0414
3.000000 9 -0.0002
3.000000 10 -0.0001
3.000000 11 -0.0200
- 3.000000 12 0.0414
- 3.000000 13 0.0200
- 3.000000 14 4.7057
+ 3.000000 12 -0.0414
+ 3.000000 13 -0.0200
+ 3.000000 14 -4.7057
4.000000 0 -0.0330
4.000000 1 -0.0226
- 4.000000 2 3.0553
+ 4.000000 2 -3.0553
4.000000 3 0.0330
4.000000 4 0.0226
- 4.000000 5 -3.0553
+ 4.000000 5 3.0553
4.000000 6 -0.0005
4.000000 7 -0.0004
4.000000 8 -0.0504
4.000000 9 -0.0004
4.000000 10 -0.0003
4.000000 11 -0.0345
- 4.000000 12 0.0504
- 4.000000 13 0.0345
- 4.000000 14 4.6674
+ 4.000000 12 -0.0504
+ 4.000000 13 -0.0345
+ 4.000000 14 -4.6674
5.000000 0 -0.0366
5.000000 1 -0.0341
- 5.000000 2 2.9720
+ 5.000000 2 -2.9720
5.000000 3 0.0366
5.000000 4 0.0341
- 5.000000 5 -2.9720
+ 5.000000 5 2.9720
5.000000 6 -0.0007
5.000000 7 -0.0006
5.000000 8 -0.0544
5.000000 9 -0.0006
5.000000 10 -0.0006
5.000000 11 -0.0506
- 5.000000 12 0.0544
- 5.000000 13 0.0506
- 5.000000 14 4.4165
+ 5.000000 12 -0.0544
+ 5.000000 13 -0.0506
+ 5.000000 14 -4.4165
6.000000 0 -0.0373
6.000000 1 -0.0470
- 6.000000 2 2.8361
+ 6.000000 2 -2.8361
6.000000 3 0.0373
6.000000 4 0.0470
- 6.000000 5 -2.8361
+ 6.000000 5 2.8361
6.000000 6 -0.0007
6.000000 7 -0.0009
6.000000 8 -0.0529
6.000000 9 -0.0009
6.000000 10 -0.0011
6.000000 11 -0.0666
- 6.000000 12 0.0529
- 6.000000 13 0.0666
- 6.000000 14 4.0218
+ 6.000000 12 -0.0529
+ 6.000000 13 -0.0666
+ 6.000000 14 -4.0218
7.000000 0 -0.0348
7.000000 1 -0.0607
- 7.000000 2 2.6773
+ 7.000000 2 -2.6773
7.000000 3 0.0348
7.000000 4 0.0607
- 7.000000 5 -2.6773
+ 7.000000 5 2.6773
7.000000 6 -0.0006
7.000000 7 -0.0011
7.000000 8 -0.0466
7.000000 9 -0.0011
7.000000 10 -0.0018
7.000000 11 -0.0813
- 7.000000 12 0.0466
- 7.000000 13 0.0813
- 7.000000 14 3.5839
+ 7.000000 12 -0.0466
+ 7.000000 13 -0.0813
+ 7.000000 14 -3.5839
8.000000 0 -0.0290
8.000000 1 -0.0746
- 8.000000 2 2.5300
+ 8.000000 2 -2.5300
8.000000 3 0.0290
8.000000 4 0.0746
- 8.000000 5 -2.5300
+ 8.000000 5 2.5300
8.000000 6 -0.0004
8.000000 7 -0.0011
8.000000 8 -0.0367
8.000000 9 -0.0011
8.000000 10 -0.0028
8.000000 11 -0.0943
- 8.000000 12 0.0367
- 8.000000 13 0.0943
- 8.000000 14 3.2006
+ 8.000000 12 -0.0367
+ 8.000000 13 -0.0943
+ 8.000000 14 -3.2006
9.000000 0 -0.0197
9.000000 1 -0.0878
- 9.000000 2 2.4265
+ 9.000000 2 -2.4265
9.000000 3 0.0197
9.000000 4 0.0878
- 9.000000 5 -2.4265
+ 9.000000 5 2.4265
9.000000 6 -0.0002
9.000000 7 -0.0009
9.000000 8 -0.0239
9.000000 9 -0.0009
9.000000 10 -0.0039
9.000000 11 -0.1065
- 9.000000 12 0.0239
- 9.000000 13 0.1065
- 9.000000 14 2.9440
+ 9.000000 12 -0.0239
+ 9.000000 13 -0.1065
+ 9.000000 14 -2.9440
10.000000 0 -0.0071
10.000000 1 -0.0997
- 10.000000 2 2.3893
+ 10.000000 2 -2.3893
10.000000 3 0.0071
10.000000 4 0.0997
- 10.000000 5 -2.3893
+ 10.000000 5 2.3893
10.000000 6 -0.0000
10.000000 7 -0.0004
10.000000 8 -0.0085
10.000000 9 -0.0004
10.000000 10 -0.0050
10.000000 11 -0.1192
- 10.000000 12 0.0085
- 10.000000 13 0.1192
- 10.000000 14 2.8544
+ 10.000000 12 -0.0085
+ 10.000000 13 -0.1192
+ 10.000000 14 -2.8544
11.000000 0 0.0087
11.000000 1 -0.1097
- 11.000000 2 2.4265
+ 11.000000 2 -2.4265
11.000000 3 -0.0087
11.000000 4 0.1097
- 11.000000 5 -2.4265
+ 11.000000 5 2.4265
11.000000 6 -0.0000
11.000000 7 0.0005
11.000000 8 0.0106
11.000000 9 0.0005
11.000000 10 -0.0060
11.000000 11 -0.1330
- 11.000000 12 -0.0106
- 11.000000 13 0.1330
- 11.000000 14 2.9440
+ 11.000000 12 0.0106
+ 11.000000 13 -0.1330
+ 11.000000 14 -2.9440
12.000000 0 0.0273
12.000000 1 -0.1169
- 12.000000 2 2.5300
+ 12.000000 2 -2.5300
12.000000 3 -0.0273
12.000000 4 0.1169
- 12.000000 5 -2.5300
+ 12.000000 5 2.5300
12.000000 6 -0.0004
12.000000 7 0.0016
12.000000 8 0.0345
12.000000 9 0.0016
12.000000 10 -0.0068
12.000000 11 -0.1478
- 12.000000 12 -0.0345
- 12.000000 13 0.1478
- 12.000000 14 3.2006
+ 12.000000 12 0.0345
+ 12.000000 13 -0.1478
+ 12.000000 14 -3.2006
13.000000 0 0.0481
13.000000 1 -0.1208
- 13.000000 2 2.6773
+ 13.000000 2 -2.6773
13.000000 3 -0.0481
13.000000 4 0.1208
- 13.000000 5 -2.6773
+ 13.000000 5 2.6773
13.000000 6 -0.0012
13.000000 7 0.0029
13.000000 8 0.0644
13.000000 9 0.0029
13.000000 10 -0.0073
13.000000 11 -0.1617
- 13.000000 12 -0.0644
- 13.000000 13 0.1617
- 13.000000 14 3.5839
+ 13.000000 12 0.0644
+ 13.000000 13 -0.1617
+ 13.000000 14 -3.5839
14.000000 0 0.0707
14.000000 1 -0.1208
- 14.000000 2 2.8361
+ 14.000000 2 -2.8361
14.000000 3 -0.0707
14.000000 4 0.1208
- 14.000000 5 -2.8361
+ 14.000000 5 2.8361
14.000000 6 -0.0025
14.000000 7 0.0043
14.000000 8 0.1002
14.000000 9 0.0043
14.000000 10 -0.0073
14.000000 11 -0.1714
- 14.000000 12 -0.1002
- 14.000000 13 0.1714
- 14.000000 14 4.0218
+ 14.000000 12 0.1002
+ 14.000000 13 -0.1714
+ 14.000000 14 -4.0218
15.000000 0 0.0942
15.000000 1 -0.1167
- 15.000000 2 2.9720
+ 15.000000 2 -2.9720
15.000000 3 -0.0942
15.000000 4 0.1167
- 15.000000 5 -2.9720
+ 15.000000 5 2.9720
15.000000 6 -0.0044
15.000000 7 0.0055
15.000000 8 0.1400
15.000000 9 0.0055
15.000000 10 -0.0068
15.000000 11 -0.1734
- 15.000000 12 -0.1400
- 15.000000 13 0.1734
- 15.000000 14 4.4165
+ 15.000000 12 0.1400
+ 15.000000 13 -0.1734
+ 15.000000 14 -4.4165
16.000000 0 0.1180
16.000000 1 -0.1081
- 16.000000 2 3.0553
+ 16.000000 2 -3.0553
16.000000 3 -0.1180
16.000000 4 0.1081
- 16.000000 5 -3.0553
+ 16.000000 5 3.0553
16.000000 6 -0.0070
16.000000 7 0.0064
16.000000 8 0.1802
16.000000 9 0.0064
16.000000 10 -0.0058
16.000000 11 -0.1651
- 16.000000 12 -0.1802
- 16.000000 13 0.1651
- 16.000000 14 4.6674
+ 16.000000 12 0.1802
+ 16.000000 13 -0.1651
+ 16.000000 14 -4.6674
17.000000 0 0.1411
17.000000 1 -0.0948
- 17.000000 2 3.0678
+ 17.000000 2 -3.0678
17.000000 3 -0.1411
17.000000 4 0.0948
- 17.000000 5 -3.0678
+ 17.000000 5 3.0678
17.000000 6 -0.0100
17.000000 7 0.0067
17.000000 8 0.2164
17.000000 9 0.0067
17.000000 10 -0.0045
17.000000 11 -0.1454
- 17.000000 12 -0.2164
- 17.000000 13 0.1454
- 17.000000 14 4.7057
+ 17.000000 12 0.2164
+ 17.000000 13 -0.1454
+ 17.000000 14 -4.7057
18.000000 0 0.1627
18.000000 1 -0.0769
- 18.000000 2 3.0068
+ 18.000000 2 -3.0068
18.000000 3 -0.1627
18.000000 4 0.0769
- 18.000000 5 -3.0068
+ 18.000000 5 3.0068
18.000000 6 -0.0132
18.000000 7 0.0063
18.000000 8 0.2447
18.000000 9 0.0063
18.000000 10 -0.0030
18.000000 11 -0.1157
- 18.000000 12 -0.2447
- 18.000000 13 0.1157
- 18.000000 14 4.5204
+ 18.000000 12 0.2447
+ 18.000000 13 -0.1157
+ 18.000000 14 -4.5204
19.000000 0 0.1820
19.000000 1 -0.0546
- 19.000000 2 2.8856
+ 19.000000 2 -2.8856
19.000000 3 -0.1820
19.000000 4 0.0546
- 19.000000 5 -2.8856
+ 19.000000 5 2.8856
19.000000 6 -0.0166
19.000000 7 0.0050
19.000000 8 0.2626
19.000000 9 0.0050
19.000000 10 -0.0015
19.000000 11 -0.0788
- 19.000000 12 -0.2626
- 19.000000 13 0.0788
- 19.000000 14 4.1634
+ 19.000000 12 0.2626
+ 19.000000 13 -0.0788
+ 19.000000 14 -4.1634
20.000000 0 0.1980
20.000000 1 -0.0282
- 20.000000 2 2.7307
+ 20.000000 2 -2.7307
20.000000 3 -0.1980
20.000000 4 0.0282
- 20.000000 5 -2.7307
+ 20.000000 5 2.7307
20.000000 6 -0.0196
20.000000 7 0.0028
20.000000 8 0.2703
20.000000 9 0.0028
20.000000 10 -0.0004
20.000000 11 -0.0385
- 20.000000 12 -0.2703
- 20.000000 13 0.0385
- 20.000000 14 3.7283
+ 20.000000 12 0.2703
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+ 20.000000 14 -3.7283
21.000000 0 0.2100
21.000000 1 0.0018
- 21.000000 2 2.5757
+ 21.000000 2 -2.5757
21.000000 3 -0.2100
21.000000 4 -0.0018
- 21.000000 5 -2.5757
+ 21.000000 5 2.5757
21.000000 6 -0.0220
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21.000000 11 0.0023
- 21.000000 12 -0.2704
- 21.000000 13 -0.0023
- 21.000000 14 3.3171
+ 21.000000 12 0.2704
+ 21.000000 13 0.0023
+ 21.000000 14 -3.3171
22.000000 0 0.2172
22.000000 1 0.0347
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22.000000 3 -0.2172
22.000000 4 -0.0347
- 22.000000 5 -2.4545
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22.000000 6 -0.0236
22.000000 7 -0.0038
22.000000 8 0.2666
22.000000 9 -0.0038
22.000000 10 -0.0006
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- 22.000000 12 -0.2666
- 22.000000 13 -0.0426
- 22.000000 14 3.0123
+ 22.000000 12 0.2666
+ 22.000000 13 0.0426
+ 22.000000 14 -3.0123
23.000000 0 0.2191
23.000000 1 0.0698
- 23.000000 2 2.3935
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23.000000 4 -0.0698
- 23.000000 5 -2.3935
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23.000000 6 -0.0240
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23.000000 8 0.2623
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23.000000 11 0.0836
- 23.000000 12 -0.2623
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+ 23.000000 12 0.2623
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+ 23.000000 14 -2.8645
24.000000 0 0.2152
24.000000 1 0.1062
- 24.000000 2 2.4060
+ 24.000000 2 -2.4060
24.000000 3 -0.2152
24.000000 4 -0.1062
- 24.000000 5 -2.4060
+ 24.000000 5 2.4060
24.000000 6 -0.0232
24.000000 7 -0.0114
24.000000 8 0.2589
24.000000 9 -0.0114
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24.000000 11 0.1278
- 24.000000 12 -0.2589
- 24.000000 13 -0.1278
- 24.000000 14 2.8945
+ 24.000000 12 0.2589
+ 24.000000 13 0.1278
+ 24.000000 14 -2.8945
25.000000 0 0.2051
25.000000 1 0.1429
- 25.000000 2 2.4893
+ 25.000000 2 -2.4893
25.000000 3 -0.2051
25.000000 4 -0.1429
- 25.000000 5 -2.4893
+ 25.000000 5 2.4893
25.000000 6 -0.0210
25.000000 7 -0.0147
25.000000 8 0.2553
25.000000 9 -0.0147
25.000000 10 -0.0102
25.000000 11 0.1778
- 25.000000 12 -0.2553
- 25.000000 13 -0.1778
- 25.000000 14 3.0983
+ 25.000000 12 0.2553
+ 25.000000 13 0.1778
+ 25.000000 14 -3.0983
26.000000 0 0.1887
26.000000 1 0.1788
- 26.000000 2 2.6252
+ 26.000000 2 -2.6252
26.000000 3 -0.1887
26.000000 4 -0.1788
- 26.000000 5 -2.6252
+ 26.000000 5 2.6252
26.000000 6 -0.0178
26.000000 7 -0.0169
26.000000 8 0.2477
26.000000 9 -0.0169
26.000000 10 -0.0160
26.000000 11 0.2347
- 26.000000 12 -0.2477
- 26.000000 13 -0.2347
- 26.000000 14 3.4458
+ 26.000000 12 0.2477
+ 26.000000 13 0.2347
+ 26.000000 14 -3.4458
27.000000 0 0.1661
27.000000 1 0.2129
- 27.000000 2 2.7841
+ 27.000000 2 -2.7841
27.000000 3 -0.1661
27.000000 4 -0.2129
- 27.000000 5 -2.7841
+ 27.000000 5 2.7841
27.000000 6 -0.0138
27.000000 7 -0.0177
27.000000 8 0.2311
27.000000 9 -0.0177
27.000000 10 -0.0227
27.000000 11 0.2964
- 27.000000 12 -0.2311
- 27.000000 13 -0.2964
- 27.000000 14 3.8755
+ 27.000000 12 0.2311
+ 27.000000 13 0.2964
+ 27.000000 14 -3.8755
28.000000 0 0.1373
28.000000 1 0.2440
- 28.000000 2 2.9313
+ 28.000000 2 -2.9313
28.000000 3 -0.1373
28.000000 4 -0.2440
- 28.000000 5 -2.9313
+ 28.000000 5 2.9313
28.000000 6 -0.0094
28.000000 7 -0.0168
28.000000 8 0.2012
28.000000 9 -0.0168
28.000000 10 -0.0298
28.000000 11 0.3577
- 28.000000 12 -0.2012
- 28.000000 13 -0.3577
- 28.000000 14 4.2963
+ 28.000000 12 0.2012
+ 28.000000 13 0.3577
+ 28.000000 14 -4.2963
29.000000 0 0.1028
29.000000 1 0.2712
- 29.000000 2 3.0348
+ 29.000000 2 -3.0348
29.000000 3 -0.1028
29.000000 4 -0.2712
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diff --git a/src/core/PlumedMain.cpp b/src/core/PlumedMain.cpp
index 280952028493d4e64092a4d5b25bb70a0e30ab7e..007cdf8ae8a6c534fdb3792a19bf5bcd7edf8806 100644
--- a/src/core/PlumedMain.cpp
+++ b/src/core/PlumedMain.cpp
@@ -548,7 +548,7 @@ void PlumedMain::readInputWords(const std::vector<std::string> & words){
for(unsigned i=0;i<interpreted.size();++i) log<<" "<<interpreted[i];
log<<"\n";
log.flush();
- plumed_merror("I cannot understand line");
+ plumed_merror("I cannot understand line " + interpreted[0] + " " + interpreted[1]);
};
action->checkRead();
actionSet.push_back(action);
diff --git a/src/multicolvar/DistanceFromContour.cpp b/src/multicolvar/DistanceFromContour.cpp
index 0de8592ace12af95d3f9419eae32fd28278f01ec..35e792a735786ebca6435e5e2de9f98eb1328f01 100644
--- a/src/multicolvar/DistanceFromContour.cpp
+++ b/src/multicolvar/DistanceFromContour.cpp
@@ -264,36 +264,31 @@ void DistanceFromContour::calculate(){
// This deals with periodic boundary conditions - if we are inside the membrane the sum of the absolute
// distances from the contours should add up to the spacing. When this is not the case we must be outside
// the contour
- if( predir==-1 && (fabs(root1[dir])+fabs(root2[dir]))>(spacing+pbc_param) ) predir=1;
+ // if( predir==-1 && (fabs(root1[dir])+fabs(root2[dir]))>(spacing+pbc_param) ) predir=1;
// Set the final value to root that is closest to the "origin" = position of atom
if( fabs(root1[dir])<fabs(root2[dir]) ){
getPntrToComponent("dist1")->set( predir*fabs(root1[dir]) );
getPntrToComponent("dist2")->set( fabs(root2[dir]) );
- getPntrToComponent("qdist")->set( predir*fabs(root1[dir])*fabs(root2[dir]) );
} else {
getPntrToComponent("dist1")->set( predir*fabs(root2[dir]) );
getPntrToComponent("dist2")->set( fabs(root1[dir]) );
- getPntrToComponent("qdist")->set( predir*fabs(root2[dir])*fabs(root1[dir]) );
}
+ getPntrToComponent("qdist")->set( root2[dir]*root1[dir] );
// Now calculate the derivatives
if( !doNotCalculateDerivatives() ){
Value* ival=myvalue_vessel->getFinalValue(); ival->clearDerivatives();
std::vector<double> root1v(3); for(unsigned i=0;i<3;++i) root1v[i]=root1[i];
derivTime=true; std::vector<double> der(3); getDifferenceFromContour( root1v, der ); double prefactor;
- if( mybasemulticolvars[0]->isDensity() ){
- if( fabs(root1[dir])<fabs(root2[dir]) ) prefactor = predir*fabs(root1[dir]) / myderiv_vessel->getOutputValue();
- else prefactor = fabs(root2[dir]);
- } else plumed_error();
+ if( mybasemulticolvars[0]->isDensity() ) prefactor = root2[dir] / myderiv_vessel->getOutputValue();
+ else plumed_error();
Value* val=getPntrToComponent("qdist");
for(unsigned i=0;i<val->getNumberOfDerivatives();++i) val->setDerivative( i, -prefactor*ival->getDerivative(i) );
ival->clearDerivatives();
std::vector<double> root2v(3); for(unsigned i=0;i<3;++i) root2v[i]=root2[i];
getDifferenceFromContour( root2v, der );
- if( mybasemulticolvars[0]->isDensity() ){
- if( fabs(root1[dir])<fabs(root2[dir]) ) prefactor = fabs(root2[dir]) / myderiv_vessel->getOutputValue();
- else prefactor = predir*fabs(root2[dir]) / myderiv_vessel->getOutputValue();
- } else plumed_error();
+ if( mybasemulticolvars[0]->isDensity() ) prefactor = root1[dir] / myderiv_vessel->getOutputValue();
+ else plumed_error();
for(unsigned i=0;i<val->getNumberOfDerivatives();++i) val->addDerivative( i, -prefactor*ival->getDerivative(i) );
}
}