Changeset 1646 for trunk/GSASIImath.py

Timestamp:

Feb 11, 2015 1:33:27 PM (8 years ago)

Author:

vondreele

Message:

allow search for negative density peaks in charge flip and Fourier maps
plot negative density in neutron maps & negative peaks in red

File:

• trunk/GSASIImath.py (modified) (3 diffs)

trunk/GSASIImath.py

@@ -2080 +2080 @@
     return mapData,map4DData
     
-def SearchMap(generalData,drawingData):
+def SearchMap(generalData,drawingData,Neg=False):
     '''Does a search of a density map for peaks meeting the criterion of peak
     height is greater than mapData['cutOff']/100 of mapData['rhoMax'] where 
     mapData is data['General']['mapData']; the map is also in mapData.
 
-    :param data: the phase data structure
+    :param generalData: the phase data structure; includes the map
+    :param drawingData: the drawing data structure
+    :param Neg:  if True then search for negative peaks (i.e. H-atoms & neutron data)
 
     :returns: (peaks,mags,dzeros) where
@@ -2158 +2160 @@
         mapData = generalData['Map']
         contLevel = mapData['cutOff']*mapData['rhoMax']/100.
-        rho = copy.copy(mapData['rho'])     #don't mess up original
+        if Neg:
+            rho = -copy.copy(mapData['rho'])     #flip +/-
+        else:
+            rho = copy.copy(mapData['rho'])     #don't mess up original
         mapHalf = np.array(rho.shape)/2
         res = mapData['Resolution']
@@ -2193 +2198 @@
         rho = rollMap(rho,-ind)        
     dzeros = np.sqrt(np.sum(np.inner(Amat,peaks)**2,axis=0))
-    return np.array(peaks),np.array([mags,]).T,np.array([dzeros,]).T
+    if Neg:     #want negative magnitudes for negative peaks
+        return np.array(peaks),-np.array([mags,]).T,np.array([dzeros,]).T
+    else:
+        return np.array(peaks),np.array([mags,]).T,np.array([dzeros,]).T
     
 def sortArray(data,pos,reverse=False):