Changeset 2927

Timestamp:

09/06/10 16:55:55 (17 months ago)

Author:

farhi

Message:

samples: updated headers, fixed usage of nb_toms = multiplicity of chemical formula within unit cell

Location:

trunk/nlib/samples

Files:

• Isotropic_Sqw.comp (modified) (5 diffs)
• PowderN.comp (modified) (7 diffs)
• Single_crystal.comp (modified) (8 diffs)

trunk/nlib/samples/Isotropic_Sqw.comp

@@ -67 +67 @@
 *   transparently, so that it can be used like a regular sample object.
 *   It supports the OFF and NOFF file format but not COFF (colored faces). 
-*   Such files may be generated from XYZ data using qhull/powercrust, and 
-*   viewed with geomview
+*   Such files may be generated from XYZ data using:
+*     qhull < coordinates.xyz Qx Qv Tv o > geomview.off 
+*   and viewed with geomview or java -jar jroff.jar (see below).
 *   The default size of the object depends of the OFF file data, but its 
 *   bounding box may be resized using xwidth,yheight and zdepth.
@@ -167 +168 @@
 * sigma_inc:[barns] Incoherent Scattering cross-section. Use -1 to unactivate.
 * sigma_abs:[barns] Absorption cross-section at 2200 m/s. Use -1 to unactivate.
-* V_rho:     [AA-3] Density of atoms (nb atoms/unit cell V_0).
+* V_rho:     [AA-3] Density of scattering elements (nb atoms/unit cell V_0).
 * T:            [K] Temperature of sample, detailed balance
 *
@@ -236 +237 @@
 * Cross sections for compounds:       http://www.ncnr.nist.gov/resources/sldcalc.html
 * %L
+* Web Elements                        http://www.webelements.com/
+* %L
+* Fullprof powder refinement:         http://www.ill.eu/sites/fullprof/index.html
+* %L
+* Crystallographica software:         http://www.crystallographica.com/
+* %L
 * Example data file <a href="../data/He4_liq_coh.sqw">He4_liq_coh.sqw</a>
 * %L
 * The <a href="PowderN.html">PowderN</a> component.
 * %L
-* Web Elements                        http://www.webelements.com/
-* %L
 * The test/example instrument <a href="../examples/Test_Isotropic_Sqw.instr">Test_Isotropic_Sqw.instr</a>.
 * %L
-* Geomview and Object File Format (OFF) <http|://www.geomview.org>
+* Geomview and Object File Format (OFF) <http://www.geomview.org>
 * %L
-* Powercrust/qhull <http://www.cs.utexas.edu/users/amenta/powercrust>
+* Java version of Geomview (display only) jroff.jar <http://www.holmes3d.net/graphics/roffview/> 
+* %L
+* Powercrust/qhull <http://qhull.org>
 * %E
 *****************************************************************************/
@@ -754 +761 @@
     "density",
     "weight",
-    "nb_atoms",
+    "nb_atoms","multiplicity",
     NULL);
   if (parsing) {
@@ -781 +788 @@
     if (parsing[22] )     mat_weight  =atof(parsing[22]);
     if (parsing[23] )     mat_at_nb   =atof(parsing[23]);
-    for (i=0; i<=23; i++) if (parsing[i]) free(parsing[i]);
+    if (parsing[24] )     mat_at_nb   =atof(parsing[24]);
+    for (i=0; i<=24; i++) if (parsing[i]) free(parsing[i]);
     free(parsing);
   }
-
+  
+  /* compute the scattering unit density from material weight and density */
+  /* the weight of the scattering element is the chemical formula molecular weight 
+   * times the nb of chemical formulae in the scattering element (nb_atoms) */
   if (!Sqw->rho && mat_density > 0 && mat_weight > 0 && mat_at_nb > 0) {
     /* molar volume [cm^3/mol] = weight [g/mol] / density [g/cm^3] */
     /* atom density per Angs^3 = [mol/cm^3] * N_Avogadro *(1e-8)^3 */
-    Sqw->rho = mat_density/mat_weight/1e24*6.02214199e23/mat_at_nb;
-    if (Sqw->verbose_output > 0) printf("Isotropic_Sqw: %s: Computing atom density V_rho=%g [AA^-3] from file %s\n", Sqw->compname, Sqw->rho, file);
+    Sqw->rho = mat_density/(mat_weight*mat_at_nb)/1e24*6.02214199e23;
+    if (Sqw->verbose_output > 0) printf("Isotropic_Sqw: %s: Computing scattering unit density V_rho=%g [AA^-3] from file %s\n", Sqw->compname, Sqw->rho, file);
+  }
+  
+  /* the scattering unit cross sections are the chemical formula onces 
+   * times the nb of chemical formulae in the scattering element */
+  if (mat_at_nb > 0) { 
+    Sqw->s_abs *= mat_at_nb; Sqw->s_inc *= mat_at_nb; Sqw->s_coh *= mat_at_nb; 
   }
 

trunk/nlib/samples/PowderN.comp

@@ -49 +49 @@
 *   transparently, so that it can be used like a regular sample object.
 *   It supports the OFF and NOFF file format but not COFF (colored faces). 
-*   Such files may be generated from XYZ data using qhull/powercrust, and 
-*   viewed with geomview
+*   Such files may be generated from XYZ data using:
+*     qhull < coordinates.xyz Qx Qv Tv o > geomview.off 
+*   and viewed with geomview or java -jar jroff.jar (see below).
 *   The default size of the object depends of the OFF file data, but its 
 *   bounding box may be resized using xwidth,yheight and zdepth.
@@ -158 +159 @@
 * weight:   Atomic/molecular weight of material [g/mol]
 * density:  Density of material. rho=density/weight/1e24*N_A. [g/cm^3]
-* nb_atoms: Number of atoms per unit cell [1]
+* nb_atoms: Number of sub-unit per unit cell, that is ratio of sigma for chemical formula to sigma per unit cell [1]
 *
 * %L
@@ -171 +172 @@
 * Cross sections for compounds:       http://www.ncnr.nist.gov/resources/sldcalc.html
 * %L
-* Fullprof powder refinement:         http://www-llb.cea.fr/fullweb/fp2k/fp2k.htm
-* %L
 * Web Elements                        http://www.webelements.com/
 * %L
-* Geomview and Object File Format (OFF) <http|://www.geomview.org>
-* %L
-* Powercrust/qhull <http://www.cs.utexas.edu/users/amenta/powercrust>
+* Fullprof powder refinement:         http://www.ill.eu/sites/fullprof/index.html
+* %L
+* Crystallographica software:         http://www.crystallographica.com/
+* %L
+* Geomview and Object File Format (OFF) <http://www.geomview.org>
+* %L
+* Java version of Geomview (display only) jroff.jar <http://www.holmes3d.net/graphics/roffview/> 
+* %L
+* Powercrust/qhull <http://qhull.org>
 *
 * %E
@@ -276 +281 @@
       "density",
       "weight",
-      "nb_atoms",
+      "nb_atoms","multiplicity",
       NULL);
 
@@ -303 +308 @@
       if (parsing[21] && !info->at_weight)     info->at_weight    =atof(parsing[21]);
       if (parsing[22] && info->at_nb <= 1)  info->at_nb    =atof(parsing[22]);
-      for (i=0; i<=22; i++) if (parsing[i]) free(parsing[i]);
+      if (parsing[23] && info->at_nb <= 1)  info->at_nb    =atof(parsing[23]);
+      for (i=0; i<=23; i++) if (parsing[i]) free(parsing[i]);
       free(parsing);
     }
@@ -535 +541 @@
   }
 
+  /* compute the scattering unit density from material weight and density */
+  /* the weight of the scattering element is the chemical formula molecular weight 
+   * times the nb of chemical formulae in the scattering element (nb_atoms) */
   if (!line_info.V_0 && line_info.at_nb > 0
     && line_info.at_weight > 0 && line_info.rho > 0) {
@@ -541 +550 @@
     line_info.V_0 = line_info.at_nb
       /(line_info.rho/line_info.at_weight/1e24*6.02214199e23);
+  }
+  
+  /* the scattering unit cross sections are the chemical formula onces 
+   * times the nb of chemical formulae in the scattering element */
+  if (line_info.at_nb > 0) { 
+    line_info.sigma_a *= line_info.at_nb; line_info.sigma_i *= line_info.at_nb;
   }
 

trunk/nlib/samples/Single_crystal.comp

@@ -36 +36 @@
 *   transparently, so that it can be used like a regular sample object.
 *   It supports the OFF and NOFF file format but not COFF (colored faces). 
-*   Such files may be generated from XYZ data using qhull/powercrust, and 
-*   viewed with geomview
+*   Such files may be generated from XYZ data using:
+*     qhull < coordinates.xyz Qx Qv Tv o > geomview.off 
+*   and viewed with geomview or java -jar jroff.jar (see below).
 *   The default size of the object depends of the OFF file data, but its 
 *   bounding box may be resized using xwidth,yheight and zdepth.
@@ -86 +87 @@
 *           ax=3.0282, by=3.0282, cz=3.0282/2)
 *
-* %BUGS:
-* The component is known not to work properly as a Bragg monochromator. The 
-* reason is likely to relate to the internal definition of reciprocal space 
-* orientation. Investigation undergoing. 
-*
 * Also, always use a non-zero value of delta_d_d.
 *
@@ -105 +101 @@
 *               The OFF file may be generated from XYZ coordinates using qhull/powercrust [str]
 * delta_d_d: Lattice spacing variance, gaussian RMS [1]
-* mosaic:    Crystal mosaic (isotropic), gaussian RMS. Puts the crystal in the isotropic mosaic model state, thus disregarding other mosaicity parameters. [arc minutes]
+* mosaic:    Crystal mosaic (isotropic), gaussian RMS. Puts the crystal in the 
+*            isotropic mosaic model state, thus disregarding other mosaicity parameters. [arc minutes]
 * mosaic_a:  Horizontal (rotation around lattice vector a) mosaic (anisotropic), gaussian RMS. 
-* Put the crystal in the anisotropic crystal vector state. I.e. model mosaicity
-* through rotation around the crystal lattice vectors. Has precedence over
-* in-plane mosaic model. [arc minutes]
-* mosaic_b:  Vertical (rotation around lattice vector b) mosaic (anisotropic), gaussian RMS. [arc minutes]
-* mosaic_c:  Out-of-plane (Rotation around lattice vector c) mosaic (anisotropic), gaussian RMS [arc minutes]
-* mosaic_AB: In Plane mosaic rotation and plane vectors (anisotropic), mosaic_A, mosaic_B, A_h,A_k,A_l, B_h,B_k,B_l. Puts the crystal in the in-plane mosaic state. Vectors A and B define plane in which the crystal roation is defined, and mosaic_A, mosaic_B, denotes the resp. mosaicities (gaussian RMS) with respect to the the two reflections chosen by A and B (Miller indices). [arc_minutes, arc_minutes,1, 1, 1, 1, 1, 1]
+*            Put the crystal in the anisotropic crystal vector state. I.e. model mosaicity
+*            through rotation around the crystal lattice vectors. Has precedence over
+*            in-plane mosaic model. [arc minutes]
+* mosaic_b:  Vertical (rotation around lattice vector b) mosaic (anisotropic), 
+*            gaussian RMS. [arc minutes]
+* mosaic_c:  Out-of-plane (Rotation around lattice vector c) mosaic (anisotropic), 
+*            gaussian RMS [arc minutes]
+* mosaic_AB: In Plane mosaic rotation and plane vectors (anisotropic), 
+*            mosaic_A, mosaic_B, A_h,A_k,A_l, B_h,B_k,B_l. Puts the crystal in 
+*            the in-plane mosaic state. Vectors A and B define plane in which 
+*            the crystal roation is defined, and mosaic_A, mosaic_B, denotes the 
+*            resp. mosaicities (gaussian RMS) with respect to the the two 
+*            reflections chosen by A and B (Miller indices). [arc_minutes, arc_minutes,1, 1, 1, 1, 1, 1]
 * 
 * recip_cell: Choice of direct/reciprocal (0/1) unit cell definition [1]
@@ -152 +156 @@
 * Cross sections for compounds:       http://www.ncnr.nist.gov/resources/sldcalc.html
 * %L
-* Geomview and Object File Format (OFF) <http|://www.geomview.org>
+* Fullprof powder refinement:         http://www.ill.eu/sites/fullprof/index.html
 * %L
-* Powercrust/qhull <http://www.cs.utexas.edu/users/amenta/powercrust>
+* Crystallographica software:         http://www.crystallographica.com/
+* %L
+* Geomview and Object File Format (OFF) <http://www.geomview.org>
+* %L
+* Java version of Geomview (display only) jroff.jar <http://www.holmes3d.net/graphics/roffview/> 
+* %L
+* Powercrust/qhull <http://qhull.org>
 *
 * %E
@@ -333 +343 @@
         "lattice_bb",
         "lattice_cc",
-        "nb_atoms",
+        "nb_atoms","multiplicity",
         NULL);
 
@@ -354 +364 @@
         if (parsing[15] && !info->m_cc)   info->m_cc=atof(parsing[15]);
         if (parsing[16])   nb_atoms=atof(parsing[16]);
-        for (i=0; i<=16; i++) if (parsing[i]) free(parsing[i]);
+        if (parsing[17])   nb_atoms=atof(parsing[17]);
+        for (i=0; i<=17; i++) if (parsing[i]) free(parsing[i]);
         free(parsing);
       }
     }
+    
+    if (nb_atoms > 1) { info->sigma_a *= nb_atoms; info->sigma_i *= nb_atoms; }
 
     /* special cases for the structure definition */
@@ -685 +698 @@
     }
     return(info->count = i);
-  }
+  } /* read_hkl_data */
 #endif /* !SINGLE_CRYSTAL_DECL */
 
@@ -719 +732 @@
   hkl_info.sigma_a = sigma_abs;
   hkl_info.sigma_i = sigma_inc;
-  hkl_info.recip = recip_cell;
+  hkl_info.recip   = recip_cell;
 
   /* default format h,k,l,F,F2  */