start building new setup for paper

.gitignore

@@ -8,6 +8,7 @@ old
 *.backup
 .project
 .settings
+.idea
 *.pyc
 *.pyo
 hosts

analysis/compress_h5.sh

@@ -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

analysis/estia_analyze.py

@@ -8,7 +8,7 @@ import sys, os
 from numpy import *
 seterr(all='ignore')
 import estia_help as eh
-import mcstas_reader as mr
+from aglib import mcstas_reader as mr
 
 
 # Scaling factor of source monitor after normalizing by area to get to brilliance.

analysis/mcstas_reader.py

@@ -1,422 +0,0 @@
-#-*- coding: utf-8 -*-
-'''
-Simple support library for reading, analyzing and plotting of McStas results
-from the Estia instrument simulations.
-Meant to be used from IPython Notebook or QtConsole, but can also be run stand alone.
-'''
-
-import os, sys
-from numpy import *
-
-try:
-    import h5py
-except ImportError:
-    print "h5py not found, modern NeXuS format will not be readable."
-
-try:
-  from IPython import display #@UnusedImport
-  from IPython.core.pylabtools import print_figure
-  from matplotlib.figure import Figure
-  from matplotlib.backends.backend_agg import FigureCanvasAgg
-  from matplotlib.colors import LogNorm
-except ImportError:
-  # IPython and/or matplotlib not available, no interactive functionalities
-  display=None
-
-MAX_EVTS_BATCH=50000
-    
-class McSim(object):
-  '''
-  Object representing complete simulation from McStas.
-  Supports either the old style McStas output with separate ASCII files 
-  or HDF5 single file output.
-  
-  Different monitors can be accessed as keys like in a dictionary. The data is only loaded when the monitor is first accessed.
-  '''
-
-  def __init__(self, path):
-    '''
-    Initialize the simulation. path should be the file name to either the NeXuS or the mccode.sim file.
-    '''
-    self._data={}
-    if path.endswith('.h5'):
-      self._init_hdf(path)
-    elif path.endswith('.sim'):
-      self._init_old(path)
-    else:
-      if os.path.exists(os.path.join(path,'mccode.h5')):
-        self._init_hdf(os.path.join(path,'mccode.h5'))
-      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
-
-  def _init_hdf(self, path):
-    self.hdf=h5py.File(path, 'r')
-    self.data_loader=DataLoaderHDF(self.hdf)
-    self.info=self.data_loader.info
-
-  def _init_old(self, path):
-    self.info=HeaderFile(path)
-    self.data_loader=DataLoaderOld(self.info, os.path.dirname(path))
-
-  def keys(self):
-    return self.info['data'].keys()
-
-  def monitors(self):
-    output=[]
-    for val in self.info['data'].values():
-      xy=(val['xvar'], val['yvar'])
-      if not xy in output:
-        output.append(xy)
-    output.sort()
-    return output
-  
-  def plot(self, monitors=None):
-    graphs={}
-    for key, val in self.info['data'].items():
-      xy=(val['xvar'], val['yvar'])
-      if monitors is not None and xy!=monitors:
-        continue
-      data=self[key]
-      if xy in graphs:
-        graphs[xy].append(data)
-      else:
-        graphs[xy]=[data]
-    for xy, datasets in sorted(graphs.items()):
-      cols=min(len(datasets), 3)
-      rows=len(datasets)/3+1
-
-      fig=Figure(figsize=(12, 5*rows), dpi=300, facecolor='#FFFFFF')
-      FigureCanvasAgg(fig)
-
-      for i, data in enumerate(datasets):
-        ax=fig.add_subplot(rows, cols, i+1)
-        data.plot(ax=ax)
-      graphs[xy]=fig
-    if monitors is None:
-      return graphs
-    else:
-      return fig
-
-  def __getitem__(self, item):
-    if item in self._data:
-      return self._data[item]
-    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
-
-class HeaderFile(object):
-  '''
-  Analyze McStas mccode.sim header files.
-  '''
-  _data=None
-
-  @property
-  def data(self):
-    return self._data['data']
-
-  def __init__(self, path):
-    self._data={}
-    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.'
-    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)
-
-  def get_data(self, data):
-    output={}
-    start_idx=0
-    while start_idx<len(data):
-      start_idx=data.find('begin data', start_idx)
-      if start_idx==-1:
-        break
-      end_idx=data.find('end data', start_idx)
-      block=data[start_idx:end_idx].splitlines()[1:]
-      block_info={}
-      for bline in block:
-        item, value=bline.strip().split(':', 1)
-        block_info[item]=value.strip()
-        if item=='component':
-          output[value.strip()]=block_info
-
-      start_idx=end_idx
-    return output
-
-  def __getitem__(self, item):
-    return self._data[item]
-
-class DataLoaderOld(object):
-  '''
-    Load and analyze a old style McStas format with a simulation and a set of data text files.
-  '''
-  def __init__(self, info, root):
-    self.info=info
-    self.root=root
-
-  def load_item(self, item):
-    item_info=self.info['data'][item]
-    if not item_info['type'].startswith('array_2d'):
-      return self.load_item_1d(item)
-
-    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     
-      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]
-      return Dataset(data, item_info)
-
-  def load_item_1d(self, item):
-    item_info=self.info['data'][item]
-    fname=os.path.join(self.root, item_info['filename'])
-    raw=loadtxt(fname).T
-    data=raw[1]
-    errors=raw[2]
-    return Dataset1D(data, errors, item_info)
-
-class DataLoaderHDF(object):
-  '''
-    Load and analyze a new style NeXuS file format.
-  '''
-  def __init__(self, hdf):
-    self.hdf=hdf['entry1']
-    self.info={}
-    self.info['data']={}
-    for item in self.hdf['data'].keys():
-      node=self.hdf['data/'+item]
-      info={}
-      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:
-        self.info['data'][info['filename']]=info
-      info['datapath']='data/'+item
-
-  def load_item(self, item):
-    item_info=self.info['data'][item]
-    if not item_info['type'].startswith('array_2d'):
-      return self.load_item_1d(item)
-
-    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
-      cols=item_info['variables'].split()
-      evds=node['events']
-      if len(evds)<=MAX_EVTS_BATCH:
-        data=evds.value.astype(float32).view(
-            dtype={'names': cols, 'formats': ['f4']*len(cols)}).flatten()
-      else:
-        ds=[]
-        sys.stdout.write('Reading large dataset:\n')
-        for i in range(len(evds)//MAX_EVTS_BATCH+1):
-          sys.stdout.write('\r%i/%i'%(i*MAX_EVTS_BATCH, len(evds)))
-          sys.stdout.flush()
-          ds.append(evds[i*MAX_EVTS_BATCH:(i+1)*MAX_EVTS_BATCH])
-        sys.stdout.write('\r%i/%i\n'%(len(evds), len(evds)))
-        data=vstack(ds).astype(float32).view(
-            dtype={'names': cols, 'formats': ['f4']*len(cols)}).flatten()
-      return TofData(data, item_info)
-    else:
-      data=node['data'].value.T
-      return Dataset(data, item_info)
-  
-  def load_item_1d(self, item):
-    item_info=self.info['data'][item]
-    node=self.hdf[item_info['datapath']]
-    data=node['data'].value
-    errors=node['errors'].value
-    return Dataset1D(data, errors, item_info)
-
-class Dataset1D(object):
-  '''
-    Representation of a standard McStas dataset of one variable.
-  '''
-  def __init__(self, data, errors, info):
-    self.data=data
-    self.errors=errors
-    self.info=info
-
-  def plot(self, log=False, ax=None):
-    if ax is None:
-      import pylab
-      ax=pylab.gca()
-
-    limits=map(float, self.info['xlimits'].split())
-    x=linspace(limits[0], limits[1], len(self.data))
-
-    ax.errorbar(x, self.data, yerr=self.errors)
-    if log:
-      ax.set_yscale('log')
-    else:
-      ax.set_yscale('linear')
-    ax.set_xlabel(self.info['xlabel'])
-    ax.set_ylabel(self.info['ylabel'])
-    ax.set_title(self.info['component'])
-
-  def _repr_png_(self):
-    '''
-      Image representation form ipython console/notebook. 
-    '''
-    fig=Figure(figsize=(8, 5), dpi=300, facecolor='#FFFFFF')
-    FigureCanvasAgg(fig)
-    ax=fig.add_subplot(111)
-
-    self.plot(ax=ax)
-
-    return print_figure(fig, dpi=72)
-
-
-class Dataset(object):
-  '''
-    Representation of a standard McStas dataset with 2D view.
-  '''
-  def __init__(self, data, info):
-    self.data=data
-    self.info=info
-
-  def plot(self, log=False, ax=None):
-    if ax is None:
-      import pylab
-      ax=pylab.gca()
-
-    limits=map(float, self.info['xylimits'].split())
-
-    if log:
-      ax.imshow(self.data, origin='lower', extent=limits, aspect='auto', norm=LogNorm())
-    else:
-      ax.imshow(self.data, origin='lower', extent=limits, aspect='auto')
-    ax.set_xlabel(self.info['xlabel'])
-    ax.set_ylabel(self.info['ylabel'])
-    ax.set_title(self.info['component'])
-
-  def _repr_png_(self):
-    '''
-      Image representation form ipython console/notebook. 
-    '''
-    fig=Figure(figsize=(8, 5), dpi=300, facecolor='#FFFFFF')
-    FigureCanvasAgg(fig)
-    ax=fig.add_subplot(111)
-
-    self.plot(ax=ax)
-
-    return print_figure(fig, dpi=72)
-
-class TofData(Dataset):
-  '''
-    Representation of a dataset collected with Monitor_nD
-  '''
-  
-  def project1d(self, col, bins=50, fltr=None, newcols=None, norm=None):
-    ''' 
-      Generate binned data for arbitrary binning and columns.
-      
-      The fltr argument can be a string with a filtering condition on the available columns.
-      Syntax for this filtering follows numpy array convetions like (x>5)&(abs(L)<0.3) would
-      be a valid statement.
-      
-      newcols can be a list of (name, code) tuples, that calculate new columns from
-      existing ones, like newcols=[('q', '4*pi/L*sin(theta)')].
-    '''
-    columns=dict([(coli, self.data[coli]) for coli in self.data.dtype.names])
-    if newcols is not None:
-      for name, code in newcols:
-        columns[name]=eval(code, globals(), columns)
-
-    if norm is None:
-      w=self.data['p']
-    else:
-      w=eval(norm+'*p', globals(), columns)
-
-    if fltr is None:
-      I, x=histogram(columns[col], bins=bins, weights=w)
-    else:
-      if isinstance(fltr, basestring):
-        fltr=eval(fltr, globals(), columns)
-      I, x=histogram(columns[col][fltr], bins=bins, weights=w[fltr])
-    return x, I
-
-  def project2d(self, xcol, ycol, bins=50, fltr=None, newcols=None):
-    ''' 
-      Generate 2D binned data for arbitrary binning and columns.
-      
-      The fltr argument can be a string with a filtering condition on the available columns.
-      Syntax for this filtering follows numpy array convetions like (x>5)&(abs(L)<0.3) would
-      be a valid statement.
-      
-      newcols can be a list of (name, code) tuples, that calculate new columns from
-      existing ones, like newcols=[('q', '4*pi/L*sin(theta)')].
-    '''
-    columns=dict([(coli, self.data[coli]) for coli in self.data.dtype.names])
-    if newcols is not None:
-      for name, code in newcols:
-        columns[name]=eval(code, globals(), columns)
-
-    if fltr is None:
-      I, y, x=histogram2d(columns[ycol], columns[xcol],
-                        bins=bins, weights=self.data['p'])
-    else:
-      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])
-    return x, y, I
-
-  def plot(self, xcol='x', ycol='y', log=False, ax=None, bins=50, fltr=None, newcols=None):
-    if ax is None:
-      import pylab
-      ax=pylab.gca()
-
-    x, y, I=self.project2d(xcol, ycol, bins=bins, fltr=fltr, newcols=newcols)
-
-    if log:
-      ax.pcolormesh(x, y, I, norm=LogNorm())
-    else:
-      ax.pcolormesh(x, y, I)
-
-    col_names=self.info['title'].split()
-    cols=self.info['variables'].split()
-
-    try:
-      ax.set_xlabel(xcol+'-'+col_names[cols.index(xcol)])
-    except ValueError:
-      ax.set_xlabel(xcol)
-    try:
-      ax.set_ylabel(ycol+'-'+col_names[cols.index(ycol)])
-    except ValueError:
-      ax.set_ylabel(ycol)
-    ax.set_title(self.info['component'])
-
-
-  def plot1d(self, col='x', log=False, ax=None, bins=50, fltr=None, newcols=None):
-    if ax is None:
-      import pylab
-      ax=pylab.gca()
-
-    x, I=self.project1d(col, bins=bins, fltr=fltr, newcols=newcols)
-
-    if log:
-      ax.semilogy((x[:-1]+x[1:])/2., I)
-    else:
-      ax.plot((x[:-1]+x[1:])/2., I)
-    col_names=self.info['title'].split()
-    cols=self.info['variables'].split()
-
-    try:
-      ax.set_xlabel(col+'-'+col_names[cols.index(col)])
-    except ValueError:
-      ax.set_xlabel(col)
-    ax.set_ylabel('Intensity')
-    ax.set_title(self.info['component'])
-

simulation/D2O.ref

@@ -1,602 +0,0 @@
-# Dataset "D2O" exported from GenX on Wed Dec 12 04:56:52 2018
-# Column lables:
-# q                      R
-1.666666666666666774e-03 1.000000000000000444e+00
-3.333333333333333547e-03 9.999999999999997780e-01
-5.000000000000000104e-03 9.999999999999997780e-01
-6.666666666666667095e-03 1.000000000000000000e+00
-8.333333333333333218e-03 1.000000000000000000e+00
-1.000000000000000021e-02 9.999999999999997780e-01
-1.166666666666666546e-02 1.000000000000000000e+00
-1.333333333333333419e-02 1.000000000000000000e+00
-1.499999999999999944e-02 1.000000000000000000e+00
-1.666666666666666644e-02 9.999999999999997780e-01
-1.833333333333333343e-02 4.278890099662767121e-01
-2.000000000000000042e-02 1.488213407917928499e-01
-2.166666666666666741e-02 7.884172397716723846e-02
-2.333333333333333440e-02 4.817452607189460362e-02
-2.500000000000000486e-02 3.189361318639775261e-02
-2.666666666666666838e-02 2.227351089491558592e-02
-2.833333333333333537e-02 1.617286323369671042e-02
-3.000000000000000236e-02 1.210130221930963597e-02
-3.166666666666666935e-02 9.275545669075232341e-03
-3.333333333333333287e-02 7.252320052814169304e-03
-3.500000000000000333e-02 5.766184773509967602e-03
-3.666666666666666685e-02 4.650893428800271893e-03
-3.833333333333333731e-02 3.798435003476626718e-03
-4.000000000000000083e-02 3.136449158010019053e-03
-4.166666666666666435e-02 2.615177649439983341e-03
-4.333333333333333481e-02 2.199624859348910891e-03
-4.500000000000000527e-02 1.864688519115220407e-03
-4.666666666666666879e-02 1.592047104649371280e-03
-4.833333333333333925e-02 1.368119547985798337e-03
-4.999999999999999584e-02 1.182697864477368077e-03
-5.166666666666666630e-02 1.028012492027462850e-03
-5.333333333333333676e-02 8.980819969847711167e-04
-5.500000000000000028e-02 7.882533389725678323e-04
-5.666666666666667074e-02 6.948721016997541113e-04
-5.833333333333334120e-02 6.150427933261069530e-04
-6.000000000000000472e-02 5.464524855421789510e-04
-6.166666666666666824e-02 4.872395943257391100e-04
-6.333333333333333870e-02 4.358952326153466895e-04
-6.500000000000000222e-02 3.911883347291949869e-04
-6.666666666666666574e-02 3.521083144256650943e-04
-6.833333333333334314e-02 3.178207833803634160e-04
-7.000000000000000666e-02 2.876330878189759703e-04
-7.166666666666667018e-02 2.609672896223826869e-04
-7.333333333333333370e-02 2.373388377584093804e-04
-7.499999999999999722e-02 2.163396222927348015e-04
-7.666666666666667462e-02 1.976244279443217474e-04
-7.833333333333333814e-02 1.809000424665311657e-04
-8.000000000000000167e-02 1.659164515183386701e-04
-8.166666666666666519e-02 1.524596832757783220e-04
-8.333333333333332871e-02 1.403459649391344810e-04
-8.500000000000000611e-02 1.294169281633042532e-04
-8.666666666666666963e-02 1.195356575005832348e-04
-8.833333333333333315e-02 1.105834197134533182e-04
-9.000000000000001055e-02 1.024569455916587762e-04
-9.166666666666667407e-02 9.506616212616428763e-05
-9.333333333333333759e-02 8.833229335679883471e-05
-9.500000000000001499e-02 8.218626426822687851e-05
-9.666666666666667851e-02 7.656735477319774488e-05
-9.833333333333332815e-02 7.142206085828434919e-05
-9.999999999999999167e-02 6.670312795820712841e-05
-1.016666666666666691e-01 6.236872801538500633e-05
-1.033333333333333326e-01 5.838175681406183431e-05
-1.049999999999999961e-01 5.470923231784354554e-05
-1.066666666666666735e-01 5.132177809103187119e-05
-1.083333333333333370e-01 4.819317860823825678e-05
-1.100000000000000006e-01 4.529999547886719982e-05
-1.116666666666666780e-01 4.262123543222435878e-05
-1.133333333333333415e-01 4.013806240326980157e-05
-1.150000000000000050e-01 3.783354729055566355e-05
-1.166666666666666824e-01 3.569244997606189424e-05
-1.183333333333333459e-01 3.370102904102350720e-05
-1.199999999999999956e-01 3.184687531417531464e-05
-1.216666666666666591e-01 3.011876597473503737e-05
-1.233333333333333365e-01 2.850653642251948946e-05
-1.250000000000000000e-01 2.700096753867208433e-05
-1.266666666666666774e-01 2.559368630616589346e-05
-1.283333333333333270e-01 2.427707805072443407e-05
-1.300000000000000044e-01 2.304420880910700020e-05
-1.316666666666666818e-01 2.188875654044092456e-05
-1.333333333333333315e-01 2.080495007345798850e-05
-1.350000000000000089e-01 1.978751483337357349e-05
-1.366666666666666863e-01 1.883162452074562727e-05
-1.383333333333333359e-01 1.793285802466960840e-05
-1.400000000000000133e-01 1.708716094682676266e-05
-1.416666666666666630e-01 1.629081119377076716e-05
-1.433333333333333404e-01 1.554038816436415657e-05
-1.449999999999999900e-01 1.483274511916031133e-05
-1.466666666666666674e-01 1.416498437028349574e-05
-1.483333333333333448e-01 1.353443497503935812e-05
-1.499999999999999944e-01 1.293863265526270861e-05
-1.516666666666666718e-01 1.237530169802975281e-05
-1.533333333333333492e-01 1.184233862257320649e-05
-1.549999999999999989e-01 1.133779742373565549e-05
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simulation/Estia_baseline.instr

@@ -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
 )
@@ -104,12 +105,20 @@ 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 analyzer_flipper_start  = 0.4; // Distance from sample to analyzer flipper
+
+
 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
 
+double Theta1_analyzer1, Theta1_analyzer2, Theta2_analyzer1, Theta2_analyzer2, dist_ana_vfocus; // quantities calculated out of values above and 1.5 degree covered divergence
+int p_int;
+%}
+
+USERVARS %{
+  int p_int; // a flag that gets incremented if a polarizer mirror scatters
 %}
 
 INITIALIZE
@@ -118,11 +127,11 @@ INITIALIZE
 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;
-
+p_int=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 +144,8 @@ 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 +211,7 @@ 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 +243,15 @@ 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(nb=21, ndiv=41, filename="vs_hordiv",
+          xmin=-0.02, xmax=0.02, ymin=-0.02, ymax=0.02, maxdiv=2.0,
+		  restore_neutron=1)
+		  AT (0, 0, -0.5*sample_length-0.001) RELATIVE arm_selene1
+
+COMPONENT vs_divergence_v = DivPos_monitor(nb=21, ndiv=41, filename="vs_verdiv",
+          xmin=-0.02, xmax=0.02, ymin=-0.02, ymax=0.02, maxdiv=2.0,
+		  restore_neutron=1, vertical=1)
+		  AT (0, 0, -0.5*sample_length-0.001) RELATIVE arm_selene1
 
 /* The actual virtual source mask, two L-shaped absorbers (first top-right) */
 COMPONENT virtual_source_TR = Slit(
@@ -282,8 +300,8 @@ 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
@@ -331,36 +349,67 @@ COMPONENT si_sample = Mirror(
     ROTATED (0, 90, 0) RELATIVE arm_sample
 
 
-COMPONENT arm_analyzer = Arm()
+
+
+
+/* Rotate spin 90 degrees*/
+COMPONENT arm_hack = Arm()
+       AT (0, 0, 0) RELATIVE arm_sample
+       EXTEND %{
+         double tmp = sy;
+         sy = sx;
+         sx = -tmp;
+       %}
+
+
+
+
+/* flipped arm detector to position analyzer correctly for beam path 1*/
+COMPONENT arm_detector2 = Arm()
     AT (0, 0, 0) RELATIVE arm_detector
-    ROTATED (-selene_theta+(Theta1_analyzer1-Theta2_analyzer1)/2.0, 0, 0) RELATIVE arm_detector
+  ROTATED (0,0,180) RELATIVE arm_detector
+
+
+
+COMPONENT arm_analyzer = Arm()
+    AT (0, 0, 0) RELATIVE arm_detector2
+    ROTATED (-selene_theta+(Theta1_analyzer1-Theta2_analyzer1)/2.0, 0, 0) RELATIVE arm_detector2
+
+COMPONENT virtual_analyzer_flipper = Arm() // Gone -> Pol_SF_ideal(ny=1, xwidth=1, yheight=1, zdepth=0.001)
+        WHEN (enable_analyzer>2)
+        AT (0, 0, analyzer_flipper_start) RELATIVE arm_analyzer
+        ROTATED (0,0,0.0) RELATIVE arm_analyzer
+    EXTEND %{
+        if(INSTRUMENT_GETPAR(enable_analyzer)>2) sx *=-1;
+    %}
 
 COMPONENT arm_analyzer2 = Arm()
-    AT (0, 0, 0) RELATIVE arm_detector
-    ROTATED (-selene_theta+(Theta1_analyzer2-Theta2_analyzer2)/2.0, 0, 0) RELATIVE arm_detector
+    AT (0, 0, 0) RELATIVE arm_detector2
+    ROTATED (-selene_theta+(Theta1_analyzer2-Theta2_analyzer2)/2.0, 0, 0) RELATIVE arm_detector2
 
 /* 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
-        AT (0, 0.0, analyzer2_start) RELATIVE arm_analyzer
-        ROTATED (0,0,0.0) RELATIVE arm_analyzer
+        AT (0, 0.0, analyzer2_start) RELATIVE arm_analyzer2
+        ROTATED (0,0,0.0) RELATIVE arm_analyzer2
 
 /* 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",
+        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
 
 /***********************************************************************/
 

simulation/Estia_feeder.instr

@@ -144,7 +144,7 @@ COMPONENT NBOA_window=Al_window(thickness=NBOA_Al_entrance_length)
     AT (0,0,NBOA_Al_entrance_start) RELATIVE ISCS
 
     
-COMPONENT NBOA_side = AbsorberFixed(xmin=NBOA_side_x, xmax=NBOA_side_x+0.012, 
+COMPONENT NBOA_side = Absorber(xmin=NBOA_side_x, xmax=NBOA_side_x+0.012,
                                       ymin=-0.2, ymax=0.2, 
                                       zmin=0.0, zmax=E02_01_01_Cu_length+E02_01_01_length+E02_01_02_length+E02_01_03_length)
     AT (0, 0, E02_01_01_Cu_start) RELATIVE ISCS
@@ -181,7 +181,7 @@ COMPONENT NBOA_Cu_collimator=Guide_gravity(
 * feeder neutron guide *
 ************************/
 
-COMPONENT E02_01_011_wedge = AbsorberFixed(xmin=-0.1, xmax=0.0, 
+COMPONENT E02_01_011_wedge = Absorber(xmin=-0.1, xmax=0.0,
                                       ymin=-E02_01_011_wh/2.0, ymax=E02_01_011_wh/2.0, 
                                       zmin=0.0, zmax=E02_01_01_length-0.5)
     AT (0, 0, E02_01_01_start) RELATIVE ISCS
@@ -190,7 +190,7 @@ COMPONENT E02_01_011_wedge = AbsorberFixed(xmin=-0.1, xmax=0.0,
         ALLOW_BACKPROP;    
         PROP_Z0;
     %}
-COMPONENT E02_01_012_wedge = AbsorberFixed(xmin=-0.1, xmax=0.0, 
+COMPONENT E02_01_012_wedge = Absorber(xmin=-0.1, xmax=0.0,
                                       ymin=-E02_01_012_wh/2.0, ymax=E02_01_012_wh/2.0, 
                                       zmin=0.5-E02_01_01_Cu_length, zmax=E02_01_01_length)
     AT (0, 0, E02_01_01_start) RELATIVE ISCS
@@ -210,7 +210,7 @@ COMPONENT E02_01_01 = Elliptic_guide_gravity(
     enableGravity=enable_gravity)
     AT (0, 0, E02_01_01_start) RELATIVE ISCS
 
-COMPONENT E02_01_021_wedge = AbsorberFixed(xmin=-0.1, xmax=0.0, 
+COMPONENT E02_01_021_wedge = Absorber(xmin=-0.1, xmax=0.0,
                                       ymin=-E02_01_021_wh/2.0, ymax=E02_01_021_wh/2.0, 
                                       zmin=0.0, zmax=E02_01_02_length/2.0)
     AT (0, 0, E02_01_02_start) RELATIVE ISCS
@@ -219,7 +219,7 @@ COMPONENT E02_01_021_wedge = AbsorberFixed(xmin=-0.1, xmax=0.0,
         ALLOW_BACKPROP;    
         PROP_Z0;
     %}
-COMPONENT E02_01_022_wedge = AbsorberFixed(xmin=-0.1, xmax=0.0, 
+COMPONENT E02_01_022_wedge = Absorber(xmin=-0.1, xmax=0.0,
                                       ymin=-E02_01_022_wh/2.0, ymax=E02_01_022_wh/2.0, 
                                       zmin=E02_01_02_length/2.0, zmax=E02_01_02_length)
     AT (0, 0, E02_01_02_start) RELATIVE ISCS
@@ -238,7 +238,7 @@ COMPONENT E02_01_02 = Elliptic_guide_gravity(
     enableGravity=enable_gravity)
     AT (0, 0, E02_01_02_start) RELATIVE ISCS
 
-COMPONENT E02_01_031_wedge = AbsorberFixed(xmin=-0.1, xmax=0.0, 
+COMPONENT E02_01_031_wedge = Absorber(xmin=-0.1, xmax=0.0,
                                       ymin=-E02_01_031_wh/2.0, ymax=E02_01_031_wh/2.0, 
                                       zmin=0.0, zmax=0.5)
     AT (0, 0, E02_01_03_start) RELATIVE ISCS
@@ -247,7 +247,7 @@ COMPONENT E02_01_031_wedge = AbsorberFixed(xmin=-0.1, xmax=0.0,
         ALLOW_BACKPROP;    
         PROP_Z0;
     %}
-COMPONENT E02_01_032_wedge = AbsorberFixed(xmin=-0.1, xmax=0.0, 
+COMPONENT E02_01_032_wedge = Absorber(xmin=-0.1, xmax=0.0,
                                       ymin=-E02_01_032_wh/2.0, ymax=E02_01_032_wh/2.0, 
                                       zmin=0.5, zmax=1.0)
     AT (0, 0, E02_01_03_start) RELATIVE ISCS
@@ -256,7 +256,7 @@ COMPONENT E02_01_032_wedge = AbsorberFixed(xmin=-0.1, xmax=0.0,
         ALLOW_BACKPROP;    
         PROP_Z0;
     %}
-COMPONENT E02_01_033_wedge = AbsorberFixed(xmin=-0.1, xmax=0.0, 
+COMPONENT E02_01_033_wedge = Absorber(xmin=-0.1, xmax=0.0,
                                       ymin=-E02_01_033_wh/2.0, ymax=E02_01_033_wh/2.0, 
                                       zmin=1.0, zmax=E02_01_03_length)
     AT (0, 0, E02_01_03_start) RELATIVE ISCS
@@ -299,7 +299,7 @@ COMPONENT NFGA_Al_window_in=Al_window(
     WHEN enable_windows
     AT (0,0,NFGA_Al_start) RELATIVE ISCS
 
-COMPONENT NFGA_side1 = AbsorberFixed(xmin=NFGA_side_x1, xmax=NFGA_side_x1+0.008, 
+COMPONENT NFGA_side1 = Absorber(xmin=NFGA_side_x1, xmax=NFGA_side_x1+0.008,
                                       ymin=-0.2, ymax=0.2, 
                                       zmin=0.002, zmax=0.502)
     AT (0, 0, E02_02_01_start-0.002) RELATIVE ISCS
@@ -309,7 +309,7 @@ COMPONENT NFGA_side1 = AbsorberFixed(xmin=NFGA_side_x1, xmax=NFGA_side_x1+0.008,
         ALLOW_BACKPROP;    
         PROP_Z0;
     %}
-COMPONENT NFGA_side2 = AbsorberFixed(xmin=NFGA_side_x2, xmax=NFGA_side_x2+0.008, 
+COMPONENT NFGA_side2 = Absorber(xmin=NFGA_side_x2, xmax=NFGA_side_x2+0.008,
                                       ymin=-0.2, ymax=0.2, 
                                       zmin=0.502, zmax=E02_02_01_length+E02_02_02_length+E02_02_03_length+0.002)
     AT (0, 0, E02_02_01_start-0.002) RELATIVE ISCS
@@ -321,7 +321,7 @@ COMPONENT NFGA_side2 = AbsorberFixed(xmin=NFGA_side_x2, xmax=NFGA_side_x2+0.008,
     %}
         
 // in-bunker feeder segments	
-COMPONENT E02_02_011_wedge = AbsorberFixed(xmin=-0.1, xmax=0.0, 
+COMPONENT E02_02_011_wedge = Absorber(xmin=-0.1, xmax=0.0,
                                       ymin=-E02_02_011_wh/2.0, ymax=E02_02_011_wh/2.0, 
                                       zmin=0.0, zmax=E02_02_01_length/2.0)
     AT (0, 0, E02_02_01_start) RELATIVE ISCS
@@ -330,7 +330,7 @@ COMPONENT E02_02_011_wedge = AbsorberFixed(xmin=-0.1, xmax=0.0,
         ALLOW_BACKPROP;    
         PROP_Z0;
     %}
-COMPONENT E02_02_012_wedge = AbsorberFixed(xmin=-0.1, xmax=0.0, 
+COMPONENT E02_02_012_wedge = Absorber(xmin=-0.1, xmax=0.0,
                                       ymin=-E02_02_012_wh/2.0, ymax=E02_02_012_wh/2.0, 
                                       zmin=E02_02_01_length/2.0, zmax=E02_02_01_length)
     AT (0, 0, E02_02_01_start) RELATIVE ISCS
@@ -349,7 +349,7 @@ COMPONENT E02_02_01 = Elliptic_guide_gravity(
     enableGravity=enable_gravity)
     AT (0, 0, E02_02_01_start) RELATIVE ISCS
     
-COMPONENT E02_02_021_wedge = AbsorberFixed(xmin=-0.1, xmax=0.0, 
+COMPONENT E02_02_021_wedge = Absorber(xmin=-0.1, xmax=0.0,
                                       ymin=-E02_02_021_wh/2.0, ymax=E02_02_021_wh/2.0, 
                                       zmin=0.0, zmax=E02_02_02_length/2.0)
     AT (0, 0, E02_02_02_start) RELATIVE ISCS
@@ -358,7 +358,7 @@ COMPONENT E02_02_021_wedge = AbsorberFixed(xmin=-0.1, xmax=0.0,
         ALLOW_BACKPROP;    
         PROP_Z0;
     %}
-COMPONENT E02_02_022_wedge = AbsorberFixed(xmin=-0.1, xmax=0.0, 
+COMPONENT E02_02_022_wedge = Absorber(xmin=-0.1, xmax=0.0,
                                       ymin=-E02_02_022_wh/2.0, ymax=E02_02_022_wh/2.0, 
                                       zmin=E02_02_02_length/2.0, zmax=E02_02_02_length)
     AT (0, 0, E02_02_02_start) RELATIVE ISCS
@@ -377,7 +377,7 @@ COMPONENT E02_02_02 = Elliptic_guide_gravity(
     enableGravity=enable_gravity)
     AT (0, 0, E02_02_02_start) RELATIVE ISCS
     
-COMPONENT E02_02_031_wedge = AbsorberFixed(xmin=-0.1, xmax=0.0, 
+COMPONENT E02_02_031_wedge = Absorber(xmin=-0.1, xmax=0.0,
                                       ymin=-E02_02_031_wh/2.0, ymax=E02_02_031_wh/2.0, 
                                       zmin=0.0, zmax=0.5)
     AT (0, 0, E02_02_03_start) RELATIVE ISCS
@@ -386,7 +386,7 @@ COMPONENT E02_02_031_wedge = AbsorberFixed(xmin=-0.1, xmax=0.0,
         ALLOW_BACKPROP;    
         PROP_Z0;
     %}
-COMPONENT E02_02_032_wedge = AbsorberFixed(xmin=-0.1, xmax=0.0, 
+COMPONENT E02_02_032_wedge = Absorber(xmin=-0.1, xmax=0.0,
                                       ymin=-E02_02_032_wh/2.0, ymax=E02_02_032_wh/2.0, 
                                       zmin=0.5, zmax=1.0)
     AT (0, 0, E02_02_03_start) RELATIVE ISCS
@@ -395,7 +395,7 @@ COMPONENT E02_02_032_wedge = AbsorberFixed(xmin=-0.1, xmax=0.0,
         ALLOW_BACKPROP;    
         PROP_Z0;
     %}
-COMPONENT E02_02_033_wedge = AbsorberFixed(xmin=-0.1, xmax=0.0, 
+COMPONENT E02_02_033_wedge = Absorber(xmin=-0.1, xmax=0.0,
                                       ymin=-E02_02_033_wh/2.0, ymax=E02_02_033_wh/2.0, 
                                       zmin=1.0, zmax=E02_02_03_length)
     AT (0, 0, E02_02_03_start) RELATIVE ISCS

simulation/Estia_liquids.instr

@@ -1,391 +0,0 @@
-/*******************************************************************************
-*         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

@@ -28,20 +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 +127,112 @@ 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,
+                                      rUpData="SNAG_m5p5_Tup.ref", rDownData="SNAG_m5p5_Tdown.ref")
+		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
+		%{
+			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,
+                                      rUpData="SNAG_m5p5_Tup.ref", rDownData="SNAG_m5p5_Tdown.ref")
+		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(nb=21, ndiv=41, filename="mf_hordiv",
+          xmin=-0.02, xmax=0.02, ymin=-0.02, ymax=0.02, maxdiv=2.0)
+		  AT (0, 0, 0) RELATIVE arm_polarizer
+
+COMPONENT mf_divergence_v = DivPos_monitor(nb=21, ndiv=41, filename="mf_verdiv",
+          xmin=-0.02, xmax=0.02, ymin=-0.02, ymax=0.02, maxdiv=2.0, vertical=1)
+		  AT (0, 0, 0) 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/SNAG_m5p5_Tdown.ref

@@ -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
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+0.056701342	0.120064418
+0.058974642	0.122922579
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+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
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+0.080833293	0.10262909
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+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
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+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

@@ -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
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+0.06548852	0.987959462
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+0.074231981	0.985149296
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+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/ScanningSlit.comp

@@ -1,93 +0,0 @@
-/*******************************************************************************
-*
-* McStas, neutron ray-tracing package
-*         Copyright (C) 1997-2011, All rights reserved
-*         Risoe National Laboratory, Roskilde, Denmark
-*         Institut Laue Langevin, Grenoble, France
-*
-* Component: ScanningSlit
-*
-* %I
-* Written by: Jochen Stahn, based on the Slip component by
-*             Kim Lefmann and Henrik M. Roennow
-* Date: 15. 10. 2013
-* Version: $Revision: 0.00 $
-* Origin: PSI
-* Release: McStas 1.12c
-*
-* moving rectangular slit with optional insignificance cut
-*
-* %D
-* A simple rectangular slit, where the blades in x-direction move with time.
-* No transmission around the slit is allowed.
-* If cutting option is used, low-weight neutron rays are ABSORBED
-*
-* Example: FastSlit(height=0.1)
-*
-* %P
-* INPUT PARAMETERS
-*
-* height: height of the opening in y, centered.
-*
-* Optional parameters:
-* cut:  Lower limit for allowed weight (1)
-*
-* %E
-*******************************************************************************/
-
-
-DEFINE COMPONENT ScanningSlit
-DEFINITION PARAMETERS ()
-SETTING PARAMETERS (xmin=0, xmax=0, ymin=0, ymax=0, height=0.1, dist=2.4, lmin=4, lmax=10, omeg=0, eps=1.25, reso=0.01, dthet=1.5, posi=33.7)
-OUTPUT PARAMETERS ()
-/* STATE PARAMETERS (x,y,z,vx,vy,vz,t,s1,s2,p) */
-
-DECLARE
- %{
-  double lact;
- %}
-
-
-INITIALIZE
-%{
-  if (height > 0) { ymax=height/2; ymin=-ymax; }
-  lmax  *= (1+reso/2) ;
-  lmin  *= (1-reso/2) ;
-  eps   *= PI/180 ;
-  omeg  *= PI/180 ;
-  dthet *= PI/180;
-%}
-
-TRACE
-%{
-    PROP_Z0;
-    lact = 3.956e3*t/posi ;
-    xmin = -dist * (1+reso/2)*( eps + 0.5*dthet - dthet*(lact-lmin)/(lmax-lmin) ) ;
-    xmax = -dist * (1-reso/2)*( eps + 0.5*dthet - dthet*(lact-lmin)/(lmax-lmin) ) ;
-    if ((x<xmin || x>xmax || y<ymin || y>ymax))
-      ABSORB;
-    else
-      SCATTER;
-%}
-
-MCDISPLAY
-%{
-  magnify("xy");
-    double xw, yh;
-    xw = (xmax - xmin)/2.0;
-    yh = (ymax - ymin)/2.0;
-    multiline(3, xmin-xw, (double)ymax, 0.0,
-              (double)xmin, (double)ymax, 0.0,
-              (double)xmin, ymax+yh, 0.0);
-    multiline(3, xmax+xw, (double)ymax, 0.0,
-              (double)xmax, (double)ymax, 0.0,
-              (double)xmax, ymax+yh, 0.0);
-    multiline(3, xmin-xw, (double)ymin, 0.0,
-              (double)xmin, (double)ymin, 0.0,
-              (double)xmin, ymin-yh, 0.0);
-    multiline(3, xmax+xw, (double)ymin, 0.0,
-              (double)xmax, (double)ymin, 0.0,
-              (double)xmax, ymin-yh, 0.0);
-%}
-
-END

simulation/Selene_geometry.instr

@@ -1,145 +0,0 @@
-/*******************************************************************************
-*         McStas instrument definition URL=http://www.mcstas.org
-*
-* Instrument: Selene_geometry
-*
-* %Identification
-* Written by: Artur Glavic (artur.glavic@psi.ch); Jochen Stahn (jochen.stahn@psi.ch); Christine Klauser (christine.klauser@psi.ch)
-* Date: 01. 11. 2017
-* Origin: PSI
-* Release: McStas 2.4.1
-* Version: 1.0
-* %INSTRUMENT_SITE: Estia (E02)
-*
-* Estia is a vertical sample, focusing reflectometer for small sample
-*
-* %Description
-* This is a test model to analyze the impact of the displacement of the two Selene guide
-* mirrors to each other and the virtual source. With this it is possible to evaluate
-* necessary engineering requirements for the guide carriers.
-*
-* %Parameters
-* sample_length: [m] Size of sample in beam direction, also controls virtual source opening
-* sample_height: [m] Size of sample in vertical direction, also controls virtual source opening
-* omegaa: [deg]  sample rotation omega
-*
-* %End
-*******************************************************************************/
-
-DEFINE INSTRUMENT Selene_geometry(double sample_length=0.01, double sample_height=0.01, omegaa=1.2,
-        double tx_1=0.0, double tz_1=0.0, double rz_1=0.0, double ry_1=0.0,
-        double tx_2=0.0, double tz_2=0.0, double rz_2=0.0, double ry_2=0.0
-        )
-
-DECLARE
-%{
-
-%}
-
-INITIALIZE
-%{
-
-%}
-TRACE
-
-COMPONENT origin = Progress_bar()
-    AT (0,0,0) ABSOLUTE
-
-COMPONENT ISCS = Arm()
-    AT (0, 0, 0) RELATIVE origin    
-    
-COMPONENT arm_selene1 = Arm()
-    AT (tx_1, 0, tz_1) RELATIVE ISCS
-    ROTATED (0, ry_1, rz_1) RELATIVE ISCS
-    
-COMPONENT arm_selene2 = Arm()
-    AT (tx_2, 0, 2*selene_c+tz_2) RELATIVE ISCS    
-    ROTATED (0, ry_2, rz_2) RELATIVE ISCS
-
-COMPONENT arm_virtual_source_beam = Arm()
-    AT (0, 0, 0) RELATIVE arm_selene1
-    ROTATED (0, 1.25, 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, omegaa, 0) RELATIVE arm_virtual_source_beam
-    
-    
-COMPONENT source = Moderator(radius = 0.01, focus_xw = selene_entry+0.002, focus_yh = selene_entry+0.002, 
-                                       target_index=3, Emin=0.75, Emax=6)
-    AT (0,0,-0.1) RELATIVE ISCS
-    ROTATED (-1.25, 1.25, 0) RELATIVE ISCS
-
-/* 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 = sample_height/2)
-    AT (0, 0, -0.5*sample_length) 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 = -sample_height/2, ymax = 1.0)
-    AT (0, 0, 0.5*sample_length) RELATIVE arm_virtual_source
-
-%include "Estia_selene.instr"
-
-COMPONENT M_n3 = Monitor_nD(
-        filename = "M_n3", 
-        options = "x limits=[-0.05 0.05] bins=1000 y limits=[-0.05 0.05] bins=1000 lambda limits=[0 35] bins=350",
-        xwidth = 0.5, yheight = 0.5)
-    AT (0, 0, 4*selene_c-0.01) RELATIVE ISCS
-    ROTATED (0, 1.25+omegaa, 0) RELATIVE ISCS
-
-COMPONENT M_n2 = Monitor_nD(
-        filename = "M_n2", 
-        options = "x limits=[-0.05 0.05] bins=1000 y limits=[-0.05 0.05] bins=1000 lambda limits=[0 35] bins=350",
-        xwidth = 0.5, yheight = 0.5)
-    AT (0, 0, 4*selene_c-0.005) RELATIVE ISCS
-    ROTATED (0, 1.25+omegaa, 0) RELATIVE ISCS
-    
-COMPONENT M_n1 = Monitor_nD(
-        filename = "M_n1", 
-        options = "x limits=[-0.05 0.05] bins=1000 y limits=[-0.05 0.05] bins=1000 lambda limits=[0 35] bins=350",
-        xwidth = 0.5, yheight = 0.5)
-    AT (0, 0, 4*selene_c-0.0025) RELATIVE ISCS
-    ROTATED (0, 1.25+omegaa, 0) RELATIVE ISCS
-    
-COMPONENT M_0 = Monitor_nD(
-        filename = "M_0", 
-        options = "x limits=[-0.05 0.05] bins=1000 y limits=[-0.05 0.05] bins=1000 lambda limits=[0 35] bins=350",
-        xwidth = 0.5, yheight = 0.5)
-    AT (0, 0, 4*selene_c) RELATIVE ISCS
-    ROTATED (0, 1.25+omegaa, 0) RELATIVE ISCS
-
-COMPONENT MFP = Monitor_nD(
-        filename = "MFP", 
-        options = "x limits=[-0.05 0.05] bins=1000 y limits=[-0.05 0.05] bins=1000 lambda limits=[0 35] bins=350",
-        xwidth = 0.5, yheight = 0.5)
-    AT (0, 0, 4*selene_c+0.0001) RELATIVE ISCS
-    ROTATED (0, 1.25+omegaa-90, 0) RELATIVE ISCS
-
-COMPONENT M_p1 = Monitor_nD(
-        filename = "M_p1", 
-        options = "x limits=[-0.05 0.05] bins=1000 y limits=[-0.05 0.05] bins=1000 lambda limits=[0 35] bins=350",
-        xwidth = 0.5, yheight = 0.5)
-    AT (0, 0, 4*selene_c+0.0025) RELATIVE ISCS
-    ROTATED (0, 1.25+omegaa, 0) RELATIVE ISCS
-
-COMPONENT M_p2 = Monitor_nD(
-        filename = "M_p2", 
-        options = "x limits=[-0.05 0.05] bins=1000 y limits=[-0.05 0.05] bins=1000 lambda limits=[0 35] bins=350",
-        xwidth = 0.5, yheight = 0.5)
-    AT (0, 0, 4*selene_c+0.005) RELATIVE ISCS
-    ROTATED (0, 1.25+omegaa, 0) RELATIVE ISCS
-
-COMPONENT M_p3 = Monitor_nD(
-        filename = "M_p3", 
-        options = "x limits=[-0.05 0.05] bins=1000 y limits=[-0.05 0.05] bins=1000 lambda limits=[0 35] bins=350",
-        xwidth = 0.5, yheight = 0.5)
-    AT (0, 0, 4*selene_c+0.01) RELATIVE ISCS
-    ROTATED (0, 1.25+omegaa, 0) RELATIVE ISCS
-
-FINALLY
-%{
-%}
-
-END

simulation/compile_if_needed.sh

@@ -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

simulation/hostnames

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

simulation/run_liquids.sh

@@ -1,174 +0,0 @@
-#!/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_monitor.sh

@@ -1,12 +0,0 @@
-#!/bin/bash
-
-mcstas -o Estia_monitor.c Estia_monitor.instr
-mpicc -O3 -o Estia_monitor.out Estia_monitor.c -lm -DUSE_MPI
-
-
-mpirun -np 6 Estia_monitor.out --ncount=1e8 --dir=../results/monitor --gravitation enable_windows=1 lambda_start=1.0 lambda_end=35.0 direct_beam=0
-mpirun -np 6 Estia_monitor.out --ncount=1e8 --dir=../results/monitor_ref --gravitation enable_windows=1 lambda_start=1.0 lambda_end=35.0 direct_beam=2
-mpirun -np 6 Estia_monitor.out --ncount=1e8 --dir=../results/monitor_trans --gravitation enable_windows=1 lambda_start=1.0 lambda_end=35.0 direct_beam=1
-
-mpirun -np 6 Estia_monitor.out --ncount=1e8 --dir=../results/monitor100 --gravitation enable_windows=1 lambda_start=1.0 lambda_end=35.0 direct_beam=0 foil_thickness=0.0001
-mpirun -np 6 Estia_monitor.out --ncount=1e8 --dir=../results/monitor001 --gravitation enable_windows=1 lambda_start=1.0 lambda_end=35.0 direct_beam=0 foil_thickness=0.000001

simulation/run_pol.sh

@@ -1,213 +0,0 @@
-#!/bin/bash
-
-DEST=../results
-ncount=2e7
-use_cores=4
-sample=4
-omega=0.8
-sample_length=0.01
-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
-
-
-###################### 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
-
-# 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 $use_cores Estia_baseline.out \
-        --dir="$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=$lambda_end enable_gravity=1 enable_chopper=0 enable_polarizer=2 enable_analyzer=0
-# 
-# ncount=5e9
-# sample_length=0.01
-# omega=1.0
-# sample_length=0.003
-# DESTi=$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=$lambda_end enable_gravity=1 enable_chopper=0 enable_polarizer=0 enable_analyzer=1
-
-# sample_height=0.001
-# DESTi=$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=$lambda_end enable_gravity=1 enable_chopper=0 enable_polarizer=0 enable_analyzer=2
-
-# sample_height=0.001
-# DESTi=$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
-       
-
-###################### Reference and Ni-layer measurement 1x1mm² sample ####################
-
-

simulation/run_selene.py

@@ -1,52 +0,0 @@
-#!/usr/bin/env python
-#-*- coding: utf8 -*-
-
-import sys, os
-from subprocess import call
-from numpy import *
-from scipy.optimize import leastsq
-
-
-CALL='/afs/psi.ch/project/sinq/sl6-64/bin/mpirun -np $SLURM_NPROCS Estia_baseline.out '
-CALL=+'--dir=../results/selene_geo --ncount=1e9 '
-CALL=+'omegaa=1.0 sample=4 sample_length=0.001 sample_height=0.01 '
-CALL=+'lambda_start=2.5 lambda_end=15.0 enable_gravity=1 enable_chopper=1 '
-CALL=+'lambda_min=3.75 selene1_foot1y=%.4f selene1_foot2y=%.4f '
-
-def B(x,w):
-    # box function with full width w
-    return float32(abs(x)<=(w/2.))
-
-def G(x,I0,x0,sigma):
-    # Gaussian with intensity I0, center x0 and standard deviation sigma
-    return I0*exp(-0.5*(x-x0)**2/sigma**2)
-
-def Intensity(x, p):
-    I0, x0, sigma, w=p
-    return convolve(B(xc,w), G(xc, I0, x0, sigma), mode='same')
-
-def Beam(x,I0,x0,sigma,w):
-    I=I0*where((x-x0)<(-w/2.), exp(-0.5*(x-x0+w/2.)**2/sigma**2),
-            where((x-x0)>(w/2.), exp(-0.5*(x-x0-w/2.)**2/sigma**2), 1.))
-    return I
-
-def residuals(p, x, y):
-    I0, x0, sigma, w=p
-    return y-Beam(x, I0, x0, sigma, w)
-
-def FWHM(pi):
-    rng=xc[where(Beam(xc, *pi)>=(pi[0]/2.))[0]]
-    return rng[-1]-rng[0]
-  
-x=linspace(-10.0005, 10.0005, 20001)
-xc=(x[1:]+x[:-1])/2.
-
-def analyze(fi):
-  sim=mr.McSim(fi)
-  det=sim['tof_sample']
-  ignore,y=det.project1d('x', bins=x/1000.)
-  p,res=leastsq(residuals, (y.max(), (xc*y).sum()/y.sum(), 0.01, 0.1), (xc, y))
-  return p,det
-
-if __name__=='__main__':
-    pass

simulation/run_simu_2.sh

@@ -1,86 +0,0 @@
-#!/bin/bash
-
-DEST=../results
-use_cores=6
-
-######################  Compile model if necessary   ####################
-bash compile_if_neede.sh
-
-######## Reference and Ni-layer conventional measurement 10x10mm² sample #############
-ncount=1e10
-sample_length=0.01
-sample_height=0.01
-lambda_start=3.25
-lambda_min=3.75
-lambda_end=12.75
-sample=1
-
-omega=1.0
-DESTi=$DEST/tof_reference_10x10_10
-if [ -e "$DESTi" ]; then
-	rm -r "$DESTi"
-fi
-
-mpirun  -np $use_cores Estia_baseline.out \
-        --dir="$DESTi" --format=NeXuS --ncount=$ncount --gravitation \
-        omegaa=$omega operationmode=1 theta_resolution=0.01 over_illumination=0.0001 \
-        sample=$sample sample_length=$sample_length sample_height=$sample_height \
-        lambda_start=$lambda_start lambda_min=$lambda_min lambda_end=$lambda_end enable_gravity=1 enable_chopper=1
-       
-#     Ni Sample
-ncount=2e10
-sample=2
-omega=0.5
-DESTi=$DEST/tof_nickle_10x10_05
-if [ -e "$DESTi" ]; then
-	rm -r "$DESTi"
-fi
-
-mpirun  -np $use_cores Estia_baseline.out \
-        --dir="$DESTi" --format=NeXuS --ncount=$ncount --gravitation \
-        omegaa=$omega operationmode=1 theta_resolution=0.03 over_illumination=0.0001 \
-        sample=$sample sample_length=$sample_length sample_height=$sample_height \
-        lambda_start=$lambda_start lambda_min=$lambda_min lambda_end=$lambda_end enable_gravity=1 enable_chopper=1
-
-ncount=1e10
-omega=1.2
-DESTi=$DEST/tof_nickle_10x10_12
-if [ -e "$DESTi" ]; then
-	rm -r "$DESTi"
-fi
-
-mpirun  -np $use_cores Estia_baseline.out \
-        --dir="$DESTi" --format=NeXuS --ncount=$ncount --gravitation \
-        omegaa=$omega operationmode=1 theta_resolution=0.03 over_illumination=0.0001 \
-        sample=$sample sample_length=$sample_length sample_height=$sample_height \
-        lambda_start=$lambda_start lambda_min=$lambda_min lambda_end=$lambda_end enable_gravity=1 enable_chopper=1
-        
-ncount=5e9
-omega=3.0
-DESTi=$DEST/tof_nickle_10x10_30
-if [ -e "$DESTi" ]; then
-	rm -r "$DESTi"
-fi
-
-mpirun  -np $use_cores Estia_baseline.out \
-        --dir="$DESTi" --format=NeXuS --ncount=$ncount --gravitation \
-        omegaa=$omega operationmode=1 theta_resolution=0.03 over_illumination=0.0001 \
-        sample=$sample sample_length=$sample_length sample_height=$sample_height \
-        lambda_start=$lambda_start lambda_min=$lambda_min lambda_end=$lambda_end enable_gravity=1 enable_chopper=1
-                
-ncount=2e9
-omega=7.5
-DESTi=$DEST/tof_nickle_10x10_75
-if [ -e "$DESTi" ]; then
-	rm -r "$DESTi"
-fi
-
-mpirun  -np $use_cores Estia_baseline.out \
-        --dir="$DESTi" --format=NeXuS --ncount=$ncount --gravitation \
-        omegaa=$omega operationmode=1 theta_resolution=0.03 over_illumination=0.0001 \
-        sample=$sample sample_length=$sample_length sample_height=$sample_height \
-        lambda_start=$lambda_start lambda_min=$lambda_min lambda_end=$lambda_end enable_gravity=1 enable_chopper=1
-
-###################### Reference and Ni-layer measurement 1x1mm² sample ####################
-
-

simulation/run_simu_3.sh

@@ -1,46 +0,0 @@
-#!/bin/bash
-
-DEST=../results
-ncount=1e9
-use_cores=6
-sample=4
-omega=0.8
-sample_length=0.01
-sample_height=0.01
-lambda_start=3.0
-lambda_end=32.0
-
-bash compile_if_neede.sh
-
-
-################# Reference and Ni-layer measurement 2 pulse skipping ####################
-ncount=4e9
-sample_length=0.01
-sample_height=0.01
-lambda_start=3.9
-lambda_end=24.0
-sample=1
-omega=2.0
-
-DESTi=$DEST/single_skip_reference
-if [ -e "$DESTi" ]; then
-	rm -r "$DESTi"
-fi
-
-mpirun  -np $use_cores Estia_baseline.out \
-        --dir="$DESTi" --format=NeXuS --ncount=$ncount --gravitation \
-        omegaa=$omega operationmode=0 theta_resolution=0.04 over_illumination=0.0002 \
-        sample=$sample sample_length=$sample_length sample_height=$sample_height \
-        lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=1 enable_chopper=3
-        
-sample=2
-DESTi=$DEST/single_skip_nickle
-if [ -e "$DESTi" ]; then
-	rm -r "$DESTi"
-fi
-
-mpirun  -np $use_cores Estia_baseline.out \
-        --dir="$DESTi" --format=NeXuS --ncount=$ncount --gravitation \
-        omegaa=$omega operationmode=0 theta_resolution=0.04 over_illumination=0.0002 \
-        sample=$sample sample_length=$sample_length sample_height=$sample_height \
-        lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=1 enable_chopper=3

simulation/run_simu_chopper.sh

@@ -1,119 +0,0 @@
-#!/bin/bash
-
-DEST=../results
-ncount=1e9
-use_cores=6
-sample=1
-omega=15.0
-sample_length=0.02
-sample_height=0.01
-
-lambda_start=3.5
-lambda_min=5.0
-lambda_end=15.5
-frame_usage=0.92
-
-###################### Brilliance Transfer 10x10mm² and 1x1mm² VS ####################
-bash compile_if_neede.sh
-
-###################### Reference and Ni-layer measurement 10x10mm² sample ####################
-
-frame_usage=0.92
-DESTi=$DEST/chopper_f1_092
-if [ -e "$DESTi" ]; then
-	rm -r "$DESTi"
-fi
-
-mpirun  -np $use_cores Estia_baseline.out \
-        --dir="$DESTi" --format=NeXuS --ncount=$ncount \
-        omegaa=$omega operationmode=0 theta_resolution=0.04 over_illumination=0.0001 \
-        sample=$sample sample_length=$sample_length sample_height=$sample_height \
-        lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=0 enable_chopper=1 \
-        frame_usage=$frame_usage lambda_min=$lambda_min
-       
-frame_usage=0.94
-DESTi=$DEST/chopper_f1_094
-if [ -e "$DESTi" ]; then
-	rm -r "$DESTi"
-fi
-
-mpirun  -np $use_cores Estia_baseline.out \
-        --dir="$DESTi" --format=NeXuS --ncount=$ncount \
-        omegaa=$omega operationmode=0 theta_resolution=0.04 over_illumination=0.0001 \
-        sample=$sample sample_length=$sample_length sample_height=$sample_height \
-        lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=0 enable_chopper=1 \
-        frame_usage=$frame_usage lambda_min=$lambda_min
-       
-frame_usage=0.96
-DESTi=$DEST/chopper_f1_096
-if [ -e "$DESTi" ]; then
-	rm -r "$DESTi"
-fi
-
-mpirun  -np $use_cores Estia_baseline.out \
-        --dir="$DESTi" --format=NeXuS --ncount=$ncount \
-        omegaa=$omega operationmode=0 theta_resolution=0.04 over_illumination=0.0001 \
-        sample=$sample sample_length=$sample_length sample_height=$sample_height \
-        lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=0 enable_chopper=1 \
-        frame_usage=$frame_usage lambda_min=$lambda_min
-       
-frame_usage=0.974
-DESTi=$DEST/chopper_f1_097s
-if [ -e "$DESTi" ]; then
-	rm -r "$DESTi"
-fi
-
-mpirun  -np $use_cores Estia_baseline.out \
-        --dir="$DESTi" --format=NeXuS --ncount=$ncount \
-        omegaa=$omega operationmode=0 theta_resolution=0.04 over_illumination=0.0001 \
-        sample=$sample sample_length=$sample_length sample_height=$sample_height \
-        lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=0 enable_chopper=1 \
-        frame_usage=$frame_usage lambda_min=$lambda_min
-       
-frame_usage=0.98
-DESTi=$DEST/chopper_f1_098
-if [ -e "$DESTi" ]; then
-	rm -r "$DESTi"
-fi
-
-mpirun  -np $use_cores Estia_baseline.out \
-        --dir="$DESTi" --format=NeXuS --ncount=$ncount \
-        omegaa=$omega operationmode=0 theta_resolution=0.04 over_illumination=0.0001 \
-        sample=$sample sample_length=$sample_length sample_height=$sample_height \
-        lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=0 enable_chopper=1 \
-        frame_usage=$frame_usage lambda_min=$lambda_min
-       
-frame_usage=0.99
-DESTi=$DEST/chopper_f1_099
-if [ -e "$DESTi" ]; then
-	rm -r "$DESTi"
-fi
-
-mpirun  -np $use_cores Estia_baseline.out \
-        --dir="$DESTi" --format=NeXuS --ncount=$ncount \
-        omegaa=$omega operationmode=0 theta_resolution=0.04 over_illumination=0.0001 \
-        sample=$sample sample_length=$sample_length sample_height=$sample_height \
-        lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=0 enable_chopper=1 \
-        frame_usage=$frame_usage lambda_min=$lambda_min
-       
-       
-frame_usage=0.98
-lambda_start=2.75
-lambda_min=3.75
-lambda_end=12.75
-DESTi=$DEST/chopper_f1_375A
-if [ -e "$DESTi" ]; then
-	rm -r "$DESTi"
-fi
-
-mpirun  -np $use_cores Estia_baseline.out \
-        --dir="$DESTi" --format=NeXuS --ncount=$ncount \
-        omegaa=$omega operationmode=0 theta_resolution=0.04 over_illumination=0.0001 \
-        sample=$sample sample_length=$sample_length sample_height=$sample_height \
-        lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=0 enable_chopper=1 \
-        frame_usage=$frame_usage lambda_min=$lambda_min
-       
-       
-###################### Reference and Ni-layer measurement 1x1mm² sample ####################
-
-

simulation/run_vs.sh

@@ -1,32 +0,0 @@
-#!/bin/bash
-
-DEST=../results
-ncount=1e8
-use_cores=6
-sample=1
-omega=0.8
-sample_length=0.01
-sample_height=0.015
-
-if [ Estia_vs.instr -nt Estia_vs.out ]; then
-	rm Estia_vs.c Estia_vs.out
-	mcstas -t -o Estia_vs.c Estia_vs.instr
-	mpicc -O3 -o Estia_vs.out Estia_vs.c -lm -DUSE_MPI -DUSE_NEXUS -lNeXus
-fi
-
-
-omega=2.0
-DESTi=$DEST/vs_data
-if [ -e "$DESTi" ]; then
-	rm -r "$DESTi"
-fi
-
-mpirun  -np $use_cores Estia_vs.out \
-        --dir="$DESTi" --format=NeXuS --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 \
-        enable_gravity=1 enable_chopper=0 source_power=5
-       
-###################### Reference and Ni-layer measurement 1x1mm² sample ####################
-
-

simulation/sbatch.sh

@@ -1,40 +0,0 @@
-#!/bin/bash
-#SBATCH -J mcEstia_1
-#SBATCH -N 2
-#SBATCH --ntasks-per-node=24
-#SBATCH --time=1-00:00:00
-#SBATCH --mail-type=fail
-#SBATCH --mail-user=artur.glavic@psi.ch
-
-#SBATCH -o stdout.log
-#SBATCH -e stderr.log
-
-#SBATCH --partition=ll_long
-
-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`"
-
-/usr/bin/modulecmd tcsh load mcstas
-bash compile_if_needed.sh
-
-for y1 in $(seq -0.009 0.001 0.009)
-  do
-  for y2 in $(seq -0.009 0.001 0.009) $(seq -0.09 0.01 -0.01) $(seq 0.01 0.01 0.09) $(seq -0.5 0.1 -0.1) $(seq 0.1 0.1 0.5)
-    do
-    printf -v Y1 %.3f $y1
-    printf -v Y2 %.3f $y2
-    echo $Y1 $Y2
-    /afs/psi.ch/project/sinq/sl6-64/bin/mpirun -np $SLURM_NPROCS Estia_baseline.out \
-            --dir=../results/selene1_geo_$Y1\_$Y2 --ncount=1e9 \
-            omegaa=1.0 sample=4 sample_length=0.00005 sample_height=0.01 \
-            lambda_start=2.5 lambda_end=15.0 enable_gravity=1 enable_chopper=1 \
-            lambda_min=3.75 selene1_foot1y=$Y1 selene1_foot2y=$Y2
-  done
-done
-
-        
-echo "Program finished with exit code $? at: `date`"
-

simulation/sbatch_2.sh

@@ -1,40 +0,0 @@
-#!/bin/bash
-#SBATCH -J mcEstia_2
-#SBATCH -N 2
-#SBATCH --ntasks-per-node=24
-#SBATCH --time=1-00:00:00
-#SBATCH --mail-type=fail
-#SBATCH --mail-user=artur.glavic@psi.ch
-
-#SBATCH -o stdout2.log
-#SBATCH -e stderr2.log
-
-#SBATCH --partition=ll_long
-
-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`"
-
-/usr/bin/modulecmd tcsh load mcstas
-bash compile_if_needed.sh
-
-for y1 in $(seq -0.09 0.01 -0.01)
-  do
-  for y2 in $(seq -0.009 0.001 0.009) $(seq -0.09 0.01 -0.01) $(seq 0.01 0.01 0.09) $(seq -0.5 0.1 -0.1) $(seq 0.1 0.1 0.5)
-    do
-    printf -v Y1 %.3f $y1
-    printf -v Y2 %.3f $y2
-    echo $Y1 $Y2
-    /afs/psi.ch/project/sinq/sl6-64/bin/mpirun -np $SLURM_NPROCS Estia_baseline.out \
-            --dir=../results/selene1_geo_$Y1\_$Y2 --ncount=1e9 \
-            omegaa=1.0 sample=4 sample_length=0.00005 sample_height=0.01 \
-            lambda_start=2.5 lambda_end=15.0 enable_gravity=1 enable_chopper=1 \
-            lambda_min=3.75 selene1_foot1y=$Y1 selene1_foot2y=$Y2
-  done
-done
-
-        
-echo "Program finished with exit code $? at: `date`"
-

simulation/sbatch_3.sh

@@ -1,40 +0,0 @@
-#!/bin/bash
-#SBATCH -J mcEstia_3
-#SBATCH -N 2
-#SBATCH --ntasks-per-node=24
-#SBATCH --time=1-00:00:00
-#SBATCH --mail-type=fail
-#SBATCH --mail-user=artur.glavic@psi.ch
-
-#SBATCH -o stdout3.log
-#SBATCH -e stderr3.log
-
-#SBATCH --partition=ll_long
-
-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`"
-
-/usr/bin/modulecmd tcsh load mcstas
-bash compile_if_needed.sh
-
-for y1 in $(seq 0.01 0.01 0.09)
-  do
-  for y2 in $(seq -0.009 0.001 0.009) $(seq -0.09 0.01 -0.01) $(seq 0.01 0.01 0.09) $(seq -0.5 0.1 -0.1) $(seq 0.1 0.1 0.5)
-    do
-    printf -v Y1 %.3f $y1
-    printf -v Y2 %.3f $y2
-    echo $Y1 $Y2
-    /afs/psi.ch/project/sinq/sl6-64/bin/mpirun -np $SLURM_NPROCS Estia_baseline.out \
-            --dir=../results/selene1_geo_$Y1\_$Y2 --ncount=1e9 \
-            omegaa=1.0 sample=4 sample_length=0.00005 sample_height=0.01 \
-            lambda_start=2.5 lambda_end=15.0 enable_gravity=1 enable_chopper=1 \
-            lambda_min=3.75 selene1_foot1y=$Y1 selene1_foot2y=$Y2
-  done
-done
-
-        
-echo "Program finished with exit code $? at: `date`"
-

simulation/sbatch_4.sh

@@ -1,40 +0,0 @@
-#!/bin/bash
-#SBATCH -J mcEstia_4
-#SBATCH -N 2
-#SBATCH --ntasks-per-node=24
-#SBATCH --time=1-00:00:00
-#SBATCH --mail-type=fail
-#SBATCH --mail-user=artur.glavic@psi.ch
-
-#SBATCH -o stdout4.log
-#SBATCH -e stderr4.log
-
-#SBATCH --partition=ll_long
-
-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`"
-
-/usr/bin/modulecmd tcsh load mcstas
-bash compile_if_needed.sh
-
-for y1 in $(seq -0.5 0.1 -0.1)
-  do
-  for y2 in $(seq -0.009 0.001 0.009) $(seq -0.09 0.01 -0.01) $(seq 0.01 0.01 0.09) $(seq -0.5 0.1 -0.1) $(seq 0.1 0.1 0.5)
-    do
-    printf -v Y1 %.3f $y1
-    printf -v Y2 %.3f $y2
-    echo $Y1 $Y2
-    /afs/psi.ch/project/sinq/sl6-64/bin/mpirun -np $SLURM_NPROCS Estia_baseline.out \
-            --dir=../results/selene1_geo_$Y1\_$Y2 --ncount=1e9 \
-            omegaa=1.0 sample=4 sample_length=0.00005 sample_height=0.01 \
-            lambda_start=2.5 lambda_end=15.0 enable_gravity=1 enable_chopper=1 \
-            lambda_min=3.75 selene1_foot1y=$Y1 selene1_foot2y=$Y2
-  done
-done
-
-        
-echo "Program finished with exit code $? at: `date`"
-

simulation/sbatch_5.sh

@@ -1,40 +0,0 @@
-#!/bin/bash
-#SBATCH -J mcEstia_5
-#SBATCH -N 2
-#SBATCH --ntasks-per-node=24
-#SBATCH --time=1-00:00:00
-#SBATCH --mail-type=fail
-#SBATCH --mail-user=artur.glavic@psi.ch
-
-#SBATCH -o stdout5.log
-#SBATCH -e stderr5.log
-
-#SBATCH --partition=ll_long
-
-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`"
-
-/usr/bin/modulecmd tcsh load mcstas
-bash compile_if_needed.sh
-
-for y1 in $(seq 0.1 0.1 0.5)
-  do
-  for y2 in $(seq -0.009 0.001 0.009) $(seq -0.09 0.01 -0.01) $(seq 0.01 0.01 0.09) $(seq -0.5 0.1 -0.1) $(seq 0.1 0.1 0.5)
-    do
-    printf -v Y1 %.3f $y1
-    printf -v Y2 %.3f $y2
-    echo $Y1 $Y2
-    /afs/psi.ch/project/sinq/sl6-64/bin/mpirun -np $SLURM_NPROCS Estia_baseline.out \
-            --dir=../results/selene1_geo_$Y1\_$Y2 --ncount=1e9 \
-            omegaa=1.0 sample=4 sample_length=0.00005 sample_height=0.01 \
-            lambda_start=2.5 lambda_end=15.0 enable_gravity=1 enable_chopper=1 \
-            lambda_min=3.75 selene1_foot1y=$Y1 selene1_foot2y=$Y2
-  done
-done
-
-        
-echo "Program finished with exit code $? at: `date`"
-