From 7bc09b7da85e4f48c1c1ee92a9ced2c198b5bc45 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=A9r=C3=B4me=20H=C3=A9nin?= Date: Fri, 30 Aug 2024 15:43:38 +0200 Subject: [PATCH 01/13] Add gridParameters to abf bias Implement in colvargid::init_from_colvars Clean up unused grid constructors --- src/colvarbias_abf.cpp | 54 ++++++++++++++++--------------- src/colvarbias_abf.h | 2 ++ src/colvargrid.cpp | 44 ++++++++++--------------- src/colvargrid.h | 73 +++++++++++++++++++++++++----------------- 4 files changed, 90 insertions(+), 83 deletions(-) diff --git a/src/colvarbias_abf.cpp b/src/colvarbias_abf.cpp index db6ee6d57..5ab693771 100644 --- a/src/colvarbias_abf.cpp +++ b/src/colvarbias_abf.cpp @@ -83,6 +83,8 @@ int colvarbias_abf::init(std::string const &conf) } } + key_lookup(conf, "gridParameters", &grid_params); + // shared ABF get_keyval(conf, "shared", shared_on, false); if (shared_on) { @@ -108,9 +110,9 @@ int colvarbias_abf::init(std::string const &conf) } // Allocate these at init time if possible - local_samples.reset(new colvar_grid_count(colvars)); - local_gradients.reset(new colvar_grid_gradient(colvars, local_samples)); - local_pmf.reset(new integrate_potential(colvars, local_gradients)); + local_samples.reset(new colvar_grid_count(colvars, grid_params)); + local_gradients.reset(new colvar_grid_gradient(colvars, local_samples, grid_params)); + local_pmf.reset(new integrate_potential(colvars, local_gradients, grid_params)); } // ************* checking the associated colvars ******************* @@ -187,8 +189,8 @@ int colvarbias_abf::init(std::string const &conf) cvm::log("Allocating count and free energy gradient grids.\n"); } - samples.reset(new colvar_grid_count(colvars)); - gradients.reset(new colvar_grid_gradient(colvars, samples)); + samples.reset(new colvar_grid_count(colvars, grid_params)); + gradients.reset(new colvar_grid_gradient(colvars, samples, grid_params)); gradients->full_samples = full_samples; gradients->min_samples = min_samples; @@ -204,11 +206,11 @@ int colvarbias_abf::init(std::string const &conf) colvarparse::parse_silent); z_bin.assign(num_variables(), 0); - z_samples.reset(new colvar_grid_count(colvars)); + z_samples.reset(new colvar_grid_count(colvars, grid_params)); z_samples->request_actual_value(); - z_gradients.reset(new colvar_grid_gradient(colvars, z_samples)); + z_gradients.reset(new colvar_grid_gradient(colvars, z_samples, grid_params)); z_gradients->request_actual_value(); - czar_gradients.reset(new colvar_grid_gradient(colvars)); + czar_gradients.reset(new colvar_grid_gradient(colvars, grid_params)); } get_keyval(conf, "integrate", b_integrate, num_variables() <= 3); // Integrate for output if d<=3 @@ -218,9 +220,9 @@ int colvarbias_abf::init(std::string const &conf) cvm::error("Error: cannot integrate free energy in dimension > 3.\n"); return COLVARS_ERROR; } - pmf.reset(new integrate_potential(colvars, gradients)); + pmf.reset(new integrate_potential(colvars, gradients, grid_params)); if (b_CZAR_estimator) { - czar_pmf.reset(new integrate_potential(colvars, czar_gradients)); + czar_pmf.reset(new integrate_potential(colvars, czar_gradients, grid_params)); } // Parameters for integrating initial (and final) gradient data get_keyval(conf, "integrateMaxIterations", integrate_iterations, 10000, colvarparse::parse_silent); @@ -234,10 +236,10 @@ int colvarbias_abf::init(std::string const &conf) if (b_CZAR_estimator && shared_on && cvm::main()->proxy->replica_index() == 0) { // The pointers below are used for outputting CZAR data // Allocate grids for collected global data, on replica 0 only - global_z_samples.reset(new colvar_grid_count(colvars)); - global_z_gradients.reset(new colvar_grid_gradient(colvars, global_z_samples)); - global_czar_gradients.reset(new colvar_grid_gradient(colvars)); - global_czar_pmf.reset(new integrate_potential(colvars, global_czar_gradients)); + global_z_samples.reset(new colvar_grid_count(colvars, grid_params)); + global_z_gradients.reset(new colvar_grid_gradient(colvars, global_z_samples, grid_params)); + global_czar_gradients.reset(new colvar_grid_gradient(colvars, grid_params)); + global_czar_pmf.reset(new integrate_potential(colvars, global_czar_gradients, grid_params)); } else { // otherwise they are just aliases for the local CZAR grids global_z_samples = z_samples; @@ -250,11 +252,11 @@ int colvarbias_abf::init(std::string const &conf) // This used to be only if "shared" was defined, // but now we allow calling share externally (e.g. from Tcl). if (b_CZAR_estimator) { - z_samples_in.reset(new colvar_grid_count(colvars)); - z_gradients_in.reset(new colvar_grid_gradient(colvars, z_samples_in)); + z_samples_in.reset(new colvar_grid_count(colvars, grid_params)); + z_gradients_in.reset(new colvar_grid_gradient(colvars, z_samples_in, grid_params)); } - last_samples.reset(new colvar_grid_count(colvars)); - last_gradients.reset(new colvar_grid_gradient(colvars, last_samples)); + last_samples.reset(new colvar_grid_count(colvars, grid_params)); + last_gradients.reset(new colvar_grid_gradient(colvars, last_samples, grid_params)); // Any data collected after now is new for shared ABF purposes shared_last_step = cvm::step_absolute(); @@ -548,9 +550,9 @@ int colvarbias_abf::replica_share() { if (!local_samples) { // We arrive here if sharing has just been enabled by a script // in which case local arrays have not been initialized yet - local_samples.reset(new colvar_grid_count(colvars)); - local_gradients.reset(new colvar_grid_gradient(colvars, local_samples)); - local_pmf.reset(new integrate_potential(colvars, local_gradients)); + local_samples.reset(new colvar_grid_count(colvars, grid_params)); + local_gradients.reset(new colvar_grid_gradient(colvars, local_samples, grid_params)); + local_pmf.reset(new integrate_potential(colvars, local_gradients, grid_params)); } // Calculate the delta gradient and count for the local replica last_gradients->delta_grid(*gradients); @@ -668,10 +670,10 @@ int colvarbias_abf::replica_share_CZAR() { // We arrive here if sharing has just been enabled by a script // Allocate grids for collective data, on replica 0 only // overriding CZAR grids that are equal to local ones by default - global_z_samples.reset(new colvar_grid_count(colvars)); - global_z_gradients.reset(new colvar_grid_gradient(colvars, global_z_samples)); - global_czar_gradients.reset(new colvar_grid_gradient(colvars)); - global_czar_pmf.reset(new integrate_potential(colvars, global_czar_gradients)); + global_z_samples.reset(new colvar_grid_count(colvars, grid_params)); + global_z_gradients.reset(new colvar_grid_gradient(colvars, global_z_samples, grid_params)); + global_czar_gradients.reset(new colvar_grid_gradient(colvars, grid_params)); + global_czar_pmf.reset(new integrate_potential(colvars, global_czar_gradients, grid_params)); } // Start with data from replica 0 @@ -879,7 +881,7 @@ int colvarbias_abf::read_gradients_samples() // Therefore the czar_gradients grid is not linked to a sampling grid // Here we define a temporary czar_gradients grid linked to z_samples, // to correctly average input gradients if overlapping - czar_gradients_in.reset(new colvar_grid_gradient(colvars, z_samples)); + czar_gradients_in.reset(new colvar_grid_gradient(colvars, z_samples, grid_params)); } for ( size_t i = 0; i < input_prefix.size(); i++ ) { diff --git a/src/colvarbias_abf.h b/src/colvarbias_abf.h index 4426a8a3f..479926137 100644 --- a/src/colvarbias_abf.h +++ b/src/colvarbias_abf.h @@ -42,6 +42,8 @@ class colvarbias_abf : public colvarbias { /// Base filename(s) for reading previous gradient data (replaces data from restart file) std::vector input_prefix; + /// Optional custom configuration string for grid parameters + std::string grid_params; /// Adapt the bias at each time step (as opposed to keeping it constant)? bool update_bias; diff --git a/src/colvargrid.cpp b/src/colvargrid.cpp index 11693a758..c4532406e 100644 --- a/src/colvargrid.cpp +++ b/src/colvargrid.cpp @@ -24,15 +24,9 @@ colvar_grid_count::colvar_grid_count() mult = 1; } -colvar_grid_count::colvar_grid_count(std::vector const &nx_i, - size_t const &def_count) - : colvar_grid(nx_i, def_count, 1) -{} - colvar_grid_count::colvar_grid_count(std::vector &colvars, - size_t const &def_count, - bool margin) - : colvar_grid(colvars, def_count, 1, margin) + std::string config) + : colvar_grid(colvars, 0, 1, false, config) {} std::string colvar_grid_count::get_state_params() const @@ -132,13 +126,10 @@ colvar_grid_scalar::colvar_grid_scalar(colvar_grid_scalar const &g) { } -colvar_grid_scalar::colvar_grid_scalar(std::vector const &nx_i) - : colvar_grid(nx_i, 0.0, 1), samples(NULL) -{ -} - -colvar_grid_scalar::colvar_grid_scalar(std::vector &colvars, bool margin) - : colvar_grid(colvars, 0.0, 1, margin), samples(NULL) +colvar_grid_scalar::colvar_grid_scalar(std::vector &colvars, + std::string config, + bool add_extra_bin) + : colvar_grid(colvars, 0.0, 1, add_extra_bin, config), samples(NULL) { } @@ -334,18 +325,15 @@ colvar_grid_gradient::colvar_grid_gradient() {} -colvar_grid_gradient::colvar_grid_gradient(std::vector const &nx_i) - : colvar_grid(nx_i, 0.0, nx_i.size()), samples(NULL), full_samples(0), min_samples(0) -{} - - -colvar_grid_gradient::colvar_grid_gradient(std::vector &colvars) - : colvar_grid(colvars, 0.0, colvars.size()), samples(NULL), full_samples(0), min_samples(0) +colvar_grid_gradient::colvar_grid_gradient(std::vector &colvars, std::string config) + : colvar_grid(colvars, 0.0, colvars.size(), false, config), samples(NULL), full_samples(0), min_samples(0) {} -colvar_grid_gradient::colvar_grid_gradient(std::vector &colvars, std::shared_ptr samples_in) - : colvar_grid(colvars, 0.0, colvars.size()), samples(samples_in), full_samples(0), min_samples(0) +colvar_grid_gradient::colvar_grid_gradient(std::vector &colvars, + std::shared_ptr samples_in, + std::string config) + : colvar_grid(colvars, 0.0, colvars.size(), false, config), samples(samples_in), full_samples(0), min_samples(0) { samples_in->has_parent_data = true; } @@ -586,12 +574,14 @@ cvm::real colvar_grid_gradient::grid_rmsd(colvar_grid_gradient const &other_grid } -integrate_potential::integrate_potential(std::vector &colvars, std::shared_ptr gradients) - : colvar_grid_scalar(colvars, true), +integrate_potential::integrate_potential(std::vector &colvars, + std::shared_ptr gradients, + std::string config) + : colvar_grid_scalar(colvars, config, true), b_smoothed(false), gradients(gradients) { - // parent class colvar_grid_scalar is constructed with margin option set to true + // parent class colvar_grid_scalar is constructed with add_extra_bin option set to true // hence PMF grid is wider than gradient grid if non-PBC if (nd > 1) { diff --git a/src/colvargrid.h b/src/colvargrid.h index 4cbbb1096..72226f6c3 100644 --- a/src/colvargrid.h +++ b/src/colvargrid.h @@ -29,7 +29,7 @@ template class colvar_grid : public colvarparse { public: // TODO create accessors for these after all instantiations work /// Number of dimensions - size_t nd; + size_t nd = 0; /// Number of points along each dimension std::vector nx; @@ -247,22 +247,24 @@ template class colvar_grid : public colvarparse { this->setup(nx_i, t, mult_i); } - /// \brief Constructor from a vector of colvars + /// \brief Constructor from a vector of colvars or an optional grid config string /// \param add_extra_bin requests that non-periodic dimensions are extended /// by 1 bin to accommodate the integral (PMF) of another gridded quantity (gradient) colvar_grid(std::vector const &colvars, T const &t = T(), size_t mult_i = 1, - bool add_extra_bin = false) + bool add_extra_bin = false, + std::string config = std::string()) : has_parent_data(false), has_data(false) { (void) t; - this->init_from_colvars(colvars, mult_i, add_extra_bin); + this->init_from_colvars(colvars, mult_i, add_extra_bin, config); } int init_from_colvars(std::vector const &colvars, size_t mult_i = 1, - bool add_extra_bin = false) + bool add_extra_bin = false, + std::string config = std::string()) { if (cvm::debug()) { cvm::log("Reading grid configuration from collective variables.\n"); @@ -298,7 +300,6 @@ template class colvar_grid : public colvarparse { widths.push_back(cv[i]->width); hard_lower_boundaries.push_back(cv[i]->is_enabled(colvardeps::f_cv_hard_lower_boundary)); hard_upper_boundaries.push_back(cv[i]->is_enabled(colvardeps::f_cv_hard_upper_boundary)); - periodic.push_back(cv[i]->periodic_boundaries()); // By default, get reported colvar value (for extended Lagrangian colvars) use_actual_value.push_back(false); @@ -310,19 +311,33 @@ template class colvar_grid : public colvarparse { use_actual_value[i-1] = true; } + // This needs to work if the boundaries are undefined in the colvars + lower_boundaries.push_back(cv[i]->lower_boundary); + upper_boundaries.push_back(cv[i]->upper_boundary); + } + + // Replace widths and boundaries with optional custom configuration + if (!config.empty()) { + this->parse_params(config); + this->check_keywords(config, "gridParameters"); + } + + // Only now can we determine periodicity + for (i = 0; i < cv.size(); i++) { + periodic.push_back(cv[i]->periodic_boundaries(lower_boundaries[i].real_value, + upper_boundaries[i].real_value)); + if (add_extra_bin) { + // Shift the grid by half the bin width (values at edges instead of center of bins) + lower_boundaries[i] -= 0.5 * widths[i]; + if (periodic[i]) { - // Shift the grid by half the bin width (values at edges instead of center of bins) - lower_boundaries.push_back(cv[i]->lower_boundary.real_value - 0.5 * widths[i]); - upper_boundaries.push_back(cv[i]->upper_boundary.real_value - 0.5 * widths[i]); + // Just shift + upper_boundaries[i] -= 0.5 * widths[i]; } else { - // Make this grid larger by one bin width - lower_boundaries.push_back(cv[i]->lower_boundary.real_value - 0.5 * widths[i]); - upper_boundaries.push_back(cv[i]->upper_boundary.real_value + 0.5 * widths[i]); + // Widen grid by one bin width + upper_boundaries[i] += 0.5 * widths[i]; } - } else { - lower_boundaries.push_back(cv[i]->lower_boundary); - upper_boundaries.push_back(cv[i]->upper_boundary); } } @@ -966,14 +981,9 @@ class colvar_grid_count : public colvar_grid virtual ~colvar_grid_count() {} - /// Constructor - colvar_grid_count(std::vector const &nx_i, - size_t const &def_count = 0); - - /// Constructor from a vector of colvars + /// Constructor from a vector of colvars or a config string colvar_grid_count(std::vector &colvars, - size_t const &def_count = 0, - bool add_extra_bin = false); + std::string config = std::string()); /// Increment the counter at given position inline void incr_count(std::vector const &ix) @@ -1255,11 +1265,9 @@ class colvar_grid_scalar : public colvar_grid /// Destructor virtual ~colvar_grid_scalar(); - /// Constructor from specific sizes arrays - colvar_grid_scalar(std::vector const &nx_i); - /// Constructor from a vector of colvars colvar_grid_scalar(std::vector &colvars, + std::string config = std::string(), bool add_extra_bin = false); /// Accumulate the value @@ -1566,17 +1574,20 @@ class colvar_grid_gradient : public colvar_grid virtual ~colvar_grid_gradient() {} - /// Constructor from specific sizes arrays - colvar_grid_gradient(std::vector const &nx_i); + // /// Constructor from specific sizes arrays + // colvar_grid_gradient(std::vector const &nx_i); /// Constructor from a vector of colvars - colvar_grid_gradient(std::vector &colvars); + colvar_grid_gradient(std::vector &colvars, + std::string config = std::string()); /// Constructor from a multicol file colvar_grid_gradient(std::string &filename); /// Constructor from a vector of colvars and a pointer to the count grid - colvar_grid_gradient(std::vector &colvars, std::shared_ptr samples_in); + colvar_grid_gradient(std::vector &colvars, + std::shared_ptr samples_in, + std::string config = std::string()); /// Parameters for smoothing data with low sampling int full_samples; @@ -1829,7 +1840,9 @@ class integrate_potential : public colvar_grid_scalar {} /// Constructor from a vector of colvars + gradient grid - integrate_potential(std::vector &colvars, std::shared_ptr gradients); + integrate_potential(std::vector &colvars, + std::shared_ptr gradients, + std::string config = std::string()); /// Constructor from a gradient grid (for processing grid files without a Colvars config) integrate_potential(std::shared_ptr gradients); From c06a99c0c92cb8aa02114dcc547b4d18c27b3544 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=A9r=C3=B4me=20H=C3=A9nin?= Date: Fri, 30 Aug 2024 18:23:15 +0200 Subject: [PATCH 02/13] Change histogramGrid to gridParameters For consistency. Update doc and tests. histogramGrid is deprecated but still works. --- doc/colvars-refman-main.tex | 16 ++++++++-------- .../test.in | 2 +- .../test.in | 2 +- .../test.in | 2 +- .../test.in | 2 +- .../test.in | 2 +- .../test.in | 2 +- .../000_distance_histogram-customgrid/test.in | 2 +- src/colvarbias_histogram.cpp | 5 +++-- src/colvargrid.h | 4 ++-- ...e-dihedral_histogram2d-periodic-customgrid.in | 2 +- tests/histogram-customgrid-periodic.in | 2 +- tests/histogram-customgrid.in | 2 +- .../test.in | 2 +- .../distance-grid_histogram-customgrid/test.in | 2 +- .../distance_histogram-customgrid/test.in | 2 +- 16 files changed, 26 insertions(+), 25 deletions(-) diff --git a/doc/colvars-refman-main.tex b/doc/colvars-refman-main.tex index 6b4cb9cf6..1ece21c22 100644 --- a/doc/colvars-refman-main.tex +++ b/doc/colvars-refman-main.tex @@ -5508,7 +5508,8 @@ \cvsubsubsec{Parameters for ABF}{sec:colvarbias_abf_params} -ABF depends on parameters from each collective variable to define the grid on which free energy gradients are computed: see \ref{sec:colvar_grid_params} for detauls. +ABF depends on parameters from each collective variable to define the grid on which free energy gradients are computed: see \ref{sec:colvar_grid_params} for details. +Alternately, grid parameters can be set directly inside the ABF block by inserting a \texttt{gridParameters} sub-block, as explained in \ref{sec:colvarbias_histogram_grid}. Other parameters to control the ABF runtime can be set in the ABF configuration block: \begin{itemize} @@ -7583,7 +7584,7 @@ \-histogram~\{\\ \-\-~~name~hist2d\\ \-\-~~colvars~r~theta\\ -\-\-~~histogramGrid~\{\\ +\-\-~~gridParameters~\{\\ \-\-~~~~widths~~0.1~1.0\\ \-\-~~~~lowerBoundaries~~~2.0~30.0\\ \-\-~~~~upperBoundaries~~10.0~90.0\\ @@ -7606,24 +7607,23 @@ \cvsubsubsec{Defining grids for multidimensional histograms}{sec:colvarbias_histogram_grid} -Grid parameters for the histogram may be provided at the level of the individual variables, or via a dedicated configuration block \texttt{histogramGrid \{ \ldots \}} inside the configuration of this \texttt{histogram}. +Grid parameters for the histogram may be provided at the level of the individual variables, or via a dedicated configuration block \texttt{gridParameters \{ \ldots \}} inside the configuration of this \texttt{histogram}. The options supported \emph{inside this block} are: \begin{itemize} - \item % \key{% lowerBoundaries}{% - \texttt{histogramGrid}}{% + \texttt{gridParameters}}{% Lower boundaries of the grid}{% list of space-separated decimals}{% This option defines the lower boundaries of the grid, overriding any values defined by the \texttt{lowerBoundary} keyword of each colvar. - Note that when \texttt{gatherVectorColvars} is \texttt{on}, each vector variable is automatically treated as a scalar, and a single value should be provided for it. + Note that when \texttt{gatherVectorColvars} is \texttt{on} in the enclosing \texttt{histogram} block, each vector variable is automatically treated as a scalar, and a single value should be provided for it. } \item % - \simkey{upperBoundaries}{\texttt{histogramGrid}}{lowerBoundaries} + \simkey{upperBoundaries}{\texttt{gridParameters}}{lowerBoundaries} \item % - \simkey{widths}{\texttt{histogramGrid}}{lowerBoundaries} + \simkey{widths}{\texttt{gridParameters}}{lowerBoundaries} \end{itemize} diff --git a/gromacs/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/test.in b/gromacs/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/test.in index 5ae19f915..3d768c4fd 100644 --- a/gromacs/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/test.in +++ b/gromacs/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/test.in @@ -38,7 +38,7 @@ colvar { histogram { colvars r phi - histogramGrid { + gridParameters { widths 0.2 6.0 lowerBoundaries 0.0 0.0 upperBoundaries 10.0 360.0 diff --git a/lammps/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/test.in b/lammps/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/test.in index 5ae19f915..3d768c4fd 100644 --- a/lammps/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/test.in +++ b/lammps/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/test.in @@ -38,7 +38,7 @@ colvar { histogram { colvars r phi - histogramGrid { + gridParameters { widths 0.2 6.0 lowerBoundaries 0.0 0.0 upperBoundaries 10.0 360.0 diff --git a/lammps/tests/library/000_distance-grid_histogram-customgrid/test.in b/lammps/tests/library/000_distance-grid_histogram-customgrid/test.in index 612947def..61603e2ad 100644 --- a/lammps/tests/library/000_distance-grid_histogram-customgrid/test.in +++ b/lammps/tests/library/000_distance-grid_histogram-customgrid/test.in @@ -26,7 +26,7 @@ colvar { histogram { colvars one - histogramGrid { + gridParameters { widths 0.2 lowerBoundaries 0.6 upperBoundaries 5.4 diff --git a/namd/tests/library/000_dihedral_histogram-customgrid-periodic/test.in b/namd/tests/library/000_dihedral_histogram-customgrid-periodic/test.in index 42f28ccdc..5883076c2 100644 --- a/namd/tests/library/000_dihedral_histogram-customgrid-periodic/test.in +++ b/namd/tests/library/000_dihedral_histogram-customgrid-periodic/test.in @@ -28,7 +28,7 @@ colvar { histogram { colvars one - histogramGrid { + gridParameters { widths 5 lowerBoundaries -60 upperBoundaries 300 diff --git a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/test.in b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/test.in index 5ae19f915..3d768c4fd 100644 --- a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/test.in +++ b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/test.in @@ -38,7 +38,7 @@ colvar { histogram { colvars r phi - histogramGrid { + gridParameters { widths 0.2 6.0 lowerBoundaries 0.0 0.0 upperBoundaries 10.0 360.0 diff --git a/namd/tests/library/000_distance-grid_histogram-customgrid/test.in b/namd/tests/library/000_distance-grid_histogram-customgrid/test.in index 612947def..61603e2ad 100644 --- a/namd/tests/library/000_distance-grid_histogram-customgrid/test.in +++ b/namd/tests/library/000_distance-grid_histogram-customgrid/test.in @@ -26,7 +26,7 @@ colvar { histogram { colvars one - histogramGrid { + gridParameters { widths 0.2 lowerBoundaries 0.6 upperBoundaries 5.4 diff --git a/namd/tests/library/000_distance_histogram-customgrid/test.in b/namd/tests/library/000_distance_histogram-customgrid/test.in index acfd48c31..1169d86ee 100644 --- a/namd/tests/library/000_distance_histogram-customgrid/test.in +++ b/namd/tests/library/000_distance_histogram-customgrid/test.in @@ -22,7 +22,7 @@ colvar { histogram { colvars one - histogramGrid { + gridParameters { widths 0.2 lowerBoundaries 0.6 upperBoundaries 5.4 diff --git a/src/colvarbias_histogram.cpp b/src/colvarbias_histogram.cpp index 98de27530..3ca60a01c 100644 --- a/src/colvarbias_histogram.cpp +++ b/src/colvarbias_histogram.cpp @@ -99,9 +99,10 @@ int colvarbias_histogram::init(std::string const &conf) { std::string grid_conf; - if (key_lookup(conf, "histogramGrid", &grid_conf)) { + if (key_lookup(conf, "histogramGrid", &grid_conf) || + key_lookup(conf, "gridParameters", &grid_conf)) { grid->parse_params(grid_conf); - grid->check_keywords(grid_conf, "histogramGrid"); + grid->check_keywords(grid_conf, "gridParameters"); } } diff --git a/src/colvargrid.h b/src/colvargrid.h index 72226f6c3..275da3fcb 100644 --- a/src/colvargrid.h +++ b/src/colvargrid.h @@ -1342,8 +1342,8 @@ class colvar_grid_scalar : public colvar_grid /// \brief Return the gradient of the scalar field from finite differences /// Input coordinates are those of gradient grid, shifted wrt scalar grid - /// Should not be called on edges of scalar grid, provided the latter has margins - /// wrt gradient grid + /// Should not be called on edges of scalar grid, provided the latter has + /// margins (extra bins) wrt gradient grid inline void vector_gradient_finite_diff( const std::vector &ix0, std::vector &grad) { cvm::real A0, A1; diff --git a/tests/distance-dihedral_histogram2d-periodic-customgrid.in b/tests/distance-dihedral_histogram2d-periodic-customgrid.in index 49f0b7b5b..3950e3e25 100644 --- a/tests/distance-dihedral_histogram2d-periodic-customgrid.in +++ b/tests/distance-dihedral_histogram2d-periodic-customgrid.in @@ -34,7 +34,7 @@ colvar { histogram { colvars r phi - histogramGrid { + gridParameters { widths 0.2 6.0 lowerBoundaries 0.0 0.0 upperBoundaries 10.0 360.0 diff --git a/tests/histogram-customgrid-periodic.in b/tests/histogram-customgrid-periodic.in index 603f68537..0ebc5025e 100644 --- a/tests/histogram-customgrid-periodic.in +++ b/tests/histogram-customgrid-periodic.in @@ -1,6 +1,6 @@ histogram { colvars one - histogramGrid { + gridParameters { widths 5 lowerBoundaries -60 upperBoundaries 300 diff --git a/tests/histogram-customgrid.in b/tests/histogram-customgrid.in index dc36c5740..7a26ae6f1 100644 --- a/tests/histogram-customgrid.in +++ b/tests/histogram-customgrid.in @@ -1,6 +1,6 @@ histogram { colvars one - histogramGrid { + gridParameters { widths 0.2 lowerBoundaries 0.6 upperBoundaries 5.4 diff --git a/tests/input_files/dihedral_histogram-customgrid-periodic/test.in b/tests/input_files/dihedral_histogram-customgrid-periodic/test.in index 42f28ccdc..5883076c2 100644 --- a/tests/input_files/dihedral_histogram-customgrid-periodic/test.in +++ b/tests/input_files/dihedral_histogram-customgrid-periodic/test.in @@ -28,7 +28,7 @@ colvar { histogram { colvars one - histogramGrid { + gridParameters { widths 5 lowerBoundaries -60 upperBoundaries 300 diff --git a/tests/input_files/distance-grid_histogram-customgrid/test.in b/tests/input_files/distance-grid_histogram-customgrid/test.in index 612947def..61603e2ad 100644 --- a/tests/input_files/distance-grid_histogram-customgrid/test.in +++ b/tests/input_files/distance-grid_histogram-customgrid/test.in @@ -26,7 +26,7 @@ colvar { histogram { colvars one - histogramGrid { + gridParameters { widths 0.2 lowerBoundaries 0.6 upperBoundaries 5.4 diff --git a/tests/input_files/distance_histogram-customgrid/test.in b/tests/input_files/distance_histogram-customgrid/test.in index acfd48c31..1169d86ee 100644 --- a/tests/input_files/distance_histogram-customgrid/test.in +++ b/tests/input_files/distance_histogram-customgrid/test.in @@ -22,7 +22,7 @@ colvar { histogram { colvars one - histogramGrid { + gridParameters { widths 0.2 lowerBoundaries 0.6 upperBoundaries 5.4 From 22f00a40d7ffe965ca583f0064f0685562ada104 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=A9r=C3=B4me=20H=C3=A9nin?= Date: Tue, 17 Sep 2024 15:55:32 +0200 Subject: [PATCH 03/13] Move grid params to base class colvar_grid_params this allows for transparent initialization of a grid from another contining a different data type. --- doc/colvars-refman-main.tex | 12 +- .../test.in | 2 +- .../test.in | 2 +- .../test.in | 2 +- .../test.in | 2 +- .../AutoDiff/test.colvars.out | 14 +- .../AutoDiff/test.colvars.state.stripped | 5 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.histogram1.dat | 6004 ++++++++--------- .../AutoDiff/test.restart.colvars.out | 18 +- .../test.restart.colvars.state.stripped | 5 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../AutoDiff/test.restart.histogram1.dat | 6004 ++++++++--------- .../namd-version.txt | 6 +- .../test.in | 2 +- .../AutoDiff/test.colvars.out | 53 +- .../AutoDiff/test.colvars.state.stripped | 3 +- .../AutoDiff/test.colvars.traj | 40 +- .../AutoDiff/test.histogram1.dat | 50 +- .../AutoDiff/test.restart.colvars.out | 57 +- .../test.restart.colvars.state.stripped | 3 +- .../AutoDiff/test.restart.colvars.traj | 42 +- .../AutoDiff/test.restart.histogram1.dat | 50 +- .../namd-version.txt | 6 +- .../test.in | 2 +- .../AutoDiff/test.colvars.out | 15 +- .../AutoDiff/test.colvars.traj | 2 +- .../AutoDiff/test.histogram1.dat | 50 +- .../AutoDiff/test.restart.colvars.out | 19 +- .../000_distance_histogram-customgrid/test.in | 2 +- src/colvarbias_abf.cpp | 67 +- src/colvarbias_abf.h | 2 - src/colvarbias_histogram.cpp | 4 +- src/colvargrid.cpp | 38 +- src/colvargrid.h | 100 +- tests/Makefile | 8 +- tests/build_tests.sh | 1 + ...ihedral_histogram2d-periodic-customgrid.in | 2 +- tests/histogram-customgrid-periodic.in | 2 +- tests/histogram-customgrid.in | 2 +- .../test.in | 2 +- .../test.in | 2 +- .../distance_histogram-customgrid/test.in | 2 +- 43 files changed, 6446 insertions(+), 6340 deletions(-) diff --git a/doc/colvars-refman-main.tex b/doc/colvars-refman-main.tex index 1ece21c22..dbdaa01a9 100644 --- a/doc/colvars-refman-main.tex +++ b/doc/colvars-refman-main.tex @@ -5509,7 +5509,7 @@ \cvsubsubsec{Parameters for ABF}{sec:colvarbias_abf_params} ABF depends on parameters from each collective variable to define the grid on which free energy gradients are computed: see \ref{sec:colvar_grid_params} for details. -Alternately, grid parameters can be set directly inside the ABF block by inserting a \texttt{gridParameters} sub-block, as explained in \ref{sec:colvarbias_histogram_grid}. +Alternately, grid parameters can be set directly inside the ABF block by inserting a \texttt{grid} sub-block, as explained in \ref{sec:colvarbias_histogram_grid}. Other parameters to control the ABF runtime can be set in the ABF configuration block: \begin{itemize} @@ -7584,7 +7584,7 @@ \-histogram~\{\\ \-\-~~name~hist2d\\ \-\-~~colvars~r~theta\\ -\-\-~~gridParameters~\{\\ +\-\-~~grid~\{\\ \-\-~~~~widths~~0.1~1.0\\ \-\-~~~~lowerBoundaries~~~2.0~30.0\\ \-\-~~~~upperBoundaries~~10.0~90.0\\ @@ -7607,23 +7607,23 @@ \cvsubsubsec{Defining grids for multidimensional histograms}{sec:colvarbias_histogram_grid} -Grid parameters for the histogram may be provided at the level of the individual variables, or via a dedicated configuration block \texttt{gridParameters \{ \ldots \}} inside the configuration of this \texttt{histogram}. +Grid parameters for the histogram may be provided at the level of the individual variables, or via a dedicated configuration block \texttt{grid \{ \ldots \}} inside the configuration of this \texttt{histogram}. The options supported \emph{inside this block} are: \begin{itemize} \item % \key{% lowerBoundaries}{% - \texttt{gridParameters}}{% + \texttt{grid}}{% Lower boundaries of the grid}{% list of space-separated decimals}{% This option defines the lower boundaries of the grid, overriding any values defined by the \texttt{lowerBoundary} keyword of each colvar. Note that when \texttt{gatherVectorColvars} is \texttt{on} in the enclosing \texttt{histogram} block, each vector variable is automatically treated as a scalar, and a single value should be provided for it. } \item % - \simkey{upperBoundaries}{\texttt{gridParameters}}{lowerBoundaries} + \simkey{upperBoundaries}{\texttt{grid}}{lowerBoundaries} \item % - \simkey{widths}{\texttt{gridParameters}}{lowerBoundaries} + \simkey{widths}{\texttt{grid}}{lowerBoundaries} \end{itemize} diff --git a/gromacs/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/test.in b/gromacs/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/test.in index 3d768c4fd..e139372dc 100644 --- a/gromacs/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/test.in +++ b/gromacs/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/test.in @@ -38,7 +38,7 @@ colvar { histogram { colvars r phi - gridParameters { + grid { widths 0.2 6.0 lowerBoundaries 0.0 0.0 upperBoundaries 10.0 360.0 diff --git a/lammps/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/test.in b/lammps/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/test.in index 3d768c4fd..e139372dc 100644 --- a/lammps/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/test.in +++ b/lammps/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/test.in @@ -38,7 +38,7 @@ colvar { histogram { colvars r phi - gridParameters { + grid { widths 0.2 6.0 lowerBoundaries 0.0 0.0 upperBoundaries 10.0 360.0 diff --git a/lammps/tests/library/000_distance-grid_histogram-customgrid/test.in b/lammps/tests/library/000_distance-grid_histogram-customgrid/test.in index 61603e2ad..8376dfbdb 100644 --- a/lammps/tests/library/000_distance-grid_histogram-customgrid/test.in +++ b/lammps/tests/library/000_distance-grid_histogram-customgrid/test.in @@ -26,7 +26,7 @@ colvar { histogram { colvars one - gridParameters { + grid { widths 0.2 lowerBoundaries 0.6 upperBoundaries 5.4 diff --git a/namd/tests/library/000_dihedral_histogram-customgrid-periodic/test.in b/namd/tests/library/000_dihedral_histogram-customgrid-periodic/test.in index 5883076c2..40a5cd78c 100644 --- a/namd/tests/library/000_dihedral_histogram-customgrid-periodic/test.in +++ b/namd/tests/library/000_dihedral_histogram-customgrid-periodic/test.in @@ -28,7 +28,7 @@ colvar { histogram { colvars one - gridParameters { + grid { widths 5 lowerBoundaries -60 upperBoundaries 300 diff --git a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.colvars.out index b48697538..5185c0ef1 100644 --- a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.colvars.out @@ -2,12 +2,14 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: colvars: https://doi.org/10.1080/00268976.2013.813594 colvars: as well as all other papers listed below for individual features used. -colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Summary of compile-time features available in this build: +colvars: - SMP parallelism: enabled (num. threads = 4) +colvars: - Lepton custom functions: available +colvars: - Tcl interpreter: available colvars: Redefining the Tcl "cv" command to the new script interface. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -111,7 +113,7 @@ colvars: Initializing a new "dihedral" component. colvars: # name = "" [default] colvars: # componentCoeff = 1 [default] colvars: # componentExp = 1 [default] -colvars: # period = 0 [default] +colvars: # period = 360 [default] colvars: # wrapAround = 0 [default] colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] @@ -229,10 +231,14 @@ colvars: - NAMD engine: colvars: - Scalable center-of-mass computation (NAMD): colvars: Phillips2020 https://doi.org/10.1063/5.0014475 colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). +colvars: Current simulation parameters: initial step = 0, integration timestep = 1 +colvars: Updating atomic parameters (masses, charges, etc). colvars: Re-initialized atom group for variable "r":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "r":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "phi":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. @@ -240,8 +246,6 @@ colvars: Re-initialized atom group for variable "phi":0/1. 4 atoms: total mass = colvars: Re-initialized atom group for variable "phi":0/2. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "phi":0/3. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Histogram histogram1 will be written to file "test.histogram1.dat" colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". colvars: Saving collective variables state to "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.colvars.state.stripped index 39cdbdd58..4ede266de 100644 --- a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.colvars.state.stripped @@ -5,12 +5,12 @@ configuration { colvar { name r - x 3.21688253464583e+00 + x 3.2168825344401 } colvar { name phi - x 6.02774557527018e+01 + x 60.277455741941 } histogram { @@ -18,6 +18,7 @@ histogram { step 20 name histogram1 } + grid 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 diff --git a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.colvars.traj index 0d258d955..0737f7787 100644 --- a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step r phi 0 3.20554673468334e+00 6.31129478791928e+01 - 1 3.20437148316546e+00 6.30795952609024e+01 - 2 3.20384028589204e+00 6.30231590817356e+01 - 3 3.20396721187433e+00 6.29423176380356e+01 - 4 3.20472817287036e+00 6.28366833861828e+01 - 5 3.20606308066645e+00 6.27068898721072e+01 - 6 3.20787989003051e+00 6.25546017866590e+01 - 7 3.21005997943917e+00 6.23824530261739e+01 - 8 3.21246460655188e+00 6.21939260051983e+01 - 9 3.21494247388772e+00 6.19931890919450e+01 - 10 3.21733851236362e+00 6.17849080688927e+01 - 11 3.21950367383415e+00 6.15740450245643e+01 - 12 3.22130499858006e+00 6.13656547661594e+01 - 13 3.22263479496346e+00 6.11646847438178e+01 - 14 3.22341769665784e+00 6.09757828950022e+01 - 15 3.22361473677138e+00 6.08031168346083e+01 - 16 3.22322417514557e+00 6.06502098509209e+01 - 17 3.22227942564879e+00 6.05198025353684e+01 - 18 3.22084479803044e+00 6.04137510912894e+01 - 19 3.21900979846930e+00 6.03329741083708e+01 - 20 3.21688253464583e+00 6.02774557527018e+01 + 1 3.20437148316484e+00 6.30795952608635e+01 + 2 3.20384028588952e+00 6.30231590815800e+01 + 3 3.20396721186862e+00 6.29423176376863e+01 + 4 3.20472817286016e+00 6.28366833855655e+01 + 5 3.20606308065050e+00 6.27068898711517e+01 + 6 3.20787989000758e+00 6.25546017852999e+01 + 7 3.21005997940810e+00 6.23824530243513e+01 + 8 3.21246460651160e+00 6.21939260028577e+01 + 9 3.21494247383722e+00 6.19931890890363e+01 + 10 3.21733851230199e+00 6.17849080653709e+01 + 11 3.21950367376059e+00 6.15740450203887e+01 + 12 3.22130499849384e+00 6.13656547612945e+01 + 13 3.22263479486396e+00 6.11646847382338e+01 + 14 3.22341769654449e+00 6.09757828886765e+01 + 15 3.22361473664369e+00 6.08031168275266e+01 + 16 3.22322417500307e+00 6.06502098430778e+01 + 17 3.22227942549106e+00 6.05198025267681e+01 + 18 3.22084479785707e+00 6.04137510819449e+01 + 19 3.21900979827991e+00 6.03329740983038e+01 + 20 3.21688253444007e+00 6.02774557419408e+01 diff --git a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.histogram1.dat b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.histogram1.dat index 4ca2d87c5..337d77a7b 100644 --- a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.histogram1.dat +++ b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.histogram1.dat @@ -1,3053 +1,3053 @@ # 2 -# 0 0.2 50 0 -# 0 6 60 1 +# 0.00000000000000e+00 2.00000000000000e-01 50 0 +# 0.00000000000000e+00 6.00000000000000e+00 60 1 - 0.1 3 0 - 0.1 9 0 - 0.1 15 0 - 0.1 21 0 - 0.1 27 0 - 0.1 33 0 - 0.1 39 0 - 0.1 45 0 - 0.1 51 0 - 0.1 57 0 - 0.1 63 0 - 0.1 69 0 - 0.1 75 0 - 0.1 81 0 - 0.1 87 0 - 0.1 93 0 - 0.1 99 0 - 0.1 105 0 - 0.1 111 0 - 0.1 117 0 - 0.1 123 0 - 0.1 129 0 - 0.1 135 0 - 0.1 141 0 - 0.1 147 0 - 0.1 153 0 - 0.1 159 0 - 0.1 165 0 - 0.1 171 0 - 0.1 177 0 - 0.1 183 0 - 0.1 189 0 - 0.1 195 0 - 0.1 201 0 - 0.1 207 0 - 0.1 213 0 - 0.1 219 0 - 0.1 225 0 - 0.1 231 0 - 0.1 237 0 - 0.1 243 0 - 0.1 249 0 - 0.1 255 0 - 0.1 261 0 - 0.1 267 0 - 0.1 273 0 - 0.1 279 0 - 0.1 285 0 - 0.1 291 0 - 0.1 297 0 - 0.1 303 0 - 0.1 309 0 - 0.1 315 0 - 0.1 321 0 - 0.1 327 0 - 0.1 333 0 - 0.1 339 0 - 0.1 345 0 - 0.1 351 0 - 0.1 357 0 + 1.00000000000000e-01 3.00000000000000e+00 0.00000000000000e+00 + 1.00000000000000e-01 9.00000000000000e+00 0.00000000000000e+00 + 1.00000000000000e-01 1.50000000000000e+01 0.00000000000000e+00 + 1.00000000000000e-01 2.10000000000000e+01 0.00000000000000e+00 + 1.00000000000000e-01 2.70000000000000e+01 0.00000000000000e+00 + 1.00000000000000e-01 3.30000000000000e+01 0.00000000000000e+00 + 1.00000000000000e-01 3.90000000000000e+01 0.00000000000000e+00 + 1.00000000000000e-01 4.50000000000000e+01 0.00000000000000e+00 + 1.00000000000000e-01 5.10000000000000e+01 0.00000000000000e+00 + 1.00000000000000e-01 5.70000000000000e+01 0.00000000000000e+00 + 1.00000000000000e-01 6.30000000000000e+01 0.00000000000000e+00 + 1.00000000000000e-01 6.90000000000000e+01 0.00000000000000e+00 + 1.00000000000000e-01 7.50000000000000e+01 0.00000000000000e+00 + 1.00000000000000e-01 8.10000000000000e+01 0.00000000000000e+00 + 1.00000000000000e-01 8.70000000000000e+01 0.00000000000000e+00 + 1.00000000000000e-01 9.30000000000000e+01 0.00000000000000e+00 + 1.00000000000000e-01 9.90000000000000e+01 0.00000000000000e+00 + 1.00000000000000e-01 1.05000000000000e+02 0.00000000000000e+00 + 1.00000000000000e-01 1.11000000000000e+02 0.00000000000000e+00 + 1.00000000000000e-01 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3.03000000000000e+02 0.00000000000000e+00 + 9.70000000000000e+00 3.09000000000000e+02 0.00000000000000e+00 + 9.70000000000000e+00 3.15000000000000e+02 0.00000000000000e+00 + 9.70000000000000e+00 3.21000000000000e+02 0.00000000000000e+00 + 9.70000000000000e+00 3.27000000000000e+02 0.00000000000000e+00 + 9.70000000000000e+00 3.33000000000000e+02 0.00000000000000e+00 + 9.70000000000000e+00 3.39000000000000e+02 0.00000000000000e+00 + 9.70000000000000e+00 3.45000000000000e+02 0.00000000000000e+00 + 9.70000000000000e+00 3.51000000000000e+02 0.00000000000000e+00 + 9.70000000000000e+00 3.57000000000000e+02 0.00000000000000e+00 - 9.9 3 0 - 9.9 9 0 - 9.9 15 0 - 9.9 21 0 - 9.9 27 0 - 9.9 33 0 - 9.9 39 0 - 9.9 45 0 - 9.9 51 0 - 9.9 57 0 - 9.9 63 0 - 9.9 69 0 - 9.9 75 0 - 9.9 81 0 - 9.9 87 0 - 9.9 93 0 - 9.9 99 0 - 9.9 105 0 - 9.9 111 0 - 9.9 117 0 - 9.9 123 0 - 9.9 129 0 - 9.9 135 0 - 9.9 141 0 - 9.9 147 0 - 9.9 153 0 - 9.9 159 0 - 9.9 165 0 - 9.9 171 0 - 9.9 177 0 - 9.9 183 0 - 9.9 189 0 - 9.9 195 0 - 9.9 201 0 - 9.9 207 0 - 9.9 213 0 - 9.9 219 0 - 9.9 225 0 - 9.9 231 0 - 9.9 237 0 - 9.9 243 0 - 9.9 249 0 - 9.9 255 0 - 9.9 261 0 - 9.9 267 0 - 9.9 273 0 - 9.9 279 0 - 9.9 285 0 - 9.9 291 0 - 9.9 297 0 - 9.9 303 0 - 9.9 309 0 - 9.9 315 0 - 9.9 321 0 - 9.9 327 0 - 9.9 333 0 - 9.9 339 0 - 9.9 345 0 - 9.9 351 0 - 9.9 357 0 + 9.90000000000000e+00 3.00000000000000e+00 0.00000000000000e+00 + 9.90000000000000e+00 9.00000000000000e+00 0.00000000000000e+00 + 9.90000000000000e+00 1.50000000000000e+01 0.00000000000000e+00 + 9.90000000000000e+00 2.10000000000000e+01 0.00000000000000e+00 + 9.90000000000000e+00 2.70000000000000e+01 0.00000000000000e+00 + 9.90000000000000e+00 3.30000000000000e+01 0.00000000000000e+00 + 9.90000000000000e+00 3.90000000000000e+01 0.00000000000000e+00 + 9.90000000000000e+00 4.50000000000000e+01 0.00000000000000e+00 + 9.90000000000000e+00 5.10000000000000e+01 0.00000000000000e+00 + 9.90000000000000e+00 5.70000000000000e+01 0.00000000000000e+00 + 9.90000000000000e+00 6.30000000000000e+01 0.00000000000000e+00 + 9.90000000000000e+00 6.90000000000000e+01 0.00000000000000e+00 + 9.90000000000000e+00 7.50000000000000e+01 0.00000000000000e+00 + 9.90000000000000e+00 8.10000000000000e+01 0.00000000000000e+00 + 9.90000000000000e+00 8.70000000000000e+01 0.00000000000000e+00 + 9.90000000000000e+00 9.30000000000000e+01 0.00000000000000e+00 + 9.90000000000000e+00 9.90000000000000e+01 0.00000000000000e+00 + 9.90000000000000e+00 1.05000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 1.11000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 1.17000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 1.23000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 1.29000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 1.35000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 1.41000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 1.47000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 1.53000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 1.59000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 1.65000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 1.71000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 1.77000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 1.83000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 1.89000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 1.95000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 2.01000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 2.07000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 2.13000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 2.19000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 2.25000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 2.31000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 2.37000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 2.43000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 2.49000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 2.55000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 2.61000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 2.67000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 2.73000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 2.79000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 2.85000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 2.91000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 2.97000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 3.03000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 3.09000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 3.15000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 3.21000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 3.27000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 3.33000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 3.39000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 3.45000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 3.51000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 3.57000000000000e+02 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.colvars.out index 5c3fb9114..f6811b00b 100644 --- a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.colvars.out @@ -2,12 +2,14 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: colvars: https://doi.org/10.1080/00268976.2013.813594 colvars: as well as all other papers listed below for individual features used. -colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Summary of compile-time features available in this build: +colvars: - SMP parallelism: enabled (num. threads = 4) +colvars: - Lepton custom functions: available +colvars: - Tcl interpreter: available colvars: Redefining the Tcl "cv" command to the new script interface. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -111,7 +113,7 @@ colvars: Initializing a new "dihedral" component. colvars: # name = "" [default] colvars: # componentCoeff = 1 [default] colvars: # componentExp = 1 [default] -colvars: # period = 0 [default] +colvars: # period = 360 [default] colvars: # wrapAround = 0 [default] colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] @@ -229,16 +231,20 @@ colvars: - NAMD engine: colvars: - Scalable center-of-mass computation (NAMD): colvars: Phillips2020 https://doi.org/10.1063/5.0014475 colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Loading state from text file "test.colvars.state". colvars: Restarting collective variable "r" from value: 3.21688 colvars: Restarting collective variable "phi" from value: 60.2775 -colvars: Restarting histogram bias "histogram1" from step number 20. +colvars: Restarted histogram bias "histogram1" with step number 20. colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (4 scalable groups, 16 atoms in total). colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). +colvars: Current simulation parameters: initial step = 20, integration timestep = 1 +colvars: Updating atomic parameters (masses, charges, etc). colvars: Re-initialized atom group for variable "r":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "r":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "phi":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. @@ -246,8 +252,6 @@ colvars: Re-initialized atom group for variable "phi":0/1. 4 atoms: total mass = colvars: Re-initialized atom group for variable "phi":0/2. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: Re-initialized atom group for variable "phi":0/3. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Histogram histogram1 will be written to file "test.restart.histogram1.dat" colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj". colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj". colvars: Saving collective variables state to "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.colvars.state.stripped index 16d91a903..caf8764ae 100644 --- a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.colvars.state.stripped @@ -5,12 +5,12 @@ configuration { colvar { name r - x 3.21404878547144e+00 + x 3.2140487849902 } colvar { name phi - x 6.08972122017851e+01 + x 60.897212181713 } histogram { @@ -18,6 +18,7 @@ histogram { step 40 name histogram1 } + grid 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 diff --git a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.colvars.traj index 6e6a9d108..604d12df3 100644 --- a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step r phi - 20 3.21688253464583e+00 6.02774557527018e+01 - 21 3.21458253157603e+00 6.02463068700288e+01 - 22 3.21223315254029e+00 6.02378794668108e+01 - 23 3.20995392032979e+00 6.02499213792704e+01 - 24 3.20785326966943e+00 6.02797520575071e+01 - 25 3.20602244845117e+00 6.03244375021622e+01 - 26 3.20453120146139e+00 6.03809430522940e+01 - 27 3.20342556480347e+00 6.04462482372788e+01 - 28 3.20272769852622e+00 6.05174152657937e+01 - 29 3.20243730776714e+00 6.05916134522643e+01 - 30 3.20253423308456e+00 6.06661106334871e+01 - 31 3.20298183362156e+00 6.07382494079973e+01 - 32 3.20373100914607e+00 6.08054278528112e+01 - 33 3.20472468746373e+00 6.08651029084488e+01 - 34 3.20590256221113e+00 6.09148265944857e+01 - 35 3.20720566184671e+00 6.09523144226767e+01 - 36 3.20858030459458e+00 6.09755306669437e+01 - 37 3.20998111854285e+00 6.09827676451462e+01 - 38 3.21137308334418e+00 6.09726956295080e+01 - 39 3.21273274315657e+00 6.09443715427968e+01 - 40 3.21404878547144e+00 6.08972122017851e+01 + 20 3.21688253444007e+00 6.02774557419408e+01 + 21 3.21458253135360e+00 6.02463068586075e+01 + 22 3.21223315230094e+00 6.02378794547661e+01 + 23 3.20995392007338e+00 6.02499213666399e+01 + 24 3.20785326939588e+00 6.02797520443279e+01 + 25 3.20602244816055e+00 6.03244374884684e+01 + 26 3.20453120115385e+00 6.03809430381164e+01 + 27 3.20342556447928e+00 6.04462482226439e+01 + 28 3.20272769818574e+00 6.05174152507230e+01 + 29 3.20243730741081e+00 6.05916134367742e+01 + 30 3.20253423271288e+00 6.06661106175892e+01 + 31 3.20298183323507e+00 6.07382493916984e+01 + 32 3.20373100874535e+00 6.08054278361138e+01 + 33 3.20472468704942e+00 6.08651028913515e+01 + 34 3.20590256178393e+00 6.09148265769848e+01 + 35 3.20720566140745e+00 6.09523144047665e+01 + 36 3.20858030414419e+00 6.09755306486173e+01 + 37 3.20998111808250e+00 6.09827676263962e+01 + 38 3.21137308287521e+00 6.09726956103264e+01 + 39 3.21273274268056e+00 6.09443715231749e+01 + 40 3.21404878499019e+00 6.08972121817130e+01 diff --git a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.histogram1.dat b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.histogram1.dat index bcd93aff0..60d272104 100644 --- a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.histogram1.dat +++ b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/AutoDiff/test.restart.histogram1.dat @@ -1,3053 +1,3053 @@ # 2 -# 0 0.2 50 0 -# 0 6 60 1 +# 0.00000000000000e+00 2.00000000000000e-01 50 0 +# 0.00000000000000e+00 6.00000000000000e+00 60 1 - 0.1 3 0 - 0.1 9 0 - 0.1 15 0 - 0.1 21 0 - 0.1 27 0 - 0.1 33 0 - 0.1 39 0 - 0.1 45 0 - 0.1 51 0 - 0.1 57 0 - 0.1 63 0 - 0.1 69 0 - 0.1 75 0 - 0.1 81 0 - 0.1 87 0 - 0.1 93 0 - 0.1 99 0 - 0.1 105 0 - 0.1 111 0 - 0.1 117 0 - 0.1 123 0 - 0.1 129 0 - 0.1 135 0 - 0.1 141 0 - 0.1 147 0 - 0.1 153 0 - 0.1 159 0 - 0.1 165 0 - 0.1 171 0 - 0.1 177 0 - 0.1 183 0 - 0.1 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1.00000000000000e-01 6.30000000000000e+01 0.00000000000000e+00 + 1.00000000000000e-01 6.90000000000000e+01 0.00000000000000e+00 + 1.00000000000000e-01 7.50000000000000e+01 0.00000000000000e+00 + 1.00000000000000e-01 8.10000000000000e+01 0.00000000000000e+00 + 1.00000000000000e-01 8.70000000000000e+01 0.00000000000000e+00 + 1.00000000000000e-01 9.30000000000000e+01 0.00000000000000e+00 + 1.00000000000000e-01 9.90000000000000e+01 0.00000000000000e+00 + 1.00000000000000e-01 1.05000000000000e+02 0.00000000000000e+00 + 1.00000000000000e-01 1.11000000000000e+02 0.00000000000000e+00 + 1.00000000000000e-01 1.17000000000000e+02 0.00000000000000e+00 + 1.00000000000000e-01 1.23000000000000e+02 0.00000000000000e+00 + 1.00000000000000e-01 1.29000000000000e+02 0.00000000000000e+00 + 1.00000000000000e-01 1.35000000000000e+02 0.00000000000000e+00 + 1.00000000000000e-01 1.41000000000000e+02 0.00000000000000e+00 + 1.00000000000000e-01 1.47000000000000e+02 0.00000000000000e+00 + 1.00000000000000e-01 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9.70000000000000e+00 3.39000000000000e+02 0.00000000000000e+00 + 9.70000000000000e+00 3.45000000000000e+02 0.00000000000000e+00 + 9.70000000000000e+00 3.51000000000000e+02 0.00000000000000e+00 + 9.70000000000000e+00 3.57000000000000e+02 0.00000000000000e+00 - 9.9 3 0 - 9.9 9 0 - 9.9 15 0 - 9.9 21 0 - 9.9 27 0 - 9.9 33 0 - 9.9 39 0 - 9.9 45 0 - 9.9 51 0 - 9.9 57 0 - 9.9 63 0 - 9.9 69 0 - 9.9 75 0 - 9.9 81 0 - 9.9 87 0 - 9.9 93 0 - 9.9 99 0 - 9.9 105 0 - 9.9 111 0 - 9.9 117 0 - 9.9 123 0 - 9.9 129 0 - 9.9 135 0 - 9.9 141 0 - 9.9 147 0 - 9.9 153 0 - 9.9 159 0 - 9.9 165 0 - 9.9 171 0 - 9.9 177 0 - 9.9 183 0 - 9.9 189 0 - 9.9 195 0 - 9.9 201 0 - 9.9 207 0 - 9.9 213 0 - 9.9 219 0 - 9.9 225 0 - 9.9 231 0 - 9.9 237 0 - 9.9 243 0 - 9.9 249 0 - 9.9 255 0 - 9.9 261 0 - 9.9 267 0 - 9.9 273 0 - 9.9 279 0 - 9.9 285 0 - 9.9 291 0 - 9.9 297 0 - 9.9 303 0 - 9.9 309 0 - 9.9 315 0 - 9.9 321 0 - 9.9 327 0 - 9.9 333 0 - 9.9 339 0 - 9.9 345 0 - 9.9 351 0 - 9.9 357 0 + 9.90000000000000e+00 3.00000000000000e+00 0.00000000000000e+00 + 9.90000000000000e+00 9.00000000000000e+00 0.00000000000000e+00 + 9.90000000000000e+00 1.50000000000000e+01 0.00000000000000e+00 + 9.90000000000000e+00 2.10000000000000e+01 0.00000000000000e+00 + 9.90000000000000e+00 2.70000000000000e+01 0.00000000000000e+00 + 9.90000000000000e+00 3.30000000000000e+01 0.00000000000000e+00 + 9.90000000000000e+00 3.90000000000000e+01 0.00000000000000e+00 + 9.90000000000000e+00 4.50000000000000e+01 0.00000000000000e+00 + 9.90000000000000e+00 5.10000000000000e+01 0.00000000000000e+00 + 9.90000000000000e+00 5.70000000000000e+01 0.00000000000000e+00 + 9.90000000000000e+00 6.30000000000000e+01 0.00000000000000e+00 + 9.90000000000000e+00 6.90000000000000e+01 0.00000000000000e+00 + 9.90000000000000e+00 7.50000000000000e+01 0.00000000000000e+00 + 9.90000000000000e+00 8.10000000000000e+01 0.00000000000000e+00 + 9.90000000000000e+00 8.70000000000000e+01 0.00000000000000e+00 + 9.90000000000000e+00 9.30000000000000e+01 0.00000000000000e+00 + 9.90000000000000e+00 9.90000000000000e+01 0.00000000000000e+00 + 9.90000000000000e+00 1.05000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 1.11000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 1.17000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 1.23000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 1.29000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 1.35000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 1.41000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 1.47000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 1.53000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 1.59000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 1.65000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 1.71000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 1.77000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 1.83000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 1.89000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 1.95000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 2.01000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 2.07000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 2.13000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 2.19000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 2.25000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 2.31000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 2.37000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 2.43000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 2.49000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 2.55000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 2.61000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 2.67000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 2.73000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 2.79000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 2.85000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 2.91000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 2.97000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 3.03000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 3.09000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 3.15000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 3.21000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 3.27000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 3.33000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 3.39000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 3.45000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 3.51000000000000e+02 0.00000000000000e+00 + 9.90000000000000e+00 3.57000000000000e+02 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/namd-version.txt b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/namd-version.txt index 017b69b3a..e1d311c69 100644 --- a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/namd-version.txt +++ b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.15alpha2 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version 2022-04-14. -colvars: Using NAMD interface, version "2022-04-06". +Info: NAMD 3.1alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2024-06-04. +colvars: Using NAMD interface, version "2023-12-05". diff --git a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/test.in b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/test.in index 3d768c4fd..e139372dc 100644 --- a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/test.in +++ b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/test.in @@ -38,7 +38,7 @@ colvar { histogram { colvars r phi - gridParameters { + grid { widths 0.2 6.0 lowerBoundaries 0.0 0.0 upperBoundaries 10.0 360.0 diff --git a/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.colvars.out index 2cb8b2826..b357252a1 100644 --- a/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.colvars.out @@ -1,9 +1,15 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. -colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: This version was built with the C++11 standard or higher. +colvars: Summary of compile-time features available in this build: +colvars: - SMP parallelism: enabled (num. threads = 4) +colvars: - Lepton custom functions: available +colvars: - Tcl interpreter: available +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +48,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +62,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -123,20 +130,32 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. -colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Histogram colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). +colvars: Current simulation parameters: initial step = 0, integration timestep = 1 +colvars: Updating atomic parameters (masses, charges, etc). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Histogram histogram1 will be written to file "test.histogram1.dat" colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". colvars: Saving collective variables state to "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.colvars.state.stripped index 48987f05a..d2fcc1e5b 100644 --- a/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21688253464583e+00 + x 3.2168825344401 } histogram { @@ -13,6 +13,7 @@ histogram { step 20 name histogram1 } + grid 0 0 0 0 0 0 0 0 0 0 0 0 0 20 0 0 diff --git a/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.colvars.traj index 2d1d01de3..edbc89eea 100644 --- a/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one 0 3.20554673468334e+00 0.00000000000000e+00 - 1 3.20437148316546e+00 0.00000000000000e+00 - 2 3.20384028589204e+00 0.00000000000000e+00 - 3 3.20396721187433e+00 0.00000000000000e+00 - 4 3.20472817287036e+00 0.00000000000000e+00 - 5 3.20606308066645e+00 0.00000000000000e+00 - 6 3.20787989003051e+00 0.00000000000000e+00 - 7 3.21005997943917e+00 0.00000000000000e+00 - 8 3.21246460655188e+00 0.00000000000000e+00 - 9 3.21494247388772e+00 0.00000000000000e+00 - 10 3.21733851236362e+00 0.00000000000000e+00 - 11 3.21950367383415e+00 0.00000000000000e+00 - 12 3.22130499858006e+00 0.00000000000000e+00 - 13 3.22263479496346e+00 0.00000000000000e+00 - 14 3.22341769665784e+00 0.00000000000000e+00 - 15 3.22361473677138e+00 0.00000000000000e+00 - 16 3.22322417514557e+00 0.00000000000000e+00 - 17 3.22227942564879e+00 0.00000000000000e+00 - 18 3.22084479803044e+00 0.00000000000000e+00 - 19 3.21900979846930e+00 0.00000000000000e+00 - 20 3.21688253464583e+00 0.00000000000000e+00 + 1 3.20437148316484e+00 0.00000000000000e+00 + 2 3.20384028588952e+00 0.00000000000000e+00 + 3 3.20396721186862e+00 0.00000000000000e+00 + 4 3.20472817286016e+00 0.00000000000000e+00 + 5 3.20606308065050e+00 0.00000000000000e+00 + 6 3.20787989000758e+00 0.00000000000000e+00 + 7 3.21005997940810e+00 0.00000000000000e+00 + 8 3.21246460651160e+00 0.00000000000000e+00 + 9 3.21494247383722e+00 0.00000000000000e+00 + 10 3.21733851230199e+00 0.00000000000000e+00 + 11 3.21950367376059e+00 0.00000000000000e+00 + 12 3.22130499849384e+00 0.00000000000000e+00 + 13 3.22263479486396e+00 0.00000000000000e+00 + 14 3.22341769654449e+00 0.00000000000000e+00 + 15 3.22361473664369e+00 0.00000000000000e+00 + 16 3.22322417500307e+00 0.00000000000000e+00 + 17 3.22227942549106e+00 0.00000000000000e+00 + 18 3.22084479785707e+00 0.00000000000000e+00 + 19 3.21900979827991e+00 0.00000000000000e+00 + 20 3.21688253444007e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.histogram1.dat b/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.histogram1.dat index 1b0ff42d4..6ff3132f9 100644 --- a/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.histogram1.dat +++ b/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.histogram1.dat @@ -1,27 +1,27 @@ # 1 -# 0.6 0.2 24 0 +# 6.00000000000000e-01 2.00000000000000e-01 24 0 - 0.7 0 - 0.9 0 - 1.1 0 - 1.3 0 - 1.5 0 - 1.7 0 - 1.9 0 - 2.1 0 - 2.3 0 - 2.5 0 - 2.7 0 - 2.9 0 - 3.1 0 - 3.3 20 - 3.5 0 - 3.7 0 - 3.9 0 - 4.1 0 - 4.3 0 - 4.5 0 - 4.7 0 - 4.9 0 - 5.1 0 - 5.3 0 + 7.00000000000000e-01 0.00000000000000e+00 + 9.00000000000000e-01 0.00000000000000e+00 + 1.10000000000000e+00 0.00000000000000e+00 + 1.30000000000000e+00 0.00000000000000e+00 + 1.50000000000000e+00 0.00000000000000e+00 + 1.70000000000000e+00 0.00000000000000e+00 + 1.90000000000000e+00 0.00000000000000e+00 + 2.10000000000000e+00 0.00000000000000e+00 + 2.30000000000000e+00 0.00000000000000e+00 + 2.50000000000000e+00 0.00000000000000e+00 + 2.70000000000000e+00 0.00000000000000e+00 + 2.90000000000000e+00 0.00000000000000e+00 + 3.10000000000000e+00 0.00000000000000e+00 + 3.30000000000000e+00 2.00000000000000e+01 + 3.50000000000000e+00 0.00000000000000e+00 + 3.70000000000000e+00 0.00000000000000e+00 + 3.90000000000000e+00 0.00000000000000e+00 + 4.10000000000000e+00 0.00000000000000e+00 + 4.30000000000000e+00 0.00000000000000e+00 + 4.50000000000000e+00 0.00000000000000e+00 + 4.70000000000000e+00 0.00000000000000e+00 + 4.90000000000000e+00 0.00000000000000e+00 + 5.10000000000000e+00 0.00000000000000e+00 + 5.30000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.restart.colvars.out index 231ed2e71..022b32247 100644 --- a/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.restart.colvars.out @@ -1,9 +1,15 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: -colvars: https://dx.doi.org/10.1080/00268976.2013.813594 -colvars: in any publication based on this calculation. -colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. colvars: This version was built with the C++11 standard or higher. +colvars: Summary of compile-time features available in this build: +colvars: - SMP parallelism: enabled (num. threads = 4) +colvars: - Lepton custom functions: available +colvars: - Tcl interpreter: available +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -42,6 +48,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -55,28 +62,28 @@ colvars: # forceNoPBC = off [default] colvars: # scalable = on [default] colvars: Initializing atom group "group1". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group1" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group1". colvars: # printAtomIDs = off [default] colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. colvars: Initializing atom group "group2". colvars: # name = "" [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "group2" colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] -colvars: # enableForces = on [default] colvars: # enableFitGradients = on [default] colvars: Enabling scalable calculation for group "group2". colvars: # printAtomIDs = off [default] @@ -123,25 +130,37 @@ colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). -colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. -colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Histogram colvar bias implementation: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "test.colvars.state". +colvars: Loading state from text file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21688 -colvars: Restarting histogram bias "histogram1" from step number 20. +colvars: Restarted histogram bias "histogram1" with step number 20. colvars: ---------------------------------------------------------------------- -colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). +colvars: Current simulation parameters: initial step = 20, integration timestep = 1 +colvars: Updating atomic parameters (masses, charges, etc). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Histogram histogram1 will be written to file "test.restart.histogram1.dat" colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj". colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj". colvars: Saving collective variables state to "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.restart.colvars.state.stripped index 35abb4af3..805a3a993 100644 --- a/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.restart.colvars.state.stripped +++ b/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.restart.colvars.state.stripped @@ -5,7 +5,7 @@ configuration { colvar { name one - x 3.21404878547144e+00 + x 3.2140487849902 } histogram { @@ -13,6 +13,7 @@ histogram { step 40 name histogram1 } + grid 0 0 0 0 0 0 0 0 0 0 0 0 0 40 0 0 diff --git a/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.restart.colvars.traj index 58d908160..52b10f39a 100644 --- a/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.restart.colvars.traj +++ b/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.restart.colvars.traj @@ -1,22 +1,22 @@ # step one fa_one - 20 3.21688253464583e+00 0.00000000000000e+00 - 21 3.21458253157603e+00 0.00000000000000e+00 - 22 3.21223315254029e+00 0.00000000000000e+00 - 23 3.20995392032979e+00 0.00000000000000e+00 - 24 3.20785326966943e+00 0.00000000000000e+00 - 25 3.20602244845117e+00 0.00000000000000e+00 - 26 3.20453120146139e+00 0.00000000000000e+00 - 27 3.20342556480347e+00 0.00000000000000e+00 - 28 3.20272769852622e+00 0.00000000000000e+00 - 29 3.20243730776714e+00 0.00000000000000e+00 - 30 3.20253423308456e+00 0.00000000000000e+00 - 31 3.20298183362156e+00 0.00000000000000e+00 - 32 3.20373100914607e+00 0.00000000000000e+00 - 33 3.20472468746373e+00 0.00000000000000e+00 - 34 3.20590256221113e+00 0.00000000000000e+00 - 35 3.20720566184671e+00 0.00000000000000e+00 - 36 3.20858030459458e+00 0.00000000000000e+00 - 37 3.20998111854285e+00 0.00000000000000e+00 - 38 3.21137308334418e+00 0.00000000000000e+00 - 39 3.21273274315657e+00 0.00000000000000e+00 - 40 3.21404878547144e+00 0.00000000000000e+00 + 20 3.21688253444007e+00 0.00000000000000e+00 + 21 3.21458253135360e+00 0.00000000000000e+00 + 22 3.21223315230094e+00 0.00000000000000e+00 + 23 3.20995392007338e+00 0.00000000000000e+00 + 24 3.20785326939588e+00 0.00000000000000e+00 + 25 3.20602244816055e+00 0.00000000000000e+00 + 26 3.20453120115385e+00 0.00000000000000e+00 + 27 3.20342556447928e+00 0.00000000000000e+00 + 28 3.20272769818574e+00 0.00000000000000e+00 + 29 3.20243730741081e+00 0.00000000000000e+00 + 30 3.20253423271288e+00 0.00000000000000e+00 + 31 3.20298183323507e+00 0.00000000000000e+00 + 32 3.20373100874535e+00 0.00000000000000e+00 + 33 3.20472468704942e+00 0.00000000000000e+00 + 34 3.20590256178393e+00 0.00000000000000e+00 + 35 3.20720566140745e+00 0.00000000000000e+00 + 36 3.20858030414419e+00 0.00000000000000e+00 + 37 3.20998111808250e+00 0.00000000000000e+00 + 38 3.21137308287521e+00 0.00000000000000e+00 + 39 3.21273274268056e+00 0.00000000000000e+00 + 40 3.21404878499019e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.restart.histogram1.dat b/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.restart.histogram1.dat index 2a16dc5f6..686fae912 100644 --- a/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.restart.histogram1.dat +++ b/namd/tests/library/000_distance-grid_histogram-customgrid/AutoDiff/test.restart.histogram1.dat @@ -1,27 +1,27 @@ # 1 -# 0.6 0.2 24 0 +# 6.00000000000000e-01 2.00000000000000e-01 24 0 - 0.7 0 - 0.9 0 - 1.1 0 - 1.3 0 - 1.5 0 - 1.7 0 - 1.9 0 - 2.1 0 - 2.3 0 - 2.5 0 - 2.7 0 - 2.9 0 - 3.1 0 - 3.3 40 - 3.5 0 - 3.7 0 - 3.9 0 - 4.1 0 - 4.3 0 - 4.5 0 - 4.7 0 - 4.9 0 - 5.1 0 - 5.3 0 + 7.00000000000000e-01 0.00000000000000e+00 + 9.00000000000000e-01 0.00000000000000e+00 + 1.10000000000000e+00 0.00000000000000e+00 + 1.30000000000000e+00 0.00000000000000e+00 + 1.50000000000000e+00 0.00000000000000e+00 + 1.70000000000000e+00 0.00000000000000e+00 + 1.90000000000000e+00 0.00000000000000e+00 + 2.10000000000000e+00 0.00000000000000e+00 + 2.30000000000000e+00 0.00000000000000e+00 + 2.50000000000000e+00 0.00000000000000e+00 + 2.70000000000000e+00 0.00000000000000e+00 + 2.90000000000000e+00 0.00000000000000e+00 + 3.10000000000000e+00 0.00000000000000e+00 + 3.30000000000000e+00 4.00000000000000e+01 + 3.50000000000000e+00 0.00000000000000e+00 + 3.70000000000000e+00 0.00000000000000e+00 + 3.90000000000000e+00 0.00000000000000e+00 + 4.10000000000000e+00 0.00000000000000e+00 + 4.30000000000000e+00 0.00000000000000e+00 + 4.50000000000000e+00 0.00000000000000e+00 + 4.70000000000000e+00 0.00000000000000e+00 + 4.90000000000000e+00 0.00000000000000e+00 + 5.10000000000000e+00 0.00000000000000e+00 + 5.30000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_histogram-customgrid/namd-version.txt b/namd/tests/library/000_distance-grid_histogram-customgrid/namd-version.txt index e2b19c981..e1d311c69 100644 --- a/namd/tests/library/000_distance-grid_histogram-customgrid/namd-version.txt +++ b/namd/tests/library/000_distance-grid_histogram-customgrid/namd-version.txt @@ -1,3 +1,3 @@ -Info: NAMD 2.14b1 for Linux-x86_64-multicore -colvars: Initializing the collective variables module, version "2020-04-09". -colvars: Using NAMD interface, version "2020-04-07". +Info: NAMD 3.1alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2024-06-04. +colvars: Using NAMD interface, version "2023-12-05". diff --git a/namd/tests/library/000_distance-grid_histogram-customgrid/test.in b/namd/tests/library/000_distance-grid_histogram-customgrid/test.in index 61603e2ad..8376dfbdb 100644 --- a/namd/tests/library/000_distance-grid_histogram-customgrid/test.in +++ b/namd/tests/library/000_distance-grid_histogram-customgrid/test.in @@ -26,7 +26,7 @@ colvar { histogram { colvars one - gridParameters { + grid { widths 0.2 lowerBoundaries 0.6 upperBoundaries 5.4 diff --git a/namd/tests/library/000_distance_histogram-customgrid/AutoDiff/test.colvars.out b/namd/tests/library/000_distance_histogram-customgrid/AutoDiff/test.colvars.out index a86d5ad83..71af64557 100644 --- a/namd/tests/library/000_distance_histogram-customgrid/AutoDiff/test.colvars.out +++ b/namd/tests/library/000_distance_histogram-customgrid/AutoDiff/test.colvars.out @@ -2,12 +2,14 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: colvars: https://doi.org/10.1080/00268976.2013.813594 colvars: as well as all other papers listed below for individual features used. -colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Summary of compile-time features available in this build: +colvars: - SMP parallelism: enabled (num. threads = 4) +colvars: - Lepton custom functions: available +colvars: - Tcl interpreter: available +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: The restart output state file will be "test.tmp.colvars.state". colvars: The final output state file will be "test.colvars.state". -colvars: Opening trajectory file "test.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -46,6 +48,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -142,15 +145,17 @@ colvars: - NAMD engine: colvars: - Scalable center-of-mass computation (NAMD): colvars: Phillips2020 https://doi.org/10.1063/5.0014475 colvars: +colvars: updating target temperature (T = 0 K). colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). +colvars: Current simulation parameters: initial step = 0, integration timestep = 1 +colvars: Updating atomic parameters (masses, charges, etc). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.tmp.colvars.state". -colvars: The final output state file will be "test.colvars.state". -colvars: Histogram histogram1 will be written to file "test.histogram1.dat" colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". colvars: Saving collective variables state to "test.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_histogram-customgrid/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance_histogram-customgrid/AutoDiff/test.colvars.traj index a3529376d..edbc89eea 100644 --- a/namd/tests/library/000_distance_histogram-customgrid/AutoDiff/test.colvars.traj +++ b/namd/tests/library/000_distance_histogram-customgrid/AutoDiff/test.colvars.traj @@ -5,7 +5,7 @@ 3 3.20396721186862e+00 0.00000000000000e+00 4 3.20472817286016e+00 0.00000000000000e+00 5 3.20606308065050e+00 0.00000000000000e+00 - 6 3.20787989000757e+00 0.00000000000000e+00 + 6 3.20787989000758e+00 0.00000000000000e+00 7 3.21005997940810e+00 0.00000000000000e+00 8 3.21246460651160e+00 0.00000000000000e+00 9 3.21494247383722e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance_histogram-customgrid/AutoDiff/test.histogram1.dat b/namd/tests/library/000_distance_histogram-customgrid/AutoDiff/test.histogram1.dat index 1b0ff42d4..6ff3132f9 100644 --- a/namd/tests/library/000_distance_histogram-customgrid/AutoDiff/test.histogram1.dat +++ b/namd/tests/library/000_distance_histogram-customgrid/AutoDiff/test.histogram1.dat @@ -1,27 +1,27 @@ # 1 -# 0.6 0.2 24 0 +# 6.00000000000000e-01 2.00000000000000e-01 24 0 - 0.7 0 - 0.9 0 - 1.1 0 - 1.3 0 - 1.5 0 - 1.7 0 - 1.9 0 - 2.1 0 - 2.3 0 - 2.5 0 - 2.7 0 - 2.9 0 - 3.1 0 - 3.3 20 - 3.5 0 - 3.7 0 - 3.9 0 - 4.1 0 - 4.3 0 - 4.5 0 - 4.7 0 - 4.9 0 - 5.1 0 - 5.3 0 + 7.00000000000000e-01 0.00000000000000e+00 + 9.00000000000000e-01 0.00000000000000e+00 + 1.10000000000000e+00 0.00000000000000e+00 + 1.30000000000000e+00 0.00000000000000e+00 + 1.50000000000000e+00 0.00000000000000e+00 + 1.70000000000000e+00 0.00000000000000e+00 + 1.90000000000000e+00 0.00000000000000e+00 + 2.10000000000000e+00 0.00000000000000e+00 + 2.30000000000000e+00 0.00000000000000e+00 + 2.50000000000000e+00 0.00000000000000e+00 + 2.70000000000000e+00 0.00000000000000e+00 + 2.90000000000000e+00 0.00000000000000e+00 + 3.10000000000000e+00 0.00000000000000e+00 + 3.30000000000000e+00 2.00000000000000e+01 + 3.50000000000000e+00 0.00000000000000e+00 + 3.70000000000000e+00 0.00000000000000e+00 + 3.90000000000000e+00 0.00000000000000e+00 + 4.10000000000000e+00 0.00000000000000e+00 + 4.30000000000000e+00 0.00000000000000e+00 + 4.50000000000000e+00 0.00000000000000e+00 + 4.70000000000000e+00 0.00000000000000e+00 + 4.90000000000000e+00 0.00000000000000e+00 + 5.10000000000000e+00 0.00000000000000e+00 + 5.30000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance_histogram-customgrid/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance_histogram-customgrid/AutoDiff/test.restart.colvars.out index cc179e493..6469216ff 100644 --- a/namd/tests/library/000_distance_histogram-customgrid/AutoDiff/test.restart.colvars.out +++ b/namd/tests/library/000_distance_histogram-customgrid/AutoDiff/test.restart.colvars.out @@ -2,12 +2,14 @@ colvars: ---------------------------------------------------------------------- colvars: Please cite Fiorin et al, Mol Phys 2013: colvars: https://doi.org/10.1080/00268976.2013.813594 colvars: as well as all other papers listed below for individual features used. -colvars: SMP parallelism is enabled; if needed, use "smp off" to override this. colvars: This version was built with the C++11 standard or higher. +colvars: Summary of compile-time features available in this build: +colvars: - SMP parallelism: enabled (num. threads = 4) +colvars: - Lepton custom functions: available +colvars: - Tcl interpreter: available +colvars: Redefining the Tcl "cv" command to the new script interface. colvars: The restart output state file will be "test.restart.tmp.colvars.state". colvars: The final output state file will be "test.restart.colvars.state". -colvars: Opening trajectory file "test.restart.colvars.traj". -colvars: Redefining the Tcl "cv" command to the new script interface. colvars: ---------------------------------------------------------------------- colvars: Reading new configuration from file "test.in": colvars: # units = "" [default] @@ -46,6 +48,7 @@ colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 10 colvars: # scriptedColvarForces = off [default] colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. colvars: # name = "one" @@ -142,20 +145,22 @@ colvars: - NAMD engine: colvars: - Scalable center-of-mass computation (NAMD): colvars: Phillips2020 https://doi.org/10.1063/5.0014475 colvars: +colvars: updating target temperature (T = 0 K). colvars: ---------------------------------------------------------------------- -colvars: Loading state from file "test.colvars.state". +colvars: Loading state from text file "test.colvars.state". colvars: Restarting collective variable "one" from value: 3.21688 -colvars: Restarting histogram bias "histogram1" from step number 20. +colvars: Restarted histogram bias "histogram1" with step number 20. colvars: ---------------------------------------------------------------------- colvars: Updating NAMD interface: colvars: updating atomic data (0 atoms). colvars: updating group data (2 scalable groups, 8 atoms in total). colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). +colvars: Current simulation parameters: initial step = 20, integration timestep = 1 +colvars: Updating atomic parameters (masses, charges, etc). colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. colvars: The restart output state file will be "test.restart.tmp.colvars.state". -colvars: The final output state file will be "test.restart.colvars.state". -colvars: Histogram histogram1 will be written to file "test.restart.histogram1.dat" colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj". colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj". colvars: Saving collective variables state to "test.restart.tmp.colvars.state". diff --git a/namd/tests/library/000_distance_histogram-customgrid/test.in b/namd/tests/library/000_distance_histogram-customgrid/test.in index 1169d86ee..02b99ab06 100644 --- a/namd/tests/library/000_distance_histogram-customgrid/test.in +++ b/namd/tests/library/000_distance_histogram-customgrid/test.in @@ -22,7 +22,7 @@ colvar { histogram { colvars one - gridParameters { + grid { widths 0.2 lowerBoundaries 0.6 upperBoundaries 5.4 diff --git a/src/colvarbias_abf.cpp b/src/colvarbias_abf.cpp index 5ab693771..cad3dea75 100644 --- a/src/colvarbias_abf.cpp +++ b/src/colvarbias_abf.cpp @@ -83,8 +83,6 @@ int colvarbias_abf::init(std::string const &conf) } } - key_lookup(conf, "gridParameters", &grid_params); - // shared ABF get_keyval(conf, "shared", shared_on, false); if (shared_on) { @@ -108,11 +106,6 @@ int colvarbias_abf::init(std::string const &conf) if ( shared_freq && output_freq % shared_freq ) { return cvm::error("Error: outputFreq must be a multiple of sharedFreq.\n"); } - - // Allocate these at init time if possible - local_samples.reset(new colvar_grid_count(colvars, grid_params)); - local_gradients.reset(new colvar_grid_gradient(colvars, local_samples, grid_params)); - local_pmf.reset(new integrate_potential(colvars, local_gradients, grid_params)); } // ************* checking the associated colvars ******************* @@ -189,12 +182,23 @@ int colvarbias_abf::init(std::string const &conf) cvm::log("Allocating count and free energy gradient grids.\n"); } - samples.reset(new colvar_grid_count(colvars, grid_params)); - gradients.reset(new colvar_grid_gradient(colvars, samples, grid_params)); + { + /// Optional custom configuration string for grid parameters + std::string grid_conf; + key_lookup(conf, "grid", &grid_conf); + + samples.reset(new colvar_grid_count(colvars, grid_conf)); + } + gradients.reset(new colvar_grid_gradient(colvars, samples)); // Also use samples as template for sizes gradients->full_samples = full_samples; gradients->min_samples = min_samples; + if (shared_on) { + local_samples.reset(new colvar_grid_count(colvars, samples)); + local_gradients.reset(new colvar_grid_gradient(colvars, local_samples)); + } + // Data for eABF z-based estimator if (is_enabled(f_cvb_extended)) { get_keyval(conf, "CZARestimator", b_CZAR_estimator, true); @@ -206,11 +210,11 @@ int colvarbias_abf::init(std::string const &conf) colvarparse::parse_silent); z_bin.assign(num_variables(), 0); - z_samples.reset(new colvar_grid_count(colvars, grid_params)); + z_samples.reset(new colvar_grid_count(colvars, samples)); z_samples->request_actual_value(); - z_gradients.reset(new colvar_grid_gradient(colvars, z_samples, grid_params)); + z_gradients.reset(new colvar_grid_gradient(colvars, z_samples)); z_gradients->request_actual_value(); - czar_gradients.reset(new colvar_grid_gradient(colvars, grid_params)); + czar_gradients.reset(new colvar_grid_gradient(colvars, nullptr, samples)); } get_keyval(conf, "integrate", b_integrate, num_variables() <= 3); // Integrate for output if d<=3 @@ -220,9 +224,12 @@ int colvarbias_abf::init(std::string const &conf) cvm::error("Error: cannot integrate free energy in dimension > 3.\n"); return COLVARS_ERROR; } - pmf.reset(new integrate_potential(colvars, gradients, grid_params)); + pmf.reset(new integrate_potential(colvars, gradients)); if (b_CZAR_estimator) { - czar_pmf.reset(new integrate_potential(colvars, czar_gradients, grid_params)); + czar_pmf.reset(new integrate_potential(colvars, czar_gradients)); + } + if (shared_on) { + local_pmf.reset(new integrate_potential(colvars, local_gradients)); } // Parameters for integrating initial (and final) gradient data get_keyval(conf, "integrateMaxIterations", integrate_iterations, 10000, colvarparse::parse_silent); @@ -236,10 +243,10 @@ int colvarbias_abf::init(std::string const &conf) if (b_CZAR_estimator && shared_on && cvm::main()->proxy->replica_index() == 0) { // The pointers below are used for outputting CZAR data // Allocate grids for collected global data, on replica 0 only - global_z_samples.reset(new colvar_grid_count(colvars, grid_params)); - global_z_gradients.reset(new colvar_grid_gradient(colvars, global_z_samples, grid_params)); - global_czar_gradients.reset(new colvar_grid_gradient(colvars, grid_params)); - global_czar_pmf.reset(new integrate_potential(colvars, global_czar_gradients, grid_params)); + global_z_samples.reset(new colvar_grid_count(colvars, samples)); + global_z_gradients.reset(new colvar_grid_gradient(colvars, global_z_samples)); + global_czar_gradients.reset(new colvar_grid_gradient(colvars, nullptr, samples)); + global_czar_pmf.reset(new integrate_potential(colvars, global_czar_gradients)); } else { // otherwise they are just aliases for the local CZAR grids global_z_samples = z_samples; @@ -252,11 +259,11 @@ int colvarbias_abf::init(std::string const &conf) // This used to be only if "shared" was defined, // but now we allow calling share externally (e.g. from Tcl). if (b_CZAR_estimator) { - z_samples_in.reset(new colvar_grid_count(colvars, grid_params)); - z_gradients_in.reset(new colvar_grid_gradient(colvars, z_samples_in, grid_params)); + z_samples_in.reset(new colvar_grid_count(colvars, samples)); + z_gradients_in.reset(new colvar_grid_gradient(colvars, z_samples_in)); } - last_samples.reset(new colvar_grid_count(colvars, grid_params)); - last_gradients.reset(new colvar_grid_gradient(colvars, last_samples, grid_params)); + last_samples.reset(new colvar_grid_count(colvars, samples)); + last_gradients.reset(new colvar_grid_gradient(colvars, last_samples)); // Any data collected after now is new for shared ABF purposes shared_last_step = cvm::step_absolute(); @@ -550,9 +557,9 @@ int colvarbias_abf::replica_share() { if (!local_samples) { // We arrive here if sharing has just been enabled by a script // in which case local arrays have not been initialized yet - local_samples.reset(new colvar_grid_count(colvars, grid_params)); - local_gradients.reset(new colvar_grid_gradient(colvars, local_samples, grid_params)); - local_pmf.reset(new integrate_potential(colvars, local_gradients, grid_params)); + local_samples.reset(new colvar_grid_count(colvars, samples)); + local_gradients.reset(new colvar_grid_gradient(colvars, local_samples)); + local_pmf.reset(new integrate_potential(colvars, local_gradients)); } // Calculate the delta gradient and count for the local replica last_gradients->delta_grid(*gradients); @@ -670,10 +677,10 @@ int colvarbias_abf::replica_share_CZAR() { // We arrive here if sharing has just been enabled by a script // Allocate grids for collective data, on replica 0 only // overriding CZAR grids that are equal to local ones by default - global_z_samples.reset(new colvar_grid_count(colvars, grid_params)); - global_z_gradients.reset(new colvar_grid_gradient(colvars, global_z_samples, grid_params)); - global_czar_gradients.reset(new colvar_grid_gradient(colvars, grid_params)); - global_czar_pmf.reset(new integrate_potential(colvars, global_czar_gradients, grid_params)); + global_z_samples.reset(new colvar_grid_count(colvars, samples)); + global_z_gradients.reset(new colvar_grid_gradient(colvars, global_z_samples)); + global_czar_gradients.reset(new colvar_grid_gradient(colvars, nullptr, samples)); + global_czar_pmf.reset(new integrate_potential(colvars, global_czar_gradients)); } // Start with data from replica 0 @@ -881,7 +888,7 @@ int colvarbias_abf::read_gradients_samples() // Therefore the czar_gradients grid is not linked to a sampling grid // Here we define a temporary czar_gradients grid linked to z_samples, // to correctly average input gradients if overlapping - czar_gradients_in.reset(new colvar_grid_gradient(colvars, z_samples, grid_params)); + czar_gradients_in.reset(new colvar_grid_gradient(colvars, z_samples)); } for ( size_t i = 0; i < input_prefix.size(); i++ ) { diff --git a/src/colvarbias_abf.h b/src/colvarbias_abf.h index 479926137..4426a8a3f 100644 --- a/src/colvarbias_abf.h +++ b/src/colvarbias_abf.h @@ -42,8 +42,6 @@ class colvarbias_abf : public colvarbias { /// Base filename(s) for reading previous gradient data (replaces data from restart file) std::vector input_prefix; - /// Optional custom configuration string for grid parameters - std::string grid_params; /// Adapt the bias at each time step (as opposed to keeping it constant)? bool update_bias; diff --git a/src/colvarbias_histogram.cpp b/src/colvarbias_histogram.cpp index 3ca60a01c..419d1634e 100644 --- a/src/colvarbias_histogram.cpp +++ b/src/colvarbias_histogram.cpp @@ -100,9 +100,9 @@ int colvarbias_histogram::init(std::string const &conf) { std::string grid_conf; if (key_lookup(conf, "histogramGrid", &grid_conf) || - key_lookup(conf, "gridParameters", &grid_conf)) { + key_lookup(conf, "grid", &grid_conf)) { grid->parse_params(grid_conf); - grid->check_keywords(grid_conf, "gridParameters"); + grid->check_keywords(grid_conf, "grid"); } } diff --git a/src/colvargrid.cpp b/src/colvargrid.cpp index c4532406e..d5cb95ffd 100644 --- a/src/colvargrid.cpp +++ b/src/colvargrid.cpp @@ -26,7 +26,12 @@ colvar_grid_count::colvar_grid_count() colvar_grid_count::colvar_grid_count(std::vector &colvars, std::string config) - : colvar_grid(colvars, 0, 1, false, config) + : colvar_grid(colvars, 0, 1, false, nullptr, config) +{} + +colvar_grid_count::colvar_grid_count(std::vector &colvars, + std::shared_ptr params) + : colvar_grid(colvars, 0, 1, false, params) {} std::string colvar_grid_count::get_state_params() const @@ -127,9 +132,9 @@ colvar_grid_scalar::colvar_grid_scalar(colvar_grid_scalar const &g) } colvar_grid_scalar::colvar_grid_scalar(std::vector &colvars, - std::string config, + std::shared_ptr params, bool add_extra_bin) - : colvar_grid(colvars, 0.0, 1, add_extra_bin, config), samples(NULL) + : colvar_grid(colvars, 0.0, 1, add_extra_bin, params), samples(NULL) { } @@ -321,24 +326,32 @@ cvm::real colvar_grid_scalar::grid_rmsd(colvar_grid_scalar const &other_grid) co colvar_grid_gradient::colvar_grid_gradient() - : colvar_grid(), samples(NULL), full_samples(0), min_samples(0) + : colvar_grid(), samples(NULL) {} -colvar_grid_gradient::colvar_grid_gradient(std::vector &colvars, std::string config) - : colvar_grid(colvars, 0.0, colvars.size(), false, config), samples(NULL), full_samples(0), min_samples(0) -{} +// colvar_grid_gradient::colvar_grid_gradient(std::vector &colvars, std::string config) +// : colvar_grid(colvars, 0.0, colvars.size(), false, nullptr, config), samples(NULL) +// {} +// colvar_grid_gradient::colvar_grid_gradient(std::vector &colvars, +// std::shared_ptr samples_in) +// : colvar_grid(colvars, 0.0, colvars.size(), false, samples_in), samples(samples_in) +// { +// if (samples_in) +// samples_in->has_parent_data = true; +// } colvar_grid_gradient::colvar_grid_gradient(std::vector &colvars, std::shared_ptr samples_in, + std::shared_ptr params, std::string config) - : colvar_grid(colvars, 0.0, colvars.size(), false, config), samples(samples_in), full_samples(0), min_samples(0) + : colvar_grid(colvars, 0.0, colvars.size(), false, params, config), samples(samples_in) { - samples_in->has_parent_data = true; + if (samples_in) + samples_in->has_parent_data = true; } - colvar_grid_gradient::colvar_grid_gradient(std::string &filename) : colvar_grid(), samples(NULL) @@ -575,9 +588,8 @@ cvm::real colvar_grid_gradient::grid_rmsd(colvar_grid_gradient const &other_grid integrate_potential::integrate_potential(std::vector &colvars, - std::shared_ptr gradients, - std::string config) - : colvar_grid_scalar(colvars, config, true), + std::shared_ptr gradients) + : colvar_grid_scalar(colvars, gradients, true), b_smoothed(false), gradients(gradients) { diff --git a/src/colvargrid.h b/src/colvargrid.h index 275da3fcb..01be047a7 100644 --- a/src/colvargrid.h +++ b/src/colvargrid.h @@ -19,15 +19,11 @@ #include "colvarparse.h" -/// \brief Grid of values of a function of several collective -/// variables \param T The data type -/// -/// Only scalar colvars supported so far: vector colvars are treated as arrays -template class colvar_grid : public colvarparse { - - //protected: -public: // TODO create accessors for these after all instantiations work +/// \brief Unified base class for grid of values of a function of several collective +/// variables +class colvar_grid_params { +public: /// Number of dimensions size_t nd = 0; @@ -37,6 +33,27 @@ template class colvar_grid : public colvarparse { /// Cumulative number of points along each dimension std::vector nxc; + /// Lower boundaries of the colvars in this grid + std::vector lower_boundaries; + + /// Upper boundaries of the colvars in this grid + std::vector upper_boundaries; + + /// Widths of the colvars in this grid + std::vector widths; +}; + + +/// \brief Grid of values of a function of several collective +/// variables \param T The data type +/// +/// Only scalar colvars supported so far: vector colvars are treated as arrays +/// All common, type-independent members are collected in the base class colvar_grid_base +template class colvar_grid : public colvar_grid_params, public colvarparse { + + //protected: +public: // TODO create accessors for these after all instantiations work + /// \brief Multiplicity of each datum (allow the binning of /// non-scalar types such as atomic gradients) size_t mult; @@ -73,13 +90,6 @@ template class colvar_grid : public colvarparse { } public: - - /// Lower boundaries of the colvars in this grid - std::vector lower_boundaries; - - /// Upper boundaries of the colvars in this grid - std::vector upper_boundaries; - /// Whether some colvars are periodic std::vector periodic; @@ -89,9 +99,6 @@ template class colvar_grid : public colvarparse { /// Whether some colvars have hard upper boundaries std::vector hard_upper_boundaries; - /// Widths of the colvars in this grid - std::vector widths; - /// True if this is a count grid related to another grid of data bool has_parent_data; @@ -218,19 +225,15 @@ template class colvar_grid : public colvarparse { /// \brief "Almost copy-constructor": only copies configuration /// parameters from another grid, but doesn't reallocate stuff; /// setup() must be called after that; - colvar_grid(colvar_grid const &g) : colvarparse(), - nd(g.nd), - nx(g.nx), + colvar_grid(colvar_grid const &g) : colvar_grid_params(colvar_grid_params(g)), + colvarparse(), mult(g.mult), data(), cv(g.cv), use_actual_value(g.use_actual_value), - lower_boundaries(g.lower_boundaries), - upper_boundaries(g.upper_boundaries), periodic(g.periodic), hard_lower_boundaries(g.hard_lower_boundaries), hard_upper_boundaries(g.hard_upper_boundaries), - widths(g.widths), has_parent_data(false), has_data(false) {} @@ -254,16 +257,18 @@ template class colvar_grid : public colvarparse { T const &t = T(), size_t mult_i = 1, bool add_extra_bin = false, + std::shared_ptr params = nullptr, std::string config = std::string()) : has_parent_data(false), has_data(false) { (void) t; - this->init_from_colvars(colvars, mult_i, add_extra_bin, config); + this->init_from_colvars(colvars, mult_i, add_extra_bin, params, config); } int init_from_colvars(std::vector const &colvars, size_t mult_i = 1, bool add_extra_bin = false, + std::shared_ptr params = nullptr, std::string config = std::string()) { if (cvm::debug()) { @@ -281,8 +286,7 @@ template class colvar_grid : public colvarparse { " collective variables, multiplicity = "+cvm::to_str(mult_i)+".\n"); } - for (i = 0; i < cv.size(); i++) { - + for (i = 0; i < nd; i++) { if (cv[i]->value().type() != colvarvalue::type_scalar) { cvm::error("Colvar grids can only be automatically " "constructed for scalar variables. " @@ -319,11 +323,29 @@ template class colvar_grid : public colvarparse { // Replace widths and boundaries with optional custom configuration if (!config.empty()) { this->parse_params(config); - this->check_keywords(config, "gridParameters"); + this->check_keywords(config, "grid"); + + if (params) { + cvm::error("Error: init_from_colvars was passed both a grid config and a template grid.", COLVARS_BUG_ERROR); + return COLVARS_BUG_ERROR; + } + } else if (params) { + // Match grid sizes with template + + if (params->nd != nd) { + cvm::error("Trying to initialize grid from template with wrong dimension (" + + cvm::to_str(params->nd) + " instead of " + + cvm::to_str(this->nd) + ")."); + return COLVARS_ERROR; + } + + widths =params->widths; + lower_boundaries =params->lower_boundaries; + upper_boundaries =params->upper_boundaries; } // Only now can we determine periodicity - for (i = 0; i < cv.size(); i++) { + for (i = 0; i < nd; i++) { periodic.push_back(cv[i]->periodic_boundaries(lower_boundaries[i].real_value, upper_boundaries[i].real_value)); @@ -341,6 +363,7 @@ template class colvar_grid : public colvarparse { } } + // Reset grid sizes based on widths and boundaries this->init_from_boundaries(); return this->setup(); } @@ -983,7 +1006,10 @@ class colvar_grid_count : public colvar_grid /// Constructor from a vector of colvars or a config string colvar_grid_count(std::vector &colvars, - std::string config = std::string()); + std::shared_ptr params = nullptr); + + colvar_grid_count(std::vector &colvars, + std::string config); /// Increment the counter at given position inline void incr_count(std::vector const &ix) @@ -1267,7 +1293,7 @@ class colvar_grid_scalar : public colvar_grid /// Constructor from a vector of colvars colvar_grid_scalar(std::vector &colvars, - std::string config = std::string(), + std::shared_ptr params = nullptr, bool add_extra_bin = false); /// Accumulate the value @@ -1577,16 +1603,17 @@ class colvar_grid_gradient : public colvar_grid // /// Constructor from specific sizes arrays // colvar_grid_gradient(std::vector const &nx_i); - /// Constructor from a vector of colvars - colvar_grid_gradient(std::vector &colvars, - std::string config = std::string()); + // /// Constructor from a vector of colvars + // colvar_grid_gradient(std::vector &colvars, + // std::string config = std::string()); /// Constructor from a multicol file colvar_grid_gradient(std::string &filename); /// Constructor from a vector of colvars and a pointer to the count grid colvar_grid_gradient(std::vector &colvars, - std::shared_ptr samples_in, + std::shared_ptr samples_in = nullptr, + std::shared_ptr params = nullptr, std::string config = std::string()); /// Parameters for smoothing data with low sampling @@ -1841,8 +1868,7 @@ class integrate_potential : public colvar_grid_scalar /// Constructor from a vector of colvars + gradient grid integrate_potential(std::vector &colvars, - std::shared_ptr gradients, - std::string config = std::string()); + std::shared_ptr gradients); /// Constructor from a gradient grid (for processing grid files without a Colvars config) integrate_potential(std::shared_ptr gradients); diff --git a/tests/Makefile b/tests/Makefile index 0439197af..9743b19bf 100644 --- a/tests/Makefile +++ b/tests/Makefile @@ -1,13 +1,15 @@ .PHONY: all functional gromacs lammps namd -all: functional gromacs lammps namd +all: functional lammps namd # gromacs + functional: ./build_tests.sh input_files/ -gromacs: - ./build_tests.sh ../gromacs/tests/library/ +# GROMACS tests need manual adjustments +# gromacs: +# ./build_tests.sh ../gromacs/tests/library/ lammps: ./build_tests.sh ../lammps/tests/library/ diff --git a/tests/build_tests.sh b/tests/build_tests.sh index 833afb149..02ad0fac4 100755 --- a/tests/build_tests.sh +++ b/tests/build_tests.sh @@ -154,6 +154,7 @@ for colvar in "distance-grid" ; do "histogram" \ "histogram-customgrid" \ "abf" \ + "abf-customgrid" \ "metadynamics" \ "metadynamics-sigmas" \ "metadynamics-wt" \ diff --git a/tests/distance-dihedral_histogram2d-periodic-customgrid.in b/tests/distance-dihedral_histogram2d-periodic-customgrid.in index 3950e3e25..9e05ed20e 100644 --- a/tests/distance-dihedral_histogram2d-periodic-customgrid.in +++ b/tests/distance-dihedral_histogram2d-periodic-customgrid.in @@ -34,7 +34,7 @@ colvar { histogram { colvars r phi - gridParameters { + grid { widths 0.2 6.0 lowerBoundaries 0.0 0.0 upperBoundaries 10.0 360.0 diff --git a/tests/histogram-customgrid-periodic.in b/tests/histogram-customgrid-periodic.in index 0ebc5025e..68b0f526e 100644 --- a/tests/histogram-customgrid-periodic.in +++ b/tests/histogram-customgrid-periodic.in @@ -1,6 +1,6 @@ histogram { colvars one - gridParameters { + grid { widths 5 lowerBoundaries -60 upperBoundaries 300 diff --git a/tests/histogram-customgrid.in b/tests/histogram-customgrid.in index 7a26ae6f1..69c096a15 100644 --- a/tests/histogram-customgrid.in +++ b/tests/histogram-customgrid.in @@ -1,6 +1,6 @@ histogram { colvars one - gridParameters { + grid { widths 0.2 lowerBoundaries 0.6 upperBoundaries 5.4 diff --git a/tests/input_files/dihedral_histogram-customgrid-periodic/test.in b/tests/input_files/dihedral_histogram-customgrid-periodic/test.in index 5883076c2..40a5cd78c 100644 --- a/tests/input_files/dihedral_histogram-customgrid-periodic/test.in +++ b/tests/input_files/dihedral_histogram-customgrid-periodic/test.in @@ -28,7 +28,7 @@ colvar { histogram { colvars one - gridParameters { + grid { widths 5 lowerBoundaries -60 upperBoundaries 300 diff --git a/tests/input_files/distance-grid_histogram-customgrid/test.in b/tests/input_files/distance-grid_histogram-customgrid/test.in index 61603e2ad..8376dfbdb 100644 --- a/tests/input_files/distance-grid_histogram-customgrid/test.in +++ b/tests/input_files/distance-grid_histogram-customgrid/test.in @@ -26,7 +26,7 @@ colvar { histogram { colvars one - gridParameters { + grid { widths 0.2 lowerBoundaries 0.6 upperBoundaries 5.4 diff --git a/tests/input_files/distance_histogram-customgrid/test.in b/tests/input_files/distance_histogram-customgrid/test.in index 1169d86ee..02b99ab06 100644 --- a/tests/input_files/distance_histogram-customgrid/test.in +++ b/tests/input_files/distance_histogram-customgrid/test.in @@ -22,7 +22,7 @@ colvar { histogram { colvars one - gridParameters { + grid { widths 0.2 lowerBoundaries 0.6 upperBoundaries 5.4 From 6e90969b2a7db8ab169c4715d7366ad1f8343f7e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=A9r=C3=B4me=20H=C3=A9nin?= Date: Tue, 17 Sep 2024 15:58:53 +0200 Subject: [PATCH 04/13] Add test for ABF with custom grid --- .../AutoDiff/test.colvars.out | 177 +++++++++++++++++ .../AutoDiff/test.colvars.state.stripped | 27 +++ .../AutoDiff/test.colvars.traj | 22 +++ .../AutoDiff/test.count | 23 +++ .../AutoDiff/test.grad | 23 +++ .../AutoDiff/test.pmf | 24 +++ .../AutoDiff/test.restart.colvars.out | 182 ++++++++++++++++++ .../test.restart.colvars.state.stripped | 27 +++ .../AutoDiff/test.restart.colvars.traj | 22 +++ .../AutoDiff/test.restart.count | 23 +++ .../AutoDiff/test.restart.grad | 23 +++ .../AutoDiff/test.restart.pmf | 24 +++ .../namd-version.txt | 3 + .../000_distance-grid_abf-customgrid/test.in | 36 ++++ .../distance-grid_abf-customgrid/test.in | 36 ++++ 15 files changed, 672 insertions(+) create mode 100644 namd/tests/library/000_distance-grid_abf-customgrid/AutoDiff/test.colvars.out create mode 100644 namd/tests/library/000_distance-grid_abf-customgrid/AutoDiff/test.colvars.state.stripped create mode 100644 namd/tests/library/000_distance-grid_abf-customgrid/AutoDiff/test.colvars.traj create mode 100644 namd/tests/library/000_distance-grid_abf-customgrid/AutoDiff/test.count create mode 100644 namd/tests/library/000_distance-grid_abf-customgrid/AutoDiff/test.grad create mode 100644 namd/tests/library/000_distance-grid_abf-customgrid/AutoDiff/test.pmf create mode 100644 namd/tests/library/000_distance-grid_abf-customgrid/AutoDiff/test.restart.colvars.out create mode 100644 namd/tests/library/000_distance-grid_abf-customgrid/AutoDiff/test.restart.colvars.state.stripped create mode 100644 namd/tests/library/000_distance-grid_abf-customgrid/AutoDiff/test.restart.colvars.traj create mode 100644 namd/tests/library/000_distance-grid_abf-customgrid/AutoDiff/test.restart.count create mode 100644 namd/tests/library/000_distance-grid_abf-customgrid/AutoDiff/test.restart.grad create mode 100644 namd/tests/library/000_distance-grid_abf-customgrid/AutoDiff/test.restart.pmf create mode 100644 namd/tests/library/000_distance-grid_abf-customgrid/namd-version.txt create mode 100644 namd/tests/library/000_distance-grid_abf-customgrid/test.in create mode 100644 tests/input_files/distance-grid_abf-customgrid/test.in diff --git a/namd/tests/library/000_distance-grid_abf-customgrid/AutoDiff/test.colvars.out b/namd/tests/library/000_distance-grid_abf-customgrid/AutoDiff/test.colvars.out new file mode 100644 index 000000000..d8e4e0e7e --- /dev/null +++ b/namd/tests/library/000_distance-grid_abf-customgrid/AutoDiff/test.colvars.out @@ -0,0 +1,177 @@ +colvars: ---------------------------------------------------------------------- +colvars: Please cite Fiorin et al, Mol Phys 2013: +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. +colvars: This version was built with the C++11 standard or higher. +colvars: Summary of compile-time features available in this build: +colvars: - SMP parallelism: enabled (num. threads = 4) +colvars: - Lepton custom functions: available +colvars: - Tcl interpreter: available +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: The final output state file will be "test.colvars.state". +colvars: ---------------------------------------------------------------------- +colvars: Reading new configuration from file "test.in": +colvars: # units = "" [default] +colvars: # indexFile = "index.ndx" +colvars: The following index groups are currently defined: +colvars: Protein (104 atoms) +colvars: Protein_noH (51 atoms) +colvars: Protein_Backbone (40 atoms) +colvars: Protein_C-alpha (10 atoms) +colvars: RMSD_atoms (10 atoms) +colvars: Protein_C-alpha_1_2 (2 atoms) +colvars: Protein_C-alpha_9_10 (2 atoms) +colvars: Protein_C-alpha_1 (1 atoms) +colvars: group1 (4 atoms) +colvars: Protein_C-alpha_2 (1 atoms) +colvars: group2 (4 atoms) +colvars: Protein_C-alpha_3 (1 atoms) +colvars: group3 (4 atoms) +colvars: Protein_C-alpha_4 (1 atoms) +colvars: group4 (4 atoms) +colvars: Protein_C-alpha_5 (1 atoms) +colvars: group5 (4 atoms) +colvars: Protein_C-alpha_6 (1 atoms) +colvars: group6 (4 atoms) +colvars: Protein_C-alpha_7 (1 atoms) +colvars: group7 (4 atoms) +colvars: Protein_C-alpha_8 (1 atoms) +colvars: group8 (4 atoms) +colvars: Protein_C-alpha_9 (1 atoms) +colvars: group9 (4 atoms) +colvars: Protein_C-alpha_10 (1 atoms) +colvars: group10 (4 atoms) +colvars: heavy_atoms (51 atoms) +colvars: # smp = on [default] +colvars: # colvarsTrajFrequency = 1 +colvars: # colvarsRestartFrequency = 10 +colvars: # scriptedColvarForces = off [default] +colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] +colvars: ---------------------------------------------------------------------- +colvars: Initializing a new collective variable. +colvars: # name = "one" +colvars: Initializing a new "distance" component. +colvars: # name = "" [default] +colvars: # componentCoeff = 1 [default] +colvars: # componentExp = 1 [default] +colvars: # period = 0 [default] +colvars: # wrapAround = 0 [default] +colvars: # forceNoPBC = off [default] +colvars: # scalable = on [default] +colvars: Initializing atom group "group1". +colvars: # name = "" [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] +colvars: # atomsOfGroup = "" [default] +colvars: # indexGroup = "group1" +colvars: # psfSegID = [default] +colvars: # atomsFile = "" [default] +colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableFitGradients = on [default] +colvars: Enabling scalable calculation for group "group1". +colvars: # printAtomIDs = off [default] +colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. +colvars: Initializing atom group "group2". +colvars: # name = "" [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] +colvars: # atomsOfGroup = "" [default] +colvars: # indexGroup = "group2" +colvars: # psfSegID = [default] +colvars: # atomsFile = "" [default] +colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableFitGradients = on [default] +colvars: Enabling scalable calculation for group "group2". +colvars: # printAtomIDs = off [default] +colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. +colvars: # oneSiteSystemForce = off [default] +colvars: # oneSiteTotalForce = off [default] +colvars: All components initialized. +colvars: # timeStepFactor = 1 [default] +colvars: # width = 0.5 +colvars: # lowerBoundary = 0 [default] +colvars: # upperBoundary = 10 +colvars: # hardLowerBoundary = on [default] +colvars: # hardUpperBoundary = off [default] +colvars: # expandBoundaries = off [default] +colvars: # extendedLagrangian = off [default] +colvars: # outputValue = on [default] +colvars: # outputVelocity = off [default] +colvars: # outputTotalForce = off [default] +colvars: # outputAppliedForce = on +colvars: # subtractAppliedForce = off [default] +colvars: # runAve = off [default] +colvars: # corrFunc = off [default] +colvars: ---------------------------------------------------------------------- +colvars: Collective variables initialized, 1 in total. +colvars: ---------------------------------------------------------------------- +colvars: Initializing a new "abf" instance. +colvars: # name = "abf1" [default] +colvars: # colvars = { one } +colvars: # stepZeroData = off [default] +colvars: # outputEnergy = off [default] +colvars: # outputFreq = 10 [default] +colvars: # timeStepFactor = 1 [default] +colvars: WARNING: ABF should not be run without a thermostat or at 0 Kelvin! +colvars: # applyBias = on [default] +colvars: # hideJacobian = off [default] +colvars: Jacobian (geometric) forces will be included in reported free energy gradients. +colvars: # fullSamples = 10 +colvars: # minSamples = 5 [default] +colvars: # inputPrefix = [default] +colvars: # historyFreq = 0 [default] +colvars: # shared = off [default] +colvars: # updateBias = on [default] +colvars: # maxForce = [default] +colvars: # lowerBoundaries = { 1 } +colvars: # upperBoundaries = { 5 } +colvars: # widths = { 0.2 } +colvars: # integrate = on [default] +colvars: Finished ABF setup. +colvars: ---------------------------------------------------------------------- +colvars: Collective variables biases initialized, 1 in total. +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module (re)initialized. +colvars: ---------------------------------------------------------------------- +colvars: Updating NAMD interface: +colvars: updating atomic data (0 atoms). +colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - ABF colvar bias implementation: +colvars: - Internal-forces free energy estimator: +colvars: Henin2010 https://doi.org/10.1021/ct9004432 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). +colvars: Updating NAMD interface: +colvars: updating atomic data (0 atoms). +colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). +colvars: Current simulation parameters: initial step = 0, integration timestep = 1 +colvars: Updating atomic parameters (masses, charges, etc). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.tmp.colvars.state". +colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". +colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". +colvars: Saving collective variables state to "test.tmp.colvars.state". +colvars: Synchronizing (emptying the buffer of) trajectory file "test.colvars.traj". +colvars: Saving collective variables state to "test.tmp.colvars.state". +colvars: Saving collective variables state to "test.colvars.state". diff --git a/namd/tests/library/000_distance-grid_abf-customgrid/AutoDiff/test.colvars.state.stripped b/namd/tests/library/000_distance-grid_abf-customgrid/AutoDiff/test.colvars.state.stripped new file mode 100644 index 000000000..6218c5e5f --- /dev/null +++ b/namd/tests/library/000_distance-grid_abf-customgrid/AutoDiff/test.colvars.state.stripped @@ -0,0 +1,27 @@ +configuration { + step 20 + dt 1.000000e+00 +} + +colvar { + name one + x 3.1950410985963 +} + +abf { + configuration { + step 20 + name abf1 + } + +samples + 0 0 0 0 0 0 0 0 + 0 0 1 19 0 0 0 0 + 0 0 0 0 + +gradient + 0 0 0 0 0 0 0 0 + 0 0 9.0035723267509 -2.579519379033 0 0 0 0 + 0 0 0 0 +} + diff --git a/namd/tests/library/000_distance-grid_abf-customgrid/AutoDiff/test.colvars.traj b/namd/tests/library/000_distance-grid_abf-customgrid/AutoDiff/test.colvars.traj new file mode 100644 index 000000000..e9640ca18 --- /dev/null +++ b/namd/tests/library/000_distance-grid_abf-customgrid/AutoDiff/test.colvars.traj @@ -0,0 +1,22 @@ +# step one fa_one + 0 3.20554673468334e+00 0.00000000000000e+00 + 1 3.20437148316484e+00 0.00000000000000e+00 + 2 3.20384028588952e+00 0.00000000000000e+00 + 3 3.20396721186862e+00 0.00000000000000e+00 + 4 3.20472817286016e+00 0.00000000000000e+00 + 5 3.20606308065050e+00 0.00000000000000e+00 + 6 3.20787989000758e+00 -7.68950954395538e+00 + 7 3.20994206782701e+00 -1.45081021954275e+01 + 8 3.21200777962688e+00 -2.01168223029416e+01 + 9 3.21384392079195e+00 -2.42708474851834e+01 + 10 3.21523959933526e+00 -2.68357715832756e+01 + 11 3.21601851659179e+00 -2.31658530843961e+01 + 12 3.21612044367303e+00 -1.94776790572419e+01 + 13 3.21551354957116e+00 -1.59170233488108e+01 + 14 3.21419762164954e+00 -1.26130067638540e+01 + 15 3.21220454729786e+00 -9.67058885249153e+00 + 16 3.20959604449941e+00 -7.16540382727146e+00 + 17 3.20645917266472e+00 -5.14219076042634e+00 + 18 3.20290044125515e+00 -3.61665560433939e+00 + 19 3.19903928567179e+00 0.00000000000000e+00 + 20 3.19504109859627e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_abf-customgrid/AutoDiff/test.count b/namd/tests/library/000_distance-grid_abf-customgrid/AutoDiff/test.count new file mode 100644 index 000000000..3ce84d350 --- /dev/null +++ b/namd/tests/library/000_distance-grid_abf-customgrid/AutoDiff/test.count @@ -0,0 +1,23 @@ +# 1 +# 1.00000000000000e+00 2.00000000000000e-01 20 0 + + 1.10000000000000e+00 0 + 1.30000000000000e+00 0 + 1.50000000000000e+00 0 + 1.70000000000000e+00 0 + 1.90000000000000e+00 0 + 2.10000000000000e+00 0 + 2.30000000000000e+00 0 + 2.50000000000000e+00 0 + 2.70000000000000e+00 0 + 2.90000000000000e+00 0 + 3.10000000000000e+00 1 + 3.30000000000000e+00 19 + 3.50000000000000e+00 0 + 3.70000000000000e+00 0 + 3.90000000000000e+00 0 + 4.10000000000000e+00 0 + 4.30000000000000e+00 0 + 4.50000000000000e+00 0 + 4.70000000000000e+00 0 + 4.90000000000000e+00 0 diff --git a/namd/tests/library/000_distance-grid_abf-customgrid/AutoDiff/test.grad b/namd/tests/library/000_distance-grid_abf-customgrid/AutoDiff/test.grad new file mode 100644 index 000000000..fa882f14e --- /dev/null +++ b/namd/tests/library/000_distance-grid_abf-customgrid/AutoDiff/test.grad @@ -0,0 +1,23 @@ +# 1 +# 0.00000000000000e+00 5.00000000000000e-01 20 0 + + 2.50000000000000e-01 0.00000000000000e+00 + 7.50000000000000e-01 0.00000000000000e+00 + 1.25000000000000e+00 0.00000000000000e+00 + 1.75000000000000e+00 0.00000000000000e+00 + 2.25000000000000e+00 0.00000000000000e+00 + 2.75000000000000e+00 0.00000000000000e+00 + 3.25000000000000e+00 0.00000000000000e+00 + 3.75000000000000e+00 0.00000000000000e+00 + 4.25000000000000e+00 0.00000000000000e+00 + 4.75000000000000e+00 0.00000000000000e+00 + 5.25000000000000e+00 9.00357232675086e+00 + 5.75000000000000e+00 -2.57951937903295e+00 + 6.25000000000000e+00 0.00000000000000e+00 + 6.75000000000000e+00 0.00000000000000e+00 + 7.25000000000000e+00 0.00000000000000e+00 + 7.75000000000000e+00 0.00000000000000e+00 + 8.25000000000000e+00 0.00000000000000e+00 + 8.75000000000000e+00 0.00000000000000e+00 + 9.25000000000000e+00 0.00000000000000e+00 + 9.75000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_abf-customgrid/AutoDiff/test.pmf b/namd/tests/library/000_distance-grid_abf-customgrid/AutoDiff/test.pmf new file mode 100644 index 000000000..0304e06b5 --- /dev/null +++ b/namd/tests/library/000_distance-grid_abf-customgrid/AutoDiff/test.pmf @@ -0,0 +1,24 @@ +# 1 +# -2.50000000000000e-01 5.00000000000000e-01 21 0 + + 0.00000000000000e+00 0.00000000000000e+00 + 5.00000000000000e-01 0.00000000000000e+00 + 1.00000000000000e+00 0.00000000000000e+00 + 1.50000000000000e+00 0.00000000000000e+00 + 2.00000000000000e+00 0.00000000000000e+00 + 2.50000000000000e+00 0.00000000000000e+00 + 3.00000000000000e+00 0.00000000000000e+00 + 3.50000000000000e+00 0.00000000000000e+00 + 4.00000000000000e+00 0.00000000000000e+00 + 4.50000000000000e+00 0.00000000000000e+00 + 5.00000000000000e+00 0.00000000000000e+00 + 5.50000000000000e+00 4.50178616337543e+00 + 6.00000000000000e+00 3.21202647385895e+00 + 6.50000000000000e+00 3.21202647385895e+00 + 7.00000000000000e+00 3.21202647385895e+00 + 7.50000000000000e+00 3.21202647385895e+00 + 8.00000000000000e+00 3.21202647385895e+00 + 8.50000000000000e+00 3.21202647385895e+00 + 9.00000000000000e+00 3.21202647385895e+00 + 9.50000000000000e+00 3.21202647385895e+00 + 1.00000000000000e+01 3.21202647385895e+00 diff --git a/namd/tests/library/000_distance-grid_abf-customgrid/AutoDiff/test.restart.colvars.out b/namd/tests/library/000_distance-grid_abf-customgrid/AutoDiff/test.restart.colvars.out new file mode 100644 index 000000000..8a5ee803a --- /dev/null +++ b/namd/tests/library/000_distance-grid_abf-customgrid/AutoDiff/test.restart.colvars.out @@ -0,0 +1,182 @@ +colvars: ---------------------------------------------------------------------- +colvars: Please cite Fiorin et al, Mol Phys 2013: +colvars: https://doi.org/10.1080/00268976.2013.813594 +colvars: as well as all other papers listed below for individual features used. +colvars: This version was built with the C++11 standard or higher. +colvars: Summary of compile-time features available in this build: +colvars: - SMP parallelism: enabled (num. threads = 4) +colvars: - Lepton custom functions: available +colvars: - Tcl interpreter: available +colvars: Redefining the Tcl "cv" command to the new script interface. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: The final output state file will be "test.restart.colvars.state". +colvars: ---------------------------------------------------------------------- +colvars: Reading new configuration from file "test.in": +colvars: # units = "" [default] +colvars: # indexFile = "index.ndx" +colvars: The following index groups are currently defined: +colvars: Protein (104 atoms) +colvars: Protein_noH (51 atoms) +colvars: Protein_Backbone (40 atoms) +colvars: Protein_C-alpha (10 atoms) +colvars: RMSD_atoms (10 atoms) +colvars: Protein_C-alpha_1_2 (2 atoms) +colvars: Protein_C-alpha_9_10 (2 atoms) +colvars: Protein_C-alpha_1 (1 atoms) +colvars: group1 (4 atoms) +colvars: Protein_C-alpha_2 (1 atoms) +colvars: group2 (4 atoms) +colvars: Protein_C-alpha_3 (1 atoms) +colvars: group3 (4 atoms) +colvars: Protein_C-alpha_4 (1 atoms) +colvars: group4 (4 atoms) +colvars: Protein_C-alpha_5 (1 atoms) +colvars: group5 (4 atoms) +colvars: Protein_C-alpha_6 (1 atoms) +colvars: group6 (4 atoms) +colvars: Protein_C-alpha_7 (1 atoms) +colvars: group7 (4 atoms) +colvars: Protein_C-alpha_8 (1 atoms) +colvars: group8 (4 atoms) +colvars: Protein_C-alpha_9 (1 atoms) +colvars: group9 (4 atoms) +colvars: Protein_C-alpha_10 (1 atoms) +colvars: group10 (4 atoms) +colvars: heavy_atoms (51 atoms) +colvars: # smp = on [default] +colvars: # colvarsTrajFrequency = 1 +colvars: # colvarsRestartFrequency = 10 +colvars: # scriptedColvarForces = off [default] +colvars: # scriptingAfterBiases = off [default] +colvars: # sourceTclFile = "" [default] +colvars: ---------------------------------------------------------------------- +colvars: Initializing a new collective variable. +colvars: # name = "one" +colvars: Initializing a new "distance" component. +colvars: # name = "" [default] +colvars: # componentCoeff = 1 [default] +colvars: # componentExp = 1 [default] +colvars: # period = 0 [default] +colvars: # wrapAround = 0 [default] +colvars: # forceNoPBC = off [default] +colvars: # scalable = on [default] +colvars: Initializing atom group "group1". +colvars: # name = "" [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] +colvars: # atomsOfGroup = "" [default] +colvars: # indexGroup = "group1" +colvars: # psfSegID = [default] +colvars: # atomsFile = "" [default] +colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableFitGradients = on [default] +colvars: Enabling scalable calculation for group "group1". +colvars: # printAtomIDs = off [default] +colvars: Atom group "group1" defined with 4 atoms requested: total mass = 54.028, total charge = -0.72. +colvars: Initializing atom group "group2". +colvars: # name = "" [default] +colvars: # centerToOrigin = off [default] +colvars: # centerToReference = off [default] +colvars: # rotateToReference = off [default] +colvars: # atomsOfGroup = "" [default] +colvars: # indexGroup = "group2" +colvars: # psfSegID = [default] +colvars: # atomsFile = "" [default] +colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableFitGradients = on [default] +colvars: Enabling scalable calculation for group "group2". +colvars: # printAtomIDs = off [default] +colvars: Atom group "group2" defined with 4 atoms requested: total mass = 54.028, total charge = -0.4. +colvars: # oneSiteSystemForce = off [default] +colvars: # oneSiteTotalForce = off [default] +colvars: All components initialized. +colvars: # timeStepFactor = 1 [default] +colvars: # width = 0.5 +colvars: # lowerBoundary = 0 [default] +colvars: # upperBoundary = 10 +colvars: # hardLowerBoundary = on [default] +colvars: # hardUpperBoundary = off [default] +colvars: # expandBoundaries = off [default] +colvars: # extendedLagrangian = off [default] +colvars: # outputValue = on [default] +colvars: # outputVelocity = off [default] +colvars: # outputTotalForce = off [default] +colvars: # outputAppliedForce = on +colvars: # subtractAppliedForce = off [default] +colvars: # runAve = off [default] +colvars: # corrFunc = off [default] +colvars: ---------------------------------------------------------------------- +colvars: Collective variables initialized, 1 in total. +colvars: ---------------------------------------------------------------------- +colvars: Initializing a new "abf" instance. +colvars: # name = "abf1" [default] +colvars: # colvars = { one } +colvars: # stepZeroData = off [default] +colvars: # outputEnergy = off [default] +colvars: # outputFreq = 10 [default] +colvars: # timeStepFactor = 1 [default] +colvars: WARNING: ABF should not be run without a thermostat or at 0 Kelvin! +colvars: # applyBias = on [default] +colvars: # hideJacobian = off [default] +colvars: Jacobian (geometric) forces will be included in reported free energy gradients. +colvars: # fullSamples = 10 +colvars: # minSamples = 5 [default] +colvars: # inputPrefix = [default] +colvars: # historyFreq = 0 [default] +colvars: # shared = off [default] +colvars: # updateBias = on [default] +colvars: # maxForce = [default] +colvars: # lowerBoundaries = { 1 } +colvars: # upperBoundaries = { 5 } +colvars: # widths = { 0.2 } +colvars: # integrate = on [default] +colvars: Finished ABF setup. +colvars: ---------------------------------------------------------------------- +colvars: Collective variables biases initialized, 1 in total. +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module (re)initialized. +colvars: ---------------------------------------------------------------------- +colvars: Updating NAMD interface: +colvars: updating atomic data (0 atoms). +colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: +colvars: SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS: +colvars: +colvars: - Colvars module: +colvars: - Colvars-NAMD interface: +colvars: - Optimal rotation via flexible fitting: +colvars: - distance colvar component: +colvars: Fiorin2013 https://doi.org/10.1080/00268976.2013.813594 +colvars: +colvars: - ABF colvar bias implementation: +colvars: - Internal-forces free energy estimator: +colvars: Henin2010 https://doi.org/10.1021/ct9004432 +colvars: +colvars: - NAMD engine: +colvars: - Scalable center-of-mass computation (NAMD): +colvars: Phillips2020 https://doi.org/10.1063/5.0014475 +colvars: +colvars: updating target temperature (T = 0 K). +colvars: ---------------------------------------------------------------------- +colvars: Loading state from text file "test.colvars.state". +colvars: Restarting collective variable "one" from value: 3.19504 +colvars: Restarted abf bias "abf1" with step number 20. +colvars: ---------------------------------------------------------------------- +colvars: Updating NAMD interface: +colvars: updating atomic data (0 atoms). +colvars: updating group data (2 scalable groups, 8 atoms in total). +colvars: updating grid object data (0 grid objects in total). +colvars: updating target temperature (T = 0 K). +colvars: Current simulation parameters: initial step = 20, integration timestep = 1 +colvars: Updating atomic parameters (masses, charges, etc). +colvars: Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 54.028, total charge = -0.72. +colvars: Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 54.028, total charge = -0.4. +colvars: The restart output state file will be "test.restart.tmp.colvars.state". +colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj". +colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj". +colvars: Saving collective variables state to "test.restart.tmp.colvars.state". +colvars: Synchronizing (emptying the buffer of) trajectory file "test.restart.colvars.traj". +colvars: Saving collective variables state to "test.restart.tmp.colvars.state". +colvars: Saving collective variables state to "test.restart.colvars.state". diff --git a/namd/tests/library/000_distance-grid_abf-customgrid/AutoDiff/test.restart.colvars.state.stripped b/namd/tests/library/000_distance-grid_abf-customgrid/AutoDiff/test.restart.colvars.state.stripped new file mode 100644 index 000000000..c7b9b2fea --- /dev/null +++ b/namd/tests/library/000_distance-grid_abf-customgrid/AutoDiff/test.restart.colvars.state.stripped @@ -0,0 +1,27 @@ +configuration { + step 40 + dt 1.000000e+00 +} + +colvar { + name one + x 3.1550316480017 +} + +abf { + configuration { + step 40 + name abf1 + } + +samples + 0 0 0 0 0 0 0 0 + 0 0 21 19 0 0 0 0 + 0 0 0 0 + +gradient + 0 0 0 0 0 0 0 0 + 0 0 -18.596622597615 -2.579519379033 0 0 0 0 + 0 0 0 0 +} + diff --git a/namd/tests/library/000_distance-grid_abf-customgrid/AutoDiff/test.restart.colvars.traj b/namd/tests/library/000_distance-grid_abf-customgrid/AutoDiff/test.restart.colvars.traj new file mode 100644 index 000000000..36292a1a7 --- /dev/null +++ b/namd/tests/library/000_distance-grid_abf-customgrid/AutoDiff/test.restart.colvars.traj @@ -0,0 +1,22 @@ +# step one fa_one + 20 3.19504109859627e+00 0.00000000000000e+00 + 21 3.19102191972704e+00 0.00000000000000e+00 + 22 3.18709720675364e+00 0.00000000000000e+00 + 23 3.18337516035850e+00 0.00000000000000e+00 + 24 3.17995068524441e+00 0.00000000000000e+00 + 25 3.17690060023898e+00 -1.70733191351305e+00 + 26 3.17425438901656e+00 -4.49848369146902e+00 + 27 3.17200310573942e+00 -8.13196505762149e+00 + 28 3.17010441301305e+00 -1.23579104029288e+01 + 29 3.16848920515434e+00 -1.69399919425882e+01 + 30 3.16706897911795e+00 -1.80599464168527e+01 + 31 3.16579864457612e+00 -1.88459693108695e+01 + 32 3.16463211540264e+00 -1.93446440423366e+01 + 33 3.16352515122836e+00 -1.96053998551592e+01 + 34 3.16243794428299e+00 -1.96786766893698e+01 + 35 3.16133719773243e+00 -1.96136510459479e+01 + 36 3.16019748810951e+00 -1.94558499141651e+01 + 37 3.15900181308568e+00 -1.92450798507875e+01 + 38 3.15774152752143e+00 -1.90145989083226e+01 + 39 3.15641592564363e+00 -1.87913372766038e+01 + 40 3.15503164800165e+00 -1.85966225976150e+01 diff --git a/namd/tests/library/000_distance-grid_abf-customgrid/AutoDiff/test.restart.count b/namd/tests/library/000_distance-grid_abf-customgrid/AutoDiff/test.restart.count new file mode 100644 index 000000000..fd78406df --- /dev/null +++ b/namd/tests/library/000_distance-grid_abf-customgrid/AutoDiff/test.restart.count @@ -0,0 +1,23 @@ +# 1 +# 1.00000000000000e+00 2.00000000000000e-01 20 0 + + 1.10000000000000e+00 0 + 1.30000000000000e+00 0 + 1.50000000000000e+00 0 + 1.70000000000000e+00 0 + 1.90000000000000e+00 0 + 2.10000000000000e+00 0 + 2.30000000000000e+00 0 + 2.50000000000000e+00 0 + 2.70000000000000e+00 0 + 2.90000000000000e+00 0 + 3.10000000000000e+00 21 + 3.30000000000000e+00 19 + 3.50000000000000e+00 0 + 3.70000000000000e+00 0 + 3.90000000000000e+00 0 + 4.10000000000000e+00 0 + 4.30000000000000e+00 0 + 4.50000000000000e+00 0 + 4.70000000000000e+00 0 + 4.90000000000000e+00 0 diff --git a/namd/tests/library/000_distance-grid_abf-customgrid/AutoDiff/test.restart.grad b/namd/tests/library/000_distance-grid_abf-customgrid/AutoDiff/test.restart.grad new file mode 100644 index 000000000..b598f0091 --- /dev/null +++ b/namd/tests/library/000_distance-grid_abf-customgrid/AutoDiff/test.restart.grad @@ -0,0 +1,23 @@ +# 1 +# 0.00000000000000e+00 5.00000000000000e-01 20 0 + + 2.50000000000000e-01 0.00000000000000e+00 + 7.50000000000000e-01 0.00000000000000e+00 + 1.25000000000000e+00 0.00000000000000e+00 + 1.75000000000000e+00 0.00000000000000e+00 + 2.25000000000000e+00 0.00000000000000e+00 + 2.75000000000000e+00 0.00000000000000e+00 + 3.25000000000000e+00 0.00000000000000e+00 + 3.75000000000000e+00 0.00000000000000e+00 + 4.25000000000000e+00 0.00000000000000e+00 + 4.75000000000000e+00 0.00000000000000e+00 + 5.25000000000000e+00 -1.85966225976150e+01 + 5.75000000000000e+00 -2.57951937903300e+00 + 6.25000000000000e+00 0.00000000000000e+00 + 6.75000000000000e+00 0.00000000000000e+00 + 7.25000000000000e+00 0.00000000000000e+00 + 7.75000000000000e+00 0.00000000000000e+00 + 8.25000000000000e+00 0.00000000000000e+00 + 8.75000000000000e+00 0.00000000000000e+00 + 9.25000000000000e+00 0.00000000000000e+00 + 9.75000000000000e+00 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_abf-customgrid/AutoDiff/test.restart.pmf b/namd/tests/library/000_distance-grid_abf-customgrid/AutoDiff/test.restart.pmf new file mode 100644 index 000000000..83a7f8cae --- /dev/null +++ b/namd/tests/library/000_distance-grid_abf-customgrid/AutoDiff/test.restart.pmf @@ -0,0 +1,24 @@ +# 1 +# -2.50000000000000e-01 5.00000000000000e-01 21 0 + + 0.00000000000000e+00 1.05880709883240e+01 + 5.00000000000000e-01 1.05880709883240e+01 + 1.00000000000000e+00 1.05880709883240e+01 + 1.50000000000000e+00 1.05880709883240e+01 + 2.00000000000000e+00 1.05880709883240e+01 + 2.50000000000000e+00 1.05880709883240e+01 + 3.00000000000000e+00 1.05880709883240e+01 + 3.50000000000000e+00 1.05880709883240e+01 + 4.00000000000000e+00 1.05880709883240e+01 + 4.50000000000000e+00 1.05880709883240e+01 + 5.00000000000000e+00 1.05880709883240e+01 + 5.50000000000000e+00 1.28975968951650e+00 + 6.00000000000000e+00 0.00000000000000e+00 + 6.50000000000000e+00 0.00000000000000e+00 + 7.00000000000000e+00 0.00000000000000e+00 + 7.50000000000000e+00 0.00000000000000e+00 + 8.00000000000000e+00 0.00000000000000e+00 + 8.50000000000000e+00 0.00000000000000e+00 + 9.00000000000000e+00 0.00000000000000e+00 + 9.50000000000000e+00 0.00000000000000e+00 + 1.00000000000000e+01 0.00000000000000e+00 diff --git a/namd/tests/library/000_distance-grid_abf-customgrid/namd-version.txt b/namd/tests/library/000_distance-grid_abf-customgrid/namd-version.txt new file mode 100644 index 000000000..e1d311c69 --- /dev/null +++ b/namd/tests/library/000_distance-grid_abf-customgrid/namd-version.txt @@ -0,0 +1,3 @@ +Info: NAMD 3.1alpha2 for Linux-x86_64-multicore +colvars: Initializing the collective variables module, version 2024-06-04. +colvars: Using NAMD interface, version "2023-12-05". diff --git a/namd/tests/library/000_distance-grid_abf-customgrid/test.in b/namd/tests/library/000_distance-grid_abf-customgrid/test.in new file mode 100644 index 000000000..bb11ed575 --- /dev/null +++ b/namd/tests/library/000_distance-grid_abf-customgrid/test.in @@ -0,0 +1,36 @@ +colvarsTrajFrequency 1 +colvarsRestartFrequency 10 +indexFile index.ndx + +colvar { + + name one + + outputAppliedForce on + + # use a non-trivial width to test bias behavior + width 0.5 + # The lower boundary is already defined at 0 for a distance function + # lowerBoundary 0.0 + upperBoundary 10.0 + + distance { + group1 { + indexGroup group1 + } + group2 { + indexGroup group2 + } + } +} + +abf { + colvars one + fullSamples 10 + + grid { + widths 0.2 + lowerBoundaries 1.0 + upperBoundaries 5.0 + } +} diff --git a/tests/input_files/distance-grid_abf-customgrid/test.in b/tests/input_files/distance-grid_abf-customgrid/test.in new file mode 100644 index 000000000..bb11ed575 --- /dev/null +++ b/tests/input_files/distance-grid_abf-customgrid/test.in @@ -0,0 +1,36 @@ +colvarsTrajFrequency 1 +colvarsRestartFrequency 10 +indexFile index.ndx + +colvar { + + name one + + outputAppliedForce on + + # use a non-trivial width to test bias behavior + width 0.5 + # The lower boundary is already defined at 0 for a distance function + # lowerBoundary 0.0 + upperBoundary 10.0 + + distance { + group1 { + indexGroup group1 + } + group2 { + indexGroup group2 + } + } +} + +abf { + colvars one + fullSamples 10 + + grid { + widths 0.2 + lowerBoundaries 1.0 + upperBoundaries 5.0 + } +} From 513a9bd70e80a0a02b984fa5056e817f367710c3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=A9r=C3=B4me=20H=C3=A9nin?= Date: Wed, 18 Sep 2024 14:23:02 +0200 Subject: [PATCH 05/13] Update doc for custom grids --- doc/colvars-refman-main.tex | 56 ++++++++++++++++++++----------------- 1 file changed, 31 insertions(+), 25 deletions(-) diff --git a/doc/colvars-refman-main.tex b/doc/colvars-refman-main.tex index dbdaa01a9..b1574a175 100644 --- a/doc/colvars-refman-main.tex +++ b/doc/colvars-refman-main.tex @@ -4457,7 +4457,7 @@ of freedom, and the actual geometric colvar (function of Cartesian coordinates) only feels the force from the harmonic spring. This is particularly useful when combined with an \refkey{abf}{sec:colvarbias_abf} bias -to perform eABF simulations (\ref{sec:eABF}). +to perform eABF simulations (\ref{sec:colvarbias_abf_extended}). Note that for some biases (\refkey{harmonicWalls}{sec:colvarbias_harmonic_walls}, \refkey{histogram}{sec:colvarbias_histogram}), this masking behavior is controlled by the keyword \refkey{bypassExtendedLagrangian}{colvarbias|bypassExtendedLagrangian}. @@ -5272,7 +5272,7 @@ This option is implemented by the \refkey{harmonicWalls}{sec:colvarbias_harmonic_walls} and \refkey{histogram}{sec:colvarbias_histogram} biases. It is only relevant if the bias is applied to one or several extended-Lagrangian colvars (\ref{sec:colvar_extended}), - for example within an eABF (\ref{sec:eABF}) simulation. + for example within an eABF (\ref{sec:colvarbias_abf_extended}) simulation. Usually, biases use the value of the extended coordinate as a proxy for the actual colvar, and their biasing forces are applied to the extended coordinates as well. If \texttt{bypassExtendedLagrangian} is enabled, the bias behaves as if there were no extended coordinates, and accesses the value of the underlying colvars, applying any biasing forces along the gradients of those variables.} @@ -5307,6 +5307,30 @@ \end{itemize} + +\cvsubsec{Defining grids for biasing and analysis methods}{sec:colvarbias_grid} + +Several methods (\hyperlink{sec:colvarbias_histogram}{histograms}, \hyperlink{sec:colvarbias_abf}{ABF} and \hyperlink{sec:colvarbias_abf_extended}{eABF}, optionally \hyperlink{sec:colvarbias_metadynamics}{metadynamics}) rely on discretizing colvars on regular grids to represent functions such as probability distributions or free energy surfaces. +Grid parameters for these may be provided at the level of the individual variables, or via a dedicated configuration block \texttt{grid \{ \ldots \}} inside the configuration of the bias. +The options supported \emph{inside this block} are: + +\begin{itemize} +\item % + \key{% + lowerBoundaries}{% + \texttt{grid}}{% + Lower boundaries of the grid}{% + list of space-separated decimals}{% + This option defines the lower boundaries of the grid, overriding any values defined by the \texttt{lowerBoundary} keyword of each colvar. + } +\item % + \simkey{upperBoundaries}{\texttt{grid}}{lowerBoundaries} +\item % + \simkey{widths}{\texttt{grid}}{lowerBoundaries} +\end{itemize} + + + \cvsubsec{Thermodynamic integration}{sec:colvarbias_ti} The methods implemented here provide a variety of estimators of conformational free-energies. @@ -5367,7 +5391,7 @@ Combining ABF with the extended Lagrangian feature (\ref{sec:colvar_extended}) of the variables produces the extended-system ABF variant of the method -(\ref{sec:eABF}). +(\ref{sec:colvarbias_abf_extended}). ABF is based on the thermodynamic integration (TI) scheme for computing free energy profiles. The free energy as a function @@ -5470,7 +5494,7 @@ The following conditions must be met for an ABF simulation to be possible and to produce an accurate estimate of the free energy profile. Note that these requirements do not apply when using the extended-system -ABF method (\ref{sec:eABF}). +ABF method (\ref{sec:colvarbias_abf_extended}). \begin{enumerate} \item \emph{Only linear combinations} of colvar components can be used in ABF calculations. @@ -5812,8 +5836,7 @@ -\cvsubsec{Extended-system Adaptive Biasing Force (eABF)}{sec:ecolvarbias_abf_extended} -\label{sec:eABF} +\cvsubsec{Extended-system Adaptive Biasing Force (eABF)}{sec:colvarbias_abf_extended} Extended-system ABF (eABF) is a variant of ABF (\ref{sec:colvarbias_abf}) where the bias is not applied @@ -7599,32 +7622,15 @@ \item \dupkey{name}{\texttt{histogram}}{sec:colvarbias}{biasing and analysis methods} \item \dupkey{colvars}{\texttt{histogram}}{sec:colvarbias}{biasing and analysis methods} -% \item \dupkey{outputEnergy}{\texttt{histogram}}{sec:colvarbias}{biasing and analysis methods} \item \dupkey{stepZeroData}{\texttt{histogram}}{sec:colvarbias}{biasing and analysis methods} \end{itemize} -\cvsubsubsec{Defining grids for multidimensional histograms}{sec:colvarbias_histogram_grid} - Grid parameters for the histogram may be provided at the level of the individual variables, or via a dedicated configuration block \texttt{grid \{ \ldots \}} inside the configuration of this \texttt{histogram}. -The options supported \emph{inside this block} are: +The options supported \emph{inside this block} are described in \ref{sec:colvarbias_grid}. -\begin{itemize} -\item % - \key{% - lowerBoundaries}{% - \texttt{grid}}{% - Lower boundaries of the grid}{% - list of space-separated decimals}{% - This option defines the lower boundaries of the grid, overriding any values defined by the \texttt{lowerBoundary} keyword of each colvar. - Note that when \texttt{gatherVectorColvars} is \texttt{on} in the enclosing \texttt{histogram} block, each vector variable is automatically treated as a scalar, and a single value should be provided for it. - } -\item % - \simkey{upperBoundaries}{\texttt{grid}}{lowerBoundaries} -\item % - \simkey{widths}{\texttt{grid}}{lowerBoundaries} -\end{itemize} +Note that when \texttt{gatherVectorColvars} is \texttt{on}, each vector variable is automatically treated as a scalar, and a single value of each grid parameter should be provided for it. \cvsubsubsec{Output options for multi-dimensional histograms}{sec:colvarbias_histogram_output} From 4a00a76ec556e4ea4c5a2aebf16990817a87d576 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=A9r=C3=B4me=20H=C3=A9nin?= Date: Sun, 22 Sep 2024 18:51:26 +0200 Subject: [PATCH 06/13] Make grid keywords singular --- doc/colvars-refman-main.tex | 29 ++++++++++++------- .../test.in | 6 ++-- .../test.in | 6 ++-- .../test.in | 6 ++-- .../test.in | 6 ++-- .../test.in | 6 ++-- .../000_distance-grid_abf-customgrid/test.in | 6 ++-- .../test.in | 6 ++-- .../000_distance_histogram-customgrid/test.in | 6 ++-- src/colvargrid_def.h | 6 ++-- ...ihedral_histogram2d-periodic-customgrid.in | 6 ++-- tests/histogram-customgrid-periodic.in | 6 ++-- tests/histogram-customgrid.in | 6 ++-- .../test.in | 6 ++-- .../distance-grid_abf-customgrid/test.in | 6 ++-- .../test.in | 6 ++-- .../distance_histogram-customgrid/test.in | 6 ++-- 17 files changed, 67 insertions(+), 58 deletions(-) diff --git a/doc/colvars-refman-main.tex b/doc/colvars-refman-main.tex index b1574a175..07d468de5 100644 --- a/doc/colvars-refman-main.tex +++ b/doc/colvars-refman-main.tex @@ -4282,6 +4282,7 @@ Many algorithms require the definition of two boundaries and a bin width for each colvar, which are necessary to compute discrete ``states'' for a collective variable's otherwise continuous values. The following keywords define these parameters for a specific variable, and will be used by all bias that refer to that variable unless otherwise specified. +Some of these parameters can be set directly within a bias configuration by inserting a \refkey{grid}{sec:colvarbias_grid} block (\ref{sec:colvarbias_grid}). \begin{itemize} @@ -5311,22 +5312,30 @@ \cvsubsec{Defining grids for biasing and analysis methods}{sec:colvarbias_grid} Several methods (\hyperlink{sec:colvarbias_histogram}{histograms}, \hyperlink{sec:colvarbias_abf}{ABF} and \hyperlink{sec:colvarbias_abf_extended}{eABF}, optionally \hyperlink{sec:colvarbias_metadynamics}{metadynamics}) rely on discretizing colvars on regular grids to represent functions such as probability distributions or free energy surfaces. -Grid parameters for these may be provided at the level of the individual variables, or via a dedicated configuration block \texttt{grid \{ \ldots \}} inside the configuration of the bias. +Grid parameters for these may be provided at the level of the individual variables (\ref{sec:colvar_grid_params}), or via a dedicated configuration block \texttt{grid \{ \ldots \}} inside the configuration of the bias. The options supported \emph{inside this block} are: \begin{itemize} \item % \key{% - lowerBoundaries}{% + lowerBoundary}{% \texttt{grid}}{% Lower boundaries of the grid}{% list of space-separated decimals}{% - This option defines the lower boundaries of the grid, overriding any values defined by the \texttt{lowerBoundary} keyword of each colvar. + This option is specified once, and takes as many parameters as there are colvars associated with this bias. + It defines the lower boundaries of the grid, overriding any values defined by the \refkey{lowerBoundary}{colvar|lowerBoundary} keyword of each colvar. } \item % - \simkey{upperBoundaries}{\texttt{grid}}{lowerBoundaries} + \simkey{upperBoundary}{\texttt{grid}}{lowerBoundary} \item % - \simkey{widths}{\texttt{grid}}{lowerBoundaries} + \key{% + lowerBoundary}{% + \texttt{grid}}{% + Bin widths of the grid}{% + list of space-separated decimals}{% + This option is specified once, and takes as many parameters as there are colvars associated with this bias. + It defines the bin widths of the grid along each dimension, overriding any values defined by the \refkey{width}{colvar|width} keyword of each colvar. + } \end{itemize} @@ -5533,7 +5542,7 @@ \cvsubsubsec{Parameters for ABF}{sec:colvarbias_abf_params} ABF depends on parameters from each collective variable to define the grid on which free energy gradients are computed: see \ref{sec:colvar_grid_params} for details. -Alternately, grid parameters can be set directly inside the ABF block by inserting a \texttt{grid} sub-block, as explained in \ref{sec:colvarbias_histogram_grid}. +Alternately, grid parameters can be set directly inside the ABF block by inserting a \texttt{grid} sub-block, as explained in \ref{sec:colvarbias_grid}. Other parameters to control the ABF runtime can be set in the ABF configuration block: \begin{itemize} @@ -7608,15 +7617,15 @@ \-\-~~name~hist2d\\ \-\-~~colvars~r~theta\\ \-\-~~grid~\{\\ -\-\-~~~~widths~~0.1~1.0\\ -\-\-~~~~lowerBoundaries~~~2.0~30.0\\ -\-\-~~~~upperBoundaries~~10.0~90.0\\ +\-\-~~~~width~~0.1~1.0\\ +\-\-~~~~lowerBoundary~~~2.0~30.0\\ +\-\-~~~~upperBoundary~~10.0~90.0\\ \-\-~~\}\\ \-\}\\ \end{cvexampleinput} -The standard keywords below are used to control the histogram's computation and to select the variables that are sampled. See also \ref{sec:colvarbias_histogram_grid} for keywords used to define the grid, \ref{sec:colvarbias_histogram_output} for output parameters and \ref{sec:colvarbias_histogram_vectors} for more advanced keywords. +The standard keywords below are used to control the histogram's computation and to select the variables that are sampled. See also \ref{sec:colvarbias_grid} for keywords used to define the grid, \ref{sec:colvarbias_histogram_output} for output parameters and \ref{sec:colvarbias_histogram_vectors} for more advanced keywords. \begin{itemize} diff --git a/gromacs/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/test.in b/gromacs/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/test.in index e139372dc..9458ca30d 100644 --- a/gromacs/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/test.in +++ b/gromacs/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/test.in @@ -39,8 +39,8 @@ colvar { histogram { colvars r phi grid { - widths 0.2 6.0 - lowerBoundaries 0.0 0.0 - upperBoundaries 10.0 360.0 + width 0.2 6.0 + lowerBoundary 0.0 0.0 + upperBoundary 10.0 360.0 } } diff --git a/lammps/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/test.in b/lammps/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/test.in index e139372dc..9458ca30d 100644 --- a/lammps/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/test.in +++ b/lammps/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/test.in @@ -39,8 +39,8 @@ colvar { histogram { colvars r phi grid { - widths 0.2 6.0 - lowerBoundaries 0.0 0.0 - upperBoundaries 10.0 360.0 + width 0.2 6.0 + lowerBoundary 0.0 0.0 + upperBoundary 10.0 360.0 } } diff --git a/lammps/tests/library/000_distance-grid_histogram-customgrid/test.in b/lammps/tests/library/000_distance-grid_histogram-customgrid/test.in index 8376dfbdb..44cca66dd 100644 --- a/lammps/tests/library/000_distance-grid_histogram-customgrid/test.in +++ b/lammps/tests/library/000_distance-grid_histogram-customgrid/test.in @@ -27,8 +27,8 @@ colvar { histogram { colvars one grid { - widths 0.2 - lowerBoundaries 0.6 - upperBoundaries 5.4 + width 0.2 + lowerBoundary 0.6 + upperBoundary 5.4 } } diff --git a/namd/tests/library/000_dihedral_histogram-customgrid-periodic/test.in b/namd/tests/library/000_dihedral_histogram-customgrid-periodic/test.in index 40a5cd78c..635d48bcc 100644 --- a/namd/tests/library/000_dihedral_histogram-customgrid-periodic/test.in +++ b/namd/tests/library/000_dihedral_histogram-customgrid-periodic/test.in @@ -29,8 +29,8 @@ colvar { histogram { colvars one grid { - widths 5 - lowerBoundaries -60 - upperBoundaries 300 + width 5 + lowerBoundary -60 + upperBoundary 300 } } diff --git a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/test.in b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/test.in index e139372dc..9458ca30d 100644 --- a/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/test.in +++ b/namd/tests/library/000_distance-dihedral_histogram2d-periodic-customgrid/test.in @@ -39,8 +39,8 @@ colvar { histogram { colvars r phi grid { - widths 0.2 6.0 - lowerBoundaries 0.0 0.0 - upperBoundaries 10.0 360.0 + width 0.2 6.0 + lowerBoundary 0.0 0.0 + upperBoundary 10.0 360.0 } } diff --git a/namd/tests/library/000_distance-grid_abf-customgrid/test.in b/namd/tests/library/000_distance-grid_abf-customgrid/test.in index bb11ed575..15940c691 100644 --- a/namd/tests/library/000_distance-grid_abf-customgrid/test.in +++ b/namd/tests/library/000_distance-grid_abf-customgrid/test.in @@ -29,8 +29,8 @@ abf { fullSamples 10 grid { - widths 0.2 - lowerBoundaries 1.0 - upperBoundaries 5.0 + width 0.2 + lowerBoundary 1.0 + upperBoundary 5.0 } } diff --git a/namd/tests/library/000_distance-grid_histogram-customgrid/test.in b/namd/tests/library/000_distance-grid_histogram-customgrid/test.in index 8376dfbdb..44cca66dd 100644 --- a/namd/tests/library/000_distance-grid_histogram-customgrid/test.in +++ b/namd/tests/library/000_distance-grid_histogram-customgrid/test.in @@ -27,8 +27,8 @@ colvar { histogram { colvars one grid { - widths 0.2 - lowerBoundaries 0.6 - upperBoundaries 5.4 + width 0.2 + lowerBoundary 0.6 + upperBoundary 5.4 } } diff --git a/namd/tests/library/000_distance_histogram-customgrid/test.in b/namd/tests/library/000_distance_histogram-customgrid/test.in index 02b99ab06..d71dc057d 100644 --- a/namd/tests/library/000_distance_histogram-customgrid/test.in +++ b/namd/tests/library/000_distance_histogram-customgrid/test.in @@ -23,8 +23,8 @@ colvar { histogram { colvars one grid { - widths 0.2 - lowerBoundaries 0.6 - upperBoundaries 5.4 + width 0.2 + lowerBoundary 0.6 + upperBoundary 5.4 } } diff --git a/src/colvargrid_def.h b/src/colvargrid_def.h index fa6531271..88303ec6c 100644 --- a/src/colvargrid_def.h +++ b/src/colvargrid_def.h @@ -205,12 +205,12 @@ template int colvar_grid::parse_params(std::string const &conf, upper_boundaries, upper_boundaries, colvarparse::parse_silent); // camel case keywords are used in config file - colvarparse::get_keyval(conf, "lowerBoundaries", + colvarparse::get_keyval(conf, "lowerBoundary", lower_boundaries, lower_boundaries, parse_mode); - colvarparse::get_keyval(conf, "upperBoundaries", + colvarparse::get_keyval(conf, "upperBoundary", upper_boundaries, upper_boundaries, parse_mode); - colvarparse::get_keyval(conf, "widths", widths, widths, parse_mode); + colvarparse::get_keyval(conf, "width", widths, widths, parse_mode); // only used in state file colvarparse::get_keyval(conf, "sizes", nx, nx, colvarparse::parse_silent); diff --git a/tests/distance-dihedral_histogram2d-periodic-customgrid.in b/tests/distance-dihedral_histogram2d-periodic-customgrid.in index 9e05ed20e..e10e3eba1 100644 --- a/tests/distance-dihedral_histogram2d-periodic-customgrid.in +++ b/tests/distance-dihedral_histogram2d-periodic-customgrid.in @@ -35,8 +35,8 @@ colvar { histogram { colvars r phi grid { - widths 0.2 6.0 - lowerBoundaries 0.0 0.0 - upperBoundaries 10.0 360.0 + width 0.2 6.0 + lowerBoundary 0.0 0.0 + upperBoundary 10.0 360.0 } } diff --git a/tests/histogram-customgrid-periodic.in b/tests/histogram-customgrid-periodic.in index 68b0f526e..57e08094d 100644 --- a/tests/histogram-customgrid-periodic.in +++ b/tests/histogram-customgrid-periodic.in @@ -1,8 +1,8 @@ histogram { colvars one grid { - widths 5 - lowerBoundaries -60 - upperBoundaries 300 + width 5 + lowerBoundary -60 + upperBoundary 300 } } diff --git a/tests/histogram-customgrid.in b/tests/histogram-customgrid.in index 69c096a15..0bcdd7873 100644 --- a/tests/histogram-customgrid.in +++ b/tests/histogram-customgrid.in @@ -1,8 +1,8 @@ histogram { colvars one grid { - widths 0.2 - lowerBoundaries 0.6 - upperBoundaries 5.4 + width 0.2 + lowerBoundary 0.6 + upperBoundary 5.4 } } diff --git a/tests/input_files/dihedral_histogram-customgrid-periodic/test.in b/tests/input_files/dihedral_histogram-customgrid-periodic/test.in index 40a5cd78c..635d48bcc 100644 --- a/tests/input_files/dihedral_histogram-customgrid-periodic/test.in +++ b/tests/input_files/dihedral_histogram-customgrid-periodic/test.in @@ -29,8 +29,8 @@ colvar { histogram { colvars one grid { - widths 5 - lowerBoundaries -60 - upperBoundaries 300 + width 5 + lowerBoundary -60 + upperBoundary 300 } } diff --git a/tests/input_files/distance-grid_abf-customgrid/test.in b/tests/input_files/distance-grid_abf-customgrid/test.in index bb11ed575..15940c691 100644 --- a/tests/input_files/distance-grid_abf-customgrid/test.in +++ b/tests/input_files/distance-grid_abf-customgrid/test.in @@ -29,8 +29,8 @@ abf { fullSamples 10 grid { - widths 0.2 - lowerBoundaries 1.0 - upperBoundaries 5.0 + width 0.2 + lowerBoundary 1.0 + upperBoundary 5.0 } } diff --git a/tests/input_files/distance-grid_histogram-customgrid/test.in b/tests/input_files/distance-grid_histogram-customgrid/test.in index 8376dfbdb..44cca66dd 100644 --- a/tests/input_files/distance-grid_histogram-customgrid/test.in +++ b/tests/input_files/distance-grid_histogram-customgrid/test.in @@ -27,8 +27,8 @@ colvar { histogram { colvars one grid { - widths 0.2 - lowerBoundaries 0.6 - upperBoundaries 5.4 + width 0.2 + lowerBoundary 0.6 + upperBoundary 5.4 } } diff --git a/tests/input_files/distance_histogram-customgrid/test.in b/tests/input_files/distance_histogram-customgrid/test.in index 02b99ab06..d71dc057d 100644 --- a/tests/input_files/distance_histogram-customgrid/test.in +++ b/tests/input_files/distance_histogram-customgrid/test.in @@ -23,8 +23,8 @@ colvar { histogram { colvars one grid { - widths 0.2 - lowerBoundaries 0.6 - upperBoundaries 5.4 + width 0.2 + lowerBoundary 0.6 + upperBoundary 5.4 } } From 86da9ca63e01456762b1121247140a8d390c8553 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=A9r=C3=B4me=20H=C3=A9nin?= Date: Sun, 22 Sep 2024 19:12:31 +0200 Subject: [PATCH 07/13] Support keyword used in state file for grids --- src/colvargrid_def.h | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/colvargrid_def.h b/src/colvargrid_def.h index 88303ec6c..bfbe59b44 100644 --- a/src/colvargrid_def.h +++ b/src/colvargrid_def.h @@ -211,6 +211,8 @@ template int colvar_grid::parse_params(std::string const &conf, upper_boundaries, upper_boundaries, parse_mode); colvarparse::get_keyval(conf, "width", widths, widths, parse_mode); + // Plural form in state file + colvarparse::get_keyval(conf, "widths", widths, widths, parse_mode); // only used in state file colvarparse::get_keyval(conf, "sizes", nx, nx, colvarparse::parse_silent); From 080b75e35c87a28b2a42aee93ddba09e4d2445c7 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Fri, 27 Sep 2024 10:47:14 -0400 Subject: [PATCH 08/13] Fix typo --- doc/colvars-refman-main.tex | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/colvars-refman-main.tex b/doc/colvars-refman-main.tex index 07d468de5..a48a3866a 100644 --- a/doc/colvars-refman-main.tex +++ b/doc/colvars-refman-main.tex @@ -5329,7 +5329,7 @@ \simkey{upperBoundary}{\texttt{grid}}{lowerBoundary} \item % \key{% - lowerBoundary}{% + width}{% \texttt{grid}}{% Bin widths of the grid}{% list of space-separated decimals}{% From bf6e8bfac66dae5732968d561d5192afdb7cf8a9 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Fri, 27 Sep 2024 10:47:41 -0400 Subject: [PATCH 09/13] Expand doc section of grid {} block, reuse example from histogram --- doc/colvars-refman-main.tex | 62 +++++++++++++++++++++---------------- 1 file changed, 35 insertions(+), 27 deletions(-) diff --git a/doc/colvars-refman-main.tex b/doc/colvars-refman-main.tex index a48a3866a..485f3bff2 100644 --- a/doc/colvars-refman-main.tex +++ b/doc/colvars-refman-main.tex @@ -5312,8 +5312,13 @@ \cvsubsec{Defining grids for biasing and analysis methods}{sec:colvarbias_grid} Several methods (\hyperlink{sec:colvarbias_histogram}{histograms}, \hyperlink{sec:colvarbias_abf}{ABF} and \hyperlink{sec:colvarbias_abf_extended}{eABF}, optionally \hyperlink{sec:colvarbias_metadynamics}{metadynamics}) rely on discretizing colvars on regular grids to represent functions such as probability distributions or free energy surfaces. -Grid parameters for these may be provided at the level of the individual variables (\ref{sec:colvar_grid_params}), or via a dedicated configuration block \texttt{grid \{ \ldots \}} inside the configuration of the bias. -The options supported \emph{inside this block} are: + +Grid parameters are specific to each variable, and some of them may even be defined automatically: for instance, periodic angles have default boundaries of -180$^\circ$ and 180$^\circ$. +When not given by default, boundaries may be also specified when defining the collective variable itself (\ref{sec:colvar_grid_params}). + +Each bias will use by default any colvar boundaries that are automatically defined or explicitly given. +Optionally, the bias may also contain a dedicated configuration block \texttt{grid \{ \ldots \}} inside its configuration. +The options supported within the \texttt{grid \{ \ldots \}} block are: \begin{itemize} \item % @@ -5338,6 +5343,33 @@ } \end{itemize} +\noindent\textbf{Example:} Definition of custom grid parameters for a histogram. Note how some of the boundaries of the variables are automatically defined, but this histogram's grid is custom-defined to also specify a finer width and narrower boundaries. +\begin{cvexampleinput} +\-colvar~\{\\ +\-\-~~name~r\\ +\-\-~~\#~lowerBoundary~0.0~is~automatically~defined\\ +\-\-~~upperBoundary~20.0\\ +\-\-~~distance~\{~...~\}\\ +\-\}\\ +\\ +\-colvar~\{\\ +\-\-~~name~theta\\ +\-\-~~\#~lowerBoundary~-180.0~is~automatically~defined\\ +\-\-~~\#~upperBoundary~180.0~is~automatically~defined\\ +\-\-~~dihedral~\{~...~\}\\ +\-\}\\ +\\ +\-histogram~\{\\ +\-\-~~name~hist2d\\ +\-\-~~colvars~r~theta\\ +\-\-~~grid~\{\\ +\-\-~~~~width~~0.1~1.0\\ +\-\-~~~~lowerBoundary~~~2.0~30.0\\ +\-\-~~~~upperBoundary~~10.0~90.0\\ +\-\-~~\}\\ +\-\}\\ +\end{cvexampleinput} + \cvsubsec{Thermodynamic integration}{sec:colvarbias_ti} @@ -7577,7 +7609,7 @@ The \texttt{histogram} feature is used to record the distribution of a set of collective variables in the form of a N-dimensional histogram. Defining such a histogram is generally useful for analysis purposes, but it has no effect on the simulation. -\noindent\textbf{Example 1:} the two-dimensional histogram of a distance and an angle can be generated using the configuration below. The histogram code requires that each variable is a scalar number that is confined within a pre-defined interval. The interval's boundaries may be specified by hand (e.g.{} through \refkey{lowerBoundary}{colvar|lowerBoundary} and \refkey{upperBoundary}{colvar|upperBoundary} in the variable definition), or auto-detected based on the type of function. In this example, the lower boundary for the distance variable ``\texttt{r}'' is automatically set to zero, and interval for the three-body angle ``\texttt{theta}'' is $0^\circ$ and $180^\circ$: however, that an upper boundary for the distance ``\texttt{r}'' still needs to be specified manually. The grid spacings for the two variables are $0.2$~\lengthunit and $3.0^\circ$, respectively. +\noindent\textbf{Example:} the two-dimensional histogram of a distance and an angle can be generated using the configuration below. The histogram code requires that each variable is a scalar number that is confined within a pre-defined interval. The interval's boundaries may be specified by hand (e.g.{} through \refkey{lowerBoundary}{colvar|lowerBoundary} and \refkey{upperBoundary}{colvar|upperBoundary} in the variable definition), or auto-detected based on the type of function. In this example, the lower boundary for the distance variable ``\texttt{r}'' is automatically set to zero, and interval for the three-body angle ``\texttt{theta}'' is $0^\circ$ and $180^\circ$: however, that an upper boundary for the distance ``\texttt{r}'' still needs to be specified manually. The grid spacings for the two variables are $0.2$~\lengthunit and $3.0^\circ$, respectively. % Note: a three-body angle is used to support NAMD users, because the % init_as_periodic_angle() function was added after the NAMD 2.14 release. \begin{cvexampleinput} @@ -7600,30 +7632,6 @@ \-\}\\ \end{cvexampleinput} -\noindent\textbf{Example 2:} This example is similar to the previous one, but with the important difference that the parameters for the histogram's grid are defined \emph{explicitly} for this histogram instance. Therefore, this histogram's grid may differ from the one defined from parameters embedded in the \texttt{colvar~\{~...~\}} block (for example, narrower intervals and finer grid spacings may be selected). -\begin{cvexampleinput} -\-colvar~\{\\ -\-\-~~name~r\\ -\-\-~~upperBoundary~20.0\\ -\-\-~~distance~\{~...~\}\\ -\-\}\\ -\\ -\-colvar~\{\\ -\-\-~~name~theta\\ -\-\-~~dihedral~\{~...~\}\\ -\-\}\\ -\\ -\-histogram~\{\\ -\-\-~~name~hist2d\\ -\-\-~~colvars~r~theta\\ -\-\-~~grid~\{\\ -\-\-~~~~width~~0.1~1.0\\ -\-\-~~~~lowerBoundary~~~2.0~30.0\\ -\-\-~~~~upperBoundary~~10.0~90.0\\ -\-\-~~\}\\ -\-\}\\ -\end{cvexampleinput} - The standard keywords below are used to control the histogram's computation and to select the variables that are sampled. See also \ref{sec:colvarbias_grid} for keywords used to define the grid, \ref{sec:colvarbias_histogram_output} for output parameters and \ref{sec:colvarbias_histogram_vectors} for more advanced keywords. From 2bb211c76cae03b85ad3bd0794a7addb301db9ca Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Thu, 3 Oct 2024 13:47:33 -0400 Subject: [PATCH 10/13] Fix library functional tests --- .../test.in | 8 ++--- .../distance-grid_abf-customgrid/test.in | 36 ------------------- 2 files changed, 4 insertions(+), 40 deletions(-) delete mode 100644 tests/input_files/distance-grid_abf-customgrid/test.in diff --git a/tests/input_files/distance-dihedral_histogram2d-periodic-customgrid/test.in b/tests/input_files/distance-dihedral_histogram2d-periodic-customgrid/test.in index 5ae19f915..9458ca30d 100644 --- a/tests/input_files/distance-dihedral_histogram2d-periodic-customgrid/test.in +++ b/tests/input_files/distance-dihedral_histogram2d-periodic-customgrid/test.in @@ -38,9 +38,9 @@ colvar { histogram { colvars r phi - histogramGrid { - widths 0.2 6.0 - lowerBoundaries 0.0 0.0 - upperBoundaries 10.0 360.0 + grid { + width 0.2 6.0 + lowerBoundary 0.0 0.0 + upperBoundary 10.0 360.0 } } diff --git a/tests/input_files/distance-grid_abf-customgrid/test.in b/tests/input_files/distance-grid_abf-customgrid/test.in deleted file mode 100644 index 15940c691..000000000 --- a/tests/input_files/distance-grid_abf-customgrid/test.in +++ /dev/null @@ -1,36 +0,0 @@ -colvarsTrajFrequency 1 -colvarsRestartFrequency 10 -indexFile index.ndx - -colvar { - - name one - - outputAppliedForce on - - # use a non-trivial width to test bias behavior - width 0.5 - # The lower boundary is already defined at 0 for a distance function - # lowerBoundary 0.0 - upperBoundary 10.0 - - distance { - group1 { - indexGroup group1 - } - group2 { - indexGroup group2 - } - } -} - -abf { - colvars one - fullSamples 10 - - grid { - width 0.2 - lowerBoundary 1.0 - upperBoundary 5.0 - } -} From 6866cd1492bc8a04cb5943827beb5fa2f86053d7 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Thu, 3 Oct 2024 13:48:15 -0400 Subject: [PATCH 11/13] Update README to mention library tests vs. engine tests; document limitations! --- tests/Makefile | 7 ++--- tests/README.md | 69 ++++++++++++++++++++++++++++++------------------- 2 files changed, 46 insertions(+), 30 deletions(-) diff --git a/tests/Makefile b/tests/Makefile index 9743b19bf..c337466d9 100644 --- a/tests/Makefile +++ b/tests/Makefile @@ -1,12 +1,13 @@ .PHONY: all functional gromacs lammps namd -all: functional lammps namd # gromacs - - functional: ./build_tests.sh input_files/ + +all: functional lammps namd # gromacs + + # GROMACS tests need manual adjustments # gromacs: # ./build_tests.sh ../gromacs/tests/library/ diff --git a/tests/README.md b/tests/README.md index 837d1796c..4859d6b99 100644 --- a/tests/README.md +++ b/tests/README.md @@ -2,7 +2,7 @@ This folder contains example configuration files that define computations via the Colvars library. Most configurations are written using features that are supported by multiple backends (GROMACS, LAMMPS, NAMD and VMD). -Because not all engines support name-based selections or PDB file-based selections, and in the interest of compactness and portability, the primary atom selection method used here is index groups, which will require one or more `indexFile` keywords to be included. For other selection methods, [engine-specific tests](#Engine-specific-tests) may be also created without using the tools from this folder. +Because not all engines support name-based selections or PDB file-based selections, and in the interest of compactness and portability, the primary atom selection method used here is index groups, which will require one or more `indexFile` keywords to be included. For other selection methods, [engine-specific tests](#MD-Engine-interface-tests) may be also created without using the tools from this folder. ### Test input syntax and dependencies @@ -17,29 +17,16 @@ The configuration files included in this folder use index groups with one or mor For the above two groups, please use the file names `rmsd_atoms_refpos.xyz` and `rmsd_atoms_refpos.xyz` to supply reference coordinates, since these files are already set up in each engine's test folder. -### Testing procedure and pass/fail criteria +### Running the library tests -For each backend, there is a folder `/tests/library`, which contains a `run_tests.sh` script and full input decks for each of the tests included here. Numerical results are compared by that script against previously recorded values (i.e. regression tests are performed). +Most of the tests contained in this folder are added to the CMake build system, and are run automatically using CTest. Nothing special is needed to run them; however, there are currently two limitations: +1. Each test runs a standalone version of the library against a pre-computed atomic trajectory, and therefore runs through most of the Colvars library functionality, but at this moment *no checks are made yet on numerical correctness*: these are currently done through MD engine regression tests (see below). +2. Algorithms that require the availability of total forces from the MD engine (e.g. ABF, TI, etc) are currently not supported. -Each test runs a short MD simulation (e.g. 20 steps) with the program exiting gracefully, followed by a second MD run of the same length, restarted from the first. Colvars trajectory files, state files, and other output files are all compared against reference values: if a relative deviation greater than 1.0e-6 is observed, that test fails. - -Tests are run in double precision wherever this is feasible: therefore, most tests match their expected results within a far smaller error than 1.0e-6. However, remember that a *full MD simulation* is performed for each test, and changes in the MD engine's version and choices of compiler may introduce differences whichever version of Colvars is used. - -In the automated tests performed on GitHub, a CentOS 7 Linux environment and the GCC 4.8 compiler are used to build Colvars and other codes (exception: GROMACS uses GCC 10 from the same environment). A text file in each test folder states which code versions were used to generate the reference output. Occasionally, reference outputs may need to be updated to reflect changes in codes unrelated to Colvars: this is done as rarely and conservatively as possible. - -Please keep the above in mind if you plan on running tests in your own environment for development purposes, and feel free to reach out via GitHub issue if a test's failure is suspicious. - - -### Engine-specific tests - -Some Colvars features are specific to a certain engine: for example, not all codes implement atom name-based or PDB file-based selections, or Colvars may be using code from that engine to perform a computation. For those cases, additional tests are also found in the `/tests/library` folder. There is also a `/tests/interface` folder to test functionality that is unique to that code. - -*Aside from the above exceptions, it is highly recommended to create test inputs at the top level, i.e. inside this folder, so that they may be reused and their features tested in every scenario.* +### Adding a new test for the library -### Adding a new test - -- First, a Colvars configuration file should be created; the default extension used is `.in` for simplicity (but any extension would otherwise work for a Colvars file). The file may either be complete on its own: +1. First, a Colvars configuration file should be created; the default extension used is `.in` for simplicity (but any extension would otherwise work for a Colvars file). The file may either be complete on its own: ``` nano my_config_name.in ``` @@ -50,7 +37,7 @@ nano bias_name.in ``` In either case, a file called simply `test.in` will be generated. This file will be placed inside a folder dedicated to running the corresponding test. This folder will contain any additional input files, as well as the reference output files for the test. -- Next, add the following lines to the script `build_tests.sh` to create a test folder: +2. Next, add the following lines to the script `build_tests.sh` to create a test folder: ``` create_test_dir ``` @@ -64,17 +51,45 @@ write_colvars_config ``` (If the new test has additional dependencies other than the Colvars config file, those would have to be copied manually as well.) -- Lastly, run the script to execute these tasks: +3. Lastly, run `make` to copy all functional input files into the folder `input_files`, where they will be taken up by CMake. Note that some configurations are not yet supported (see [above](#Adding-a-new-test-for-the-library)), and should not be committed to Git yet. ``` -./build_tests.sh ..//tests/library +make ``` -and navigate to the test's parent folder to run it for the first time and generate reference files: + + +## MD engine regression tests + +For each engine, the folder `/tests/library` contains a `run_tests.sh` script and full input decks for each of the tests included here. Numerical results are compared by that script against previously recorded values (i.e. regression tests are performed). + +Each test runs a short MD simulation (e.g. 20 steps) with the program exiting gracefully, followed by a second MD run of the same length, restarted from the first. Colvars trajectory files, state files, and other output files are all compared against reference values: if a relative deviation greater than 1.0e-6 is observed, that test fails. + +Tests are run in double precision wherever this is feasible: therefore, most tests match their expected results within a far smaller error than 1.0e-6. However, remember that a *full MD simulation* is performed for each test, and changes in the MD engine's version and choices of compiler may introduce differences whichever version of Colvars is used. + +In the automated tests performed on GitHub, a container is typically used to build Colvars and other codes: this reduces the possible sources of variability from using different compilers. A text file in each test folder states which code versions were used to generate the reference output. Occasionally, reference outputs may need to be updated to reflect changes in codes unrelated to Colvars: this is done as rarely and conservatively as possible. + +Please keep the above in mind if you plan on running tests in your own environment for development purposes, and feel free to reach out via GitHub issue if a test's failure is suspicious. + + +### Adding a MD engine regression test + +Please use the same steps 1 and 2 for the [library tests](#Adding-a-new-test-for-the-library), but instead of step 3 please use the following instead: +``` +make ``` -cd ..//tests/library +Then, navigate to the test's parent folder to run it for the first time and generate reference files, using the "`-g`" flag: +``` +cd //tests/library ./run_tests.sh -g 000_ ``` - -- It is always a good idea to check that the test matches the reference files just generated: +It is always a good idea to immediately check that the script can correctly match against the reference files just generated: ``` ./run_tests.sh 000_ ``` +**NOTE:** due to changes in the unit system, adding GROMACS tests requires manual edits in addition to the steps above. + + +### MD engine interface tests + +Some Colvars features are specific to a certain engine: for example, not all codes implement atom name-based or PDB file-based selections, or Colvars may be using code from that engine to perform a computation. For those cases, additional tests are also found in the `/tests/library` folder. There is also a `/tests/interface` folder to test functionality that is unique to that code. + +*Aside from the above exceptions, it is highly recommended to create test inputs at the top level, i.e. inside this folder, so that they may be reused and their features tested in every scenario.* From aa5af96fd51550eb5371681fb2110b6e5ee510c8 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Fri, 18 Oct 2024 11:57:07 -0400 Subject: [PATCH 12/13] Remove unused function parameter --- src/colvarbias_meta.cpp | 34 +++++++--------------------------- src/colvarbias_meta.h | 21 +++++++++++---------- 2 files changed, 18 insertions(+), 37 deletions(-) diff --git a/src/colvarbias_meta.cpp b/src/colvarbias_meta.cpp index ee9a5d601..d46d059b8 100644 --- a/src/colvarbias_meta.cpp +++ b/src/colvarbias_meta.cpp @@ -318,33 +318,15 @@ colvarbias_meta::~colvarbias_meta() { colvarbias_meta::clear_state_data(); colvarproxy *proxy = cvm::main()->proxy; - proxy->close_output_stream(replica_hills_file); - proxy->close_output_stream(hills_traj_file_name()); - - if (target_dist) { - delete target_dist; - target_dist = NULL; - } } int colvarbias_meta::clear_state_data() { - if (hills_energy) { - delete hills_energy; - hills_energy = NULL; - } - - if (hills_energy_gradients) { - delete hills_energy_gradients; - hills_energy_gradients = NULL; - } - hills.clear(); hills_off_grid.clear(); - return COLVARS_OK; } @@ -626,8 +608,7 @@ int colvarbias_meta::update_grid_data() { if ((cvm::step_absolute() % grids_freq) == 0) { // map the most recent gaussians to the grids - project_hills(new_hills_begin, hills.end(), - hills_energy, hills_energy_gradients); + project_hills(new_hills_begin, hills.end(), hills_energy.get(), hills_energy_gradients.get()); new_hills_begin = hills.end(); // TODO: we may want to condense all into one replicas array, @@ -636,8 +617,8 @@ int colvarbias_meta::update_grid_data() for (size_t ir = 0; ir < replicas.size(); ir++) { replicas[ir]->project_hills(replicas[ir]->new_hills_begin, replicas[ir]->hills.end(), - replicas[ir]->hills_energy, - replicas[ir]->hills_energy_gradients); + replicas[ir]->hills_energy.get(), + replicas[ir]->hills_energy_gradients.get()); replicas[ir]->new_hills_begin = replicas[ir]->hills.end(); } } @@ -962,8 +943,7 @@ void colvarbias_meta::project_hills(colvarbias_meta::hill_iter h_first, void colvarbias_meta::recount_hills_off_grid(colvarbias_meta::hill_iter h_first, - colvarbias_meta::hill_iter h_last, - colvar_grid_scalar * /* he */) + colvarbias_meta::hill_iter h_last) { hills_off_grid.clear(); @@ -1471,9 +1451,9 @@ void colvarbias_meta::rebin_grids_after_restart() if (restart_keep_hills && !hills.empty()) { // if there are hills, recompute the new grids from them cvm::log("Rebinning the energy and forces grids from "+ - cvm::to_str(hills.size())+" hills (this may take a while)...\n"); - project_hills(hills.begin(), hills.end(), - new_hills_energy, new_hills_energy_gradients, true); + cvm::to_str(hills.size())+" hills (this may take a bit)...\n"); + project_hills(hills.begin(), hills.end(), new_hills_energy.get(), + new_hills_energy_gradients.get(), true); cvm::log("rebinning done.\n"); } else { diff --git a/src/colvarbias_meta.h b/src/colvarbias_meta.h index a765a60c7..50dc512d7 100644 --- a/src/colvarbias_meta.h +++ b/src/colvarbias_meta.h @@ -15,7 +15,10 @@ #include #include "colvarbias.h" -#include "colvargrid.h" + +class colvar_grid_scalar; +class colvar_grid_gradient; + /// Metadynamics bias (implementation of \link colvarbias \endlink) @@ -123,8 +126,7 @@ class colvarbias_meta hill_iter new_hills_off_grid_begin; /// Regenerate the hills_off_grid list - void recount_hills_off_grid(hill_iter h_first, hill_iter h_last, - colvar_grid_scalar *ge); + void recount_hills_off_grid(hill_iter h_first, hill_iter h_last); template OST &write_hill_template_(OST &os, colvarbias_meta::hill const &h); @@ -211,7 +213,7 @@ class colvarbias_meta bool ebmeta; /// Target distribution for EBmeta - colvar_grid_scalar* target_dist; + std::shared_ptr target_dist; /// Number of equilibration steps for EBmeta cvm::step_number ebmeta_equil_steps; @@ -223,15 +225,14 @@ class colvarbias_meta bool safely_read_restart; /// Hill energy, cached on a grid - colvar_grid_scalar *hills_energy; + std::shared_ptr hills_energy; /// Hill forces, cached on a grid - colvar_grid_gradient *hills_energy_gradients; + std::shared_ptr hills_energy_gradients; - /// \brief Project the selected hills onto grids - void project_hills(hill_iter h_first, hill_iter h_last, - colvar_grid_scalar *ge, colvar_grid_gradient *gf, - bool print_progress = false); + /// Project the selected hills onto grids + void project_hills(hill_iter h_first, hill_iter h_last, colvar_grid_scalar *ge, + colvar_grid_gradient *gf, bool print_progress = false); // Multiple Replicas variables and functions From 6f1ab534c395611233a0f3b661b7660efd6e3bda Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Fri, 18 Oct 2024 12:10:18 -0400 Subject: [PATCH 13/13] Use smart pointers to manage metadynamics grid data --- src/colvarbias_meta.cpp | 82 ++++++++++++++++++++--------------------- src/colvarbias_meta.h | 11 +++--- 2 files changed, 46 insertions(+), 47 deletions(-) diff --git a/src/colvarbias_meta.cpp b/src/colvarbias_meta.cpp index d46d059b8..a559006e8 100644 --- a/src/colvarbias_meta.cpp +++ b/src/colvarbias_meta.cpp @@ -14,6 +14,7 @@ #include "colvarmodule.h" #include "colvarproxy.h" #include "colvar.h" +#include "colvargrid.h" #include "colvarbias_meta.h" #include "colvars_memstream.h" @@ -31,8 +32,6 @@ colvarbias_meta::colvarbias_meta(char const *key) use_grids = true; grids_freq = 0; rebin_grids = false; - hills_energy = NULL; - hills_energy_gradients = NULL; dump_fes = true; keep_hills = false; @@ -143,9 +142,9 @@ int colvarbias_meta::init(std::string const &conf) get_keyval(conf, "keepHills", keep_hills, keep_hills); get_keyval(conf, "keepFreeEnergyFiles", dump_fes_save, dump_fes_save); - if (hills_energy == NULL) { - hills_energy = new colvar_grid_scalar(colvars); - hills_energy_gradients = new colvar_grid_gradient(colvars); + if (!hills_energy) { + hills_energy.reset(new colvar_grid_scalar(colvars)); + hills_energy_gradients.reset(new colvar_grid_gradient(colvars)); } } else { @@ -254,7 +253,6 @@ int colvarbias_meta::init_ebmeta_params(std::string const &conf) { int error_code = COLVARS_OK; // for ebmeta - target_dist = NULL; get_keyval(conf, "ebMeta", ebmeta, false); if(ebmeta){ cvm::main()->cite_feature("Ensemble-biased metadynamics (ebMetaD)"); @@ -265,7 +263,7 @@ int colvarbias_meta::init_ebmeta_params(std::string const &conf) "targetDistFile accordingly.\n", COLVARS_INPUT_ERROR); } - target_dist = new colvar_grid_scalar(); + target_dist.reset(new colvar_grid_scalar()); error_code |= target_dist->init_from_colvars(colvars); std::string target_dist_file; get_keyval(conf, "targetDistFile", target_dist_file); @@ -523,10 +521,8 @@ int colvarbias_meta::update_grid_params() new_hills_energy->map_grid(*hills_energy); new_hills_energy_gradients->map_grid(*hills_energy_gradients); - delete hills_energy; - delete hills_energy_gradients; - hills_energy = new_hills_energy; - hills_energy_gradients = new_hills_energy_gradients; + hills_energy.reset(new_hills_energy); + hills_energy_gradients.reset(new_hills_energy_gradients); curr_bin = hills_energy->get_colvars_index(); if (cvm::debug()) @@ -1061,8 +1057,8 @@ int colvarbias_meta::update_replicas_registry() (replicas.back())->comm = multiple_replicas; if (use_grids) { - (replicas.back())->hills_energy = new colvar_grid_scalar(colvars); - (replicas.back())->hills_energy_gradients = new colvar_grid_gradient(colvars); + (replicas.back())->hills_energy.reset(new colvar_grid_scalar(colvars)); + (replicas.back())->hills_energy_gradients.reset(new colvar_grid_gradient(colvars)); } if (is_enabled(f_cvb_calc_ti_samples)) { (replicas.back())->enable(f_cvb_calc_ti_samples); @@ -1319,34 +1315,40 @@ template IST &colvarbias_meta::read_state_data_template_(IST &is) { if (use_grids) { - colvar_grid_scalar *hills_energy_backup = NULL; - colvar_grid_gradient *hills_energy_gradients_backup = NULL; + std::unique_ptr hills_energy_backup; + std::unique_ptr hills_energy_gradients_backup; - if (has_data) { + bool const need_backup = has_data; + + if (need_backup) { if (cvm::debug()) - cvm::log("Backupping grids for metadynamics bias \""+ - this->name+"\""+ - ((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+".\n"); - hills_energy_backup = hills_energy; - hills_energy_gradients_backup = hills_energy_gradients; - hills_energy = new colvar_grid_scalar(colvars); - hills_energy_gradients = new colvar_grid_gradient(colvars); + cvm::log("Backing up grids for metadynamics bias \"" + this->name + "\"" + + ((comm != single_replica) ? ", replica \"" + replica_id + "\"" : "") + ".\n"); + + hills_energy_backup = std::move(hills_energy); + hills_energy_gradients_backup = std::move(hills_energy_gradients); + hills_energy.reset(new colvar_grid_scalar(colvars)); + hills_energy_gradients.reset(new colvar_grid_gradient(colvars)); } - read_grid_data_template_(is, "hills_energy", hills_energy, - hills_energy_backup); + read_grid_data_template_(is, "hills_energy", hills_energy.get(), + hills_energy_backup.get()); - read_grid_data_template_( - is, "hills_energy_gradients", hills_energy_gradients, hills_energy_gradients_backup); + read_grid_data_template_(is, "hills_energy_gradients", + hills_energy_gradients.get(), + hills_energy_gradients_backup.get()); if (is) { cvm::log(" successfully read the biasing potential and its gradients from grids.\n"); - if (hills_energy_backup != nullptr) { - // Now that we have successfully updated the grids, delete the backup copies - delete hills_energy_backup; - delete hills_energy_gradients_backup; - } } else { + if (need_backup) { + if (cvm::debug()) + cvm::log("Restoring grids from backup for metadynamics bias \"" + this->name + "\"" + + ((comm != single_replica) ? ", replica \"" + replica_id + "\"" : "") + ".\n"); + // Restoring content from original grid + hills_energy->copy_grid(*hills_energy_backup); + hills_energy_gradients->copy_grid(*hills_energy_gradients_backup); + } return is; } } @@ -1434,10 +1436,8 @@ void colvarbias_meta::rebin_grids_after_restart() // read from the configuration file), and project onto them the // grids just read from the restart file - colvar_grid_scalar *new_hills_energy = - new colvar_grid_scalar(colvars); - colvar_grid_gradient *new_hills_energy_gradients = - new colvar_grid_gradient(colvars); + std::unique_ptr new_hills_energy(new colvar_grid_scalar(colvars)); + std::unique_ptr new_hills_energy_gradients(new colvar_grid_gradient(colvars)); if (cvm::debug()) { std::ostringstream tmp_os; @@ -1464,15 +1464,13 @@ void colvarbias_meta::rebin_grids_after_restart() new_hills_energy_gradients->map_grid(*hills_energy_gradients); } - delete hills_energy; - delete hills_energy_gradients; - hills_energy = new_hills_energy; - hills_energy_gradients = new_hills_energy_gradients; + hills_energy = std::move(new_hills_energy); + hills_energy_gradients = std::move(new_hills_energy_gradients); // assuming that some boundaries have expanded, eliminate those // off-grid hills that aren't necessary any more if (!hills.empty()) - recount_hills_off_grid(hills.begin(), hills.end(), hills_energy); + recount_hills_off_grid(hills.begin(), hills.end()); } } @@ -1813,7 +1811,7 @@ template OST &colvarbias_meta::write_state_data_template_(OST &os // this is a very good time to project hills, if you haven't done // it already! - project_hills(new_hills_begin, hills.end(), hills_energy, hills_energy_gradients); + project_hills(new_hills_begin, hills.end(), hills_energy.get(), hills_energy_gradients.get()); new_hills_begin = hills.end(); // write down the grids to the restart file diff --git a/src/colvarbias_meta.h b/src/colvarbias_meta.h index 50dc512d7..27cd6bbff 100644 --- a/src/colvarbias_meta.h +++ b/src/colvarbias_meta.h @@ -10,9 +10,10 @@ #ifndef COLVARBIAS_META_H #define COLVARBIAS_META_H -#include -#include #include +#include +#include +#include #include "colvarbias.h" @@ -213,7 +214,7 @@ class colvarbias_meta bool ebmeta; /// Target distribution for EBmeta - std::shared_ptr target_dist; + std::unique_ptr target_dist; /// Number of equilibration steps for EBmeta cvm::step_number ebmeta_equil_steps; @@ -225,10 +226,10 @@ class colvarbias_meta bool safely_read_restart; /// Hill energy, cached on a grid - std::shared_ptr hills_energy; + std::unique_ptr hills_energy; /// Hill forces, cached on a grid - std::shared_ptr hills_energy_gradients; + std::unique_ptr hills_energy_gradients; /// Project the selected hills onto grids void project_hills(hill_iter h_first, hill_iter h_last, colvar_grid_scalar *ge,