Bug fix related to change of variable name for all analysis

Improved the generic converter
Reintroduced and refactored rigid-body trajectory analysis
Implemented the dipole autocorrelation function analysis

MDANSE/Framework/Configurators/PythonScriptConfigurator.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
+'''
+
+from Scientific.IO.NetCDF import NetCDFFile
+
+from MDANSE.Framework.Configurators.IConfigurator import ConfiguratorError
+from MDANSE.Framework.Configurators.InputFileConfigurator import InputFileConfigurator
+
+class PythonScriptConfigurator(InputFileConfigurator):
+    """
+    This configurator allows to input a Python script.
+    """
+    
+    type = 'python_script'
+    
+    _default = ''
+        
+    def __init__(self, name, variables=None, **kwargs):
+        '''
+        Initializes the configurator.
+        
+        :param name: the name of the configurator as it will appear in the configuration.
+        :type name: str
+        :param variables: the list of NetCDF variables that must be present in the input NetCDF file or None if there is no compulsory variable.
+        :type variables: list of str or None
+        '''        
+
+        # The base class constructor.
+        InputFileConfigurator.__init__(self, name, **kwargs)
+        
+        self._variables = variables if variables is not None else []
+           
+    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 
+        '''
+                
+        InputFileConfigurator.configure(self, configuration, value)
+        
+        namespace = {}
+        
+        execfile(value,self.__dict__,namespace)
+                
+        for v in self._variables:
+            if not namespace.has_key(v):
+                raise ConfiguratorError("The variable %r is not defined in the %r python script file" % (v,self["value"]))
+            
+        self.update(namespace)
+        
+    @property
+    def variables(self):
+        '''
+        Returns the list of NetCDF variables that must be present in the NetCDF file.
+        
+        :return: the list of NetCDF variables that must be present in the NetCDF file.
+        :rtype: list of str
+        '''
+        
+        return self._variables
+
+    def get_information(self):
+        '''
+        Returns some basic informations about the contents of the MMTK trajectory file.
+        
+        :return: the informations about the contents of the MMTK trajectory file.
+        :rtype: str
+        '''
+        
+        info = ["NetCDF input file: %r" % self["value"]]
+        
+        if self.has_key('instance'):
+            info.append("Contains the following variables:")
+            for v in self['instance'].variables:
+                info.append(v)
+            
+        return "\n".join(info)
\ No newline at end of file

MDANSE/Framework/Jobs/AngularCorrelation.py

@@ -148,6 +148,6 @@ class AngularCorrelation(IJob):
              
         self._outputData['ac'] /= self.configuration['axis_selection']['n_axis']
                 
-        self._outputData.write(self.configuration['output_files']['root'], self.configuration['output_files']['formats'], self.header)
+        self._outputData.write(self.configuration['output_files']['root'], self.configuration['output_files']['formats'], self._info)
         
         self.configuration['trajectory']['instance'].close()  
\ No newline at end of file

MDANSE/Framework/Jobs/AreaPerMolecule.py

@@ -125,5 +125,5 @@ class AreaPerMolecule(IJob):
         Finalize the analysis (close trajectory, write output data ...)
         """
         
-        self._outputData.write(self.configuration['output_files']['root'], self.configuration['output_files']['formats'], self.header)
+        self._outputData.write(self.configuration['output_files']['root'], self.configuration['output_files']['formats'], self._info)
         self.configuration['trajectory']['instance'].close()     
\ No newline at end of file

MDANSE/Framework/Jobs/Converters/Generic.py

@@ -48,6 +48,116 @@ class GenericConverterError(Error):
                                                   
 class GenericConverter(Converter):
     """
+    Converts a trajectory written in ASCII to a MMTK trajectory file.
+    
+    This converter can be useful when using MD packages that are currently not supported by MDANSE. 
+    
+    Here is an example of ASCII trajectory that can be converted using this converter to a MMTk trajectory.
+    
+    MOLECULAR_CONTENTS
+    2
+    
+    ETHYNE
+    C1 C
+    C2 C
+    H2 H
+    H2 H
+    
+    WATER
+    O1 O
+    H1 H
+    H2 H
+    
+    MOLECULES
+    ETHYNE 1
+    WATER 2
+    
+    NSTEPS
+    4
+    
+    TIMESTEP
+    10
+    
+    STEP
+    10
+    
+    CELL
+    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
+    
+    STEP
+    20
+    
+    CELL
+    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
+    
+    STEP
+    30
+    
+    CELL
+    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
+    
+    STEP
+    40
+    
+    CELL
+    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
+
     """
 
     type = 'generic'
@@ -115,53 +225,69 @@ class GenericConverter(Converter):
             line=self._gtFile.readline().strip()
                                  
         # Read the number of steps
-        if self._gtFile.readline().strip() != "NSTEPS":
-            raise GenericConverterError("Invalid keyword#4: must be 'NSTEPS'")         
+        if self._gtFile.readline().strip() != "NFRAMES":
+            raise GenericConverterError("Invalid keyword#3: must be 'NFRAMES'")         
         try:
             self.numberOfSteps=int(self._gtFile.readline())
         except ValueError:
-            raise GenericConverterError("Invalid type for 'NSTEPS' keyword. Must be an integer corresponding to the number of steps of the simulation.")
+            raise GenericConverterError("Invalid type for 'NFRAMES' keyword. Must be an integer corresponding to the number of frames of the simulation.")
 
         # Read a blank line
         self._gtFile.readline()
 
-        # Read the number of steps
-        if self._gtFile.readline().strip() != "TIMESTEP":
-            raise GenericConverterError("Invalid keyword#5: must be 'TIMESTEP'")
-         
-        # Read the time step        
+        # Read the time step
+        if self._gtFile.readline().strip() != "FRAMETIME":
+            raise GenericConverterError("Invalid keyword#4: must be 'FRAMETIME'")
         try:
             self._timeStep=float(self._gtFile.readline())
         except ValueError:
-            raise GenericConverterError("Invalid type for 'TIMESTEP' keyword. Must be a float corresponding to the actual timestep of the simulation.")
+            raise GenericConverterError("Invalid type for 'FRAMETIME' keyword. Must be a float corresponding to the time between two frames of the simulation.")
 
         # Read a blank line
         self._gtFile.readline()
 
-        self._headerBlockSize=self._gtFile.tell()
-        
-        # Read the first frame to define the size of various data block
-
-        # Read the current step number
-        if self._gtFile.readline().strip() != "STEP":
-            raise GenericConverterError("Invalid frame block. Must start with 'STEP' keyword.")
+        # Read the box coordinates
+        if self._gtFile.readline().strip() != "BOX_COORDINATES":
+            raise GenericConverterError("Invalid keyword#5: must be 'BOX_COORDINATES'")
         try:
-            _=int(self._gtFile.readline())
+            self._box=bool(self._gtFile.readline())
         except ValueError:
-            raise GenericConverterError("Invalid type for 'STEP' keyword. Must be a in corresponding to the current step number of the simulation.")
-                    
+            raise GenericConverterError("Invalid type for 'BOX_COORDINATES' keyword. Must be a boolean indicating whether or not the coordinates are in box.")
+        
         # Read a blank line
         self._gtFile.readline()
 
-        self._pbc = (self._gtFile.readline().strip() == "CELL")
-                        
-        if self._pbc:
+        self._headerBlockSize=self._gtFile.tell()
+        
+        # Read the beginning of the first frame to define the size of various data block
+        
+        self._pbc = []
+        if self._gtFile.readline().strip() == "CELL":
+            
+            for _ in range(self.numberOfSteps):
+                cell = numpy.array([self._gtFile.readline().strip().split(",") for _ in range(3)],dtype=numpy.float64)
+                if cell.shape != (3,3):
+                    raise GenericConverterError('Invalid cell shape. Must be a 3x3 matrix.')
+                self._pbc.append(cell)
+                    
+                # Read a blank line
+                self._gtFile.readline()
+                
+                pos = self._gtFile.tell()
+                            
+                if self._gtFile.readline().strip == "CONFIGURATION":
+                    break
+                else:
+                    self._gtFile.seek(pos,0)
+                    
+        if self._pbc:                         
             self._universe = ParallelepipedicPeriodicUniverse()
-            pos = self._gtFile.tell()
-            self._gtFile.readline()
-            self._gtFile.readline()
-            self._gtFile.readline()
-            self._cellBlockSize=self._gtFile.tell()-pos
+            # Case of NVT simulation
+            if len(self._pbc)==1:
+                self._universe.setShape(self._pbc.pop(0))
+            else:
+                if len(self._pbc) != self.numberOfSteps:
+                    raise GenericConverterError('Invalid number of cell definitions. Must be equal to the number of frames for a NPT simulation.')      
         else:
             self._universe = InfiniteUniverse()
 
@@ -176,51 +302,44 @@ class GenericConverter(Converter):
                     self._universe.addObject(temp[0])
                 else:
                     self._universe.addObject(AtomCluster(temp,name=molName))
-                    
-        # Read a blank line
-        self._gtFile.readline()
-        
+                            
         # Read the current configuration
         if self._gtFile.readline().strip() != "CONFIGURATION":
             raise GenericConverterError("Invalid frame block. Must contain 'CONFIGURATION' keyword.")
-        
+
         pos = self._gtFile.tell()
         
-        for _ in range(self._universe.numberOfAtoms()):
-            line=self._gtFile.readline()
-        self._dataBlockSize=self._gtFile.tell()-pos
+        line=self._gtFile.readline()
         line=line.split(',')
         n=len(line)
-        if n==3:
-            self._hasVelocities=False
-            self._hasForces=False
-        elif n==6:
+        self._hasVelocities=False
+        self._hasForces=False
+        if n==6:
             self._hasVelocities=True
             self._hasForces=False
         elif n==9:
             self._hasVelocities=True
             self._hasForces=True          
-        else:
-            raise GenericConverterError("Invalid configuration line. Must contain3, 6 0r 9 comma-separated fixed-formatted floats.")
         
-        # Read a blank line
-        self._gtFile.readline()
+        self._gtFile.seek(pos,0)
         
-        if (self._hasVelocities or self._hasForces):
+        if self._hasVelocities:
             self._universe.initializeVelocitiesToTemperature(0.0)
             self._velocities = ParticleVector(self._universe)
-        
-        if self._hasForces:
-            self._forces = ParticleVector(self._universe)
+            if self._hasForces:        
+                self._forces = ParticleVector(self._universe)
+                self._dataShape=(self._universe.numberOfAtoms(),9)
+            else:
+                self._dataShape=(self._universe.numberOfAtoms(),6)
+        else:
+            self._dataShape=(self._universe.numberOfAtoms(),3)
                                     
         # A MMTK trajectory is opened for writing.
         self._trajectory = Trajectory(self._universe, self.configuration['output_file']['files'][0], mode='w')
  
         # A frame generator is created.
         self._snapshot = SnapshotGenerator(self._universe, actions = [TrajectoryOutput(self._trajectory, ["all"], 0, None, 1)])
-        
-        self._frameBlockSize = self._gtFile.tell() - self._headerBlockSize
-    
+            
     def run_step(self, index):
         """Runs a single step of the job.
         
@@ -229,39 +348,27 @@ class GenericConverter(Converter):
 
         @note: the argument index is the index of the loop note the index of the frame.      
         """
-        
-        self._gtFile.seek(self._headerBlockSize+index*self._frameBlockSize)
-        
-        # Read a blank line
-        self._gtFile.readline()
-        try:
-            step=int(self._gtFile.readline())
-        except ValueError:
-            raise GenericConverterError('Invalid step number value.')
+                        
+        if self._pbc:                    
+            self._universe.setShape(self._pbc[index])
+                        
+        config = numpy.array([self._gtFile.readline().split(",") for _ in range(self._universe.numberOfAtoms())],dtype=numpy.float64)
+        if config.shape != self._dataShape:
+            raise GenericConverterError('Invalid data shape. Must be a %s matrix.' % (self._dataShape,))
 
-        if self._pbc:        
-            # Read two junk lines
-            self._gtFile.readline()
-            self._gtFile.readline()
-            
-            cell = numpy.array([v.split(",") for v in self._gtFile.read(self._cellBlockSize).splitlines()],dtype=numpy.float64)
-            
-            if cell.shape != (3,3):
-                raise GenericConverterError('Invalid cell data.')
-            
-            self._universe.setShape(cell)
-            
-        # Read two junk lines
+        # Read a junk line
         self._gtFile.readline()
-        self._gtFile.readline()
-            
-        config = numpy.array([v.split(",") for v in self._gtFile.read(self._dataBlockSize).splitlines()],dtype=numpy.float64)
         
-        self._universe.setConfiguration(Configuration(self._universe, config[:,0:3]))
         
-        self._universe.foldCoordinatesIntoBox()
+        conf = Configuration(self._universe, config[:,0:3])
+        if self._box:
+            conf.convertFromBoxCoordinates()
+        
+        self._universe.setConfiguration(conf)
         
-        data = {"time" : step*self._timeStep}
+        self._universe.foldCoordinatesIntoBox()
+                
+        data = {"time" : index*self._timeStep}
         
         if self._hasVelocities:
             self._velocities.array = config[:,3:6]

MDANSE/Framework/Jobs/CoordinationNumber.py

@@ -129,7 +129,7 @@ class CoordinationNumber(DistanceHistogram):
             self._outputData["cn_inter_%s%s" % invPair][:] = self.averageDensity*cAlpha*cnInter        
             self._outputData["cn_total_%s%s" % invPair][:] = self.averageDensity*cAlpha*cnTotal 
 
-        self._outputData.write(self.configuration['output_files']['root'], self.configuration['output_files']['formats'], self.header)
+        self._outputData.write(self.configuration['output_files']['root'], self.configuration['output_files']['formats'], self._info)
         
         self.configuration['trajectory']['instance'].close()     
   

MDANSE/Framework/Jobs/CurrentCorrelationFunction.py

@@ -235,6 +235,6 @@ class CurrentCorrelationFunction(IJob):
         sqfTransTotal = weight(props,self._outputData,self.configuration['atom_selection']['n_atoms_per_element'],2,"J(q,f)_trans_%s%s")
         self._outputData["J(q,f)_trans_total"][:] = sqfTransTotal
     
-        self._outputData.write(self.configuration['output_files']['root'], self.configuration['output_files']['formats'], self.header)
+        self._outputData.write(self.configuration['output_files']['root'], self.configuration['output_files']['formats'], self._info)
         
         self.configuration['trajectory']['instance'].close()
\ No newline at end of file

MDANSE/Framework/Jobs/Density.py

@@ -112,6 +112,6 @@ class Density(IJob):
         Finalize the job.
         """        
 
-        self._outputData.write(self.configuration['output_files']['root'], self.configuration['output_files']['formats'], self.header)
+        self._outputData.write(self.configuration['output_files']['root'], self.configuration['output_files']['formats'], self._info)
         
         self.configuration['trajectory']['instance'].close()                                         
\ No newline at end of file

MDANSE/Framework/Jobs/DensityOfStates.py

@@ -166,6 +166,6 @@ class DensityOfStates(IJob):
                           "dos_%s")
         self._outputData["dos_total"][:] = dosTotal        
         
-        self._outputData.write(self.configuration['output_files']['root'], self.configuration['output_files']['formats'], self.header)
+        self._outputData.write(self.configuration['output_files']['root'], self.configuration['output_files']['formats'], self._info)
         
         self.configuration['trajectory']['instance'].close()     

MDANSE/Framework/Jobs/DensityProfile.py

@@ -160,6 +160,6 @@ class DensityProfile(IJob):
         rValues = self._extent*numpy.linspace(0,1,self._nBins+1)
         self._outputData["r"][:] = (rValues[1:]+rValues[:-1])/2
 
-        self._outputData.write(self.configuration['output_files']['root'], self.configuration['output_files']['formats'], self.header)
+        self._outputData.write(self.configuration['output_files']['root'], self.configuration['output_files']['formats'], self._info)
          
         self.configuration['trajectory']['instance'].close()
\ No newline at end of file

MDANSE/Framework/Jobs/DipoleAutoCorrelationFunction.py

+#MDANSE : Molecular Dynamics Analysis for Neutron Scattering Experiments
+#------------------------------------------------------------------------------------------
+#Copyright (C)
+#2015- Eric C. Pellegrini Institut Laue-Langevin
+#BP 156
+#71 avenue des Martyrs
+#38000 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: Bachir Aoun and Eric C. Pellegrini
+'''
+
+import collections
+
+import numpy
+
+from MDANSE.Framework.Jobs.IJob import IJob, JobError
+from MDANSE.Mathematics.Signal import correlation
+
+class DipoleAutoCorrelationFunction(IJob):
+    """
+    """
+    
+    type = 'dacf'
+
+    label = "Dipole AutoCorrelation Function"
+    
+    category = ('Infrared',)
+    
+    ancestor = "mmtk_trajectory"
+    
+    settings = collections.OrderedDict()
+    settings['trajectory'] = ('mmtk_trajectory',{})
+    settings['frames'] = ('frames', {'dependencies':{'trajectory':'trajectory'}})
+    settings['atom_selection'] = ('atom_selection',{'dependencies':{'trajectory':'trajectory'}})
+    settings['atom_charges'] = ('python_script',{'variables':['charges']})
+    settings['output_files'] = ('output_files', {'formats':["netcdf","ascii"]})
+    settings['running_mode'] = ('running_mode',{})
+    
+    def initialize(self):
+        """
+        Initialize the input parameters and analysis self variables
+        """
+
+        self.numberOfSteps = self.configuration['frames']['number']
+                        
+        # Will store the time.
+        self._outputData.add("time","line", self.configuration['frames']['time'], units='ps')
+        
+        self._dipoleMoments = numpy.zeros((self.configuration['frames']['number'],3),dtype=numpy.float64)
+            
+        self._outputData.add("dacf","line", (self.configuration['frames']['number'],), axis="time")
+        
+        if not isinstance(self.configuration["atom_charges"]["charges"],dict):
+            raise JobError(self,'Invalid type for partial charges. Must be a dictionary that maps atom index to to partial charge.')
+            
+        for idx, in self.configuration['atom_selection']["groups"]: 
+            if not self.configuration["atom_charges"]["charges"].has_key(idx):
+                raise JobError(self,'Partial charge not defined for atom: %d' % idx)                         
+        
+    def run_step(self, index):