Warning: Trying to access array offset on value of type null in /home/site/wwwroot/lib/plugins/move/action/rename.php on line 42

Warning: Cannot modify header information - headers already sent by (output started at /home/site/wwwroot/lib/plugins/move/action/rename.php:42) in /home/site/wwwroot/inc/common.php on line 1955

Warning: Cannot modify header information - headers already sent by (output started at /home/site/wwwroot/lib/plugins/move/action/rename.php:42) in /home/site/wwwroot/inc/actions.php on line 38
wppm_macros [topas wiki]

topas wiki

User Tools

Site Tools

Trace:
wppm_macros

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revisionPrevious revision
wppm_macros [2020/03/04 07:24] – old revision restored (2018/10/24 16:38) rowlesmr3wppm_macros [2022/11/03 15:08] (current) – external edit 127.0.0.1
Line 1: Line 1:
 +====== WPPM Macros ======
  
 +Paolo Scardi and co-workers have provided a set of macros for their WPPM methods in TOPAS.  The macros are listed below.  Save these as WPPM_macros.inc in your main TOPAS directory and add a line to your local.inc saying "#include WPPM_macros.inc".  
 +
 +The publication is at: [[ http://scripts.iucr.org/cgi-bin/paper?S160057671801289X|J. Appl. Cryst 2018]], and the abstract says:
 +
 +Macros implementing the main concepts of the whole powder pattern modelling approach have been written for TOPAS. Size and strain broadening components of the diffraction line profiles can be convolved with the instrumental profile already available among the standard commands of TOPAS. Specific macros are presented with examples of applications including plastically deformed powders and atomistic simulations. A macro is presented for the modelling of surface relaxation effects in spherical nanocrystals.
 +
 +Note: delete any old wppm macros you have around before using these.
 +
 +<code topas>
 +
 +' WPPM macros by P. Scardi, C. Perez-Demydenko & C.L. Azanza Ricardo
 +' See also: P. Scardi, C. Perez-Demydenko, C.L. Azanza Ricardo & A. Coelho, Journal of Applied Crystallography, 2018
 +' The following macros can be used with any space group; additional macros specific to cubic phases are available
 +' email: Paolo.Scardi@unitn.it
 +
 +macro WPPM_Sphere(RRc, RRv)
 +   {
 +      If_Prm_Eqn_Rpt(RRc, RRv, min .1 max = Min(2 Val + .3, 10000);)
 +      WPPM_ft_conv = 1 - 0.75*WPPM_L/RRv + 0.0625*(WPPM_L/RRv)^3 ;
 +
 +      'WPPM_break_on_small = 1e-7;
 +      WPPM_L_max = 2*CeV(RRc, RRv);
 +      WPPM_th2_range = 55;
 +   }
 +macro WPPM_Sphere_LogNormDIST(muc, muv, sigc, sigv)
 +   {
 +      #m_argu muc
 +      #m_argu sigc
 +      If_Prm_Eqn_Rpt(muc, muv, min .1 max = Min(2 Val + .3, 100);)
 +      If_Prm_Eqn_Rpt(sigc, sigv, min .01 max = Min(2 Val + .01, 3);)
 +      WPPM_ft_conv =
 +         {
 +            def u = CeV(muc, muv);
 +            def sig = CeV(sigc, sigv);
 +            fn M(n) = 0.5 Exp(- n (u + (3 - 0.5 n) sig^2));
 +            fn wppm_Ln(kc) = Get(WPPM_Ln_k) + Ln(kc Get(WPPM_dL));
 +            fn q(n) {
 +               return
 +                  Erfc_Approx( ( wppm_Ln(1) - u - (3-n) sig^2) / (sig Sqrt(2)))
 +                  WPPM_L^n
 +                  M(n);
 +               }
 +            return q(0) - 1.5 q(1) + 0.5 q(3);
 +         }
 +         WPPM_break_on_small = 1e-7;
 +         WPPM_L_max 1000
 +         WPPM_th2_range = 30;
 +   }
 +macro getInvariant(sg, E1, E2, E3, E4, E5, E6, E7, E8, E9, E10, E11, E12, E13, E14, E15)
 +   {
 +      #if Or(sg == 1, sg == 2); 'Triclinic, -1
 +         E1*H^4 + E2*K^4 + E3*L^4 + 2*(E4*H*H*K*K + E5*K*K*L*L + E6*H*H*L*L) + 4*(E7*(H^3)*K + E8*(H^3)*L + E9*H*(K^3) + E10*(K^3)*L + E11*H*(L^3) + E12*K*(L^3) + E13*H*H*K*L + E14*H*K*K*L + E15*H*K*L*L)
 +      
 +      #elseif And(sg >= 3, sg <= 15); 'Monoclinic, 2/m
 +         If (And(Constant(Get(al)) == 90, Constant(Get(ga)) == 90), ' unique axis b 
 +            E1*H^4 + E2*K^4 + E3*L^4 + 2*(E4*H*H*L*L + E5*K*K*L*L + E6*H*H*K*K) + 4*(E7*(H^3)*L + E8*H*(L^3) + E9*H*K*K*L),
 +            If (And(Constant(Get(al)) == 90, Constant(Get(be)) == 90), ' unique axis c 
 +               E1*H^4 + E2*K^4 + E3*L^4 + 2*(E4*H*H*K*K + E5*K*K*L*L + E6*H*H*L*L) + 4*(E7*(H^3)*K + E8*H*(K^3) + E9*H*K*L*L),
 +               "Invalid Monoclinic lattice parameters"
 +            )
 +         )
 +      #elseif And(sg >= 16, sg <= 74); 'Orthorhombic, mmm
 +         E1*H^4 + E2*K^4 + E3*L^4 + 2*(E4*H*H*K*K + E5*K*K*L*L + E6*H*H*L*L)
 +
 +      #elseif And(sg >= 75, sg <= 88); 'Tetragonal, 4/m
 +         E1*(H^4 + K^4) + E2*L^4 + 2*E3*H*H*K*K + 2*E4*(H*H + K*K)*L*L + 4*E5*H*K*(H*H - K*K)
 +       
 +      #elseif And(sg >= 89, sg <= 142); 'Tetragonal, 4/mmm
 +         E1*(H^4 + K^4) + E2*L^4 + 2*E3*H*H*K*K + 2*E4*(H*H + K*K)*L*L
 +
 +      #elseif And(sg >= 143, sg <= 148); 'Trigonal, -3
 +         #if Or(sg == 146, sg == 148); 'Trigonal space groups supporting also rhombohedral axes      
 +            If (Constant(Get(ga)) == 120,
 +               E1*(H*H - H*K + K*K)^2 + 2*E2*(H*H - H*K + K*K)*L*L + E3*L^4 + 4*E5*(H^3 - 3*H*K*K + (K^3))*L + 4*E4*H*(H - K)*K*L,
 +               If (Constant(Get(ga)) == 60,
 +                  E1*(H*H + H*K + K*K)^2 + 2*E2*L*L*(H*H + H*K + K*K) + E3*L^4 + (4/3)*E4*L*(H^3 + 3*H*H*K - K^3) + (4/3)*E5*L*(-H^3 + 3*H*K*K + K^3), ' 60deg
 +                  E1*(H^4 + K^4 + L^4) + 2*E2*(H*H*K*K + H*H*L*L + K*K*L*L) + 4*E3*((H^3)*K + (K^3)*L + H*(L^3)) + 4*E4*(H*(K^3) + (H^3)*L + K*(L^3))+ 4*E5*H*K*L*(H + K + L)
 +               )
 +            )
 +         #else      
 +            If (Constant(Get(ga)) == 120,
 +               E1*(H*H - H*K + K*K)^2 + 2*E2*(H*H - H*K + K*K)*L*L + E3*L^4 + 4*E5*(H^3 - 3*H*K*K + (K^3))*L + 4*E4*H*(H - K)*K*L,
 +               E1*(H*H + H*K + K*K)^2 + 2*E2*L*L*(H*H + H*K + K*K) + E3*L^4 + (4/3)*E4*L*(H^3 + 3*H*H*K - K^3) + (4/3)*E5*L*(-H^3 + 3*H*K*K + K^3) ' 60
 +            )
 +         #endif
 +      
 +      #elseif And(sg >= 149, sg <= 167); 'Trigonal, -3m
 +         #if Or(sg ==150, sg ==152, sg ==154, sg ==155, sg ==156, sg ==158, sg ==160, sg ==161, sg ==164, sg ==165 , sg ==166, sg ==167); 'Trigonal, -3m1
 +            #if Or(sg == 155, sg == 160, sg == 161, sg == 166, sg == 167); 'Trigonal space groups supporting also rhombohedral axes      
 +               If (Constant(Get(ga)) == 120,
 +                  E1*(H*H - H*K + K*K)^2 + 2*E2*L*L*(H*H - H*K + K*K) + E3*L^4 + 4*E4*H*K*L*(H - K),
 +                  If (Constant(Get(ga)) == 60,
 +                     E1*(H*H + H*K + K*K)^2 + 2*E2*L*L*(H*H + H*K + K*K) + E3*L^4 + 4*E4*H*K*L*(H + K), ' 60deg
 +                     E1*(H^4 + K^4 + L^4) + 2*E2*(H*H*K*K + H*H*L*L + K*K*L*L) + 4*E3*(H*K*(H*H + K*K) + H*L*(H*H + L*L) + K*L*(K*K + L*L)) + 4*E4*H*K*L*(H + K + L)
 +                  )
 +               )
 +            #else      
 +               If (Constant(Get(ga)) == 120,
 +                  E1*(H*H - H*K + K*K)^2 + 2*E2*L*L*(H*H - H*K + K*K) + E3*L^4 + 4*E4*H*K*L*(H - K),
 +                  E1*(H*H + H*K + K*K)^2 + 2*E2*L*L*(H*H + H*K + K*K) + E3*L^4 + 4*E4*H*K*L*(H + K) ' 60deg
 +               )
 +            #endif            
 +         #else 'Trigonal, -31m
 +            If (Constant(Get(ga)) == 120,
 +               E1*(H*H - H*K + K*K)^2 + 2*E2*L*L*(H*H - H*K + K*K) + E3*L^4 + E4*L*(4*(H^3) - 6*H*H*K - 6*H*K*K + 4*(K^3)),
 +               E1*(H*H + H*K + K*K)^2 + 2*E2*L*L*(H*H + H*K + K*K) + E3*L^4 + (4/3)*E4*L*(2*(H^3) + 3*H*H*K - 3*H*K*K - 2*(K^3)) ' 60deg
 +            )
 +         #endif
 +      
 +      #elseif And(sg >= 168, sg <= 194); 'Hexagonal, 6/m and 6/mmm
 +         If (Constant(Get(ga)) == 120,
 +            E1*(H*H - H*K + K*K)^2 + 2*E2*L*L*(H*H - H*K + K*K) + E3*L^4,
 +            E1*(H*H + H*K + K*K)^2 + 2*E2*L*L*(H*H + H*K + K*K) + E3*L^4 ' 60deg
 +         )
 +      #elseif And(sg >= 195, sg <= 230); 'Cubic, m-3 and m-3m
 +         E1*(H^4 + K^4 + L^4) + 2*E2*(H*H*K*K + H*H*L*L + K*K*L*L)
 +      #else
 +      #endif
 +   }
 +macro Out_Invariant(file,sg, E1, E2, E3, E4, E5, E6, E7, E8, E9)    
 +   {
 +      ' E1 to E9 for space groups 3 to 15 (2/m)
 +      Out_Invariant(file,sg, E1, E2, E3, E4, E5, E6, E7, E8, E9,,,,,,) 
 +   }
 +macro Out_Invariant(file,sg, E1, E2, E3, E4, E5, E6) 
 +   {
 +      ' E1 to E6 for space groups 16 to 64 (mmm)
 +      Out_Invariant(file,sg, E1, E2, E3, E4, E5, E6,,,,,,,,,) 
 +   }
 +
 +macro Out_Invariant(file,sg, E1, E2, E3, E4, E5) 
 +   {
 +      ' E1 to E5 for space groups 75 to 88 (4/m) and 143 to 148 (-3)
 +      Out_Invariant(file,sg, E1, E2, E3, E4, E5,,,,,,,,,,) 
 +   }
 +macro Out_Invariant(file,sg, E1, E2, E3, E4) 
 +   {
 +      ' E1 to E4 for space groups 89 to 142 (4/mmm) and 149 to 167 (-3m)
 +      Out_Invariant(file,sg, E1, E2, E3, E4,,,,,,,,,,,) 
 +   }
 +macro Out_Invariant(file,sg, E1, E2, E3) 
 +   {
 +      ' E1 to E3 for space groups 168 to 194 (6/m and 6/mmm)
 +      Out_Invariant(file,sg, E1, E2, E3,,,,,,,,,,,,) 
 +   }
 +macro Out_Invariant(file,sg, E1, E2) 
 +   {
 +      ' E1 to E2 for space groups 195 to 230 (m-3 and m-3m)
 +      Out_Invariant(file,sg, E1, E2,,,,,,,,,,,,,) 
 +   }
 +macro Out_Invariant(file,sg,E1, E2, E3, E4, E5, E6, E7, E8, E9, E10, E11, E12, E13, E14, E15)
 +   {
 +      out file
 +         Out_String("\nCell Parameters")
 +         Out(Get(a), "\na =  %V;")
 +         Out(Get(b), "\tb = %V;")
 +         Out(Get(c), "\tc = %V")
 +         Out(Get(al), "\nalpha = %V;")
 +         Out(Get(be), "\tbeta = %V;")
 +         Out(Get(ga), "\tgamma = %V")
 +
 +         Out_String("\n\n/")
 +         Out_String("*")
 +         Out_String(" H - K - L ------ Inv")
 +         Out_String(" *")
 +         Out_String("/")
 +
 +         phase_out file append
 +            load out_record out_fmt out_eqn
 +            {
 +               "\n%4.0f" = H;
 +               "%4.0f" = K;
 +               "%4.0f" = L;
 +               "%12.2f" = getInvariant(sg, E1, E2, E3, E4, E5, E6, E7, E8, E9, E10, E11, E12, E13, E14, E15) ;
 +            }
 +    }
 +macro WPPM_Strain_InvariantWilkens(rhoc, rhov, Rec, Rev, burger, wsg, E1, E2, E3, E4, E5, E6, E7, E8, E9) 
 +   {
 +      ' E1 to E9 for space groups 3 to 15 (2/m)
 +      WPPM_Strain_InvariantWilkens(rhoc, rhov, Rec, Rev, burger, wsg, E1, E2, E3, E4, E5, E6, E7, E8, E9,,,,,,) 
 +   }
 +macro WPPM_Strain_InvariantWilkens(rhoc, rhov, Rec, Rev, burger, wsg, E1, E2, E3, E4, E5, E6) 
 +   {
 +      ' E1 to E6 for space groups 16 to 64 (mmm)
 +      WPPM_Strain_InvariantWilkens(rhoc, rhov, Rec, Rev, burger, wsg, E1, E2, E3, E4, E5, E6,,,,,,,,,) 
 +   }
 +macro WPPM_Strain_InvariantWilkens(rhoc, rhov, Rec, Rev, burger, wsg, E1, E2, E3, E4, E5) 
 +   {
 +      ' E1 to E5 for space groups 75 to 88 (4/m) and 143 to 148 (-3)
 +      WPPM_Strain_InvariantWilkens(rhoc, rhov, Rec, Rev, burger, wsg, E1, E2, E3, E4, E5,,,,,,,,,,) 
 +   }
 +macro WPPM_Strain_InvariantWilkens(rhoc, rhov, Rec, Rev, burger, wsg, E1, E2, E3, E4) 
 +   {
 +      ' E1 to E4 for space groups 89 to 142 (4/mmm) and 149 to 167 (-3m)
 +      WPPM_Strain_InvariantWilkens(rhoc, rhov, Rec, Rev, burger, wsg, E1, E2, E3, E4,,,,,,,,,,,) 
 +   }
 +macro WPPM_Strain_InvariantWilkens(rhoc, rhov, Rec, Rev, burger, wsg, E1, E2, E3) 
 +   {
 +      ' E1 to E3 for space groups 168 to 194 (6/m and 6/mmm)
 +      WPPM_Strain_InvariantWilkens(rhoc, rhov, Rec, Rev, burger, wsg, E1, E2, E3,,,,,,,,,,,,) 
 +   }
 +macro WPPM_Strain_InvariantWilkens(rhoc, rhov, Rec, Rev, burger, wsg, E1, E2) 
 +   {
 +      ' E1 to E2 for space groups 195 to 230 (m-3 and m-3m)
 +      WPPM_Strain_InvariantWilkens(rhoc, rhov, Rec, Rev, burger, wsg, E1, E2,,,,,,,,,,,,,) 
 +   }
 +macro WPPM_Strain_InvariantWilkens(rhoc, rhov, Rec, Rev, burgers, wsg, E1, E2, E3, E4, E5, E6, E7, E8, E9, E10, E11, E12, E13, E14, E15)
 +   {
 +      #m_argu rhoc
 +      #m_argu Rec
 +      If_Prm_Eqn_Rpt(rhoc, rhov, min 0 max = Min(2 Val + .0001, 0.100);)
 +      If_Prm_Eqn_Rpt(Rec , Rev , min 1 max = Min(2 Val + .0001, 0.100);)
 +      
 +      WPPM_ft_conv = {                   
 +         def invariantTerm_0 = getInvariant(wsg, E1, E2, E3, E4, E5, E6, E7, E8, E9, E10, E11, E12, E13, E14, E15);
 +         def invariantTerm = If (invariantTerm_0 < 0, 1000, invariantTerm_0);
 +         def dstar = 1/(D_spacing 0.1);
 +         def aa = Constant(Get(a) 0.1); 
 +         def strainINV = invariantTerm/((aa dstar)^4);
 +         def rhoVal = CeV(rhoc, rhov);
 +         def fact = Pi burgers burgers rhoVal dstar dstar strainINV 0.01 0.5;
 +         def Reval = CeV(Rec, Rev);
 +         def eta = Abs(WPPM_L/Reval);
 +         def fstar = If ( eta < 1, -Ln(eta) + 7/4 - Ln(2) + eta*eta/6 - (32*eta*eta*eta)/(225*Pi), 256.0/(45.0*Pi*eta)-(11.0/24.0 + (Ln(2)+Ln(eta))/4.0)/(eta*eta));
 +         def result = If (WPPM_L == 0, 1, Exp(-fact*(WPPM_L*WPPM_L*fstar)));
 +           return result;
 +      }
 +      WPPM_break_on_small = 1e-7;
 +      WPPM_L_max 1000
 +      WPPM_th2_range = 30;
 +    }
 +macro WPPM_Strain_InvariantPAH(ac, av, bc, bv, wsg, E1, E2, E3, E4, E5, E6, E7, E8, E9) 
 +   {
 +      ' E1 to E9 for space groups 3 to 15 (2/m)
 +      WPPM_Strain_InvariantPAH(ac, av, bc, bv, wsg, E1, E2, E3, E4, E5, E6, E7, E8, E9,,,,,,) 
 +   }
 +macro WPPM_Strain_InvariantPAH(ac, av, bc, bv, wsg, E1, E2, E3, E4, E5, E6) 
 +   {
 +      ' E1 to E6 for space groups 16 to 64 (mmm)
 +      WPPM_Strain_InvariantPAH(ac, av, bc, bv, wsg, E1, E2, E3, E4, E5, E6,,,,,,,,,) 
 +   }
 +macro WPPM_Strain_InvariantPAH(ac, av, bc, bv, wsg, E1, E2, E3, E4, E5) 
 +   {
 +      ' E1 to E5 for space groups 75 to 88 (4/m) and 143 to 148 (-3)
 +      WPPM_Strain_InvariantPAH(ac, av, bc, bv, wsg, E1, E2, E3, E4, E5,,,,,,,,,,) 
 +   }
 +macro WPPM_Strain_InvariantPAH(ac, av, bc, bv, wsg, E1, E2, E3, E4) 
 +   {
 +      ' E1 to E4 for space groups 89 to 142 (4/mmm) and 149 to 167 (-3m)
 +      WPPM_Strain_InvariantPAH(ac, av, bc, bv, wsg, E1, E2, E3, E4,,,,,,,,,,,) 
 +   }
 +macro WPPM_Strain_InvariantPAH(ac, av, bc, bv, wsg, E1, E2, E3) 
 +   {
 +      ' E1 to E3 for space groups 168 to 194 (6/m and 6/mmm)
 +      WPPM_Strain_InvariantPAH(ac, av, bc, bv, wsg, E1, E2, E3,,,,,,,,,,,,) 
 +   }
 +macro WPPM_Strain_InvariantPAH(ac, av, bc, bv, wsg, E1, E2) 
 +   {
 +      ' E1 to E2 for space groups 195 to 230 (m-3 and m-3m)
 +      WPPM_Strain_InvariantPAH(ac, av, bc, bv, wsg, E1, E2,,,,,,,,,,,,,) 
 +   }
 +macro WPPM_Strain_InvariantPAH(ac, av, bc, bv, wsg, E1, E2, E3, E4, E5, E6, E7, E8, E9, E10, E11, E12, E13, E14, E15)
 +   {
 +      #m_argu ac
 +      #m_argu bc
 +      If_Prm_Eqn_Rpt(ac, av, min 0 max = Min(2 Val + .0001, 0.100);)
 +      If_Prm_Eqn_Rpt(bc, bv, min 0 max = Min(2 Val + .0001, 0.100);)
 +      WPPM_ft_conv = {
 +        def invariantTerm_0 = getInvariant(wsg, E1, E2, E3, E4, E5, E6, E7, E8, E9, E10, E11, E12, E13, E14, E15) ;
 +        def invariantTerm  = If (invariantTerm_0 < 0, 1000, invariantTerm_0);
 +        def dstar = 1/(D_spacing*0.1);
 +        def aa = Constant(Get(a) 0.1);
 +        def strainINV = invariantTerm/((aa*dstar)^4);
 +        def fact = 2*Pi*Pi*dstar*dstar*strainINV;
 +        def aVal = CeV(ac, av)*1e-5;
 +        def bVal = CeV(bc, bv)*1e-5;
 +        return Exp(-fact*(aVal*WPPM_L+bVal*WPPM_L*WPPM_L));
 +      }
 +      WPPM_break_on_small = 1e-7;
 +      WPPM_L_max 1000
 +      WPPM_th2_range = 30;
 +    }
 +
 +
 +</code>