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SQUASHING COMMITS for sum_hills except regtest
This implements sum_hills tool via command line it is called via a cltool that creates a fake set of CVs and then creates an function actionwitharguments which acts as hills integrator in the initial phase (no calculate phase. It dies immediately). Hypothetically this structure should allow also an integration of the hills while doing the simulations (not yet implemented). It makes use of the Kernels instead of the internals of metad. (TODO: replace meta with kernels) See the documentation on cltool/SumHills.cpp So it implementes: added FakeCv to be used with sum_hills sum hills accepts stride (--stride) projections (--idw) via names automatically grid sizing (beware, sometimes is crazy), histogram correction for multivariate gaussians (--histo) A one-line gaussian reader for metadynamics (more flexible) A BiasRepresentation class which is intended to keep the list of kernels and the grid representation in a single bunch. Can be useful when replacing metad with kernels. TODO: when periodic automatically sets the boundary. this must be fixed in a more clever way TODO when projecting handle the derivatives so to have a grid that is usable for restaring on a lower dimension
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- src/bias/MetaD.cpp 107 additions, 59 deletionssrc/bias/MetaD.cpp
- src/cltools/SumHills.cpp 508 additions, 0 deletionssrc/cltools/SumHills.cpp
- src/colvar/Fake.cpp 132 additions, 0 deletionssrc/colvar/Fake.cpp
- src/function/FuncSumHills.cpp 516 additions, 0 deletionssrc/function/FuncSumHills.cpp
- src/tools/BiasRepresentation.cpp 245 additions, 0 deletionssrc/tools/BiasRepresentation.cpp
- src/tools/BiasRepresentation.h 84 additions, 0 deletionssrc/tools/BiasRepresentation.h
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