some modifications to add lipid models

2021-10-11 14:22:07 +02:00
5 changed files with 2383 additions and 0 deletions
@@ -330,6 +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
@@ -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
+