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--- p [2009/08/27 11:17] – clare
+++ p [2022/11/03 15:08] (current) – external edit 127.0.0.1
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+====== p ======
+**[//peak_typ//****//e//** **$type]**
+Sets the peak type for a phase. The following //peak_type//’s are available:
+| **Peak type** | **$type** | **Parameters** |
+| Fundamental Parameters | fp |   |
+| Pseudo-Voigt   | pv | [//pv_lor E  pv_fwhm E//] //pv_lor// is the Lorentzian fraction of the peak profile(s). //pv_fwhm// is the FWHM of the peak profile(s). |
+| Split-PearsonVII   | spvii | [//h1// E  //h2// E  //m1// E  //m2// E] The sum of //h1// and //h2// gives the FWHM of the composite peak. //m1, m//2 are the PearsonVII exponents of the left and right composite peak, respectively. |
+| Split-PseudoVoigt   | spv | [//spv_h1// E  //spv_h2// E  //spv_l1// E  //spv_l2// E] The sum of //spv_h1// and //spv_h2// gives the full width at half maximum of the composite peak. //spv_l1, spv_l2//: the Lorentzian fractions of the left and right composite peak, respectively. |
+**[//peak_buffer_step// E [//report_on//]]**
+As the shapes of phase peaks do not change significantly over a short 2q range, a new peak shape is calculated only if the position of the last peak shape calculated is more than the distance defined by //peak_buffer_step//. Various stretching and interpolation procedures are used in order to calculate in-between peaks. See also section 6.4.
+The reserved parameter names of H, K, L, M or parameter names associated with the keywords //sh_Cij_prm// and //hkl_angle// when used in the peak convolution equations result in irregular peak shapes over short 2q ranges and thus a separate peak shape is calculated for each peak.
+When defined //report_on// causes the display of the number of peaks in the peaks buffer.
+//peak_buffer_step// is set to 500*//Peak_Calculation_Step// by default.
+**[//penalty// !E]...**
+Defines a penalty function that can be a function of other parameters. Penalties are useful for stabilizing refinements as in for example their use in bond-length restraints.
+Example HOCK.INP uses penalties to minimize on the Hock and Schittkowski problem number 65 function.
+prm x1 1 min -4.5 max 4.5  val_on_continue = Rand(-4.5, 4.5); del .01
+prm x2 1 min -4.5 max 4.5  val_on_continue = Rand(-4.5, 4.5); del .01
+prm x3 1 min -5.0 max 5.0  val_on_continue = Rand(-5.0, 5.0); del .01
+' Hock and Schittkowski problem number 65 function
+penalty = (x1-x2)^2 + (1/9) (x1 + x2 - 10)^2 + (x3 - 5)^2; : 0
+prm contraint_1 = x1^2 + x2^2 + x3^2;
+penalty = If(contraint_1 < 48, 0, (contraint_1-48)^2); : 0
+The next example applies a User defined penalty function to lattice and crystallite size parameters, which are expected to be 5.41011 Å and 200 nm respectively:
+str...
+Cubic(lp_ceo2 5.41011)
+penalty = (lp_ceo2-5.41011)^2;
+CS_L(cs_l, 200)
+penalty =(cs_l-200)^2;
+Minimizing on penalty functions in the presence of observed data is possible with the use of the //only_penalties// keyword.
+**[//penalties_weighting_K1// !E]**
+Defines the weighting K<sub>1</sub> given to penalty functions as defined in Eq. (5‑2). //penalties_weighting_K1// is set to 1 by default.
+**[//percent_zeros_before_sparse_A// #]**
+Defines the percentage of the A matrix than can be zero before sparse matrix methods are invoked. The default value is 60%.
+**[//phase_MAC// !E]**
+Calculates the mass absorption coefficient in cm<sup>2</sup>/g for the current phase. See description for //[[#k038|mixture_MAC]]//.
+**[//phase_out// $file [//append//] ]...**
+Used for writing phase dependent details to file. See the keyword //out// for a description of //[[#k045|out_record]]//. The Create_hklm_d_Th2_Ip_file uses //phase_out//.
+**[//pk_xo// E]**
+Provides a mechanism for transforming peak position to an x-axis position. For example, the peak position for neutron time-of-flight data is typically calculated in time-of-flight space, tof, or:
+tof = t0 + t1 d<sub>hkl</sub> + t2 d<sub>hkl</sub><sup>2</sup>
+where t0 and t1 and t2 are diffractometer constants. //pk_xo// can be used to refine TOF data as shown in examples TOF_Balzar_sh1.inp and TOF_Balzar_br1.inp.
+**[//phase_name// $phase_name]**
+The name given to a phase; used for reporting purposes.
+**[//phase_penalties//** **$sites N]...****[//hkl_Re_Im// #h #k #l #Re #Im]...**
+**[//accumulate_phases_and_save_to_file// $file]**
+**[//accumulate_phases_when// !E]**
+//phase_penalties// for a single hkl is defined as follows:
+<sub>{{techref_files:image162.gif?444x50}}</sub>where <sub>{{techref_files:image164.gif?21x29}}</sub>= assigned phase, <sub>{{techref_files:image166.gif?20x25}}</sub>= calculated phase, I<sub>c</sub> = calculated intensity and //d// is the reflection d-spacing.  The name N returns the sum of the //phase_penalties// and it can be used in equations and in particular //penalty// equations. <sub>{{techref_files:image166.gif?20x25}}</sub> is calculated from sites identified in [[#k142|$sites]].
+#h, #k, #l are user defined hkls; they are used for formulating the phase penalties. #Re and #Im are the real and imaginary parts of <sub>{{techref_files:image164.gif?21x29}}</sub>. An example use of phase penalties (see examples AE14-12.INP and AE5-AUTO.inp) is as follows:
+penalty = pp1;
+phase_penalties * pp1
+load hkl_Re_Im
+{
+   1   2   1  0
+   0  -2   1  0
+  -2  -1   1  0
+}
+hkls chosen for phase penalties should comprise those that are of high intensity, large d-spacing and isolated from other peaks to avoid peak overlap. Origin defining hkls are typically chosen.
+//accumulate_phases_and_save_to_file// saves the average phases collected to $file//.// Phases are collected when //accumulate_phases_when// evaluates to true; //accumulate_phases_when// defaults to true. Here’s an example use:
+temperature 1
+temperature 1
+temperature 1
+temperature 1
+temperature 10
+...move_to_the_next_temperature_regardless_of_the_change_in_rwp
+accumulate_phases_and_save_to_file SOME_FILE.TXT
+accumulate_phases_when = T == 10;
+Here phases with the best Rwp since the last accumulation are accumulated when the current temperature is 10.
+** [//process_times//]**
+Displays process times on termination of refinement.