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Commit ffe1b1f9 authored by Giovanni Bussi's avatar Giovanni Bussi
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Merge branch 'v2.2' into v2.3

parents ed4a929b b965e5b6
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CHANGES/v2.2.txt
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......@@ -189,6 +189,7 @@ See branch \branch{v2.2} on git repository.
For users:
- Fixed a problem with large step numbers in driver (see \issue{209}).
- Fixed a problem leading to crashes when using switching functions without cutoff with some compiler (see \issue{210}).
- Fixed a bug when using \ref FIT_TO_TEMPLATE and domain decomposition (see \issue{214}).
- Root dir is logged to allow easier debugging of problems.
*/
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include ../../scripts/test.make
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ATOM 1 HH31 ACE 1 -0.000 -0.000 00.000 1.00 0.00
ATOM 2 HH31 ACE 1 -0.000 -0.000 00.000 0.50 0.00
END
regtest/basic/rt63-mpi/config 0 → 100644
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type=driver
mpiprocs=2
arg="--plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --igro helix.input.gro --dump-forces ff --dump-full-virial --debug-dd"
regtest/basic/rt63-mpi/ff.0.reference 0 → 100644
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regtest/basic/rt63-mpi/ff.1.reference 0 → 100644
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regtest/basic/rt63-mpi/helix.input.gro 0 → 100644
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regtest/basic/rt63-mpi/helix.pdb 0 → 100644
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ATOM 1 HH31 ACE 1 -9.105 -2.402 21.804 0.00 0.00
ATOM 2 CH3 ACE 1 -8.930 -3.352 22.308 0.00 0.00
ATOM 3 HH32 ACE 1 -9.504 -3.501 23.223 0.00 0.00
ATOM 4 HH33 ACE 1 -9.067 -4.173 21.604 0.00 0.00
ATOM 5 C ACE 1 -7.450 -3.303 22.659 0.00 0.00
ATOM 6 O ACE 1 -6.909 -2.213 22.834 0.00 0.00
ATOM 7 N ALA 2 -6.812 -4.475 22.683 0.00 0.00
ATOM 8 H ALA 2 -7.324 -5.304 22.418 0.00 0.00
ATOM 9 CA ALA 2 -5.397 -4.597 22.969 1.00 1.00
ATOM 10 HA ALA 2 -4.882 -3.860 22.353 0.00 0.00
ATOM 11 CB ALA 2 -5.075 -4.366 24.443 0.00 0.00
ATOM 12 HB1 ALA 2 -4.010 -4.351 24.674 0.00 0.00
ATOM 13 HB2 ALA 2 -5.438 -5.144 25.114 0.00 0.00
ATOM 14 HB3 ALA 2 -5.561 -3.425 24.701 0.00 0.00
ATOM 15 C ALA 2 -4.909 -5.948 22.466 0.00 0.00
ATOM 16 O ALA 2 -4.728 -6.129 21.264 0.00 0.00
ATOM 17 N ALA 3 -4.848 -6.965 23.328 0.00 0.00
ATOM 18 H ALA 3 -5.121 -6.790 24.285 0.00 0.00
ATOM 19 CA ALA 3 -4.722 -8.399 23.159 1.00 1.00
ATOM 20 HA ALA 3 -3.768 -8.522 22.645 0.00 0.00
ATOM 21 CB ALA 3 -4.609 -9.090 24.515 0.00 0.00
ATOM 22 HB1 ALA 3 -3.760 -8.709 25.082 0.00 0.00
ATOM 23 HB2 ALA 3 -4.510 -10.142 24.246 0.00 0.00
ATOM 24 HB3 ALA 3 -5.489 -9.125 25.158 0.00 0.00
ATOM 25 C ALA 3 -5.753 -9.060 22.256 0.00 0.00
ATOM 26 O ALA 3 -5.359 -9.754 21.321 0.00 0.00
ATOM 27 N ALA 4 -7.036 -8.865 22.568 0.00 0.00
ATOM 28 H ALA 4 -7.040 -8.063 23.182 0.00 0.00
ATOM 29 CA ALA 4 -8.201 -9.234 21.789 1.00 1.00
ATOM 30 HA ALA 4 -7.869 -9.845 20.949 0.00 0.00
ATOM 31 CB ALA 4 -9.165 -9.957 22.726 0.00 0.00
ATOM 32 HB1 ALA 4 -8.633 -10.787 23.190 0.00 0.00
ATOM 33 HB2 ALA 4 -10.099 -10.329 22.305 0.00 0.00
ATOM 34 HB3 ALA 4 -9.400 -9.257 23.527 0.00 0.00
ATOM 35 C ALA 4 -8.724 -7.907 21.258 0.00 0.00
ATOM 36 O ALA 4 -8.269 -6.846 21.676 0.00 0.00
ATOM 37 N ALA 5 -9.566 -7.899 20.221 0.00 0.00
ATOM 38 H ALA 5 -9.630 -8.819 19.810 0.00 0.00
ATOM 39 CA ALA 5 -9.923 -6.793 19.356 1.00 1.00
ATOM 40 HA ALA 5 -10.138 -5.948 20.009 0.00 0.00
ATOM 41 CB ALA 5 -8.791 -6.404 18.409 0.00 0.00
ATOM 42 HB1 ALA 5 -8.531 -7.143 17.651 0.00 0.00
ATOM 43 HB2 ALA 5 -7.859 -6.290 18.963 0.00 0.00
ATOM 44 HB3 ALA 5 -8.983 -5.483 17.859 0.00 0.00
ATOM 45 C ALA 5 -11.178 -7.047 18.532 0.00 0.00
ATOM 46 O ALA 5 -11.516 -8.217 18.366 0.00 0.00
ATOM 47 N ALA 6 -11.927 -6.054 18.049 0.00 0.00
ATOM 48 H ALA 6 -11.603 -5.097 18.052 0.00 0.00
ATOM 49 CA ALA 6 -13.240 -6.259 17.469 1.00 1.00
ATOM 50 HA ALA 6 -13.121 -7.160 16.866 0.00 0.00
ATOM 51 CB ALA 6 -14.367 -6.396 18.489 0.00 0.00
ATOM 52 HB1 ALA 6 -15.329 -6.504 17.990 0.00 0.00
ATOM 53 HB2 ALA 6 -14.356 -5.552 19.178 0.00 0.00
ATOM 54 HB3 ALA 6 -14.135 -7.227 19.155 0.00 0.00
ATOM 55 C ALA 6 -13.632 -5.087 16.582 0.00 0.00
ATOM 56 O ALA 6 -13.364 -3.936 16.918 0.00 0.00
ATOM 57 N ALA 7 -14.207 -5.433 15.428 0.00 0.00
ATOM 58 H ALA 7 -14.289 -6.440 15.399 0.00 0.00
ATOM 59 CA ALA 7 -14.898 -4.580 14.482 1.00 1.00
ATOM 60 HA ALA 7 -15.364 -3.792 15.074 0.00 0.00
ATOM 61 CB ALA 7 -13.891 -3.800 13.642 0.00 0.00
ATOM 62 HB1 ALA 7 -14.478 -3.098 13.049 0.00 0.00
ATOM 63 HB2 ALA 7 -13.232 -4.434 13.048 0.00 0.00
ATOM 64 HB3 ALA 7 -13.289 -3.155 14.282 0.00 0.00
ATOM 65 C ALA 7 -15.946 -5.170 13.549 0.00 0.00
ATOM 66 O ALA 7 -17.154 -5.054 13.744 0.00 0.00
ATOM 67 N ALA 8 -15.477 -6.023 12.635 0.00 0.00
ATOM 68 H ALA 8 -14.472 -6.108 12.571 0.00 0.00
ATOM 69 CA ALA 8 -16.137 -7.083 11.902 1.00 1.00
ATOM 70 HA ALA 8 -17.209 -7.030 12.095 0.00 0.00
ATOM 71 CB ALA 8 -15.913 -6.901 10.403 0.00 0.00
ATOM 72 HB1 ALA 8 -16.476 -6.072 9.975 0.00 0.00
ATOM 73 HB2 ALA 8 -16.105 -7.811 9.835 0.00 0.00
ATOM 74 HB3 ALA 8 -14.837 -6.728 10.420 0.00 0.00
ATOM 75 C ALA 8 -15.549 -8.405 12.374 0.00 0.00
ATOM 76 O ALA 8 -14.368 -8.711 12.226 0.00 0.00
ATOM 77 N ALA 9 -16.457 -9.114 13.049 0.00 0.00
ATOM 78 H ALA 9 -17.362 -8.674 13.143 0.00 0.00
ATOM 79 CA ALA 9 -16.134 -10.157 14.001 1.00 1.00
ATOM 80 HA ALA 9 -17.002 -10.541 14.537 0.00 0.00
ATOM 81 CB ALA 9 -15.583 -11.305 13.160 0.00 0.00
ATOM 82 HB1 ALA 9 -14.572 -10.975 12.918 0.00 0.00
ATOM 83 HB2 ALA 9 -16.217 -11.496 12.294 0.00 0.00
ATOM 84 HB3 ALA 9 -15.599 -12.271 13.664 0.00 0.00
ATOM 85 C ALA 9 -15.269 -9.591 15.119 0.00 0.00
ATOM 86 O ALA 9 -15.214 -8.375 15.293 0.00 0.00
ATOM 87 N ALA 10 -14.681 -10.478 15.924 0.00 0.00
ATOM 88 H ALA 10 -14.907 -11.462 15.897 0.00 0.00
ATOM 89 CA ALA 10 -13.672 -10.148 16.910 1.00 1.00
ATOM 90 HA ALA 10 -13.288 -9.136 16.780 0.00 0.00
ATOM 91 CB ALA 10 -14.348 -10.169 18.278 0.00 0.00
ATOM 92 HB1 ALA 10 -14.897 -9.229 18.335 0.00 0.00
ATOM 93 HB2 ALA 10 -13.581 -10.251 19.048 0.00 0.00
ATOM 94 HB3 ALA 10 -14.889 -11.094 18.478 0.00 0.00
ATOM 95 C ALA 10 -12.514 -11.131 16.810 0.00 0.00
ATOM 96 O ALA 10 -12.670 -12.212 16.247 0.00 0.00
ATOM 97 N ALA 11 -11.304 -10.734 17.209 0.00 0.00
ATOM 98 H ALA 11 -11.300 -9.774 17.523 0.00 0.00
ATOM 99 CA ALA 11 -10.028 -11.384 16.987 1.00 1.00
ATOM 100 HA ALA 11 -10.121 -12.468 16.930 0.00 0.00
ATOM 101 CB ALA 11 -9.496 -11.025 15.603 0.00 0.00
ATOM 102 HB1 ALA 11 -8.583 -11.593 15.421 0.00 0.00
ATOM 103 HB2 ALA 11 -9.380 -9.942 15.574 0.00 0.00
ATOM 104 HB3 ALA 11 -10.131 -11.309 14.763 0.00 0.00
ATOM 105 C ALA 11 -9.012 -11.121 18.089 0.00 0.00
ATOM 106 O ALA 11 -9.298 -10.314 18.971 0.00 0.00
ATOM 107 N ALA 12 -7.836 -11.750 18.022 0.00 0.00
ATOM 108 H ALA 12 -7.676 -12.430 17.292 0.00 0.00
ATOM 109 CA ALA 12 -6.626 -11.294 18.676 1.00 1.00
ATOM 110 HA ALA 12 -6.953 -10.965 19.663 0.00 0.00
ATOM 111 CB ALA 12 -5.678 -12.473 18.875 0.00 0.00
ATOM 112 HB1 ALA 12 -5.215 -12.710 17.917 0.00 0.00
ATOM 113 HB2 ALA 12 -6.285 -13.303 19.237 0.00 0.00
ATOM 114 HB3 ALA 12 -4.881 -12.167 19.553 0.00 0.00
ATOM 115 C ALA 12 -6.012 -10.138 17.899 0.00 0.00
ATOM 116 O ALA 12 -6.378 -9.893 16.752 0.00 0.00
ATOM 117 N ALA 13 -5.091 -9.417 18.543 0.00 0.00
ATOM 118 H ALA 13 -5.077 -9.637 19.529 0.00 0.00
ATOM 119 CA ALA 13 -4.233 -8.407 17.956 1.00 1.00
ATOM 120 HA ALA 13 -3.980 -8.732 16.947 0.00 0.00
ATOM 121 CB ALA 13 -4.967 -7.073 17.857 0.00 0.00
ATOM 122 HB1 ALA 13 -4.295 -6.295 17.497 0.00 0.00
ATOM 123 HB2 ALA 13 -5.447 -6.756 18.783 0.00 0.00
ATOM 124 HB3 ALA 13 -5.784 -7.235 17.154 0.00 0.00
ATOM 125 C ALA 13 -2.955 -8.248 18.767 0.00 0.00
ATOM 126 O ALA 13 -1.984 -8.964 18.535 0.00 0.00
ATOM 127 N NME 14 -2.923 -7.389 19.788 0.00 0.00
ATOM 128 H NME 14 -3.729 -6.821 20.007 0.00 0.00
ATOM 129 CH3 NME 14 -1.690 -7.089 20.487 0.00 0.00
ATOM 130 HH31 NME 14 -1.873 -6.629 21.459 0.00 0.00
ATOM 131 HH32 NME 14 -1.152 -6.284 19.986 0.00 0.00
ATOM 132 HH33 NME 14 -1.135 -8.020 20.602 0.00 0.00
END
regtest/basic/rt63-mpi/plumed.dat 0 → 100644
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src/core/ActionAtomistic.h
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src/core/Atoms.cpp
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......@@ -58,6 +58,7 @@ Atoms::Atoms(PlumedMain&plumed):
naturalUnits(false),
timestep(0.0),
forceOnEnergy(0.0),
zeroallforces(false),
kbT(0.0),
asyncSent(false),
atomsNeeded(false),
......@@ -165,7 +166,7 @@ void Atoms::shareAll(){
void Atoms::share(const std::set<AtomNumber>& unique){
plumed_assert( positionsHaveBeenSet==3 && massesHaveBeenSet );
virial.zero();
if(int(gatindex.size())==natoms){
if(zeroallforces || int(gatindex.size())==natoms){
for(int i=0;i<natoms;i++) forces[i].zero();
} else {
for(unsigned i=0;i<gatindex.size();i++) forces[gatindex[i]].zero();
......
src/core/Atoms.h
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src/generic/FitToTemplate.cpp
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