Implement reflecting boundary conditions for metadynamics bias#525

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fabsugar wants to merge 53 commits intomasterfrom meta_reflection

+1,297-49

Commits on Dec 15, 2023

Starting to implement interval (forces removal beyond boundaries) and hills reflection

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Introduced init_reflection

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Introduced init_interval

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Added reflection & interval routines

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Added calls to reflected hills when required

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Introduced reflection and iontervals vars in colvarbias_meta.h

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Removed forces beyond CVs intervals when defined in colvarbias_meta.cpp

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Update argument of hill() to match recent version of colvars

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Corrected INPUT_ERROR with COLVARS_INPUT_ERROR in colvarbias_meta.cpp

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Added declaration of reflection routines in colvarbias_meta.h

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Modified sigmas and call to set_ones

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h_w substituted with colvar_sigmas

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Changed some variables from int to size_t, this was giving error in the checks

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Changed some size_t to int

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Introduced nvars and int of num_variables as the latter is size_t

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Trying to remove warnings causing problems in checks

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Trying to resolve "error: '>>' should be '> >' within a nested template argument list" in colvarbias_meta.h

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Removed monodimensional reflection

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In calc_hills_force, boundary check is now outside the hills loop for efficiency

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Modified init_reflection introducing lower and upper boundaries of the grid the default limits of reflection

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reflection_type removed

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reflection states generated only if reflection is active

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removed i index onn interval in calc_hills_force

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modifed cal_hills to account for interval

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Finished adding curr_values to calc_hills to account for interval

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some changes of declaratins leading to compilation error

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Modified calc_energy and project_hills to account for hills reflection+interval

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condition for reflection+interval added externally to calc_hills_force

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Remove requiremend of hard boundaries as a default for grid + reflection

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a few changes to resolve compilation errors

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changed variables->values with colvar_values in calc_energy

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Added errors/warning and defaults to account for periodic variables + hills refletions,

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Resolved compilation errors due to curr_values on calc energy

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Updated calc_energy in case reflection boundaries are grid boundaries,

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cal_energy modified to put interval upper boundaries inside the grid by subtracting half width

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Corretted bug on allocation of ref_state array for reflection

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Corrected bug in multidimensional reflection visible in 3D

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Fix leftover compiler issues; also remove trailing whitespace via Git hooks
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Resolving compilers issues, chenged limits of CVs to integers so control for negative values should work

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num_variables casted to int when required

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corrected bug on calc_energy at the boundary

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Corrected calc_force to take into account that also the force components

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Corrected calc_energy and calc_forces function to check that upper limit of reflection is in the boundary

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Removed some spaces

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Added >= to check values out of upper boundary just to be extra precise

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Introdiced error if reflection limits are explicity specified out of grid boundaries

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Modified implementation of interval in calc_energy and calc_forces

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removed obsolete/unused h_replica in reflect_multid routine

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Added interval vectors as argument of project hills function. This fixes the seg fault when using

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Integrate change to stream access
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Fix remaining merge conflicts
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Commits on Feb 6, 2024