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Commit 518a4bc

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Gareth Aneurin Tribello
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Fix for issue with PLANE command
If you calculate the colvar PLANE with only one PLANE (as opposed to a vector of PLANES) the code doesn't work at the moment becuase the data is not passed correctly to the values. This fixes this problem.
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5 files changed

+142
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lines changed

‎regtest/basic/rt-plane/DERIVATIVES.reference‎

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#! FIELDS time parameter p1.x p1.y p1.z p1n.x p1n.y p1n.z
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0.000000 0 0.00000 2.44705 0.80805 0.00000 2.44705 0.80805
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0.000000 1 -2.44705 0.00000 0.02851 -2.44705 0.00000 0.02851
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0.000000 2 -0.80805 -0.02851 0.00000 -0.80805 -0.02851 0.00000
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0.000000 3 0.00000 -2.44705 -0.80805 0.00000 -2.44705 -0.80805
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0.000000 4 2.44705 0.00000 -0.02851 2.44705 0.00000 -0.02851
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0.000000 5 0.80805 0.02851 0.00000 0.80805 0.02851 0.00000
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0.000000 6 0.00000 1.64577 -0.05614 0.00000 1.64577 -0.05614
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0.000000 7 -1.64577 0.00000 -0.05161 -1.64577 0.00000 -0.05161
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0.000000 8 0.05614 0.05161 0.00000 0.05614 0.05161 0.00000
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0.000000 9 0.00000 -1.64577 0.05614 0.00000 -1.64577 0.05614
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0.000000 10 1.64577 0.00000 0.05161 1.64577 0.00000 0.05161
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0.000000 11 -0.05614 -0.05161 0.00000 -0.05614 -0.05161 0.00000
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0.000000 12 0.00000 -0.17322 -0.04011 -0.00000 -0.17322 -0.04011
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0.000000 13 0.17322 0.00000 0.00000 0.17322 0.00000 0.00000
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0.000000 14 0.04011 0.00000 0.00000 0.04011 -0.00000 0.00000
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0.000000 15 0.00000 1.46726 0.00000 -0.00000 1.46726 -0.00000
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0.000000 16 -1.46726 0.00000 -0.04011 -1.46726 0.00000 -0.04011
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0.000000 17 0.00000 0.04011 0.00000 -0.00000 0.04011 0.00000
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0.000000 18 0.00000 0.00000 1.46726 -0.00000 -0.00000 1.46726
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0.000000 19 0.00000 0.00000 0.17322 -0.00000 0.00000 0.17322
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0.000000 20 -1.46726 -0.17322 0.00000 -1.46726 -0.17322 0.00000
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0.050000 0 0.00000 2.40244 0.78108 0.00000 2.40244 0.78108
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0.050000 1 -2.40244 0.00000 0.02046 -2.40244 0.00000 0.02046
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0.050000 2 -0.78108 -0.02046 0.00000 -0.78108 -0.02046 0.00000
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0.050000 3 0.00000 -2.40244 -0.78108 0.00000 -2.40244 -0.78108
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0.050000 4 2.40244 0.00000 -0.02046 2.40244 0.00000 -0.02046
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0.050000 5 0.78108 0.02046 0.00000 0.78108 0.02046 0.00000
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0.050000 6 0.00000 1.64198 -0.09163 0.00000 1.64198 -0.09163
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0.050000 7 -1.64198 0.00000 -0.10765 -1.64198 0.00000 -0.10765
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0.050000 8 0.09163 0.10765 0.00000 0.09163 0.10765 0.00000
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0.050000 9 0.00000 -1.64198 0.09163 0.00000 -1.64198 0.09163
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0.050000 10 1.64198 0.00000 0.10765 1.64198 0.00000 0.10765
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0.050000 11 -0.09163 -0.10765 0.00000 -0.09163 -0.10765 0.00000
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0.050000 12 0.00000 -0.29224 -0.08221 0.00000 -0.29224 -0.08221
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0.050000 13 0.29224 0.00000 0.00000 0.29224 -0.00000 -0.00000
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0.050000 14 0.08221 0.00000 0.00000 0.08221 -0.00000 -0.00000
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0.050000 15 0.00000 1.50265 0.00000 0.00000 1.50265 0.00000
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0.050000 16 -1.50265 0.00000 -0.08221 -1.50265 -0.00000 -0.08221
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0.050000 17 0.00000 0.08221 0.00000 0.00000 0.08221 -0.00000
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0.050000 18 0.00000 0.00000 1.50265 0.00000 -0.00000 1.50265
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0.050000 19 0.00000 0.00000 0.29224 0.00000 -0.00000 0.29224
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0.050000 20 -1.50265 -0.29224 0.00000 -1.50265 -0.29224 -0.00000
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0.100000 0 0.00000 2.40342 0.74357 0.00000 2.40342 0.74357
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0.100000 1 -2.40342 0.00000 0.00469 -2.40342 0.00000 0.00469
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0.100000 2 -0.74357 -0.00469 0.00000 -0.74357 -0.00469 0.00000
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0.100000 3 0.00000 -2.40342 -0.74357 0.00000 -2.40342 -0.74357
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0.100000 4 2.40342 0.00000 -0.00469 2.40342 0.00000 -0.00469
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0.100000 5 0.74357 0.00469 0.00000 0.74357 0.00469 0.00000
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0.100000 6 0.00000 1.62939 -0.10927 0.00000 1.62939 -0.10927
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0.100000 7 -1.62939 0.00000 -0.16810 -1.62939 0.00000 -0.16810
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0.100000 8 0.10927 0.16810 0.00000 0.10927 0.16810 0.00000
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0.100000 9 0.00000 -1.62939 0.10927 0.00000 -1.62939 0.10927
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0.100000 10 1.62939 0.00000 0.16810 1.62939 0.00000 0.16810
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0.100000 11 -0.10927 -0.16810 0.00000 -0.10927 -0.16810 0.00000
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0.100000 12 0.00000 -0.41166 -0.12449 0.00000 -0.41166 -0.12449
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0.100000 13 0.41166 0.00000 0.00000 0.41166 0.00000 0.00000
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0.100000 14 0.12449 0.00000 0.00000 0.12449 -0.00000 0.00000
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0.100000 15 0.00000 1.47421 0.00000 0.00000 1.47421 0.00000
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0.100000 16 -1.47421 0.00000 -0.12449 -1.47421 0.00000 -0.12449
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0.100000 17 0.00000 0.12449 0.00000 -0.00000 0.12449 0.00000
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0.100000 18 0.00000 0.00000 1.47421 0.00000 0.00000 1.47421
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0.100000 19 0.00000 0.00000 0.41166 0.00000 0.00000 0.41166
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0.100000 20 -1.47421 -0.41166 0.00000 -1.47421 -0.41166 0.00000
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0.150000 0 0.00000 2.44419 0.69638 0.00000 2.44419 0.69638
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0.150000 1 -2.44419 0.00000 -0.02175 -2.44419 0.00000 -0.02175
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0.150000 2 -0.69638 0.02175 0.00000 -0.69638 0.02175 0.00000
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0.150000 3 0.00000 -2.44419 -0.69638 0.00000 -2.44419 -0.69638
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0.150000 4 2.44419 0.00000 0.02175 2.44419 0.00000 0.02175
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0.150000 5 0.69638 -0.02175 0.00000 0.69638 -0.02175 0.00000
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0.150000 6 0.00000 1.61477 -0.11830 0.00000 1.61477 -0.11830
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0.150000 7 -1.61477 0.00000 -0.22124 -1.61477 0.00000 -0.22124
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0.150000 8 0.11830 0.22124 0.00000 0.11830 0.22124 0.00000
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0.150000 9 0.00000 -1.61477 0.11830 0.00000 -1.61477 0.11830
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0.150000 10 1.61477 0.00000 0.22124 1.61477 0.00000 0.22124
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0.150000 11 -0.11830 -0.22124 0.00000 -0.11830 -0.22124 0.00000
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0.150000 12 0.00000 -0.50563 -0.15664 0.00000 -0.50563 -0.15664
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0.150000 13 0.50563 0.00000 0.00000 0.50563 0.00000 -0.00000
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0.150000 14 0.15664 0.00000 0.00000 0.15664 0.00000 0.00000
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0.150000 15 0.00000 1.41365 0.00000 0.00000 1.41365 0.00000
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0.150000 16 -1.41365 0.00000 -0.15664 -1.41365 0.00000 -0.15664
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0.150000 17 0.00000 0.15664 0.00000 0.00000 0.15664 0.00000
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0.150000 18 0.00000 0.00000 1.41365 0.00000 0.00000 1.41365
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0.150000 19 0.00000 0.00000 0.50563 0.00000 0.00000 0.50563
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0.150000 20 -1.41365 -0.50563 0.00000 -1.41365 -0.50563 0.00000
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0.200000 0 0.00000 2.47711 0.64867 0.00000 2.47711 0.64867
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0.200000 1 -2.47711 0.00000 -0.04847 -2.47711 0.00000 -0.04847
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0.200000 2 -0.64867 0.04847 0.00000 -0.64867 0.04847 0.00000
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0.200000 3 0.00000 -2.47711 -0.64867 0.00000 -2.47711 -0.64867
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0.200000 4 2.47711 0.00000 0.04847 2.47711 0.00000 0.04847
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0.200000 5 0.64867 -0.04847 0.00000 0.64867 -0.04847 0.00000
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0.200000 6 0.00000 1.62124 -0.15580 0.00000 1.62124 -0.15580
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0.200000 7 -1.62124 0.00000 -0.23917 -1.62124 0.00000 -0.23917
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0.200000 8 0.15580 0.23917 0.00000 0.15580 0.23917 0.00000
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0.200000 9 0.00000 -1.62124 0.15580 0.00000 -1.62124 0.15580
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0.200000 10 1.62124 0.00000 0.23917 1.62124 0.00000 0.23917
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0.200000 11 -0.15580 -0.23917 0.00000 -0.15580 -0.23917 0.00000
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0.200000 12 0.00000 -0.51386 -0.16269 0.00000 -0.51386 -0.16269
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0.200000 13 0.51386 0.00000 0.00000 0.51386 0.00000 0.00000
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0.200000 14 0.16269 0.00000 0.00000 0.16269 0.00000 0.00000
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0.200000 15 0.00000 1.43758 0.00000 0.00000 1.43758 -0.00000
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0.200000 16 -1.43758 0.00000 -0.16269 -1.43758 0.00000 -0.16269
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0.200000 17 0.00000 0.16269 0.00000 0.00000 0.16269 0.00000
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0.200000 18 0.00000 0.00000 1.43758 0.00000 0.00000 1.43758
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0.200000 19 0.00000 0.00000 0.51386 0.00000 0.00000 0.51386
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0.200000 20 -1.43758 -0.51386 0.00000 -1.43758 -0.51386 0.00000

‎regtest/basic/rt-plane/Makefile‎

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include ../../scripts/test.make

‎regtest/basic/rt-plane/config‎

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type=driver
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# this is to test a different name
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arg="--plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f"
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extra_files="../../trajectories/trajectory.xyz"

‎regtest/basic/rt-plane/plumed.dat‎

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p1: PLANE ATOMS=2,6,3
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p1n: PLANE ATOMS=2,6,3 NUMERICAL_DERIVATIVES
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DUMPDERIVATIVES ...
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STRIDE=10
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ARG=p1.*,p1n.*
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FILE=DERIVATIVES
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FMT=%8.5f
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... DUMPDERIVATIVES
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ENDPLUMED
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‎src/colvar/Plane.cpp‎

Lines changed: 19 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -149,11 +149,27 @@ void Plane::calculate() {
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makeWhole();
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}
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calculateCV( 0, masses, charges, getPositions(), value, derivs, virial, this );
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setValue( value[0] );
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Value* valuex=getPntrToComponent("x");
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Value* valuey=getPntrToComponent("y");
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Value* valuez=getPntrToComponent("z");
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153156
for(unsigned i=0; i<derivs[0].size(); ++i) {
154-
setAtomsDerivatives( i, derivs[0][i] );
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setAtomsDerivatives( valuex, i, derivs[0][i] );
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}
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setBoxDerivatives( valuex, virial[0] );
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valuex->set( value[0] );
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for(unsigned i=0; i<derivs[1].size(); ++i) {
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setAtomsDerivatives( valuey, i, derivs[1][i] );
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}
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setBoxDerivatives( valuey, virial[1] );
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valuey->set( value[1] );
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for(unsigned i=0; i<derivs[2].size(); ++i) {
169+
setAtomsDerivatives( valuez, i, derivs[2][i] );
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}
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setBoxDerivatives( virial[0] );
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setBoxDerivatives( valuez, virial[2] );
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valuez->set( value[2] );
157173
}
158174

159175
void Plane::calculateCV( const unsigned& mode, const std::vector<double>& masses, const std::vector<double>& charges,

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