Add D2O sample

analysis/compress_h5.sh

@@ -1,9 +0,0 @@
- #!/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

analysis/mcstas_reader.py

@@ -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 list(self.info['data'].keys())
+    return self.info['data'].keys()
 
   def monitors(self):
     output=[]
-    for val in list(self.info['data'].values()):
+    for val in 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 list(self.info['data'].items()):
+    for key, val in 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 list(self.keys()):
+    elif item in 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 in ['Li', 'List'] and y_col=='p': # Detector_nD     
+    if x_col=='Li' 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 list(self.hdf['data'].keys()):
+    for item in self.hdf['data'].keys():
       node=self.hdf['data/'+item]
       info={}
-      for key, value in list(node.attrs.items()):
-        info[key.strip()]=value.strip().decode('ascii')
+      for key, value in node.attrs.items():
+        info[key.strip()]=value.strip()
       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 in ['Li', 'List'] and y_col=='p': # Detector_nD
+    if x_col=='Li' 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=list(map(float, self.info['xlimits'].split()))
+    limits=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=list(map(float, self.info['xylimits'].split()))
+    limits=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, str):
+      if isinstance(fltr, basestring):
         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, str):
+      if isinstance(fltr, basestring):
         fltr=eval(fltr, globals(), columns)
       I, y, x=histogram2d(columns[ycol][fltr], columns[xcol][fltr],
                         bins=bins, weights=columns['p'][fltr])

simulation/D2O.ref

@@ -0,0 +1,602 @@
+# Dataset "D2O" exported from GenX on Wed Dec 12 04:56:52 2018
+# Column lables:
+# q                      R
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+9.983333333333334059e-01 6.502101313897288710e-09

simulation/Estia_baseline.instr

@@ -53,8 +53,7 @@ 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, 
- double pol1_start=0.3, double pol1_angle=1.66, double pol2_start=0.3, double pol2_angle=1.66,
+ int enable_polarizer = 0, int enable_analyzer = 0,
 double source_power = 2,
 double selene1_foot1y =0.0, double selene1_foot2y = 0.0
 )
@@ -79,8 +78,6 @@ 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
 
 
@@ -125,7 +122,7 @@ 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
@@ -138,8 +135,8 @@ 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
@@ -205,7 +202,7 @@ 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=3, Lmin = lambda_start, Lmax = lambda_end,
+    target_index=4, Lmin = lambda_start, Lmax = lambda_end,
     n_pulses = 1+enable_chopper, acc_power=source_power)
     AT (0, 0, 0) RELATIVE origin 
 
@@ -237,17 +234,6 @@ 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(
@@ -296,8 +282,8 @@ COMPONENT ac_slit = Slit(
  * Sample area *
  ***************/
     COMPONENT tof_sample = Monitor_nD(
-        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",
+        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",
         xwidth=0.05, yheight = 0.05)
         WHEN sample==4
         AT (0, 0, 0) RELATIVE arm_sample_beam
@@ -354,14 +340,14 @@ COMPONENT arm_analyzer2 = Arm()
     ROTATED (-selene_theta+(Theta1_analyzer2-Theta2_analyzer2)/2.0, 0, 0) RELATIVE arm_detector
 
 /* polarization analyser */
-COMPONENT analyzer1 = Polariser(enable_ref=1, d_substrate = 5e-4, reflect_d=0, reflect_u=0, lin=analyzer1_start, length=analyzer1_length,
+COMPONENT analyzer1 = Polariser(nIncRefr=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(enable_ref=1, d_substrate = 5e-4, reflect_d=0, reflect_u=0, lin=analyzer2_start, length=analyzer2_length,
+COMPONENT analyzer2 = Polariser(nIncRefr=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
@@ -370,12 +356,11 @@ COMPONENT analyzer2 = Polariser(enable_ref=1, d_substrate = 5e-4, reflect_d=0, r
 
 /* detector */
     COMPONENT tof_detector = Monitor_nD(
-        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",
+        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",
         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
 
 /***********************************************************************/
 

simulation/Estia_liquids.instr

@@ -0,0 +1,391 @@
+/*******************************************************************************
+*         McStas instrument definition URL=http://www.mcstas.org
+*
+* Instrument: ESS_reflectometer_Estia
+*
+* %Identification
+* Written by: Artur Glavic (artur.glavic@psi.ch); Jochen Stahn (jochen.stahn@psi.ch); Christine Klauser (christine.klauser@psi.ch)
+* Date: 01. 03. 2018
+* Origin: PSI
+* Release: McStas 2.4.1
+* Version: 1.0
+* %INSTRUMENT_SITE: ESS (E02)
+*
+* Estia is a vertical sample, focusing reflectometer for small sample
+*
+* %Description
+* The instrument consists of a two part elliptical feeder that focuses onto 
+* a slit mask that defines the sample footprint, called virtual source.
+* The virtual source is imaged on the sample position with a Selene 
+* type neutron guide (two ellipses).
+* This version of the instrument, used in the ESS butterfly moderator, 
+* has two vertical Selene guide systems that share the same focal points.
+* The two guides are only implemented in the feeder as the selene mirrors
+* are part of the upgrade program.
+*
+* %Parameters
+* omegaa: [deg]  incident angle selected by slit
+* sample: flag to switch between     (0) sample D2O surface
+*                                    (1) reference ( R(q_z) = 1 for all q_z )
+*                                    (2) Ni-film on silicon
+*                                    (3) Natural SiO2 on silicon
+*                                    (4) monitor instead of sample (normal to beam)
+* sample_length: [m] Size of sample in beam direction
+* sample_width:  [m] Size of sample in perpendicular to beam
+* 
+* over_illumination: [m] Extra opening of virtual source compared to sample size
+* theta_resolution: Delta theta / theta
+* 
+* lambda_start: [A] Beginning of simulated wavelength range
+* lambda_end:   [A] End of simulated wavelength range
+* reflector:    [0/1/2] Direct beam on sample or moved down to use reflector 1 or 2 setup
+* enable_gravity: [0/1] Use gravity in elliptical guide model.
+* enable_chopper: [0/1/2/3] Activate chopper component if !=0. Numbers larger than
+*                           1 define the number of pulses per chopper opening.
+*                           (pulses skipped=enable_chopper-1)
+*
+* %End
+*******************************************************************************/
+
+DEFINE INSTRUMENT ESS_reflectometer_Estia
+(int sample = 0,  double sample_length   = 0.25, double sample_width   = 0.1,
+double omegaa = 0.0, double theta_resolution = 0.04, int reflector = 0,
+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,
+double source_power = 2)
+
+DECLARE
+%{
+/* Geometrical parameters from CAD model of Estia (ESS-0050413)
+* TCS coordinate and directional rotation first focus point 
+* refered to as focus_moderator_y_rot
+*/
+//TCS position of ISCS: (110,-105,137)
+double iscs_x=0.0199717;
+double iscs_y=0.0;
+double iscs_z=0.0547095; // ISCS in McStas coordinates using mod-view-opt.instr
+double iscs_rot_y=0.4; // ISCS is at TCS-35.6 degree, McStas at -36 degree
+double iscs_rot_x=0.7; // downward tilt of Estia axis
+
+double selene1_foot1y =0.0;
+double selene1_foot2y = 0.0;
+
+// Selene 1 geometry parameters (optics parameters in Estia_selene1.instr)
+double selene1_foot1   =  4.20; // distance of first foot to VS focus
+double selene1_foot2   =  7.00; // distance of second foot to VS focus
+double selene1_center;
+double selene1_shift;
+double selene1_rot;
+
+// Selene 2
+
+
+    
+/* general instrument geometry parameters */
+double total_length    = 35.0 ;     // m    distance moderator-sample (2*c_feeder+4*c_Selene)
+double detector_arm    =  4.0 ;     // m    distance sample-detector
+
+
+/* chopper parameters */
+double chopper_diameter = 0.7;
+double chopper_pos     = 10.895;     // m  distance source-chopper
+double chopper_phase          ;       // deg phase between pulse and chopper opening
+double chopper_open           ;       // deg of opening angle in the chopper
+double pulse_zero      =   0.00175;   // ms  intensity weighted average time of emitted neutron pulse
+double opening_time    =   0.0015; // ms time to reach full intensity on detector, used to adjust phase to get full intensity at beginning of selected band
+double chopper_freq    =  14.0 ;     // Hz  chopper frequency
+
+double slit_distance   =   1.775; //m, distance slit to sample
+
+/* derived quantities */
+double selene_theta    =    1.25;
+double velocity_max           ;     // m/s  neutron velocity of lambda_min
+
+
+double analyzer_max_height = 0.01; // Maximum sample height to be covered by te polarization analyzers
+double analyzer1_start  = 0.65; // Distance to sample to start the first analyzer
+double analyzer1_length = 1.3; // length of first analyzer
+double analyzer2_start  = 0.7; // Distance to sample to start the first analyzer
+double analyzer2_length = 1.6; // length of first analyzer
+double Theta1_analyzer1, Theta1_analyzer2, Theta2_analyzer1, Theta2_analyzer2, dist_ana_vfocus; // quantities calculated out of values above and 1.5 degree covered divergence
+
+%}
+
+INITIALIZE
+%{
+// chopper coupling together
+velocity_max= 3.956034E3 / lambda_min; // h/m_n over lambda - ((3.9..e-7m^2/s))/(1e-10m)
+chopper_phase=360.0*(chopper_pos*chopper_freq/velocity_max+(pulse_zero-opening_time)*chopper_freq);
+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);
+
+
+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
+
+Theta1_analyzer1=atan((dist_ana_vfocus+analyzer1_start)/dist_ana_vfocus*analyzer_max_height/2.0/analyzer1_start)*180.0/PI;
+Theta2_analyzer1=atan((dist_ana_vfocus+analyzer1_start+analyzer1_length)/dist_ana_vfocus*analyzer_max_height/2.0/(analyzer1_start+analyzer1_length))*180.0/PI;
+Theta1_analyzer2=atan((dist_ana_vfocus+analyzer2_start)/dist_ana_vfocus*analyzer_max_height/2.0/analyzer2_start)*180.0/PI;
+Theta2_analyzer2=atan((dist_ana_vfocus+analyzer2_start+analyzer2_length)/dist_ana_vfocus*analyzer_max_height/2.0/(analyzer2_start+analyzer2_length))*180.0/PI;
+
+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);
+
+%}
+TRACE
+
+/********************************************************************************
+ * Initial geometry coordinate axes for important components of the simulation. *
+ ********************************************************************************/
+COMPONENT origin = Progress_bar()
+    AT (0,0,0) ABSOLUTE
+    
+/* The ISCS is the instrument coordinate system with directions where y points upwards and z lies on the instrument axes. */
+COMPONENT ISCS_rot1 = Arm() // position correctly and rotate around z-axis (x points in beam direction)
+    AT (iscs_x,iscs_y,iscs_z) RELATIVE origin
+    ROTATED (0,iscs_rot_y,0) RELATIVE origin
+COMPONENT ISCS = Arm() // rotate around y-axis (slight downward tilt)
+    AT (0,0,0) RELATIVE ISCS_rot1
+    ROTATED (iscs_rot_x,0,0) RELATIVE ISCS_rot1
+
+    
+/***********************
+* Instrument Skeleton *
+***********************/
+// Axes system parallel to the c-axis of the feeder
+COMPONENT arm_feeder = Arm()
+    AT (0, 0, 0) RELATIVE ISCS
+    ROTATED (0, 0, 0) RELATIVE ISCS
+COMPONENT arm_selene1_center = Arm()
+    AT (selene1_shift, 0, 2*NBOA_c+selene1_center) RELATIVE ISCS
+    ROTATED (0, selene1_rot, 0) RELATIVE ISCS
+// Axes starting at focus of feeder parallel to c-axis of Selene guides
+COMPONENT arm_selene1 = Arm()
+    AT (0, 0, -selene1_center) RELATIVE arm_selene1_center
+COMPONENT arm_selene2 = Arm()
+    AT (0, 0, 2*NBOA_c+2*selene_c) RELATIVE ISCS
+    ROTATED (0, 0, 0) RELATIVE ISCS
+// Axes of the center of usable beam passing through the virtual source
+COMPONENT arm_virtual_source_beam = Arm()
+    AT (0, 0, 0) RELATIVE arm_selene1
+    ROTATED (0, selene_theta, 0) RELATIVE ISCS
+// Axes used for the virtual source masks, this depends on the sample angle to achieve the correct footprint
+COMPONENT arm_virtual_source = Arm()
+    AT (0, 0, 0) RELATIVE arm_virtual_source_beam
+    ROTATED (0, 10.0, 0) RELATIVE arm_virtual_source_beam
+// Sample position with Axes pointing to the center of the beam
+COMPONENT arm_sample_beam = Arm()
+    AT (0, 0, 4.0*selene_c) RELATIVE arm_selene1
+    ROTATED (0, selene_theta, 0) RELATIVE ISCS
+// Sample position with sample angle rotation
+COMPONENT arm_addon1_beam = Arm()
+    AT (0, 0, 0) RELATIVE arm_sample_beam
+    ROTATED (omegaa-iscs_rot_x, 0, 0) RELATIVE arm_sample_beam
+COMPONENT arm_addon1 = Arm()
+    AT (0, 0, -0.2) RELATIVE arm_addon1_beam
+COMPONENT arm_addon2_beam = Arm()
+    AT (0, 0, 0) RELATIVE arm_sample_beam
+    ROTATED (-omegaa-iscs_rot_x, 0, 0) RELATIVE arm_sample_beam
+COMPONENT arm_addon2 = Arm()
+    AT (0, 0, 0.2) RELATIVE arm_addon2_beam
+// Sample position with sample angle rotation
+COMPONENT arm_sample = Arm()
+    AT (0, -0.2*((reflector==1)*0.024439474+(reflector==2)*0.062914667), 0) RELATIVE arm_sample_beam
+    ROTATED (0, 0, 0) RELATIVE arm_sample_beam
+// Detector arm rotation at sample position
+COMPONENT arm_detector = Arm()
+    AT (0, 0, 0) RELATIVE arm_sample_beam
+    ROTATED (0, 0, 0) RELATIVE arm_sample_beam
+
+
+
+/**********
+ * Source *
+ **********/
+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,
+    n_pulses = 1+enable_chopper, acc_power=source_power)
+    AT (0, 0, 0) RELATIVE origin 
+
+
+/***************************************
+ * Geometry of neutron feeder separate *
+ ***************************************/
+%include "Estia_feeder.instr"
+
+/**************************************************** 
+ * Beam manipulation area around the virtual source *
+ ****************************************************/
+/* Absorber to reduce beam to needed size an for shielding purposes (CPC1 in CAD model) */
+COMPONENT CPC1_in = Slit(xwidth=0.0303, yheight=0.0792)
+    AT (0, 0, -0.890) RELATIVE arm_virtual_source_beam
+
+COMPONENT CPC1_monitor = Slit(xwidth=0.016344, yheight=0.05547)
+    AT (0, 0, -0.3573) RELATIVE arm_virtual_source_beam
+
+COMPONENT CPC1_out = Slit(xwidth=0.013, yheight=0.038)
+    AT (0, 0, -0.220) RELATIVE arm_virtual_source_beam
+
+
+/* bandwidth definition chopper */
+COMPONENT chopper = DiskChopper(radius=chopper_diameter/2.0, yheight=0.02,
+    theta_0=chopper_open, phase=chopper_phase+chopper_open/2.0,
+    nu=chopper_freq,  nslit=1)
+    WHEN enable_chopper==1
+    AT (0, 0, chopper_pos-2*NBOA_c) RELATIVE arm_virtual_source_beam
+    
+
+
+/* The actual virtual source mask, two L-shaped absorbers (first top-right) */
+COMPONENT virtual_source_TR = Slit(
+    xmin = 0.0, xmax = 1.0, ymin = -1.0, ymax = 0.006)
+    WHEN sample!=4
+    AT (0, 0, -0.015) RELATIVE arm_virtual_source
+
+//     
+/* The actual virtual source mask, two L-shaped absorbers (second bottom-left) */
+COMPONENT virtual_source_BL = Slit(
+    xmin = -1.0, xmax = 0.0, ymin = -0.006, ymax = 1.0)
+    WHEN sample!=4
+    AT (0, 0, 0.015) RELATIVE arm_virtual_source
+
+
+/*************************************
+ * Geometry of Selene guide separate *
+ *************************************/
+%include "Estia_selene1.instr"
+
+%include "Estia_selene2.instr"
+
+/**********************************
+ * Optical components within cave *
+ **********************************/
+COMPONENT ac_slit = Slit(
+    xwidth = 0.2,
+    ymin = slit_distance*tan((PI/180.0)*(omegaa*(1.0-theta_resolution/2.0)-iscs_rot_x)),
+    ymax = slit_distance*tan((PI/180.0)*(omegaa*(1.0+theta_resolution/2.0)-iscs_rot_x)))
+    AT (0, 0, -slit_distance) RELATIVE arm_sample_beam
+
+/**************************************************
+ * Reflector to increase incident angle on sample *
+ * ************************************************/
+COMPONENT addon_slit = Slit(
+    xwidth = 0.2, yheight=0.0009*(reflector!=2)+0.0023*(reflector==2))
+    AT (0, 0, -0.0376) RELATIVE arm_addon1
+
+COMPONENT addon_11 = Mirror(
+    xwidth = sample_width, yheight = 0.075,
+    m = 2, center = 1, transmit = 0
+    )
+    WHEN reflector==1
+    AT (0, 0, 0) RELATIVE arm_addon1
+    ROTATED (-89.3, 0, 0) RELATIVE arm_addon1
+
+COMPONENT addon_12 = Mirror(
+    xwidth = sample_width, yheight = 0.075,
+    m = 5, center = 1, transmit = 0
+    )
+    WHEN reflector==2
+    AT (0, 0, 0) RELATIVE arm_addon1
+    ROTATED (-88.2, 0, 0) RELATIVE arm_addon1
+
+    
+
+/***************
+ * 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",
+        xwidth=0.05, yheight = 0.05)
+        WHEN sample==4
+        AT (0, 0, 0) RELATIVE arm_sample_beam
+        ROTATED (0, 0, 0) RELATIVE arm_sample_beam
+                
+
+/* NiTi multilayer sample */
+COMPONENT sample = Mirror(
+    xwidth = sample_width, yheight = sample_length,
+    center = 1, transmit = 0,
+    reflect = "D2O.ref"
+    )
+    WHEN sample==0
+    AT (0, 0, 0) RELATIVE arm_sample
+    ROTATED (90-iscs_rot_x, 0, 0) RELATIVE arm_sample
+
+/* ideal reflector as reference */
+COMPONENT reference_sample = Mirror(
+    xwidth = sample_width, yheight = sample_length,
+    center = 1, transmit = 0,
+    R0 = 0.999, alpha = 0.001, m = 50, center = 1, transmit = 0
+    )
+    WHEN sample==1
+    AT (0, 0, 0) RELATIVE arm_sample
+    ROTATED (90-iscs_rot_x, 0, 0) RELATIVE arm_sample
+
+/* Nickel film on silicon */
+COMPONENT ni_sample = Mirror(
+    xwidth = sample_width, yheight = sample_length,
+    center = 1, transmit = 0,
+    reflect = "Si-Ni.ref"
+    )
+    WHEN sample==2
+    AT (0, 0, 0) RELATIVE arm_sample
+    ROTATED (90-iscs_rot_x, 0, 0) RELATIVE arm_sample
+
+/* Silicon with natural oxide */
+COMPONENT si_sample = Mirror(
+    xwidth = sample_width, yheight = sample_length,
+    center = 1, transmit = 0,
+    reflect = "Si-SiO2.ref"
+    )
+    WHEN sample==3
+    AT (0, 0, 0) RELATIVE arm_sample
+    ROTATED (90-iscs_rot_x, 0, 0) RELATIVE arm_sample
+
+
+/**************************************************
+ * Reflector to increase incident angle on sample *
+ * ************************************************/
+COMPONENT addon_21 = Mirror(
+    xwidth = sample_width, yheight = 0.075,
+    m = 2, center = 1, transmit = 0
+    )
+    WHEN reflector==1
+    AT (0, 0, 0) RELATIVE arm_addon2
+    ROTATED (89.3, 0, 0) RELATIVE arm_addon2
+
+COMPONENT addon_22 = Mirror(
+    xwidth = sample_width, yheight = 0.075,
+    m = 5, center = 1, transmit = 0
+    )
+    WHEN reflector==2
+    AT (0, 0, 0) RELATIVE arm_addon2
+    ROTATED (88.2, 0, 0) RELATIVE arm_addon2
+
+    
+    
+/* 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",
+        xwidth = 0.5, yheight = 1.0)
+        WHEN sample!=4
+        AT (0, 0, detector_arm+0.00001) RELATIVE arm_detector
+
+/***********************************************************************/
+
+FINALLY
+%{
+%}
+
+END

simulation/Estia_mf.instr

@@ -28,80 +28,20 @@ DEFINE INSTRUMENT Estia_selene(int enable_gravity=0)
 
 DECLARE
 %{
-
-// 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;
+    
+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
 
 %}
 
 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
 
-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);
+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;
 
 %}
 TRACE
@@ -127,116 +67,26 @@ REMOVABLE COMPONENT source = Moderator(radius = 0.001, focus_xw = selene_entry+0
 /**************************************
 * Middle focus between Selene guides *
 **************************************/
-COMPONENT arm_polref = Arm()
+COMPONENT arm_polarizer = Arm()
     AT (0, 0, 2*selene_c) RELATIVE arm_selene1
     ROTATED (selene_theta, -selene_theta, 0) RELATIVE ISCS
 
-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
+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 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
+/* 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 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

simulation/Pol_SF_ideal.comp

@@ -1,91 +0,0 @@
-/*******************************************************************************
-*
-* 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

simulation/PolarizerTest.instr

@@ -1,108 +0,0 @@
-/*******************************************************************************
-*         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
-
-

simulation/SNAG_m5p5_Tdown.ref

@@ -1,58 +0,0 @@
-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		

simulation/SNAG_m5p5_Tup.ref

@@ -1,58 +0,0 @@
-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

simulation/compile_if_needed.sh

@@ -1,6 +1,4 @@
 #!/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 ] \
@@ -8,6 +6,6 @@ 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 --trace
-	mpicc -O2 -o Estia_baseline.out Estia_baseline.c -lm -DUSE_MPI -DUSE_NEXUS -lNeXus
+	mcstas -o Estia_baseline.c Estia_baseline.instr
+	mpicc -O3 -o Estia_baseline.out Estia_baseline.c -lm -DUSE_MPI
 fi

simulation/hostnames

@@ -1,3 +0,0 @@
-mcc05:72
-mcc06:72
-

simulation/pol_sweep_analyze.py

@@ -1,83 +0,0 @@
-#!/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')
-            

simulation/polarizer_coating.sh

@@ -1,7 +0,0 @@
-!#/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

simulation/run_liquids.sh

@@ -0,0 +1,174 @@
+#!/bin/bash
+
+DEST=../results
+ncount=1e10
+use_cores=64
+use_host=mcc05,mcc06
+lambda_min=3.75
+lambda_start=3.0
+lambda_end=30.0
+
+if [ Estia_liquids.instr -nt Estia_liquids.out ] || [ ! -f Estia_liquids.out ] \
+   || [ Estia_feeder.instr -nt Estia_liquids.out ] \
+   || [ Estia_selene1.instr -nt Estia_liquids.out ] \
+   || [ Estia_mf.instr -nt Estia_liquids.out ] \
+   || [ Estia_selene2.instr -nt Estia_liquids.out ]; then
+	rm Estia_liquids.c Estia_liquids.out
+	mcstas -o Estia_liquids.c Estia_liquids.instr
+	mpicc -O3 -o Estia_liquids.out Estia_liquids.c -lm -DUSE_MPI
+fi
+
+###################### Reference measurement ####################
+
+sample=1
+omega=1.3
+DESTi=$DEST/liquids_ref_13
+if [ -e "$DESTi" ]; then
+	rm -r "$DESTi"
+fi
+
+mpirun  -np $use_cores --host $use_host Estia_liquids.out \
+        --dir="$DESTi" --format=NeXuS --ncount=$ncount \
+        omegaa=$omega theta_resolution=0.04 \
+        sample=$sample reflector=0 \
+        lambda_end=$lambda_end lambda_min=$lambda_min lambda_start=$lambda_start
+       
+omega=2.5
+DESTi=$DEST/liquids_ref_25
+if [ -e "$DESTi" ]; then
+	rm -r "$DESTi"
+fi
+
+mpirun  -np $use_cores --host $use_host Estia_liquids.out \
+        --dir="$DESTi" --format=NeXuS --ncount=$ncount \
+        omegaa=$omega theta_resolution=0.04 \
+        sample=$sample reflector=0 \
+        lambda_end=$lambda_end lambda_min=$lambda_min lambda_start=$lambda_start
+       
+omega=2.5
+DESTi=$DEST/liquids_ref_39
+if [ -e "$DESTi" ]; then
+	rm -r "$DESTi"
+fi
+
+mpirun  -np $use_cores --host $use_host Estia_liquids.out \
+        --dir="$DESTi" --format=NeXuS --ncount=$ncount \
+        omegaa=$omega theta_resolution=0.04 \
+        sample=$sample reflector=1 \
+        lambda_end=$lambda_end lambda_min=$lambda_min lambda_start=$lambda_start
+       
+omega=2.5
+DESTi=$DEST/liquids_ref_61
+if [ -e "$DESTi" ]; then
+	rm -r "$DESTi"
+fi
+
+mpirun  -np $use_cores --host $use_host Estia_liquids.out \
+        --dir="$DESTi" --format=NeXuS --ncount=$ncount \
+        omegaa=$omega theta_resolution=0.04 \
+        sample=$sample reflector=2 \
+        lambda_end=$lambda_end lambda_min=$lambda_min lambda_start=$lambda_start
+       
+###################### Ni-layer measurement ####################
+
+sample=2
+omega=1.3
+DESTi=$DEST/liquids_ni_13
+if [ -e "$DESTi" ]; then
+	rm -r "$DESTi"
+fi
+
+mpirun  -np $use_cores --host $use_host Estia_liquids.out \
+        --dir="$DESTi" --format=NeXuS --ncount=$ncount \
+        omegaa=$omega theta_resolution=0.04 \
+        sample=$sample reflector=0 \
+        lambda_end=$lambda_end lambda_min=$lambda_min lambda_start=$lambda_start
+       
+omega=2.5
+DESTi=$DEST/liquids_ni_25
+if [ -e "$DESTi" ]; then
+	rm -r "$DESTi"
+fi
+
+mpirun  -np $use_cores --host $use_host Estia_liquids.out \
+        --dir="$DESTi" --format=NeXuS --ncount=$ncount \
+        omegaa=$omega theta_resolution=0.04 \
+        sample=$sample reflector=0 \
+        lambda_end=$lambda_end lambda_min=$lambda_min lambda_start=$lambda_start
+       
+omega=2.5
+DESTi=$DEST/liquids_ni_39
+if [ -e "$DESTi" ]; then
+	rm -r "$DESTi"
+fi
+
+mpirun  -np $use_cores --host $use_host Estia_liquids.out \
+        --dir="$DESTi" --format=NeXuS --ncount=$ncount \
+        omegaa=$omega theta_resolution=0.04 \
+        sample=$sample reflector=1 \
+        lambda_end=$lambda_end lambda_min=$lambda_min lambda_start=$lambda_start
+       
+omega=2.5
+DESTi=$DEST/liquids_ni_61
+if [ -e "$DESTi" ]; then
+	rm -r "$DESTi"
+fi
+
+mpirun  -np $use_cores --host $use_host Estia_liquids.out \
+        --dir="$DESTi" --format=NeXuS --ncount=$ncount \
+        omegaa=$omega theta_resolution=0.04 \
+        sample=$sample reflector=2 \
+        lambda_end=$lambda_end lambda_min=$lambda_min lambda_start=$lambda_start
+       
+###################### D2O measurement ####################
+
+sample=0
+omega=1.3
+DESTi=$DEST/liquids_d2o_13
+if [ -e "$DESTi" ]; then
+	rm -r "$DESTi"
+fi
+
+mpirun  -np $use_cores --host $use_host Estia_liquids.out \
+        --dir="$DESTi" --format=NeXuS --ncount=$ncount \
+        omegaa=$omega theta_resolution=0.04 \
+        sample=$sample reflector=0 \
+        lambda_end=$lambda_end lambda_min=$lambda_min lambda_start=$lambda_start
+       
+omega=2.5
+DESTi=$DEST/liquids_d2o_25
+if [ -e "$DESTi" ]; then
+	rm -r "$DESTi"
+fi
+
+mpirun  -np $use_cores --host $use_host Estia_liquids.out \
+        --dir="$DESTi" --format=NeXuS --ncount=$ncount \
+        omegaa=$omega theta_resolution=0.04 \
+        sample=$sample reflector=0 \
+        lambda_end=$lambda_end lambda_min=$lambda_min lambda_start=$lambda_start
+       
+omega=2.5
+DESTi=$DEST/liquids_d2o_39
+if [ -e "$DESTi" ]; then
+	rm -r "$DESTi"
+fi
+
+mpirun  -np $use_cores --host $use_host Estia_liquids.out \
+        --dir="$DESTi" --format=NeXuS --ncount=$ncount \
+        omegaa=$omega theta_resolution=0.04 \
+        sample=$sample reflector=1 \
+        lambda_end=$lambda_end lambda_min=$lambda_min lambda_start=$lambda_start
+       
+omega=2.5
+DESTi=$DEST/liquids_d2o_61
+if [ -e "$DESTi" ]; then
+	rm -r "$DESTi"
+fi
+
+mpirun  -np $use_cores --host $use_host Estia_liquids.out \
+        --dir="$DESTi" --format=NeXuS --ncount=$ncount \
+        omegaa=$omega theta_resolution=0.04 \
+        sample=$sample reflector=2 \
+        lambda_end=$lambda_end lambda_min=$lambda_min lambda_start=$lambda_start
+       
+

simulation/run_pol.sh

@@ -1,77 +1,213 @@
 #!/bin/bash
 
 DEST=../results
-ncount=1e8
-use_cores=16
+ncount=2e7
+use_cores=4
 sample=4
-sample_length=0.005
+omega=0.8
+sample_length=0.01
 sample_height=0.01
 lambda_start=3.0
 lambda_end=32.0
 
-bash compile_if_needed.sh
+###################### 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
 
-###################### Reference measurement 10x5mm² and 10x0.5mm² VS ####################
 
-ncount=1e8
-sample_length=0.005
+###################### Reference and Ni-layer measurement 10x10mm² sample ####################
+# ncount=1e10
+sample_length=0.01
 sample_height=0.01
+lambda_start=3.5
+lambda_end=30.0
+sample=1
 
-DESTi=$DEST/pol_ref_10x5
+# omega=1.0
+# DESTi=$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
 if [ -e "$DESTi" ]; then
 	rm -r "$DESTi"
 fi
 
-mpirun  -np $use_cores --hostfile hostnames Estia_baseline.out \
-        --dir="$DESTi" --format=NeXus --ncount=$ncount \
+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=$lambda_end enable_gravity=0 enable_chopper=0 \
-		enable_polarizer=0 enable_analyzer=0
-       
-ncount=5e8
-sample_length=0.0005
-sample_height=0.01
+        lambda_start=$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
 
-DESTi=$DEST/pol_ref_10x0p5
-if [ -e "$DESTi" ]; then
-	rm -r "$DESTi"
-fi
+# sample_height=0.001
+# DESTi=$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
 
-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
+# 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
        
 
-###################### Polarizers 10x5mm² and 10x0.5mm² VS ####################
+###################### Reference and Ni-layer measurement 1x1mm² sample ####################
 
-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

simulation/sbatch.tsh

@@ -1,38 +0,0 @@
-#!/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."