Merge pull request #25 from PyCOMPLETE/develop

Prepare release v1.7.0

Author: giadarol

Makefile

@@ -0,0 +1,7 @@
+all: PyHEADTAIL
+
+PyHEADTAIL:
+	python setup.py build_ext --inplace
+
+clean:
+	python setup.py build_ext --inplace cleanall

_version.py

@@ -7,5 +7,10 @@
         worktree + ' describe --long --dirty --abbrev=10 --tags', shell=True)
     __version__ = __version__.rstrip() # remove trailing \n
     __version__ = __version__[1:] # remove leading v
+    # remove commit hash to conform to PEP440:
+    split_ = __version__.split('-')
+    __version__ = split_[0]
+    if split_[1] != '0':
+        __version__ += '.' + split_[1]
 except:
     __version__ = '(no git available to determine version)'

install

@@ -0,0 +1,2 @@
+from .. import Element, Printing, clean_slices, utils
+from .. import __version__

machines/__init__.py

@@ -0,0 +1,290 @@
+from __future__ import division
+
+import numpy as np
+from scipy.constants import c, e
+
+from PyHEADTAIL.general.element import Element
+import PyHEADTAIL.particles.generators as gen
+
+try:
+        from PyHEADTAIL.trackers.transverse_tracking_cython import TransverseMap
+        from PyHEADTAIL.trackers.detuners_cython import (Chromaticity,
+                                                     AmplitudeDetuning)
+except ImportError as e:
+        print ("*** Warning: could not import cython variants of trackers, "
+           "did you cythonize (use the following command)?\n"
+           "$ ./install \n"
+           "Falling back to (slower) python version.")
+        from PyHEADTAIL.trackers.transverse_tracking import TransverseMap
+        from PyHEADTAIL.trackers.detuners import Chromaticity, AmplitudeDetuning
+
+from PyHEADTAIL.trackers.simple_long_tracking import LinearMap, RFSystems
+
+class BasicSynchrotron(Element):
+    def __init__(self, optics_mode, circumference=None, n_segments=None, s=None, name=None,
+            alpha_x=None, beta_x=None, D_x=None, alpha_y=None, beta_y=None, D_y=None,
+            accQ_x=None, accQ_y=None, Qp_x=0, Qp_y=0, app_x=0, app_y=0, app_xy=0,
+            alpha_mom_compaction=None, longitudinal_mode=None, Q_s=None,
+            h_RF=None, V_RF=None, dphi_RF=None, p0=None, p_increment=None,
+            charge=None, mass=None, **kwargs):
+
+            
+            self.optics_mode = optics_mode
+            self.longitudinal_mode = longitudinal_mode
+            self.charge = charge
+            self.mass = mass
+            self.p0 = p0
+            
+            self.one_turn_map = []
+            
+            detuners = []
+            if Qp_x != 0 or Qp_y != 0:
+                    detuners.append(Chromaticity(Qp_x, Qp_y))
+            if app_x != 0 or app_y != 0 or app_xy != 0:
+                    detuners.append(AmplitudeDetuning(app_x, app_y, app_xy))
+
+            # construct transverse map 
+            self._contruct_transverse_map(optics_mode=optics_mode, circumference=circumference, n_segments=n_segments, s=s, name=name,
+                alpha_x=alpha_x, beta_x=beta_x, D_x=D_x, alpha_y=alpha_y, beta_y=beta_y, D_y=D_y,
+                accQ_x=accQ_x, accQ_y=accQ_y, detuners=detuners)
+            
+            # construct longitudinal map 
+            self._contruct_longitudinal_map(alpha_mom_compaction=alpha_mom_compaction, longitudinal_mode=longitudinal_mode, Q_s=Q_s,
+            h_RF=h_RF, V_RF=V_RF, dphi_RF=dphi_RF, p_increment=p_increment)
+
+
+
+    @property
+    def gamma(self):
+            return self._gamma
+    @gamma.setter
+    def gamma(self, value):
+            self._gamma = value
+            self._beta = np.sqrt(1 - self.gamma**-2)
+            self._betagamma = np.sqrt(self.gamma**2 - 1)
+            self._p0 = self.betagamma * self.mass * c
+
+    @property
+    def beta(self):
+            return self._beta
+    @beta.setter
+    def beta(self, value):
+            self.gamma = 1. / np.sqrt(1-value**2)
+
+    @property
+    def betagamma(self):
+            return self._betagamma
+    @betagamma.setter
+    def betagamma(self, value):
+            self.gamma = np.sqrt(value**2 + 1)
+
+    @property
+    def p0(self):
+            return self._p0
+    @p0.setter
+    def p0(self, value):
+            self.gamma = 1 / (c * self.mass) * np.sqrt(value**2+self.mass**2*c**2)
+            
+    @property
+    def Q_x(self):    
+		return np.atleast_1d(self.transverse_map.accQ_x)[-1]
+	
+    @property
+    def Q_y(self):    
+		return np.atleast_1d(self.transverse_map.accQ_y)[-1]      
+                   
+    def track(self, bunch, verbose=False):
+        for m in self.one_turn_map:
+            if verbose:
+                self.prints('Tracking through:\n' + str(m))
+            m.track(bunch)
+
+    def install_after_each_transverse_segment(self, element_to_add):
+        '''Attention: Do not add any elements which update the dispersion!'''
+        one_turn_map_new = []
+        for element in self.one_turn_map:
+            one_turn_map_new.append(element)
+            if element in self.transverse_map:
+                one_turn_map_new.append(element_to_add)
+        self.one_turn_map = one_turn_map_new
+
+    def generate_6D_Gaussian_bunch(self, n_macroparticles, intensity,
+                                   epsn_x, epsn_y, sigma_z):
+        '''Generate a 6D Gaussian distribution of particles which is
+        transversely matched to the Synchrotron. Longitudinally, the
+        distribution is matched only in terms of linear focusing.
+        For a non-linear bucket, the Gaussian distribution is cut along
+        the separatrix (with some margin). It will gradually filament
+        into the bucket. This will change the specified bunch length.
+        '''
+        if self.longitudinal_mode == 'linear':
+            check_inside_bucket = lambda z,dp : np.array(len(z)*[True])
+        elif self.longitudinal_mode == 'non-linear':
+            check_inside_bucket = self.longitudinal_map.get_bucket(
+                gamma=self.gamma).make_is_accepted(margin=0.05)
+        else:
+            raise NotImplementedError(
+                'Something wrong with self.longitudinal_mode')
+    
+        eta = self.longitudinal_map.alpha_array[0] - self.gamma**-2
+        beta_z    = np.abs(eta)*self.circumference/2./np.pi/self.longitudinal_map.Qs
+        sigma_dp  = sigma_z/beta_z
+        epsx_geo = epsn_x/self.betagamma
+        epsy_geo = epsn_y/self.betagamma
+        
+        injection_optics = self.transverse_map.get_injection_optics()
+        
+        bunch = gen.ParticleGenerator(macroparticlenumber=n_macroparticles,
+                                     intensity=intensity, charge=self.charge, mass=self.mass,
+                                     circumference=self.circumference, gamma=self.gamma,
+                                     distribution_x = gen.gaussian2D(epsx_geo), alpha_x=injection_optics['alpha_x'], beta_x=injection_optics['beta_x'], D_x=injection_optics['D_x'],
+                                     distribution_y = gen.gaussian2D(epsy_geo), alpha_y=injection_optics['alpha_y'], beta_y=injection_optics['beta_y'], D_y=injection_optics['D_y'],
+                                     distribution_z = gen.cut_distribution(gen.gaussian2D_asymmetrical(sigma_u=sigma_z, sigma_up=sigma_dp),is_accepted=check_inside_bucket),
+                                     ).generate()
+    
+        return bunch
+    
+    def generate_6D_Gaussian_bunch_matched(
+            self, n_macroparticles, intensity, epsn_x, epsn_y,
+            sigma_z=None, epsn_z=None):
+        '''Generate a 6D Gaussian distribution of particles which is
+        transversely as well as longitudinally matched.
+        The distribution is found iteratively to exactly yield the
+        given bunch length while at the same time being stationary in
+        the non-linear bucket. Thus, the bunch length should amount
+        to the one specificed and should not change significantly
+        during the synchrotron motion.
+    
+        Requires self.longitudinal_mode == 'non-linear'
+        for the bucket.
+        '''
+        assert self.longitudinal_mode == 'non-linear'
+        epsx_geo = epsn_x/self.betagamma
+        epsy_geo = epsn_y/self.betagamma
+        
+        injection_optics = self.transverse_map.get_injection_optics()
+        
+        bunch = gen.ParticleGenerator(macroparticlenumber=n_macroparticles,
+                                     intensity=intensity, charge=self.charge, mass=self.mass,
+                                     circumference=self.circumference, gamma=self.gamma,
+                                     distribution_x = gen.gaussian2D(epsx_geo), alpha_x=injection_optics['alpha_x'], beta_x=injection_optics['beta_x'], D_x=injection_optics['D_x'],
+                                     distribution_y = gen.gaussian2D(epsy_geo), alpha_y=injection_optics['alpha_y'], beta_y=injection_optics['beta_y'], D_y=injection_optics['D_y'],
+                                     distribution_z = gen.RF_bucket_distribution(self.longitudinal_map.get_bucket(gamma=self.gamma), sigma_z=sigma_z, epsn_z=epsn_z),
+                                     ).generate()
+    
+        return bunch
+    
+    def _contruct_transverse_map(self, optics_mode=None, circumference=None, n_segments=None, s=None, name=None,
+            alpha_x=None, beta_x=None, D_x=None, alpha_y=None, beta_y=None, D_y=None,
+            accQ_x=None, accQ_y=None, detuners=[]):    
+    
+        if optics_mode == 'smooth':
+            if circumference is None:
+                    raise ValueError('circumference has to be specified if optics_mode = "smooth"')
+
+            if  n_segments is None:
+                    raise ValueError('n_segments has to be specified if optics_mode = "smooth"')
+
+            if s is not None:
+                    raise ValueError('s vector cannot be provided if optics_mode = "smooth"')
+
+
+            s = (np.arange(0, n_segments + 1)
+                      * circumference / n_segments)
+
+            alpha_x=0.*s
+            beta_x=0.*s+beta_x
+            D_x=0.*s+D_x
+            alpha_y=0.*s
+            beta_y=0.*s+beta_y
+            D_y=0.*s+D_y
+
+        elif optics_mode == 'non-smooth':
+            if circumference is not None:
+                    raise ValueError('circumference cannot be provided if optics_mode = "non-smooth"')
+
+            if  n_segments is not None:
+                    raise ValueError('n_segments cannot be provided if optics_mode = "non-smooth"')
+
+            if s is None:
+                    raise ValueError('s has to be specified if optics_mode = "smooth"')
+
+        else:
+            raise ValueError('optics_mode not recognized')
+        
+        self.transverse_map = TransverseMap(s=s,
+            alpha_x=alpha_x,
+            beta_x=beta_x,
+            D_x=D_x,
+            alpha_y=alpha_y,
+            beta_y=beta_y,
+            D_y=D_y,
+            accQ_x=accQ_x, accQ_y=accQ_y, detuners=detuners)
+    
+        self.circumference = s[-1]
+        self.transverse_map.n_segments = len(s)-1
+        
+        if name is None:
+            self.transverse_map.name = ['P_%d'%ip for ip in xrange(len(s)-1)]            
+            self.transverse_map.name.append('end_ring')
+        else:
+            self.transverse_map.name = name
+            
+        for i_seg, m in enumerate(self.transverse_map):
+            m.i0 = i_seg
+            m.i1 = i_seg+1
+            m.s0 = self.transverse_map.s[i_seg]
+            m.s1 = self.transverse_map.s[i_seg+1]
+            m.name0 = self.transverse_map.name[i_seg]
+            m.name1 = self.transverse_map.name[i_seg+1]
+            m.beta_x0 = self.transverse_map.beta_x[i_seg]
+            m.beta_x1 = self.transverse_map.beta_x[i_seg+1]
+            m.beta_y0 = self.transverse_map.beta_y[i_seg]
+            m.beta_y1 = self.transverse_map.beta_y[i_seg+1]          
+    
+        # insert transverse map in the ring
+        for m in self.transverse_map:
+            self.one_turn_map.append(m)
+
+    def _contruct_longitudinal_map(self, alpha_mom_compaction=None, longitudinal_mode=None, Q_s=None,
+            h_RF=None, V_RF=None, dphi_RF=None, p_increment=None):
+        
+        # compute the index of the element before which to insert
+        # the longitudinal map
+        if longitudinal_mode is not None:
+                for insert_before, si in enumerate(self.transverse_map.s):
+                        if si > 0.5 * self.circumference:
+                                break
+
+        if longitudinal_mode == 'linear':
+        	
+        	eta = alpha_mom_compaction - self.gamma**-2
+        	
+        	if Q_s == None:
+        		if p_increment!=0 or dphi_RF!=0:
+        	   		raise ValueError('Formula not valid in this case!!!!')
+        		else:
+       				Q_s = np.sqrt( e*np.abs(eta)*(h_RF*V_RF)
+                        		/ (2*np.pi*self.p0*self.beta*c) )
+
+                self.longitudinal_map = LinearMap(
+                        np.atleast_1d(alpha_mom_compaction),
+                        self.circumference, Q_s,
+                        D_x=self.transverse_map.D_x[insert_before],
+                        D_y=self.transverse_map.D_y[insert_before])
+                        
+                        
+        elif longitudinal_mode == 'non-linear':
+                self.longitudinal_map = RFSystems(
+                        self.circumference, np.atleast_1d(h_RF),
+                        np.atleast_1d(V_RF), np.atleast_1d(dphi_RF),
+                        np.atleast_1d(alpha_mom_compaction), self.gamma, p_increment,
+                        D_x=self.transverse_map.D_x[insert_before],
+                        D_y=self.transverse_map.D_y[insert_before],
+                        mass=self.mass, charge=self.charge
+                )
+        else:
+                raise NotImplementedError(
+                        'Something wrong with longitudinal_mode')
+                
+        self.one_turn_map.insert(insert_before, self.longitudinal_map)

machines/synchrotron.py

@@ -18,7 +18,7 @@
 from . import Printing
 
 from functools import partial
-from scipy.constants import e, m_p, c
+from scipy.constants import e, c
 
 
 def generate_Gaussian6DTwiss(macroparticlenumber, intensity, charge, mass,
@@ -33,7 +33,7 @@ def generate_Gaussian6DTwiss(macroparticlenumber, intensity, charge, mass,
     Returns: A particle instance with the phase space matched to the arguments
     """
     beta = np.sqrt(1.-gamma**(-2))
-    p0 = np.sqrt(gamma**2 -1) * m_p * c
+    p0 = np.sqrt(gamma**2 -1) * mass * c
     eps_geo_x = epsn_x/(beta*gamma)
     eps_geo_y = epsn_y/(beta*gamma)
     eps_geo_z = epsn_z * e / (4. * np.pi * p0)
@@ -194,7 +194,8 @@ def __init__(self, macroparticlenumber, intensity, charge, mass,
                  circumference, gamma,
                  distribution_x=None, alpha_x=0., beta_x=1., D_x=None,
                  distribution_y=None, alpha_y=0., beta_y=1., D_y=None,
-                 distribution_z=None, Qs=None, eta=None):
+                 distribution_z=None, Qs=None, eta=None,
+                 *args, **kwargs):
         '''
         Specify the distribution for each phase space seperately. Only
         the phase spaces for which a distribution has been specified