Make grid keywords singular

Colvars · Sep 23, 2024 · 3a40dbb · 3a40dbb
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diff --git a/doc/colvars-refman-main.tex b/doc/colvars-refman-main.tex
@@ -4203,6 +4203,7 @@
 
 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}
 
@@ -5232,22 +5233,30 @@
 \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}
 
 
@@ -5454,7 +5463,7 @@
 \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}
@@ -7144,15 +7153,15 @@
 \-\-~~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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -205,12 +205,12 @@ template <class T> int colvar_grid<T>::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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
     }
 }