Merge pull request #62 from molssi-seamm/dev

Bugfix: charts with multiple exes, plus units for force constants
molssi-seamm · Aug 22, 2024 · 66aaa3f · 66aaa3f
2 parents 77d391b + 1df4bf2
commit 66aaa3f
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Showing 5 changed files with 48 additions and 29 deletions.
diff --git a/HISTORY.rst b/HISTORY.rst
@@ -1,6 +1,10 @@
 =======
 History
 =======
+2024.8.22 -- Bugfix: charts with multiple exes, plus units for force constants
+    * Add units for force constants (kJ/mol/Å^2,...)
+    * Fixed an issue naming axes in plots with multiple axes
+
 2024.8.1 -- Added default units for viscosity and fixed a bug in handling dimensions
     * Added more default units: dynamic viscosity (cP, etc) and kinematic viscosity
       (cSt, etc)

diff --git a/seamm_util/plotting.py b/seamm_util/plotting.py
@@ -301,22 +301,29 @@ def dumps(self):
             plot.bottom = bottom
 
         # Number the axes sequentially and set their limits
-        axis_number = 1
+        axis_number = {"x": 0, "y": 0, "z": 0}
         for plot in plots:
             for axis in plot.axes:
                 xyz = axis.direction
+                axis_number[xyz] += 1
+                anum = axis_number[xyz]
                 axis.update(
                     {
-                        "number": axis_number,
-                        "name": xyz + "axis" + str(axis_number),
-                        "short_name": xyz + str(axis_number),
+                        "number": axis_number[xyz],
+                        "name": xyz + "axis" + ("" if anum == 1 else str(anum)),
+                        "short_name": xyz + ("" if anum == 1 else str(anum)),
                     }
                 )
                 if xyz == "x":
-                    axis.update({"start": plot.left, "stop": plot.right})
+                    length = plot.right - plot.left
+                    left = plot.left + length * axis.start
+                    right = plot.left + length * axis.stop
+                    axis.update({"start": left, "stop": right})
                 elif xyz == "y":
-                    axis.update({"start": plot.bottom, "stop": plot.top})
-                axis_number += 1
+                    length = plot.top - plot.bottom
+                    bottom = plot.bottom + length * axis.start
+                    top = plot.bottom + length * axis.stop
+                    axis.update({"start": bottom, "stop": top})
 
         # Sort out any anchors between axes and get the data
         axes = []
@@ -326,7 +333,6 @@ def dumps(self):
                     axis.update(anchor="free")
                 else:
                     axis.update(anchor=axis.anchor["short_name"])
-
                 axes.append(axis.to_dict())
 
         # And, finally, set up the traces
@@ -441,7 +447,7 @@ class Axis(Dictionary):
     for the axis.
     """
 
-    def __init__(self, direction, *args, anchor=None, **kwargs):
+    def __init__(self, direction, *args, anchor=None, start=0.0, stop=1.0, **kwargs):
         """Initialize an axis, optionally with data.
 
         Parameters
@@ -459,10 +465,10 @@ def __init__(self, direction, *args, anchor=None, **kwargs):
 
         self.anchor = anchor
         self.direction = direction
+        self.start = start
+        self.stop = stop
         self["label"] = ""
         self["number"] = None
-        self["start"] = 0.0
-        self["stop"] = 1.0
 
         self.update(*args, **kwargs)
 

diff --git a/seamm_util/units.py b/seamm_util/units.py
@@ -80,6 +80,15 @@
         "E_h/a_0",
         "Ry/a_0",
     ],
+    "[mass] / [substance] / [time] ** 2": [
+        "kcal/mol/Å^2",
+        "kJ/mol/Å^2",
+        "eV/Å^2",
+        "E_h/Å^2",
+        "Ry/Å^2",
+        "E_h/a_0^2",
+        "Ry/a_0^2",
+    ],
     "[length] * [mass] / [time] ** 2": [
         "kcal/mol/Å",
         "kJ/mol/Å",

diff --git a/tests/results/simple_plot.html b/tests/results/simple_plot.html
@@ -30,9 +30,9 @@
 			    "type": "scatter",
 			    "x0": 0,
 			    "dx": 1.0,
-			    "xaxis": "x1",
+			    "xaxis": "x",
 			    "y": [110.0, 111.0, 110.0, 109.0, 110.0],
-			    "yaxis": "y2"
+			    "yaxis": "y"
 			}
                     ],
                     {
@@ -46,8 +46,8 @@
 			    "text": "Simple plot",
 			    "xanchor": "center"
 			},    
-			"xaxis1": {
-			    "anchor": "y2",
+			"xaxis": {
+			    "anchor": "y",
 			    "domain": [
 				0.0,
 				1.0
@@ -56,8 +56,8 @@
 				"text": "Time (ps)"
 			    }
 			},    
-			"yaxis2": {
-			    "anchor": "x1",
+			"yaxis": {
+			    "anchor": "x",
 			    "domain": [
 				0.0,
 				1.0

diff --git a/tests/results/two_plots.html b/tests/results/two_plots.html
@@ -30,9 +30,9 @@
 			    "type": "scatter",
 			    "x0": 0,
 			    "dx": 1.0,
-			    "xaxis": "x1",
+			    "xaxis": "x",
 			    "y": [110.0, 111.0, 110.0, 109.0, 110.0],
-			    "yaxis": "y2"
+			    "yaxis": "y"
 			},    
 			{
 			    "hoverlabel": {
@@ -50,9 +50,9 @@
 			    "type": "scatter",
 			    "x0": 0,
 			    "dx": 1.0,
-			    "xaxis": "x3",
+			    "xaxis": "x2",
 			    "y": [10.0, 11.0, 10.0, 9.0, 10.0],
-			    "yaxis": "y4"
+			    "yaxis": "y2"
 			}
                     ],
                     {
@@ -66,8 +66,8 @@
 			    "text": "Two plots",
 			    "xanchor": "center"
 			},    
-			"xaxis1": {
-			    "anchor": "y2",
+			"xaxis": {
+			    "anchor": "y",
 			    "domain": [
 				0.0,
 				0.6466666666666666
@@ -76,8 +76,8 @@
 				"text": "Time (ps)"
 			    }
 			},    
-			"yaxis2": {
-			    "anchor": "x1",
+			"yaxis": {
+			    "anchor": "x",
 			    "domain": [
 				0.0,
 				1.0
@@ -86,8 +86,8 @@
 				"text": "Energy (kcal/mol)"
 			    }
 			},    
-			"xaxis3": {
-			    "anchor": "y4",
+			"xaxis2": {
+			    "anchor": "y2",
 			    "domain": [
 				0.6666666666666666,
 				1.0
@@ -96,8 +96,8 @@
 				"text": "Time (ps)"
 			    }
 			},    
-			"yaxis4": {
-			    "anchor": "x3",
+			"yaxis2": {
+			    "anchor": "x2",
 			    "domain": [
 				0.0,
 				0.48