- Many fixes to the triple axis stuff

* update after a1-a6 drive
  * intrduction of targets
- POLDI writing
- Moved HKL calculation 4 TRICS to fourlib
This commit is contained in:
cvs
2002-01-25 14:48:50 +00:00
parent 8c043c8cd1
commit 1e60f3be82
39 changed files with 3513 additions and 1160 deletions

791
fourlib.c Normal file
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/*
F O U R L I B
This is a library of routines for doing transformations between the
various coordinate systems used on a four circle diffractometer as
used for neutron or X-ray diffraction. The coordinate systems used are
described in Busing, Levy, Acta Cryst (1967),22, 457 ff.
Generally we have:
Z = [OM][CHI][PHI][UB]h
where: Z is a vector in the diffractometer coordinate system
OM CHI PHI are rotation matrices around the respective angles
UB is the UB matrix
h is the reciprocal lattice vector.
The vector Z cannot only be expressed in terms of the angles stt, om, chi,
and phi put also by polar coordinates gamma and nu.
This code is a reimplementation based on a F77 code from Gary McIntyre, ILL
and code extracted from the ILL MAD control program.
Mark Koennecke, November-December 2001
*/
#include <stdio.h>
#include <assert.h>
#include <math.h>
#include "fortify.h"
#include "fourlib.h"
#define PI 3.141592653589793
#define RD 57.30
#define ABS(x) (x < 0 ? -(x) : (x))
/*------------------------------------------------------------------------
a safe routine for calculating the atan of y/x
------------------------------------------------------------------------*/
static double myatan(double y, double x){
if(ABS(x) < 0.0001){
if(y > .0){
return PI/2;
}else {
return -PI/2;
}
}
if(x > .0){
return atan(y/x);
} else {
if(y > .0){
return PI + atan(y/x);
} else {
return -PI + atan(y/x);
}
}
}
/*-------------------------------------------------------------------------*/
static double rtan(double y, double x){
double val;
if( (x == 0.) && (y == 0.) ) {
return .0;
}
if( x == 0.) {
if(y < 0.){
return -PI/2.;
} else {
return PI/2.;
}
}
if(ABS(y) < ABS(x)) {
val = atan(ABS(y/x));
if(x < 0.) {
val = PI - val;
}
if(y < 0.){
val = -val;
}
return val;
} else {
val = PI/2. - atan(ABS(x/y));
if(x < 0.) {
val = PI - val;
}
if( y < 0.) {
val = - val;
}
}
return val;
}
/*----------------------------------------------------------------------
clear3x3 sets a 3x3 matrix to 0
-----------------------------------------------------------------------*/
static void clear3x3(MATRIX target){
int i, j;
for(i = 0; i < 3; i++){
for(j = 0; j < 3; j++){
target[i][j] = .0;
}
}
}
/*---------------------------------------------------------------------*/
MATRIX vectorToMatrix(double z[3]){
int i;
MATRIX res;
res = mat_creat(3,1,ZERO_MATRIX);
for(i = 0; i < 3; i++){
res[i][0] = z[i];
}
return res;
}
/*---------------------------------------------------------------------*/
void matrixToVector(MATRIX zm, double z[3]){
int i;
for(i = 0; i < 3; i++){
z[i] = zm[i][0];
}
}
/*----------------------------------------------------------------------
A Busing & levy PSI matrix
----------------------------------------------------------------------*/
static void psimat(MATRIX target, double psi){
double psird = psi/RD;
clear3x3(target);
target[0][0] = 1.;
target[1][1] = cos(psird);
target[1][2] = sin(psird);
target[2][1] = -target[1][2];
target[2][2] = target[1][1];
}
/*----------------------------------------------------------------------
A Busing & levy CHI matrix
----------------------------------------------------------------------*/
void chimat(MATRIX target, double chi){
double chird = chi/RD;
clear3x3(target);
target[0][0] = cos(chird);
target[0][2] = sin(chird);
target[1][1] = 1.;
target[2][0] = -target[0][2];
target[2][2] = target[0][0];
}
/*----------------------------------------------------------------------
A Busing & levy PHI matrix
----------------------------------------------------------------------*/
void phimat(MATRIX target, double phi){
double phird = phi/RD;
clear3x3(target);
target[0][0] = cos(phird);
target[0][1] = sin(phird);
target[1][0] = -target[0][1];
target[1][1] = target[0][0];
target[2][2] = 1.;
}
/*------------------- PSD specific code ----------------------------*/
void det2pol(psdDescription *psd, int x, int y, double *gamma, double *nu) {
double xobs, yobs, b, z, d;
assert(ABS(psd->distance ) > .001);
xobs = (x - psd->xZero)*psd->xScale;
yobs = (y - psd->yZero)*psd->yScale;
b = psd->distance*cos(yobs/psd->distance);
z = psd->distance*sin(yobs/psd->distance);
d = sqrt(xobs*xobs + b*b);
*gamma = psd->gamma + myatan(xobs,b)*RD;
*nu = psd->nu + myatan(z,d)*RD;
}
/*----------------------------------------------------------------------*/
void pol2det(psdDescription *psd, double gamma, double nu, int *x, int *y){
double delga, delnu, td, tn, e, f, g, zobs, xobs;
delga = gamma - psd->gamma;
delnu = nu - psd->nu;
td = tan(delga/RD);
tn = tan(delnu/RD);
e = sqrt(1. + td*td);
f = tn*e;
g = psd->distance*(1. + tn*tn +tn*tn*td*td);
zobs = psd->distance*(atan(tn*e) + asin(f/g));
xobs = td*(psd->distance*cos(zobs/psd->distance));
*y = (int)nint(psd->yZero + zobs/psd->yScale);
*x = (int)nint(psd->xZero + xobs/psd->xScale);
}
/*--------------- bisecting geometry code -----------------------------*/
/*
turn chi and phi in order to get Z1 into the equatorial plane
*/
static void turnEquatorial(MATRIX z1, double *chi, double *phi){
if(ABS(z1[0][0]) < .0001 || ABS(z1[1][0]) < .0001){
*phi = .0;
*chi = 90.;
if(z1[2][0] < .0){
*chi = - *chi;
}
} else {
*phi = myatan(z1[1][0],z1[0][0])*RD;
*chi = myatan(z1[2][0],
sqrt(z1[0][0]*z1[0][0] + z1[1][0]*z1[1][0]))*RD;
}
}
/*----------------------------------------------------------------------
calculate d-spacing and theta from z1
-----------------------------------------------------------------------*/
static int calcTheta(double lambda, MATRIX z1, double *d, double *theta){
double dstar, sintheta;
dstar = sqrt(z1[0][0]*z1[0][0] + z1[1][0]*z1[1][0] + z1[2][0]*z1[2][0]);
if(dstar < .0001){
*d = .0;
*theta = 0;
return 0;
}
*d = 1./dstar;
sintheta = lambda * dstar/2.;
if(ABS(sintheta) > 1.0){
*d = .0;
*theta = .0;
return 0;
}
*theta = asin(sintheta)*RD;
return 1;
}
/*-------------------------------------------------------------------*/
int z1ToBisecting(double lambda, double z1[3], double *stt, double *om,
double *chi, double *phi) {
MATRIX zz1;
int status;
zz1 = vectorToMatrix(z1);
status = z1mToBisecting(lambda,zz1,stt,om,chi,phi);
mat_free(zz1);
return status;
}
/*------------------------------------------------------------------------*/
int z1mToBisecting(double lambda, MATRIX z1, double *stt, double *om,
double *chi, double *phi) {
double d;
int status;
status = calcTheta(lambda,z1,&d,om);
if(!status){
*stt = .0;
*om = .0;
*chi = .0;
*phi = .0;
return status;
}
turnEquatorial(z1,chi,phi);
*stt = *om*2.;
*chi = 180. - *chi;
*phi = 180. + *phi;
return 1;
}
/*---------------------------------------------------------------------*/
int z1ToAnglesWithOffset(double lambda, MATRIX z1m,double omOffset,
double *stt, double *om,
double *chi, double *phi){
int status, i;
double d, delOm, sinchi, q, cosp, sinp, dstar;
MATRIX z1;
status = calcTheta(lambda,z1m,&d,om);
if(!status){
*stt = .0;
*om = .0;
*chi = .0;
*phi = .0;
return status;
}
*stt = 2. * *om;
*om += omOffset;
z1 = mat_copy(z1m); /* routine messes z1m up! */
dstar = sqrt(z1[0][0]*z1[0][0] + z1[1][0]*z1[1][0] + z1[2][0]*z1[2][0]);
for(i = 0; i < 3; i++){
z1[i][0] /= dstar;
}
delOm = -omOffset/RD;
sinchi = z1[2][0]/cos(delOm);
if(ABS(sinchi) > 1.){
mat_free(z1);
return 0;
}
*chi = asin(sinchi);
*chi = PI - *chi;
if(*chi > PI){
*chi = *chi - 2* PI;
}
q = cos(delOm)*cos(*chi);
cosp = (sin(delOm)*z1[0][0] + q*z1[1][0])/
(sin(delOm)*sin(delOm) + q*q);
sinp = (z1[0][0] - sin(delOm)*cosp)/ q;
*phi = rtan(cosp,sinp);
*phi *= RD;
*chi *= RD;
mat_free(z1);
return 1;
}
/*---------------------------------------------------------------------*/
int psiForOmegaOffset(MATRIX z1m, double omOffset,
double chi, double phi, double *psi){
double chibi, sinps, cosps, sinchi, dstar;
MATRIX z1;
z1 = mat_copy(z1m); /* routine messes z1m up! */
dstar = sqrt(z1[0][0]*z1[0][0] + z1[1][0]*z1[1][0] + z1[2][0]*z1[2][0]);
z1[2][0] /= dstar;
omOffset /= RD;
if(-z1[2][0] == 1.){
*psi = phi;
} else {
chibi = PI - asin(-z1[2][0]);
if(chibi > PI){
chibi -= 2*PI;
}
sinps = tan(chibi)*tan(-omOffset);
sinchi = -z1[2][0]/cos(-omOffset);
if(ABS(sinchi) > 1.){
mat_free(z1);
return 0;
}
cosps = (cos(chibi) - sinps*sin(-omOffset)*sinchi)/cos(chi/RD);
*psi = -rtan(sinps,cosps)*RD;
}
mat_free(z1);
return 1;
}
/*----------------------------------------------------------------------*/
void rotatePsi(double om, double chi, double phi, double psi,
double *newom, double *newchi, double *newphi){
MATRIX chim, phim, psim, r0, r0psi;
chim = mat_creat(3,3,ZERO_MATRIX);
chimat(chim,chi);
phim = mat_creat(3,3,ZERO_MATRIX);
phimat(phim,phi);
r0 = mat_mul(chim,phim);
psim = mat_creat(3,3,ZERO_MATRIX);
psimat(psim,psi);
r0psi = mat_mul(psim,r0);
*newchi = rtan(sqrt(r0psi[2][0]*r0psi[2][0] + r0psi[2][1]*r0psi[2][1]),
r0psi[2][2])*RD;
*newphi = rtan(-r0psi[2][1],-r0psi[2][0])*RD;
*newom = om + rtan(-r0psi[1][2],r0psi[0][2])*RD;
mat_free(chim);
mat_free(phim);
mat_free(psim);
mat_free(r0);
mat_free(r0psi);
}
/*--------------------------------------------------------------------
calculate Z1 = [PHI]TZ3
The T means transposed matrixes for the return calculation!
---------------------------------------------------------------------*/
static void z1fromz2(double z1[3], MATRIX z2,
double phi){
MATRIX phim, phimt, zz1;
phim = mat_creat(3,3,ZERO_MATRIX);
phimat(phim, phi);
phimt = mat_tran(phim);
zz1 = mat_mul(phimt,z2);
matrixToVector(zz1,z1);
mat_free(phim);
mat_free(phimt);
mat_free(zz1);
}
/*--------------------------------------------------------------------
calculate Z1 = [PHI]T*[CHI]T*Z3
The T means transposed matrixes for the return calculation!
---------------------------------------------------------------------*/
static void z1fromz3(double z1[3], MATRIX z3, double chi,
double phi){
MATRIX chim, chimt, z2;
chim = mat_creat(3,3,ZERO_MATRIX);
chimat(chim, chi);
chimt = mat_tran(chim);
z2 = mat_mul(chimt,z3);
z1fromz2(z1,z2,phi);
mat_free(chim);
mat_free(chimt);
mat_free(z2);
}
/*--------------------------------------------------------------------
calculate Z1 = [PHI]T*[CHI]T*[OM]T*Z4
The T means transposed matrixes for the return calculation!
---------------------------------------------------------------------*/
static void z1fromz4(double z1[3], MATRIX z4, double om, double chi,
double phi){
MATRIX oma, oma2, z3;
oma = mat_creat(3,3,ZERO_MATRIX);
phimat(oma, om);
oma2 = mat_tran(oma);
z3 = mat_mul(oma2,z4);
z1fromz3(z1,z3,chi,phi);
mat_free(oma);
mat_free(oma2);
mat_free(z3);
}
/*---------------------------------------------------------------------*/
void z1FromAngles(double lambda, double stt, double om,
double chi, double phi, double z1[3]){
MATRIX z4;
double th;
z4 = mat_creat(3,1,ZERO_MATRIX);
th = (stt/2.)/RD;
z4[0][0] = (2. * sin(th)*cos(th))/lambda;
z4[1][0] = (-2. *sin(th)*sin(th))/lambda;
z4[2][0] = .0;
z1fromz4(z1,z4,om,chi,phi);
mat_free(z4);
}
/*----------------------------------------------------------------------
Normal Beam geometry specific calculations. This means the reflection is
expressed through the three angles omega, gamma (two theta detector) and
nu (detector tilt).
bisToNormalBeam was lifted from HKLGEN.
-----------------------------------------------------------------------*/
double sign(double a, double b){
if(b >= .0){
return ABS(a);
} else {
-ABS(a);
}
}
/*----------------------------------------------------------------------*/
int bisToNormalBeam(double twotheta, double omega, double chi, double phi,
double *omeganb, double *gamma, double *nu){
double tth, fom, fchi, fphi, sint, sinnu, del;
tth = twotheta/RD;
fom = omega/RD;
fchi = chi/RD;
fphi = phi/RD;
/* nu calculation */
sint = sin(tth/2.);
*nu = 2. * sin(fchi)*sint;
if(*nu > 1.){
return 0;
}
*nu = asin(*nu);
*nu = ABS(*nu)*sign(1.,fchi);
sinnu = sin(*nu);
/* gamma calculation */
*gamma = cos(tth)/cos(*nu);
if(ABS(*gamma) > 1.0){
return 0;
}
*gamma = acos(*gamma);
*gamma = *gamma * sign(1.,tth);
/* omega normal beam */
del = asin(sint/cos(fchi));
*omeganb = del + fphi;
*omeganb *= RD;
*gamma *= RD;
*nu *= RD;
if(ABS(*omeganb) > 180.){
if(*omeganb < -180.){
*omeganb += 360.;
}
if(*omeganb > 180.){
*omeganb -= 360.;
}
}
return 1;
}
/* --------------------------------------------------------------------*/
static void z4FromNormalBeam(MATRIX z4, double lambda, double gamma,
double nu){
double gar, nur;
gar = gamma/RD;
nur = nu/RD;
/*
this is basically a conversion from polar coordinates to
x,y,z coordinates. However, sin and cos are exchanged in
comparison to textbook formulas for this conversion. But this
is only a shift of origin
*/
z4[0][0] = (sin(gar) * cos(nur))/lambda;
z4[1][0] = (cos (gar) * cos(nur) -1.)/lambda;
z4[2][0] = (sin(nur))/lambda;
}
/*----------------------------------------------------------------------*/
void z1FromNormalBeam(double lambda, double omega, double gamma,
double nu, double z1[3]){
MATRIX z4, omm, omt, z1m;
z4 = mat_creat(3,1,ZERO_MATRIX);
z4FromNormalBeam(z4,lambda, gamma,nu);
omm = mat_creat(3,3,ZERO_MATRIX);
phimat(omm,omega);
omt = mat_tran(omm);
z1m = mat_mul(omt,z4);
matrixToVector(z1m,z1);
mat_free(z4);
mat_free(omm);
mat_free(omt);
mat_free(z1m);
}
/*--------------------------------------------------------------------*/
double circlify(double val){
while(val > 360.){
val -= 360.;
}
while(val < 0.){
val += 360.;
}
return val;
}
/*----------------------------------------------------------------------*/
void z1FromAllAngles(double lambda, double omega , double gamma,
double nu, double chi, double phi, double z1[3]){
MATRIX z3;
z1FromNormalBeam(lambda, omega, gamma, nu, z1);
z3 = vectorToMatrix(z1);
z1fromz3(z1,z3,chi,phi);
mat_free(z3);
}
/*------------------- a test program ------------------------------------*/
#ifdef TESTCODE
int main(int argc, char *argv[]){
psdDescription psd;
double gamma,nu, lambda, stt, om, chi, phi, z1[3], psi;
double psiom, psichi, psiphi;
double sttex, omex, chiex, phiex;
int x, y, status, i;
MATRIX UB, UBinv, zz1,zz1b, hkl, hklback;
double gaex, omnbex, nuex, omeganb;
/* initializations */
UB = mat_creat(3,3,ZERO_MATRIX);
UB[0][0] = 0.016169;
UB[0][1] = 0.011969;
UB[0][2] = 0.063195;
UB[1][0] = -.000545;
UB[1][1] = 0.083377;
UB[1][2] = -0.009117;
UB[2][0] = -0.162051;
UB[2][1] = 0.000945;
UB[2][2] = 0.006321;
UBinv = mat_inv(UB);
lambda = 1.179;
/* test PSD code */
psd.xScale = .7;
psd.yScale = 1.4;
psd.xZero = 128;
psd.yZero = 64;
psd.distance = 450.;
psd.gamma = 43.;
psd.nu = 12.3;
det2pol(&psd,200, 111,&gamma, &nu);
pol2det(&psd,gamma,nu, &x, &y);
if(x == 200 && y == 111){
printf("PSD test: OK\n");
}
/* test bisecting calculations. The tests were taken from a system known
to work
*/
status = 1;
sttex = 30.58704;
omex = 15.293520;
chiex = 129.053604;
phiex = 134.191132;
hkl = mat_creat(3,1,ZERO_MATRIX);
hkl[0][0] = -2.;
hkl[1][0] = -2.;
hkl[2][0] = 4.;
zz1 = mat_mul(UB,hkl);
z1mToBisecting(lambda,zz1,&stt,&om,&chi,&phi);
if(ABS(stt - sttex) > .01 ||
ABS(om - omex) > .01 ||
ABS(chi - chiex) > .01 ||
ABS(phi - phiex) > .01){
printf("Bisecting Angles calculation FAILED!!!!!!!!!\n");
printf("Expected: %12.4f %12.4f %12.4f %12.4f\n", sttex, omex, chiex,phiex);
printf("Got: %12.4f %12.4f %12.4f %12.4f\n", stt,om,chi,phi);
status = 0;
}
z1FromAngles(lambda,sttex,omex,chiex,phiex,z1);
for(i = 0; i < 3; i++){
if(ABS(zz1[i][0] - z1[i]) > .0001){
printf("Calculation of Z1 from Angles FAILED!!!!\n");
printf("Expected: %8.4f %8.4f %8.4f\n", zz1[0][0], zz1[1][0],
zz1[2][0]);
printf("GOT: %8.4f %8.4f %8.4f\n",z1[0],z1[1],z1[2]);
status = 0;
}
}
hklback = mat_mul(UBinv,zz1);
for(i = 0; i < 3; i++){
if(ABS(hklback[i][0] - hkl[i][0]) > .0001){
printf("Back Calculation of HKL FAILED!!!!!!!!!\n");
printf("Expected: %8.4f %8.4f %8.4f\n", hkl[0][0], hkl[1][0],
hkl[2][0]);
printf("GOT: %8.4f %8.4f %8.4f\n",hklback[0][0],
hklback[1][0],hklback[2][0]);
status = 0;
}
}
if(status == 1){
printf("Bisecting test: OK\n");
}
/* try turning in psi */
rotatePsi(omex,chiex,phiex,30.,&psiom,&psichi,&psiphi);
omex = 37.374298;
chiex = 123.068192;
phiex = 170.8209099;
if(ABS(psiom - omex) > .01 ||
ABS(psichi - chiex) > .01 ||
ABS(psiphi - phiex) > .01){
printf("Psi Rotation test FAILED!!!!!!!!!\n");
printf("Expected: %12.4f %12.4f %12.4f\n", omex, chiex,phiex);
printf("Got: %12.4f %12.4f %12.4f\n", psiom,psichi,psiphi);
status = 0;
} else {
printf("Psi rotation test: OK\n");
}
/*
try to calculate a psi for a given omega offset
*/
omex = 15.293520;
chiex = 129.053604;
phiex = 134.191132;
if(psiForOmegaOffset(zz1,-5.,chiex, phiex, &psi) != 1){
printf("Failed to calculate PSI for a Omega Offset\n");
} else {
rotatePsi(omex,chiex,phiex,psi,&psiom,&psichi,&psiphi);
if(ABS(psiom +5. - omex) > .5){
printf("Failed to reach desired omega with calculated psi\n");
printf("Expected: %12.4f Got: %12.4f PSI = %12.4f\n", omex -10.,
psiom, psi);
} else {
printf("Psi for Omega Offset: OK\n");
}
}
/*
try to calculate angles with a omega offset
*/
omex = 10.29;
chiex = 128.78;
phiex = 126.24;
sttex = 30.59;
z1ToAnglesWithOffset(lambda, zz1, -5., &stt, &om, &chi, &phi);
if(ABS(stt - sttex) > .01 ||
ABS(om - omex) > .01 ||
ABS(chi - chiex) > .01 ||
ABS(phi - phiex) > .01){
printf("Angles calculation with Omega Offset FAILED!!!!!!!!!\n");
printf("Expected: %12.4f %12.4f %12.4f %12.4f\n", sttex, omex, chiex,phiex);
printf("Got: %12.4f %12.4f %12.4f %12.4f\n", stt,om,chi,phi);
status = 0;
} else {
printf("Angles with Omega Offset: OK\n");
}
/*
test normal beam codes
*/
omex = 37.374298;
gaex = 19.322;
omnbex = -21.057;
nuex = 24.186;
z1mToBisecting(lambda,zz1,&stt,&om,&chi,&phi);
chi = 50.949;
phi = -45.8088;
if(!bisToNormalBeam(stt,om,chi,phi,
&omeganb, &gamma, &nu)){
printf("Error on normal beam calculation!!\n");
}
if(ABS(omeganb - omnbex) > .01 ||
ABS(gamma - gaex) > .01 ||
ABS(nu - nuex) > .01){
printf("Normal Beam Calculation test FAILED!!!!!!!!!\n");
printf("Expected: %12.4f %12.4f %12.4f\n", omnbex, gaex,nuex);
printf("Got: %12.4f %12.4f %12.4f\n", omeganb,gamma,nu);
} else {
printf("Normal Beam Angle Calculation: OK\n");
}
z1FromNormalBeam(lambda, omnbex, gaex, nuex,z1);
status = 1;
for(i = 0; i < 3; i++){
if(ABS(zz1[i][0] - z1[i]) > .0001){
printf("Calculation of Z1 from Normal Beam Angles FAILED!!!!\n");
printf("Expected: %8.4f %8.4f %8.4f\n", zz1[0][0], zz1[1][0],
zz1[2][0]);
printf("GOT: %8.4f %8.4f %8.4f\n",z1[0],z1[1],z1[2]);
break;
status = 0;
}
}
if(status){
printf("Normal Beam Backwards Calculation: OK\n");
}
/*
for interest: try to see how normal beam angles go if we rotate psi
*/
/*
sttex = 30.58704;
om = 15.293520;
chi = 50.949;
phi = -45.8088;
printf(" PSI Omega Gamma Nu\n");
for(i = 0; i < 36; i++){
psi = i*10.;
rotatePsi(om,chi,phi,psi,&psiom,&psichi,&psiphi);
status = bisToNormalBeam(sttex,psiom,psichi,psiphi,&omeganb, &gamma, &nu);
if(status){
printf("%12.4f%12.4f%12.4f%12.4f\n",psi,omeganb,gamma,nu);
}
}
*/
}
#endif