3e89b270fd
Notable features are the umbrella-integration based free energy estimator for eABF, and the traditional thermodynamic integration estimator now available for umbrella sampling, SMD, metadynamics. Also included are several small fixes. Below is a list of relevant commits in the Colvars repository since the last update. 321d06a 2017-10-10 Add macros to manage colvarscript commands [Giacomo Fiorin] 26c3bec 2017-10-09 Document coming availability of Lepton in LAMMPS [Giacomo Fiorin] cc8f249 2017-10-04 Clarify that SMP depends on code build [Giacomo Fiorin] 0b2ffac 2017-10-04 Summarize colvar definition options, clarify some details [Giacomo Fiorin] 28002e0 2017-10-01 Separate writing of restart file from other output (e.g. PMFs) [Giacomo Fiorin] 92f7c1d 2017-10-01 Deprecate colvarsTrajAppend [Giacomo Fiorin] 12a707f 2017-09-26 Accurate Jacobian calculation for RMSD variants [Jérôme Hénin] fe389c9 2017-09-21 Allow subtractAppliedForce with extended-L again [Jérôme Hénin] c050ce0 2017-09-18 Silence compiler warnings, remove Tabs [Giacomo Fiorin] cb41905 2017-01-11 Add base class for TI estimator in other biases than ABF [Giacomo Fiorin] a1bc676 2017-09-14 Avoid writing to unopened traj file [Jérôme Hénin] b58d8cd 2017-09-08 Function to check for overlapping groups [Jérôme Hénin] 1e5efec 2017-09-07 Check for overlapping groups in coordNum [Jérôme Hénin] 03a61a4 2017-04-06 Add UI-based estimator [fhh2626] ae43754 2017-08-17 Fix outputCenters parsing [Josh Vermaas] 1619e0e 2017-08-14 Delete static feature arrays in cvm destructor [Jérôme Hénin]
130 lines
4.0 KiB
C++
130 lines
4.0 KiB
C++
// -*- c++ -*-
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// This file is part of the Collective Variables module (Colvars).
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// The original version of Colvars and its updates are located at:
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// https://github.com/colvars/colvars
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// Please update all Colvars source files before making any changes.
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// If you wish to distribute your changes, please submit them to the
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// Colvars repository at GitHub.
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#ifndef COLVARBIAS_ABF_H
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#define COLVARBIAS_ABF_H
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#include <vector>
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#include <list>
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#include <sstream>
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#include <iomanip>
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#include "colvarbias.h"
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#include "colvargrid.h"
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#include "colvar_UIestimator.h"
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typedef cvm::real* gradient_t;
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/// ABF bias
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class colvarbias_abf : public colvarbias {
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public:
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colvarbias_abf(char const *key);
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virtual int init(std::string const &conf);
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virtual ~colvarbias_abf();
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virtual int update();
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private:
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/// Filename prefix for human-readable gradient/sample count output
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std::string output_prefix;
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/// Base filename(s) for reading previous gradient data (replaces data from restart file)
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std::vector<std::string> input_prefix;
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bool update_bias;
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bool hide_Jacobian;
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size_t full_samples;
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size_t min_samples;
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/// frequency for updating output files
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int output_freq;
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/// Write combined files with a history of all output data?
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bool b_history_files;
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/// Write CZAR output file for stratified eABF (.zgrad)
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bool b_czar_window_file;
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size_t history_freq;
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/// Umbrella Integration estimator of free energy from eABF
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UIestimator::UIestimator eabf_UI;
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// Run UI estimator?
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bool b_UI_estimator;
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// Run CZAR estimator?
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bool b_CZAR_estimator;
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/// Cap applied biasing force?
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bool cap_force;
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std::vector<cvm::real> max_force;
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// Internal data and methods
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std::vector<int> bin, force_bin, z_bin;
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gradient_t system_force, applied_force;
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/// n-dim grid of free energy gradients
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colvar_grid_gradient *gradients;
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/// n-dim grid of number of samples
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colvar_grid_count *samples;
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/// n-dim grid: average force on "real" coordinate for eABF z-based estimator
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colvar_grid_gradient *z_gradients;
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/// n-dim grid of number of samples on "real" coordinate for eABF z-based estimator
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colvar_grid_count *z_samples;
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/// n-dim grid contining CZAR estimator of "real" free energy gradients
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colvar_grid_gradient *czar_gradients;
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inline int update_system_force(size_t i)
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{
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if (colvars[i]->is_enabled(f_cv_subtract_applied_force)) {
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// this colvar is already subtracting the ABF force
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system_force[i] = colvars[i]->total_force().real_value;
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} else {
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system_force[i] = colvars[i]->total_force().real_value
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- colvar_forces[i].real_value;
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}
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if (cvm::debug())
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cvm::log("ABF System force calc: cv " + cvm::to_str(i) +
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" fs " + cvm::to_str(system_force[i]) +
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" = ft " + cvm::to_str(colvars[i]->total_force().real_value) +
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" - fa " + cvm::to_str(colvar_forces[i].real_value));
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return COLVARS_OK;
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}
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// shared ABF
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bool shared_on;
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size_t shared_freq;
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int shared_last_step;
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// Share between replicas -- may be called independently of update
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virtual int replica_share();
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// Store the last set for shared ABF
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colvar_grid_gradient *last_gradients;
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colvar_grid_count *last_samples;
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// For Tcl implementation of selection rules.
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/// Give the total number of bins for a given bias.
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virtual int bin_num();
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/// Calculate the bin index for a given bias.
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virtual int current_bin();
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//// Give the count at a given bin index.
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virtual int bin_count(int bin_index);
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/// Write human-readable FE gradients and sample count
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void write_gradients_samples(const std::string &prefix, bool append = false);
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void write_last_gradients_samples(const std::string &prefix, bool append = false);
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/// Read human-readable FE gradients and sample count (if not using restart)
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void read_gradients_samples();
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std::istream& read_state_data(std::istream&);
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std::ostream& write_state_data(std::ostream&);
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};
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#endif
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