Update Colvars to version 2022-05-09
This update includes one new feature (neural-network based collective variables), several small enhancements (including an automatic definition of grid boundaries for angle-based CVs, and a normalization option for eigenvector-based CVs), bugfixes and documentation improvements. Usage information for specific features included in the Colvars library (i.e. not just the library as a whole) is now also reported to the screen or LAMMPS logfile (as is done already in other LAMMPS classes). Notable to LAMMPS code development are the removals of duplicated code and of ambiguously-named preprocessor defines in the Colvars headers. Since the last PR, the existing regression tests have also been running automatically via GitHub Actions. The following pull requests in the Colvars repository are relevant to LAMMPS: - 475 Remove fatal error condition https://github.com/Colvars/colvars/pull/475 (@jhenin, @giacomofiorin) - 474 Allow normalizing eigenvector vector components to deal with unit change https://github.com/Colvars/colvars/pull/474 (@giacomofiorin, @jhenin) - 470 Better error handling in the initialization of NeuralNetwork CV https://github.com/Colvars/colvars/pull/470 (@HanatoK) - 468 Add examples of histogram configuration, with and without explicit grid parameters https://github.com/Colvars/colvars/pull/468 (@giacomofiorin) - 464 Fix #463 using more fine-grained features https://github.com/Colvars/colvars/pull/464 (@jhenin, @giacomofiorin) - 447 [RFC] New option "scaledBiasingForce" for colvarbias https://github.com/Colvars/colvars/pull/447 (@HanatoK, @jhenin) - 444 [RFC] Implementation of dense neural network as CV https://github.com/Colvars/colvars/pull/444 (@HanatoK, @giacomofiorin, @jhenin) - 443 Fix explicit gradient dependency of sub-CVs https://github.com/Colvars/colvars/pull/443 (@HanatoK, @jhenin) - 442 Persistent bias count https://github.com/Colvars/colvars/pull/442 (@jhenin, @giacomofiorin) - 437 Return type of bias from scripting interface https://github.com/Colvars/colvars/pull/437 (@giacomofiorin) - 434 More flexible use of boundaries from colvars by grids https://github.com/Colvars/colvars/pull/434 (@jhenin) - 433 Prevent double-free in linearCombination https://github.com/Colvars/colvars/pull/433 (@HanatoK) - 428 More complete documentation for index file format (NDX) https://github.com/Colvars/colvars/pull/428 (@giacomofiorin) - 426 Integrate functional version of backup_file() into base proxy class https://github.com/Colvars/colvars/pull/426 (@giacomofiorin) - 424 Track CVC inheritance when documenting feature usage https://github.com/Colvars/colvars/pull/424 (@giacomofiorin) - 419 Generate citation report while running computations https://github.com/Colvars/colvars/pull/419 (@giacomofiorin, @jhenin) - 415 Rebin metadynamics bias from explicit hills when available https://github.com/Colvars/colvars/pull/415 (@giacomofiorin) - 312 Ignore a keyword if it has content to the left of it (regardless of braces) https://github.com/Colvars/colvars/pull/312 (@giacomofiorin) Authors: @giacomofiorin, @HanatoK, @jhenin
This commit is contained in:
Giacomo Fiorin
@ -135,13 +135,41 @@ public:
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/// Get value of alchemical lambda parameter from back-end (if available)
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virtual int get_alch_lambda(cvm::real* lambda);
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/// Set value of alchemical lambda parameter in back-end (if available)
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virtual int set_alch_lambda(cvm::real* lambda);
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/// Set value of alchemical lambda parameter to be sent to back-end at end of timestep
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void set_alch_lambda(cvm::real lambda);
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/// Send cached value of alchemical lambda parameter to back-end (if available)
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virtual int send_alch_lambda();
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/// Get energy derivative with respect to lambda (if available)
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virtual int get_dE_dLambda(cvm::real* force);
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virtual int get_dE_dlambda(cvm::real* dE_dlambda);
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/// Apply a scalar force on dE_dlambda (back-end distributes it onto atoms)
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virtual int apply_force_dE_dlambda(cvm::real* force);
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/// Get energy second derivative with respect to lambda (if available)
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virtual int get_d2E_dlambda2(cvm::real* d2E_dlambda2);
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/// Force to be applied onto alch. lambda, propagated from biasing forces on dE_dlambda
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cvm::real indirect_lambda_biasing_force;
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/// Get weight factor from accelMD
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virtual cvm::real get_accelMD_factor() const {
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cvm::error("Error: accessing the reweighting factor of accelerated MD "
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"is not yet implemented in the MD engine.\n",
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COLVARS_NOT_IMPLEMENTED);
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return 1.0;
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}
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virtual bool accelMD_enabled() const {
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return false;
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}
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protected:
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/// Next value of lambda to be sent to back-end
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cvm::real cached_alch_lambda;
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/// Whether lambda has been set and needs to be updated in backend
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bool cached_alch_lambda_changed;
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/// Whether the total forces have been requested
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bool total_force_requested;
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@ -652,9 +680,6 @@ public:
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/// (does not need to be allocated in a new interface)
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colvarscript *script;
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/// is a user force script defined?
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bool force_script_defined;
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/// Do we have a scripting interface?
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bool have_scripts;
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@ -702,7 +727,7 @@ public:
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}
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/// Remove the given file (on Windows only, rename to filename.old)
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int remove_file(char const *filename);
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virtual int remove_file(char const *filename);
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/// Remove the given file (on Windows only, rename to filename.old)
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inline int remove_file(std::string const &filename)
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@ -711,7 +736,7 @@ public:
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}
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/// Rename the given file
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int rename_file(char const *filename, char const *newfilename);
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virtual int rename_file(char const *filename, char const *newfilename);
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/// Rename the given file
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inline int rename_file(std::string const &filename,
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@ -779,7 +804,6 @@ protected:
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/// \brief Interface between the collective variables module and
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/// the simulation or analysis program (NAMD, VMD, LAMMPS...).
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/// This is the base class: each interfaced program is supported by a derived class.
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/// Only pure virtual functions ("= 0") must be reimplemented to ensure baseline functionality.
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class colvarproxy
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: public colvarproxy_system,
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public colvarproxy_atoms,
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@ -864,6 +888,12 @@ public:
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/// Called at the end of a simulation segment (i.e. "run" command)
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int post_run();
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/// Print a full list of all input atomic arrays for debug purposes
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void print_input_atomic_data();
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/// Print a full list of all applied forces for debug purposes
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void print_output_atomic_data();
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/// Convert a version string "YYYY-MM-DD" into an integer
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int get_version_from_string(char const *version_string);
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@ -910,6 +940,9 @@ protected:
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/// Integer representing the version string (allows comparisons)
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int version_int;
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/// Track which features have been acknowledged during the last run
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size_t features_hash;
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/// Raise when the output stream functions are used on threads other than 0
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void smp_stream_error();
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