some modifications to add lipid models

Add monitor model and update CPC1 entrance and middle geometry
Fix reader plotting for 2D datasets
2021-10-11 14:22:07 +02:00 · 2018-09-15 14:13:56 +02:00 · 2018-09-15 14:11:19 +02:00 · 2018-08-18 11:15:15 +02:00 · 2018-07-03 08:22:36 +02:00 · 2018-07-03 08:21:55 +02:00
20 changed files with 3457 additions and 441 deletions
@@ -294,9 +294,9 @@ class Dataset(object):
    limits=map(float, self.info['xylimits'].split())

    if log:
-      ax.imshow(self.data, extent=limits, aspect='auto', norm=LogNorm())
+      ax.imshow(self.data, origin='lower', extent=limits, aspect='auto', norm=LogNorm())
    else:
-      ax.imshow(self.data, extent=limits, aspect='auto')
+      ax.imshow(self.data, origin='lower', extent=limits, aspect='auto')
    ax.set_xlabel(self.info['xlabel'])
    ax.set_ylabel(self.info['ylabel'])
    ax.set_title(self.info['component'])
@@ -54,7 +54,8 @@ int operationmode = 0, double over_illumination = 0.0, double theta_resolution =
 double lambda_min      =  3.75, double lambda_start    =  3.0, double lambda_end      = 12.0,
 int enable_chopper = 0, int enable_gravity=0, int enable_windows=1,
 int enable_polarizer = 0, int enable_analyzer = 0,
-double source_power = 2, double frame_usage     =   0.98
+double source_power = 2,
+double selene1_foot1y =0.0, double selene1_foot2y = 0.0
 )

 DECLARE
@@ -70,8 +71,12 @@ 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 (Will follow later with detailed parameters)
-
+// 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

@@ -97,9 +102,6 @@ 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
@@ -115,7 +117,7 @@ INITIALIZE
 // chopper coupling together
 velocity_max= 3.956034E3 / lambda_min; // h/m_n over lambda - ((3.9..e-7m^2/s))/(1e-10m)
 chopper_phase=360.0*(chopper_pos*chopper_freq/velocity_max+(pulse_zero-opening_time)*chopper_freq);
-chopper_open =360.0*(chopper_pos/(total_length+detector_arm))*frame_usage;
+chopper_open = 98.0;


 /* print out some calculated parameter for checking purposes */
@@ -130,7 +132,11 @@ 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
@@ -157,10 +163,12 @@ 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, 2*NBOA_c) RELATIVE ISCS
-    ROTATED (0, 0, 0) RELATIVE ISCS
+    AT (0, 0, -selene1_center) RELATIVE arm_selene1_center
 COMPONENT arm_selene2 = Arm()
    AT (0, 0, 2*NBOA_c+2*selene_c) RELATIVE ISCS
    ROTATED (0, 0, 0) RELATIVE ISCS
@@ -199,15 +207,6 @@ COMPONENT moderator = ESS_butterfly(
    AT (0, 0, 0) RELATIVE origin 


-// monitor used for brilliance transfer calculations
-COMPONENT tof_source = Monitor_nD(
-    filename = "tof_source",
-    options = "xdiv limits=[-0.75 0.75] bins=15 ydiv limits=[-2.0 2.0] bins=40 time limits=[0 0.6] bins=600 lambda limits=[0 35] bins=350",
-    xwidth=0.01, yheight = 0.01)
-    WHEN sample==4
-    AT (0, 0, 0.03) RELATIVE ISCS
-        ROTATED (0,-selene_theta,0) RELATIVE ISCS
-
 /***************************************
 * Geometry of neutron feeder separate *
 ***************************************/
@@ -216,11 +215,14 @@ COMPONENT tof_source = Monitor_nD(
 /**************************************************** 
 * Beam manipulation area around the virtual source *
 ****************************************************/
-/* 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
+/* 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 FeNi_out = Slit(xwidth=0.013, yheight=0.038)
+COMPONENT CPC1_monitor = Slit(xwidth=0.016344, yheight=0.05547)
+    AT (0, 0, -0.3573) RELATIVE arm_virtual_source_beam
+
+COMPONENT CPC1_out = Slit(xwidth=0.013, yheight=0.038)
    AT (0, 0, -0.220) RELATIVE arm_virtual_source_beam


@@ -231,30 +233,6 @@ COMPONENT chopper = DiskChopper(radius=chopper_diameter/2.0, yheight=0.02,
    WHEN enable_chopper==1
    AT (0, 0, chopper_pos-2*NBOA_c) RELATIVE arm_virtual_source_beam
    
-    // Beam monitoring before VS
-    COMPONENT DP_before_virtual_source = DivPos_monitor(
-        filename = "DP_before_virtual_source" ,
-        nh = 200, ndiv = 200,
-        xwidth = 0.2, yheight = 0.2,
-        maxdiv_h = 6,
-        restore_neutron = 1)
-        AT (0, 0, -0.022) RELATIVE arm_virtual_source_beam
-
-    COMPONENT PP_small_before_virtual_source = PSD_monitor(
-        filename = "PP_small_before_virtual_source",
-        nx = 200, ny = 200,
-        xwidth = 0.1, yheight = 0.1,
-        restore_neutron = 1)
-        WHEN PP_small ==1
-        AT (0, 0, -0.021) RELATIVE arm_virtual_source_beam
-
-    COMPONENT PP_large_before_virtual_source = PSD_monitor(
-        filename = "PP_large_before_virtual_source",
-        nx = 200, ny = 200,
-        xmin = -1.8, xmax = 1.8, ymin = -1.8, ymax = 1.8,
-        restore_neutron = 1)
-        WHEN PP_large ==1
-        AT (0, 0, 2*NBOA_c-0.02) RELATIVE ISCS


 /* The actual virtual source mask, two L-shaped absorbers (first top-right) */
@@ -263,66 +241,26 @@ COMPONENT virtual_source_TR = Slit(
    WHEN sample!=4
    AT (-over_illumination, 0, -0.5*sample_length) RELATIVE arm_virtual_source

-// 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)
+// window to cut down to defined size for test setting
+COMPONENT virtual_source_HC = Slit(xwidth=sample_length, yheight=sample_height)
    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

-    
-    // Beam monitoring after VS
-    COMPONENT tof_virtual_source = Monitor_nD(
-        filename = "tof_virtual_source",
-        options = "xdiv limits=[-0.75 0.75] bins=15 ydiv limits=[-2.0 2.0] bins=40 time limits=[0 0.6] bins=600 lambda limits=[0 35] bins=350",
-        xwidth=sample_length, yheight = sample_height)
-        WHEN sample==4
-        AT (0, 0, 0.019) RELATIVE arm_virtual_source_beam
-                
-    COMPONENT DL_behind_virtual_source = DivLambda_monitor(
-        filename = "DL_behind_virtual_source",
-        nL = 200, nh = 200,
-        xwidth = 0.02, yheight = 0.06,
-        maxdiv_h = 3,
-        Lmin = lambda_start, Lmax = lambda_end, 
-        restore_neutron = 1)
-        AT (0, 0, 0.02) RELATIVE arm_virtual_source_beam
-
-    COMPONENT DP_behind_virtual_source = DivPos_monitor(
-        filename = "DP_behind_virtual_source" ,
-        nh = 200, ndiv = 200,
-        xwidth = 0.2, yheight = 0.2,
-        maxdiv_h = 3,
-        restore_neutron = 1)
-        AT (0, 0, 0.021) RELATIVE arm_virtual_source_beam
-
-    COMPONENT PP_small_behind_virtual_source = PSD_monitor(
-        filename = "PP_small_behind_virtual_source",
-        nx = 200, ny = 200, 
-        xwidth = 0.02, yheight = 0.05,
-        restore_neutron = 1)
-        WHEN PP_small ==1
-        AT (0, 0, 0.022) RELATIVE arm_virtual_source_beam
-
-    COMPONENT PP_large_behind_virtual_source = PSD_monitor(
-        filename = "PP_large_behind_virtual_source",
-        nx = 200, ny = 200,
-        xmin = -1.8, xmax = 1.8, ymin = -1.8, ymax = 1.8,
-        restore_neutron = 1)
-        WHEN PP_large ==1
-        AT (0, 0, 2*NBOA_c+0.023) RELATIVE ISCS

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

+%include "Estia_mf.instr"
+
+%include "Estia_selene2.instr"

 /**********************************
 * Optical components within cave *
@@ -343,60 +281,14 @@ COMPONENT ac_slit = Slit(
 /***************
 * Sample area *
 ***************/
-    // Beam monitoring before sample
-    COMPONENT PP_small_sample_focus = PSD_monitor(
-        filename = "PP_small_sample_focus",
-        nx = 200, ny = 200, 
-        xwidth = 0.02, yheight = 0.05,
-        restore_neutron = 1)
-        WHEN PP_small ==1
-        AT (0, 0, -0.001) RELATIVE arm_sample
-
-    COMPONENT DL_sample_focus = DivLambda_monitor(
-        filename = "DL_sample_focus",
-        nL = 200, nh = 200,
-        xwidth = 0.02, yheight = 0.06,
-        maxdiv_h = 3,
-        Lmin = lambda_start, Lmax = lambda_end, 
-        restore_neutron = 1)
-        AT (0, 0, -0.001) RELATIVE arm_sample
-
-    /* monitor at sample position for footprint */
-    COMPONENT PL_sample = Monitor_nD(
-        filename = "PL_sample",
-        options = "lambda limits=[0 35] bins=350 x limits=[-0.02 0.02] bins 160",
-        xwidth = 0.04, yheight = 0.02, restore_neutron=1)
-        WHEN sample!=4
-        AT (0, 0, -0.001) RELATIVE arm_sample
-        ROTATED (0, -90, 0) RELATIVE arm_sample
-
-    COMPONENT PSD_sample = PSD_monitor(
-        filename = "PSD_sample", 
-        nx = 100, ny = 100,
-        xwidth = 4*sample_length, yheight = 4*sample_height,
-        restore_neutron = 1)
-        WHEN sample!=4
-        AT (0, 0, -0.001) RELATIVE arm_sample
-        ROTATED (0, -90, 0) RELATIVE arm_sample
-
    COMPONENT tof_sample = Monitor_nD(
        filename = "tof_sample",
-        options = "xdiv limits=[-0.75 0.75] bins=15 ydiv limits=[-2.0 2.0] bins=40 time limits=[0 0.6] bins=600 lambda limits=[0 35] bins=350",
-        xwidth=sample_length, yheight = sample_height)
+        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, -0.0005) RELATIVE arm_sample_beam
-        ROTATED (0, 0, 0) RELATIVE arm_sample_beam
-                
-    /* monitor for full beam at sample position ( n/cm²/s ) */
-    COMPONENT PP_small_sample = PSD_monitor(
-        filename = "PSD_sample_perp",
-        nx = 200, ny = 200, 
-        xwidth = 0.05, yheight = 0.05,
-        restore_neutron = 1)
-        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(
@@ -438,6 +330,32 @@ COMPONENT si_sample = Mirror(
    AT (0, 0, 0) RELATIVE arm_sample
    ROTATED (0, 90, 0) RELATIVE arm_sample

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

 COMPONENT arm_analyzer = Arm()
    AT (0, 0, 0) RELATIVE arm_detector
@@ -463,31 +381,12 @@ COMPONENT analyzer2 = Polariser(nIncRefr=1, d_substrate = 5e-4, reflect_d=0, ref
        ROTATED (0,0,0.0) RELATIVE arm_analyzer

 /* detector */
-    // Beam monitoring at detector position
-    COMPONENT PP_large_detector = PSD_monitor(
-        filename = "PP_large_detector",
-        nx = 200, ny = 200, 
-        xmin = -1.8, xmax = 1.8, ymin = -1.8, ymax = 1.8,
-        restore_neutron = 1)
-        AT (0, 0, total_length+detector_arm-0.001) RELATIVE ISCS
-
-    // Detector with 0.5x1mm² resolution
-    COMPONENT PP_detector = PSD_monitor(
-        filename = "PP_detector",
-        nx = 1000, ny = 500,
-        xwidth = 0.5, yheight = 0.5,
-        restore_neutron = 1)
-        AT (0, 0, detector_arm) RELATIVE arm_detector
-
    COMPONENT tof_detector = Monitor_nD(
        filename = "tof_detector",
        options = "x limits=[-0.25 0.25] bins=1000 y limits=[-0.5 0.5] bins=1000 time limits=[0 0.6] bins=6000 lambda limits=[0 35] bins=3500 sx limits=[-1 1] bins=1000 sy limits=[-1 1] bins=1000, list all",
        xwidth = 0.5, yheight = 1.0)
        WHEN sample!=4
        AT (0, 0, detector_arm+0.00001) RELATIVE arm_detector
-    /*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

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

@@ -0,0 +1,96 @@
+/*******************************************************************************
+*         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
+
+
+/**************************************
+* 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
+
+
+/* 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
@@ -0,0 +1,204 @@
+/*******************************************************************************
+*         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
@@ -1,240 +0,0 @@
-/*******************************************************************************
-*         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 *
-**************************************/
-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 polmon_mfocus=PolLambda_monitor(Lmin=lambda_start, Lmax=lambda_end, nL=30, npol=101, my=1, filename="polmon_mfocus")
-        WHEN enable_polarizer
-            AT (0, 0, 2*selene_c) RELATIVE arm_selene1
-            ROTATED (0.0,0.0,0.0) RELATIVE arm_selene1
-
-  
-    COMPONENT PP_small_before_middle_focus = PSD_monitor(
-        filename = "PP_small_before_middle_focus",
-        nx = 200, ny = 200, 
-        xwidth = 0.1, yheight = 0.1,
-        restore_neutron = 1)
-        AT (0, 0, 2*selene_c) RELATIVE arm_selene1
-
-/* 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
-        
-
-
-/**************************
-* 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
-
-/*COMPONENT block_within_selene_guide_2 = Absorber(
-    xmin =-1, xmax=1,
-    ymin =-selene_b*0.25+0.001, 
-    ymax = selene_b*0.25-0.001,
-    zmin=0.0, zmax=0.0001)
-    AT (0, 0, 3.0*selene_c+0.0001) 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
@@ -0,0 +1,270 @@
+/*******************************************************************************
+*         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
@@ -0,0 +1,210 @@
+/*******************************************************************************
+*         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
@@ -2,8 +2,10 @@

 if [ Estia_baseline.instr -nt Estia_baseline.out ] || [ ! -f Estia_baseline.out ] \
   || [ Estia_feeder.instr -nt Estia_baseline.out ] \
-   || [ Estia_selene.instr -nt Estia_baseline.out ]; then
+   || [ Estia_selene1.instr -nt Estia_baseline.out ] \
+   || [ Estia_mf.instr -nt Estia_baseline.out ] \
+   || [ Estia_selene2.instr -nt Estia_baseline.out ]; then
 	rm Estia_baseline.c Estia_baseline.out
 	mcstas -o Estia_baseline.c Estia_baseline.instr
-	mpicc -O3 -o Estia_baseline.out Estia_baseline.c -lm -DUSE_MPI -DUSE_NEXUS -lNeXus
+	mpicc -O3 -o Estia_baseline.out Estia_baseline.c -lm -DUSE_MPI
 fi
@@ -0,0 +1,102 @@
+0.00	1.000
+0.01	0.0099682
+0.0149	0.0042479
+0.0198	0.0022557
+0.0247	0.0013447
+0.0296	0.00086176
+0.0345	0.000582
+0.0394	0.0004107
+0.0443	0.00030205
+0.0492	0.00023151
+0.0541	0.0001849
+0.059	0.00015356
+0.0639	0.00013197
+0.0688	0.00011657
+0.0737	0.00010502
+0.0786	9.58E-05
+0.0835	8.80E-05
+0.0884	8.11E-05
+0.0933	7.47E-05
+0.0982	6.88E-05
+0.1031	6.33E-05
+0.108	5.82E-05
+0.1129	5.35E-05
+0.1178	4.94E-05
+0.1227	4.57E-05
+0.1276	4.24E-05
+0.1325	3.96E-05
+0.1374	3.71E-05
+0.1423	3.48E-05
+0.1472	3.27E-05
+0.1521	3.08E-05
+0.157	2.89E-05
+0.1619	2.71E-05
+0.1668	2.53E-05
+0.1717	2.35E-05
+0.1766	2.17E-05
+0.1815	2.00E-05
+0.1864	1.83E-05
+0.1913	1.66E-05
+0.1962	1.51E-05
+0.2011	1.36E-05
+0.206	1.22E-05
+0.2109	1.08E-05
+0.2158	9.61E-06
+0.2207	8.46E-06
+0.2256	7.39E-06
+0.2305	6.39E-06
+0.2354	5.46E-06
+0.2403	4.61E-06
+0.2452	3.84E-06
+0.2501	3.16E-06
+0.255	2.55E-06
+0.2599	2.04E-06
+0.2648	1.61E-06
+0.2697	1.26E-06
+0.2746	9.93E-07
+0.2795	7.98E-07
+0.2844	6.64E-07
+0.2893	5.82E-07
+0.2942	5.39E-07
+0.2991	5.24E-07
+0.304	5.28E-07
+0.3089	5.41E-07
+0.3138	5.58E-07
+0.3187	5.73E-07
+0.3236	5.83E-07
+0.3285	5.88E-07
+0.3334	5.88E-07
+0.3383	5.84E-07
+0.3432	5.77E-07
+0.3481	5.69E-07
+0.353	5.62E-07
+0.3579	5.57E-07
+0.3628	5.53E-07
+0.3677	5.52E-07
+0.3726	5.53E-07
+0.3775	5.56E-07
+0.3824	5.61E-07
+0.3873	5.67E-07
+0.3922	5.74E-07
+0.3971	5.81E-07
+0.402	5.89E-07
+0.4069	5.96E-07
+0.4118	6.04E-07
+0.4167	6.12E-07
+0.4216	6.19E-07
+0.4265	6.27E-07
+0.4314	6.35E-07
+0.4363	6.43E-07
+0.4412	6.50E-07
+0.4461	6.58E-07
+0.451	6.66E-07
+0.4559	6.74E-07
+0.4608	6.82E-07
+0.4657	6.89E-07
+0.4706	6.97E-07
+0.4755	7.04E-07
+0.4804	7.11E-07
+0.4853	7.16E-07
+0.4902	7.20E-07
+0.4951	7.21E-07
+0.5	7.23E-07
@@ -0,0 +1,12 @@
+#!/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
@@ -2,45 +2,51 @@
 #-*- coding: utf8 -*-

 import sys, os
-import numpy as np
 from subprocess import call
+from numpy import *
+from scipy.optimize import leastsq

-FOLDER='../results2/'
-PREFIX='selene_geo_'
-SEED=3798
-ITEMS=1000

-CALL='mpirun -np 6 Selene_geometry.out --dir=%s --ncount=4e8 enable_gravity=0 sample_length=0.003 '
-CALL+='tx_1=%f tz_1=%f ry_1=%f rz_1=%f tx_2=%f tz_2=%f ry_2=%f rz_2=%f '
+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 '

-TX=[-0.001, 0.001]
-TZ=[-0.005, 0.005]
-RY=[-0.001, 0.001]
-RZ=[-2.5, 2.5]
+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__':
-    call('mcstas -t -o Selene_geometry.c Selene_geometry.instr'.split())
-    call('mpicc -O2 -o Selene_geometry.out Selene_geometry.c -lm -DUSE_MPI'.split())
-    
-    np.random.seed(SEED)
-    fh=open(os.path.join(FOLDER, PREFIX+'sims.dat'), 'w')
-    fh.write('# index tx_1 tz_1 ry_1 rz_1 tx_2 tz_2 ry_2 rz_2\n')
-    fh.write('# seed = %i\n'%SEED)
-    
-    for i in range(ITEMS):
-        tx_1=np.random.random()*(TX[1]-TX[0])+TX[0]
-        tx_2=np.random.random()*(TX[1]-TX[0])+TX[0]
-        tz_1=np.random.random()*(TZ[1]-TZ[0])+TZ[0]
-        tz_2=np.random.random()*(TZ[1]-TZ[0])+TZ[0]
-        ry_1=np.random.random()*(RY[1]-RY[0])+RY[0]
-        ry_2=np.random.random()*(RY[1]-RY[0])+RY[0]
-        rz_1=np.random.random()*(RZ[1]-RZ[0])+RZ[0]
-        rz_2=np.random.random()*(RZ[1]-RZ[0])+RZ[0]
-        ln=' '.join(['%f'%val for val in [tx_1, tz_1, ry_1, rz_1, tx_2, tz_2, ry_2, rz_2]])
-        fh.write(ln+'\n')
-        print i, ':', ln
-        call((CALL%(os.path.join(FOLDER, PREFIX+'%05i/'%i), tx_1, tz_1, ry_1, rz_1, tx_2, tz_2, ry_2, rz_2)).split())
-    
-    fh.close()
-    
+    pass
@@ -0,0 +1,251 @@
+#!/bin/tcsh
+#SBATCH -J mcEstia
+#SBATCH -N 6
+#SBATCH --ntasks-per-node=24
+#SBATCH --time=2-00:00:00
+#SBATCH --mail-type=fail
+#SBATCH --mail-user=artur.glavic@psi.ch
+
+#SBATCH -o stdout.log
+#SBATCH -e stderr.log
+
+#SBATCH --partition=medium
+
+echo "Starting at `date`"
+echo "Running on hosts: $SLURM_NODELIST"
+echo "Running on $SLURM_NNODES nodes."
+echo "Running on $SLURM_NPROCS processors."
+echo "Current working directory is `pwd`"
+
+module load mcstas
+bash compile_if_needed.sh
+
+set DEST=../results
+set ncount=1e10
+set use_cores=4
+set sample=1
+set sample_length=0.03
+set sample_height=0.01
+set lambda_start=3.5
+set lambda_end=14.0
+
+
+################## Reference ########################
+set omega=1.0
+set DESTi=$DEST/solid_liquid_reference
+if ( -e "$DESTi" ) then
+	rm -r "$DESTi"
+endif
+
+mpirun  -np $use_cores Estia_baseline.out \
+        --dir="$DESTi" --ncount=$ncount --gravitation \
+        omegaa=$omega operationmode=1 theta_resolution=0.04 over_illumination=0.0025 \
+        sample=$sample sample_length=$sample_length sample_height=$sample_height \
+        lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=1 enable_chopper=1 enable_polarizer=0 enable_analyzer=0
+
+################## H2O ########################
+set ncount=1e11
+set sample=5
+set omega=0.2
+set DESTi=$DEST/solid_liquid_h2o_02
+if ( -e "$DESTi" ) then
+	rm -r "$DESTi"
+endif
+
+mpirun  -np $use_cores Estia_baseline.out \
+        --dir="$DESTi" --ncount=$ncount --gravitation \
+        omegaa=$omega operationmode=1 theta_resolution=0.04 over_illumination=0.0025 \
+        sample=$sample sample_length=$sample_length sample_height=$sample_height \
+        lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=1 enable_chopper=1 enable_polarizer=0 enable_analyzer=0
+
+set ncount=1e10
+set omega=0.5
+set DESTi=$DEST/solid_liquid_h2o_05
+if ( -e "$DESTi" ) then
+	rm -r "$DESTi"
+endif
+
+mpirun  -np $use_cores Estia_baseline.out \
+        --dir="$DESTi" --ncount=$ncount --gravitation \
+        omegaa=$omega operationmode=1 theta_resolution=0.04 over_illumination=0.0025 \
+        sample=$sample sample_length=$sample_length sample_height=$sample_height \
+        lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=1 enable_chopper=1 enable_polarizer=0 enable_analyzer=0
+
+set ncount=4e9
+set omega=1.2
+set DESTi=$DEST/solid_liquid_h2o_12
+if ( -e "$DESTi" ) then
+	rm -r "$DESTi"
+endif
+
+mpirun  -np $use_cores Estia_baseline.out \
+        --dir="$DESTi" --ncount=$ncount --gravitation \
+        omegaa=$omega operationmode=1 theta_resolution=0.04 over_illumination=0.0025 \
+        sample=$sample sample_length=$sample_length sample_height=$sample_height \
+        lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=1 enable_chopper=1 enable_polarizer=0 enable_analyzer=0
+
+set ncount=2e9
+set omega=3.1
+set DESTi=$DEST/solid_liquid_h2o_31
+if ( -e "$DESTi" ) then
+	rm -r "$DESTi"
+endif
+
+mpirun  -np $use_cores Estia_baseline.out \
+        --dir="$DESTi" --ncount=$ncount --gravitation \
+        omegaa=$omega operationmode=1 theta_resolution=0.04 over_illumination=0.0025 \
+        sample=$sample sample_length=$sample_length sample_height=$sample_height \
+        lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=1 enable_chopper=1 enable_polarizer=0 enable_analyzer=0
+
+set ncount=1e9
+set omega=7.8
+set DESTi=$DEST/solid_liquid_h2o_78
+if ( -e "$DESTi" ) then
+	rm -r "$DESTi"
+endif
+
+mpirun  -np $use_cores Estia_baseline.out \
+        --dir="$DESTi" --ncount=$ncount --gravitation \
+        omegaa=$omega operationmode=1 theta_resolution=0.04 over_illumination=0.0025 \
+        sample=$sample sample_length=$sample_length sample_height=$sample_height \
+        lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=1 enable_chopper=1 enable_polarizer=0 enable_analyzer=0
+
+
+################## D2O ########################
+set ncount=1e11
+set sample=6
+set omega=0.2
+set DESTi=$DEST/solid_liquid_d2o_02
+if ( -e "$DESTi" ) then
+	rm -r "$DESTi"
+endif
+
+mpirun  -np $use_cores Estia_baseline.out \
+        --dir="$DESTi" --ncount=$ncount --gravitation \
+        omegaa=$omega operationmode=1 theta_resolution=0.04 over_illumination=0.0025 \
+        sample=$sample sample_length=$sample_length sample_height=$sample_height \
+        lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=1 enable_chopper=1 enable_polarizer=0 enable_analyzer=0
+
+set ncount=1e10
+set omega=0.5
+set DESTi=$DEST/solid_liquid_d2o_05
+if ( -e "$DESTi" ) then
+	rm -r "$DESTi"
+endif
+
+mpirun  -np $use_cores Estia_baseline.out \
+        --dir="$DESTi" --ncount=$ncount --gravitation \
+        omegaa=$omega operationmode=1 theta_resolution=0.04 over_illumination=0.0025 \
+        sample=$sample sample_length=$sample_length sample_height=$sample_height \
+        lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=1 enable_chopper=1 enable_polarizer=0 enable_analyzer=0
+
+set ncount=4e9
+set omega=1.2
+set DESTi=$DEST/solid_liquid_d2o_12
+if ( -e "$DESTi" ) then
+	rm -r "$DESTi"
+endif
+
+mpirun  -np $use_cores Estia_baseline.out \
+        --dir="$DESTi" --ncount=$ncount --gravitation \
+        omegaa=$omega operationmode=1 theta_resolution=0.04 over_illumination=0.0025 \
+        sample=$sample sample_length=$sample_length sample_height=$sample_height \
+        lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=1 enable_chopper=1 enable_polarizer=0 enable_analyzer=0
+
+set ncount=2e9
+set omega=3.1
+set DESTi=$DEST/solid_liquid_d2o_31
+if ( -e "$DESTi" ) then
+	rm -r "$DESTi"
+endif
+
+mpirun  -np $use_cores Estia_baseline.out \
+        --dir="$DESTi" --ncount=$ncount --gravitation \
+        omegaa=$omega operationmode=1 theta_resolution=0.04 over_illumination=0.0025 \
+        sample=$sample sample_length=$sample_length sample_height=$sample_height \
+        lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=1 enable_chopper=1 enable_polarizer=0 enable_analyzer=0
+
+set ncount=1e9
+set omega=7.8
+set DESTi=$DEST/solid_liquid_d2o_78
+if ( -e "$DESTi" ) then
+	rm -r "$DESTi"
+endif
+
+mpirun  -np $use_cores Estia_baseline.out \
+        --dir="$DESTi" --ncount=$ncount --gravitation \
+        omegaa=$omega operationmode=1 theta_resolution=0.04 over_illumination=0.0025 \
+        sample=$sample sample_length=$sample_length sample_height=$sample_height \
+        lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=1 enable_chopper=1 enable_polarizer=0 enable_analyzer=0
+
+################## SMW ########################
+set ncount=1e11
+set sample=7
+set omega=0.2
+set DESTi=$DEST/solid_liquid_smw_02
+if ( -e "$DESTi" ) then
+	rm -r "$DESTi"
+endif
+
+mpirun  -np $use_cores Estia_baseline.out \
+        --dir="$DESTi" --ncount=$ncount --gravitation \
+        omegaa=$omega operationmode=1 theta_resolution=0.04 over_illumination=0.0025 \
+        sample=$sample sample_length=$sample_length sample_height=$sample_height \
+        lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=1 enable_chopper=1 enable_polarizer=0 enable_analyzer=0
+
+set ncount=1e10
+set sample=5
+set omega=0.5
+set DESTi=$DEST/solid_liquid_smw_05
+if ( -e "$DESTi" ) then
+	rm -r "$DESTi"
+endif
+
+mpirun  -np $use_cores Estia_baseline.out \
+        --dir="$DESTi" --ncount=$ncount --gravitation \
+        omegaa=$omega operationmode=1 theta_resolution=0.04 over_illumination=0.0025 \
+        sample=$sample sample_length=$sample_length sample_height=$sample_height \
+        lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=1 enable_chopper=1 enable_polarizer=0 enable_analyzer=0
+
+set ncount=4e9
+set sample=5
+set omega=1.2
+set DESTi=$DEST/solid_liquid_smw_12
+if ( -e "$DESTi" ) then
+	rm -r "$DESTi"
+endif
+
+mpirun  -np $use_cores Estia_baseline.out \
+        --dir="$DESTi" --ncount=$ncount --gravitation \
+        omegaa=$omega operationmode=1 theta_resolution=0.04 over_illumination=0.0025 \
+        sample=$sample sample_length=$sample_length sample_height=$sample_height \
+        lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=1 enable_chopper=1 enable_polarizer=0 enable_analyzer=0
+
+set ncount=2e9
+set sample=5
+set omega=3.1
+set DESTi=$DEST/solid_liquid_smw_31
+if ( -e "$DESTi" ) then
+	rm -r "$DESTi"
+endif
+
+mpirun  -np $use_cores Estia_baseline.out \
+        --dir="$DESTi" --ncount=$ncount --gravitation \
+        omegaa=$omega operationmode=1 theta_resolution=0.04 over_illumination=0.0025 \
+        sample=$sample sample_length=$sample_length sample_height=$sample_height \
+        lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=1 enable_chopper=1 enable_polarizer=0 enable_analyzer=0
+
+set ncount=1e9
+set sample=5
+set omega=7.8
+set DESTi=$DEST/solid_liquid_smw_78
+if ( -e "$DESTi" ) then
+	rm -r "$DESTi"
+endif
+
+mpirun  -np $use_cores Estia_baseline.out \
+        --dir="$DESTi" --ncount=$ncount --gravitation \
+        omegaa=$omega operationmode=1 theta_resolution=0.04 over_illumination=0.0025 \
+        sample=$sample sample_length=$sample_length sample_height=$sample_height \
+        lambda_start=$lambda_start lambda_end=$lambda_end enable_gravity=1 enable_chopper=1 enable_polarizer=0 enable_analyzer=0
+
@@ -0,0 +1,40 @@
+#!/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`"
+
@@ -0,0 +1,40 @@
+#!/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`"
+
@@ -0,0 +1,40 @@
+#!/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`"
+
@@ -0,0 +1,40 @@
+#!/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`"
+
@@ -0,0 +1,40 @@
+#!/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	1415a39ff0	some modifications to add lipid models	2021-10-11 14:22:07 +02:00
glavic_a	0cc9f0ae5d	Add monitor model and update CPC1 entrance and middle geometry	2018-09-15 14:13:56 +02:00
glavic_a	00bd8b18c0	Fix reader plotting for 2D datasets	2018-09-15 14:11:19 +02:00
ll_glavic	7a49a0f22c	Added selene guide position error based on foot missalignment and MCC Slurm job so sweep the parameters.	2018-08-18 11:15:15 +02:00
glavic_a	a58b2d3030	Separate Selene 1/2 and middle focus	2018-07-03 08:22:36 +02:00
glavic_a	6dee3c98c1	Start monitor cleanup by removing all put the essential nD detectors.	2018-07-03 08:21:55 +02:00
glavic_a	8c10d63987	Selene guide m-value per segment	2018-06-26 17:53:46 +02:00