Fix feeder not beeing fully illuminated and add VS and MF divergence monitors

Add polarization parameters of SNAG mirrors and run file
Implement geometry of double V-style polarizer, straight not correct reflection, yet
2021-10-13 11:39:24 +02:00 · 2021-10-13 10:00:11 +02:00 · 2021-10-11 22:55:53 +02:00 · 2019-11-18 16:45:24 +01:00 · 2019-08-02 19:23:48 +02:00 · 2019-07-28 19:23:31 +02:00
23 changed files with 1367 additions and 3147 deletions
@@ -0,0 +1,9 @@
+ #!/bin/bash
+# compress McStas hdf5 files to increase performance and save disk space
+
+for fi in $*
+do
+  echo $fi
+  h5repack -i $fi -o $fi.c -f /entry1/data/detector_list_p_x_y_t_L_sx_sy_sz/events:GZIP=5 -l /entry1/data/detector_list_p_x_y_t_L_sx_sy_sz/events:CHUNK=3072x8
+  mv $fi.c $fi
+done
@@ -11,7 +11,7 @@ from numpy import *
 try:
    import h5py
 except ImportError:
-    print "h5py not found, modern NeXuS format will not be readable."
+    print("h5py not found, modern NeXuS format will not be readable.")

 try:
  from IPython import display #@UnusedImport
@@ -49,7 +49,7 @@ class McSim(object):
      elif os.path.exists(os.path.join(path, 'mccode.sim')):
        self._init_old(os.path.join(path, 'mccode.sim'))
      else:
-        raise IOError, "Can't locate mccode.h5 of mccode.sim file in %s"%path
+        raise IOError("Can't locate mccode.h5 of mccode.sim file in %s"%path)

  def _init_hdf(self, path):
    self.hdf=h5py.File(path, 'r')
@@ -61,11 +61,11 @@ class McSim(object):
    self.data_loader=DataLoaderOld(self.info, os.path.dirname(path))

  def keys(self):
-    return self.info['data'].keys()
+    return list(self.info['data'].keys())

  def monitors(self):
    output=[]
-    for val in self.info['data'].values():
+    for val in list(self.info['data'].values()):
      xy=(val['xvar'], val['yvar'])
      if not xy in output:
        output.append(xy)
@@ -74,7 +74,7 @@ class McSim(object):
  
  def plot(self, monitors=None):
    graphs={}
-    for key, val in self.info['data'].items():
+    for key, val in list(self.info['data'].items()):
      xy=(val['xvar'], val['yvar'])
      if monitors is not None and xy!=monitors:
        continue
@@ -102,12 +102,12 @@ class McSim(object):
  def __getitem__(self, item):
    if item in self._data:
      return self._data[item]
-    elif item in self.keys():
+    elif item in list(self.keys()):
      data=self.data_loader.load_item(item)
      self._data[item]=data
      return data
    else:
-      raise KeyError, "Can't find dataset %s"%item
+      raise KeyError("Can't find dataset %s"%item)

 class HeaderFile(object):
  '''
@@ -124,7 +124,7 @@ class HeaderFile(object):
    data=open(path, 'r').read()
    data_lines=data.splitlines()
    if not data.startswith('McStas simulation description file'):
-      raise IOError, 'Not a valid McStas description file.'
+      raise IOError('Not a valid McStas description file.')
    self._data['start_time']=data_lines[1].split(':', 1)[1].strip()
    self._data['program_name']=data_lines[2].split(':', 1)[1].strip()
    self._data['data']=self.get_data(data)
@@ -167,13 +167,13 @@ class DataLoaderOld(object):
    fname=os.path.join(self.root, item_info['filename'])
    x_col=item_info['xvar']
    y_col=item_info['yvar']
-    if x_col=='Li' and y_col=='p': # Detector_nD     
+    if x_col in ['Li', 'List'] and y_col=='p': # Detector_nD     
      cols=item_info['variables'].split() 
      data=loadtxt(fname, dtype={'names': cols, 'formats': ['f4']*len(cols)})
      return TofData(data, item_info)
    else:
      raw=loadtxt(fname)
-      data=raw[:len(raw)/3]
+      data=raw[:len(raw)//3]
      return Dataset(data, item_info)

  def load_item_1d(self, item):
@@ -192,11 +192,11 @@ class DataLoaderHDF(object):
    self.hdf=hdf['entry1']
    self.info={}
    self.info['data']={}
-    for item in self.hdf['data'].keys():
+    for item in list(self.hdf['data'].keys()):
      node=self.hdf['data/'+item]
      info={}
-      for key, value in node.attrs.items():
-        info[key.strip()]=value.strip()
+      for key, value in list(node.attrs.items()):
+        info[key.strip()]=value.strip().decode('ascii')
      if info['filename'][-4:]=='.dat' or '_list.' in info['filename']:
        self.info['data'][info['component']]=info
      else:
@@ -211,7 +211,7 @@ class DataLoaderHDF(object):
    node=self.hdf[item_info['datapath']]
    x_col=item_info['xvar']
    y_col=item_info['yvar']
-    if x_col=='Li' and y_col=='p': # Detector_nD
+    if x_col in ['Li', 'List'] and y_col=='p': # Detector_nD
      cols=item_info['variables'].split()
      evds=node['events']
      if len(evds)<=MAX_EVTS_BATCH:
@@ -253,7 +253,7 @@ class Dataset1D(object):
      import pylab
      ax=pylab.gca()

-    limits=map(float, self.info['xlimits'].split())
+    limits=list(map(float, self.info['xlimits'].split()))
    x=linspace(limits[0], limits[1], len(self.data))

    ax.errorbar(x, self.data, yerr=self.errors)
@@ -291,7 +291,7 @@ class Dataset(object):
      import pylab
      ax=pylab.gca()

-    limits=map(float, self.info['xylimits'].split())
+    limits=list(map(float, self.info['xylimits'].split()))

    if log:
      ax.imshow(self.data, origin='lower', extent=limits, aspect='auto', norm=LogNorm())
@@ -342,7 +342,7 @@ class TofData(Dataset):
    if fltr is None:
      I, x=histogram(columns[col], bins=bins, weights=w)
    else:
-      if isinstance(fltr, basestring):
+      if isinstance(fltr, str):
        fltr=eval(fltr, globals(), columns)
      I, x=histogram(columns[col][fltr], bins=bins, weights=w[fltr])
    return x, I
@@ -367,7 +367,7 @@ class TofData(Dataset):
      I, y, x=histogram2d(columns[ycol], columns[xcol],
                        bins=bins, weights=self.data['p'])
    else:
-      if isinstance(fltr, basestring):
+      if isinstance(fltr, str):
        fltr=eval(fltr, globals(), columns)
      I, y, x=histogram2d(columns[ycol][fltr], columns[xcol][fltr],
                        bins=bins, weights=columns['p'][fltr])
@@ -53,7 +53,8 @@ DEFINE INSTRUMENT ESS_reflectometer_Estia
 int operationmode = 0, double over_illumination = 0.0, double theta_resolution = 0.04,
 double lambda_min      =  3.75, double lambda_start    =  3.0, double lambda_end      = 12.0,
 int enable_chopper = 0, int enable_gravity=0, int enable_windows=1,
- int enable_polarizer = 0, int enable_analyzer = 0,
+ int enable_polarizer = 0, int enable_analyzer = 0, 
+ double pol1_start=0.3, double pol1_angle=1.66, double pol2_start=0.3, double pol2_angle=1.66,
 double source_power = 2,
 double selene1_foot1y =0.0, double selene1_foot2y = 0.0
 )
@@ -78,6 +79,8 @@ double selene1_center;
 double selene1_shift;
 double selene1_rot;

+int p_int=0; // a flag that gets incremented if a polarizer mirror scatters
+
 // Selene 2


@@ -122,7 +125,7 @@ chopper_open = 98.0;

 /* print out some calculated parameter for checking purposes */
 printf(" Chopper phase = %.1f deg\n", chopper_phase);
-printf(" Chopper open  = %.1f deg\n", chopper_open);
+//printf(" Chopper open  = %.1f deg\n", chopper_open);


 dist_ana_vfocus=analyzer_max_height/2.0/tan(1.5*PI/360.0); // the virtual focus point infront of the actual sample focus where the beams furthest out meet
@@ -135,8 +138,8 @@ Theta2_analyzer2=atan((dist_ana_vfocus+analyzer2_start+analyzer2_length)/dist_an
 selene1_center=(selene1_foot1+selene1_foot2)/2.;
 selene1_shift=(selene1_foot1y+selene1_foot2y)/1000.0;
 selene1_rot=atan((selene1_foot2y-selene1_foot1y)/(selene1_foot2-selene1_foot1)/1000.0)*180.0/PI;
-printf(" Selene 1 rotation  = %.4f deg\n", selene1_rot);
-printf(" Selene 1 shift  = %.1f mm\n", selene1_shift*1e3);
+//printf(" Selene 1 rotation  = %.4f deg\n", selene1_rot);
+//printf(" Selene 1 shift  = %.1f mm\n", selene1_shift*1e3);

 %}
 TRACE
@@ -202,7 +205,7 @@ COMPONENT moderator = ESS_butterfly(
    sector = "E", beamline = 2, yheight = 0.03, cold_frac = 0.9,
        focus_xw = E02_01_01_Cu_in_xmax-E02_01_01_Cu_in_xmin+0.002, 
        focus_yh = E02_01_01_Cu_in_yheight+0.002,
-    target_index=4, Lmin = lambda_start, Lmax = lambda_end,
+    target_index=3, Lmin = lambda_start, Lmax = lambda_end,
    n_pulses = 1+enable_chopper, acc_power=source_power)
    AT (0, 0, 0) RELATIVE origin 

@@ -234,6 +237,17 @@ COMPONENT chopper = DiskChopper(radius=chopper_diameter/2.0, yheight=0.02,
    AT (0, 0, chopper_pos-2*NBOA_c) RELATIVE arm_virtual_source_beam
    

+COMPONENT vs_divergence_h = DivPos_monitor(nh=21, ndiv=41, filename="vs_hordiv",
+          xmin=-0.02, xmax=0.02, ymin=-0.02, ymax=0.02, maxdiv_h=2.0,
+		  restore_neutron=1)
+		  AT (0, 0, -0.5*sample_length-0.001) RELATIVE arm_selene1
+
+COMPONENT vs_divergence_v = DivPos_monitor(nh=21, ndiv=41, filename="vs_verdiv",
+          xmin=-0.02, xmax=0.02, ymin=-0.02, ymax=0.02, maxdiv_h=2.0,
+		  restore_neutron=1)
+		  AT (0, 0, -0.5*sample_length-0.001) RELATIVE arm_selene1
+		  ROTATED (0,0,90) RELATIVE arm_selene1
+

 /* The actual virtual source mask, two L-shaped absorbers (first top-right) */
 COMPONENT virtual_source_TR = Slit(
@@ -282,8 +296,8 @@ COMPONENT ac_slit = Slit(
 * Sample area *
 ***************/
    COMPONENT tof_sample = Monitor_nD(
-        filename = "tof_sample",
-        options = "x limits=[-0.025 0.025] bins=1000 y limits=[-0.025 0.025] bins=1000 xdiv limits=[-0.75 0.75] bins=150 ydiv limits=[-2.0 2.0] bins=400 time limits=[0 0.6] bins=6000 lambda limits=[0 35] bins=3500 list all",
+        filename = "tof_sample", user1=p_int,
+        options = "x limits=[-0.025 0.025] bins=1000 y limits=[-0.025 0.025] bins=1000 xdiv limits=[-0.75 0.75] bins=150 ydiv limits=[-2.0 2.0] bins=400 time limits=[0 0.6] bins=6000 lambda limits=[0 35] bins=3500 sy limits=[-1 1] bins=2000 user1 list all",
        xwidth=0.05, yheight = 0.05)
        WHEN sample==4
        AT (0, 0, 0) RELATIVE arm_sample_beam
@@ -330,32 +344,6 @@ COMPONENT si_sample = Mirror(
    AT (0, 0, 0) RELATIVE arm_sample
    ROTATED (0, 90, 0) RELATIVE arm_sample

-/* Asymmetric lipid bilayer */
-COMPONENT lipid_h20_sample = Mirror(
-    xwidth = sample_length, yheight = sample_height,
-    center = 1, transmit = 0,
-    reflect = "lipid_h2o.ref"
-    )
-    WHEN sample==4
-    AT (0, 0, 0) RELATIVE arm_sample
-    ROTATED (0, 90, 0) RELATIVE arm_sample
-COMPONENT lipid_d20_sample = Mirror(
-    xwidth = sample_length, yheight = sample_height,
-    center = 1, transmit = 0,
-    reflect = "lipid_d2o.ref"
-    )
-    WHEN sample==5
-    AT (0, 0, 0) RELATIVE arm_sample
-    ROTATED (0, 90, 0) RELATIVE arm_sample
-COMPONENT lipid_smw_sample = Mirror(
-    xwidth = sample_length, yheight = sample_height,
-    center = 1, transmit = 0,
-    reflect = "lipid_smw.ref"
-    )
-    WHEN sample==6
-    AT (0, 0, 0) RELATIVE arm_sample
-    ROTATED (0, 90, 0) RELATIVE arm_sample
-

 COMPONENT arm_analyzer = Arm()
    AT (0, 0, 0) RELATIVE arm_detector
@@ -366,14 +354,14 @@ COMPONENT arm_analyzer2 = Arm()
    ROTATED (-selene_theta+(Theta1_analyzer2-Theta2_analyzer2)/2.0, 0, 0) RELATIVE arm_detector

 /* polarization analyser */
-COMPONENT analyzer1 = Polariser(nIncRefr=1, d_substrate = 5e-4, reflect_d=0, reflect_u=0, lin=analyzer1_start, length=analyzer1_length,
+COMPONENT analyzer1 = Polariser(enable_ref=1, d_substrate = 5e-4, reflect_d=0, reflect_u=0, lin=analyzer1_start, length=analyzer1_length,
                                delta_theta=(Theta1_analyzer1+Theta2_analyzer1+0.05)*PI/180.0, h2=0.14, h1=0.05, abs_ref=0, 
                                m_u=5.5, m_d=0.45, both_coated=0, alpha=2.3, W = 0.0014)
        WHEN enable_analyzer
        AT (0, 0.0, analyzer1_start) RELATIVE arm_analyzer
        ROTATED (0,0,0.0) RELATIVE arm_analyzer

-COMPONENT analyzer2 = Polariser(nIncRefr=1, d_substrate = 5e-4, reflect_d=0, reflect_u=0, lin=analyzer2_start, length=analyzer2_length,
+COMPONENT analyzer2 = Polariser(enable_ref=1, d_substrate = 5e-4, reflect_d=0, reflect_u=0, lin=analyzer2_start, length=analyzer2_length,
                                delta_theta=(Theta1_analyzer2+Theta2_analyzer2+0.05)*PI/180.0, h2=0.2, h1=0.05, abs_out=0, 
                                m_u=5.0, m_d=0.65, both_coated=1, alpha=2.3, W = 0.0014)
        WHEN enable_analyzer==2
@@ -382,11 +370,12 @@ COMPONENT analyzer2 = Polariser(nIncRefr=1, d_substrate = 5e-4, reflect_d=0, ref

 /* detector */
    COMPONENT tof_detector = Monitor_nD(
-        filename = "tof_detector",
-        options = "x limits=[-0.25 0.25] bins=1000 y limits=[-0.5 0.5] bins=1000 time limits=[0 0.6] bins=6000 lambda limits=[0 35] bins=3500 sx limits=[-1 1] bins=1000 sy limits=[-1 1] bins=1000, list all",
+        filename = "tof_detector", user1=p_int,
+        options = "x limits=[-0.25 0.25] bins=1000 y limits=[-0.5 0.5] bins=1000 time limits=[0 0.6] bins=6000 lambda limits=[0 35] bins=3500 sx sy sz user1, list all",
        xwidth = 0.5, yheight = 1.0)
        WHEN sample!=4
        AT (0, 0, detector_arm+0.00001) RELATIVE arm_detector
+        ROTATED (0, 0, 0) RELATIVE arm_detector

 /***********************************************************************/

@@ -28,20 +28,80 @@ DEFINE INSTRUMENT Estia_selene(int enable_gravity=0)

 DECLARE
 %{
-    
-double polarizer_max_width = 0.0015; // Maximum sample height to be covered by te polarization analyzers
-double polarizer_start  = 0.3; // Distance to sample to start the first analyzer
-double polarizer_length = 0.6; // length of first analyzer
-double Theta1_polarizer, Theta2_polarizer, dist_pol_vfocus; // quantities calculated out of values above and 1.5 degree covered divergence
+
+// Polarizer parameters used for the detailed design
+double pol1_xstart = 1.007; // [m] up-stream of focus point
+double pol1_ystart = 0.0064; // [m] (relative to c-axis)
+double pol1_xend = 0.365; // [m] up-stream of focus point
+double pol1_yend = 0.013; // [m]
+double pol1_gamma = 1.65; // [deg] optimal incident angle for beams passing through focus point
+double pol1_m = 5.08;
+double pol1_lin_xstart = 1.007; //[m]
+double pol1_lin_ystart = 0.0064; //[m]
+double pol1_lin_xend = 0.812; //[m]
+double pol1_lin_yend = -0.0014; //[m]
+double pol1_lin_m = 5.5;
+
+
+double pol2_xstart = 1.286; // [m] up-stream of focus point
+double pol2_ystart = 0.009; // [m] (relative to c-axis)
+double pol2_xend = 0.500; // [m] up-stream of focus point
+double pol2_yend = 0.0175; // [m]
+double pol2_gamma = 1.70; // [deg] optimal incident angle for beams passing through focus point
+double pol2_m = 5.08;
+double pol2_lin_xstart = 1.286; //[m]
+double pol2_lin_ystart = 0.009; //[m]
+double pol2_lin_xend = 1.093; //[m]
+double pol2_lin_yend = 0.0014; //[m]
+double pol2_lin_m = 5.08;
+
+double pol_hclose = 0.12; // [m] height of entrance
+double pol_hfar = 0.12; // [m] height of exit
+
+// parameters for polarizer component calculated from the above
+double pol1_length, pol2_length, pol1_lin_length, pol2_lin_length;
+double Theta_pol1, Theta_pol2, Theta_rot1, Theta_rot2;
+double Theta1_pol1, Theta1_pol2, Theta2_pol1, Theta2_pol2;
+double pol1_lin_rot, pol2_lin_rot;

 %}

 INITIALIZE
 %{
-dist_pol_vfocus=polarizer_max_width/2.0/tan(1.5*PI/360.0); // the virtual focus point infront of the actual sample focus where the beams furthest out meet

-Theta1_polarizer=atan((dist_pol_vfocus+polarizer_start)/dist_pol_vfocus*polarizer_max_width/2.0/polarizer_start)*180.0/PI;
-Theta2_polarizer=atan((dist_pol_vfocus+polarizer_start+polarizer_length)/dist_pol_vfocus*polarizer_max_width/2.0/(polarizer_start+polarizer_length))*180.0/PI;
+pol1_length = pol1_xstart-pol1_xend;
+pol2_length = pol2_xstart-pol2_xend;
+pol1_lin_length = pol1_lin_xstart-pol1_lin_xend;
+pol2_lin_length = pol2_lin_xstart-pol2_lin_xend;
+
+Theta1_pol1=atan2(pol1_ystart, pol1_xstart); // [rad] angle between c-axis and entrance point
+Theta2_pol1=atan2(pol1_yend, pol1_xend); // [rad] angle between c-axis and exit point
+Theta1_pol2=atan2(pol2_ystart, pol2_xstart); // [rad] angle between c-axis and entrance point
+Theta2_pol2=atan2(pol2_yend, pol2_xend); // [rad] angle between c-axis and exit point
+
+Theta_pol1=(Theta2_pol1-Theta1_pol1)*180.0/PI; // [deg] full covered divergence angle
+Theta_pol2=(Theta2_pol2-Theta1_pol2)*180.0/PI; // [deg]
+Theta_rot1=(Theta1_pol1+Theta2_pol1)/2.0*180.0/PI; // [deg] rotation of center of polarizer
+Theta_rot2=(Theta1_pol2+Theta2_pol2)/2.0*180.0/PI; // [deg]
+
+pol1_lin_rot=atan2(pol1_lin_ystart-pol1_lin_yend, 
+                   pol1_lin_xstart-pol1_lin_xend)*180.0/PI; // [deg] rotation angle of polarizer
+pol2_lin_rot=atan2(pol2_lin_ystart-pol2_lin_yend, 
+                   pol2_lin_xstart-pol2_lin_xend)*180.0/PI; // [deg] rotation angle of polarizer
+   
+
+
+printf(" Polarizer 1 angle      = %.2f deg\n", Theta_rot1);
+printf(" Polarizer 1 divergence = %.2f deg\n", Theta_pol1);
+printf(" Polarizer 1 distance   = %.1f mm\n", pol1_xstart*1000.0);
+printf(" Polarizer 1 length     = %.1f mm\n", pol1_length*1000.0);
+printf(" PolStraight 1 angle      = %.2f deg\n", pol1_lin_rot);
+
+printf(" Polarizer 2 angle      = %.2f deg\n", Theta_rot1);
+printf(" Polarizer 2 divergence = %.2f deg\n", Theta_pol2);
+printf(" Polarizer 2 distance   = %.1f mm\n", pol2_xstart*1000.0);
+printf(" Polarizer 2 length     = %.1f mm\n", pol2_length*1000.0);
+printf(" PolStraight 2 angle      = %.2f deg\n", pol2_lin_rot);

 %}
 TRACE
@@ -67,26 +127,116 @@ REMOVABLE COMPONENT source = Moderator(radius = 0.001, focus_xw = selene_entry+0
 /**************************************
 * Middle focus between Selene guides *
 **************************************/
-COMPONENT arm_polarizer = Arm()
+COMPONENT arm_polref = Arm()
    AT (0, 0, 2*selene_c) RELATIVE arm_selene1
    ROTATED (selene_theta, -selene_theta, 0) RELATIVE ISCS

-COMPONENT polarizer1 = Polariser(nIncRefr=1, d_substrate = 5e-4, reflect_d=0, reflect_u=0, lin=-(polarizer_start+polarizer_length), length=polarizer_length,
-                                 delta_theta=(Theta1_polarizer+Theta2_polarizer)*PI/180.0, h2=0.1, h1=0.05, abs_ref=1, m_u=4.0, m_d=0.65, both_coated=1, alpha=2.3, W = 0.0014)
-        WHEN enable_polarizer
-        AT (0, 0, -(polarizer_start+polarizer_length)) RELATIVE arm_polarizer
-        ROTATED (0,0,90.0) RELATIVE arm_polarizer
+COMPONENT arm_polarizer = Arm()
+    AT (0, 0, 2*selene_c) RELATIVE arm_selene1
+    ROTATED (0, 0, 0) RELATIVE arm_selene1
+
+COMPONENT arm_pol1 = Arm()
+    AT (0, 0, 0) RELATIVE arm_polarizer
+    ROTATED (0, -Theta_rot1, 0) RELATIVE arm_polarizer
+
+COMPONENT arm_pol2 = Arm()
+    AT (0, 0, 0) RELATIVE arm_polarizer
+    ROTATED (0, -Theta_rot2, 0) RELATIVE arm_polarizer


-/* The proximal polariser comes next */
-COMPONENT polarizer2 = Polariser(nIncRefr=1, d_substrate = 5e-4, reflect_d=0, reflect_u=0, lin=polarizer_start, length=polarizer_length,
-                                 delta_theta=(Theta1_polarizer+Theta2_polarizer)*PI/180.0, h2=0.1, h1=0.05, abs_ref=1, m_u=4.0, m_d=0.65, both_coated=1, alpha=2.3, W = 0.0014)
-        WHEN (enable_polarizer>1)
-        AT (0, 0, polarizer_start) RELATIVE arm_polarizer
-        ROTATED (0.0,0,90.0) RELATIVE arm_polarizer
-        
+COMPONENT polarizer2_lin = Pol_mirror(zwidth = pol2_lin_length, yheight = pol_hfar, p_reflect=0,
+                                      rUpFunc=TableReflecFunc, rUpPar="SNAG_m5p5_Tup.ref", 
+									  rDownFunc=TableReflecFunc, rDownPar="SNAG_m5p5_Tdown.ref", useTables=1)
+		WHEN (enable_polarizer>0)
+        AT ((pol2_lin_ystart+pol2_lin_yend)/2.0, 0, -(pol2_lin_xstart+pol2_lin_xend)/2.0) RELATIVE arm_polarizer
+        ROTATED (0,-pol2_lin_rot,0.0) RELATIVE arm_polarizer
+		GROUP polarizer2_set
+		EXTEND
+		%{
+			p_int=0; // reset for each trace
+			if (SCATTERED==2) {
+				p_int +=2;
+				}
+		%}
+
+COMPONENT polarizer2 = Polariser(lin=-pol2_xstart, length=pol2_length,
+                                 enable_ref=1, abs_ref=1, abs_out=1, both_coated=1,
+                                 d_substrate = 5e-4, T_loss=4.0e3,
+                                 m_u=pol2_m, m_d=0.6, m_residual=0.55,
+                                 alpha=2.3, W = 0.0014,  reflect_d=0, reflect_u=0, 
+                                 delta_theta=Theta_pol2*PI/180.0, 
+                                 h2=pol_hfar, h1=pol_hclose)
+		WHEN (enable_polarizer>0)
+        AT (0, 0, -pol2_xstart) RELATIVE arm_pol2
+        ROTATED (0,0,90.0) RELATIVE arm_pol2
+		GROUP polarizer2_set
+		EXTEND
+		%{
+			if (SCATTERED) {
+				ALLOW_BACKPROP;    
+				PROP_Z0;
+				p_int +=1;
+				} else ABSORB;
+		%}
+
+COMPONENT replacement_pol2_set = Slit(xwidth=0.2, yheight=0.2)
+	WHEN (enable_polarizer==0)
+    AT (0, 0, -0.2) RELATIVE arm_polarizer
+	GROUP polarizer2_set
+
+COMPONENT polarizer1_lin = Pol_mirror(zwidth = pol1_lin_length, yheight = pol_hfar, p_reflect=0,
+                                      rUpFunc=TableReflecFunc, rUpPar="SNAG_m5p5_Tup.ref", 
+									  rDownFunc=TableReflecFunc, rDownPar="SNAG_m5p5_Tdown.ref", useTables=1)
+		WHEN (enable_polarizer>0)
+        AT ((pol1_lin_ystart+pol1_lin_yend)/2.0, 0, -(pol1_lin_xstart+pol1_lin_xend)/2.0) RELATIVE arm_polarizer
+        ROTATED (0,-pol1_lin_rot,0.0) RELATIVE arm_polarizer
+		GROUP polarizer1_set
+		EXTEND
+		%{
+			if (SCATTERED==2) {
+				p_int +=8;
+			}
+		%}
+
+COMPONENT polarizer1 = Polariser(lin=-pol1_xstart, length=pol1_length,
+                                 enable_ref=1, abs_ref=1, abs_out=1, both_coated=1,
+                                 d_substrate = 5e-4, T_loss=4.0e3,
+                                 m_u=pol1_m, m_d=0.6, m_residual=0.55,
+                                 alpha=2.3, W = 0.0014,  reflect_d=0, reflect_u=0, 
+                                 delta_theta=Theta_pol1*PI/180.0, 
+                                 h2=pol_hfar, h1=pol_hclose)
+		WHEN (enable_polarizer>0)
+        AT (0, 0, -pol1_xstart) RELATIVE arm_pol1
+        ROTATED (0,0,90.0) RELATIVE arm_pol1
+		GROUP polarizer1_set
+		EXTEND
+		%{
+			if (SCATTERED) {
+				p_int +=4;
+			}
+		%}
+
+COMPONENT replacement_pol1_set = Slit(xwidth=0.2, yheight=0.2)
+	WHEN (enable_polarizer==0)
+    AT (0, 0, -0.1) RELATIVE arm_polarizer
+	GROUP polarizer1_set


+
+COMPONENT mf_divergence_h = DivPos_monitor(nh=21, ndiv=41, filename="mf_hordiv",
+          xmin=-0.02, xmax=0.02, ymin=-0.02, ymax=0.02, maxdiv_h=2.0)
+		  AT (0, 0, 0) RELATIVE arm_polarizer
+
+COMPONENT mf_divergence_v = DivPos_monitor(nh=21, ndiv=41, filename="mf_verdiv",
+          xmin=-0.02, xmax=0.02, ymin=-0.02, ymax=0.02, maxdiv_h=2.0)
+		  AT (0, 0, 0) RELATIVE arm_polarizer
+		  ROTATED (0,0,90) RELATIVE arm_polarizer
+
+
+
+COMPONENT virtual_flipper = Pol_SF_ideal(ny=1, xwidth=0.1, yheight=0.1, zdepth=0.001)
+        WHEN (enable_polarizer>2)
+        AT (0, 0, 0) RELATIVE arm_polarizer
    

 FINALLY
@@ -102,7 +102,7 @@ REMOVABLE COMPONENT source = Moderator(radius = 0.001, focus_xw = selene_entry+0
 /* Absorber to cut direct view beam (Copper in CAD model) */
 COMPONENT slit_before_selene_guide_1 = Slit(
    xmin = 0, xmax = selene_entry+0.001,
-    ymin = 0, ymax = selene_entry+0.005)
+    ymin = -selene_entry-0.005, ymax = 0)
    AT (0, 0, selene_distance-0.01) RELATIVE arm_selene1

 COMPONENT block_before_selene_guide_1 = Absorber(
@@ -118,7 +118,7 @@ COMPONENT E02_03_01 = Elliptic_guide_gravity(
    linyh = selene_distance, loutyh= selene_distance+14*selene_segment,
    linxw = selene_distance, loutxw= selene_distance+14*selene_segment,
    xwidth=selene_b*2, yheight=selene_b*2,
-    mright=0, mleft=scoating_01, mtop=scoating_01, mbottom=0,
+    mright=0, mleft=scoating_01, mbottom=scoating_01, mtop=0,
    enableGravity=enable_gravity) 
    AT (0, 0, selene_distance) RELATIVE arm_selene1

@@ -127,7 +127,7 @@ COMPONENT E02_03_02 = Elliptic_guide_gravity(
    linyh = selene_distance+1*selene_segment, loutyh= selene_distance+13*selene_segment,
    linxw = selene_distance+1*selene_segment, loutxw= selene_distance+13*selene_segment,
    xwidth=selene_b*2, yheight=selene_b*2,
-    mright=0, mleft=scoating_02, mtop=scoating_02, mbottom=0,
+    mright=0, mleft=scoating_02, mbottom=scoating_02, mtop=0,
    enableGravity=enable_gravity) 
    AT (0, 0, selene_distance+1*selene_segment) RELATIVE arm_selene1

@@ -136,7 +136,7 @@ COMPONENT E02_03_03 = Elliptic_guide_gravity(
    linyh = selene_distance+2*selene_segment, loutyh= selene_distance+12*selene_segment,
    linxw = selene_distance+2*selene_segment, loutxw= selene_distance+12*selene_segment,
    xwidth=selene_b*2, yheight=selene_b*2,
-    mright=0, mleft=scoating_03, mtop=scoating_03, mbottom=0,
+    mright=0, mleft=scoating_03, mbottom=scoating_03, mtop=0,
    enableGravity=enable_gravity) 
    AT (0, 0, selene_distance+2*selene_segment) RELATIVE arm_selene1

@@ -145,7 +145,7 @@ COMPONENT E02_03_04 = Elliptic_guide_gravity(
    linyh = selene_distance+3*selene_segment, loutyh= selene_distance+11*selene_segment,
    linxw = selene_distance+3*selene_segment, loutxw= selene_distance+11*selene_segment,
    xwidth=selene_b*2, yheight=selene_b*2,
-    mright=0, mleft=scoating_04, mtop=scoating_04, mbottom=0,
+    mright=0, mleft=scoating_04, mbottom=scoating_04, mtop=0,
    enableGravity=enable_gravity) 
    AT (0, 0, selene_distance+3*selene_segment) RELATIVE arm_selene1

@@ -154,7 +154,7 @@ COMPONENT E02_03_05 = Elliptic_guide_gravity(
    linyh = selene_distance+4*selene_segment, loutyh= selene_distance+10*selene_segment,
    linxw = selene_distance+4*selene_segment, loutxw= selene_distance+10*selene_segment,
    xwidth=selene_b*2, yheight=selene_b*2,
-    mright=0, mleft=scoating_05, mtop=scoating_05, mbottom=0,
+    mright=0, mleft=scoating_05, mbottom=scoating_05, mtop=0,
    enableGravity=enable_gravity) 
    AT (0, 0, selene_distance+4*selene_segment) RELATIVE arm_selene1

@@ -163,7 +163,7 @@ COMPONENT E02_03_06 = Elliptic_guide_gravity(
    linyh = selene_distance+5*selene_segment, loutyh= selene_distance+9*selene_segment,
    linxw = selene_distance+5*selene_segment, loutxw= selene_distance+9*selene_segment,
    xwidth=selene_b*2, yheight=selene_b*2,
-    mright=0, mleft=scoating_06, mtop=scoating_06, mbottom=0,
+    mright=0, mleft=scoating_06, mbottom=scoating_06, mtop=0,
    enableGravity=enable_gravity) 
    AT (0, 0, selene_distance+5*selene_segment) RELATIVE arm_selene1

@@ -172,7 +172,7 @@ COMPONENT E02_03_07 = Elliptic_guide_gravity(
    linyh = selene_distance+6*selene_segment, loutyh= selene_distance+8*selene_segment,
    linxw = selene_distance+6*selene_segment, loutxw= selene_distance+8*selene_segment,
    xwidth=selene_b*2, yheight=selene_b*2,
-    mright=0, mleft=scoating_07, mtop=scoating_07, mbottom=0,
+    mright=0, mleft=scoating_07, mbottom=scoating_07, mtop=0,
    enableGravity=enable_gravity) 
    AT (0, 0, selene_distance+6*selene_segment) RELATIVE arm_selene1

@@ -181,7 +181,7 @@ COMPONENT E02_03_08 = Elliptic_guide_gravity(
    linyh = selene_distance+7*selene_segment, loutyh= selene_distance+7*selene_segment,
    linxw = selene_distance+7*selene_segment, loutxw= selene_distance+7*selene_segment,
    xwidth=selene_b*2, yheight=selene_b*2,
-    mright=0, mleft=scoating_08, mtop=scoating_08, mbottom=0,
+    mright=0, mleft=scoating_08, mbottom=scoating_08, mtop=0,
    enableGravity=enable_gravity) 
    AT (0, 0, selene_distance+7*selene_segment) RELATIVE arm_selene1

@@ -190,7 +190,7 @@ COMPONENT E02_03_09 = Elliptic_guide_gravity(
    linyh = selene_distance+8*selene_segment, loutyh= selene_distance+6*selene_segment,
    linxw = selene_distance+8*selene_segment, loutxw= selene_distance+6*selene_segment,
    xwidth=selene_b*2, yheight=selene_b*2,
-    mright=0, mleft=scoating_09, mtop=scoating_09, mbottom=0,
+    mright=0, mleft=scoating_09, mbottom=scoating_09, mtop=0,
    enableGravity=enable_gravity) 
    AT (0, 0, selene_distance+8*selene_segment) RELATIVE arm_selene1

@@ -199,7 +199,7 @@ COMPONENT E02_03_10 = Elliptic_guide_gravity(
    linyh = selene_distance+9*selene_segment, loutyh= selene_distance+5*selene_segment,
    linxw = selene_distance+9*selene_segment, loutxw= selene_distance+5*selene_segment,
    xwidth=selene_b*2, yheight=selene_b*2,
-    mright=0, mleft=scoating_10, mtop=scoating_10, mbottom=0,
+    mright=0, mleft=scoating_10, mbottom=scoating_10, mtop=0,
    enableGravity=enable_gravity) 
    AT (0, 0, selene_distance+9*selene_segment) RELATIVE arm_selene1

@@ -208,7 +208,7 @@ COMPONENT E02_03_11 = Elliptic_guide_gravity(
    linyh = selene_distance+10*selene_segment, loutyh= selene_distance+4*selene_segment,
    linxw = selene_distance+10*selene_segment, loutxw= selene_distance+4*selene_segment,
    xwidth=selene_b*2, yheight=selene_b*2,
-    mright=0, mleft=scoating_11, mtop=scoating_11, mbottom=0,
+    mright=0, mleft=scoating_11, mbottom=scoating_11, mtop=0,
    enableGravity=enable_gravity) 
    AT (0, 0, selene_distance+10*selene_segment) RELATIVE arm_selene1

@@ -217,7 +217,7 @@ COMPONENT E02_03_12 = Elliptic_guide_gravity(
    linyh = selene_distance+11*selene_segment, loutyh= selene_distance+3*selene_segment,
    linxw = selene_distance+11*selene_segment, loutxw= selene_distance+3*selene_segment,
    xwidth=selene_b*2, yheight=selene_b*2,
-    mright=0, mleft=scoating_12, mtop=scoating_12, mbottom=0,
+    mright=0, mleft=scoating_12, mbottom=scoating_12, mtop=0,
    enableGravity=enable_gravity) 
    AT (0, 0, selene_distance+11*selene_segment) RELATIVE arm_selene1

@@ -226,7 +226,7 @@ COMPONENT E02_03_13 = Elliptic_guide_gravity(
    linyh = selene_distance+12*selene_segment, loutyh= selene_distance+2*selene_segment,
    linxw = selene_distance+12*selene_segment, loutxw= selene_distance+2*selene_segment,
    xwidth=selene_b*2, yheight=selene_b*2,
-    mright=0, mleft=scoating_13, mtop=scoating_13, mbottom=0,
+    mright=0, mleft=scoating_13, mbottom=scoating_13, mtop=0,
    enableGravity=enable_gravity) 
    AT (0, 0, selene_distance+12*selene_segment) RELATIVE arm_selene1

@@ -235,7 +235,7 @@ COMPONENT E02_03_14 = Elliptic_guide_gravity(
    linyh = selene_distance+13*selene_segment, loutyh= selene_distance+1*selene_segment,
    linxw = selene_distance+13*selene_segment, loutxw= selene_distance+1*selene_segment,
    xwidth=selene_b*2, yheight=selene_b*2,
-    mright=0, mleft=scoating_14, mtop=scoating_14, mbottom=0,
+    mright=0, mleft=scoating_14, mbottom=scoating_14, mtop=0,
    enableGravity=enable_gravity) 
    AT (0, 0, selene_distance+13*selene_segment) RELATIVE arm_selene1

@@ -244,14 +244,14 @@ COMPONENT E02_03_15 = Elliptic_guide_gravity(
    linyh = selene_distance+14*selene_segment, loutyh= selene_distance,
    linxw = selene_distance+14*selene_segment, loutxw= selene_distance,
    xwidth=selene_b*2, yheight=selene_b*2,
-    mright=0, mleft=scoating_15, mtop=scoating_15, mbottom=0,
+    mright=0, mleft=scoating_15, mbottom=scoating_15, mtop=0,
    enableGravity=enable_gravity) 
    AT (0, 0, selene_distance+14*selene_segment) RELATIVE arm_selene1

 /* Absorber to cut direct view beam (Copper in CAD model) */    
 COMPONENT slit_after_selene_guide_1 = Slit(
    xmin = 0, xmax = selene_entry+0.005,
-    ymin = 0, ymax = selene_entry+0.01)
+    ymin = -selene_entry-0.005, ymax = 0)
    AT (0, 0, 2*selene_c-selene_distance+0.001) RELATIVE arm_selene1

 COMPONENT block_after_selene_guide_1 = Absorber(
@@ -42,7 +42,7 @@ TRACE
 /* Absorber to cut direct view beam (Bor-Al in CAD model) */
 COMPONENT slit_before_selene_guide_2 = Slit(
        xmin = -selene_entry-0.005, xmax=0,
-        ymin = -selene_entry-0.01, ymax = 0)
+        ymin = 0, ymax = selene_entry+0.01)
        AT (0, 0, selene_distance-0.002) RELATIVE arm_selene2

 COMPONENT block_before_selene_guide_2 = Absorber(
@@ -59,7 +59,7 @@ COMPONENT E02_04_01 = Elliptic_guide_gravity(
    linyh = selene_distance, loutyh= selene_distance+14*selene_segment,
    linxw = selene_distance, loutxw= selene_distance+14*selene_segment,
    xwidth=selene_b*2, yheight=selene_b*2,
-    mright=scoating_15, mleft=0, mtop=0, mbottom=scoating_15,
+    mright=scoating_15, mleft=0, mbottom=0, mtop=scoating_15,
    enableGravity=enable_gravity) 
    AT (0, 0, selene_distance) RELATIVE arm_selene2

@@ -68,7 +68,7 @@ COMPONENT E02_04_02 = Elliptic_guide_gravity(
    linyh = selene_distance+1*selene_segment, loutyh= selene_distance+13*selene_segment,
    linxw = selene_distance+1*selene_segment, loutxw= selene_distance+13*selene_segment,
    xwidth=selene_b*2, yheight=selene_b*2,
-    mright=scoating_14, mleft=0, mtop=0, mbottom=scoating_14,
+    mright=scoating_14, mleft=0, mbottom=0, mtop=scoating_14,
    enableGravity=enable_gravity) 
    AT (0, 0, selene_distance+1*selene_segment) RELATIVE arm_selene2

@@ -77,7 +77,7 @@ COMPONENT E02_04_03 = Elliptic_guide_gravity(
    linyh = selene_distance+2*selene_segment, loutyh= selene_distance+12*selene_segment,
    linxw = selene_distance+2*selene_segment, loutxw= selene_distance+12*selene_segment,
    xwidth=selene_b*2, yheight=selene_b*2,
-    mright=scoating_13, mleft=0, mtop=0, mbottom=scoating_13,
+    mright=scoating_13, mleft=0, mbottom=0, mtop=scoating_13,
    enableGravity=enable_gravity) 
    AT (0, 0, selene_distance+2*selene_segment) RELATIVE arm_selene2

@@ -86,7 +86,7 @@ COMPONENT E02_04_04 = Elliptic_guide_gravity(
    linyh = selene_distance+3*selene_segment, loutyh= selene_distance+11*selene_segment,
    linxw = selene_distance+3*selene_segment, loutxw= selene_distance+11*selene_segment,
    xwidth=selene_b*2, yheight=selene_b*2,
-    mright=scoating_12, mleft=0, mtop=0, mbottom=scoating_12,
+    mright=scoating_12, mleft=0, mbottom=0, mtop=scoating_12,
    enableGravity=enable_gravity) 
    AT (0, 0, selene_distance+3*selene_segment) RELATIVE arm_selene2

@@ -95,7 +95,7 @@ COMPONENT E02_04_05 = Elliptic_guide_gravity(
    linyh = selene_distance+4*selene_segment, loutyh= selene_distance+10*selene_segment,
    linxw = selene_distance+4*selene_segment, loutxw= selene_distance+10*selene_segment,
    xwidth=selene_b*2, yheight=selene_b*2,
-    mright=scoating_11, mleft=0, mtop=0, mbottom=scoating_11,
+    mright=scoating_11, mleft=0, mbottom=0, mtop=scoating_11,
    enableGravity=enable_gravity) 
    AT (0, 0, selene_distance+4*selene_segment) RELATIVE arm_selene2

@@ -104,7 +104,7 @@ COMPONENT E02_04_06 = Elliptic_guide_gravity(
    linyh = selene_distance+5*selene_segment, loutyh= selene_distance+9*selene_segment,
    linxw = selene_distance+5*selene_segment, loutxw= selene_distance+9*selene_segment,
    xwidth=selene_b*2, yheight=selene_b*2,
-    mright=scoating_10, mleft=0, mtop=0, mbottom=scoating_10,
+    mright=scoating_10, mleft=0, mbottom=0, mtop=scoating_10,
    enableGravity=enable_gravity) 
    AT (0, 0, selene_distance+5*selene_segment) RELATIVE arm_selene2

@@ -113,7 +113,7 @@ COMPONENT E02_04_07 = Elliptic_guide_gravity(
    linyh = selene_distance+6*selene_segment, loutyh= selene_distance+8*selene_segment,
    linxw = selene_distance+6*selene_segment, loutxw= selene_distance+8*selene_segment,
    xwidth=selene_b*2, yheight=selene_b*2,
-    mright=scoating_09, mleft=0, mtop=0, mbottom=scoating_09,
+    mright=scoating_09, mleft=0, mbottom=0, mtop=scoating_09,
    enableGravity=enable_gravity) 
    AT (0, 0, selene_distance+6*selene_segment) RELATIVE arm_selene2

@@ -122,7 +122,7 @@ COMPONENT E02_04_08 = Elliptic_guide_gravity(
    linyh = selene_distance+7*selene_segment, loutyh= selene_distance+7*selene_segment,
    linxw = selene_distance+7*selene_segment, loutxw= selene_distance+7*selene_segment,
    xwidth=selene_b*2, yheight=selene_b*2,
-    mright=scoating_08, mleft=0, mtop=0, mbottom=scoating_08,
+    mright=scoating_08, mleft=0, mbottom=0, mtop=scoating_08,
    enableGravity=enable_gravity) 
    AT (0, 0, selene_distance+7*selene_segment) RELATIVE arm_selene2

@@ -131,7 +131,7 @@ COMPONENT E02_04_09 = Elliptic_guide_gravity(
    linyh = selene_distance+8*selene_segment, loutyh= selene_distance+6*selene_segment,
    linxw = selene_distance+8*selene_segment, loutxw= selene_distance+6*selene_segment,
    xwidth=selene_b*2, yheight=selene_b*2,
-    mright=scoating_07, mleft=0, mtop=0, mbottom=scoating_07,
+    mright=scoating_07, mleft=0, mbottom=0, mtop=scoating_07,
    enableGravity=enable_gravity) 
    AT (0, 0, selene_distance+8*selene_segment) RELATIVE arm_selene2

@@ -140,7 +140,7 @@ COMPONENT E02_04_10 = Elliptic_guide_gravity(
    linyh = selene_distance+9*selene_segment, loutyh= selene_distance+5*selene_segment,
    linxw = selene_distance+9*selene_segment, loutxw= selene_distance+5*selene_segment,
    xwidth=selene_b*2, yheight=selene_b*2,
-    mright=scoating_06, mleft=0, mtop=0, mbottom=scoating_06,
+    mright=scoating_06, mleft=0, mbottom=0, mtop=scoating_06,
    enableGravity=enable_gravity) 
    AT (0, 0, selene_distance+9*selene_segment) RELATIVE arm_selene2

@@ -149,7 +149,7 @@ COMPONENT E02_04_11 = Elliptic_guide_gravity(
    linyh = selene_distance+10*selene_segment, loutyh= selene_distance+4*selene_segment,
    linxw = selene_distance+10*selene_segment, loutxw= selene_distance+4*selene_segment,
    xwidth=selene_b*2, yheight=selene_b*2,
-    mright=scoating_05, mleft=0, mtop=0, mbottom=scoating_05,
+    mright=scoating_05, mleft=0, mbottom=0, mtop=scoating_05,
    enableGravity=enable_gravity) 
    AT (0, 0, selene_distance+10*selene_segment) RELATIVE arm_selene2

@@ -158,7 +158,7 @@ COMPONENT E02_04_12 = Elliptic_guide_gravity(
    linyh = selene_distance+11*selene_segment, loutyh= selene_distance+3*selene_segment,
    linxw = selene_distance+11*selene_segment, loutxw= selene_distance+3*selene_segment,
    xwidth=selene_b*2, yheight=selene_b*2,
-    mright=scoating_04, mleft=0, mtop=0, mbottom=scoating_04,
+    mright=scoating_04, mleft=0, mbottom=0, mtop=scoating_04,
    enableGravity=enable_gravity) 
    AT (0, 0, selene_distance+11*selene_segment) RELATIVE arm_selene2

@@ -167,7 +167,7 @@ COMPONENT E02_04_13 = Elliptic_guide_gravity(
    linyh = selene_distance+12*selene_segment, loutyh= selene_distance+2*selene_segment,
    linxw = selene_distance+12*selene_segment, loutxw= selene_distance+2*selene_segment,
    xwidth=selene_b*2, yheight=selene_b*2,
-    mright=scoating_03, mleft=0, mtop=0, mbottom=scoating_03,
+    mright=scoating_03, mleft=0, mbottom=0, mtop=scoating_03,
    enableGravity=enable_gravity) 
    AT (0, 0, selene_distance+12*selene_segment) RELATIVE arm_selene2

@@ -176,7 +176,7 @@ COMPONENT E02_04_14 = Elliptic_guide_gravity(
    linyh = selene_distance+13*selene_segment, loutyh= selene_distance+1*selene_segment,
    linxw = selene_distance+13*selene_segment, loutxw= selene_distance+1*selene_segment,
    xwidth=selene_b*2, yheight=selene_b*2,
-    mright=scoating_02, mleft=0, mtop=0, mbottom=scoating_02,
+    mright=scoating_02, mleft=0, mbottom=0, mtop=scoating_02,
    enableGravity=enable_gravity) 
    AT (0, 0, selene_distance+13*selene_segment) RELATIVE arm_selene2

@@ -185,14 +185,14 @@ COMPONENT E02_04_15 = Elliptic_guide_gravity(
    linyh = selene_distance+14*selene_segment, loutyh= selene_distance,
    linxw = selene_distance+14*selene_segment, loutxw= selene_distance,
    xwidth=selene_b*2, yheight=selene_b*2,
-    mright=scoating_01, mleft=0, mtop=0, mbottom=scoating_01,
+    mright=scoating_01, mleft=0, mbottom=0, mtop=scoating_01,
    enableGravity=enable_gravity) 
    AT (0, 0, selene_distance+14*selene_segment) RELATIVE arm_selene2

 /* Absorber to cut direct view beam (Bor-Al in CAD model) */
 COMPONENT slit_after_selene_guide_2 = Slit(
    xmin = -selene_entry-0.001, xmax=0, xmax = 0.0,
-    ymin = -selene_entry-0.005, ymax = 0)
+    ymin = 0, ymax = selene_entry+0.01)
    AT (0, 0, 2*selene_c-selene_distance+0.001) RELATIVE arm_selene2

 COMPONENT block_after_selene_guide_2 = Absorber(
@@ -0,0 +1,91 @@
+/*******************************************************************************
+*
+* McStas, neutron ray-tracing package
+*         Copyright 1997-2002, All rights reserved
+*         Risoe National Laboratory, Roskilde, Denmark
+*         Institut Laue Langevin, Grenoble, France
+*
+* Written by: Erik B Knudsen
+* Date: May 2017
+* Version: $Revision$
+* Release: McStas 2.4
+* Origin: DTU Physics
+*
+* Component: Pol_RFSF_ideal
+*
+*
+* %I
+*
+* Ideal model of a spin flipper
+*
+* %D
+* This component simply mirrors the polarization vector of the neutron
+* ray in the plane through (0,0,0) with normal nx,ny,nz.
+* The flipper is surrounded by a perfectly absorbing box. Neutron rays not hitting
+* the box are left untouched.
+*
+* %P
+* Input parameters:
+* nx:    [ ] x-component of the normal vector of the flipping plane.
+* ny:    [ ] y-component of the normal vector of the flipping plane.
+* nz:    [ ] z-component of the normal vector of the flipping plane.
+* xwidth: [m] width of the spin flipper.
+* yheight: [m] height of the spin flipper.
+* zdepth: [m] length of the spin flipper.
+*
+*
+* %E
+*******************************************************************************/
+
+DEFINE COMPONENT Pol_SF_ideal
+DEFINITION PARAMETERS ()
+SETTING PARAMETERS (nx=0, ny=1, nz=0, xwidth=0.1, yheight=0.1, zdepth=0.1)
+OUTPUT PARAMETERS ()
+/* Neutron parameters: (x,y,z,vx,vy,vz,t,sx,sy,sz,p) */
+TRACE
+%{
+    int hit;
+    double t0,t1;
+    hit=box_intersect(&t0,&t1, x,y,z,vx,vy,vz, xwidth,yheight,zdepth);
+    if(hit){
+        PROP_DT(t0);
+        if(fabs(z- -zdepth*0.5)>DBL_EPSILON){
+            /*neutron must have hit the side walls*/
+            ABSORB;
+        }
+        /*move to center of box and flip*/
+        PROP_Z0;
+        SCATTER;
+        double s=scalar_prod(sx,sy,sz,nx,ny,nz);
+        if (s!=0){
+            sx-=2*s*nx;
+            sy-=2*s*ny;
+            sz-=2*s*nz;
+        }
+        PROP_DT((t1-t0)/2);/*propagate the remaining distance to the box exit*/
+        if(fabs(z-zdepth*0.5)>DBL_EPSILON){
+            ABSORB;
+        }
+    }
+
+
+%}
+
+MCDISPLAY
+%{
+    double dx=xwidth/16;
+    double dy=yheight/8;
+  
+  box(0,0,0,xwidth,yheight,zdepth);
+  
+  line(dx,-dy,0,dx,-dy+yheight/2.0,0);
+  line(-dx,dy,0,-dx,dy-yheight/2.0,0);
+  line(dx,-dy+yheight/2.0,0, dx+xwidth/16,-dy+yheight-yheight/16,0);
+  line(dx,-dy+yheight/2.0,0, dx-xwidth/16,-dy+yheight-yheight/16,0);
+  
+  line(-dx,dy-yheight/2.0,0, -dx+xwidth/16,dy-yheight+yheight/16,0);
+  line(-dx,dy-yheight/2.0,0, -dx-xwidth/16,dy-yheight+yheight/16,0);
+
+%}
+
+END
@@ -0,0 +1,108 @@
+/*******************************************************************************
+*         McStas instrument definition URL=http://www.mcstas.org
+*
+* Instrument: PolarizerTest
+*
+* %Identification
+* Written by: Artur Glavic (artur.glavic@psi.ch)
+* Date: 25. 07. 2019
+* Origin: PSI
+* Release: McStas 2.5
+* Version: 1.0
+*
+* Test for polarization parameters of curved transmission polarizer
+*
+* %Description
+* 
+*
+* %Parameters
+*
+* %End
+*******************************************************************************/
+
+DEFINE INSTRUMENT PolarizerTest(m_up=5.08, m_down=0.6, R0=1.00,
+                                m_residual=0.55, Theta=1.5,
+                                lambda_min=2.0, lambda_max=32.0,
+                                gamma=1.66, focus_height=0.00001,
+                                phi=0.0, polarizer_start=0.2
+                               )
+
+DECLARE
+%{
+double lambda_mean,delta_lambda,polarizer_length,zero_position;
+double source_div, detector_height;
+
+int use_streight=0;
+  
+%}
+
+INITIALIZE
+%{
+lambda_mean=(lambda_min+lambda_max)/2.0;
+delta_lambda=(lambda_max-lambda_min)/2.0;
+
+polarizer_length=(exp(Theta/gamma)-1.0)*polarizer_start;
+zero_position=exp(0.5*Theta/gamma)*polarizer_start;
+
+source_div=0.1*Theta/180.*PI;
+detector_height=source_div/0.1*(polarizer_length+polarizer_start+0.5);
+
+%}
+
+TRACE
+
+COMPONENT origin = Progress_bar()
+    AT (0,0,0) ABSOLUTE
+
+COMPONENT focus  = Arm()
+    AT (0,0,0) RELATIVE origin
+    ROTATED (phi,0,0) RELATIVE origin
+
+COMPONENT Source = Source_simple(xwidth = 0.00001, yheight = focus_height, 
+                                 dist = 0.1, focus_xw = 0.0001, 
+                                 focus_yh = source_div, 
+                                 lambda0 = lambda_mean, dlambda = delta_lambda, 
+                                 gauss=0)
+        AT (0, 0, 0) RELATIVE origin
+
+COMPONENT FluxIn = L_monitor(xwidth = 0.5, yheight = 0.5, filename="fluxin", 
+          nL=601, Lmin=lambda_min, Lmax=lambda_max)
+         AT (0, 0, 0.101) RELATIVE origin
+
+COMPONENT polarizer = Polariser(enable_ref=1, abs_ref=0, 
+                                reflect_d=0, reflect_u=0, T_loss=4.0e3,
+                                m_substrate=0.469522, d_substrate = 5e-4, 
+                                m_u=m_up, m_d=m_down, R0=R0,
+                                m_residual=m_residual,
+                                lin=polarizer_start, length=polarizer_length,
+                                delta_theta=(Theta)*PI/180.0, h2=0.1, h1=0.05,
+                                both_coated=1, alpha=2.3, W = 0.0014)
+        WHEN use_streight==0
+        AT (0, -5e-4, polarizer_start) RELATIVE focus
+
+COMPONENT streight = Mirror(xwidth = 0.2, yheight = 0.2, 
+                            m=5.0, center=1, transmit=0)
+        WHEN use_streight==1
+        AT (0, 0, zero_position) RELATIVE origin
+        ROTATED (90.0-gamma,0,0) RELATIVE origin
+
+
+COMPONENT FluxOut = L_monitor(xwidth = 0.5, yheight = detector_height, 
+                              filename="fluxout", 
+          nL=601, Lmin=lambda_min, Lmax=lambda_max)
+        AT (0, 0, polarizer_length+polarizer_start+0.5) RELATIVE origin
+COMPONENT PolMon = MeanPolLambda_monitor(xwidth=0.5, yheight=detector_height, 
+                                         mx=-1, 
+                      nL=601, Lmin=lambda_min, Lmax=lambda_max, 
+                      filename="polarization")
+        AT (0, 0, polarizer_length+polarizer_start+0.5) RELATIVE origin
+
+
+    
+FINALLY
+%{
+%}
+
+END
+
+
@@ -0,0 +1,58 @@
+4.37173E-05	0.253838498
+0.001967279	0.548126562
+0.004240578	0.781912929
+0.006513878	0.831781609
+0.008656026	0.935568791
+0.010841891	0.996046699
+0.012984039	0.994254859
+0.015038752	0.780745054
+0.017443204	0.571166135
+0.019497917	0.421992388
+0.021771217	0.347878292
+0.023913365	0.314863976
+0.026317816	0.273648917
+0.028241378	0.248910367
+0.030514678	0.229613667
+0.032700543	0.210315136
+0.034711539	0.201079179
+0.03711599	0.179153501
+0.039301855	0.174572119
+0.041444003	0.161570874
+0.043629868	0.159330731
+0.045772016	0.158627627
+0.047957881	0.133760075
+0.050231181	0.128230852
+0.052373329	0.135460425
+0.054559194	0.125901964
+0.056701342	0.120064418
+0.058974642	0.122922579
+0.061160507	0.127084935
+0.063171503	0.12641248
+0.06548852	0.117637177
+0.067630668	0.105706827
+0.069903968	0.112415362
+0.072089833	0.119429932
+0.074231981	0.105676178
+0.076417846	0.107716872
+0.078428842	0.107129046
+0.080833293	0.10262909
+0.082888007	0.094164854
+0.085161306	0.092239896
+0.087303454	0.085655788
+0.089620471	0.081615114
+0.091631467	0.076984785
+0.093817332	0.076157254
+0.096090632	0.070972035
+0.09823278	0.060551277
+0.100287493	0.071366358
+0.102691945	0.065426801
+0.104834093	0.059045344
+0.107019958	0.056229269
+0.109162106	0.061290519
+0.111347971	0.051160701
+0.113490119	0.053836338
+0.115763418	0.05839439
+0.117949284	0.057514252
+0.120091431	0.047536765
+0.122364731	0.04877829
+0.300000000 0.000000000		
@@ -0,0 +1,58 @@
+4.37173E-05	0.224586133
+0.001967279	0.518057252
+0.004240578	0.775672976
+0.006513878	0.825879049
+0.008656026	0.899985882
+0.010841891	0.967789786
+0.012984039	0.99196296
+0.015038752	0.992909754
+0.017443204	0.994177124
+0.019497917	0.991424846
+0.021771217	0.993887344
+0.023913365	0.998648926
+0.026317816	0.999361915
+0.028241378	0.998678679
+0.030514678	0.998109885
+0.032700543	0.997772638
+0.034711539	0.997392554
+0.03711599	0.999600524
+0.039301855	0.994779551
+0.041444003	0.996274647
+0.043629868	0.996149207
+0.045772016	0.998305774
+0.047957881	0.99658353
+0.050231181	0.995950077
+0.052373329	0.995563046
+0.054559194	0.995479284
+0.056701342	0.993347667
+0.058974642	0.990508095
+0.061160507	0.990476431
+0.063171503	0.988754593
+0.06548852	0.987959462
+0.067630668	0.987058572
+0.069903968	0.988939946
+0.072089833	0.986821236
+0.074231981	0.985149296
+0.076417846	0.987362592
+0.078428842	0.986507086
+0.080833293	0.98295765
+0.082888007	0.983313364
+0.085161306	0.983817788
+0.087303454	0.983554288
+0.089620471	0.979763465
+0.091631467	0.975348682
+0.093817332	0.975887375
+0.096090632	0.972236927
+0.09823278	0.965515882
+0.100287493	0.962852402
+0.102691945	0.956266464
+0.104834093	0.953509902
+0.107019958	0.945236222
+0.109162106	0.808306574
+0.111347971	0.186001557
+0.113490119	0.078929784
+0.115763418	0.051976893
+0.117949284	0.05338487
+0.120091431	0.04844847
+0.122364731	0.053399168
+0.300000000 0.000000000
@@ -1,4 +1,6 @@
 #!/bin/bash
+export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/afs/psi.ch/project/sinq/sl6-64/mcstas2.4/mcstas/2.4/libs
+

 if [ Estia_baseline.instr -nt Estia_baseline.out ] || [ ! -f Estia_baseline.out ] \
   || [ Estia_feeder.instr -nt Estia_baseline.out ] \
@@ -6,6 +8,6 @@ if [ Estia_baseline.instr -nt Estia_baseline.out ] || [ ! -f Estia_baseline.out
   || [ Estia_mf.instr -nt Estia_baseline.out ] \
   || [ Estia_selene2.instr -nt Estia_baseline.out ]; then
 	rm Estia_baseline.c Estia_baseline.out
-	mcstas -o Estia_baseline.c Estia_baseline.instr
-	mpicc -O3 -o Estia_baseline.out Estia_baseline.c -lm -DUSE_MPI
+	mcstas -o Estia_baseline.c Estia_baseline.instr --trace
+	mpicc -O2 -o Estia_baseline.out Estia_baseline.c -lm -DUSE_MPI -DUSE_NEXUS -lNeXus
 fi
@@ -0,0 +1,3 @@
+mcc05:72
+mcc06:72
+
@@ -1,102 +0,0 @@
-0.00	1.000
-0.01	0.0099682
-0.0149	0.0042479
-0.0198	0.0022557
-0.0247	0.0013447
-0.0296	0.00086176
-0.0345	0.000582
-0.0394	0.0004107
-0.0443	0.00030205
-0.0492	0.00023151
-0.0541	0.0001849
-0.059	0.00015356
-0.0639	0.00013197
-0.0688	0.00011657
-0.0737	0.00010502
-0.0786	9.58E-05
-0.0835	8.80E-05
-0.0884	8.11E-05
-0.0933	7.47E-05
-0.0982	6.88E-05
-0.1031	6.33E-05
-0.108	5.82E-05
-0.1129	5.35E-05
-0.1178	4.94E-05
-0.1227	4.57E-05
-0.1276	4.24E-05
-0.1325	3.96E-05
-0.1374	3.71E-05
-0.1423	3.48E-05
-0.1472	3.27E-05
-0.1521	3.08E-05
-0.157	2.89E-05
-0.1619	2.71E-05
-0.1668	2.53E-05
-0.1717	2.35E-05
-0.1766	2.17E-05
-0.1815	2.00E-05
-0.1864	1.83E-05
-0.1913	1.66E-05
-0.1962	1.51E-05
-0.2011	1.36E-05
-0.206	1.22E-05
-0.2109	1.08E-05
-0.2158	9.61E-06
-0.2207	8.46E-06
-0.2256	7.39E-06
-0.2305	6.39E-06
-0.2354	5.46E-06
-0.2403	4.61E-06
-0.2452	3.84E-06
-0.2501	3.16E-06
-0.255	2.55E-06
-0.2599	2.04E-06
-0.2648	1.61E-06
-0.2697	1.26E-06
-0.2746	9.93E-07
-0.2795	7.98E-07
-0.2844	6.64E-07
-0.2893	5.82E-07
-0.2942	5.39E-07
-0.2991	5.24E-07
-0.304	5.28E-07
-0.3089	5.41E-07
-0.3138	5.58E-07
-0.3187	5.73E-07
-0.3236	5.83E-07
-0.3285	5.88E-07
-0.3334	5.88E-07
-0.3383	5.84E-07
-0.3432	5.77E-07
-0.3481	5.69E-07
-0.353	5.62E-07
-0.3579	5.57E-07
-0.3628	5.53E-07
-0.3677	5.52E-07
-0.3726	5.53E-07
-0.3775	5.56E-07
-0.3824	5.61E-07
-0.3873	5.67E-07
-0.3922	5.74E-07
-0.3971	5.81E-07
-0.402	5.89E-07
-0.4069	5.96E-07
-0.4118	6.04E-07
-0.4167	6.12E-07
-0.4216	6.19E-07
-0.4265	6.27E-07
-0.4314	6.35E-07
-0.4363	6.43E-07
-0.4412	6.50E-07
-0.4461	6.58E-07
-0.451	6.66E-07
-0.4559	6.74E-07
-0.4608	6.82E-07
-0.4657	6.89E-07
-0.4706	6.97E-07
-0.4755	7.04E-07
-0.4804	7.11E-07
-0.4853	7.16E-07
-0.4902	7.20E-07
-0.4951	7.21E-07
-0.5	7.23E-07
@@ -0,0 +1,83 @@
+#!/usr/bin/env python
+'''
+Run a simulation through various values of polarizer 1/2 distance to focus
+and generate a datafile with analyzed values for polarization and transmission
+for the short and long wavelength area.
+'''
+
+import sys, os
+from numpy import *
+sys.path.append('../analysis')
+from mcstas_reader import McSim
+
+Iref=1.0
+L=linspace(1.95, 32.05, 302)
+Lc=(L[:-1]+L[1:])/2.
+
+gamma1=1.8
+gamma2=1.66
+command_s_ref="mpiexec -np 60 --hostfile hostnames Estia_baseline.out --ncount=1e10 --dir=../results/polarizer_s_ref --format=NeXus sample=1 omegaa=2.0 over_illumination=0.001  lambda_start=2.0 lambda_end=32.0 sample_length=0.01 enable_polarizer=0"
+command_l_ref="mpiexec -np 60 --hostfile hostnames Estia_baseline.out --ncount=2e9 --dir=../results/polarizer_l_ref --format=NeXus sample=1 omegaa=6.0 over_illumination=0.001  lambda_start=2.0 lambda_end=32.0 sample_length=0.048 enable_polarizer=0"
+command_s="mpiexec -np 60 --hostfile hostnames Estia_baseline.out --ncount=5e9 --dir=../results/polarizer_s --format=NeXus sample=1 omegaa=2.0 over_illumination=0.001 pol1_start=%%f pol1_angle=%f pol2_start=%%f pol2_angle=%f lambda_start=2.0 lambda_end=32.0 sample_length=0.01 enable_polarizer=3"%(gamma1, gamma2)
+command_l="mpiexec -np 60 --hostfile hostnames Estia_baseline.out --ncount=1e9 --dir=../results/polarizer_l --format=NeXus sample=1 omegaa=6.0 over_illumination=0.001 pol1_start=%%f pol1_angle=%f pol2_start=%%f pol2_angle=%f lambda_start=2.0 lambda_end=32.0 sample_length=0.048 enable_polarizer=3"%(gamma1, gamma2)
+
+lengths=linspace(0.1, 0.6, 25)  
+
+def get_polarization(ds):
+    N,ignore=histogram(ds.data['L'], bins=L)
+    PN,ignore=histogram(ds.data['L'], bins=L, weights=sqrt(ds.data['sx']**2+ds.data['sy']**2+ds.data['sz']**2))
+    return PN/maximum(N,1)
+                       
+
+def get_intensity(ds):
+    I, ignore=histogram(ds.data['L'], bins=L, weights=ds.data['p'])
+    return I
+
+def analyze(ds):
+    P=get_polarization(ds)
+    I=get_intensity(ds)
+    T=I/maximum(Iref, Iref[Iref>0].min())
+    return P,T
+
+def get_data(fname):
+    det=McSim(fname)['tof_detector']
+    P,T=analyze(det)
+    return [P[17], P[230], T[17], T[230]]
+
+def simulate_and_analyze(pol1_start, pol2_start):
+    print pol1_start, pol2_start
+    os.system('rm -rf ../results/polarizer_?')
+    os.system(command_s%(pol1_start, pol2_start))
+    os.system(command_l%(pol1_start, pol2_start))
+    
+    global Iref
+    Iref=Iref_s
+    ds=get_data('../results/polarizer_s')
+    Iref=Iref_l
+    dl=get_data('../results/polarizer_l')
+    with open('../results/polarizer_data.dat', 'a') as fh:
+        fh.write((10*'%.6f '+'\n')%tuple([pol1_start, pol2_start]+ds+dl))
+
+if __name__=='__main__':
+    if not (os.path.exists('../results/polarizer_s_ref') and 
+            os.path.exists('../results/polarizer_l_ref')):
+        os.system('rm -rf ../results/polarizer_?_ref')
+        print 'Simulate reference intensities'
+        os.system(command_s_ref)
+        os.system(command_l_ref)
+      
+    
+    ref=McSim('../results/polarizer_s_ref')['tof_detector']
+    Iref_s=get_intensity(ref)
+    ref=McSim('../results/polarizer_l_ref')['tof_detector']
+    Iref_l=get_intensity(ref)
+    
+    with open('../results/polarizer_data.dat', 'w') as fh:
+        fh.write('# pol1   pol2     P3.7_s   P25_s    T3.7_s   T25_s    P3.7_l   P25_l    T3.7_l   T25_l\n')
+    
+    for pol1 in lengths:
+        for pol2 in lengths:
+            simulate_and_analyze(pol1, pol2)
+        with open('../results/polarizer_data.dat', 'a') as fh:
+            fh.write('\n')
+            
@@ -0,0 +1,7 @@
+!#/bin/sh
+rm PolarizerTest.c PolarizerTest.out
+rm -r ../results/polarizer_coating
+mcstas -o PolarizerTest.c PolarizerTest.instr --trace
+#mpicc -O2 -o PolarizerTest.out PolarizerTest.c -lm -DUSE_MPI
+mpicc -O2 -o PolarizerTest.out PolarizerTest.c -lm -DUSE_MPI -DUSE_NEXUS -lNeXus -I/usr/local/include/nexus
+LD_LIBRARY_PATH=/usr/local/lib/ mpirun -np 6 ./PolarizerTest.out --ncount=1e8 --format=NeXus --dir=../results/polarizer_coating R0=1.0 gamma=1.66
@@ -1,213 +1,77 @@
 #!/bin/bash

 DEST=../results
-ncount=2e7
-use_cores=4
+ncount=1e8
+use_cores=16
 sample=4
-omega=0.8
-sample_length=0.01
+sample_length=0.005
 sample_height=0.01
 lambda_start=3.0
 lambda_end=32.0

-###################### Brilliance Transfer 10x10mm² and 1x1mm² VS ####################
-if [ Estia_baseline.instr -nt Estia_baseline.out ]; then
-	rm Estia_baseline.c Estia_baseline.out
-	mcstas -o Estia_baseline.c Estia_baseline.instr
-	mpicc -O3 -o Estia_baseline.out Estia_baseline.c -lm -DUSE_MPI -DUSE_NEXUS -lNeXus
-fi
-# 
-# if [ Estia_baseline_ana1.instr -nt Estia_baseline_ana1.out ]; then
-# 	rm Estia_baseline_ana1.c Estia_baseline_ana1.out
-# 	mcstas -o Estia_baseline_ana1.c Estia_baseline_ana1.instr
-# 	mpicc -O3 -o Estia_baseline_ana1.out Estia_baseline_ana1.c -lm -DUSE_MPI -DUSE_NEXUS -lNeXus
-# fi
-# 
-# if [ Estia_baseline_ana2.instr -nt Estia_baseline_ana2.out ]; then
-# 	rm Estia_baseline_ana2.c Estia_baseline_ana2.out
-# 	mcstas -o Estia_baseline_ana2.c Estia_baseline_ana2.instr
-# 	mpicc -O3 -o Estia_baseline_ana2.out Estia_baseline_ana2.c -lm -DUSE_MPI -DUSE_NEXUS -lNeXus
-# fi
+bash compile_if_needed.sh

+###################### Reference measurement 10x5mm² and 10x0.5mm² VS ####################

-###################### Reference and Ni-layer measurement 10x10mm² sample ####################
-# ncount=1e10
-sample_length=0.01
+ncount=1e8
+sample_length=0.005
 sample_height=0.01
-lambda_start=3.5
-lambda_end=30.0
-sample=1

-# omega=1.0
-# DESTi=$DEST/pol_ref_10x10_10
-# if [ -e "$DESTi" ]; then
-# 	rm -r "$DESTi"
-# fi
-# 
-# mpirun  -np $use_cores Estia_baseline.out \
-#         --dir="$DESTi" --ncount=$ncount --gravitation \
-#         omegaa=$omega operationmode=0 theta_resolution=0.04 over_illumination=0.000 \
-#         sample=$sample sample_length=$sample_length sample_height=$sample_height \
-#         lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=1 enable_chopper=0 enable_polarizer=0 enable_analyzer=0
-# 
-# DESTi=$DEST/pol1_10x10_10
-# if [ -e "$DESTi" ]; then
-# 	rm -r "$DESTi"
-# fi
-# 
-# mpirun  -np $use_cores Estia_baseline.out \
-#         --dir="$DESTi" --ncount=$ncount --gravitation \
-#         omegaa=$omega operationmode=0 theta_resolution=0.04 over_illumination=0.000 \
-#         sample=$sample sample_length=$sample_length sample_height=$sample_height \
-#         lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=1 enable_chopper=0 enable_polarizer=1 enable_analyzer=0
-# 
-# DESTi=$DEST/pol2_10x10_10
-# if [ -e "$DESTi" ]; then
-# 	rm -r "$DESTi"
-# fi
-# 
-# mpirun  -np $use_cores Estia_baseline.out \
-#         --dir="$DESTi" --ncount=$ncount --gravitation \
-#         omegaa=$omega operationmode=0 theta_resolution=0.04 over_illumination=0.000 \
-#         sample=$sample sample_length=$sample_length sample_height=$sample_height \
-#         lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=1 enable_chopper=0 enable_polarizer=2 enable_analyzer=0
-# # 
-# omega=7.0
-# DESTi=$DEST/pol1_10x10_70
-# if [ -e "$DESTi" ]; then
-# 	rm -r "$DESTi"
-# fi
-# 
-# mpirun  -np $use_cores Estia_baseline.out \
-#         --dir="$DESTi" --ncount=$ncount --gravitation \
-#         omegaa=$omega operationmode=0 theta_resolution=0.04 over_illumination=0.000 \
-#         sample=$sample sample_length=$sample_length sample_height=$sample_height \
-#         lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=1 enable_chopper=0 enable_polarizer=1 enable_analyzer=0
-# 
-# DESTi=$DEST/pol2_10x10_70
-# if [ -e "$DESTi" ]; then
-# 	rm -r "$DESTi"
-# fi
-# 
-# mpirun  -np $use_cores Estia_baseline.out \
-#         --dir="$DESTi" --ncount=$ncount --gravitation \
-#         omegaa=$omega operationmode=0 theta_resolution=0.04 over_illumination=0.000 \
-#         sample=$sample sample_length=$sample_length sample_height=$sample_height \
-#         lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=1 enable_chopper=0 enable_polarizer=2 enable_analyzer=0
-# 
-
-# ncount=1e8
-omega=0.0
-# DESTi=$DEST/pol1_10x50_70
-# if [ -e "$DESTi" ]; then
-# 	rm -r "$DESTi"
-# fi
-# 
-# mpirun  -np $use_cores Estia_baseline.out \
-#         --dir="$DESTi" --ncount=$ncount --gravitation \
-#         omegaa=$omega operationmode=0 theta_resolution=0.04 over_illumination=0.0025 \
-#         sample=$sample sample_length=$sample_length sample_height=$sample_height \
-#         lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=1 enable_chopper=0 enable_polarizer=1 enable_analyzer=0
-
-DESTi=$DEST/pol2_10x50_70
+DESTi=$DEST/pol_ref_10x5
 if [ -e "$DESTi" ]; then
 	rm -r "$DESTi"
 fi

-mpirun  -np $use_cores Estia_baseline.out \
-        --dir="$DESTi" --ncount=$ncount --gravitation \
-        omegaa=$omega operationmode=0 theta_resolution=0.04 over_illumination=0.0025 \
+mpirun  -np $use_cores --hostfile hostnames Estia_baseline.out \
+        --dir="$DESTi" --format=NeXus --ncount=$ncount \
        sample=$sample sample_length=$sample_length sample_height=$sample_height \
-        lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=1 enable_chopper=0 enable_polarizer=2 enable_analyzer=0
-# 
-# ncount=5e9
-# sample_length=0.01
-# omega=1.0
-# sample_length=0.003
-# DESTi=$DEST/pol_ref_3x10_10
-# if [ -e "$DESTi" ]; then
-# 	rm -r "$DESTi"
-# fi
-# 
-# mpirun  -np $use_cores Estia_baseline.out \
-#         --dir="$DESTi" --ncount=$ncount --gravitation \
-#         omegaa=$omega operationmode=0 theta_resolution=0.04 over_illumination=0.000 \
-#         sample=$sample sample_length=$sample_length sample_height=$sample_height \
-#         lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=1 enable_chopper=0 enable_polarizer=0 enable_analyzer=0
-# 
-# DESTi=$DEST/pol1_3x10_10
-# if [ -e "$DESTi" ]; then
-# 	rm -r "$DESTi"
-# fi
-# 
-# mpirun  -np $use_cores Estia_baseline.out \
-#         --dir="$DESTi" --ncount=$ncount --gravitation \
-#         omegaa=$omega operationmode=0 theta_resolution=0.04 over_illumination=0.000 \
-#         sample=$sample sample_length=$sample_length sample_height=$sample_height \
-#         lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=1 enable_chopper=0 enable_polarizer=1 enable_analyzer=0
-# 
-# DESTi=$DEST/pol2_3x10_10
-# if [ -e "$DESTi" ]; then
-# 	rm -r "$DESTi"
-# fi
-# 
-# mpirun  -np $use_cores Estia_baseline.out \
-#         --dir="$DESTi" --ncount=$ncount --gravitation \
-#         omegaa=$omega operationmode=0 theta_resolution=0.04 over_illumination=0.000 \
-#         sample=$sample sample_length=$sample_length sample_height=$sample_height \
-#         lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=1 enable_chopper=0 enable_polarizer=2 enable_analyzer=0
-# 
-# 
-# sample_height=0.01
-# sample_length=0.01
-# DESTi=$DEST/ana1_10x10_10
-# if [ -e "$DESTi" ]; then
-# 	rm -r "$DESTi"
-# fi
-# 
-# mpirun  -np $use_cores Estia_baseline.out \
-#         --dir="$DESTi" --ncount=$ncount --gravitation \
-#         omegaa=$omega operationmode=0 theta_resolution=0.04 over_illumination=0.000 \
-#         sample=$sample sample_length=$sample_length sample_height=$sample_height \
-#         lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=1 enable_chopper=0 enable_polarizer=0 enable_analyzer=1
+        lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=0 enable_chopper=0 \
+		enable_polarizer=0 enable_analyzer=0
+       
+ncount=5e8
+sample_length=0.0005
+sample_height=0.01

-# sample_height=0.001
-# DESTi=$DEST/ana1_10x1_10
-# if [ -e "$DESTi" ]; then
-# 	rm -r "$DESTi"
-# fi
-# 
-# mpirun  -np $use_cores Estia_baseline_ana1.out \
-#         --dir="$DESTi" --ncount=$ncount --gravitation \
-#         omegaa=$omega operationmode=0 theta_resolution=0.04 over_illumination=0.000 \
-#         sample=$sample sample_length=$sample_length sample_height=$sample_height \
-#         lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=1 enable_chopper=0 enable_polarizer=0 enable_analyzer=1
-#        
-# sample_height=0.01
-# DESTi=$DEST/ana2_10x10_10
-# if [ -e "$DESTi" ]; then
-# 	rm -r "$DESTi"
-# fi
-# 
-# mpirun  -np $use_cores Estia_baseline.out \
-#         --dir="$DESTi" --ncount=$ncount --gravitation \
-#         omegaa=$omega operationmode=0 theta_resolution=0.04 over_illumination=0.000 \
-#         sample=$sample sample_length=$sample_length sample_height=$sample_height \
-#         lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=1 enable_chopper=0 enable_polarizer=0 enable_analyzer=2
+DESTi=$DEST/pol_ref_10x0p5
+if [ -e "$DESTi" ]; then
+	rm -r "$DESTi"
+fi

-# sample_height=0.001
-# DESTi=$DEST/ana2_10x1_10
-# if [ -e "$DESTi" ]; then
-# 	rm -r "$DESTi"
-# fi
-# 
-# mpirun  -np $use_cores Estia_baseline_ana2.out \
-#         --dir="$DESTi" --ncount=$ncount --gravitation \
-#         omegaa=$omega operationmode=0 theta_resolution=0.04 over_illumination=0.000 \
-#         sample=$sample sample_length=$sample_length sample_height=$sample_height \
-#         lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=1 enable_chopper=0 enable_polarizer=0 enable_analyzer=2
+mpirun  -np $use_cores --hostfile hostnames Estia_baseline.out \
+        --dir="$DESTi" --format=NeXus --ncount=$ncount \
+        sample=$sample sample_length=$sample_length sample_height=$sample_height \
+        lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=0 enable_chopper=0 \
+		enable_polarizer=0 enable_analyzer=0
       

-###################### Reference and Ni-layer measurement 1x1mm² sample ####################
+###################### Polarizers 10x5mm² and 10x0.5mm² VS ####################

+ncount=2e8
+sample_length=0.005
+sample_height=0.01

+DESTi=$DEST/pol_10x5
+if [ -e "$DESTi" ]; then
+	rm -r "$DESTi"
+fi
+
+mpirun  -np $use_cores --hostfile hostnames Estia_baseline.out \
+        --dir="$DESTi" --format=NeXus --ncount=$ncount \
+        sample=$sample sample_length=$sample_length sample_height=$sample_height \
+        lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=0 enable_chopper=0 \
+		enable_polarizer=1 enable_analyzer=0
+       
+ncount=1e9
+sample_length=0.0005
+sample_height=0.01
+
+DESTi=$DEST/pol_10x0p5
+if [ -e "$DESTi" ]; then
+	rm -r "$DESTi"
+fi
+
+mpirun  -np $use_cores --hostfile hostnames Estia_baseline.out \
+        --dir="$DESTi" --format=NeXus --ncount=$ncount \
+        sample=$sample sample_length=$sample_length sample_height=$sample_height \
+        lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=0 enable_chopper=0 \
+		enable_polarizer=1 enable_analyzer=0
@@ -1,251 +0,0 @@
-#!/bin/tcsh
-#SBATCH -J mcEstia
-#SBATCH -N 6
-#SBATCH --ntasks-per-node=24
-#SBATCH --time=2-00:00:00
-#SBATCH --mail-type=fail
-#SBATCH --mail-user=artur.glavic@psi.ch
-
-#SBATCH -o stdout.log
-#SBATCH -e stderr.log
-
-#SBATCH --partition=medium
-
-echo "Starting at `date`"
-echo "Running on hosts: $SLURM_NODELIST"
-echo "Running on $SLURM_NNODES nodes."
-echo "Running on $SLURM_NPROCS processors."
-echo "Current working directory is `pwd`"
-
-module load mcstas
-bash compile_if_needed.sh
-
-set DEST=../results
-set ncount=1e10
-set use_cores=4
-set sample=1
-set sample_length=0.03
-set sample_height=0.01
-set lambda_start=3.5
-set lambda_end=14.0
-
-
-################## Reference ########################
-set omega=1.0
-set DESTi=$DEST/solid_liquid_reference
-if ( -e "$DESTi" ) then
-	rm -r "$DESTi"
-endif
-
-mpirun  -np $use_cores Estia_baseline.out \
-        --dir="$DESTi" --ncount=$ncount --gravitation \
-        omegaa=$omega operationmode=1 theta_resolution=0.04 over_illumination=0.0025 \
-        sample=$sample sample_length=$sample_length sample_height=$sample_height \
-        lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=1 enable_chopper=1 enable_polarizer=0 enable_analyzer=0
-
-################## H2O ########################
-set ncount=1e11
-set sample=5
-set omega=0.2
-set DESTi=$DEST/solid_liquid_h2o_02
-if ( -e "$DESTi" ) then
-	rm -r "$DESTi"
-endif
-
-mpirun  -np $use_cores Estia_baseline.out \
-        --dir="$DESTi" --ncount=$ncount --gravitation \
-        omegaa=$omega operationmode=1 theta_resolution=0.04 over_illumination=0.0025 \
-        sample=$sample sample_length=$sample_length sample_height=$sample_height \
-        lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=1 enable_chopper=1 enable_polarizer=0 enable_analyzer=0
-
-set ncount=1e10
-set omega=0.5
-set DESTi=$DEST/solid_liquid_h2o_05
-if ( -e "$DESTi" ) then
-	rm -r "$DESTi"
-endif
-
-mpirun  -np $use_cores Estia_baseline.out \
-        --dir="$DESTi" --ncount=$ncount --gravitation \
-        omegaa=$omega operationmode=1 theta_resolution=0.04 over_illumination=0.0025 \
-        sample=$sample sample_length=$sample_length sample_height=$sample_height \
-        lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=1 enable_chopper=1 enable_polarizer=0 enable_analyzer=0
-
-set ncount=4e9
-set omega=1.2
-set DESTi=$DEST/solid_liquid_h2o_12
-if ( -e "$DESTi" ) then
-	rm -r "$DESTi"
-endif
-
-mpirun  -np $use_cores Estia_baseline.out \
-        --dir="$DESTi" --ncount=$ncount --gravitation \
-        omegaa=$omega operationmode=1 theta_resolution=0.04 over_illumination=0.0025 \
-        sample=$sample sample_length=$sample_length sample_height=$sample_height \
-        lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=1 enable_chopper=1 enable_polarizer=0 enable_analyzer=0
-
-set ncount=2e9
-set omega=3.1
-set DESTi=$DEST/solid_liquid_h2o_31
-if ( -e "$DESTi" ) then
-	rm -r "$DESTi"
-endif
-
-mpirun  -np $use_cores Estia_baseline.out \
-        --dir="$DESTi" --ncount=$ncount --gravitation \
-        omegaa=$omega operationmode=1 theta_resolution=0.04 over_illumination=0.0025 \
-        sample=$sample sample_length=$sample_length sample_height=$sample_height \
-        lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=1 enable_chopper=1 enable_polarizer=0 enable_analyzer=0
-
-set ncount=1e9
-set omega=7.8
-set DESTi=$DEST/solid_liquid_h2o_78
-if ( -e "$DESTi" ) then
-	rm -r "$DESTi"
-endif
-
-mpirun  -np $use_cores Estia_baseline.out \
-        --dir="$DESTi" --ncount=$ncount --gravitation \
-        omegaa=$omega operationmode=1 theta_resolution=0.04 over_illumination=0.0025 \
-        sample=$sample sample_length=$sample_length sample_height=$sample_height \
-        lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=1 enable_chopper=1 enable_polarizer=0 enable_analyzer=0
-
-
-################## D2O ########################
-set ncount=1e11
-set sample=6
-set omega=0.2
-set DESTi=$DEST/solid_liquid_d2o_02
-if ( -e "$DESTi" ) then
-	rm -r "$DESTi"
-endif
-
-mpirun  -np $use_cores Estia_baseline.out \
-        --dir="$DESTi" --ncount=$ncount --gravitation \
-        omegaa=$omega operationmode=1 theta_resolution=0.04 over_illumination=0.0025 \
-        sample=$sample sample_length=$sample_length sample_height=$sample_height \
-        lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=1 enable_chopper=1 enable_polarizer=0 enable_analyzer=0
-
-set ncount=1e10
-set omega=0.5
-set DESTi=$DEST/solid_liquid_d2o_05
-if ( -e "$DESTi" ) then
-	rm -r "$DESTi"
-endif
-
-mpirun  -np $use_cores Estia_baseline.out \
-        --dir="$DESTi" --ncount=$ncount --gravitation \
-        omegaa=$omega operationmode=1 theta_resolution=0.04 over_illumination=0.0025 \
-        sample=$sample sample_length=$sample_length sample_height=$sample_height \
-        lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=1 enable_chopper=1 enable_polarizer=0 enable_analyzer=0
-
-set ncount=4e9
-set omega=1.2
-set DESTi=$DEST/solid_liquid_d2o_12
-if ( -e "$DESTi" ) then
-	rm -r "$DESTi"
-endif
-
-mpirun  -np $use_cores Estia_baseline.out \
-        --dir="$DESTi" --ncount=$ncount --gravitation \
-        omegaa=$omega operationmode=1 theta_resolution=0.04 over_illumination=0.0025 \
-        sample=$sample sample_length=$sample_length sample_height=$sample_height \
-        lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=1 enable_chopper=1 enable_polarizer=0 enable_analyzer=0
-
-set ncount=2e9
-set omega=3.1
-set DESTi=$DEST/solid_liquid_d2o_31
-if ( -e "$DESTi" ) then
-	rm -r "$DESTi"
-endif
-
-mpirun  -np $use_cores Estia_baseline.out \
-        --dir="$DESTi" --ncount=$ncount --gravitation \
-        omegaa=$omega operationmode=1 theta_resolution=0.04 over_illumination=0.0025 \
-        sample=$sample sample_length=$sample_length sample_height=$sample_height \
-        lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=1 enable_chopper=1 enable_polarizer=0 enable_analyzer=0
-
-set ncount=1e9
-set omega=7.8
-set DESTi=$DEST/solid_liquid_d2o_78
-if ( -e "$DESTi" ) then
-	rm -r "$DESTi"
-endif
-
-mpirun  -np $use_cores Estia_baseline.out \
-        --dir="$DESTi" --ncount=$ncount --gravitation \
-        omegaa=$omega operationmode=1 theta_resolution=0.04 over_illumination=0.0025 \
-        sample=$sample sample_length=$sample_length sample_height=$sample_height \
-        lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=1 enable_chopper=1 enable_polarizer=0 enable_analyzer=0
-
-################## SMW ########################
-set ncount=1e11
-set sample=7
-set omega=0.2
-set DESTi=$DEST/solid_liquid_smw_02
-if ( -e "$DESTi" ) then
-	rm -r "$DESTi"
-endif
-
-mpirun  -np $use_cores Estia_baseline.out \
-        --dir="$DESTi" --ncount=$ncount --gravitation \
-        omegaa=$omega operationmode=1 theta_resolution=0.04 over_illumination=0.0025 \
-        sample=$sample sample_length=$sample_length sample_height=$sample_height \
-        lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=1 enable_chopper=1 enable_polarizer=0 enable_analyzer=0
-
-set ncount=1e10
-set sample=5
-set omega=0.5
-set DESTi=$DEST/solid_liquid_smw_05
-if ( -e "$DESTi" ) then
-	rm -r "$DESTi"
-endif
-
-mpirun  -np $use_cores Estia_baseline.out \
-        --dir="$DESTi" --ncount=$ncount --gravitation \
-        omegaa=$omega operationmode=1 theta_resolution=0.04 over_illumination=0.0025 \
-        sample=$sample sample_length=$sample_length sample_height=$sample_height \
-        lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=1 enable_chopper=1 enable_polarizer=0 enable_analyzer=0
-
-set ncount=4e9
-set sample=5
-set omega=1.2
-set DESTi=$DEST/solid_liquid_smw_12
-if ( -e "$DESTi" ) then
-	rm -r "$DESTi"
-endif
-
-mpirun  -np $use_cores Estia_baseline.out \
-        --dir="$DESTi" --ncount=$ncount --gravitation \
-        omegaa=$omega operationmode=1 theta_resolution=0.04 over_illumination=0.0025 \
-        sample=$sample sample_length=$sample_length sample_height=$sample_height \
-        lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=1 enable_chopper=1 enable_polarizer=0 enable_analyzer=0
-
-set ncount=2e9
-set sample=5
-set omega=3.1
-set DESTi=$DEST/solid_liquid_smw_31
-if ( -e "$DESTi" ) then
-	rm -r "$DESTi"
-endif
-
-mpirun  -np $use_cores Estia_baseline.out \
-        --dir="$DESTi" --ncount=$ncount --gravitation \
-        omegaa=$omega operationmode=1 theta_resolution=0.04 over_illumination=0.0025 \
-        sample=$sample sample_length=$sample_length sample_height=$sample_height \
-        lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=1 enable_chopper=1 enable_polarizer=0 enable_analyzer=0
-
-set ncount=1e9
-set sample=5
-set omega=7.8
-set DESTi=$DEST/solid_liquid_smw_78
-if ( -e "$DESTi" ) then
-	rm -r "$DESTi"
-endif
-
-mpirun  -np $use_cores Estia_baseline.out \
-        --dir="$DESTi" --ncount=$ncount --gravitation \
-        omegaa=$omega operationmode=1 theta_resolution=0.04 over_illumination=0.0025 \
-        sample=$sample sample_length=$sample_length sample_height=$sample_height \
-        lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=1 enable_chopper=1 enable_polarizer=0 enable_analyzer=0
-
@@ -0,0 +1,38 @@
+#!/bin/tcsh
+#SBATCH -J mcEstia_S
+#SBATCH -N 2
+#SBATCH --ntasks-per-node=24
+#SBATCH --time=2:00:00
+#SBATCH --mail-type=fail
+#SBATCH --mail-user=artur.glavic@psi.ch
+
+#SBATCH -o stdout.log
+#SBATCH -e stderr.log
+
+#SBATCH --partition=ll_short
+
+echo "Starting at `date`"
+echo "Running on hosts: $SLURM_NODELIST"
+echo "Running on $SLURM_NNODES nodes."
+echo "Running on $SLURM_NPROCS processors."
+echo "Current working directory is `pwd`"
+
+#module unload intel
+#module load intel
+module load mcstas
+bash compile_if_needed.sh
+
+mpirun -np $SLURM_NPROCS Estia_baseline.out --format=NeXus \
+        --dir=$*
+#        --dir=../results/$1 --ncount=1e9 \
+#        sample=1 enable_polarizer=1 \
+#        omegaa=6.0 sample_length=0.048 sample_height=0.01
+
+echo "Program finished with exit code $? at: `date`"
+
+
+echo "Compressing hdf5 file..."
+h5repack -i ../results/$1/mccode.h5 -o ../results/$1/mccode.h5.c -f /entry1/data/detector_list_p_x_y_t_L_sx_sy_sz/events:GZIP=5 -l /entry1/data/detector_list_p_x_y_t_L_sx_sy_sz/events:CHUNK=3072x8
+mv ../results/$1/mccode.h5.c ../results/$1/mccode.h5
+
+echo "Scipt finished."
Author	SHA1	Message	Date
glavic_a	b570182e5d	Fix feeder not beeing fully illuminated and add VS and MF divergence monitors	2021-10-13 11:39:24 +02:00
glavic_a	41533faaa1	Add polarization parameters of SNAG mirrors and run file	2021-10-13 10:00:11 +02:00
glavic_a	1cbe0c628f	Implement geometry of double V-style polarizer, straight not correct reflection, yet	2021-10-11 22:55:53 +02:00
glavic_a	c2a947a923	Minor changes to run on cluster	2019-11-18 16:45:24 +01:00
glavic_a	c011bdad07	First version for polarizer distance sweep	2019-08-02 19:23:48 +02:00
glavic_a	f6a77d0dfe	Fix issue with multiple polarizer instances reintroduced in update	2019-07-28 19:23:31 +02:00
glavic_a	7323c7fd8a	Remove monitors, add geometry parameters and slurm job. Some strange behavior	2019-07-28 17:40:21 +02:00
glavic_a	fb84f6fb5b	Update polarizer and optimize parameters for m=5 mirror from SNAG	2019-07-28 14:50:31 +02:00
glavic_a	fe44ee1edd	Add updated Polarizer component	2019-07-25 15:40:51 +02:00
glavic_a	6016ffba54	Replace Selene guide top/bottom order	2019-07-25 15:40:28 +02:00