More fixes in docu

doc/Makefile

@@ -48,6 +48,9 @@ clean:
 html:
 	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
 	@echo
+	mkdir -p _static/water _static/benzene
+	cp ../share/validation/water/trajectory-*.png _static/water/.
+	cp ../share/validation/benzene/trajectory-*.png _static/benzene/.
 	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
 
 dirhtml:

doc/vl.rst

@@ -64,7 +64,7 @@ Finally, two validations are performed for each system:
 
 .. _seclab_vl_water:
 
-Validation 1 - Water
+Validation 1 - water
 **********************
 
 Force field construction
@@ -124,21 +124,21 @@ trajectories, two bonds and one bend.
 
 * **First O-H bond**:
 
-.. image:: ../../../share/validation/water/trajectory-BondHarm-H.O-0_Ehc3.png
+.. image:: ../../_static/water/trajectory-BondHarm-H.O-0_Ehc3.png
     :width: 400
-    :target: ../../../share/validation/water/trajectory-BondHarm-H.O-0_Ehc3.png    
+    :target: ../../_static/water/trajectory-BondHarm-H.O-0_Ehc3.png    
 
 * **Second O-H bond**:
 
-.. image:: ../../../share/validation/water/trajectory-BondHarm-H.O-1_Ehc3.png
+.. image:: ../../_static/water/trajectory-BondHarm-H.O-1_Ehc3.png
     :width: 400
-    :target: ../../../share/validation/water/trajectory-BondHarm-H.O-1_Ehc3.png
+    :target: ../../_static/water/trajectory-BondHarm-H.O-1_Ehc3.png
 
 * **H-O-H bend**:
 
-.. image:: ../../../share/validation/water/trajectory-BendAHarm-H.O.H-2_Ehc3.png
+.. image:: ../../_static/water/trajectory-BendAHarm-H.O.H-2_Ehc3.png
     :width: 400
-    :target: ../../../share/validation/water/trajectory-BendAHarm-H.O.H-2_Ehc3.png
+    :target: ../../_static/water/trajectory-BendAHarm-H.O.H-2_Ehc3.png
 
 
 Geometry and frequencies
@@ -149,9 +149,9 @@ Geometry and frequencies
 
 |
 
-.. _seclab_vl_benzene:
+.. _seclab_vl__static/benzene:
 
-Validation 2 - Benzene
+Validation 2 - benzene
 **********************
 
 Force field construction
@@ -211,137 +211,137 @@ trajectories, two bonds and one bend.
 
 * **C-H bonds**:
 
-.. image:: ../../../share/validation/benzene/trajectory-BondHarm-C.H-0_Ehc3.png
+.. image:: ../../_static/benzene/trajectory-BondHarm-C.H-0_Ehc3.png
     :width: 400
-    :target: ../../../share/validation/benzene/trajectory-BondHarm-C.H-0_Ehc3.png    
+    :target: ../../_static/benzene/trajectory-BondHarm-C.H-0_Ehc3.png    
 
-.. image:: ../../../share/validation/benzene/trajectory-BondHarm-C.H-7_Ehc3.png
+.. image:: ../../_static/benzene/trajectory-BondHarm-C.H-7_Ehc3.png
     :width: 400
-    :target: ../../../share/validation/benzene/trajectory-BondHarm-C.H-7_Ehc3.png
+    :target: ../../_static/benzene/trajectory-BondHarm-C.H-7_Ehc3.png
 
-.. image:: ../../../share/validation/benzene/trajectory-BondHarm-C.H-8_Ehc3.png
+.. image:: ../../_static/benzene/trajectory-BondHarm-C.H-8_Ehc3.png
     :width: 400
-    :target: ../../../share/validation/benzene/trajectory-BondHarm-C.H-8_Ehc3.png
+    :target: ../../_static/benzene/trajectory-BondHarm-C.H-8_Ehc3.png
 
-.. image:: ../../../share/validation/benzene/trajectory-BondHarm-C.H-9_Ehc3.png
+.. image:: ../../_static/benzene/trajectory-BondHarm-C.H-9_Ehc3.png
     :width: 400
-    :target: ../../../share/validation/benzene/trajectory-BondHarm-C.H-9_Ehc3.png
+    :target: ../../_static/benzene/trajectory-BondHarm-C.H-9_Ehc3.png
 
-.. image:: ../../../share/validation/benzene/trajectory-BondHarm-C.H-10_Ehc3.png
+.. image:: ../../_static/benzene/trajectory-BondHarm-C.H-10_Ehc3.png
     :width: 400
-    :target: ../../../share/validation/benzene/trajectory-BondHarm-C.H-10_Ehc3.png
+    :target: ../../_static/benzene/trajectory-BondHarm-C.H-10_Ehc3.png
 
-.. image:: ../../../share/validation/benzene/trajectory-BondHarm-C.H-11_Ehc3.png
+.. image:: ../../_static/benzene/trajectory-BondHarm-C.H-11_Ehc3.png
     :width: 400
-    :target: ../../../share/validation/benzene/trajectory-BondHarm-C.H-11_Ehc3.png
+    :target: ../../_static/benzene/trajectory-BondHarm-C.H-11_Ehc3.png
 
 
 * **C-C bonds**:
 
-.. image:: ../../../share/validation/benzene/trajectory-BondHarm-C.C-1_Ehc3.png
+.. image:: ../../_static/benzene/trajectory-BondHarm-C.C-1_Ehc3.png
     :width: 400
-    :target: ../../../share/validation/benzene/trajectory-BondHarm-C.C-1_Ehc3.png
+    :target: ../../_static/benzene/trajectory-BondHarm-C.C-1_Ehc3.png
 
-.. image:: ../../../share/validation/benzene/trajectory-BondHarm-C.C-2_Ehc3.png
+.. image:: ../../_static/benzene/trajectory-BondHarm-C.C-2_Ehc3.png
     :width: 400
-    :target: ../../../share/validation/benzene/trajectory-BondHarm-C.C-2_Ehc3.png
+    :target: ../../_static/benzene/trajectory-BondHarm-C.C-2_Ehc3.png
 
-.. image:: ../../../share/validation/benzene/trajectory-BondHarm-C.C-3_Ehc3.png
+.. image:: ../../_static/benzene/trajectory-BondHarm-C.C-3_Ehc3.png
     :width: 400
-    :target: ../../../share/validation/benzene/trajectory-BondHarm-C.C-3_Ehc3.png
+    :target: ../../_static/benzene/trajectory-BondHarm-C.C-3_Ehc3.png
 
-.. image:: ../../../share/validation/benzene/trajectory-BondHarm-C.C-4_Ehc3.png
+.. image:: ../../_static/benzene/trajectory-BondHarm-C.C-4_Ehc3.png
     :width: 400
-    :target: ../../../share/validation/benzene/trajectory-BondHarm-C.C-4_Ehc3.png
+    :target: ../../_static/benzene/trajectory-BondHarm-C.C-4_Ehc3.png
 
-.. image:: ../../../share/validation/benzene/trajectory-BondHarm-C.C-5_Ehc3.png
+.. image:: ../../_static/benzene/trajectory-BondHarm-C.C-5_Ehc3.png
     :width: 400
-    :target: ../../../share/validation/benzene/trajectory-BondHarm-C.C-5_Ehc3.png
+    :target: ../../_static/benzene/trajectory-BondHarm-C.C-5_Ehc3.png
 
-.. image:: ../../../share/validation/benzene/trajectory-BondHarm-C.C-6_Ehc3.png
+.. image:: ../../_static/benzene/trajectory-BondHarm-C.C-6_Ehc3.png
     :width: 400
-    :target: ../../../share/validation/benzene/trajectory-BondHarm-C.C-6_Ehc3.png   
+    :target: ../../_static/benzene/trajectory-BondHarm-C.C-6_Ehc3.png   
 
 
 * **C-C-C bends**:
 
-.. image:: ../../../share/validation/benzene/trajectory-BendAHarm-C.C.C-24_Ehc3.png
+.. image:: ../../_static/benzene/trajectory-BendAHarm-C.C.C-24_Ehc3.png
     :width: 400
-    :target: ../../../share/validation/benzene/trajectory-BendAHarm-C.C.C-24_Ehc3.png
+    :target: ../../_static/benzene/trajectory-BendAHarm-C.C.C-24_Ehc3.png
 
-.. image:: ../../../share/validation/benzene/trajectory-BendAHarm-C.C.C-25_Ehc3.png
+.. image:: ../../_static/benzene/trajectory-BendAHarm-C.C.C-25_Ehc3.png
     :width: 400
-    :target: ../../../share/validation/benzene/trajectory-BendAHarm-C.C.C-25_Ehc3.png
+    :target: ../../_static/benzene/trajectory-BendAHarm-C.C.C-25_Ehc3.png
 
-.. image:: ../../../share/validation/benzene/trajectory-BendAHarm-C.C.C-26_Ehc3.png
+.. image:: ../../_static/benzene/trajectory-BendAHarm-C.C.C-26_Ehc3.png
     :width: 400
-    :target: ../../../share/validation/benzene/trajectory-BendAHarm-C.C.C-26_Ehc3.png
+    :target: ../../_static/benzene/trajectory-BendAHarm-C.C.C-26_Ehc3.png
 
-.. image:: ../../../share/validation/benzene/trajectory-BendAHarm-C.C.C-27_Ehc3.png
+.. image:: ../../_static/benzene/trajectory-BendAHarm-C.C.C-27_Ehc3.png
     :width: 400
-    :target: ../../../share/validation/benzene/trajectory-BendAHarm-C.C.C-27_Ehc3.png
+    :target: ../../_static/benzene/trajectory-BendAHarm-C.C.C-27_Ehc3.png
 
-.. image:: ../../../share/validation/benzene/trajectory-BendAHarm-C.C.C-28_Ehc3.png
+.. image:: ../../_static/benzene/trajectory-BendAHarm-C.C.C-28_Ehc3.png
     :width: 400
-    :target: ../../../share/validation/benzene/trajectory-BendAHarm-C.C.C-28_Ehc3.png
+    :target: ../../_static/benzene/trajectory-BendAHarm-C.C.C-28_Ehc3.png
 
-.. image:: ../../../share/validation/benzene/trajectory-BendAHarm-C.C.C-29_Ehc3.png
+.. image:: ../../_static/benzene/trajectory-BendAHarm-C.C.C-29_Ehc3.png
     :width: 400
-    :target: ../../../share/validation/benzene/trajectory-BendAHarm-C.C.C-29_Ehc3.png
+    :target: ../../_static/benzene/trajectory-BendAHarm-C.C.C-29_Ehc3.png
 
 
 * **C-C-H bends**:
 
-.. image:: ../../../share/validation/benzene/trajectory-BendAHarm-C.C.H-12_Ehc3.png
+.. image:: ../../_static/benzene/trajectory-BendAHarm-C.C.H-12_Ehc3.png
     :width: 400
-    :target: ../../../share/validation/benzene/trajectory-BendAHarm-C.C.H-12_Ehc3.png
+    :target: ../../_static/benzene/trajectory-BendAHarm-C.C.H-12_Ehc3.png
 
-.. image:: ../../../share/validation/benzene/trajectory-BendAHarm-C.C.H-13_Ehc3.png
+.. image:: ../../_static/benzene/trajectory-BendAHarm-C.C.H-13_Ehc3.png
     :width: 400
-    :target: ../../../share/validation/benzene/trajectory-BendAHarm-C.C.H-13_Ehc3.png
+    :target: ../../_static/benzene/trajectory-BendAHarm-C.C.H-13_Ehc3.png
 
-.. image:: ../../../share/validation/benzene/trajectory-BendAHarm-C.C.H-14_Ehc3.png
+.. image:: ../../_static/benzene/trajectory-BendAHarm-C.C.H-14_Ehc3.png
     :width: 400
-    :target: ../../../share/validation/benzene/trajectory-BendAHarm-C.C.H-14_Ehc3.png
+    :target: ../../_static/benzene/trajectory-BendAHarm-C.C.H-14_Ehc3.png
 
-.. image:: ../../../share/validation/benzene/trajectory-BendAHarm-C.C.H-15_Ehc3.png
+.. image:: ../../_static/benzene/trajectory-BendAHarm-C.C.H-15_Ehc3.png
     :width: 400
-    :target: ../../../share/validation/benzene/trajectory-BendAHarm-C.C.H-15_Ehc3.png
+    :target: ../../_static/benzene/trajectory-BendAHarm-C.C.H-15_Ehc3.png
 
-.. image:: ../../../share/validation/benzene/trajectory-BendAHarm-C.C.H-16_Ehc3.png
+.. image:: ../../_static/benzene/trajectory-BendAHarm-C.C.H-16_Ehc3.png
     :width: 400
-    :target: ../../../share/validation/benzene/trajectory-BendAHarm-C.C.H-16_Ehc3.png
+    :target: ../../_static/benzene/trajectory-BendAHarm-C.C.H-16_Ehc3.png
 
-.. image:: ../../../share/validation/benzene/trajectory-BendAHarm-C.C.H-17_Ehc3.png
+.. image:: ../../_static/benzene/trajectory-BendAHarm-C.C.H-17_Ehc3.png
     :width: 400
-    :target: ../../../share/validation/benzene/trajectory-BendAHarm-C.C.H-17_Ehc3.png
+    :target: ../../_static/benzene/trajectory-BendAHarm-C.C.H-17_Ehc3.png
 
 
 * **C-C-H-C out-of-plane distances**:
 
-.. image:: ../../../share/validation/benzene/trajectory-Oopdist-C.C.H.C-54_Ehc3.png
+.. image:: ../../_static/benzene/trajectory-Oopdist-C.C.H.C-54_Ehc3.png
     :width: 400
-    :target: ../../../share/validation/benzene/trajectory-Oopdist-C.C.H.C-54_Ehc3.png
+    :target: ../../_static/benzene/trajectory-Oopdist-C.C.H.C-54_Ehc3.png
 
-.. image:: ../../../share/validation/benzene/trajectory-Oopdist-C.C.H.C-55_Ehc3.png
+.. image:: ../../_static/benzene/trajectory-Oopdist-C.C.H.C-55_Ehc3.png
     :width: 400
-    :target: ../../../share/validation/benzene/trajectory-Oopdist-C.C.H.C-55_Ehc3.png
+    :target: ../../_static/benzene/trajectory-Oopdist-C.C.H.C-55_Ehc3.png
 
-.. image:: ../../../share/validation/benzene/trajectory-Oopdist-C.C.H.C-56_Ehc3.png
+.. image:: ../../_static/benzene/trajectory-Oopdist-C.C.H.C-56_Ehc3.png
     :width: 400
-    :target: ../../../share/validation/benzene/trajectory-Oopdist-C.C.H.C-56_Ehc3.png
+    :target: ../../_static/benzene/trajectory-Oopdist-C.C.H.C-56_Ehc3.png
 
-.. image:: ../../../share/validation/benzene/trajectory-Oopdist-C.C.H.C-57_Ehc3.png
+.. image:: ../../_static/benzene/trajectory-Oopdist-C.C.H.C-57_Ehc3.png
     :width: 400
-    :target: ../../../share/validation/benzene/trajectory-Oopdist-C.C.H.C-57_Ehc3.png
+    :target: ../../_static/benzene/trajectory-Oopdist-C.C.H.C-57_Ehc3.png
 
-.. image:: ../../../share/validation/benzene/trajectory-Oopdist-C.C.H.C-58_Ehc3.png
+.. image:: ../../_static/benzene/trajectory-Oopdist-C.C.H.C-58_Ehc3.png
     :width: 400
-    :target: ../../../share/validation/benzene/trajectory-Oopdist-C.C.H.C-58_Ehc3.png
+    :target: ../../_static/benzene/trajectory-Oopdist-C.C.H.C-58_Ehc3.png
 
-.. image:: ../../../share/validation/benzene/trajectory-Oopdist-C.C.H.C-59_Ehc3.png
+.. image:: ../../_static/benzene/trajectory-Oopdist-C.C.H.C-59_Ehc3.png
     :width: 400
-    :target: ../../../share/validation/benzene/trajectory-Oopdist-C.C.H.C-59_Ehc3.png
+    :target: ../../_static/benzene/trajectory-Oopdist-C.C.H.C-59_Ehc3.png
 
 
 Geometry and frequencies

quickff/perturbation.py

@@ -378,15 +378,15 @@ def estimate(self, trajectory, ai, ffrefs=[], do_valence=False, energy_noise=Non
             do_valence
                 If set to True, the current valence force field (stored in
                 self.valence) will be used to compute the valence contribution
-            
+
             energy_noise
-                If set to a float, the parabolic fitting will be repeated 
+                If set to a float, the parabolic fitting will be repeated
                 Nerrorsteps times including normal noise on top of the reference
-                value. The mean of the noise is 0, while the std equals the 
-                number given by energy_noise. The resulting fits give a 
-                distribution of force  constants and rest values instead of 
-                single value, the std is used to identify bad estimates, the 
-                mean is used for the actual FF parametrs. If set to nan, the 
+                value. The mean of the noise is 0, while the std equals the
+                number given by energy_noise. The resulting fits give a
+                distribution of force  constants and rest values instead of
+                single value, the std is used to identify bad estimates, the
+                mean is used for the actual FF parametrs. If set to nan, the
                 parabolic fit is performed only once without any noise.
         '''
         with log.section('PTEST', 3, timer='PT Estimate'):

quickff/tools.py

@@ -398,11 +398,11 @@ def get_ei_radii(numbers):
         'Li': 1.2951*angstrom, 'B' : 1.2020*angstrom, 'C' : 1.1703*angstrom,
         'N' : 1.1048*angstrom, 'O' : 1.1325*angstrom, 'F' : 1.1096*angstrom,
         'Na': 1.7093*angstrom, 'Mg': 1.6155*angstrom, 'Al': 1.6742*angstrom,
-        'Si': 1.6376*angstrom, 'P' : 1.5727*angstrom, 'S' : 1.6011*angstrom, 
-        'Cl': 1.5798*angstrom, 'Ca': 1.6541*angstrom, 'Sc': 2.0559*angstrom, 
-        'Ti': 2.0502*angstrom, 'V' : 2.0654*angstrom, 'Cr': 2.0692*angstrom, 
-        'Mn': 2.0323*angstrom, 'Fe': 2.0695*angstrom, 'Co': 2.0377*angstrom, 
-        'Ni': 2.0579*angstrom, 'Cu': 2.0573*angstrom, 'Zn': 1.9896*angstrom, 
+        'Si': 1.6376*angstrom, 'P' : 1.5727*angstrom, 'S' : 1.6011*angstrom,
+        'Cl': 1.5798*angstrom, 'Ca': 1.6541*angstrom, 'Sc': 2.0559*angstrom,
+        'Ti': 2.0502*angstrom, 'V' : 2.0654*angstrom, 'Cr': 2.0692*angstrom,
+        'Mn': 2.0323*angstrom, 'Fe': 2.0695*angstrom, 'Co': 2.0377*angstrom,
+        'Ni': 2.0579*angstrom, 'Cu': 2.0573*angstrom, 'Zn': 1.9896*angstrom,
         'Ga': 2.0820*angstrom, 'Br': 2.0088*angstrom,
     }