Add pulse skipping simulation to run script

Extend q-range of simulated data to region measured up to 11.7 deg
update script, process hdf files to add compression
2018-10-04 09:34:08 +02:00 · 2018-09-27 14:47:52 +02:00 · 2018-09-16 14:09:15 +02:00 · 2018-08-18 12:21:48 +02:00 · 2018-06-26 07:51:35 +02:00 · 2018-06-26 07:26:05 +02:00
41 changed files with 9389 additions and 111387 deletions
@@ -0,0 +1,9 @@
+ #!/bin/bash
+# compress McStas hdf5 files to increase performance and save disk space
+
+for fi in $*
+do
+  echo $fi
+  h5repack -i $fi -o $fi.c -f /entry1/data/of_detector_list_p_x_y_t_L_sx_sy/events:GZIP=5 -l /entry1/data/of_detector_list_p_x_y_t_L_sx_sy/events:CHUNK=3072x7
+  mv $fi.c $fi
+done
@@ -1,93 +0,0 @@
-#!/usr/bin/env python
-
-from numpy import *
-
-import mcstas_reader as mr
-
-l=arange(3,11,0.01)
-lp=(l[1:]+l[:-1])/2.
-
-t=arange(0.0, 0.18, 0.0001)
-tp=(t[1:]+t[:-1])/2.
-
-def get_pulses(fn, freq, offset=0.002):
-    det=mr.McSim(fn)['tof_detector']
-    pulses=[]
-    for i in range(int(freq/7)):
-        li, Ii=det.project1d('L', bins=l, newcols=[('tc', 't-L*0.00406-%f'%offset)], 
-                             fltr='(tc>%f)&(tc<%f)'%(i*1./freq, (i+1)*1./freq))
-        ti, Iti=det.project1d('t', bins=t, newcols=[('tc', 't-L*0.00406-%f'%offset)], 
-                              fltr='(tc>%f)&(tc<%f)'%(i*1./freq, (i+1)*1./freq))
-        pulses.append(((li[1:]+li[:-1])/2., Ii, (ti[1:]+ti[:-1])/2., Iti))
-    return det, pulses
-
-def get_filtered_pulses(det, pulses, freq, offset=0.0001, threashold=0.01):
-    Is=array([pi[3] for pi in pulses])
-    fpulses=[]
-    for i in range(1,int(freq/7)-1):
-        fltr=(Is[:i].sum(axis=0)+Is[i+1:].sum(axis=0))<(threashold*Is[i])
-        tf=tp[fltr]
-        if len(tf)<2:
-            continue
-        li, Ii=det.project1d('L', bins=l, fltr='(t>%f)&(t<%f)'%(tf[0], tf[-1]))
-        ti, Iti=det.project1d('t', bins=t, fltr='(t>%f)&(t<%f)'%(tf[0], tf[-1]))
-        fpulses.append(((li[1:]+li[:-1])/2., Ii, (ti[1:]+ti[:-1])/2., Iti))
-    return fpulses
-    
-
-def calc_usable(pulses, threashold=0.01):
-    Is=array([pi[3] for pi in pulses])
-    sI=0.
-    for i in range(1,Is.shape[0]):
-        sI+=Is[i][(Is[:i].sum(axis=0)+Is[i+1:].sum(axis=0))<(threashold*Is[i])].sum()
-    return sI
-
-def calc_sum(pulses):
-    Is=array([pi[3] for pi in pulses])
-    return Is.sum(axis=0)
-
-def tof_plot(det, pulses):
-    figure(figsize=(18,10))
-    for i, pi in enumerate(pulses):
-        semilogy(tp, pi[3], label='%i'%i)
-    ylim(100,1e5)
-
-def tof_th_plot(det, pulses, threashold=0.01):
-    figure(figsize=(18,10))
-    Is=array([pi[3] for pi in pulses])
-    for i, pi in enumerate(pulses):
-        fltr=(Is[:i].sum(axis=0)+Is[i+1:].sum(axis=0))<(threashold*Is[i])
-        semilogy(tp[fltr], pi[3][fltr], label='%i'%i)
-    ylim(100,1e5)
-
-def lambda_plot(det, pulses):
-    figure(figsize=(18,10))
-    for i, pi in enumerate(pulses):
-        semilogy(lp, pi[1])
-    semilogy(lp, det.project1d('L', bins=l)[1])
-    semilogy(lp, Ir)
-    ylim(100,1e6)
-    xlim(3,11)
-
-def export(fn, pulses):
-    It=calc_sum(pulses)
-    savetxt(fn+'_lpulses.dat', array([pules[0][0], It, Ir]+[pi[1] for pi in pulses]).T)
-    savetxt(fn+'_tpulses.dat', array([pules[0][2]]+[pi[3] for pi in pulses]).T)
-
-ref=mr.McSim('../results/ersa_ref/')['tof_detector']
-Ir=ref.project1d('L', bins=l)[1]
-
-freq_offsets={245: 0.00007, 280: 0.002, 308: 0.0015, 350: 0.003}
-rfreq_offsets={245: 0.0000, 280: 0.0002, 308: 0.0015, 350: 0.0007}
-
-results={}
-for key,val in freq_offsets.items():
-    results['%i'%key]=get_pulses('../results/ersa_%iHz/'%key, 2.*key, val)
-    try:
-        results['r300-%i'%key]=get_pulses('../results/ersa_r300_%iHz/'%key, 2.*key, val)
-    except:
-        continue
-
-for key,val in rfreq_offsets.items():
-        results['rev-%i'%key]=get_pulses('../results/ersa_reverse_%iHz/'%key, 2.*key, val)
-
@@ -10,147 +10,36 @@ seterr(all='ignore')
 import estia_help as eh
 import mcstas_reader as mr

-
-# Scaling factor of source monitor after normalizing by area to get to brilliance.
-# Converts from 1.5x4.0 degree² acceptance range to 1/steradian
-# Factor 10 due to 0.1 Angstrom binning.
-BT_SOURCE_SCALE=10.*(180.**2/pi**2)/1.5/4.0
-BT_SAMPLE_SCALE=10.*(180.**2/pi**2)/1.5/1.5
-
+# work around for wrong wavelength calculation in pulse skipping mode
+eh.l_code='((t-0.0335)%%(%f/14.)+0.0335-0.0015)*101.436605'

 if __name__=='__main__':
-  if not os.path.exists('../results/analyzed'):
-    os.mkdir('../results/analyzed')
+  if not os.path.exists('../results/mooc_analyzed'):
+    os.mkdir('../results/mooc_analyzed')
  
-  if len(sys.argv)>1:
-    only_items=map(int, sys.argv[1:])
-  else:
-    only_items=range(100)

-  if 1 in only_items:
-    print "Brilliance Transfer 5x10"
-    bt_10=mr.McSim('../results/brilliance_5x10/mccode.h5')
-    d=bt_10['tof_sample.L']
-    vs=bt_10['tof_virtual_source.L']
-    r=bt_10['tof_source.L']
-    x, y, e=eh.calc_brilliance_transfer(d, BT_SAMPLE_SCALE*2., r, BT_SOURCE_SCALE)
-    savetxt('../results/analyzed/brilliance_transfer_5x10.dat', array([x, y, e]).T)
-    savetxt('../results/analyzed/brilliance_5x10.dat', array([x, d.data*BT_SAMPLE_SCALE*2.,
-                                           d.errors*BT_SAMPLE_SCALE*2.]).T)
-    x, y, e=eh.calc_brilliance_transfer(vs, BT_SAMPLE_SCALE, r, BT_SOURCE_SCALE)
-    savetxt('../results/analyzed/brilliance_transfer_vs_5x10.dat', array([x, y, e]).T)
-    
-    btn_10=mr.McSim('../results/brilliance_nowindow_5x10/mccode.h5')
-    d=btn_10['tof_sample.L']
-    vs=btn_10['tof_virtual_source.L']
-    r=btn_10['tof_source.L']
-    x, y, e=eh.calc_brilliance_transfer(d, BT_SAMPLE_SCALE*2., r, BT_SOURCE_SCALE)
-    savetxt('../results/analyzed/brilliance_transfer_nowindow_5x10.dat', array([x, y, e]).T)
-    x, y, e=eh.calc_brilliance_transfer(vs, BT_SAMPLE_SCALE, r, BT_SOURCE_SCALE)
-    savetxt('../results/analyzed/brilliance_transfer_nowindow_vs_5x10.dat', array([x, y, e]).T)
+  print "pulse skipping mode"
+  opts=dict(qres=0.02, qmin=0.007, qmax=0.2, mindq=2e-5, crop_overlap=False)
+  names=['q_z', 'Intensity(ToF)', 'Reflectivity(ToF)', 
+         '1s-Stat(ToF)', '1pulse-Stat(ToF)', '10s-Statistics(ToF)', 
+         'Intensity(λ)', 'Reflectivity(λ)']
+  units=['A^{-1}', 'cts/s', '1', 'cts/s', '1']
+  info='Reflectivity simulation for 50x10mm² sample, 2-pulse skipping'

-
-  if 2 in only_items:
-    print "Brilliance Transfer 1x1"
-    bt_1=mr.McSim('../results/brilliance_1x1/mccode.h5')
-    d=bt_1['tof_sample.L']
-    r=bt_1['tof_source.L']
-    x, y, e=eh.calc_brilliance_transfer(d, BT_SAMPLE_SCALE*100, r, BT_SOURCE_SCALE)
-    savetxt('../results/analyzed/brilliance_transfer_1x1.dat', array([x, y, e]).T)
-    savetxt('../results/analyzed/brilliance_1x1.dat', array([x, d.data*BT_SAMPLE_SCALE*100,
-                                           d.errors*BT_SAMPLE_SCALE*100]).T)
-
-  if 3 in only_items:
-    print "Refelctiviy 10x10 sample"
-    opts=dict(qres=0.01, qmin=0.003, qmax=0.5, mindq=5e-4)
-    names=['q_z', 'Intensity(ToF)', 'Reflectivity(ToF)', 'dR (1s ToF)', 'Intensity(λ)', 'Reflectivity(λ)']
-    units=['A^{-1}', 'cts/s', '1', 'cts/s', '1']
-    info='Reflectivity simulation for 10x10mm² sample, omega=%.1f deg'
-
-    print "0.8 degree"
-    ref=mr.McSim('../results/reference_10x10_10/mccode.h5')['tof_detector']
-    ni_08=mr.McSim('../results/nickle_10x10_08/mccode.h5')['tof_detector']
-    q, I, R=eh.calcR(ni_08, ref, 0.8, 1.0, detcorr=True, **opts)
-    q, I_real, R_real=eh.calcR(ni_08, ref, 0.8, 1.0, use_tof=False, **opts)
-    idx_start, idx_end=where((I>0.)&(I_real>0.))[0][[0,-1]]
-    eh.save_w_header('../results/analyzed/reflectivity_10x10_08.dat',
-                     [q[idx_start:idx_end+1],
-                      I[idx_start:idx_end+1], R[idx_start:idx_end+1],
-                      (R/sqrt(I))[idx_start:idx_end+1],
-                      I_real[idx_start:idx_end+1], R_real[idx_start:idx_end+1]],
-                     info, names, units)
-    del(ni_08)
-
-    print "3.0 degree"
-    ni_30=mr.McSim('../results/nickle_10x10_30/mccode.h5')['tof_detector']
-    q, I, R=eh.calcR(ni_30, ref, 3.0, 1.0, detcorr=True, **opts)
-    q, I_real, R_real=eh.calcR(ni_30, ref, 3.0, 1.0, use_tof=False, **opts)
-    idx_start, idx_end=where((I>0.)&(I_real>0.))[0][[0,-1]]
-    eh.save_w_header('../results/analyzed/reflectivity_10x10_30.dat',
-                     [q[idx_start:idx_end+1],
-                      I[idx_start:idx_end+1], R[idx_start:idx_end+1],
-                      (R/sqrt(I))[idx_start:idx_end+1],
-                      I_real[idx_start:idx_end+1], R_real[idx_start:idx_end+1]],
-                     info, names, units)
-    del(ni_30)
-
-    print "8.0 degree"
-    ni_80=mr.McSim('../results/nickle_10x10_80/mccode.h5')['tof_detector']
-    q, I, R=eh.calcR(ni_80, ref, 8.0, 1.0, detcorr=True, **opts)
-    q, I_real, R_real=eh.calcR(ni_80, ref, 8.0, 1.0, use_tof=False, **opts)
-    idx_start, idx_end=where((I>0.)&(I_real>0.))[0][[0,-1]]
-    eh.save_w_header('../results/analyzed/reflectivity_10x10_80.dat',
-                     [q[idx_start:idx_end+1],
-                      I[idx_start:idx_end+1], R[idx_start:idx_end+1],
-                      (R/sqrt(I))[idx_start:idx_end+1],
-                      I_real[idx_start:idx_end+1], R_real[idx_start:idx_end+1]],
-                     info, names, units)
-
-  if 4 in only_items:
-    print "10x10 sample pulse skipping mode."
-    opts=dict(qres=0.04, qmin=0.003, qmax=0.2, mindq=2e-4)
-    names=['q_z', 'Intensity(ToF)', 'Reflectivity(ToF)', 'Intensity(λ)', 'Reflectivity(λ)']
-    units=['A^{-1}', 'cts/s', '1', 'cts/s', '1']
-    info='Reflectivity simulation for 10x10mm² sample, 2-pulse skipping'
-
-    ref=mr.McSim('../results/single_skip_reference/mccode.h5')['tof_detector']
-    ni=mr.McSim('../results/single_skip_nickle/mccode.h5')['tof_detector']
-    q, I, R=eh.calcR(ni, ref, 2.0, skip_pulses=2, **opts)
-    q, I_real, R_real=eh.calcR(ni, ref, 2.0, skip_pulses=2, use_tof=False, **opts)
+  ref=mr.McSim('../results/mooc_reference_ps')['tof_detector']
+  
+  for i in range(6):
+    print "dataset",i
+    sample=mr.McSim('../results/mooc_model_ps_%i'%i)['tof_detector']
+    q, I, R=eh.calcR(sample, ref, 1.5, 1.5, skip_pulses=2, **opts)
+    q, I_real, R_real=eh.calcR(sample, ref, 1.5, 1.5, skip_pulses=2, use_tof=False, **opts)
    idx_start, idx_end=where((I>0.))[0][[0,-1]]
-    eh.save_w_header('../results/analyzed/single_skip_reflectivity.dat',
-                     [q[idx_start:idx_end+1],
-                      I[idx_start:idx_end+1], R[idx_start:idx_end+1],
+    eh.save_w_header('../results/mooc_analyzed/model%i_skip_reflectivity.dat'%i,
+                      [q[idx_start:idx_end+1],
+                      I[idx_start:idx_end+1], R[idx_start:idx_end+1], 
+                      random.poisson(I[idx_start:idx_end+1])/I[idx_start:idx_end+1]*R[idx_start:idx_end+1],
+                      random.poisson(I[idx_start:idx_end+1]*3./14.)/I[idx_start:idx_end+1]*14./3.*R[idx_start:idx_end+1],
+                      random.poisson(I[idx_start:idx_end+1]*10.)/I[idx_start:idx_end+1]/10.*R[idx_start:idx_end+1],
                      I_real[idx_start:idx_end+1], R_real[idx_start:idx_end+1]],
-                     info, names, units)
+                      info, names, units)

-  if 5 in only_items:
-    print "Extracting event statistics."
-    fh=open('../results/analyzed/event_stats.dat', 'w')
-    fh.write('# event statistics for Estia\n')
-    fh.write('# item      avg. total     peak total     avg. ROI       peak ROI\n')
-    fh.write('#           [cps]          [cps]          [cps/mm²]      [cps/mm²]\n')
-    line='%(name)s  %(total) 12e  %(peak) 12e  %(roi) 12e  %(roi_peak) 12e\n'
-
-    ds=mr.McSim('../results/reference_10x10_10/mccode.h5')['tof_detector']
-    res=eh.calcStat(ds)
-    res['name']='Reference'
-    fh.write(line%res)
-
-    ds=mr.McSim('../results/nickle_10x10_08/mccode.h5')['tof_detector']
-    res=eh.calcStat(ds)
-    res['name']='Ni-0.8deg'
-    fh.write(line%res)
-
-    ds=mr.McSim('../results/nickle_10x10_30/mccode.h5')['tof_detector']
-    res=eh.calcStat(ds)
-    res['name']='Ni-3.0deg'
-    fh.write(line%res)
-
-    ds=mr.McSim('../results/nickle_10x10_80/mccode.h5')['tof_detector']
-    res=eh.calcStat(ds)
-    res['name']='Ni-8.0deg'
-    fh.write(line%res)
-
-    fh.close()
-    
@@ -294,9 +294,9 @@ class Dataset(object):
    limits=map(float, self.info['xylimits'].split())

    if log:
-      ax.imshow(self.data, origin='lower', extent=limits, aspect='auto', norm=LogNorm())
+      ax.imshow(self.data, extent=limits, aspect='auto', norm=LogNorm())
    else:
-      ax.imshow(self.data, origin='lower', extent=limits, aspect='auto')
+      ax.imshow(self.data, extent=limits, aspect='auto')
    ax.set_xlabel(self.info['xlabel'])
    ax.set_ylabel(self.info['ylabel'])
    ax.set_title(self.info['component'])
@@ -49,14 +49,13 @@
 *******************************************************************************/

 DEFINE INSTRUMENT ESS_reflectometer_Estia
-(double omegaa = 1.2,  int sample = 0,  double sample_length   = 0.01, double sample_height   = 0.01,
+(double omegaa = 1.2,  int sample = 1,  string sample_file="alessandra_model_2_nores_000.dat", 
+double sample_length   = 0.01, double sample_height   = 0.01,
 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, 
-double wfm_freq=0.0, double wfm_shift=0.0, double wfm_radius=0.15,
-int enable_polarizer = 0, int enable_analyzer = 0,
-double source_power = 2,
-double selene1_foot1y =0.0, double selene1_foot2y = 0.0
+int enable_chopper = 0, int enable_gravity=0, int enable_windows=1,
+ int enable_polarizer = 0, int enable_analyzer = 0,
+double source_power = 2, double frame_usage     =   0.98
 )

 DECLARE
@@ -72,12 +71,8 @@ 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

-// 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 1 (Will follow later with detailed parameters)
+

 // Selene 2

@@ -95,7 +90,7 @@ double chopper_phase          ;       // deg phase between pulse and chopper ope
 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 chopper_freq = 14.0;     // Hz  chopper frequency

 double slit_distance   =   1.775; //m, distance slit to sample

@@ -103,6 +98,9 @@ double slit_distance   =   1.775; //m, distance slit to sample
 double selene_theta    =    1.25;
 double velocity_max           ;     // m/s  neutron velocity of lambda_min

+/* flags */
+int PP_small         = 1 ;   // plot all PSD with small area
+int PP_large         = 1 ;   // plot all PSD with large area

 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
@@ -115,10 +113,12 @@ double Theta1_analyzer1, Theta1_analyzer2, Theta2_analyzer1, Theta2_analyzer2, d

 INITIALIZE
 %{
+
+chopper_freq/=fmax(1.0, enable_chopper);
 // 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;
+chopper_open =360.0*(chopper_pos/(total_length+detector_arm))*frame_usage;


 /* print out some calculated parameter for checking purposes */
@@ -133,11 +133,7 @@ Theta2_analyzer1=atan((dist_ana_vfocus+analyzer1_start+analyzer1_length)/dist_an
 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
@@ -164,12 +160,10 @@ COMPONENT ISCS = Arm() // rotate around y-axis (slight downward tilt)
 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
+    AT (0, 0, 2*NBOA_c) RELATIVE ISCS
+    ROTATED (0, 0, 0) RELATIVE ISCS
 COMPONENT arm_selene2 = Arm()
    AT (0, 0, 2*NBOA_c+2*selene_c) RELATIVE ISCS
    ROTATED (0, 0, 0) RELATIVE ISCS
@@ -207,7 +201,6 @@ COMPONENT moderator = ESS_butterfly(
    n_pulses = 1+enable_chopper, acc_power=source_power)
    AT (0, 0, 0) RELATIVE origin 

-
 /***************************************
 * Geometry of neutron feeder separate *
 ***************************************/
@@ -216,14 +209,11 @@ COMPONENT moderator = ESS_butterfly(
 /**************************************************** 
 * 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
+/* Absorber to reduce beam to needed size an for shielding purposes (FeNi in CAD model) */
+COMPONENT FeNi_in = Slit(xwidth=0.028, yheight=0.078)
+    AT (0, 0, -0.800) 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)
+COMPONENT FeNi_out = Slit(xwidth=0.013, yheight=0.038)
    AT (0, 0, -0.220) RELATIVE arm_virtual_source_beam


@@ -231,37 +221,34 @@ COMPONENT CPC1_out = Slit(xwidth=0.013, yheight=0.038)
 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
+    WHEN enable_chopper!=0
    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 = sample_height/2+over_illumination*5)
    WHEN sample!=4
    AT (-over_illumination, 0, -0.5*sample_length) RELATIVE arm_virtual_source

-// window to cut down to defined size for test setting
-COMPONENT virtual_source_HC = Slit(xwidth=sample_length, yheight=sample_height)
+// window to absorb neutron not passing through heavy collimation
+COMPONENT virtual_source_HC = Slit(
+    xmin = -0.015, xmax = 0.015,
+    ymin = -0.015, ymax = 0.015)
    WHEN sample==4
    AT (0, 0, 0) 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-over_illumination*5, ymax = 1.0)
    WHEN sample!=4
    AT (over_illumination, 0, 0.5*sample_length) RELATIVE arm_virtual_source

-
 /*************************************
 * Geometry of Selene guide separate *
 *************************************/
-%include "Estia_selene1.instr"
+%include "Estia_selene.instr"

-%include "Estia_mf.instr"
-
-%include "Estia_selene2.instr"

 /**********************************
 * Optical components within cave *
@@ -282,24 +269,6 @@ 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",
-        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_length, yheight = sample_height,
-    center = 1, transmit = 0,
-    reflect = "NiTiML.ref"
-    )
-    WHEN sample==0
-    AT (0, 0, 0) RELATIVE arm_sample
-    ROTATED (0, 90, 0) RELATIVE arm_sample

 /* ideal reflector as reference */
 COMPONENT reference_sample = Mirror(
@@ -311,50 +280,18 @@ COMPONENT reference_sample = Mirror(
    AT (0, 0, 0) RELATIVE arm_sample
    ROTATED (0, 90, 0) RELATIVE arm_sample

-/* Nickel film on silicon */
-COMPONENT ni_sample = Mirror(
+/* User defined sample file */
+COMPONENT mooc_sample = Mirror(
    xwidth = sample_length, yheight = sample_height,
    center = 1, transmit = 0,
-    reflect = "Si-Ni.ref"
+    reflect = sample_file
    )
    WHEN sample==2
    AT (0, 0, 0) RELATIVE arm_sample
    ROTATED (0, 90, 0) RELATIVE arm_sample

-/* Silicon with natural oxide */
-COMPONENT si_sample = Mirror(
-    xwidth = sample_length, yheight = sample_height,
-    center = 1, transmit = 0,
-    reflect = "Si-SiO2.ref"
-    )
-    WHEN sample==3
-    AT (0, 0, 0) RELATIVE arm_sample
-    ROTATED (0, 90, 0) RELATIVE arm_sample


-COMPONENT arm_analyzer = Arm()
-    AT (0, 0, 0) RELATIVE arm_detector
-    ROTATED (-selene_theta+(Theta1_analyzer1-Theta2_analyzer1)/2.0, 0, 0) RELATIVE arm_detector
-
-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
-
-/* polarization analyser */
-COMPONENT analyzer1 = Polariser(nIncRefr=1, d_substrate = 5e-4, reflect_d=0, reflect_u=0, lin=analyzer1_start, length=analyzer1_length,
-                                delta_theta=(Theta1_analyzer1+Theta2_analyzer1+0.05)*PI/180.0, h2=0.14, h1=0.05, abs_ref=0, 
-                                m_u=5.5, m_d=0.45, both_coated=0, alpha=2.3, W = 0.0014)
-        WHEN enable_analyzer
-        AT (0, 0.0, analyzer1_start) RELATIVE arm_analyzer
-        ROTATED (0,0,0.0) RELATIVE arm_analyzer
-
-COMPONENT analyzer2 = Polariser(nIncRefr=1, d_substrate = 5e-4, reflect_d=0, reflect_u=0, lin=analyzer2_start, length=analyzer2_length,
-                                delta_theta=(Theta1_analyzer2+Theta2_analyzer2+0.05)*PI/180.0, h2=0.2, h1=0.05, abs_out=0, 
-                                m_u=5.0, m_d=0.65, both_coated=1, alpha=2.3, W = 0.0014)
-        WHEN enable_analyzer==2
-        AT (0, 0.0, analyzer2_start) RELATIVE arm_analyzer
-        ROTATED (0,0,0.0) RELATIVE arm_analyzer
-
 /* detector */
    COMPONENT tof_detector = Monitor_nD(
        filename = "tof_detector",
@@ -362,6 +299,9 @@ COMPONENT analyzer2 = Polariser(nIncRefr=1, d_substrate = 5e-4, reflect_d=0, ref
        xwidth = 0.5, yheight = 1.0)
        WHEN sample!=4
        AT (0, 0, detector_arm+0.00001) RELATIVE arm_detector
+    /*COMPONENT detector = PSD_TOF_monitor(xwidth=0.5, yheight=0.5,
+            nx=1000, ny=250, tmin=35000, tmax=115000, nt=160, filename="detector")
+        AT (0, 0, detector_arm) RELATIVE arm_detector

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

@@ -1,172 +0,0 @@
-/*******************************************************************************
-*         McStas instrument definition URL=http://www.mcstas.org
-*
-* Instrument: Estia_mf
-*
-* %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
-* These are the components near the middle focus between the Selene guide 1 and 2.
-* This file is not intended for stand alone use but is included in the Estia instrument model. 
-* The removable components, however, allow for a stand alone use for debugging purpose.
-*
-* %Parameters
-* enable_gravity: [0/1] Use gravity in elliptical guide model.
-*
-* %End
-*******************************************************************************/
-
-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
-
-%}
-
-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;
-
-%}
-TRACE
-
-REMOVABLE COMPONENT origin = Progress_bar()
-    AT (0,0,0) ABSOLUTE
-
-REMOVABLE COMPONENT ISCS = Arm()
-    AT (0, 0, 0) RELATIVE origin    
-    
-REMOVABLE COMPONENT arm_selene1 = Arm()
-    AT (0, 0, 0) RELATIVE ISCS    
-    
-REMOVABLE COMPONENT arm_selene2 = Arm()
-    AT (0, 0, 2*selene_c) RELATIVE ISCS    
-
-REMOVABLE COMPONENT source = Moderator(radius = 0.001, focus_xw = selene_entry+0.002, focus_yh = selene_entry+0.002, 
-                                       target_index=3, Emin=1, Emax=15)
-    AT (0,0,0) RELATIVE ISCS
-    ROTATED (-1.25, 1.25, 0) RELATIVE ISCS
-
-COMPONENT arm_ersa = Arm()
-    AT (0, 0, 0) RELATIVE arm_selene2
-    ROTATED (0, -selene_theta, 0) RELATIVE arm_selene2
-
-
-/**************************************
-* Middle focus between Selene guides *
-**************************************/
-COMPONENT arm_polarizer = 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 ersa_01 = DiskChopper(radius=wfm_radius, yheight=0.05,
-    theta_0=120, phase=60+wfm_shift*180,
-    nu=wfm_freq,  nslit=2)
-    WHEN wfm_freq>0
-    AT (0, 0, -0.08) RELATIVE arm_ersa
-
-COMPONENT ersa_02 = DiskChopper(radius=wfm_radius, yheight=0.05,
-    theta_0=120, phase=75+wfm_shift*180,
-    nu=wfm_freq,  nslit=2)
-    WHEN wfm_freq>0
-    AT (0, 0, -0.07) RELATIVE arm_ersa
-
-COMPONENT ersa_03 = DiskChopper(radius=wfm_radius, yheight=0.05,
-    theta_0=120, phase=90+wfm_shift*180,
-    nu=wfm_freq,  nslit=2)
-    WHEN wfm_freq>0
-    AT (0, 0, -0.06) RELATIVE arm_ersa
-
-COMPONENT ersa_04 = DiskChopper(radius=wfm_radius, yheight=0.05,
-    theta_0=120, phase=105+wfm_shift*180,
-    nu=wfm_freq,  nslit=2)
-    WHEN wfm_freq>0
-    AT (0, 0, -0.05) RELATIVE arm_ersa
-
-COMPONENT ersa_05 = DiskChopper(radius=wfm_radius, yheight=0.05,
-    theta_0=120, phase=120+wfm_shift*180,
-    nu=wfm_freq,  nslit=2)
-    WHEN wfm_freq>0
-    AT (0, 0, -0.04) RELATIVE arm_ersa
-
-COMPONENT ersa_05b = DiskChopper(radius=wfm_radius, yheight=0.05,
-    theta_0=45, phase=-22.5+wfm_shift*180,
-    nu=wfm_freq,  nslit=2)
-    WHEN wfm_freq<0
-    AT (0, 0, -0.04) RELATIVE arm_ersa
-
-COMPONENT ersa_11b = DiskChopper(radius=wfm_radius, yheight=0.05,
-    theta_0=45, phase=22.5+wfm_shift*180,
-    nu=wfm_freq,  nslit=2)
-    WHEN wfm_freq<0
-    AT (0, 0, 0.04) RELATIVE arm_ersa
-
-COMPONENT ersa_11 = DiskChopper(radius=wfm_radius, yheight=0.05,
-    theta_0=120, phase=120+wfm_shift*180,
-    nu=wfm_freq,  nslit=2)
-    WHEN wfm_freq>0
-    AT (0, 0, 0.04) RELATIVE arm_ersa
-
-COMPONENT ersa_12 = DiskChopper(radius=wfm_radius, yheight=0.05,
-    theta_0=120, phase=135+wfm_shift*180,
-    nu=wfm_freq,  nslit=2)
-    WHEN wfm_freq>0
-    AT (0, 0, 0.05) RELATIVE arm_ersa
-
-COMPONENT ersa_13 = DiskChopper(radius=wfm_radius, yheight=0.05,
-    theta_0=120, phase=150+wfm_shift*180,
-    nu=wfm_freq,  nslit=2)
-    WHEN wfm_freq>0
-    AT (0, 0, 0.06) RELATIVE arm_ersa
-
-COMPONENT ersa_14 = DiskChopper(radius=wfm_radius, yheight=0.05,
-    theta_0=120, phase=165+wfm_shift*180,
-    nu=wfm_freq,  nslit=2)
-    WHEN wfm_freq>0
-    AT (0, 0, 0.07) RELATIVE arm_ersa
-
-COMPONENT ersa_15 = DiskChopper(radius=wfm_radius, yheight=0.05,
-    theta_0=120, phase=180+wfm_shift*180,
-    nu=wfm_freq,  nslit=2)
-    WHEN wfm_freq>0
-    AT (0, 0, 0.08) RELATIVE arm_ersa
-
-/* 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
-        
-
-
-    
-
-FINALLY
-%{
-%}
-
-END
@@ -1,204 +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]  sample rotation omega
-* sample: flag to switch between     (0) sample Ni/Ti-multilayer
-*                                    (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, also controls virtual source opening
-* sample_height: [m] Size of sample in vertical direction, also controls virtual source opening
-* 
-* operationmode: operation mode      (0) high-intensity specular reflectivity
-*                                    (1) almost conventional TOF
-* over_illumination: [m] Extra opening of virtual source compared to sample size
-* theta_resolution: Delta theta / theta  adjusted with the slit (operationmode=1)
-* 
-* lambda_start: [A] Beginning of simulated wavelength range
-* lambda_end:   [A] End of simulated wavelength range
-* 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
-(double lambda_start    =  3.0, double lambda_end      = 12.0,
-int enable_gravity=1, int enable_windows=1, direct_beam=0,
-double source_power = 5, foil_thickness=0.00001)
-
-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
-
-// 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;
-
-%}
-
-INITIALIZE
-%{
-
-%}
-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
-// 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
-// 90 degree to main beam is the monitors detector position
-COMPONENT arm_monitor = Arm()
-    AT (0, 0, -0.320) RELATIVE arm_virtual_source_beam
-    ROTATED (-90, 0, 0) RELATIVE arm_virtual_source_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, 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
-
-// As TOF detector is rectangular, use focus_r size to limit to actual
-// detector size of 0.5'' diameter cylinder
-COMPONENT Vanadium_Foil = Incoherent(focus_r=0.00635, p_interact=0.9,
-                                     xwidth=0.018, yheight=0.055, zdepth=foil_thickness,
-                                     sigma_abs=5.08, sigma_inc=5.08, Vc=13.827,
-                                     target_index=1)
-    WHEN direct_beam<2
-    AT (0, 0, -0.320) RELATIVE arm_virtual_source_beam
-    ROTATED (34.3, 0, 0) RELATIVE arm_virtual_source_beam
-
-COMPONENT tof_monitor = TOFLambda_monitor(
-    filename = "monitor",
-    tmin=0, tmax=120000, nt=1200,
-    Lmin=0,Lmax=35,nL=350,
-    xwidth = 0.025, yheight = 0.025)
-    WHEN direct_beam==0
-    AT (0, 0, 0.1) RELATIVE arm_monitor
-
-COMPONENT tof_direct = TOFLambda_monitor(
-    filename = "VS",
-    tmin=0, tmax=120000, nt=1200,
-    Lmin=0,Lmax=35,nL=350,
-    xwidth = 0.05, yheight = 0.05)
-    WHEN direct_beam>0
-    AT (0, 0, 0.08) RELATIVE arm_virtual_source_beam
-
-
-FINALLY
-%{
-%}
-
-END
@@ -0,0 +1,204 @@
+/*******************************************************************************
+*         McStas instrument definition URL=http://www.mcstas.org
+*
+* Instrument: Estia_selene
+*
+* %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
+* This is the beam extraction part of the instrument, it is not intended for use but is
+* included in the Estia instrument model. The removable components, however,
+* allow for a stand alone use for debugging purpose.
+*
+* %Parameters
+* enable_gravity: [0/1] Use gravity in elliptical guide model.
+*
+* %End
+*******************************************************************************/
+
+DEFINE INSTRUMENT Estia_selene(int enable_gravity=0)
+
+DECLARE
+%{
+    
+// Selene 1 (Will follow later with detailed parameters)
+
+
+// Selene 2
+
+    
+/* selene parameters */
+double selene_xi       =  0.6 ;     //      length of neutron guide over 2*c of ellipses, xi
+double selene_b        =  0.1047;     // m selene short half axis c
+double selene_c        =  6.0000;     // m selene focus half distance c
+double selene_coating  =  3.8;        //   m-value of selene coating
+
+
+/* other variables */
+double selene_entry ;
+double selene_length ;
+double selene_distance ;
+
+double polarizer_max_width = 0.0015; // Maximum sample height to be covered by te polarization analyzers
+double polarizer_start  = 0.3; // Distance to sample to start the first analyzer
+double polarizer_length = 0.6; // length of first analyzer
+double Theta1_polarizer, Theta2_polarizer, dist_pol_vfocus; // quantities calculated out of values above and 1.5 degree covered divergence
+
+%}
+
+INITIALIZE
+%{
+/* derived parameters for the selene guides */
+selene_length   = 2.0 * selene_c * selene_xi;
+selene_distance = ( 1.0 - selene_xi ) * selene_c;
+selene_entry    = selene_b * sqrt( 1.0 - pow(selene_xi,2.0) );
+
+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;
+
+%}
+TRACE
+
+REMOVABLE COMPONENT origin = Progress_bar()
+    AT (0,0,0) ABSOLUTE
+
+REMOVABLE COMPONENT ISCS = Arm()
+    AT (0, 0, 0) RELATIVE origin    
+    
+REMOVABLE COMPONENT arm_selene1 = Arm()
+    AT (0, 0, 0) RELATIVE ISCS    
+    
+REMOVABLE COMPONENT arm_selene2 = Arm()
+    AT (0, 0, 2*selene_c) RELATIVE ISCS    
+
+REMOVABLE COMPONENT source = Moderator(radius = 0.001, focus_xw = selene_entry+0.002, focus_yh = selene_entry+0.002, 
+                                       target_index=3, Emin=1, Emax=15)
+    AT (0,0,0) RELATIVE ISCS
+    ROTATED (-1.25, 1.25, 0) RELATIVE ISCS
+
+/**************************
+* Selene 1 neutron guide *
+**************************/
+/* Absorber to cut direct view beam (Copper in CAD model) */
+COMPONENT slit_before_selene_guide_1 = Slit(
+    xmin = 0, xmax = selene_entry+0.001,
+    ymin = 0, ymax = selene_entry+0.005)
+    AT (0, 0, selene_distance-0.01) RELATIVE arm_selene1
+
+COMPONENT block_before_selene_guide_1 = Absorber(
+    xmin=-1, xmax=1, 
+    ymin=-selene_entry/4.0+0.005, 
+    ymax=selene_entry/4.0-0.005,
+    zmin=0.0, zmax=0.001)
+    AT (0, 0, selene_distance-0.0095) RELATIVE arm_selene1
+
+/* Selene 1 elliptic guide */
+COMPONENT selene_guide_1 = Elliptic_guide_gravity(
+    l=selene_length, dimensionsAt = "mid",
+    linyh = selene_distance, loutyh= selene_distance,
+    linxw = selene_distance, loutxw= selene_distance,
+    xwidth=selene_b*2, yheight=selene_b*2,
+    mright=0, mleft=selene_coating, mtop=selene_coating, mbottom=0,
+    enableGravity=enable_gravity) 
+    AT (0, 0, selene_distance) RELATIVE arm_selene1
+
+/* Absorber to cut direct view beam (Copper in CAD model) */    
+COMPONENT slit_after_selene_guide_1 = Slit(
+    xmin = 0, xmax = selene_entry+0.005,
+    ymin = 0, ymax = selene_entry+0.01)
+    AT (0, 0, 2*selene_c-selene_distance+0.001) RELATIVE arm_selene1
+
+COMPONENT block_after_selene_guide_1 = Absorber(
+    xmin=-1, xmax=1, 
+    ymin=-selene_entry/4.0+0.015, 
+    ymax=selene_entry/4.0-0.015,
+    zmin=0.0, zmax=0.001)
+    AT (0, 0, 2*selene_c-selene_distance+0.0015) RELATIVE arm_selene1
+        
+
+/**************************************
+* Middle focus between Selene guides *
+**************************************/  
+
+
+
+/**************************
+* Selene 2 neutron guide *
+**************************/                
+/* Absorber to cut direct view beam (Copper in CAD model) */    
+COMPONENT slit_before_selene_guide_2 = Slit(
+        xmin = -selene_entry-0.005, xmax=0,
+        ymin = -selene_entry-0.01, ymax = 0)
+        AT (0, 0, selene_distance-0.002) RELATIVE arm_selene2
+
+COMPONENT block_before_selene_guide_2 = Absorber(
+    xmin=-1, xmax=1, 
+    ymin=-selene_entry/4.0+0.015, 
+    ymax=selene_entry/4.0-0.015,
+    zmin=0.0, zmax=0.001)
+    AT (0, 0, selene_distance-0.0015) RELATIVE arm_selene2
+
+    
+/* Selene 2 elliptic guide first half */
+COMPONENT selene_guide_21 = Elliptic_guide_gravity(
+    l=0.5*selene_length-0.001, dimensionsAt = "mid",
+    linyh = selene_distance, loutyh= selene_c+0.001,
+    linxw = selene_distance, loutxw= selene_c+0.001,
+    xwidth=selene_b*2, yheight=selene_b*2,
+    mright=selene_coating, mleft=0, mtop=0, mbottom=selene_coating,
+    enableGravity=enable_gravity) 
+    AT (0, 0, selene_distance) RELATIVE arm_selene2
+
+/* Absorber to cut direct view beam (Copper in CAD model) */    
+COMPONENT slit_within_selene_guide_2 = Slit(
+    xmin = -selene_b, xmax=-selene_b*0.45+0.005,
+    ymin = -selene_b, ymax=-selene_b*0.45+0.005)
+    AT (0, 0, 1.0*selene_c) RELATIVE arm_selene2
+
+/* Selene 2 elliptic guide first half */
+COMPONENT selene_guide_22 = Elliptic_guide_gravity(
+    l=0.5*selene_length-0.001, dimensionsAt = "mid",
+    linyh = selene_c+0.001, loutyh= selene_distance,
+    linxw = selene_c+0.001, loutxw= selene_distance,
+    xwidth=selene_b*2, yheight=selene_b*2,
+    mright=selene_coating, mleft=0, mtop=0, mbottom=selene_coating,
+    enableGravity=enable_gravity) 
+    AT (0, 0, 1.0*selene_c+0.001) RELATIVE arm_selene2
+
+/* Absorber to cut direct view beam (Copper in CAD model) */    
+COMPONENT slit_after_selene_guide_2 = Slit(
+    xmin = -selene_entry-0.001, xmax=0, xmax = 0.0,
+    ymin = -selene_entry-0.005, ymax = 0)
+    AT (0, 0, 2*selene_c-selene_distance+0.001) RELATIVE arm_selene2
+
+COMPONENT block_after_selene_guide_2 = Absorber(
+    xmin=-1, xmax=1, 
+    ymin=-selene_entry/4.0+0.015, 
+    ymax=selene_entry/4.0-0.015,
+    zmin=0.0, zmax=0.001)
+    AT (0, 0, 2*selene_c-selene_distance+0.0015) RELATIVE arm_selene2
+
+REMOVABLE COMPONENT FocusMonitor = PSD_monitor(
+        filename = "Focus", 
+        nx = 100, ny = 100,
+        xwidth = 0.005, yheight = 0.005,
+        restore_neutron = 1)
+    AT (0, 0, 4*selene_c) RELATIVE ISCS
+    ROTATED (0, 1.25, 0) RELATIVE ISCS
+    
+
+FINALLY
+%{
+%}
+
+END
@@ -1,270 +0,0 @@
-/*******************************************************************************
-*         McStas instrument definition URL=http://www.mcstas.org
-*
-* Instrument: Estia_selene1
-*
-* %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
-* This is the Selene guide 1 part of the instrument, it is not intended for use but is
-* included in the Estia instrument model. The removable components, however,
-* allow for a stand alone use for debugging purpose.
-*
-* %Parameters
-* enable_gravity: [0/1] Use gravity in elliptical guide model.
-*
-* %End
-*******************************************************************************/
-
-DEFINE INSTRUMENT Estia_selene(int enable_gravity=0)
-
-DECLARE
-%{
-    
-// Selene 1
-
-
-// Selene 2
-
-    
-/* selene parameters */
-double selene_xi       =  0.6 ;     //      length of neutron guide over 2*c of ellipses, xi
-double selene_b        =  0.1047;     // m selene short half axis c
-double selene_c        =  6.0000;     // m selene focus half distance c
-
-/* Coating along the elliptic guide to allow sharp wavelenth cut-off */
-double scoating_01     =  3.58;  // coating at Selene 1 start/ Selene 2 end
-double scoating_02     =  3.36;
-double scoating_03     =  3.19;
-double scoating_04     =  3.07;
-double scoating_05     =  2.98;
-double scoating_06     =  2.92;
-double scoating_07     =  2.88;
-double scoating_08     =  2.86;  // coating in center
-double scoating_09     =  2.86;  
-double scoating_10     =  2.87;  
-double scoating_11     =  2.91;  
-double scoating_12     =  2.98;  
-double scoating_13     =  3.07;  
-double scoating_14     =  3.20;  
-double scoating_15     =  3.38;  // coating at Selene 1 end/ Selene 2 start
-
-
-/* other variables */
-double selene_entry ;
-double selene_length ;
-double selene_distance ;
-
-double selene_segment ; 
-
-%}
-
-INITIALIZE
-%{
-/* derived parameters for the selene guides */
-selene_length   = 2.0 * selene_c * selene_xi;
-selene_distance = ( 1.0 - selene_xi ) * selene_c;
-selene_entry    = selene_b * sqrt( 1.0 - pow(selene_xi,2.0) );
-selene_segment  = selene_length / 15.;
-
-%}
-TRACE
-
-REMOVABLE COMPONENT origin = Progress_bar()
-    AT (0,0,0) ABSOLUTE
-
-REMOVABLE COMPONENT ISCS = Arm()
-    AT (0, 0, 0) RELATIVE origin    
-    
-REMOVABLE COMPONENT arm_selene1 = Arm()
-    AT (0, 0, 0) RELATIVE ISCS
-    ROTATED (0, 0, 0) RELATIVE ISCS
-    
-REMOVABLE COMPONENT arm_selene2 = Arm()
-    AT (0, 0, 2*selene_c) RELATIVE ISCS    
-
-REMOVABLE COMPONENT source = Moderator(radius = 0.001, focus_xw = selene_entry+0.002, focus_yh = selene_entry+0.002, 
-                                       target_index=3, Emin=1, Emax=15)
-    AT (0,0,0) RELATIVE ISCS
-    ROTATED (-1.25, 1.25, 0) RELATIVE ISCS
-
-/**************************
-* Selene 1 neutron guide *
-**************************/
-/* Absorber to cut direct view beam (Copper in CAD model) */
-COMPONENT slit_before_selene_guide_1 = Slit(
-    xmin = 0, xmax = selene_entry+0.001,
-    ymin = 0, ymax = selene_entry+0.005)
-    AT (0, 0, selene_distance-0.01) RELATIVE arm_selene1
-
-COMPONENT block_before_selene_guide_1 = Absorber(
-    xmin=-1, xmax=1, 
-    ymin=-selene_entry/4.0+0.005, 
-    ymax=selene_entry/4.0-0.005,
-    zmin=0.0, zmax=0.001)
-    AT (0, 0, selene_distance-0.0095) RELATIVE arm_selene1
-
-/* Selene 1 elliptic guide */
-COMPONENT E02_03_01 = Elliptic_guide_gravity(
-    l=selene_segment, dimensionsAt = "mid",
-    linyh = selene_distance, loutyh= selene_distance+14*selene_segment,
-    linxw = selene_distance, loutxw= selene_distance+14*selene_segment,
-    xwidth=selene_b*2, yheight=selene_b*2,
-    mright=0, mleft=scoating_01, mtop=scoating_01, mbottom=0,
-    enableGravity=enable_gravity) 
-    AT (0, 0, selene_distance) RELATIVE arm_selene1
-
-COMPONENT E02_03_02 = Elliptic_guide_gravity(
-    l=selene_segment, dimensionsAt = "mid",
-    linyh = selene_distance+1*selene_segment, loutyh= selene_distance+13*selene_segment,
-    linxw = selene_distance+1*selene_segment, loutxw= selene_distance+13*selene_segment,
-    xwidth=selene_b*2, yheight=selene_b*2,
-    mright=0, mleft=scoating_02, mtop=scoating_02, mbottom=0,
-    enableGravity=enable_gravity) 
-    AT (0, 0, selene_distance+1*selene_segment) RELATIVE arm_selene1
-
-COMPONENT E02_03_03 = Elliptic_guide_gravity(
-    l=selene_segment, dimensionsAt = "mid",
-    linyh = selene_distance+2*selene_segment, loutyh= selene_distance+12*selene_segment,
-    linxw = selene_distance+2*selene_segment, loutxw= selene_distance+12*selene_segment,
-    xwidth=selene_b*2, yheight=selene_b*2,
-    mright=0, mleft=scoating_03, mtop=scoating_03, mbottom=0,
-    enableGravity=enable_gravity) 
-    AT (0, 0, selene_distance+2*selene_segment) RELATIVE arm_selene1
-
-COMPONENT E02_03_04 = Elliptic_guide_gravity(
-    l=selene_segment, dimensionsAt = "mid",
-    linyh = selene_distance+3*selene_segment, loutyh= selene_distance+11*selene_segment,
-    linxw = selene_distance+3*selene_segment, loutxw= selene_distance+11*selene_segment,
-    xwidth=selene_b*2, yheight=selene_b*2,
-    mright=0, mleft=scoating_04, mtop=scoating_04, mbottom=0,
-    enableGravity=enable_gravity) 
-    AT (0, 0, selene_distance+3*selene_segment) RELATIVE arm_selene1
-
-COMPONENT E02_03_05 = Elliptic_guide_gravity(
-    l=selene_segment, dimensionsAt = "mid",
-    linyh = selene_distance+4*selene_segment, loutyh= selene_distance+10*selene_segment,
-    linxw = selene_distance+4*selene_segment, loutxw= selene_distance+10*selene_segment,
-    xwidth=selene_b*2, yheight=selene_b*2,
-    mright=0, mleft=scoating_05, mtop=scoating_05, mbottom=0,
-    enableGravity=enable_gravity) 
-    AT (0, 0, selene_distance+4*selene_segment) RELATIVE arm_selene1
-
-COMPONENT E02_03_06 = Elliptic_guide_gravity(
-    l=selene_segment, dimensionsAt = "mid",
-    linyh = selene_distance+5*selene_segment, loutyh= selene_distance+9*selene_segment,
-    linxw = selene_distance+5*selene_segment, loutxw= selene_distance+9*selene_segment,
-    xwidth=selene_b*2, yheight=selene_b*2,
-    mright=0, mleft=scoating_06, mtop=scoating_06, mbottom=0,
-    enableGravity=enable_gravity) 
-    AT (0, 0, selene_distance+5*selene_segment) RELATIVE arm_selene1
-
-COMPONENT E02_03_07 = Elliptic_guide_gravity(
-    l=selene_segment, dimensionsAt = "mid",
-    linyh = selene_distance+6*selene_segment, loutyh= selene_distance+8*selene_segment,
-    linxw = selene_distance+6*selene_segment, loutxw= selene_distance+8*selene_segment,
-    xwidth=selene_b*2, yheight=selene_b*2,
-    mright=0, mleft=scoating_07, mtop=scoating_07, mbottom=0,
-    enableGravity=enable_gravity) 
-    AT (0, 0, selene_distance+6*selene_segment) RELATIVE arm_selene1
-
-COMPONENT E02_03_08 = Elliptic_guide_gravity(
-    l=selene_segment, dimensionsAt = "mid",
-    linyh = selene_distance+7*selene_segment, loutyh= selene_distance+7*selene_segment,
-    linxw = selene_distance+7*selene_segment, loutxw= selene_distance+7*selene_segment,
-    xwidth=selene_b*2, yheight=selene_b*2,
-    mright=0, mleft=scoating_08, mtop=scoating_08, mbottom=0,
-    enableGravity=enable_gravity) 
-    AT (0, 0, selene_distance+7*selene_segment) RELATIVE arm_selene1
-
-COMPONENT E02_03_09 = Elliptic_guide_gravity(
-    l=selene_segment, dimensionsAt = "mid",
-    linyh = selene_distance+8*selene_segment, loutyh= selene_distance+6*selene_segment,
-    linxw = selene_distance+8*selene_segment, loutxw= selene_distance+6*selene_segment,
-    xwidth=selene_b*2, yheight=selene_b*2,
-    mright=0, mleft=scoating_09, mtop=scoating_09, mbottom=0,
-    enableGravity=enable_gravity) 
-    AT (0, 0, selene_distance+8*selene_segment) RELATIVE arm_selene1
-
-COMPONENT E02_03_10 = Elliptic_guide_gravity(
-    l=selene_segment, dimensionsAt = "mid",
-    linyh = selene_distance+9*selene_segment, loutyh= selene_distance+5*selene_segment,
-    linxw = selene_distance+9*selene_segment, loutxw= selene_distance+5*selene_segment,
-    xwidth=selene_b*2, yheight=selene_b*2,
-    mright=0, mleft=scoating_10, mtop=scoating_10, mbottom=0,
-    enableGravity=enable_gravity) 
-    AT (0, 0, selene_distance+9*selene_segment) RELATIVE arm_selene1
-
-COMPONENT E02_03_11 = Elliptic_guide_gravity(
-    l=selene_segment, dimensionsAt = "mid",
-    linyh = selene_distance+10*selene_segment, loutyh= selene_distance+4*selene_segment,
-    linxw = selene_distance+10*selene_segment, loutxw= selene_distance+4*selene_segment,
-    xwidth=selene_b*2, yheight=selene_b*2,
-    mright=0, mleft=scoating_11, mtop=scoating_11, mbottom=0,
-    enableGravity=enable_gravity) 
-    AT (0, 0, selene_distance+10*selene_segment) RELATIVE arm_selene1
-
-COMPONENT E02_03_12 = Elliptic_guide_gravity(
-    l=selene_segment, dimensionsAt = "mid",
-    linyh = selene_distance+11*selene_segment, loutyh= selene_distance+3*selene_segment,
-    linxw = selene_distance+11*selene_segment, loutxw= selene_distance+3*selene_segment,
-    xwidth=selene_b*2, yheight=selene_b*2,
-    mright=0, mleft=scoating_12, mtop=scoating_12, mbottom=0,
-    enableGravity=enable_gravity) 
-    AT (0, 0, selene_distance+11*selene_segment) RELATIVE arm_selene1
-
-COMPONENT E02_03_13 = Elliptic_guide_gravity(
-    l=selene_segment, dimensionsAt = "mid",
-    linyh = selene_distance+12*selene_segment, loutyh= selene_distance+2*selene_segment,
-    linxw = selene_distance+12*selene_segment, loutxw= selene_distance+2*selene_segment,
-    xwidth=selene_b*2, yheight=selene_b*2,
-    mright=0, mleft=scoating_13, mtop=scoating_13, mbottom=0,
-    enableGravity=enable_gravity) 
-    AT (0, 0, selene_distance+12*selene_segment) RELATIVE arm_selene1
-
-COMPONENT E02_03_14 = Elliptic_guide_gravity(
-    l=selene_segment, dimensionsAt = "mid",
-    linyh = selene_distance+13*selene_segment, loutyh= selene_distance+1*selene_segment,
-    linxw = selene_distance+13*selene_segment, loutxw= selene_distance+1*selene_segment,
-    xwidth=selene_b*2, yheight=selene_b*2,
-    mright=0, mleft=scoating_14, mtop=scoating_14, mbottom=0,
-    enableGravity=enable_gravity) 
-    AT (0, 0, selene_distance+13*selene_segment) RELATIVE arm_selene1
-
-COMPONENT E02_03_15 = Elliptic_guide_gravity(
-    l=selene_segment, dimensionsAt = "mid",
-    linyh = selene_distance+14*selene_segment, loutyh= selene_distance,
-    linxw = selene_distance+14*selene_segment, loutxw= selene_distance,
-    xwidth=selene_b*2, yheight=selene_b*2,
-    mright=0, mleft=scoating_15, mtop=scoating_15, mbottom=0,
-    enableGravity=enable_gravity) 
-    AT (0, 0, selene_distance+14*selene_segment) RELATIVE arm_selene1
-
-/* Absorber to cut direct view beam (Copper in CAD model) */    
-COMPONENT slit_after_selene_guide_1 = Slit(
-    xmin = 0, xmax = selene_entry+0.005,
-    ymin = 0, ymax = selene_entry+0.01)
-    AT (0, 0, 2*selene_c-selene_distance+0.001) RELATIVE arm_selene1
-
-COMPONENT block_after_selene_guide_1 = Absorber(
-    xmin=-1, xmax=1, 
-    ymin=-selene_entry/4.0+0.015, 
-    ymax=selene_entry/4.0-0.015,
-    zmin=0.0, zmax=0.001)
-    AT (0, 0, 2*selene_c-selene_distance+0.0015) RELATIVE arm_selene1
-        
-    
-
-FINALLY
-%{
-%}
-
-END
@@ -1,210 +0,0 @@
-/*******************************************************************************
-*         McStas instrument definition URL=http://www.mcstas.org
-*
-* Instrument: Estia_selene2
-*
-* %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
-* This is the second Selene guide part of the instrument, it is not intended for use but is
-* included in the Estia instrument model. This file does not work no its own, as it
-* requires the definitions specified in the Estia_selene1.instr DECLAR and INITIALIZE.
-*
-* %End
-*******************************************************************************/
-
-DEFINE INSTRUMENT Estia_selene2()
-
-DECLARE
-%{
-    
-
-%}
-
-INITIALIZE
-%{
-
-%}
-TRACE
-
-
-/**************************
-* Selene 2 neutron guide *
-**************************/                
-/* Absorber to cut direct view beam (Bor-Al in CAD model) */
-COMPONENT slit_before_selene_guide_2 = Slit(
-        xmin = -selene_entry-0.005, xmax=0,
-        ymin = -selene_entry-0.01, ymax = 0)
-        AT (0, 0, selene_distance-0.002) RELATIVE arm_selene2
-
-COMPONENT block_before_selene_guide_2 = Absorber(
-    xmin=-1, xmax=1, 
-    ymin=-selene_entry/4.0+0.015, 
-    ymax=selene_entry/4.0-0.015,
-    zmin=0.0, zmax=0.001)
-    AT (0, 0, selene_distance-0.0015) RELATIVE arm_selene2
-
-    
-/* Selene 2 elliptic guide first half */
-COMPONENT E02_04_01 = Elliptic_guide_gravity(
-    l=selene_segment, dimensionsAt = "mid",
-    linyh = selene_distance, loutyh= selene_distance+14*selene_segment,
-    linxw = selene_distance, loutxw= selene_distance+14*selene_segment,
-    xwidth=selene_b*2, yheight=selene_b*2,
-    mright=scoating_15, mleft=0, mtop=0, mbottom=scoating_15,
-    enableGravity=enable_gravity) 
-    AT (0, 0, selene_distance) RELATIVE arm_selene2
-
-COMPONENT E02_04_02 = Elliptic_guide_gravity(
-    l=selene_segment, dimensionsAt = "mid",
-    linyh = selene_distance+1*selene_segment, loutyh= selene_distance+13*selene_segment,
-    linxw = selene_distance+1*selene_segment, loutxw= selene_distance+13*selene_segment,
-    xwidth=selene_b*2, yheight=selene_b*2,
-    mright=scoating_14, mleft=0, mtop=0, mbottom=scoating_14,
-    enableGravity=enable_gravity) 
-    AT (0, 0, selene_distance+1*selene_segment) RELATIVE arm_selene2
-
-COMPONENT E02_04_03 = Elliptic_guide_gravity(
-    l=selene_segment, dimensionsAt = "mid",
-    linyh = selene_distance+2*selene_segment, loutyh= selene_distance+12*selene_segment,
-    linxw = selene_distance+2*selene_segment, loutxw= selene_distance+12*selene_segment,
-    xwidth=selene_b*2, yheight=selene_b*2,
-    mright=scoating_13, mleft=0, mtop=0, mbottom=scoating_13,
-    enableGravity=enable_gravity) 
-    AT (0, 0, selene_distance+2*selene_segment) RELATIVE arm_selene2
-
-COMPONENT E02_04_04 = Elliptic_guide_gravity(
-    l=selene_segment, dimensionsAt = "mid",
-    linyh = selene_distance+3*selene_segment, loutyh= selene_distance+11*selene_segment,
-    linxw = selene_distance+3*selene_segment, loutxw= selene_distance+11*selene_segment,
-    xwidth=selene_b*2, yheight=selene_b*2,
-    mright=scoating_12, mleft=0, mtop=0, mbottom=scoating_12,
-    enableGravity=enable_gravity) 
-    AT (0, 0, selene_distance+3*selene_segment) RELATIVE arm_selene2
-
-COMPONENT E02_04_05 = Elliptic_guide_gravity(
-    l=selene_segment, dimensionsAt = "mid",
-    linyh = selene_distance+4*selene_segment, loutyh= selene_distance+10*selene_segment,
-    linxw = selene_distance+4*selene_segment, loutxw= selene_distance+10*selene_segment,
-    xwidth=selene_b*2, yheight=selene_b*2,
-    mright=scoating_11, mleft=0, mtop=0, mbottom=scoating_11,
-    enableGravity=enable_gravity) 
-    AT (0, 0, selene_distance+4*selene_segment) RELATIVE arm_selene2
-
-COMPONENT E02_04_06 = Elliptic_guide_gravity(
-    l=selene_segment, dimensionsAt = "mid",
-    linyh = selene_distance+5*selene_segment, loutyh= selene_distance+9*selene_segment,
-    linxw = selene_distance+5*selene_segment, loutxw= selene_distance+9*selene_segment,
-    xwidth=selene_b*2, yheight=selene_b*2,
-    mright=scoating_10, mleft=0, mtop=0, mbottom=scoating_10,
-    enableGravity=enable_gravity) 
-    AT (0, 0, selene_distance+5*selene_segment) RELATIVE arm_selene2
-
-COMPONENT E02_04_07 = Elliptic_guide_gravity(
-    l=selene_segment, dimensionsAt = "mid",
-    linyh = selene_distance+6*selene_segment, loutyh= selene_distance+8*selene_segment,
-    linxw = selene_distance+6*selene_segment, loutxw= selene_distance+8*selene_segment,
-    xwidth=selene_b*2, yheight=selene_b*2,
-    mright=scoating_09, mleft=0, mtop=0, mbottom=scoating_09,
-    enableGravity=enable_gravity) 
-    AT (0, 0, selene_distance+6*selene_segment) RELATIVE arm_selene2
-
-COMPONENT E02_04_08 = Elliptic_guide_gravity(
-    l=selene_segment, dimensionsAt = "mid",
-    linyh = selene_distance+7*selene_segment, loutyh= selene_distance+7*selene_segment,
-    linxw = selene_distance+7*selene_segment, loutxw= selene_distance+7*selene_segment,
-    xwidth=selene_b*2, yheight=selene_b*2,
-    mright=scoating_08, mleft=0, mtop=0, mbottom=scoating_08,
-    enableGravity=enable_gravity) 
-    AT (0, 0, selene_distance+7*selene_segment) RELATIVE arm_selene2
-
-COMPONENT E02_04_09 = Elliptic_guide_gravity(
-    l=selene_segment, dimensionsAt = "mid",
-    linyh = selene_distance+8*selene_segment, loutyh= selene_distance+6*selene_segment,
-    linxw = selene_distance+8*selene_segment, loutxw= selene_distance+6*selene_segment,
-    xwidth=selene_b*2, yheight=selene_b*2,
-    mright=scoating_07, mleft=0, mtop=0, mbottom=scoating_07,
-    enableGravity=enable_gravity) 
-    AT (0, 0, selene_distance+8*selene_segment) RELATIVE arm_selene2
-
-COMPONENT E02_04_10 = Elliptic_guide_gravity(
-    l=selene_segment, dimensionsAt = "mid",
-    linyh = selene_distance+9*selene_segment, loutyh= selene_distance+5*selene_segment,
-    linxw = selene_distance+9*selene_segment, loutxw= selene_distance+5*selene_segment,
-    xwidth=selene_b*2, yheight=selene_b*2,
-    mright=scoating_06, mleft=0, mtop=0, mbottom=scoating_06,
-    enableGravity=enable_gravity) 
-    AT (0, 0, selene_distance+9*selene_segment) RELATIVE arm_selene2
-
-COMPONENT E02_04_11 = Elliptic_guide_gravity(
-    l=selene_segment, dimensionsAt = "mid",
-    linyh = selene_distance+10*selene_segment, loutyh= selene_distance+4*selene_segment,
-    linxw = selene_distance+10*selene_segment, loutxw= selene_distance+4*selene_segment,
-    xwidth=selene_b*2, yheight=selene_b*2,
-    mright=scoating_05, mleft=0, mtop=0, mbottom=scoating_05,
-    enableGravity=enable_gravity) 
-    AT (0, 0, selene_distance+10*selene_segment) RELATIVE arm_selene2
-
-COMPONENT E02_04_12 = Elliptic_guide_gravity(
-    l=selene_segment, dimensionsAt = "mid",
-    linyh = selene_distance+11*selene_segment, loutyh= selene_distance+3*selene_segment,
-    linxw = selene_distance+11*selene_segment, loutxw= selene_distance+3*selene_segment,
-    xwidth=selene_b*2, yheight=selene_b*2,
-    mright=scoating_04, mleft=0, mtop=0, mbottom=scoating_04,
-    enableGravity=enable_gravity) 
-    AT (0, 0, selene_distance+11*selene_segment) RELATIVE arm_selene2
-
-COMPONENT E02_04_13 = Elliptic_guide_gravity(
-    l=selene_segment, dimensionsAt = "mid",
-    linyh = selene_distance+12*selene_segment, loutyh= selene_distance+2*selene_segment,
-    linxw = selene_distance+12*selene_segment, loutxw= selene_distance+2*selene_segment,
-    xwidth=selene_b*2, yheight=selene_b*2,
-    mright=scoating_03, mleft=0, mtop=0, mbottom=scoating_03,
-    enableGravity=enable_gravity) 
-    AT (0, 0, selene_distance+12*selene_segment) RELATIVE arm_selene2
-
-COMPONENT E02_04_14 = Elliptic_guide_gravity(
-    l=selene_segment, dimensionsAt = "mid",
-    linyh = selene_distance+13*selene_segment, loutyh= selene_distance+1*selene_segment,
-    linxw = selene_distance+13*selene_segment, loutxw= selene_distance+1*selene_segment,
-    xwidth=selene_b*2, yheight=selene_b*2,
-    mright=scoating_02, mleft=0, mtop=0, mbottom=scoating_02,
-    enableGravity=enable_gravity) 
-    AT (0, 0, selene_distance+13*selene_segment) RELATIVE arm_selene2
-
-COMPONENT E02_04_15 = Elliptic_guide_gravity(
-    l=selene_segment, dimensionsAt = "mid",
-    linyh = selene_distance+14*selene_segment, loutyh= selene_distance,
-    linxw = selene_distance+14*selene_segment, loutxw= selene_distance,
-    xwidth=selene_b*2, yheight=selene_b*2,
-    mright=scoating_01, mleft=0, mtop=0, mbottom=scoating_01,
-    enableGravity=enable_gravity) 
-    AT (0, 0, selene_distance+14*selene_segment) RELATIVE arm_selene2
-
-/* Absorber to cut direct view beam (Bor-Al in CAD model) */
-COMPONENT slit_after_selene_guide_2 = Slit(
-    xmin = -selene_entry-0.001, xmax=0, xmax = 0.0,
-    ymin = -selene_entry-0.005, ymax = 0)
-    AT (0, 0, 2*selene_c-selene_distance+0.001) RELATIVE arm_selene2
-
-COMPONENT block_after_selene_guide_2 = Absorber(
-    xmin=-1, xmax=1, 
-    ymin=-selene_entry/4.0+0.015, 
-    ymax=selene_entry/4.0-0.015,
-    zmin=0.0, zmax=0.001)
-    AT (0, 0, 2*selene_c-selene_distance+0.0015) RELATIVE arm_selene2
-    
-
-FINALLY
-%{
-%}
-
-END
@@ -2,10 +2,8 @@

 if [ Estia_baseline.instr -nt Estia_baseline.out ] || [ ! -f Estia_baseline.out ] \
   || [ Estia_feeder.instr -nt Estia_baseline.out ] \
-   || [ Estia_selene1.instr -nt Estia_baseline.out ] \
-   || [ Estia_mf.instr -nt Estia_baseline.out ] \
-   || [ Estia_selene2.instr -nt Estia_baseline.out ]; then
+   || [ Estia_selene.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
+	mpicc -O3 -o Estia_baseline.out Estia_baseline.c -lm -DUSE_MPI -DUSE_NEXUS -lNeXus
 fi
@@ -1,4 +0,0 @@
-foreach z ( `seq -0.5 0.125 0.5` )
-  echo $z
-  ./run_simu.sh $z
-end
@@ -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
@@ -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 ####################
-
-
@@ -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
@@ -1,121 +1,117 @@
 #!/bin/bash

 DEST=../results
-ncount=1e9
-use_cores=6
-sample=4
-omega=0.8
-sample_length=0.005
-sample_height=0.01
-lambda_start=3.0
-lambda_end=32.0
-
-###################### Brilliance Transfer 10x10mm² and 1x1mm² VS ####################
-bash compile_if_needed.sh
-
-DESTi=$DEST/brilliance_nowindow_5x10
-if [ -e "$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=0.000 \
-        sample=$sample sample_length=$sample_length sample_height=$sample_height \
-        enable_windows=0 \
-        lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=1 enable_chopper=0
-
-DESTi=$DEST/brilliance_5x10
-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=0.000 \
-        sample=$sample sample_length=$sample_length sample_height=$sample_height \
-        lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=1 enable_chopper=0
-
-
-ncount=1e10
-sample_length=0.001
-sample_height=0.001
-
-DESTi=$DEST/brilliance_1x1
-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=0.000 \
-        sample=$sample sample_length=$sample_length sample_height=$sample_height \
-        lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=1 enable_chopper=0
-
-
-# ###################### Reference and Ni-layer measurement 10x10mm² sample ####################
-ncount=1e10
-sample_length=0.01
+ncount=4e9
+use_cores=${SLURM_NPROCS:-6}
+sample_length=0.05
 sample_height=0.01
 lambda_start=3.25
-lambda_end=12.75
-sample=1
+lambda_end=25.5

-omega=1.0
-DESTi=$DEST/reference_10x10_10
+bash compile_if_needed.sh
+echo "Running with $use_cores threads"
+
+# ###################### Reference and sample measurement pulse skipping ####################
+
+#
+#      Reference in pulse skipping mode
+omega=1.5
+DESTi=$DEST/mooc_reference_ps
+echo "Reference, pulse skipping"
+echo "Results saved to $DESTi"
 if [ -e "$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=0.000 \
-        sample=$sample sample_length=$sample_length sample_height=$sample_height \
-        lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=1 enable_chopper=1
-       
-#     Ni Sample
-        
-ncount=6e9
-sample=2
-omega=0.8
-DESTi=$DEST/nickle_10x10_08
-if [ -e "$DESTi" ]; then
-	rm -r "$DESTi"
-fi
+        --dir="$DESTi" --ncount=$ncount --gravitation --format=NeXus \
+        omegaa=$omega operationmode=0 theta_resolution=0.04 over_illumination=0.0002 \
+        sample=1 sample_length=$sample_length sample_height=$sample_height \
+        lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=1 enable_chopper=3
+#        
+#     Sample models in pulse skipping mode
+for MODEL in 0 1 2 3 4 5
+do
+  omega=1.5
+  DESTi="$DEST/mooc_model_ps_$MODEL"
+  echo "Model $MODEL, pulse skipping"
+  echo "Results saved to $DESTi"
+  if [ -e "$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=0.0001 \
-        sample=$sample sample_length=$sample_length sample_height=$sample_height \
-        lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=1 enable_chopper=1
+  mpirun  -np $use_cores Estia_baseline.out \
+          --dir="$DESTi" --ncount=$ncount --gravitation --format=NeXus  \
+          omegaa=$omega operationmode=0 theta_resolution=0.04 over_illumination=0.0002 \
+          sample=2 sample_length=$sample_length sample_height=$sample_height \
+          lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=1 enable_chopper=3 \
+          sample_file="alessandra_model_2_nores_00$MODEL.dat"

-ncount=2e9
-omega=3.0
-DESTi=$DEST/nickle_10x10_30
-if [ -e "$DESTi" ]; then
-	rm -r "$DESTi"
-fi
+done

-mpirun  -np $use_cores Estia_baseline.out \
-        --dir="$DESTi" --format=NeXuS --ncount=$ncount --gravitation \
-        omegaa=$omega operationmode=0 theta_resolution=0.04 over_illumination=0.0001 \
-        sample=$sample sample_length=$sample_length sample_height=$sample_height \
-        lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=1 enable_chopper=1
-        
-        
-ncount=1e9
-omega=8.0
-DESTi=$DEST/nickle_10x10_80
-if [ -e "$DESTi" ]; then
-	rm -r "$DESTi"
-fi
+#        
+#     Sample models in pulse skipping mode, larger angle
+for MODEL in 0 1 2 3 4 5
+do
+  omega=4.0
+  DESTi="$DEST/mooc_model_ps2_$MODEL"
+  echo "Model $MODEL, pulse skipping"
+  echo "Results saved to $DESTi"
+  if [ -e "$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=0.0001 \
-        sample=$sample sample_length=$sample_length sample_height=$sample_height \
-        lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=1 enable_chopper=1
+  mpirun  -np $use_cores Estia_baseline.out \
+          --dir="$DESTi" --ncount=$ncount --gravitation --format=NeXus  \
+          omegaa=$omega operationmode=0 theta_resolution=0.04 over_illumination=0.0002 \
+          sample=2 sample_length=$sample_length sample_height=$sample_height \
+          lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=1 enable_chopper=3 \
+          sample_file="alessandra_model_2_nores_00$MODEL.dat"

-# ###################### Reference and Ni-layer measurement 1x1mm² sample ####################
+done
+
+# ###################### Reference and samples in conventional mode ####################
 # 
 # 
+#
+#      Reference in conventional mode
+ncount=4e9
+lambda_end=13.5
+theta_resolution=0.1
+
+omega=1.5
+DESTi=$DEST/mooc_reference_tof
+echo "Reference, omega=$omega, Delta omega=$theta_resolution"
+echo "Results saved to $DESTi"
+if [ -e "$DESTi" ]; then
+	rm -r "$DESTi"
+fi
+
+mpirun  -np $use_cores Estia_baseline.out \
+        --dir="$DESTi" --ncount=$ncount --gravitation --format=NeXus  \
+        omegaa=$omega operationmode=1 theta_resolution=$theta_resolution over_illumination=0.0002 \
+        sample=1 sample_length=$sample_length sample_height=$sample_height \
+        lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=1 enable_chopper=1
+#        
+#     Sample models in pulse skipping mode
+for MODEL in 0 1 2 3 4 5
+do
+  for omega in 0.3 0.75 1.875 4.6875 11.71875
+  do
+    ncount=$(bc <<< "5000000000/$omega/$omega")
+    theta_resolution=$(bc <<< "scale=10;0.05*$omega")
+    DESTi="$DEST/mooc_model_tof_$MODEL-$omega"
+    echo "Model $MODEL, omega=$omega, Delta omega=$theta_resolution, n=$ncount"
+    echo "Results saved to $DESTi"
+    if [ -e "$DESTi" ]; then
+            rm -r "$DESTi"
+    fi
+
+    mpirun  -np $use_cores Estia_baseline.out \
+            --dir="$DESTi" --ncount=$ncount --gravitation --format=NeXus  \
+            omegaa=$omega operationmode=1 theta_resolution=$theta_resolution over_illumination=0.0002 \
+            sample=2 sample_length=$sample_length sample_height=$sample_height \
+            lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=1 enable_chopper=1 \
+            sample_file="alessandra_model_2_nores_00$MODEL.dat"
+  done
+done
@@ -1,5 +1,5 @@
 #!/bin/tcsh
-#SBATCH -J wfm_McEstia
+#SBATCH -J mooc_McEstia
 #SBATCH -N 2
 #SBATCH --ntasks-per-node=24
 #SBATCH --time=1-00:00:00
@@ -20,5 +20,4 @@ echo "Current working directory is `pwd`"

 module load mcstas

-bash compile_if_needed.sh
-bash run_wfm.sh
+bash run_simu.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 ####################
-
-
@@ -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=$lambda_end enable_gravity=1 enable_chopper=3
@@ -1,119 +0,0 @@
-#!/bin/bash
-
-DEST=../results
-ncount=1e9
-use_cores=6
-sample=1
-omega=15.0
-sample_length=0.02
-sample_height=0.01
-
-lambda_start=3.5
-lambda_min=5.0
-lambda_end=15.5
-frame_usage=0.92
-
-###################### Brilliance Transfer 10x10mm² and 1x1mm² VS ####################
-bash compile_if_neede.sh
-
-###################### Reference and Ni-layer measurement 10x10mm² sample ####################
-
-frame_usage=0.92
-DESTi=$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=$lambda_min
-       
-       
-###################### Reference and Ni-layer measurement 1x1mm² sample ####################
-
-
@@ -1,32 +0,0 @@
-#!/bin/bash
-
-DEST=../results
-ncount=1e8
-use_cores=6
-sample=1
-omega=0.8
-sample_length=0.01
-sample_height=0.015
-
-if [ Estia_vs.instr -nt Estia_vs.out ]; then
-	rm Estia_vs.c Estia_vs.out
-	mcstas -t -o Estia_vs.c Estia_vs.instr
-	mpicc -O3 -o Estia_vs.out Estia_vs.c -lm -DUSE_MPI -DUSE_NEXUS -lNeXus
-fi
-
-
-omega=2.0
-DESTi=$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=$sample_height \
-        enable_gravity=1 enable_chopper=0 source_power=5
-       
-###################### Reference and Ni-layer measurement 1x1mm² sample ####################
-
-
@@ -1,177 +0,0 @@
-#!/bin/bash
-
-DEST=../results
-ncount=2e10
-use_cores=$SLURM_NPROCS
-sample=1
-omega=5.0
-sample_length=0.01
-sample_height=0.01
-lambda_start=3.00
-lambda_end=15.0
-
-######################## 1% WFM for 30cm and 60cm device #######################
-
-DESTi=$DEST/ersa_245Hz
-if [ -e "$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=0.001 \
-        sample=$sample sample_length=$sample_length sample_height=$sample_height \
-        enable_windows=0 wfm_freq=245 wfm_shift=0.0 \
-        lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=1 enable_chopper=1
-
-
-DESTi=$DEST/ersa_280Hz
-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=0.001 \
-        sample=$sample sample_length=$sample_length sample_height=$sample_height \
-        enable_windows=0 wfm_freq=280 wfm_shift=0.0 \
-        lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=1 enable_chopper=1
-
-
-DESTi=$DEST/ersa_308Hz
-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=0.001 \
-        sample=$sample sample_length=$sample_length sample_height=$sample_height \
-        enable_windows=0 wfm_freq=308 wfm_shift=0.0 \
-        lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=1 enable_chopper=1
-
-
-DESTi=$DEST/ersa_350Hz
-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=0.001 \
-        sample=$sample sample_length=$sample_length sample_height=$sample_height \
-        enable_windows=0 wfm_freq=350 wfm_shift=0.0 \
-        lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=1 enable_chopper=1
-
-
-
-DESTi=$DEST/ersa_r300_245Hz
-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=0.001 \
-        sample=$sample sample_length=$sample_length sample_height=$sample_height \
-        enable_windows=0 wfm_freq=245 wfm_shift=0.0 wfm_radius=0.3 \
-        lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=1 enable_chopper=1
-
-
-DESTi=$DEST/ersa_r300_280Hz
-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=0.001 \
-        sample=$sample sample_length=$sample_length sample_height=$sample_height \
-        enable_windows=0 wfm_freq=280 wfm_shift=0.0 wfm_radius=0.3 \
-        lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=1 enable_chopper=1
-
-
-
-DESTi=$DEST/ersa_r300_308Hz
-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=0.001 \
-        sample=$sample sample_length=$sample_length sample_height=$sample_height \
-        enable_windows=0 wfm_freq=308 wfm_shift=0.0 wfm_radius=0.3 \
-        lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=1 enable_chopper=1
-
-
-
-DESTi=$DEST/ersa_r300_350Hz
-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=0.001 \
-        sample=$sample sample_length=$sample_length sample_height=$sample_height \
-        enable_windows=0 wfm_freq=350 wfm_shift=0.0 wfm_radius=0.3 \
-        lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=1 enable_chopper=1
-
-###################### 0.5% WFM ########################
-
-ncount=4e10
-DESTi=$DEST/ersa_reverse_280Hz
-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=0.001 \
-        sample=$sample sample_length=$sample_length sample_height=$sample_height \
-        enable_windows=0 wfm_freq=-280 wfm_shift=0.0 \
-        lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=0 enable_chopper=1
-
-
-DESTi=$DEST/ersa_reverse_308Hz
-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=0.001 \
-        sample=$sample sample_length=$sample_length sample_height=$sample_height \
-        enable_windows=0 wfm_freq=-308 wfm_shift=0.0 \
-        lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=0 enable_chopper=1
-
-
-DESTi=$DEST/ersa_reverse_350Hz
-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=0.001 \
-        sample=$sample sample_length=$sample_length sample_height=$sample_height \
-        enable_windows=0 wfm_freq=-350 wfm_shift=0.0 \
-        lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=0 enable_chopper=1
-
-
-##################### Reference run ###############################
-ncount=1e10
-
-DESTi=$DEST/ersa_ref
-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=0.001 \
-        sample=$sample sample_length=$sample_length sample_height=$sample_height \
-        enable_windows=0 wfm_freq=0 \
-        lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=1 enable_chopper=1
-
@@ -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`"
-
@@ -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`"
-
@@ -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`"
-
@@ -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`"
-
@@ -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`"
-
Author	SHA1	Message	Date
glavic_a	b520d1c9d1	Add pulse skipping simulation to run script	2018-10-04 09:34:08 +02:00
glavic_a	e73d512b9c	Extend q-range of simulated data to region measured up to 11.7 deg	2018-09-27 14:47:52 +02:00
glavic_a	52db780c96	update script, process hdf files to add compression	2018-09-16 14:09:15 +02:00
glavic_a	2b780d8f1f	Update script for slurm and add ToF mode runs	2018-08-18 12:21:48 +02:00
glavic_a	ef1dc84488	minor wavelength shift	2018-06-26 07:51:35 +02:00
glavic_a	1857f9b0dd	Simulate and analyze pulse skipping mode models	2018-06-26 07:26:05 +02:00
glavic_a	29b537efce	fix chopper for pulse skipping	2018-06-25 23:31:09 +02:00
glavic_a	c938f456bf	Simplify instrument and add model files.	2018-06-25 22:08:16 +02:00