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out_mem [topas wiki]

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out_mem [2023/09/12 23:06] – [The macros] iangieout_mem [2023/09/12 23:14] (current) – external edit 127.0.0.1
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 +====== Macro to output .mem file and .prf file for MEM analysis in Dysnomia ======
  
 +The macros in this page output .mem file and .prf file for [[https://jp-minerals.org/dysnomia/en/|Dysnomia]] to calculate electron density in unit cell based on Maximum Entropy Method (MEM) analysis.
 +The format of .mem and .prf files are based on the Dysnomia example files.
 +
 +This macro calls other macros "[[atomic_number|Atomic_Number]]" and "[[space_group_number|sg_num]]".
 +
 +This macro has been tested working in TOPAS v6.
 +
 +==== The macros ====
 +=== Out_MEM ===
 +This macro exports the real part and imaginary part of observed structure factors, and their errors for each reflection.
 +This macro also calls "Out_PRF" macro to export a Preference file .prf for Dysnomia to perform MEM analysis.
 +The macro parameter "sgs", Space Group Symbel needs be in lower case without any gap nor underscore, but needs be quoted by double quotes, e.g. "r-3c"
 +
 +<code topas>
 +macro Out_MEM(phasename, sgs) {  'space group symbel 'sgs' needs be lower case without gap nor underscore, but with double quotes, e.g. "r-3c"
 +  #if (Run_Number == 0)
 + out phasename##_dys.mem append 
 + Out_String("# Title (up to 70 character) \n")
 + Out(Get(phase_name), "%s ( Powder X-ray Data )\n")
 + Out_String("#        a         b         c     alpha      beta     gamma\n")
 + Out(Get(a), "%10.5f")
 + Out(Get(b), "%10.5f")
 + Out(Get(c), "%10.5f")
 + Out(Get(al), "%10.5f")
 + Out(Get(be), "%10.5f")
 + Out(Get(ga), "%10.5f\n")
 + Out_String("# P.O. correction\n")
 + Out_String("# When TORAYA & MARUMO type function is used add P option.\n")
 + Out_String("# IPTYP : -1 = No Correction   0 = Plate Like   1 = Needle Like\n")
 + Out_String("#          POP1           POP2  IPTYP  JPH  JPK  JPL\n")
 + Out_String("      0.0000000      0.0000000     -1    0    0    0     P\n")
 + Out_String("# SPG  ORG   NX   NY   NZ\n")
 + Out(sg_num(sgs), "  %.0f    1   ")
 + Out(6(Round(Get(a)/0.07/6)+1), "%.0f  ")
 + Out(6(Round(Get(b)/0.07/6)+1), "%.0f  ")
 + Out(6(Round(Get(c)/0.07/6)+1), "%.0f\n")
 + Out_String("#  Total charge         lambda\n")
 + Out(Total_e_in_Cell, "%14.7f")
 + Out_String("      0.0010000\n")
 + Out_String("# NREF1 need to count manually\n")
 + Out_String("   64\n")
 + Out_String("#   h    k    l          Fo(R)          Fo(I)       sigma(F)")
 + phase_out phasename##_dys.mem append 
 + load out_record out_fmt out_eqn
 +             {  "\n%5.0f" = H;
 +                " %4.0f" = K;
 +                " %4.0f" = L;
 +       '" %4.0f" = M;
 +       '" %12.2f" = I_no_scale_pks/M/Get(scale);  '|F|^2
 +       '" %11.4f" = A01-B11; 'Real
 +       '" %11.4f" = A11+B01; 'Imaginary
 +                " %14.7f" = Sqrt(Iobs_no_scale_pks/M/Get(scale)) Cos(If((A01-B11)>0, ArcTan((A11+B01)/(A01-B11)), ArcTan((A11+B01)/(A01-B11)) +Pi));
 +                " %14.7f" = Sqrt(Iobs_no_scale_pks/M/Get(scale)) Sin(If((A01-B11)>0, ArcTan((A11+B01)/(A01-B11)), ArcTan((A11+B01)/(A01-B11)) +Pi));
 +                " %14.7f" = Sqrt(Iobs_no_scale_pks)/Get(scale) Sqrt((Iobs_no_scale_pks_err/Iobs_no_scale_pks)^2+ (Error(scf)/Get(scale))^2 )/2 /Sqrt(M/Get(scale));
 +             }
 + Out_PRF(phasename)
 + #else
 + out phasename##_dys.mem append             
 + Out_String("\n# NREF2 fix to 0\n")
 + Out_String("    0\n")
 + Out_String("# NREF3 need to count manually\n")
 + Out_String("   11\n")
 + Out_String("#   h    k    l")
 + phase_out phasename##_dys.mem append 
 + load out_record out_fmt out_eqn
 + {  "\n%5.0f" = H;
 +    " %4.0f" = K;
 +                   " %4.0f" = L; }
 + #endif
 +}
 +</code>   
 +
 +=== Out_PRF ===
 +The "Out_PRF" macro from below link generate a .prf preference file for Dysnomia to execute. For some reason, this TOPAS Wiki site does not display certain Out_String function, so I have to place it on my google drive:
 +
 +https://drive.google.com/file/d/1wH5K6pJriHAAQyXCOpRfOQiowZXpKYGf/view?usp=sharing
 +
 +==== Application Example: Working .inp to export .mem and .prf files ====
 +To use this function, please save the macros "Out_MEM"(on this page), "Out_PRF"(on this page), "[[atomic_number|Atomic_Number]]" and "[[space_group_number|sg_num]]" into your TOPAS' local.inc, or #include them in your .inp files.
 +
 +Below example .inp file will be executed twice automatically. 
 +
 +The first run performs conventional Rietveld refinement and export information for the measured hkls. 
 +
 +The second run exports Miller indexes of unmeasured d-spacing reflections of higher spacing resolution, down to 0.7 Angstrom.
 +
 +<code topas>
 +num_runs 2 
 + 
 +'r_p    0 r_p_dash    0 
 +'r_wp   0 r_wp_dash   0 
 +'r_exp  0 r_exp_dash  0 
 +'gof    0 
 +'weighted_Durbin_Watson   0 
 +
 + #if (Run_Number == 0)
 + RAW(corundum)  
 + do_errors 
 +            CuKa5(0.001) ' Radiation used to measure the data
 +            out DMIN.txt Out(Lam /2/Sin(X2 Deg/2)) 'Export the min d_obs
 +        #else
 +            iters 0
 +            yobs_eqn = 1; min 1 max 180 del 0.01
 +            MoKa2(0.001) ' Dummy hard radiation to generate high Miller hkls 
 + prm DMIN = #include DMIN.txt;
 + start_X = 2 ArcSin(Lam /2 /DMIN) Rad;  'calculate only the range between min d_obs to 0.7 Angstrom  
 + finish_X = 2 ArcSin(Lam /2 /0.7) Rad;  'The limit 0.7 Angstrom can be adapted according to your phase
 +        #endif
 +
 +        Radius(173)
 +        LP_Factor(26.6)
 +        Full_Axial_Model(12, 15, 12, 4.6, 4.6)
 +        Slit_Width(0.3)
 +        Divergence(1)
 +   
 +        Absorption(@, 30) 
 +        ZE(@,0)     
 +        One_on_X(@, 1000) 
 +        bkg  @ 0 0 0 0 0 0
 +    
 +        STR(R_-3_C) 
 + phase_name "Corundum" 
 + prm Total_e_in_Cell = Al_electrons + O_electrons;:0  ' Total Number of Electron in Unit Cell
 + Trigonal(@  4.75847, @  12.99036) 
 + site Al num_posns 0 x 0    y 0   z @ 0.35228`_0.00003 occ Al 1 beq @ 0.29860`_0.00866 prm Al_electrons =Get(num_posns) * Atomic_Number("Al");
 + site O  num_posns 0 x @ 0.30607`_0.00014 y 0 z   0.25 occ O  1 beq @ 0.16724`_0.01427 prm O_electrons =Get(num_posns) * Atomic_Number("O");
 + scale scf 0.00208062929`_5.482e-06  'name the scale factor as "scf" to export its error.
 + CS_L(@, 274.753078`_7.43125129) 
 + Strain_L(@, 0.0166526397`_0.00141211878)
 + r_bragg  3.76972174
 + 
 +
 +  Out_MEM(Corundum,"r-3c")
 +</code>  
 +
 +N.B.: the number of reflections "NREF1" and "NREF3" need be manually count and updated in the generated .mem file.
 +
 +N.B.2: According to the Dysnomia examples, it seems do not need F_imaginary part for MEM analysis, therefore the imaginary part can be set to 0 in the generated .mem file.
 +
 +N.B.3: Reflections of zero Fo(R) should be avoided, otherwise Dysnomia won't work.
 +
 +If any user in our open TOPAS community has suggestion or idea, or bug report on these macros, please kindly let me know and I am happy to learn from you: [[tony.wang@qut.edu.au]]
 +
 +Thanks for Dr. Koichi Momma's inspiring education in the IUCr Crystallographic Computing School (Melbourne, 2023). :)