Merge pull request #1972 from farhi/mcxtrace-fluo-sx-1

Mcxtrace fluo sx 1

Author: willend

mcxtrace-comps/data/C-diamond.lau

@@ -1,4 +1,4 @@
-# TITLE *Diamond-C-[FD3-MS] Fayos, J.[1999]
+# TITLE C [FD3-MS] Diamond - Fayos, J.[1999]
 # CELL 3.567000 3.567000 3.567000 90.000000 90.000000 90.000000
 # SPCGRP F D 3 M   CUBIC STRUCTURE
 # ATOM C 1 0.000000 0.000000 0.000000

mcxtrace-comps/data/C_diamond.laz

@@ -1,4 +1,4 @@
-# TITLE *Diamond-C-[FD3-MS] Fayos, J.[1999]
+# TITLE C [FD3-MS] Diamond - Fayos, J.[1999]
 # CELL 3.567000 3.567000 3.567000 90.000000 90.000000 90.000000
 # SPCGRP F D 3 M   CUBIC STRUCTURE
 # ATOM C 1 0.000000 0.000000 0.000000

mcxtrace-comps/data/Fe.lau

@@ -1,4 +1,4 @@
-# TITLE *Iron-Fe-[IM3-M] Swanson, H.E.;Tatge, E.[1954] [Iron alpha phase]
+# TITLE Fe [IM3-M] Iron - Swanson, H.E.;Tatge, E.[1954] [Iron alpha phase]
 # CELL 2.886000 2.886000 2.886000 90.000000 90.000000 90.000000
 # SPCGRP I M 3 M   CUBIC STRUCTURE
 # ATOM FE 1 0.000000 0.000000 0.000000

mcxtrace-comps/data/Fe_bcc229_lt13deg.dat

@@ -1,4 +1,4 @@
-# TITLE *Iron-Fe-[IM3-M] Swanson, H.E.;Tatge, E.[1954] [Iron alpha phase]
+# TITLE Fe [IM3-M] Iron - Swanson, H.E.;Tatge, E.[1954] [Iron alpha phase]
 # CELL 2.886000 2.886000 2.886000 90.000000 90.000000 90.000000
 # SPCGRP I M 3 M   CUBIC STRUCTURE
 # ATOM FE 1 0.000000 0.000000 0.000000

mcxtrace-comps/data/adrenaline.lau

@@ -1,4 +1,4 @@
-# TITLE *Adrenaline C9H13NO3 (epinephrine, (R)-4-(1-hydroxy-2-(méthylamino)éthyl)benzène-1,2-dio)
+# TITLE C9H13NO3 Adrenaline (epinephrine, (R)-4-(1-hydroxy-2-(méthylamino)éthyl)benzène-1,2-dio)
 # L-Adrenaline: P 21 (4) monoclinic
 # a=7.873, b=6.790, c=8.638; aa=cc=90, bb=98.02;
 # Reference: A.M. Anderson; Acta Chem.Scand.Ser.B, 29, (1975), 239

mcxtrace-comps/examples/Tests_samples/Test_FluoPowder/Test_FluoPowder.instr

@@ -45,6 +45,7 @@ USERVARS %{
 %}
 
 INITIALIZE %{
+  MPI_MASTER(
   switch (index) {
     case 1:
       printf("%s: Using PowderN (pure diffraction)\n", NAME_INSTRUMENT); break;
@@ -58,7 +59,7 @@ INITIALIZE %{
       printf("%s: Using Fluorescence+PowderN in a GROUP (fluorescence+diffraction)\n", NAME_INSTRUMENT); break;
     default:
       exit(printf("%s: Unknown sample index %i. Use index=1-4.", NAME_INSTRUMENT, index));
-  }
+  });
 %}
 
 TRACE
@@ -95,7 +96,8 @@ EXTEND %{
 %}
 
 COMPONENT FL_pow = FluoPowder(
-    radius=0.5e-6, material=material)
+    radius=0.5e-6, material=material,
+    escape_ratio=0.01, pileup_ratio=0.01)
 WHEN (index == 3)
 AT (0, 0, 0) RELATIVE sample_cradle
 EXTEND %{
@@ -125,7 +127,7 @@ WHEN (index == 5)
 AT (0, 0, 0) RELATIVE sample_cradle
 GROUP FluPow
 EXTEND %{
-  if (SCATTERED) scatt_type=3;
+  if (SCATTERED) scatt_type=DIFFRACTION;
   else ABSORB;
 %}
 
@@ -136,11 +138,11 @@ COMPONENT Sph_mon = PSD_monitor_4PI(nx=512,ny=512,
   AT (0, 0, 0) RELATIVE PREVIOUS
 
 COMPONENT Sph_mon_pow = COPY(Sph_mon)(filename="Sphere_pow")
-  WHEN (scatt_type == 3)
+  WHEN (scatt_type == DIFFRACTION)
   AT (0, 0, 0) RELATIVE PREVIOUS
 
   COMPONENT Sph_mon_flu = COPY(Sph_mon)(filename="Sphere_fluo")
-  WHEN (scatt_type != 3)
+  WHEN (scatt_type != DIFFRACTION)
   AT (0, 0, 0) RELATIVE PREVIOUS
 
 COMPONENT E_mon = Monitor_nD(
@@ -149,11 +151,16 @@ COMPONENT E_mon = Monitor_nD(
   AT(0,0,0) RELATIVE PREVIOUS
 
 COMPONENT E_mon_pow = COPY(E_mon)(filename="Energy_pow")
-  WHEN (scatt_type == 3)
+  WHEN (scatt_type == DIFFRACTION)
   AT (0, 0, 0) RELATIVE PREVIOUS
 
 COMPONENT E_mon_flu = COPY(E_mon)(filename="Energy_flu")
-  WHEN (scatt_type != 3)
+  WHEN (scatt_type != DIFFRACTION)
   AT (0, 0, 0) RELATIVE PREVIOUS
 
+// ideal "banana" detector
+COMPONENT det_angle = Monitor_nD(options="abs theta limits=[5 90]",
+                                 radius=0.6, yheight=1e-2, bins=10000)
+AT (0,0,0) RELATIVE PREVIOUS
+
 END

mcxtrace-comps/examples/Tests_samples/Test_Fluorescence/Test_Fluorescence.instr

@@ -59,14 +59,15 @@ AT(0,0,3) RELATIVE Origin
 
 COMPONENT sample=Fluorescence(material=material,
   xwidth=0.001,yheight=0.001,zdepth=0.0001, p_interact=0.99,
-  target_index=1, focus_xw=0.0005, focus_yh=0.0005)
+  target_index=1, focus_xw=0.0005, focus_yh=0.0005, 
+  escape_ratio=0.01, pileup_ratio=0.01)
 AT (0,0,0) RELATIVE sample_mount_point
 EXTEND %{
   if (!SCATTERED) ABSORB;
   Stype=type;
 %}
 
-COMPONENT emon = E_monitor(restore_xray=1,nE=2001,Emin=0, Emax=1.2*E0, 
+COMPONENT emon = E_monitor(restore_xray=1,nE=2001,Emin=0, Emax=1.5*E0, 
   filename="emon.dat",xwidth=0.007, yheight=0.007)
 AT(0,0,0.1) RELATIVE PREVIOUS
 
@@ -85,5 +86,13 @@ COMPONENT emon_Rayleigh = COPY(emon)(filename="Rayleigh.dat")
 WHEN (Stype == RAYLEIGH)
 AT(0,0,0.1) RELATIVE PREVIOUS
 
+COMPONENT emon_Escape = COPY(emon)(filename="Si_Escape.dat")
+WHEN (Stype == FLUORESCENCE_ESCAPE)
+AT(0,0,0.1) RELATIVE PREVIOUS
+
+COMPONENT emon_PileUp = COPY(emon)(filename="Si_PileUp.dat")
+WHEN (Stype == FLUORESCENCE_PILEUP)
+AT(0,0,0.1) RELATIVE PREVIOUS
+
 
 END

mcxtrace-comps/examples/Tests_samples/Test_PowderN/Test_PowderN.instr

@@ -15,33 +15,28 @@
 * %Description
 * Simply a model source illuminating a powder sample.
 * The default sample itself is an LaB6-powder. 
-* Alternatively, the Single_crystal component can also be tested in powder mode.
+* Alternatively, the Single_crystal (powder mode) and FluoPowder components can also be tested.
 *
-* %Example: Test_PowderN.instr reflections="Fe_bcc229_lt13deg.dat" -n1e7 TTH=13.4 d_phi=45 frac_i=0 Detector: Sph_mon_I=2.68295e-14
-* %Example: Test_PowderN.instr E0=15 Detector: Sph_mon_I=6.24257e-12
-* %Example: Test_PowderN.instr E0=15 d_phi=10 Detector: Sph_mon_I=6.59782e-13
-* %Example: Test_PowderN.instr E0=15 directbeam=1 SPLITS=2 Detector: Sph_mon_I=7.94366e-10
-* %Example: Test_PowderN.instr E0=15 directbeam=1 SPLITS=5 Detector: Sph_mon_I=7.94366e-10
-* %Example: Test_PowderN.instr E0=15 directbeam=1 SPLITS=10 Detector: Sph_mon_I=7.94366e-10
-* %Example: Test_PowderN.instr E0=15 directbeam=1 SPLITS=20 Detector: Sph_mon_I=7.94366e-10
+* %Example: index=1 Detector: Sph_mon_I=1.26755e-11
+* %Example: index=2 Detector: Sph_mon_I=4.44793e-13
+* %Example: index=3 Detector: Sph_mon_I=5.23579e-11
 *
 * %Parameters
 * E0:          [keV]  Source energy (width 1 keV)
 * L1:          [m]    Source-sample distance
 * directbeam:  [1]    Suppress direct beam (0) or not (1)
-* reflections: [str]  List of powder reflections, LAU/CIF format.
+* reflections: [str]  List of powder reflections, LAU/LAZ/CIF format.
 * SPLITS:      [1]    Number of SPLIT's before sample
 * frac_c:      [1]    Fraction of stats assigned to coherent scattering
 * frac_i:      [1]    Fraction of stats assigned to incoherent scattering
 * frac_t:      [1]    Fraction of stats assigned to unscattered, "direct beam"
-* TTH:         [deg]  Rotation of secondary detector arm.
 * d_phi:       [deg]  Angle corresponding to the vertical angular range to focus to, e.g. detector height. 0 for no focusing.
-* index:       [1]    Index of the sample component to use. 1=PowderN, 2=Single_crystal
+* index:       [1]    Index of the sample component to use. 1=PowderN, 2=Single_crystal, 3=FluoPowder
 *
 * %End
 *******************************************************************************/
-DEFINE INSTRUMENT Test_PowderN(E0=15, L1=10, int directbeam=0, string reflections="LaB6_660b_AVID2.hkl", 
-  int SPLITS=1, frac_c=0.8, frac_i=0.1, frac_t=0.1, d_phi=0, TTH=0, int index=1)
+DEFINE INSTRUMENT Test_PowderN(E0=15, L1=10, int directbeam=0, string reflections="LaB6.cif",
+  int SPLITS=1, frac_c=0.8, frac_i=0.1, frac_t=0.1, d_phi=0, int index=1)
 
 TRACE
 
@@ -55,11 +50,13 @@ COMPONENT src = Source_flat(
 
 SPLIT SPLITS COMPONENT sample_cradle = Arm()
   AT (0, 0, L1) RELATIVE PREVIOUS
+  
+// samples -------------------------------------------------------------------
 
 COMPONENT Pow = PowderN(
     radius=0.5e-4, yheight=1e-3, reflections=reflections,format={ 4,5,7,0,0,0,0,0 },
     p_inc=frac_i, p_transmit=frac_t, p_interact=frac_c,
-    d_phi=d_phi, pack = 0.5, Vc = 123)
+    d_phi=d_phi, pack = 0.5)
 WHEN (index == 1)
 AT (0, 0, 0) RELATIVE sample_cradle
 EXTEND %{
@@ -72,7 +69,7 @@ EXTEND %{
 
 COMPONENT SX = Single_crystal(
     radius=0.5e-4, yheight=1e-3, reflections=reflections,powder=1,
-    p_transmit=frac_t, mosaic=5, sigma_inc=-1)
+    p_transmit=frac_t, mosaic=1, sigma_inc=-1)
 WHEN (index == 2)
 AT (0, 0, 0) RELATIVE sample_cradle
 EXTEND %{
@@ -83,19 +80,24 @@ EXTEND %{
   }
 %}
 
+COMPONENT FlPow = FluoPowder(
+  radius=0.5e-4, yheight=1e-3, material=reflections, powder_d_phi=d_phi,
+  packing_factor = 0.5, p_interact=frac_c)
+WHEN (index == 3)
+AT (0, 0, 0) RELATIVE sample_cradle
+EXTEND %{
+  if(INSTRUMENT_GETPAR(directbeam) == 0) {
+    if (!SCATTERED) {
+      ABSORB;
+    }
+  }
+  %}
+
+// detectors -------------------------------------------------------------------
 
 COMPONENT Sph_mon = PSD_monitor_4PI(nx=200,ny=200, radius=1, restore_xray=1, filename="Sphere")
   AT (0, 0, 0) RELATIVE PREVIOUS
 
-COMPONENT ttharm= Arm()
-AT(0,0,0) RELATIVE Pow
-ROTATED (0,TTH,0) RELATIVE Pow
-
-COMPONENT detector2 = PSD_monitor(
-    nx=200, ny=200, xwidth=2e-3, yheight=1e-2, filename="psd2",restore_xray=1
-)
-AT(0,0,0.1) RELATIVE ttharm
-
 // ideal "banana" detector
 COMPONENT det_angle = Monitor_nD(options="abs theta limits=[5 90]",
   radius=0.6, yheight=1e-2, bins=10000)

mcxtrace-comps/examples/Tests_samples/Test_SX/Test_SX.instr

@@ -15,47 +15,56 @@
 * Simply a model source illuminating a SX sample.
 * The sample itself is a Mo bulk crystal.
 *
-* %Example: TTH=13.4 Detector: psd4pi_I=7.95747e-10
+* %Example: index=1 Detector: psd4pi_I=1.18843e-13
+* %Example: index=2 Detector: psd4pi_I=4.80386e-13
 *
 * %Parameters
-* TTH: [deg.] Two theta rotation. Only places the last detector.
+* reflections: [str] List of powder reflections, LAU/CIF format.
+* index:       [1]   Index of the sample component to use. 1=Single_crystal, 2=FluoCrystal
 *
 * %End
 *******************************************************************************/
 
-DEFINE INSTRUMENT Test_SX(TTH=13.4)
+DEFINE INSTRUMENT Test_SX(string reflections="Mo.lau", index=1)
+
+USERVARS %{
+  int Stype;
+%}
 
 TRACE
 COMPONENT src = Source_flat(
     yheight = 1e-3, xwidth = 1e-3, dist = 10, focus_xw = 1e-3,
     focus_yh = 1e-3, E0 = 7, dE = 6.9)
 AT (0, 0, 0) ABSOLUTE
 
-COMPONENT psd0 = PSD_monitor(
-    nx = 100, ny = 100, filename = "psd0", xwidth = 2e-3, yheight = 2e-3)
-AT (0, 0, 1e-9) RELATIVE src
-
-COMPONENT sample = Single_crystal(reflections="Mo.lau", material_datafile="NULL", 
-    radius = .5e-4, yheight = 1e-3,mosaic=1e-4)
+COMPONENT sample_pos=Arm()
 AT (0, 0, 10) RELATIVE PREVIOUS
-ROTATED (0,0,0) RELATIVE PREVIOUS
-/*EXTEND %{*/
-/*  if(!SCATTERED) ABSORB;*/
-/*%}*/
+
+COMPONENT sample = Single_crystal(reflections=reflections, material_datafile="NULL", 
+    radius = .5e-4, yheight = 1e-3, mosaic=1)
+    WHEN(index==1)
+AT (0, 0, 0) RELATIVE sample_pos
+EXTEND %{
+  if(!SCATTERED) ABSORB;
+  else Stype=DIFFRACTION;
+%}
+
+COMPONENT sampleF = FluoCrystal(material=reflections,
+    radius = .5e-4, yheight = 1e-3, sx_mosaic=5)
+    WHEN(index==2)
+AT (0, 0, 0) RELATIVE sample_pos
+EXTEND %{
+  if(!SCATTERED) ABSORB;
+  else Stype=type;
+%}
 
 COMPONENT psd4pi = PSD_monitor_4PI(
     nx = 180, ny = 180, filename = "psd4pi", radius = 0.1, restore_xray = 1)
 AT (0, 0, 0) RELATIVE sample
 
-/*COMPONENT detector = PSD_monitor(*/
-/*    nx=200, ny=200, xwidth=0.1, yheight=0.1, filename="psd1",restore_xray=1)*/
-/*AT(0,0,0.1) RELATIVE sample*/
-/**/
-/*COMPONENT ttharm= Arm()*/
-/*AT(0,0,0) RELATIVE sample*/
-/*ROTATED (TTH,TTH,0) RELATIVE sample*/
-/**/
-/*COMPONENT detector2 = PSD_monitor(*/
-/*    nx=200, ny=200, xwidth=2e-3, yheight=1e-2, filename="psd2",restore_xray=1)*/
-/*AT(0,0,0.1) RELATIVE ttharm*/
+COMPONENT psd_Diff = PSD_monitor_4PI(
+    nx = 180, ny = 180, filename = "psd4pi_diff", radius = 0.1, restore_xray = 1)
+WHEN (Stype == DIFFRACTION)
+AT (0, 0, 0) RELATIVE sample
+
 END