some modifications to add lipid models

2021-10-11 14:22:07 +02:00
9 changed files with 2385 additions and 373 deletions
@@ -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)
-
@@ -52,9 +52,8 @@ DEFINE INSTRUMENT ESS_reflectometer_Estia
 (double omegaa = 1.2,  int sample = 0,  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,
+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 selene1_foot1y =0.0, double selene1_foot2y = 0.0
 )
@@ -331,6 +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
@@ -63,10 +63,6 @@ REMOVABLE COMPONENT source = Moderator(radius = 0.001, focus_xw = selene_entry+0
    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 *
@@ -82,78 +78,6 @@ COMPONENT polarizer1 = Polariser(nIncRefr=1, d_substrate = 5e-4, reflect_d=0, re
        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)
@@ -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 +1,251 @@
+#!/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=$lambda_end enable_gravity=1 enable_chopper=1 enable_polarizer=0 enable_analyzer=0
+
@@ -1,177 +0,0 @@
-#!/bin/bash
-
-DEST=../results
-ncount=2e10
-use_cores=$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
-
@@ -1,24 +0,0 @@
-#!/bin/tcsh
-#SBATCH -J wfm_McEstia
-#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`"
-
-
-module load mcstas
-
-bash compile_if_needed.sh
-bash run_wfm.sh