Fixed many many many bugs due to the protage of nmoldyn to MDANSE.

Reduced the size of PDB example file.
Added the generated functional tests for all MDANSE analysis.
Bug fix in spatial density cython file

Data/Trajectories/Generic/test.gtf

+MOLECULAR_CONTENTS
+2
+
+ETHYNE
+C1 C
+C2 C
+H2 H
+H2 H
+
+WATER
+O1 O
+H1 H
+H2 H
+
+MOLECULES
+ETHYNE 1
+WATER 2
+
+NFRAMES
+4
+
+FRAMETIME
+1.5
+
+BOX_COORDINATES
+False
+
+CELL
+10,0,0
+0,10,0
+0,0,10
+
+10,0,0
+0,10,0
+0,0,10
+
+10,0,0
+0,10,0
+0,0,10
+
+10,0,0
+0,10,0
+0,0,10
+
+CONFIGURATION
+0,0,0
+0,0,1
+0,1,0
+0,1,1
+1,0,0
+1,0,1
+1,1,0
+1,1,1
+2,2,2
+3,3,3
+
+0,0,0
+0,0,1
+0,1,0
+0,1,1
+1,0,0
+1,0,1
+1,1,0
+1,1,1
+2,2,2
+3,3,3
+
+0,0,0
+0,0,1
+0,1,0
+0,1,1
+1,0,0
+1,0,1
+1,1,0
+1,1,1
+2,2,2
+3,3,3
+
+0,0,0
+0,0,1
+0,1,0
+0,1,1
+1,0,0
+1,0,1
+1,1,0
+1,1,1
+2,2,2
+3,3,3
+
+

Extensions/sd_fast_calc.pyx

@@ -35,10 +35,9 @@ def spatial_density(ndarray[np.float64_t, ndim=2]  config not None,
 
     cdef double x, y, z, sdx, sdy, sdz, minix, miniy, miniz
     cdef double xorigin, yorigin, zorigin, orthx, orthy, orthz
-    cdef double aa, bb, cc, dd, ee, ff, gg, hh, ii,  denum, micx, micy, micz, xscaledOrigin, yscaledOrigin, zscaledOrigin
+    cdef double aa, bb, cc, dd, ee, ff, gg, hh, ii,  denum, micx, micy, micz, xscaledOrigin, yscaledOrigin, zscaledOrigin, xscaledMin, yscaledMin, zscaledMin
     cdef int i, j,k, bin, nbins, nbases, nindexes, xind, yind, zind
     
-    
     nbases = bases.shape[0]
     nindexes = indexes.shape[0]
         
@@ -49,7 +48,7 @@ def spatial_density(ndarray[np.float64_t, ndim=2]  config not None,
     cdef ndarray[np.float64_t, ndim=2] invBasis = np.zeros((3,3), dtype = np.float64)
     cdef ndarray[np.float64_t, ndim=2] basis = np.zeros((3,3), dtype = np.float64)
     cdef ndarray[np.float64_t, ndim=2] scaleconfig = np.zeros((nindexes,3), dtype = np.float64)
-    
+        
     for 0 <= i < nindexes:
 
         x = <float> config[i,0]
@@ -72,33 +71,36 @@ def spatial_density(ndarray[np.float64_t, ndim=2]  config not None,
         
         basis = bases[i,:,:]
 
-        aa = <float>basis[0,0]
-        bb = <float>basis[0,1]
-        cc = <float>basis[0,2]
-        
-        dd = <float>basis[1,0]
-        ee = <float>basis[1,1]
-        ff = <float>basis[1,2]
-        
-        gg = <float>basis[2,0]
-        hh = <float>basis[2,1]
-        ii = <float>basis[2,2]
-        
-        denum = -cc*ee*gg+bb*ff*gg+cc*dd*hh-aa*ff*hh-bb*dd*ii+aa*ee*ii
-        
-        invBasis[0,0] = (-ff*hh+ee*ii)/denum
-        invBasis[0,1] = (cc*hh-bb*ii)/denum
-        invBasis[0,2] = (-cc*ee+bb*ff)/denum
-        
-        invBasis[1,0] = (ff*gg-dd*ii)/denum
-        invBasis[1,1] = (-cc*gg+aa*ii)/denum
-        invBasis[1,2] = (cc*dd-aa*ff)/denum
-        
-        invBasis[2,0] = (-ee*gg+dd*hh)/denum
-        invBasis[2,1] = (bb*gg-aa*hh)/denum
-        invBasis[2,2] = (-bb*dd+aa*ee)/denum
-        
-        
+        m00 = <float>basis[0,0]
+        m01 = <float>basis[0,1]
+        m02 = <float>basis[0,2]
+        
+        m10 = <float>basis[1,0]
+        m11 = <float>basis[1,1]
+        m12 = <float>basis[1,2]
+        
+        m20 = <float>basis[2,0]
+        m21 = <float>basis[2,1]
+        m22 = <float>basis[2,2]
+        
+        denum = -m02*m11*m20 + m01*m12*m20 + m02*m10*m21 - m00*m12*m21- m01*m10*m22 + m00*m11*m22
+        
+        invBasis[0,0] = (-m12*m21+m11*m22)/denum
+        invBasis[0,1] = ( m02*m21-m01*m22)/denum
+        invBasis[0,2] = (-m02*m11+m01*m12)/denum
+        
+        invBasis[1,0] = ( m12*m20-m10*m22)/denum
+        invBasis[1,1] = (-m02*m20+m00*m22)/denum
+        invBasis[1,2] = ( m02*m10-m00*m12)/denum
+        
+        invBasis[2,0] = (-m11*m20+m10*m21)/denum
+        invBasis[2,1] = ( m02*m20-m00*m21)/denum
+        invBasis[2,2] = (-m02*m10+m00*m11)/denum
+                
+        xscaledMin = <float> (invBasis[0,0]*minix + invBasis[0,1]*miniy + invBasis[0,2]*miniz) 
+        yscaledMin = <float> (invBasis[1,0]*minix + invBasis[1,1]*miniy + invBasis[1,2]*miniz)
+        zscaledMin = <float> (invBasis[2,0]*minix + invBasis[2,1]*miniy + invBasis[2,2]*miniz)
+                
         for 0 <= j < nindexes:
  
             sdx = scaleconfig[j,0] - xscaledOrigin
@@ -113,23 +115,18 @@ def spatial_density(ndarray[np.float64_t, ndim=2]  config not None,
             micy =  sdx*cell[1,0] + sdy*cell[1,1] + sdz*cell[1,2]
             micz =  sdx*cell[2,0] + sdy*cell[2,1] + sdz*cell[2,2]
             
-            orthx = <float> (invBasis[0,0]*micx + invBasis[0,1]*micy  + invBasis[0,2]*micz) 
-            orthy = <float> (invBasis[1,0]*micx + invBasis[1,1]*micy  + invBasis[1,2]*micz)
-            orthz = <float> (invBasis[2,0]*micx + invBasis[2,1]*micy  + invBasis[2,2]*micz)
+            orthx = <float> (invBasis[0,0]*micx + invBasis[0,1]*micy + invBasis[0,2]*micz) 
+            orthy = <float> (invBasis[1,0]*micx + invBasis[1,1]*micy + invBasis[1,2]*micz)
+            orthz = <float> (invBasis[2,0]*micx + invBasis[2,1]*micy + invBasis[2,2]*micz)
             
-            x = (orthx-minix)/resolution
-            y = (orthy-miniy)/resolution
-            z = (orthz-miniz)/resolution
+            x = (orthx-xscaledMin)/resolution
+            y = (orthy-yscaledMin)/resolution
+            z = (orthz-zscaledMin)/resolution
             
             xind = <int> x
             yind = <int> y
             zind = <int> z
-
+            
             hist[xind,yind,zind] += 1
 
-    return hist
-        
-        
-        
-        
-        
\ No newline at end of file
+    return hist
\ No newline at end of file

MDANSE/App/GUI/Framework/Plugins/Plotter/PlotterPlugin.py

@@ -27,7 +27,7 @@
 ''' 
 Created on Apr 10, 2015
 
-@author: Gael Goret, Eric C. Pellegrini
+@author: Gael Goret and Eric C. Pellegrini
 '''
 
 import collections
@@ -444,7 +444,7 @@ class PlotterFrame(wx.Frame):
             data = collections.OrderedDict()
             for k in _vars:
                 data[k]={}
-                if hasattr(vars[k], 'axis'):
+                if hasattr(_vars[k], 'axis'):
                     if _vars[k].axis:
                         data[k]['axis'] =  _vars[k].axis.split('|')
                     else:

MDANSE/Framework/Configurable.py

@@ -97,6 +97,17 @@ class Configurable(object):
         if isinstance(settings,dict):
             cls.settings.update(settings)        
     
+    @property
+    def configuration(self):
+        '''
+        Return the configuration bound to the Configurable object.
+        
+        :return: the configuration bound to the Configurable object.
+        :rtype: dict
+        '''
+        
+        return self._configuration
+    
     def setup(self,parameters):
         '''
         Setup the configuration according to a set of input parameters.

MDANSE/Framework/Configurators/InstrumentResolutionConfigurator.py

@@ -63,7 +63,7 @@ class InstrumentResolutionConfigurator(IConfigurator):
     
     type = "instrument_resolution"
         
-    _default = ('gaussian', {'mu': 0.0, 'sigma': 0.0001})
+    _default = ('gaussian', {'mu': 0.0, 'sigma': 10.0})
         
     def configure(self, configuration, value):
         '''
@@ -129,10 +129,10 @@ You should change your resolution function settings to make it sharper.''',self)
         if not self.has_key("kernel"):
             return "No configured yet"
         
-        info = ["Instrument resolution kernel:" % self["kernel"]]
+        info = ["Instrument resolution kernel: %s" % self["kernel"]]
         if self["parameters"]:
             info.append("Parameters:")
-            for k,v in self["parameters"]:
+            for k,v in self["parameters"].items():
                 info.append("%s = %s" % (k,v))
                 
         info = "\n".join(info)

MDANSE/Framework/Configurators/MMTKTrajectoryConfigurator.py

@@ -50,7 +50,7 @@ class MMTKNetCDFTrajectoryConfigurator(InputFileConfigurator):
     
     type = 'mmtk_trajectory'
     
-    _default = 'waterbox_in_periodic_universe.nc'
+    _default = os.path.join('..','..','..','Data','Trajectories','MMTK','waterbox_in_periodic_universe.nc')
                         
     def configure(self, configuration, value):
         '''

MDANSE/Framework/Configurators/PartialChargeConfigurator.py

+#MDANSE : Molecular Dynamics Analysis for Neutron Scattering Experiments
+#------------------------------------------------------------------------------------------
+#Copyright (C)
+#2015- Eric C. Pellegrini Institut Laue-Langevin
+#BP 156
+#6, rue Jules Horowitz
+#38042 Grenoble Cedex 9
+#France
+#pellegrini[at]ill.fr
+#goret[at]ill.fr
+#aoun[at]ill.fr
+#
+#This library is free software; you can redistribute it and/or
+#modify it under the terms of the GNU Lesser General Public
+#License as published by the Free Software Foundation; either
+#version 2.1 of the License, or (at your option) any later version.
+#
+#This library is distributed in the hope that it will be useful,
+#but WITHOUT ANY WARRANTY; without even the implied warranty of
+#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+#Lesser General Public License for more details.
+#
+#You should have received a copy of the GNU Lesser General Public
+#License along with this library; if not, write to the Free Software
+#Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+
+''' 
+Created on Jun 9, 2015
+
+@author: Eric C. Pellegrini
+'''
+
+import os
+
+from MDANSE.Framework.Configurators.IConfigurator import IConfigurator,ConfiguratorError
+from MDANSE.Framework.UserDefinitionsStore import UD_STORE
+
+class PartialChargeConfigurator(IConfigurator):
+    """
+    This configurator allows to input partial charges.
+    """
+    
+    type = 'partial_charges'
+    
+    _default = ''
+                   
+    def configure(self, configuration, value):
+        '''
+        Configure a python script. 
+                
+        :param configuration: the current configuration.
+        :type configuration: a MDANSE.Framework.Configurable.Configurable object
+        :param value: the path for the python script.
+        :type value: str 
+        '''
+
+        trajConfig = configuration[self._dependencies['trajectory']]
+        
+        if UD_STORE.has_definition(trajConfig["basename"],'partial_charges',value):
+            self['charges'] = UD_STORE[trajConfig["basename"],'partial_charges',value]
+        else:
+            if isinstance(value,basestring):                
+                # Case of a python script
+                if os.path.exists(value):
+                    namespace = {}
+                    
+                    execfile(value,self.__dict__,namespace)
+                            
+                    if not namespace.has_key('charges'):
+                        raise ConfiguratorError("The variable 'charges' is not defined in the %r python script file" % (self["value"],))
+                        
+                    self.update(namespace)
+                else:
+                    raise ConfiguratorError("The python script defining partial charges %s could not be found." % value)
+                    
+            elif isinstance(value,dict):
+                self['charges'] = value
+            else:
+                raise ConfiguratorError("Invalid type for partial charges.")
+                
+            
+    def get_information(self):
+        '''
+        Returns some basic informations about the partial charges.
+        
+        :return: the informations about the partial charges.
+        :rtype: str
+        '''
+        
+        info = 'Sum of partial charges = %8.3f' % sum(self['charges'].values())
+        
+        return info

MDANSE/Framework/Configurators/PythonScriptConfigurator.py

@@ -30,8 +30,6 @@ Created on Jun 9, 2015
 @author: Eric C. Pellegrini
 '''
 
-from Scientific.IO.NetCDF import NetCDFFile
-
 from MDANSE.Framework.Configurators.IConfigurator import ConfiguratorError
 from MDANSE.Framework.Configurators.InputFileConfigurator import InputFileConfigurator
 

MDANSE/Framework/Configurators/QVectorsConfigurator.py

@@ -78,22 +78,22 @@ class QVectorsConfigurator(IConfigurator):
             generator, parameters = value
             generator = REGISTRY["q_vectors"][generator](trajConfig["instance"])
             generator.setup(parameters)
-            data = generator.generate()
+            generator.generate()
                         
-            if not data:
+            if not generator.configuration['q_vectors']:
                 raise ConfiguratorError("no Q vectors could be generated", self)
+
+            self["parameters"] = parameters
+            self["type"] = generator.type
+            self["is_lattice"] = generator.is_lattice
+            self["q_vectors"] = generator.configuration['q_vectors']
         
         else:                        
             self["parameters"] = ud['parameters']
             self["type"] = ud['generator']
             self["is_lattice"] = ud['is_lattice']
             self["q_vectors"] = ud['q_vectors']
-
-            self["parameters"] = parameters
-            self["type"] = generator.type
-            self["is_lattice"] = generator.is_lattice
-            self["q_vectors"] = data
-                                                
+                                
         self["shells"] = self["q_vectors"].keys()
         self["n_shells"] = len(self["q_vectors"])    
         self["value"] = self["q_vectors"]

MDANSE/Framework/Configurators/RangeConfigurator.py

@@ -201,7 +201,7 @@ class RangeConfigurator(IConfigurator):
         :rtype: str
         '''
         
-        info = "$d values from %s to %s" % (self['number'],self['first'],self['last'])
+        info = "%d values from %s to %s" % (self['number'],self['first'],self['last'])
         
         if self._includeLast:
             info += ("last value included")

MDANSE/Framework/InstrumentResolutions/GaussianResolution.py

@@ -42,9 +42,9 @@ class GaussianInstrumentResolution(IInstrumentResolution):
     
     type = 'gaussian'
 
-    configurators = collections.OrderedDict()
-    configurators['mu'] = ('float', {"default":0.0})
-    configurators['sigma'] = ('float', {"default":1.0})
+    settings = collections.OrderedDict()
+    settings['mu'] = ('float', {"default":0.0})
+    settings['sigma'] = ('float', {"default":1.0})
 
     def set_kernel(self, frequencies, dt):
 

MDANSE/Framework/InstrumentResolutions/IdealResolution.py

@@ -42,7 +42,7 @@ class IdealInstrumentResolution(IInstrumentResolution):
     
     type = 'ideal'
     
-    configurators = collections.OrderedDict()
+    settings = collections.OrderedDict()
 
     def set_kernel(self, frequencies, dt):
                 

MDANSE/Framework/InstrumentResolutions/LorentzianResolution.py

@@ -43,9 +43,9 @@ class LorentzianInstrumentResolution(IInstrumentResolution):
     
     type = 'lorentzian'
 
-    configurators = collections.OrderedDict()
-    configurators['mu'] = ('float', {"default":0.0})
-    configurators['sigma'] = ('float', {"default":1.0})
+    settings = collections.OrderedDict()
+    settings['mu'] = ('float', {"default":0.0})
+    settings['sigma'] = ('float', {"default":1.0})
 
     def set_kernel(self, frequencies, dt):
 

MDANSE/Framework/InstrumentResolutions/PseudoVoigtResolution.py

@@ -42,12 +42,12 @@ class PseudoVoigtInstrumentResolution(IInstrumentResolution):
 
     type = 'pseudo-voigt'
 
-    configurators = collections.OrderedDict()
-    configurators['eta'] = ('float', {"mini":0.0, "maxi":1.0, "default":0.5})
-    configurators['mu_lorentzian'] = ('float', {"default":0.0})
-    configurators['sigma_lorentzian'] = ('float', {"default":1.0})
-    configurators['mu_gaussian'] = ('float', {"default":0.0})
-    configurators['sigma_gaussian'] = ('float', {"default":1.0})
+    settings = collections.OrderedDict()
+    settings['eta'] = ('float', {"mini":0.0, "maxi":1.0, "default":0.5})
+    settings['mu_lorentzian'] = ('float', {"default":0.0})
+    settings['sigma_lorentzian'] = ('float', {"default":1.0})
+    settings['mu_gaussian'] = ('float', {"default":0.0})
+    settings['sigma_gaussian'] = ('float', {"default":1.0})
 
     def set_kernel(self, frequencies, dt):
 

MDANSE/Framework/InstrumentResolutions/SquareResolution.py

@@ -42,9 +42,9 @@ class SquareInstrumentResolution(IInstrumentResolution):
     
     type = 'square'
 
-    configurators = collections.OrderedDict()
-    configurators['mu'] = ('float', {"default":0.0})
-    configurators['sigma'] = ('float', {"default":1.0})
+    settings = collections.OrderedDict()
+    settings['mu'] = ('float', {"default":0.0})
+    settings['sigma'] = ('float', {"default":1.0})
 
     def set_kernel(self, frequencies, dt):
                                 

MDANSE/Framework/InstrumentResolutions/TriangularResolution.py

@@ -42,9 +42,9 @@ class TriangularInstrumentResolution(IInstrumentResolution):
     
     type = 'triangular'
 
-    configurators = collections.OrderedDict()
-    configurators['mu'] = ('float', {"default":0.0})
-    configurators['sigma'] = ('float', {"default":1.0})
+    settings = collections.OrderedDict()
+    settings['mu'] = ('float', {"default":0.0})
+    settings['sigma'] = ('float', {"default":1.0})
 
     def set_kernel(self, frequencies, dt):
 

MDANSE/Framework/Jobs/AngularCorrelation.py

@@ -27,7 +27,7 @@
 ''' 
 Created on Apr 10, 2015
 
-@author: pellegrini
+@author: Eric C. Pellegrini
 '''
 
 import collections
@@ -72,7 +72,8 @@ class AngularCorrelation(IJob):
     settings = collections.OrderedDict()    
     settings['trajectory'] = ('mmtk_trajectory',{})
     settings['frames'] = ('frames', {"dependencies":{'trajectory':'trajectory'}})
-    settings['axis_selection'] = ('axis_selection',{"dependencies":{'trajectory':'trajectory'}})
+    settings['axis_selection'] = ('axis_selection',{"dependencies":{'trajectory':'trajectory'},
+                                                    'default' : {'molecule':'Water', 'endpoint1':('OW',), 'endpoint2':('HW',)}})
     settings['per_axis'] = ('boolean', {"label":"output contribution per axis", "default":False})
     settings['output_files'] = ('output_files', {"formats":["netcdf","ascii"]})
     settings['running_mode'] = ('running_mode',{})
@@ -124,7 +125,7 @@ class AngularCorrelation(IJob):
                                 
         diff /= modulus[:,numpy.newaxis]
 
-        ac = correlation(diff,axis=0,reduce=1)
+        ac = correlation(diff,axis=0,average=1)
                         
         return index, ac
 

MDANSE/Framework/Jobs/AreaPerMolecule.py

@@ -27,10 +27,11 @@
 ''' 
 Created on Apr 10, 2015
 
-@author: pellegrini
+@author: Bachir Aoun and Eric C. Pellegrini
 '''
 
 import collections
+import os
 
 import numpy
 
@@ -58,13 +59,10 @@ class AreaPerMolecule(IJob):
     ancestor = "mmtk_trajectory"
 
     settings = collections.OrderedDict()
-    settings['trajectory'] = ('mmtk_trajectory',{})
+    settings['trajectory'] = ('mmtk_trajectory',{'default':os.path.join('..','..','..','Data','Trajectories','MMTK','dmpc_in_periodic_universe.nc')})
     settings['frames'] = ('frames', {"dependencies":{'trajectory':'trajectory'}})
-    settings['axis'] = ('multiple_choices', {'label':'area vectors',
-                                                  'choices':['a','b','c'],
-                                                  'nChoices':2,
-                                                  'default':['a','b']})
-    settings['name'] = ('string', {'label':'molecule name'})    
+    settings['axis'] = ('multiple_choices', {'label':'area vectors','choices':['a','b','c'],'nChoices':2,'default':['a','b']})
+    settings['name'] = ('string', {'label':'molecule name','default':'DMPC'})    
     settings['output_files'] = ('output_files', {'formats':["netcdf","ascii"]})
     settings['running_mode'] = ('running_mode',{})
     

MDANSE/Framework/Jobs/Converters/CHARMM.py

@@ -27,7 +27,7 @@
 ''' 
 Created on Apr 10, 2015
 
-@author: pellegrini
+@author: Eric C. Pellegrini
 '''
 
 from MDANSE.Framework.Jobs.Converters.DCDConverter import DCDConverter

MDANSE/Framework/Jobs/Converters/Castep.py

@@ -31,6 +31,7 @@ Created on Apr 10, 2015
 '''
 
 import collections
+import os
 import itertools
 import re
 
@@ -145,7 +146,7 @@ class CASTEPConverter(Converter):
     ancestor = None
 
     settings = collections.OrderedDict()
-    settings['castep_file'] = ('input_file', {})
+    settings['castep_file'] = ('input_file', {'default':os.path.join('..','..','..','Data','Trajectories','CASTEP','PBAnew.md')})
     settings['output_file'] = ('output_files', {'formats':["netcdf"]})
                 
     def initialize(self):

MDANSE/Framework/Jobs/Converters/DCDConverter.py

@@ -31,6 +31,7 @@ Created on Apr 10, 2015