From d08bf9d0ab129ca58e66d8fd216e34ecf4ed415d Mon Sep 17 00:00:00 2001
From: gianlum33 <g.marcozzi@fu-berlin.de>
Date: Mon, 2 Sep 2024 16:31:42 +0200
Subject: [PATCH] Bsweep trEPR with new defin of lw
---
from_bittl/src/p2 | Bin 0 -> 41096 bytes
from_bittl/src/p2.c | 752 +++++++++++++++++++
from_bittl/src/p2.h | 52 ++
from_bittl/src/p2.txt | 40 +
from_bittl/src/p2_utils.c | 155 ++++
from_bittl/src/test2_Pabs.asc | 1024 ++++++++++++++++++++++++++
from_bittl/src/test2_Pem.asc | 1024 ++++++++++++++++++++++++++
from_bittl/src/test2_Qabs.asc | 1024 ++++++++++++++++++++++++++
from_bittl/src/test2_Qem.asc | 1024 ++++++++++++++++++++++++++
from_bittl/src/test2_spec.asc | 1024 ++++++++++++++++++++++++++
from_bittl/src/test2_sum.asc | 1024 ++++++++++++++++++++++++++
trEPR_spectrumIntegral.asv | 256 +++++++
trEPR_spectrumIntegral.m | 257 +++++++
zech_psiOopEseem_trEPRstickSpectra.m | 484 +++++++++---
14 files changed, 8049 insertions(+), 91 deletions(-)
create mode 100755 from_bittl/src/p2
create mode 100755 from_bittl/src/p2.c
create mode 100755 from_bittl/src/p2.h
create mode 100755 from_bittl/src/p2.txt
create mode 100755 from_bittl/src/p2_utils.c
create mode 100755 from_bittl/src/test2_Pabs.asc
create mode 100755 from_bittl/src/test2_Pem.asc
create mode 100755 from_bittl/src/test2_Qabs.asc
create mode 100755 from_bittl/src/test2_Qem.asc
create mode 100755 from_bittl/src/test2_spec.asc
create mode 100755 from_bittl/src/test2_sum.asc
create mode 100644 trEPR_spectrumIntegral.asv
create mode 100644 trEPR_spectrumIntegral.m
diff --git a/from_bittl/src/p2 b/from_bittl/src/p2
new file mode 100755
index 0000000000000000000000000000000000000000..f237429ab78f673f9726e77f882a18909d0f9b83
GIT binary patch
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diff --git a/from_bittl/src/p2.c b/from_bittl/src/p2.c
new file mode 100755
index 0000000..b81b82d
--- /dev/null
+++ b/from_bittl/src/p2.c
@@ -0,0 +1,752 @@
+/***************************************************************
+* p2.c *
+* cc p2.c -o p2 -lm *
+****************************************************************
+* Versions:
+* - ESEEM_FTs and Tr EPR Spectra! (21.08.98 SZ)
+* - ESEEM with or without Hfc's (27.08.98 SZ)
+* - Whole program derived vom p2k.c (version 31.08.98)
+*
+****************************************************************/
+
+#include <stdio.h>
+#include <ctype.h>
+#include <stdlib.h>
+#include <string.h>
+#include <unistd.h>
+#include <math.h>
+#include "p2.h"
+#include "p2_utils.c"
+
+
+int ReadInput()
+{
+ short i, k;
+ FILE *fp, *fopen();
+
+ if ((fp = fopen("p2.txt","r")) == NULL) {
+ printf("file p2.txt cannot be opened");
+ return(-1);
+ }
+ fscanf(fp,"%lf %*s %lf %lf %d %*s %d %d %*s", &fmw, &h1, &h2,
+ &NumOfPoints, &nt, &np);
+ dh = (h2-h1)/(NumOfPoints-1);
+ for (i=0;i<=2;i++)
+ for (k=0;k<=2;k++)
+ fscanf(fp, "%lf ", &gP[i][k]);
+ NewLine(fp);
+ fscanf(fp,"%lf", &hbP);
+ NewLine(fp);
+ for(i=0;i<=2;i++)
+ for (k=0;k<=2;k++)
+ fscanf(fp, "%lf", &gA1[i][k]);
+ NewLine(fp);
+ fscanf(fp, "%lf", &hbA1);
+ NewLine(fp);
+ reference_syst=getc(fp);
+ NewLine(fp);
+ switch (toupper(reference_syst)) {
+ case 'Q':
+ fscanf(fp, "%lf %lf %*s",&phi1,&theta1);
+ fscanf(fp, "%lf %lf %lf %*s",&euler_PQ[0],&euler_PQ[1],&euler_PQ[2]);
+ break;
+/*
+ case 'Z':
+ fscanf(fp, "%lf %lf %lf %*s",&euler_zP[0],&euler_zP[1],&euler_zP[2]);
+ fscanf(fp, "%lf %lf %lf %*s",&euler_zQ[0],&euler_zQ[1],&euler_zQ[2]);
+ break;
+ case 'P':
+ fscanf(fp, "%lf %lf %*s",&phi1,&theta1);
+ fscanf(fp, "%lf %lf %lf %*s",&euler_PQ[0],&euler_PQ[1],&euler_PQ[2]);
+ break;
+*/
+ default:
+ printf("Up to now, only Q as reference system possible (SORRY!) ");
+ fclose(fp);
+ return -1;
+ }
+ fscanf(fp, "%lf %lf %*s", &J, &d);
+ NewLine(fp);
+ print_orient = getc(fp);
+ NewLine(fp);
+ print_Powder = getc(fp);
+ NewLine(fp);
+ print_ESEEM_FT = getc(fp);
+ NewLine(fp);
+ fscanf(fp, "%20s %*s", outfile);
+ fscanf(fp, "%lf %d %*s", &max_freq, &num_freq_points);
+ fscanf(fp, "%d %*s", &delta_w_steps);
+ fscanf(fp, "%lf %*s", &lorentz_hb);
+ fscanf(fp,"%d %*s",&number_of_protons);
+ for(i=0;i<=2;i++)
+ for (k=0;k<=2;k++)
+ fscanf(fp, "%lf", &aA1[i][k]);
+ fscanf(fp,"%d %*s",&n_protons_p);
+ for(i=0;i<=2;i++)
+ for (k=0;k<=2;k++)
+ fscanf(fp, "%lf", &aP[i][k]);
+ fclose(fp);
+ return(0);
+}
+
+
+void WriteInput()
+{
+ short i, k;
+
+ printf("CCRP simulation for P+Q- powder spectra\n");
+ printf("Microwave frequency: %.2f MHz \n",fmw);
+ printf("Magnetic field: from %.2f to %.2f Gauss in steps of %.4f Gauss\n"
+ ,h1,h2,dh);
+ printf("\nNumber of Fieldpoints = %d \n",NumOfPoints);
+ printf("Theta steps: %d Phi steps: %d\n",nt,np);
+ printf("\n ANGLES:\n");
+ printf("zPQ_gQ: Phi1: %f Theta1: %f\n ",phi1, theta1);
+ printf("Euler(gP_gQ) %f, %f, %f\n ",euler_PQ[0],euler_PQ[1], euler_PQ[2]);
+ PrintMatrix(gP,"g-Tensor for P+");
+ PrintMatrix(gA1,"g-Tensor for A1-");
+ printf("Linewidth P: %.2f Q: %.2f\n",hbP,hbA1);
+ printf("Dipol-Dipol-Coupling %.3f Exchange Coupling %.3f\n", d,J);
+ if (number_of_protons != 0) {
+ printf("Acceptor Q has %d aequivalent protons\n",number_of_protons);
+ PrintMatrix(aA1,"Hyperfine tensor");
+ }
+ if (n_protons_p != 0) {
+ printf("Donor P has %d aequivalent protons\n",n_protons_p);
+ PrintMatrix(aP,"Hyperfine tensor");
+ }
+ printf("Output filename %-20s\n",outfile);
+}
+
+void PrintOutRelOrntPQ(o_sys)
+ char o_sys;
+{
+ printf("\n RELATIVE ORIENTATION PQ \n");
+ PrintMatrix(rPQ,"Transformation matrix P->Q");
+ PrintMatrix(rtPQ,"Transformation matrix Q->P");
+ printf("in g%c system:\n",reference_syst);
+ printf(" alpha = %.2f\n",euler_PQ[0]*deg);
+ printf(" beta = %.2f\n",euler_PQ[1]*deg);
+ printf(" gamma = %.2f\n",euler_PQ[2]*deg);
+ printf("in g%c system:\n",o_sys);
+ printf(" alpha = %.2f \n",180-euler_PQ[2]*deg);
+ printf(" beta = %.2f \n",euler_PQ[1]*deg);
+ printf(" gamma = %.2f \n",180-euler_PQ[0]*deg);
+}
+
+void PrintOutAngles_zPQ(sys, theta, phi, vec)
+ char sys;
+ DataT theta, phi;
+ vector vec;
+{
+ char axis[9];
+
+ switch (toupper(sys)){
+ case 'Q':
+ strncpy(axis, "zPQ", sizeof(axis));
+ printf("\n ORIENTATION of Dipolar Vector relative to g%c\n",sys);
+ break;
+ case 'P':
+ strncpy(axis, "zPQ", sizeof(axis));
+ printf("\n ORIENTATION of Dipolar Vector relative to g%c\n",sys);
+ break;
+/*
+ case 'C':
+ strncpy(axis, "c-axis", sizeof(axis));
+ sys = 'Q';
+ printf("\n ORIENTATION of crystall c-axis relative to g%c\n",sys);
+ break;
+ case 'D':
+ strncpy(axis, "c-axis", sizeof(axis));
+ sys = 'P';
+ printf("\n ORIENTATION of crystall c-axis relative to g%c\n",sys);
+ break;
+*/
+ case 'B':
+ strncpy(axis, "B0-field", sizeof(axis));
+ sys = 'Q';
+ printf("\n ORIENTATION of B0-field relative to g%c\n",sys);
+ break;
+ default:
+ return;
+ }
+ printf(" theta = %.2f (%.2f) phi = %.2f (%.2f) \n",
+ theta*deg,180-theta*deg,phi*deg,180-phi*deg);
+ printf(" Angle: %s g%cx = %.2f (%.2f)\n", axis, sys,
+ vec[0]*deg,180-vec[0]*deg);
+ printf(" Angle: %s g%cy = %.2f (%.2f)\n", axis, sys,
+ vec[1]*deg,180-vec[1]*deg);
+ printf(" Angle: %s g%cz = %.2f (%.2f)\n", axis, sys,
+ vec[2]*deg,180-vec[2]*deg);
+}
+
+
+/* calcu. rotation matrix from Euler anlges
+ R = Rz(gamma) Ry(beta) Rz(alpha) */
+void GetR(r,euler)
+ matrix r;
+ vector euler;
+{
+ matrix a, b, c;
+
+ RotationMatrix(a,euler[0]*deg,'z');
+ RotationMatrix(b,euler[1]*deg,'y');
+ RotationMatrix(c,euler[2]*deg,'z');
+ MulMat(r,c,b);
+ MulMat(r,r,a);
+}
+
+/* Dipolar axis in Q axis system
+ rpA1 = Rz(phi) Ry(theta) (0,0,1) */
+void GetrpA1()
+{
+ rpA1[0] = -sin(theta1) * cos(phi1);
+ rpA1[1] = sin(theta1) * sin(phi1);
+ rpA1[2] = cos(theta1);
+}
+
+/* Angle between dipolar axis and Q axes system */
+void GetzQ()
+{
+ zQ[0] = acos(rpA1[0]);
+ zQ[1] = acos(rpA1[1]);
+ zQ[2] = theta1;
+}
+
+/* Angle between dipolar axis and P axes system */
+void GetzP()
+{
+ matrix r;
+ short i,k;
+
+ GetR(r,euler_PQ);
+ Transpose(r,r);
+ for(i=0;i<3;i++) {
+ for(zP[i]=0.0, k=0; k<3; k++)
+ zP[i] += r[i][k]*rpA1[k];
+ zP[i] = acos(zP[i]);
+ }
+}
+
+void GetAngles()
+{
+ short i;
+ char other_sys;
+ float phiP, phiC;
+
+ if (reference_syst == 'P')
+ other_sys = 'Q';
+ else
+ other_sys = 'P';
+ GetrpA1(); /* ----> zPQ in gQ axis system */
+ GetzQ();
+ GetzP();
+ PrintOutAngles_zPQ('Q',theta1,phi1,zQ);
+ phiP = atan(-cos(zP[1])/cos(zP[0]));
+ PrintOutAngles_zPQ('P',zP[2],phiP,zP);
+ PrintOutRelOrntPQ(other_sys);
+}
+
+
+/* Transf. gP in gQ axis system */
+void RotateGP()
+{
+ PrintMatrix(gP," gP in gP");
+ GetR(rPQ, euler_PQ);
+ Transpose(rtPQ, rPQ);
+ MulMat(gP,gP,rtPQ);
+ MulMat(gP,rPQ,gP);
+ PrintMatrix(gP," gP in gQ");
+}
+
+
+void GetHyperfineProbs(hyperfine_prob,np)
+vector10 hyperfine_prob;
+int np;
+{
+ vector10 b;
+ double hnorm;
+ short i, j;
+
+ for(i=0; i<=np+1; i++)
+ hyperfine_prob[i] = 0.0;
+ hyperfine_prob[1] = 1.0;
+ if (np != 0 ) {
+ for (b[0] = 0,i=1; i<=np+1; i++) {
+ for (j=1; j<=i; j++)
+ b[j] = hyperfine_prob[j] + hyperfine_prob[j-1];
+ for (j=1; j<=i; j++)
+ hyperfine_prob[j] = b[j];
+ }
+ for (hnorm=0,i=0;i<10;i++)
+ hnorm += hyperfine_prob[i];
+ for (i=0;i<10;i++)
+ hyperfine_prob[i] /= hnorm;
+ }
+}
+
+void RotDipolarMatrix()
+{
+ short i, j;
+ matrix Rd, Rdt, Rdz, Rdy; /*, Djunk1, Djunk2; */
+
+ for (i=0; i<3; i++)
+ for(j=0; j<3; j++)
+ Dm[i][j] = 0.0;
+ Dm[0][0] = -d/3.0;
+ Dm[1][1] = -d/3.0;
+ Dm[2][2] = 2*d/3.0;
+ PrintMatrix(Dm, "Dipol-Tensor vor Drehung");
+ /* Rotationsmatrix: 1. Rot. um y-Achse um theta, 2. Rot. um z um phi
+ D' = Rz(phi) Ry(theta) D Ryt(theta) Rzt(phi) */
+ RotationMatrix(Rdy, theta1 * deg, 'y');
+ RotationMatrix(Rdz, phi1 * deg, 'z');
+ MulMat(Rd, Rdz, Rdy);
+ Transpose(Rdt,Rd);
+ MulMat(Dm, Rd, Dm);
+ MulMat(Dm, Dm, Rdt);
+/* vandenBrink et al. 1995 wieder gel�scht. SZ 20/08/98
+ for(i=0; i<3; i++)
+ for(j=0; j<3; j++)
+ Djunk1[i][j] = 0.0;
+ MulMat(Djunk1, gA12, Dm);
+ MulMat(Djunk1, Djunk1, gP2);
+ for(i=0; i<3; i++)
+ for(j=0; j<3; j++)
+ Djunk2[i][j] = 0.0;
+ MulMat(Djunk2, gP2, Dm);
+ MulMat(Djunk2, Djunk2, gA12);
+ for (i=0; i<3; i++)
+ for(j=0; j<3; j++)
+ Dm[i][j] = (Djunk1[i][j] + Djunk2[i][j])/2.0;
+ PrintMatrix(Dm, "Dipol-Tensor 1/2 (gA2 D gP2 + gP2 D gA2");
+ MulMat(Dm, gA12, Dm);
+ MulMat(Dm, Dm, gP2);
+ PrintMatrix(Dm, "Dipol-Tensor nach g-Mat. mult.");
+*/
+}
+
+/* Calc. actual dipolar coupling: deff = Bvec D Bvec */
+double Get_deff(B0vector)
+vector B0vector;
+{
+ short i, j;
+ double deff; /*, teiler; */
+
+ /* teiler = geffA1*geffP*4.0092053; */
+ for (deff=0.0, i=0; i<3; i++)
+ for (j=0; j<3; j++)
+ deff += B0vector[i] * B0vector[j] * Dm[i][j];
+ return(deff);
+ /* Bei Multiplikation mit G-tensoren: Normierung
+ return(deff/teiler);
+ */
+}
+
+
+
+void InitPar()
+{
+ double ct, st, sp, cp;
+ short i;
+ matrix gPt, gA1t;
+
+ step_size = nt*np;
+ J = GBETA*J;
+ d = GBETA*d;
+ hbP = 0.5*SQR(GBETA*hbP);
+ hbA1 = 0.5*SQR(GBETA*hbA1);
+ hbPA1 = (hbP + hbA1)/2.0;
+ theta1 = theta1 * rad;
+ phi1 = phi1 * rad;
+ for (i=0; i<3; i++){
+ euler_PQ[i] *= rad;
+ }
+ RotateGP();
+ GetAngles();
+ Transpose(gPt, gP);
+ Transpose(gA1t, gA1);
+ MulMat(gP2,gP,gPt);
+ MulMat(gA12,gA1,gA1t);
+ RotDipolarMatrix();
+ PrintMatrix(gP2,"g-Tensor fuer P2+");
+ PrintMatrix(gA12,"g-Tensor fuer A12");
+ if (number_of_protons != 0) {
+ MulMat(ga2,gA1,aA1);
+ MulMat(ga2,ga2,ga2);
+ }
+ if (n_protons_p != 0) {
+ MulMat(gaP2,gP,aP);
+ MulMat(gaP2,gaP2,gaP2);
+ }
+ GetHyperfineProbs(hyperfine_prob_P,n_protons_p);
+ PrintVec10(hyperfine_prob_P," Hyperfein-Wahrscheinlichkeiten fuer P");
+ GetHyperfineProbs(hyperfine_prob_A1,number_of_protons);
+ PrintVec10(hyperfine_prob_A1," Hyperfein-Wahrscheinlichkeiten fuer A1");
+}
+
+void Getgeff(B0vector)
+vector B0vector;
+{
+ double deff;
+ short i, k;
+
+ for (geffA1=geffP=0,i=0; i<3; i++) {
+ for (k=0; k<3; k++)
+ geffA1 += B0vector[i] * B0vector[k] * gA12[i][k];
+ for (k=0; k<3; k++)
+ geffP += B0vector[i] * B0vector[k] * gP2[i][k];
+ }
+ geffP = sqrt(geffP);
+ geffA1 = sqrt(geffA1);
+ if (number_of_protons != 0) {
+ for (aeffA1=0,i=0; i<3; i++)
+ for (k=0; k<3; k++)
+ aeffA1 += B0vector[i] * B0vector[k] * ga2[i][k];
+ aeffA1 = sqrt(aeffA1)/geffA1;
+ }
+ if (n_protons_p != 0) {
+ for (aeffP=0,i=0; i<3; i++)
+ for (k=0; k<3; k++)
+ aeffP += B0vector[i] * B0vector[k] * gaP2[i][k];
+ aeffP = sqrt(aeffP)/geffP;
+ }
+ deff = Get_deff(B0vector);
+ Jpd = J + deff/2.0;
+ Jmd = J - deff;
+}
+
+
+void GetTransitionFrequencies(h)
+double h;
+{
+ double w0, q, inten, p_character, hb12, hb34, norm12, norm34, x;
+
+ w0 = BE * h * (geffA1 + geffP) / 2.0
+ + miA1 * aeffA1/2.0 + miP * aeffP/2.0;
+ q = BE * h * (geffP-geffA1)/2.0
+ -miA1 * aeffA1/2.0 + miP * aeffP/2.0;
+
+ x = sqrt(Jpd*Jpd + q*q)*q/fabs(q);
+ p_character = 0.5 * (1 + q/x);
+ hb12 = p_character * hbP + (1. - p_character) * hbA1;
+ hb34 = p_character * hbA1 + (1. - p_character) * hbP;
+ trans[0] = -SQR(-fmw + w0 + Jmd + x)/hb12;
+ trans[1] = -SQR(-fmw + w0 - Jmd + x)/hb12;
+ trans[2] = -SQR(-fmw + w0 + Jmd - x)/hb34;
+ trans[3] = -SQR(-fmw + w0 - Jmd - x)/hb34;
+ inten = q*q/(4 * (Jpd*Jpd + q*q))
+ * hyperfine_prob_A1[imiA1] * hyperfine_prob_P[imiP];
+ intens[0] = -inten * FACTOR / hb12;
+ intens[1] = inten * FACTOR / hb12;
+ intens[2] = -inten * FACTOR / hb34;
+ intens[3] = inten * FACTOR / hb34;
+}
+
+
+void SingleOrientationSpectrum(B0vector)
+vector B0vector;
+{
+ double h;
+ short field_pt, k;
+
+ Getgeff(B0vector);
+ for (miA1 = -number_of_protons/2.0,imiA1 = 1;
+ imiA1 <= number_of_protons + 1; imiA1++) {
+ for (miP = -n_protons_p/2.0, imiP = 1;
+ imiP <= n_protons_p + 1; imiP++) {
+ for (h=h1,field_pt=0; field_pt < NumOfPoints; field_pt++) {
+ GetTransitionFrequencies(h);
+ if ((imiA1 == 1) && (imiP == 1))
+ orient_spec[field_pt] = 0.0;
+ for (k = 0; k < 4; k++) {
+ if (trans[k] > -15.0) {
+ Transpec[k][field_pt] += intens[k]* exp(trans[k])/step_size;
+ orient_spec[field_pt] += intens[k]* exp(trans[k])/step_size;
+ }
+ }
+ if ((imiA1 == number_of_protons + 1) && (imiP == n_protons_p +1))
+ spec[field_pt] += orient_spec[field_pt];
+ h += dh;
+ }
+ miP += 1.0;
+ }
+ miA1 += 1.0;
+ }
+}
+
+
+
+/* Direction of B0 in Q axes system */
+void GetB0vector(B0vector, cos_theta_B0, phi_B0)
+ vector B0vector;
+ double cos_theta_B0, phi_B0;
+{
+ double sin_theta_B0;
+
+ sin_theta_B0 = Compliment(cos_theta_B0);
+ B0vector[0] = sin_theta_B0 * cos(phi_B0);
+ B0vector[1] = sin_theta_B0 * sin(phi_B0);
+ B0vector[2] = cos_theta_B0;
+}
+
+
+void MakeTensorWithHfc(B0vector)
+vector B0vector;
+{
+ double freq, faktor, A, B, breite, delta_w, delta_w_i, R_2, R;
+ double exponent, y, inten;
+ long int freq_point, i;
+
+ Getgeff(B0vector);
+ A = 2*Jmd;
+ B = 2*Jpd;
+ delta_w = BE * 0.5*(h1+h2) * (geffP - geffA1);
+ breite = sqrt(2*hbPA1);
+ for (delta_w_i = delta_w - 3*breite ; delta_w_i <= delta_w + 3*breite;
+ delta_w_i += 6*breite/delta_w_steps) {
+ exponent = -SQR(delta_w - delta_w_i)/hbPA1;
+ inten = exp(exponent);
+ R_2 = SQR(delta_w_i) + SQR(B);
+ if (delta_w_i != delta_w)
+ R = sqrt(R_2) * (delta_w_i-delta_w)/fabs(delta_w_i-delta_w);
+ else
+ R = sqrt(R_2);
+ if (R_2 != 0.0)
+ faktor = SQR(delta_w_i) * SQR(B) / SQR(R_2);
+ for (freq_point = 0, freq = - max_freq ;
+ freq_point < num_freq_points; freq_point++) {
+ if ((y = SQR((A-freq)/lorentz_hb)) < 1e+03) {
+ tens[0][freq_point] += faktor/(1 + y);
+ tensor[freq_point] += faktor/(1 + y);
+ }
+ if ((y = SQR((A-R-freq)/lorentz_hb)) < 1e+03) {
+ tens[1][freq_point] += -0.5*inten*faktor/(1 + y);
+ tensor[freq_point] += - 0.5*inten*faktor/(1 + y);
+ }
+ if ((y = SQR((A+R-freq)/lorentz_hb)) < 1e+03) {
+ tens[2][freq_point] += -0.5*inten*faktor/(1 + y);
+ tensor[freq_point] += -0.5*inten*faktor/(1 + y);
+ }
+
+ freq += 2*max_freq/(num_freq_points-1);
+ }
+ }
+}
+
+/* ESEEM FTs without consideration of Hfc's ot G-anisotropy --
+ only dipolar and exchange interaction Gamma = 2 (J - d)
+ with Lorentzian broadening */
+
+void MakeTensor(B0vector)
+vector B0vector;
+{
+ double freq, Gamma, y;
+ long int freq_point, i;
+
+ Getgeff(B0vector);
+ Gamma = 2*Jmd;
+
+ for (freq_point = 0, freq = - max_freq ; freq_point < num_freq_points;
+ freq_point++) {
+ if ((y = SQR((Gamma-freq)/lorentz_hb)) < 1e+03) {
+ tensor[freq_point] += 1/(1 + y);
+ }
+ freq += 2*max_freq/(num_freq_points-1);
+ }
+}
+
+/* Add Gamma and -Gamma contribution (Point Symmetry of SFT) */
+void MakeESEEMFourier()
+{
+ double *temp;
+ int i, k;
+
+ if ((temp = (double *)malloc(num_freq_points*sizeof(double))) == NULL) {
+ printf("Couldn't allocate memory for TEMP\n");
+ }
+
+ for (i=0; i<num_freq_points; i++)
+ temp[i] = tensor[num_freq_points - 1 - i];
+ for (i=0; i<num_freq_points; i++)
+ tensor[i] -= temp[i];
+}
+
+void MakeESEEMFourierWithHfc()
+{
+ double *temp;
+ int i, k;
+
+ if ((temp = (double *)malloc(num_freq_points*sizeof(double))) == NULL) {
+ printf("Couldn't allocate memory for TEMP\n");
+ }
+
+ for (i=0; i<num_freq_points; i++)
+ temp[i] = tensor[num_freq_points - 1 - i];
+ for (i=0; i<num_freq_points; i++) {
+ tensor[i] -= temp[i];
+ /*
+ tensor[i] /= delta_w_steps;
+ */
+ }
+ for (k=0; k<3; k++) {
+ for (i=0; i<num_freq_points; i++)
+ temp[i] = tens[k][num_freq_points - 1 - i];
+ for (i=0; i<num_freq_points; i++) {
+ tens[k][i] -= temp[i];
+ /*
+ tens[k][i] /= delta_w_steps;
+ */
+ }
+ }
+}
+
+void Write_FT_Files()
+{
+ char spec_fn[20];
+
+ sprintf(spec_fn, "%s_ten", outfile);
+ printf("%s\n", spec_fn);
+ WriteSpec(-max_freq, max_freq, tensor, num_freq_points, spec_fn);
+ sprintf(spec_fn, "%s_A", outfile);
+ WriteSpec(-max_freq, max_freq, tens[0], num_freq_points, spec_fn);
+ sprintf(spec_fn, "%s_AmR", outfile);
+ WriteSpec(-max_freq, max_freq, tens[1], num_freq_points, spec_fn);
+ sprintf(spec_fn, "%s_ApR", outfile);
+ WriteSpec(-max_freq, max_freq, tens[2], num_freq_points, spec_fn);
+}
+
+void Write_TrEPR_Files()
+{
+ int i,k;
+ char spec_fn[20];
+
+ sprintf(spec_fn, "%s_spec", outfile);
+ printf("%s\n", spec_fn);
+ WriteSpec(h1, h2, spec, NumOfPoints, spec_fn);
+ sprintf(spec_fn, "%s_Pem", outfile);
+ WriteSpec(h1, h2, Transpec[0], NumOfPoints, spec_fn);
+ sprintf(spec_fn, "%s_Pabs", outfile);
+ WriteSpec(h1, h2, Transpec[1], NumOfPoints, spec_fn);
+ sprintf(spec_fn, "%s_Qem", outfile);
+ WriteSpec(h1, h2, Transpec[2], NumOfPoints, spec_fn);
+ sprintf(spec_fn, "%s_Qabs", outfile);
+ WriteSpec(h1, h2, Transpec[3], NumOfPoints, spec_fn);
+ for (i = 0; i < NumOfPoints; i++) {
+ spec[i] = 0.;
+ for (k = 0; k < 4; k++) spec[i] += Transpec[k][i];
+ }
+ sprintf(spec_fn, "%s_sum", outfile);
+ WriteSpec(h1, h2, spec, NumOfPoints, spec_fn);
+}
+
+void MakeSpec()
+{
+ double cos_theta_B0, phi_B0, delta_cos_theta, delta_phi;
+ vector B0vector;
+ short i, i_cos_theta, i_phi;
+
+ delta_cos_theta = 2.0/nt;
+ delta_phi = PI/np;
+
+ for (cos_theta_B0 = 1 - delta_cos_theta/2, i_cos_theta = 1;
+ i_cos_theta <= nt; i_cos_theta++) {
+ printf("%d\t%f\n", nt - i_cos_theta, cos_theta_B0); fflush(stdout);
+ for (phi_B0 = 0.0, i_phi=1; i_phi <= np; i_phi++) {
+ GetB0vector(B0vector, cos_theta_B0, phi_B0);
+ if (tolower(print_Powder) == 'y')
+ SingleOrientationSpectrum(B0vector);
+ if (tolower(print_ESEEM_FT) == 'y') {
+ if (delta_w_steps == 0) {
+ MakeTensor(B0vector);
+ }
+ else {
+ MakeTensorWithHfc(B0vector);
+ }
+ }
+ phi_B0 += delta_phi;
+ }
+ cos_theta_B0 -= delta_cos_theta;
+ }
+ if (tolower(print_Powder) == 'y')
+ Write_TrEPR_Files();
+ if (tolower(print_ESEEM_FT) == 'y') {
+ if (delta_w_steps == 0)
+ MakeESEEMFourier();
+ else
+ MakeESEEMFourierWithHfc();
+ Write_FT_Files();
+ }
+}
+
+void RingBell(n)
+int n;
+{
+ short i;
+
+ for (i=1; i<=n; i++) {
+ printf("\7 \n");
+ }
+ printf("Fertig! \n");
+}
+
+
+void InitVariables(NumOfPoints, FreqPkt)
+int NumOfPoints, FreqPkt;
+{
+ int i, k;
+
+
+ if ((tensor = (double *)malloc(FreqPkt*sizeof(double))) == NULL)
+ printf("Couldn't allocate memory for TENSOR\n");
+
+ if ((tens = (void *)malloc(3*sizeof(double *))) == NULL)
+ printf("No Memory for TENS-Pointer\n");
+
+ for (k=0; k<3; k++) {
+ if ((tens[k] = (double *)malloc(FreqPkt*sizeof(double))) == NULL)
+ printf("Couldn't allocate memory for Tens\n");
+ for (i=0; i<FreqPkt; i++)
+ tens[k][i] = 0.0;
+ }
+
+ for (i = 0; i < FreqPkt; i++)
+ tensor[i] = 0.0;
+
+ if ((Transpec = (void *)malloc(4*sizeof(double *))) == NULL)
+ printf("No Memory for Transpec-Pointer\n");
+
+
+ for (k=0; k < 4; k++) {
+ if ((Transpec[k] = (double *)malloc(NumOfPoints*sizeof(double))) == NULL)
+ printf("Couldn't allocate memory for Transpec\n");
+ for (i=0; i < NumOfPoints; i++)
+ Transpec[k][i] = 0.0;
+ }
+
+ if ((spec = (double *)malloc(NumOfPoints*sizeof(double))) == NULL)
+ printf("Couldn't allocate memory for SPEC\n");
+ if ((orient_spec = (double *)malloc(NumOfPoints*sizeof(double))) == NULL)
+ printf("Couldn't allocate memory for ORIENT_SPEC\n");
+ for (i=0; i < NumOfPoints; i++) {
+ spec[i] = 0.0;
+ orient_spec[i] = 0.0;
+ }
+}
+
+int main() {
+
+ int k;
+
+ if (ReadInput() == 0) {
+ WriteInput();
+ InitVariables(NumOfPoints, num_freq_points);
+ InitPar();
+ MakeSpec();
+ /*
+ WriteGnuInput();
+ */
+ RingBell(1);
+ }
+}
+
diff --git a/from_bittl/src/p2.h b/from_bittl/src/p2.h
new file mode 100755
index 0000000..45aab17
--- /dev/null
+++ b/from_bittl/src/p2.h
@@ -0,0 +1,52 @@
+#define PI M_PI
+#define DataT double
+#define MAX_NUMBER_POINTS 32
+#define BE 1.399624167 /* beta/h; (vorher 1.39968) SZ 9/8/96 */
+#define GBETA (2.0023193*BE)
+#define FACTOR 0.398942 /*(1/sqrt(2*PI))*/
+#define SQR(x) ((x)*(x))
+#define asc ".asc\0"
+#define deg (180.0/PI)
+#define rad (PI/180.0)
+/*#define register short*/ /* SZ 26/8/95 */
+
+typedef DataT
+ vector[3],
+ vector4[4],
+ vector10[10];
+
+typedef vector
+ matrix[3];
+
+typedef char
+ strg[16];
+
+strg filename[9], orient_name[3];
+
+double *spec, **Transpec, **tens, *orient_spec;
+
+double *tensor;
+
+matrix aA1, aP, gP, gP2, gA1, gA12, gaP2, ga2, Dm,
+ rPQ, rtPQ, rCQ, rtCQ, rBC, rtBC, Ra,
+ Rz180, Rz120, Rz240;
+
+vector rpA1, euler_PQ, euler_zP, euler_zQ, zP, zQ;
+
+
+vector4 intens, trans;
+
+vector10 hyperfine_prob_P, hyperfine_prob_A1;
+
+DataT fmw, h1, h2, dh, phi1, theta1, J, d, Jpd, Jmd, geffP,
+ geffA1, aeffP, aeffA1, hbP, hbA1, hbPA1, miA1, miP,
+ lorentz_hb, max_freq;
+
+int imiA1, imiP, nt, np, step_size, number_of_protons,
+ n_protons_p, NumOfPoints, delta_w_steps, num_freq_points,
+ alpha_step, astep, num_spec;
+
+char reference_syst, print_orient, print_Powder,
+ print_ESEEM_FT, outfile[20];
+
+
diff --git a/from_bittl/src/p2.txt b/from_bittl/src/p2.txt
new file mode 100755
index 0000000..0b3d5fb
--- /dev/null
+++ b/from_bittl/src/p2.txt
@@ -0,0 +1,40 @@
+9700. MIKROWELLEN-FREQUENZ
+3450. 3470. 1024 MAGNETFELD
+181 181 GENAUIGKEIT
+2.00300 0.00000 0.00000
+0.00000 2.00260 0.00000
+0.00000 0.00000 2.00230 G-TENSOR P700+
+0.2 LINIENBREITE P
+2.00620 0.00000 0.00000
+0.00000 2.00510 0.00000
+0.00000 0.00000 2.00220 G-TENSOR Qb-
+0.2 LINIENBREITE Q
+Q REFERENZSYSTEM
+0.0 90.0 PHI,THETA
+83.0 128.0 10.0 ALPHA,BETA,GAMMA
++0.01 -1.7 J,D
+Y ORIENTIERUNGSSPEKTREN?
+Y PULVERSPEKTRUM?
+N ESEEM_FT?
+test2 OUTPUT_FILENAME
+31.25 512 MAX.ESEEM-FT-FREQUENZ,FREQ-PUNKTE
+256 HYPERFEIN_SCHRITTE
+0. LORENTZ_BREITE(MHz)
+3 ANZAHL_DER_PROTONEN_AM_A1-
+-10.25 -1.472 0.000
+-1.472 -11.95 0.000
+0.000 0.000 -9.000
+0 ANZAHL_DER_PROTONEN_AM_P+
+ 0.1 0.0 0.0
+ 0.0 0.1 0.0
+ 0.0 0.0 0.1
+
+10.25 1.472 0.000
+ 1.472 11.95 0.000
+ 0.000 0.000 9.000
+
+-4.5 0.0 0.0
+ 0.0 -4.0 0.0
+ 0.0 0.0 -3.5
+
+ HFC Tensor A1- (9.4,12.8,9.0) 30 grd gedreht.
diff --git a/from_bittl/src/p2_utils.c b/from_bittl/src/p2_utils.c
new file mode 100755
index 0000000..3f8be1b
--- /dev/null
+++ b/from_bittl/src/p2_utils.c
@@ -0,0 +1,155 @@
+void PrintMatrix(a,title)
+matrix a;
+char title[];
+{
+ int i, j;
+
+ printf("\n %s \n",title);
+ for (i=0;i<=2;i++) {
+ printf(" ");
+ for (j=0;j<=2;j++)
+ printf("%9.5f%c",a[i][j],' ');
+ printf("\n");
+ }
+}
+
+void PrintVec(a,title)
+vector a;
+char title[];
+{
+ int i;
+
+ printf("\n %s \n",title);
+ for (i=0;i<=2;i++)
+ printf("%9.5f%c",a[i],' ');
+ printf("\n");
+}
+
+void PrintVec10(a,title)
+vector10 a;
+char title[];
+{
+ int i;
+
+ printf("\n %s \n",title);
+ for (i=0;i<=4;i++)
+ printf("%9.5f%c",a[i],' ');
+ printf("\n");
+ for (i=5;i<=9;i++)
+ printf("%9.5f%c",a[i],' ');
+ printf("\n");
+ printf("\n");
+}
+
+void CopyMatrix (a,b)
+matrix a, b;
+{
+ short i, j;
+
+ for (i=0; i<3; i++)
+ for (j=0; j<3; j++)
+ a[i][j] = b[i][j];
+}
+
+void MulMat(a,b,c)
+matrix a, b, c;
+{
+ double dummy;
+ matrix d, e;
+ short i, j, k;
+
+ CopyMatrix(d,b);
+ CopyMatrix(e,c);
+ for (i=0; i<3; i++)
+ for (j=0; j<3; j++) {
+ for (dummy=0, k=0; k<3; k++)
+ dummy += d[i][k] * e[k][j];
+ a[i][j] = dummy;
+ }
+}
+
+void Transpose (a,b)
+matrix a, b;
+{
+ short i, j;
+ matrix c;
+
+ CopyMatrix(c,b);
+ for (i=0; i<3; i++)
+ for (j=0; j<3; j++)
+ a[j][i] = c[i][j];
+}
+
+void RotationMatrix(a,winkel,axis)
+matrix a;
+double winkel;
+char axis;
+{
+ short i, j, k;
+
+ winkel = winkel * PI /180.0;
+ for (i=0; i<3; i++)
+ for (j=0; j<3; j++)
+ a[i][j] = 0.0;
+ switch (axis) {
+ case 'x':
+ i=0;
+ j=1;
+ k=2;
+ break;
+ case 'y':
+ i=1;
+ j=2;
+ k=0;
+ break;
+ case 'z':
+ i=2;
+ j=0;
+ k=1;
+ break;
+ }
+ a[i][i] = 1.0;
+ a[j][j] = cos(winkel);
+ a[k][k] = cos(winkel);
+ a[j][k] = sin(winkel);
+ a[k][j] = -sin(winkel);
+}
+
+void NewLine(fp)
+FILE *fp;
+{
+ char c;
+
+ while ((c = getc(fp)) != '\n');
+}
+
+
+double Compliment(a)
+double a;
+{
+ if (a*a > 1.0) {
+ printf(" Warning: Function \"Compliment\" called with a value greater than 1.0!! Returns a value of 0.0 ");
+ return 0.0;
+ }
+ else
+ return sqrt(1.0 - a*a);
+}
+
+void WriteSpec(low, high, sp, n,name)
+double low, high, *sp;
+int n;
+char name[];
+{
+ int i;
+ FILE *fp, *fopen();
+ double range;
+
+ range = high - low;
+ strncat(name,asc,sizeof(asc));
+ if ((fp = fopen(name,"w")) == NULL)
+ printf("file %s cannot be opened",name);
+ for (i=0; i<n; i++)
+ fprintf(fp,"%.3f\t%.9f\n",low + i*range/(n-1), sp[i]);
+ fclose(fp);
+}
+
diff --git a/from_bittl/src/test2_Pabs.asc b/from_bittl/src/test2_Pabs.asc
new file mode 100755
index 0000000..f65f2fa
--- /dev/null
+++ b/from_bittl/src/test2_Pabs.asc
@@ -0,0 +1,1024 @@
+3450.000 0.000000000
+3450.020 0.000000000
+3450.039 0.000000000
+3450.059 0.000000000
+3450.078 0.000000000
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diff --git a/from_bittl/src/test2_Pem.asc b/from_bittl/src/test2_Pem.asc
new file mode 100755
index 0000000..5a30571
--- /dev/null
+++ b/from_bittl/src/test2_Pem.asc
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diff --git a/from_bittl/src/test2_Qabs.asc b/from_bittl/src/test2_Qabs.asc
new file mode 100755
index 0000000..e101310
--- /dev/null
+++ b/from_bittl/src/test2_Qabs.asc
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diff --git a/from_bittl/src/test2_Qem.asc b/from_bittl/src/test2_Qem.asc
new file mode 100755
index 0000000..bd95999
--- /dev/null
+++ b/from_bittl/src/test2_Qem.asc
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diff --git a/from_bittl/src/test2_spec.asc b/from_bittl/src/test2_spec.asc
new file mode 100755
index 0000000..1d8f4b3
--- /dev/null
+++ b/from_bittl/src/test2_spec.asc
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diff --git a/from_bittl/src/test2_sum.asc b/from_bittl/src/test2_sum.asc
new file mode 100755
index 0000000..1d8f4b3
--- /dev/null
+++ b/from_bittl/src/test2_sum.asc
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diff --git a/trEPR_spectrumIntegral.asv b/trEPR_spectrumIntegral.asv
new file mode 100644
index 0000000..73ca950
--- /dev/null
+++ b/trEPR_spectrumIntegral.asv
@@ -0,0 +1,256 @@
+%
+clearvars
+
+Sys.S = [1/2 1/2];
+Sys.g = [2, 2.0075];
+
+Sys.initState = 'singlet';
+
+% Exchange coupling
+nj = 100;
+Js = linspace(1e-2, 100, nj); % MHz
+
+gPlus = (Sys.g(1) + Sys.g(2))/2;
+mwFreq = 9.7; % GHz
+B0 = planck/bmagn/gPlus*mwFreq*1e12; % mT
+nPoint = 5000;
+msAx = linspace(9.4, 10, nPoint); % GHz, mw sweep axis
+bsAx = mhz2mt(msAx*1e3, gPlus); % mT, b field sweep
+
+%
+% Frequency sweep
+%
+mhzLw = 10;
+Sys.lw = mhzLw; % MHz
+
+Exp.mwRange = [min(msAx), max(msAx)];
+Exp.Field = B0;
+Exp.nPoints = nPoint;
+Exp.Harmonic = 0;
+
+msSim = zeros(nj, nPoint);
+
+for ij = 1:nj
+ Sys.J = Js(ij);
+ msSim(ij, :) = pepper(Sys, Exp);
+ % msSim(ij, :) = msSim(ij, :)/max(abs(msSim(ij, :)));
+end
+
+msTotIntegral = sum(msSim, 2)/nPoint;
+
+%
+% Field sweep
+%
+clear("Exp")
+
+Sys.lw = mhz2mt(mhzLw); % mT
+
+Exp.Range = [min(bsAx), max(bsAx)];
+Exp.mwFreq = mwFreq;
+Exp.nPoints = nPoint;
+Exp.Harmonic = 0;
+
+bsSim = zeros(nj, nPoint);
+
+for ij = 1:nj
+ Sys.J = Js(ij);
+ bsSim(ij, :) = pepper(Sys, Exp);
+ % bsSim(ij, :) = bsSim(ij, :)/max(abs(bsSim(ij, :)));
+end
+
+bsTotIntegral = sum(bsSim, 2)/nPoint;
+
+clf
+plot(Js, msTotIntegral, 'o-', 'DisplayName', 'Mw sweep')
+yyaxis right
+plot(Js, bsTotIntegral, 'o-', 'DisplayName', 'B0 sweep')
+xlabel('J / MHz')
+yyaxis left
+ylabel('Integral of trEPR spectrum')
+legend()
+
+%%
+
+ij = 100;
+clf
+plot(msAx, msSim(ij, :))
+yyaxis right
+plot(msAx, flip(bsSim(ij, :)))
+
+%%
+clearvars
+
+Sys.S = [1/2 1/2];
+Sys.g = [2, 2.0075];
+
+Sys.initState = 'singlet';
+
+% Dipolar coupling
+ndip = 100;
+dips = linspace(1, 100, ndip); % MHz
+
+gPlus = (Sys.g(1) + Sys.g(2))/2;
+mwFreq = 9.7; % GHz
+B0 = planck/bmagn/gPlus*mwFreq*1e12; % mT
+nPoint = 5000;
+msAx = linspace(9.4, 10, nPoint); % GHz, mw sweep axis
+bsAx = mhz2mt(msAx*1e3, gPlus); % mT, b field sweep
+
+%
+% Frequency sweep
+%
+mhzLw = 10;
+Sys.lw = mhzLw; % MHz
+
+Exp.mwRange = [min(msAx), max(msAx)];
+Exp.Field = B0;
+Exp.nPoints = nPoint;
+Exp.Harmonic = 0;
+
+msSim = zeros(ndip, nPoint);
+
+for ij = 1:ndip
+ Sys.dip = dips(ij);
+ msSim(ij, :) = pepper(Sys, Exp);
+ % msSim(ij, :) = msSim(ij, :)/max(abs(msSim(ij, :)));
+end
+
+msTotIntegral = sum(msSim, 2)/nPoint;
+
+%
+% Field sweep
+%
+clear("Exp")
+
+Sys.lw = mhz2mt(mhzLw); % mT
+
+Exp.Range = [min(bsAx), max(bsAx)];
+Exp.mwFreq = mwFreq;
+Exp.nPoints = nPoint;
+Exp.Harmonic = 0;
+
+bsSim = zeros(ndip, nPoint);
+
+for ij = 1:ndip
+ Sys.dip = dips(ij);
+ bsSim(ij, :) = pepper(Sys, Exp);
+ % bsSim(ij, :) = bsSim(ij, :)/max(abs(bsSim(ij, :)));
+end
+
+bsTotIntegral = sum(bsSim, 2)/nPoint;
+
+clf
+plot(dips, msTotIntegral, 'o-', 'DisplayName', 'Mw sweep')
+yyaxis right
+plot(dips, bsTotIntegral, 'o-', 'DisplayName', 'B0 sweep')
+xlabel('J / MHz')
+yyaxis left
+ylabel('Integral of trEPR spectrum')
+legend()
+
+%%
+ij = 100;
+clf
+plot(msAx, msSim(ij, :))
+yyaxis right
+plot(msAx, flip(bsSim(ij, :)))
+
+%%
+clearvars
+
+Sys.S = [1/2 1/2];
+Sys.g = [2, 2.0075];
+Sys.dip = 5; % MHz
+
+Sys.initState = 'singlet';
+
+gPlus = (Sys.g(1) + Sys.g(2))/2;
+mwFreq = 9.7; % GHz
+B0 = planck/bmagn/gPlus*mwFreq*1e12; % mT
+nPoint = 5000;
+msAx = linspace(9.4, 10, nPoint); % GHz, mw sweep axis
+bsAx = mhz2mt(msAx*1e3, gPlus); % mT, b field sweep
+
+%
+% Frequency sweep
+%
+mhzLw = 10;
+Sys.lw = mhzLw; % MHz
+
+Exp.mwRange = [min(msAx), max(msAx)];
+Exp.Field = B0;
+Exp.nPoints = nPoint;
+Exp.Harmonic = 0;
+
+Opt.GridSize = [91 0]; % 181 orientations
+Opt.GridSymmetry = 'C1';
+
+% Powder average
+msSim = pepper(Sys, Exp, Opt);
+
+clear("Opt")
+
+Exp.CrystalSymmetry = 1;
+Exp.MolFrame = [0 0 0]*pi/180;
+Exp.SampleFrame = [0 0 0]*pi/180;
+
+Opt.separate = 'orientations';
+rho = deg2rad(linspace(0, 180, 181)); % 10 degree increments
+solidAngleWeight = sin(rho')/sum(sin(rho), 'all');
+
+% Rotation around x
+Exp.SampleRotation = {'x', rho};
+msSimRotX = pepper(Sys, Exp, Opt);
+msPowderRotX = sum(solidAngleWeight.*msSimRotX);
+
+% Rotation around y
+Exp.SampleRotation = {'y', rho};
+msSimRotY = pepper(Sys, Exp, Opt);
+msPowderRotY = sum(solidAngleWeight.*msSimRotY);
+
+%
+% Field sweep
+%
+clear("Exp")
+
+Sys.lw = mhz2mt(mhzLw); % mT
+
+Exp.Range = [min(bsAx), max(bsAx)];
+Exp.mwFreq = mwFreq;
+Exp.nPoints = nPoint;
+Exp.Harmonic = 0;
+
+clear("Opt")
+Opt.GridSize = [91 0]; % 181 orientations
+Opt.GridSymmetry = 'C1';
+
+% Powder average
+bsSim = pepper(Sys, Exp, Opt);
+
+clear("Opt")
+
+Exp.CrystalSymmetry = 1;
+Exp.MolFrame = [0 0 0]*pi/180;
+Exp.SampleFrame = [0 0 0]*pi/180;
+
+Opt.separate = 'orientations';
+rho = deg2rad(linspace(0, 180, 181));
+solidAngleWeight = sin(rho')/sum(sin(rho), 'all');
+
+% Rotation around x
+Exp.SampleRotation = {'x', rho};
+bsSimRotX = pepper(Sys, Exp, Opt);
+bsPowderRotX = sum(solidAngleWeight.*bsSimRotX);
+
+% Rotation around y
+Exp.SampleRotation = {'y', rho};
+bsSimRotY = pepper(Sys, Exp, Opt);
+bsPowderRotY = sum(solidAngleWeight.*bsSimRotY);
+
+%%
+
+clf
+plot(msAx, msPowderRotX, msAx, msPowderRotY)
+% clf
+% plot(bsAx, bsPowderRotX, bsAx, bsPowderRotY)
+
diff --git a/trEPR_spectrumIntegral.m b/trEPR_spectrumIntegral.m
new file mode 100644
index 0000000..6600b3b
--- /dev/null
+++ b/trEPR_spectrumIntegral.m
@@ -0,0 +1,257 @@
+%% 1. Exhange coupling
+clearvars
+
+Sys.S = [1/2 1/2];
+Sys.g = [2, 2.0075];
+
+Sys.initState = 'singlet';
+
+% Exchange coupling
+nj = 100;
+Js = linspace(1e-2, 100, nj); % MHz
+
+gPlus = (Sys.g(1) + Sys.g(2))/2;
+mwFreq = 9.7; % GHz
+B0 = planck/bmagn/gPlus*mwFreq*1e12; % mT
+nPoint = 5000;
+msAx = linspace(9.4, 10, nPoint); % GHz, mw sweep axis
+bsAx = mhz2mt(msAx*1e3, gPlus); % mT, b field sweep
+
+%
+% Frequency sweep
+%
+mhzLw = 10;
+Sys.lw = mhzLw; % MHz
+
+Exp.mwRange = [min(msAx), max(msAx)];
+Exp.Field = B0;
+Exp.nPoints = nPoint;
+Exp.Harmonic = 0;
+
+msSim = zeros(nj, nPoint);
+
+for ij = 1:nj
+ Sys.J = Js(ij);
+ msSim(ij, :) = pepper(Sys, Exp);
+ % msSim(ij, :) = msSim(ij, :)/max(abs(msSim(ij, :)));
+end
+
+msTotIntegral = sum(msSim, 2)/nPoint;
+
+%
+% Field sweep
+%
+clear("Exp")
+
+Sys.lw = mhz2mt(mhzLw); % mT
+
+Exp.Range = [min(bsAx), max(bsAx)];
+Exp.mwFreq = mwFreq;
+Exp.nPoints = nPoint;
+Exp.Harmonic = 0;
+
+bsSim = zeros(nj, nPoint);
+
+for ij = 1:nj
+ Sys.J = Js(ij);
+ bsSim(ij, :) = pepper(Sys, Exp);
+ % bsSim(ij, :) = bsSim(ij, :)/max(abs(bsSim(ij, :)));
+end
+
+bsTotIntegral = sum(bsSim, 2)/nPoint;
+
+clf
+plot(Js, msTotIntegral, 'o-', 'DisplayName', 'Mw sweep')
+yyaxis right
+plot(Js, bsTotIntegral, 'o-', 'DisplayName', 'B0 sweep')
+xlabel('J / MHz')
+yyaxis left
+ylabel('Integral of trEPR spectrum')
+legend()
+
+%% Plot
+
+ij = 100;
+clf
+plot(msAx, msSim(ij, :))
+yyaxis right
+plot(msAx, flip(bsSim(ij, :)))
+
+%% Dipolar coupling
+clearvars
+
+Sys.S = [1/2 1/2];
+Sys.g = [2, 2.0075];
+
+Sys.initState = 'singlet';
+
+% Dipolar coupling
+ndip = 100;
+dips = linspace(1, 100, ndip); % MHz
+
+gPlus = (Sys.g(1) + Sys.g(2))/2;
+mwFreq = 9.7; % GHz
+B0 = planck/bmagn/gPlus*mwFreq*1e12; % mT
+nPoint = 5000;
+msAx = linspace(9.4, 10, nPoint); % GHz, mw sweep axis
+bsAx = mhz2mt(msAx*1e3, gPlus); % mT, b field sweep
+
+%
+% Frequency sweep
+%
+mhzLw = 10;
+Sys.lw = mhzLw; % MHz
+
+Exp.mwRange = [min(msAx), max(msAx)];
+Exp.Field = B0;
+Exp.nPoints = nPoint;
+Exp.Harmonic = 0;
+
+msSim = zeros(ndip, nPoint);
+
+for ij = 1:ndip
+ Sys.dip = dips(ij);
+ msSim(ij, :) = pepper(Sys, Exp);
+ % msSim(ij, :) = msSim(ij, :)/max(abs(msSim(ij, :)));
+end
+
+msTotIntegral = sum(msSim, 2)/nPoint;
+
+%
+% Field sweep
+%
+clear("Exp")
+
+Sys.lw = mhz2mt(mhzLw); % mT
+
+Exp.Range = [min(bsAx), max(bsAx)];
+Exp.mwFreq = mwFreq;
+Exp.nPoints = nPoint;
+Exp.Harmonic = 0;
+
+bsSim = zeros(ndip, nPoint);
+
+for ij = 1:ndip
+ Sys.dip = dips(ij);
+ bsSim(ij, :) = pepper(Sys, Exp);
+ % bsSim(ij, :) = bsSim(ij, :)/max(abs(bsSim(ij, :)));
+end
+
+bsTotIntegral = sum(bsSim, 2)/nPoint;
+
+clf
+plot(dips, msTotIntegral, 'o-', 'DisplayName', 'Mw sweep')
+yyaxis right
+plot(dips, bsTotIntegral, 'o-', 'DisplayName', 'B0 sweep')
+xlabel('J / MHz')
+yyaxis left
+ylabel('Integral of trEPR spectrum')
+legend()
+
+%% Plot
+
+ij = 100;
+clf
+plot(msAx, msSim(ij, :))
+yyaxis right
+plot(msAx, flip(bsSim(ij, :)))
+
+%% Crystal rotation
+clearvars
+
+Sys.S = [1/2 1/2];
+Sys.g = [2, 2.0075];
+Sys.dip = 5; % MHz
+
+Sys.initState = 'singlet';
+
+gPlus = (Sys.g(1) + Sys.g(2))/2;
+mwFreq = 9.7; % GHz
+B0 = planck/bmagn/gPlus*mwFreq*1e12; % mT
+nPoint = 5000;
+msAx = linspace(9.4, 10, nPoint); % GHz, mw sweep axis
+bsAx = mhz2mt(msAx*1e3, gPlus); % mT, b field sweep
+
+%
+% Frequency sweep
+%
+mhzLw = 10;
+Sys.lw = mhzLw; % MHz
+
+Exp.mwRange = [min(msAx), max(msAx)];
+Exp.Field = B0;
+Exp.nPoints = nPoint;
+Exp.Harmonic = 0;
+
+Opt.GridSize = [91 0]; % 181 orientations
+Opt.GridSymmetry = 'C1';
+
+% Powder average
+msSim = pepper(Sys, Exp, Opt);
+
+clear("Opt")
+
+Exp.CrystalSymmetry = 1;
+Exp.MolFrame = [0 0 0]*pi/180;
+Exp.SampleFrame = [0 0 0]*pi/180;
+
+Opt.separate = 'orientations';
+rho = deg2rad(linspace(0, 180, 181)); % 10 degree increments
+solidAngleWeight = sin(rho')/sum(sin(rho), 'all');
+
+% Rotation around x
+Exp.SampleRotation = {'x', rho};
+msSimRotX = pepper(Sys, Exp, Opt);
+msPowderRotX = sum(solidAngleWeight.*msSimRotX);
+
+% Rotation around y
+Exp.SampleRotation = {'y', rho};
+msSimRotY = pepper(Sys, Exp, Opt);
+msPowderRotY = sum(solidAngleWeight.*msSimRotY);
+
+%
+% Field sweep
+%
+clear("Exp")
+
+Sys.lw = mhz2mt(mhzLw); % mT
+
+Exp.Range = [min(bsAx), max(bsAx)];
+Exp.mwFreq = mwFreq;
+Exp.nPoints = nPoint;
+Exp.Harmonic = 0;
+
+clear("Opt")
+Opt.GridSize = [91 0]; % 181 orientations
+Opt.GridSymmetry = 'C1';
+
+% Powder average
+bsSim = pepper(Sys, Exp, Opt);
+
+clear("Opt")
+
+Exp.CrystalSymmetry = 1;
+Exp.MolFrame = [0 0 0]*pi/180;
+Exp.SampleFrame = [0 0 0]*pi/180;
+
+Opt.separate = 'orientations';
+rho = deg2rad(linspace(0, 180, 181));
+solidAngleWeight = sin(rho')/sum(sin(rho), 'all');
+
+% Rotation around x
+Exp.SampleRotation = {'x', rho};
+bsSimRotX = pepper(Sys, Exp, Opt);
+bsPowderRotX = sum(solidAngleWeight.*bsSimRotX);
+
+% Rotation around y
+Exp.SampleRotation = {'y', rho};
+bsSimRotY = pepper(Sys, Exp, Opt);
+bsPowderRotY = sum(solidAngleWeight.*bsSimRotY);
+
+%% Plot
+
+clf
+plot(msAx, msPowderRotX, msAx, msPowderRotY)
+% clf
+% plot(bsAx, bsPowderRotX, bsAx, bsPowderRotY)
+
diff --git a/zech_psiOopEseem_trEPRstickSpectra.m b/zech_psiOopEseem_trEPRstickSpectra.m
index 2960014..ea050e9 100755
--- a/zech_psiOopEseem_trEPRstickSpectra.m
+++ b/zech_psiOopEseem_trEPRstickSpectra.m
@@ -7,53 +7,51 @@ addpath(genpath('/net/storage/gianlum33/soft/matlab/'))
tic
% Taken from Easyspin example
-clear('Sys', 'Exp', 'Vary', 'VaryExp')
+clear('Sys', 'Exp', 'Vary', 'VaryExp', "Opt")
Sys.S = [1/2 1/2];
Sys.g = [2.0030 2.0026 2.0023; ... % P700+
2.0062 2.0051 2.0022]; % A1-
-% Sys.gFrame = [-10 -128 -83; ...
-Sys.gFrame = [0 0 0;
+Sys.gFrame = [-10 -128 -83; ...
0 0 0]*pi/180;
-Sys.eeFrame = [0 0 0]*pi/180; % zD direction is along -x of A1-
+Sys.eeFrame = [0 90 0]*pi/180; % zD direction is along -x of A1-
-% Factor 1/1.5 coming from different definition of spin Hamiltonian?
-Sys.J = unitconvert(-1e-3,'mT->MHz')*2; % MHz
-Sys.dip = unitconvert(+0.177,'mT->MHz')/1.5; % MHz
-Sys.lw = mt2mhz(0.35); % MHz
-% Sys.lw = mhz2mt(11); % MHz
+Sys.J = (-1/2)*unitconvert(1e-3,'mT->MHz'); % MHz
+Sys.dip = unitconvert(0.170,'mT->MHz')/1.5; % MHz
+Sys.lwpp = 0.35; % mT
Sys.initState = 'singlet';
-% nNuc = 1;
-% Sys.Nucs = '1H';
-% Sys.Nucs = repmat(append(Sys.Nucs, ', '), [1, nNuc]);
-% Sys.Nucs = Sys.Nucs(1:end - 2);
-% % Sys.A = [zeros(1, 3), 9, 9, 9];
-% % Sys.A = 10*ones(1, 6);
+nNuc = 3;
+Sys.Nucs = '1H';
+Sys.Nucs = repmat(append(Sys.Nucs, ', '), [1, nNuc]);
+Sys.Nucs = Sys.Nucs(1:end - 2);
+Sys.A = [zeros(1, 3), 9, 9.4, 12.8];
+% Sys.A = 10*ones(1, 6);
% Sys.A = 0*ones(1, 6);
-% Sys.A = repmat(Sys.A, [nNuc, 1]);
-% Sys.AFrame = [0 0 0 0 -0 0]*pi/180;
-% Sys.AFrame = repmat(Sys.AFrame, [nNuc, 1]);
-
-B0 = 345.9*1; % mT
-mwFreq = 9.7*1;
-mwRange = mwFreq/1*1e-2;
-xxSim = linspace(mwFreq - mwRange/2, mwFreq + mwRange/2, 4096); % GHz
-xxSim1 = mhz2mt(xxSim*1e3); % mT
+Sys.A = repmat(Sys.A, [nNuc, 1]);
+Sys.AFrame = [0 0 0 60 -90 0]*pi/180;
+Sys.AFrame = repmat(Sys.AFrame, [nNuc, 1]);
+
+% gPlus = (Sys.g(1) + Sys.g(2))/2;
+mwFreq = 9.7;
+% B0 = planck/bmagn/gfree*mwFreq*1e12; % mT
+% xxSim = linspace(mwFreq - 100e-3, mwFreq + 100e-3, 1024); % GHz
+xxSim1 = linspace(344.5, 347, 1024); % mT
% Frequency sweep
-Exp.mwCenterSweep = [mean(xxSim), max(xxSim) - min(xxSim)];
-Exp.Field = B0;
+% Exp.mwCenterSweep = [mean(xxSim), max(xxSim) - min(xxSim)];
+% Exp.Field = B0;
% Magnetic field sweep
-% Exp.CenterSweep = [mean(xxSim1), max(xxSim1) - min(xxSim1)]; % mT
-% Exp.mwFreq = mwFreq; % GHz
+Exp.CenterSweep = [mean(xxSim1), max(xxSim1) - min(xxSim1)]; % mT
+Exp.mwFreq = mwFreq; % GHz
Exp.nPoints = numel(xxSim1);
Exp.Harmonic = 0;
-Opt.GridSize = [91 0]; % Equivalent to steps of 1 degree
-Opt.GridSymmetry = 'C1';
+Opt.GridSize = [91 0];
+Opt.GridSymmetry = '';
+
% Opt.separate = 'transitions';
FitOpt.Verbosity = 0;
FitOpt.maxTime = 0.5;
@@ -61,27 +59,244 @@ FitOpt.maxTime = 0.5;
% Exp.CrystalSymmetry = 1;
% Exp.MolFrame = [0 -0 -0]*pi/180; % molecular frame aligned with crystal/sample frame
% Exp.SampleFrame = [-0 -0 -0]*pi/180;
+% %
+% nRot_L = [0;0;1]; % sample rotation axis in lab frame (lab x axis here)
+% rho = deg2rad(0:1:180); % 10 degree increments
+% Exp.SampleRotation = {'y',rho};
+% Opt.separate = 'orientations';
+%
+
+%
+% % ySimNoHfi = pepper(Sys, Exp);
-% ySimNoHfi = pepper(Sys, Exp);
-% ySim = pepper(Sys, Exp, Opt);
+ySim = pepper(Sys, Exp, Opt);
+% yySim = ySim;
+ySim = ySim'/max(abs(ySim));
-Ham = ham(Sys, [0, 0, B0]);
-[Ham0, mux, muy, muz] = ham(Sys);
+% Ham = ham(Sys, [0, 0, B0]);
+% [Ham0, mux, muy, muz] = ham(Sys);
toc
+clf
+plot(xxSim1, ySim) %, xxSim, yySim)
+% clf
-% hold on
+%% Functions
+% Expected input: B0 in mT
+% Output: frequency nu in MHz
+g2wFunc = @(B0, g) bmagn*B0/planck*g*1e-9;
+
+% Expected input: deltaw in MHz, J in MHz, d in MHz
+% Output: Omega in MHz
+OmegaFunc = @(deltaw, J, d) sqrt(deltaw.^2 + (J + d/2).^2);
+% OmegaFuncEasy = @(deltaw, J, d) sqrt(deltaw.^2 + (J/2 + d/2).^2);
+
+% Dipolar interaction
+% Makes use of the fact that cos(thetaD) = dotProduct(B0, zD)
+% Expected input:
+% dip: 1 x 1
+% nVers: 3 x nTheta x nPhi
+% zD: 3 x 1
+dipFunc = @(dip, nVers, zD) dip*((sum(nVers.*zD)).^2 - 1/3);
+% dipFuncEasy = @(dip, nVers, zD) -3/2*dip*((sum(nVers.*zD)).^2 - 1/3);
+
+
+%% My powder average (only for equivalent nuclei)
+
+tic
+dip = -mt2mhz(0.170);
+JJ = mt2mhz(0.001);
+nHfiLine = nNuc + 1;
+trlwpp = 0.02; % mT
+
+% Theta, phi grid
+nTheta = 181;
+nPhi = 181;
+thetas = linspace(0, 180, nTheta)*pi/180;
+thetas = thetas';
+phis = linspace(0, 360, nPhi)*pi/180;
+
+% Direction of B0
+nVers = ang2vec(ones(nTheta, 1)*phis, thetas*ones(1, nPhi));
+% Effective g-values
+euMatrixg1 = erot(Sys.gFrame(1, :))';
+g1Tensor = euMatrixg1*diag(Sys.g(1, :))*euMatrixg1';
+g1 = sqrt( sum( (g1Tensor*nVers).^2, 1));
+euMatrixg2 = erot(Sys.gFrame(2, :))';
+g2Tensor = euMatrixg2*diag(Sys.g(2, :))*euMatrixg2';
+g2 = sqrt( sum( (g2Tensor*nVers).^2, 1));
+% Dipolar interaction
+zD = erot(Sys.eeFrame)*[0, 0, 1]';
+dd = dipFunc(dip, nVers, zD);
+
+% Hyperfine interaction with a number nNuc of equal nuclei
+if nNuc ~= 0
+ euMatrixHfi1 = erot(Sys.AFrame(1, 1:3));
+ Ahfi1Tensor = euMatrixHfi1'*diag(Sys.A(1, 1:3))*euMatrixHfi1;
+ Ahfi1 = squeeze( ...
+ sqrt( sum( (pagemtimes(Ahfi1Tensor', nVers)).^2)));
+ % For spin 2
+ euMatrixHfi2 = erot(Sys.AFrame(1, 4:6));
+ Ahfi2Tensor = euMatrixHfi2'*diag(Sys.A(1, 4:6))*euMatrixHfi2;
+ Ahfi2 = squeeze( ...
+ sqrt( sum( (pagemtimes(Ahfi2Tensor', nVers)).^2)));
+
+ % Shift resonances due to hyperfine interaction
+ Aplus = (Ahfi1 + Ahfi2)/2; % MHz
+ Aminus = (Ahfi1 - Ahfi2)/2; % MHz
+
+ % Pascal triangle for hfi interaction
+ pascalMatrix = pascal(nHfiLine);
+ pascalFactor = pascalMatrix(nHfiLine:nHfiLine - 1:end - 1); % Antidiag
+else
+ Aplus = 0;
+ Aminus = 0;
+ pascalFactor = 1;
+end
+
+w0 = g2wFunc(xxSim1', (g1 + g2)/2); % MHz
+deltaw = g2wFunc(xxSim1', (g1 - g2)/2); % MHz
+% Signs for different transitions
+signJmd = [-1, 1, -1, 1];
+signOmega = [-1, -1, 1, 1];
+signIntens = [1, -1, 1, -1];
+% Possible values of sum of nuclear spin quantum numbers
+quantNumNuc = -nNuc/2:1:nNuc/2;
+% Initialization
+trSignal = zeros(numel(xxSim1), nTheta*nPhi);
+% Spectra
+for itrans = 1:4
+ for ihfi = 1:nHfiLine
+ w0_ = w0 + quantNumNuc(ihfi)*Aplus;
+ deltaw_ = deltaw + quantNumNuc(ihfi)*Aminus;
+ Omega = OmegaFunc(deltaw_, JJ, dd);
+ wReson = w0_ + signJmd(itrans)*(JJ - dd) + signOmega(itrans)*Omega;
+ % intensityReson correct only for case of equal lws
+ intensityReson = signIntens(itrans)*1/8*(deltaw_.^2)./(Omega.^2);
+ trSignal_ = ...
+ gaussianbs(wReson*1e-3, mwFreq, mt2mhz(trlwpp)*1e-3, "lwpp");
+ trSignal = trSignal + intensityReson.*trSignal_*pascalFactor(ihfi);
+ end
+end
+trSignal = reshape(trSignal, [numel(xxSim1), nTheta, nPhi]);
+% Sum over solid angle distribution
+solidAngleWeight = sin(thetas')/sum(sin(thetas)*ones(1, nPhi), 'all');
+trSignalPowder = sum(squeeze(sum(trSignal.*solidAngleWeight, 3)), 2);
+% Normalized signal to max = 1
+ntrSignal = trSignalPowder/abs(max(trSignalPowder));
+
+% zfile = load('/net/storage/gianlum33/projects/oop_ciss_calculations/from_bittl/src/test2_spec.asc');
+zfile = load('S:\projects\oop_ciss_calculations\from_bittl\src\test2_spec.asc');
+xxz = zfile(:, 1);
+yyz = zfile(:, 2);
+% figure()
+clf
+plot(xxz/10, yyz/max(yyz), 'DisplayName', 'Zech')
+hold on
+plot(xxSim1, ntrSignal, 'DisplayName', 'Gianluca')
+hold on
+plot(xxSim1, ySim/max(ySim), 'DisplayName', 'Easyspin')
+legend()
+xlim([min(xxSim1) max(xxSim1)])
+toc
+
+%%
+%{
+% if numel(trlw) == 1
+% trlw = repmat(repelem(trlw, 4), [1, nHfiLine*nTheta*nPhi]);
+% elseif numel(trlw) == 2
+% trlw = repmat(repelem(trlw, 2), [1, nHfiLine*nTheta*nPhi]);
+% else
+% error('trlw should be of size (1, 1) or (1, 2)')
+% end
+
+
+
+% Intensities
+intensityReson = 1/8*(deltaw(1, :).^2)./(Omega(1, :).^2);
+intensityReson = ...
+ repmat([1, -1, 1, -1], [1, max(size(dd))]).* ...
+ repelem(intensityReson, 4);
+intensityNorm = intensityReson ./ sum(abs(trSignal), 1);
+pascalFactor = repmat(repelem(pascalFactor, 4), [1, nTheta*nPhi]);
+
+trSignal = trSignal.*intensityNorm.*pascalFactor;
+% trSignalSumHfi = squeeze(sum(trSignal, 3)); % Sum over hfi lines
+% trSignalSum = squeeze(sum(trSignalSumHfi, 2)); % Sum over transitions
+
+trSignal = reshape(trSignal, [numel(xxSim1), 4, nHfiLine, nTheta, nPhi]);
+if nNuc ~= 0
+ trSignalSumHfi = squeeze(sum(trSignal, 2)); % Sum over hfi lines
+ trSignalSum = squeeze(sum(trSignalSumHfi, 2)); % Sum over transitions
+else
+ trSignalSum = squeeze(sum(trSignal, 2)); % Sum over transitions
+end
+
+solidAngleWeight = sin(thetas')/sum(sin(thetas)*ones(1, nPhi), 'all');
+trSignalPowder = sum(squeeze(sum(trSignalSum.*solidAngleWeight, 3)), 2);
+
+% [~, ith] = min(abs(Exp.SampleFrame(2) + thetas));
+% ntrSignal = trSignalSum(:, ith, 1)/abs(max(trSignalSum(:, ith, 1)));
+ntrSignal = trSignalPowder/abs(max(trSignalPowder));
+
+diff = ySim - ntrSignal;
+% toc
+%
% clf
-% % plot(xxSim1, ySim/max(ySim), xxSim1 - 0.21, flip(trSignalPowder/max(trSignalPowder)))
-% plot(xxSim, ySim/max(ySim))
% hold on
-% plot(xxSim, trSignalPowder/max(trSignalPowder))
+% plot(xxSim, ySim, xxSim, ntrSignal)
% yyaxis right
-% plot(xxSim, ySim'/max(ySim) - trSignalPowder/max(trSignalPowder))
-% % plot(xxSim, ySimNoHfi/max(ySimNoHfi), xxSim, ySim/max(ySim))
-% % legend('Easyspin', 'Gianluca')
+% plot(xxSim, diff)
+
+% if abs(round(sum(diff), 5)) == abs(round(sum(ySim), 5))
+% disp("Same areas. Area of my norm. signal is: " + string(sum(ntrSignal)))
+% else
+% disp("Not the same areas!!!!!!!")
+% end
+
+toc
+
+
+
+%%
+clf
+plot(Js, sum(ySim, 2), 'o')
+hold on
+% plot(Js, sum(diff, 2), 'o')
+% plot(Js, sum(ntrSignalPowder, 2), 'o')
+
+%%
+
+% figure()
+ij = 1;
+clf
+plot(xxSim, ySim(ij, :), xxSim, trSignalPowder/max(trSignalPowder))
+yyaxis right
+plot(xxSim, ySim(ij, :)' - trSignalPowder/max(trSignalPowder))
%%
+clf
+for ij = 1
+ plot(xxSim, diff(ij, :))
+ hold on
+end
+legend()
+%%
+
+[~, ith] = min(abs(Exp.SampleFrame(2) - thetas));
+% figure(1)
+clf
+plot(xxSim, ySim/max(ySim))
+hold on
+plot(xxSim, trSignalSum(:, ith, 1)/max(trSignalSum(:, ith, 1)))
+% plot(xxSim, trSignal(:, 1, 1, ith, 1)/max(trSignal(:, 1, 1, ith, 1)))
+% plot(xxSim, trSignal(:, 2, 1, ith, 1)/max(trSignal(:, 1, 1, ith, 1)))
+% plot(xxSim, trSignal(:, 3, 1, ith, 1)/max(trSignal(:, 1, 1, ith, 1)))
+% plot(xxSim, trSignal(:, 4, 1, ith, 1)/max(trSignal(:, 1, 1, ith, 1)))
+yyaxis right
+plot(xxSim, ySim/max(ySim) - trSignalSum(:, ith, 1)/max(trSignalSum(:, ith, 1)))
+
+%%
[Vary, VaryExp] = deal(struct());
% Vary.gFrame = [1.5, 1.5, 1.5; 0, 0, 0];
% Vary.lw = 5;
@@ -120,39 +335,19 @@ Om = sqrt(Om);
eigen1 = Om - (Sys.J/4 - Sys.dip/2)
eigen2 = - Om - (Sys.J/4 - Sys.dip/2)
-%% My powder average (only for equivalent nuclei)
-
-tic
-dip = unitconvert(-0.177,'mT->MHz'); % MHz, -4.9 MHz
-JJ = unitconvert(1e-3,'mT->MHz'); % MHz
-% ONLY gaussian lw implemented for now
-% One linewidth for each transition (w12, w34, w13, w24)
-% trlw = [Sys.lw*2*42/35, Sys.lw*2*42/35, Sys.lw*42/35, Sys.lw*42/35]*1e-3; % GHz, 0.7 and 0.35 mT
-trlw = Sys.lw; % MHz
-if isfield(Exp, 'mwFreq')
- trlw = mt2mhz(trlw);
-end
-
-% Expected input: B0 in mT
-% Output: frequency nu in MHz
-g2wFunc = @(B0, g) bmagn*B0/planck*g*1e-9;
-% Expected input: deltaw in MHz, J in MHz, d in MHz
-% Output: Omega in MHz
-OmegaFunc = @(deltaw, J, d) sqrt(deltaw.^2 + (J + d/2).^2);
-% Dipolar interaction
-% Makes use of the fact that cos(thetaD) = dotProduct(B0, zD)
-% Expected input:
-% dip: 1 x 1
-% nVers: 3 x nTheta x nPhi
-% zD: 3 x 1
-dipFunc = @(dip, nVers, zD) dip*((sum(nVers.*zD)).^2 - 1/3);
+load("vik.mat")
+clf
+imagesc(squeeze(reshapeThPh(ddn)) - dd)
+colormap(vik)
+colorbar
+%%
% Theta, phi grid
nTheta = 91*2 - 1;
thetas = linspace(0, 180, nTheta)*pi/180;
% thetas = 10*pi/180;
nTheta = numel(thetas);
-nPhi = 91*2*2 - 3;
+nPhi = 91*2*2 - 1;
phis = linspace(0, 360, nPhi)*pi/180;
% Direction of B0
@@ -188,6 +383,21 @@ else
nHfiLine = 0;
end
+%
+% Hyperfine interaction with a number nNuc of equal nuclei
+%
+
+%
+% hfi
+%
+if isfield(Sys, 'Nucs')
+ nNuc = numel(strsplit(Sys.Nucs, ',')); % Number of equivalent nuclei
+ nHfiLine = nNuc + 1;
+else
+ nNuc = 0;
+ nHfiLine = 0;
+end
+
%
% Hyperfine interaction with a number nNuc of equal nuclei
%
@@ -205,7 +415,7 @@ if nNuc ~= 0
% Shift resonances due to hyperfine interaction
Aplus = (Ahfi1 + Ahfi2)/2; % MHz
- % Make w0 have size [nHfiLine, nTheta, nPhi]
+ % Make w0 have size [nHfiLine, nTheta, nPhi]qrt(deltaw.^2 + (J + d/2).^2);
w0 = insertDimensionPos1(w0, nHfiLine);
% Make Aplus have size [1, nTheta, nPhi]
Aplus = reshape(Aplus, [1, size(Aplus)]);
@@ -248,7 +458,7 @@ wReson(4, :, :, :) = w0 + dipInteraction + (Omega) ; % w24
% Lineshapes for each transition - (xxSim(2) - xxSim(1))/8
trSignal = ...
- gaussiantransitions(xxSim', wReson*1e-3, trlw*1e-3, "fwhm");
+ gaussiantransitions(xxSim', wReson*1e-3, trlw*1e-3, "var");
% trSignal = ...
% gaussiantransitions(xxSim', wReson, trlw*1e-3, "fwhm");
@@ -271,14 +481,14 @@ solidAngleWeight = sin(thetas)/sum(sin(thetas')*ones(1, nPhi), 'all');
trSignalPowder = sum(squeeze(sum(trSignalSum.*solidAngleWeight, 3)), 2);
% hold on
-clf
-% plot(xxSim1, ySim/max(ySim), xxSim1 - 0.21, flip(trSignalPowder/max(trSignalPowder)))
-plot(xxSim, ySim/max(ySim))
-hold on
-% plot(xxSim(1:end - 1), trSignalPowder(2:end)/max(trSignalPowder))
-plot(xxSim, trSignalPowder/max(trSignalPowder(:)))
+% clf
+% % plot(xxSim1, ySim/max(ySim), xxSim1 - 0.21, flip(trSignalPowder/max(trSignalPowder)))
+% plot(xxSim, ySim/max(ySim))
+% hold on
+% % plot(xxSim(1:end - 1), trSignalPowder(2:end)/max(trSignalPowder))
+% plot(xxSim, trSignalPowder/max(trSignalPowder(:)))
-yyaxis right
+% yyaxis right
% plot(xxSim, ySim'/max(ySim) - trSignalPowder/max(trSignalPowder))
% xlim([9.695, 9.708])
toc
@@ -298,19 +508,6 @@ yyaxis right
plot(xxSim, ySim/max(ySim) - newsig)
% xlim([9.695, 9.708])
toc
-%%
-[~, ith] = min(abs(Exp.SampleFrame(2) - thetas));
-% figure(1)
-clf
-plot(xxSim, ySim/max(ySim))
-hold on
-plot(xxSim, trSignalSum(:, ith, 1)/max(trSignalSum(:, ith, 1)))
-% plot(xxSim, trSignal(:, 1, 1, ith, 1)/max(trSignal(:, 1, 1, ith, 1)))
-% plot(xxSim, trSignal(:, 2, 1, ith, 1)/max(trSignal(:, 1, 1, ith, 1)))
-% plot(xxSim, trSignal(:, 3, 1, ith, 1)/max(trSignal(:, 1, 1, ith, 1)))
-% plot(xxSim, trSignal(:, 4, 1, ith, 1)/max(trSignal(:, 1, 1, ith, 1)))
-yyaxis right
-plot(xxSim, ySim'/max(ySim) - trSignalSum(:, ith, 1)/max(trSignalSum(:, ith, 1)))
%% Plot
@@ -360,6 +557,15 @@ tan2alpha = squeeze(deltaw) ./ ((JJ + dd/2)*1e-3);
%%
%{
+2.00300 0.00000 0.00000
+0.00000 2.00260 0.00000
+0.00000 0.00000 2.00230 G-TENSOR P700+
+
+2.00620 0.00000 0.00000
+0.00000 2.00510 0.00000
+0.00000 0.00000 2.00220 G-TENSOR Qb-
+
+
tic
clear('Sys', 'Exp', 'Vary', 'VaryExp')
@@ -581,9 +787,105 @@ xlabel('X')
title('g1')
%}
-
+%}
%%
+function y1 = gaussianbs(wReson, mwFreq, c, mode)
+ arguments
+ wReson
+ mwFreq
+ c (1, 1) double
+ mode string = "lwpp"
+ end
+
+ if strcmp(mode, "fwhm")
+ % If the input is fwhm, multiply the input parameters to have var
+ c = c/(2*sqrt(2*log(2)));
+ elseif strcmp(mode, "lwpp")
+ c = c/2;
+ elseif strcmp(mode, "var")
+ % Do nothing
+ else
+ error("Indicate if c is 'lwpp', 'fwhm'(=lw) or" ...
+ + "'var'(=variance) of the gaussian.")
+ end
+
+ % Adjust dimensions of xx if needed
+ % [nAx, dim2] = size(xx);
+ % if nAx < dim2
+ % xx = xx';
+ % nAx = dim2;
+ % end
+ % nTotLine = size(x0, 2);
+ %
+ % xx = repmat(xx, [1, nTotLine]);
+ % x0 = repmat(x0, [nAx, ones(1, nTotLine)]);
+ % c = repmat(c, [nAx, ones(1, nTotLine)]);
+
+ y1 = exp(-1/2 * (wReson - mwFreq).^2 ./ c^2);
+
+end
+function y1 = newlorentziantransitions(xx, x0, c, mode)
+ % Output:
+ % y1:
+ arguments
+ xx % [nAx, 1] equally spaced values
+ x0
+ c
+ mode string = "fwhm"
+ end
+
+ if strcmp(mode, "fwhm")
+ % If the input is fwhm, multiply the input parameters to have var
+ c = c/sqrt(3);
+ end
+
+ % Adjust dimensions of xx if needed
+ [nAx, dim2] = size(xx);
+ if nAx < dim2
+ xx = xx';
+ nAx = dim2;
+ end
+ nTotLine = size(x0, 2);
+
+ xx = repmat(xx, [1, nTotLine]);
+ x0 = repmat(x0, [nAx, ones(1, nTotLine)]);
+ c = repmat(c, [nAx, ones(1, nTotLine)]);
+
+ y1 = (1 + 4/3*(xx - x0).^2 ./ c.^2).^(-1);
+end
+
+function y1 = newgaussiantransitions(xx, x0, c, mode)
+ % Output:
+ % y1:
+ arguments
+ xx % [nAx, 1] equally spaced values
+ x0
+ c
+ mode string = "fwhm"
+ end
+
+ if strcmp(mode, "fwhm")
+ % If the input is fwhm, multiply the input parameters to have var
+ c = c/(2*sqrt(2*log(2)));
+ disp('fwhm')
+ end
+
+ % Adjust dimensions of xx if needed
+ [nAx, dim2] = size(xx);
+ if nAx < dim2
+ xx = xx';
+ nAx = dim2;
+ end
+ nTotLine = size(x0, 2);
+
+ xx = repmat(xx, [1, nTotLine]);
+ x0 = repmat(x0, [nAx, ones(1, nTotLine)]);
+ c = repmat(c, [nAx, ones(1, nTotLine)]);
+
+ y1 = exp(-1/2 * (xx - x0).^2 ./ c.^2);
+end
+
function y1 = gaussiantransitions(xx, x0, c, mode)
% Output:
% y1:
--
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