Files
sics/ubfour.c
2014-03-14 09:48:14 +01:00

726 lines
16 KiB
C

/**
* This is a library for calculating UB matrices for four circle diffraction.
* The algorithm and settings definition is from:
*
* Busing & Levy, Acta Cryst. (1967), 22, 457ff
*
* Implemented:
* - UB from cell cell constants and two reflections.
* - Brute force index search
*
* Mark Koennecke, March 2005
*/
#include <math.h>
#include "ubfour.h"
#include <assert.h>
#include "vector.h"
#include "trigd.h"
#include "fourlib.h"
#include "lld.h"
#define ABS(x) (x < 0 ? -(x) : (x))
/*--------------------------------------------------------------------------------------*/
static MATRIX calcUVectorFromAngles(reflection r)
{
MATRIX u;
double om;
u = makeVector();
if (u == NULL) {
return NULL;
}
/*
* the tricky bit is set again: Busing and Levy's omega is 0 in bisecting
* position. This is why we have to correct for two_theta/2 here in order
* to arrive at the proper rotation around the omega axis.
*/
om = r.om - r.s2t / 2.;
vectorSet(u, 0,
Cosd(om) * Cosd(r.chi) * Cosd(r.phi) - Sind(om) * Sind(r.phi));
vectorSet(u, 1,
Cosd(om) * Cosd(r.chi) * Sind(r.phi) + Sind(om) * Cosd(r.phi));
vectorSet(u, 2, Cosd(om) * Sind(r.chi));
return u;
}
/*--------------------------------------------------------------------------------------
* The code for this was directly lifted from rafnb from ILL, routine UBH in rafnbb.f.
* I have yet to find a proper description of normal beam geometry calculations.
*--------------------------------------------------------------------------------------*/
static MATRIX calcNBUVectorFromAngles(reflection r)
{
MATRIX u;
double om, gamma, nu;
u = makeVector();
if (u == NULL) {
return NULL;
}
/*
VAB(1,I) = SN(1)*CS(2)*CS(3) + SN(2)*(1.-CS(1)*CS(3))
VAB(2,I) = SN(1)*SN(2)*CS(3) - CS(2)*(1.-CS(1)*CS(3))
VAB(3,I) = SN(3)
1 = gamma, 2 = om, 3 = nu, CS = cos, SN = sin
*/
gamma = r.gamma;
om = r.omnb;
nu = r.nu;
vectorSet(u, 0,
Sind(gamma)*Cosd(om)*Cosd(nu) + Sind(om)*(1. - Cosd(gamma)*Cosd(nu)));
vectorSet(u, 1,
Sind(gamma)*Sind(om)*Cosd(nu) - Cosd(om)*(1. - Cosd(gamma)*Cosd(nu)));
vectorSet(u, 2, Sind(nu));
return u;
}
/*--------------------------------------------------------------------------------------*/
static MATRIX reflectionToHC(reflection r, MATRIX B)
{
MATRIX h = NULL, hc = NULL;
h = makeVector();
if (h == NULL) {
return NULL;
}
vectorSet(h, 0, r.h);
vectorSet(h, 1, r.k);
vectorSet(h, 2, r.l);
hc = mat_mul(B, h);
killVector(h);
return hc;
}
/*---------------------------------------------------------------------------------------*/
MATRIX calcUBFromCellAndReflections(lattice direct, reflection r1,
reflection r2, int *errCode)
{
MATRIX B, HT, UT, U, UB, HTT;
MATRIX u1, u2, h1, h2;
double ud[3];
int status;
reflection r;
*errCode = 1;
/*
calculate the B matrix and the HT matrix
*/
B = mat_creat(3, 3, ZERO_MATRIX);
status = calculateBMatrix(direct, B);
if (status < 0) {
*errCode = status;
return NULL;
}
h1 = reflectionToHC(r1, B);
h2 = reflectionToHC(r2, B);
if (h1 == NULL || h2 == NULL) {
*errCode = UBNOMEMORY;
return NULL;
}
HT = matFromTwoVectors(h1, h2);
if (HT == NULL) {
*errCode = UBNOMEMORY;
return NULL;
}
/*
calculate U vectors and UT matrix
*/
u1 = calcUVectorFromAngles(r1);
u2 = calcUVectorFromAngles(r2);
if (u1 == NULL || u2 == NULL) {
*errCode = UBNOMEMORY;
return NULL;
}
UT = matFromTwoVectors(u1, u2);
if (UT == NULL) {
*errCode = UBNOMEMORY;
return NULL;
}
/*
debugging output
printf("B-matrix\n");
mat_dump(B);
printf("HT-matrix\n");
mat_dump(HT);
printf("UT-matrix\n");
mat_dump(UT);
*/
/*
UT = U * HT
*/
HTT = mat_tran(HT);
if (HTT == NULL) {
*errCode = UBNOMEMORY;
return NULL;
}
U = mat_mul(UT, HTT);
if (U == NULL) {
*errCode = UBNOMEMORY;
return NULL;
}
UB = mat_mul(U, B);
if (UB == NULL) {
*errCode = UBNOMEMORY;
}
/*
clean up
*/
killVector(h1);
killVector(h2);
mat_free(HT);
mat_free(HTT);
killVector(u1);
killVector(u2);
mat_free(UT);
mat_free(U);
mat_free(B);
return UB;
}
/*---------------------------------------------------------------------------------------*/
MATRIX calcNBUBFromCellAndReflections(lattice direct, reflection r1,
reflection r2, int *errCode)
{
MATRIX B, HT, UT, U, UB, HTT;
MATRIX u1, u2, h1, h2;
double ud[3];
int status;
reflection r;
*errCode = 1;
/*
calculate the B matrix and the HT matrix
*/
B = mat_creat(3, 3, ZERO_MATRIX);
status = calculateBMatrix(direct, B);
if (status < 0) {
*errCode = status;
return NULL;
}
h1 = reflectionToHC(r1, B);
h2 = reflectionToHC(r2, B);
if (h1 == NULL || h2 == NULL) {
*errCode = UBNOMEMORY;
return NULL;
}
HT = matFromTwoVectors(h1, h2);
if (HT == NULL) {
*errCode = UBNOMEMORY;
return NULL;
}
/*
calculate U vectors and UT matrix
*/
u1 = calcNBUVectorFromAngles(r1);
u2 = calcNBUVectorFromAngles(r2);
if (u1 == NULL || u2 == NULL) {
*errCode = UBNOMEMORY;
return NULL;
}
UT = matFromTwoVectors(u1, u2);
if (UT == NULL) {
*errCode = UBNOMEMORY;
return NULL;
}
/*
debugging output
printf("B-matrix\n");
mat_dump(B);
printf("HT-matrix\n");
mat_dump(HT);
printf("UT-matrix\n");
mat_dump(UT);
*/
/*
UT = U * HT
*/
HTT = mat_tran(HT);
if (HTT == NULL) {
*errCode = UBNOMEMORY;
return NULL;
}
U = mat_mul(UT, HTT);
if (U == NULL) {
*errCode = UBNOMEMORY;
return NULL;
}
UB = mat_mul(U, B);
if (UB == NULL) {
*errCode = UBNOMEMORY;
}
/*
clean up
*/
killVector(h1);
killVector(h2);
mat_free(HT);
mat_free(HTT);
killVector(u1);
killVector(u2);
mat_free(UT);
mat_free(U);
mat_free(B);
return UB;
}
/*-----------------------------------------------------------------------------------*/
static void storeReflection(reflection r, double two_theta_obs,
double two_theta_calc, int list)
{
refIndex ri, test;
int count = 0, status, pos = 0;
ri.h = r.h;
ri.k = r.k;
ri.l = r.l;
ri.t2obs = two_theta_obs;
ri.t2calc = two_theta_calc;
ri.t2diff = ABS(two_theta_obs - two_theta_calc);
/*
locate the last entry bigger then us
*/
status = LLDnodePtr2First(list);
while (status == 1) {
LLDnodeDataTo(list, &test);
count++;
if (test.t2diff == ri.t2diff) {
LLDnodeDataFrom(list, &ri);
return;
}
if (test.t2diff > ri.t2diff) {
break;
}
status = LLDnodePtr2Next(list);
}
/*
special case: empty list
*/
if (count == 0) {
LLDnodeAppendFrom(list, &ri);
return;
}
/*
special case: append after last
*/
LLDnodePtr2Last(list);
LLDnodeDataTo(list, &test);
if (ri.t2diff > test.t2diff) {
LLDnodeAppendFrom(list, &ri);
return;
}
status = LLDnodePtr2First(list);
pos = 0;
while (status == 1) {
LLDnodeDataTo(list, &test);
pos++;
if (pos == count) {
LLDnodeInsertFrom(list, &ri);
return;
}
status = LLDnodePtr2Next(list);
}
}
/*----------------------------------------------------------------------------
u_transform(i) = u(i)*(2*sin(theta)/lambda)
-----------------------------------------------------------------------------*/
static void uToScatteringVector(MATRIX u, double theta, double lambda)
{
double scale;
int i;
scale = (2. * Sind(theta)) / lambda;
for (i = 0; i < 3; i++) {
u[i][0] *= scale;
}
}
/*----------------------------------------------------------------------------*/
static MATRIX buildHCHIMatrix(MATRIX u1, MATRIX u2, MATRIX u3)
{
int i;
MATRIX HCHI;
HCHI = mat_creat(3, 3, ZERO_MATRIX);
if (HCHI == NULL) {
return NULL;
}
for (i = 0; i < 3; i++) {
HCHI[i][0] = u1[i][0];
HCHI[i][1] = u2[i][0];
HCHI[i][2] = u3[i][0];
}
return HCHI;
}
/*----------------------------------------------------------------------------*/
static MATRIX buildIndexMatrix(reflection r1, reflection r2, reflection r3)
{
MATRIX HI;
int i;
HI = mat_creat(3, 3, ZERO_MATRIX);
if (HI == NULL) {
return NULL;
}
HI[0][0] = r1.h;
HI[1][0] = r1.k;
HI[2][0] = r1.l;
HI[0][1] = r2.h;
HI[1][1] = r2.k;
HI[2][1] = r2.l;
HI[0][2] = r3.h;
HI[1][2] = r3.k;
HI[2][2] = r3.l;
return HI;
}
/*-----------------------------------------------------------------------------*/
MATRIX calcUBFromThreeReflections(reflection r1, reflection r2,
reflection r3, double lambda,
int *errCode)
{
MATRIX u1, u2, u3, HCHI, HI, HIINV, UB;
double det, z1[3];
if (lambda <= .1) {
*errCode = INVALID_LAMBDA;
return NULL;
}
*errCode = 1;
u1 = calcUVectorFromAngles(r1);
u2 = calcUVectorFromAngles(r2);
u3 = calcUVectorFromAngles(r3);
uToScatteringVector(u1, r1.s2t / 2., lambda);
uToScatteringVector(u2, r2.s2t / 2., lambda);
uToScatteringVector(u3, r3.s2t / 2., lambda);
HCHI = buildHCHIMatrix(u1, u2, u3);
HI = buildIndexMatrix(r1, r2, r3);
if (HCHI == NULL || HI == NULL) {
*errCode = UBNOMEMORY;
killVector(u1);
killVector(u2);
killVector(u3);
return NULL;
}
HIINV = mat_inv(HI);
if (HIINV == NULL) {
*errCode = NOTRIGHTHANDED;
killVector(u1);
killVector(u2);
killVector(u3);
mat_free(HI);
mat_free(HCHI);
return NULL;
}
UB = mat_mul(HCHI, HIINV);
det = mat_det(UB);
if (det < .0) {
mat_free(UB);
UB = NULL;
*errCode = NOTRIGHTHANDED;
}
killVector(u1);
killVector(u2);
killVector(u3);
mat_free(HI);
mat_free(HCHI);
mat_free(HIINV);
return UB;
}
/*-----------------------------------------------------------------------------*/
MATRIX calcNBUBFromThreeReflections(reflection r1, reflection r2,
reflection r3, double lambda,
int *errCode)
{
MATRIX u1, u2, u3, HCHI, HI, HIINV, UB;
double det, z1[3];
if (lambda <= .1) {
*errCode = INVALID_LAMBDA;
return NULL;
}
*errCode = 1;
z1FromNormalBeam(lambda,r1.gamma,r1.omnb, r1.nu,z1);
u1 = vectorToMatrix(z1);
z1FromNormalBeam(lambda,r2.gamma,r2.omnb, r2.nu,z1);
u2 = vectorToMatrix(z1);
z1FromNormalBeam(lambda,r3.gamma,r3.omnb, r3.nu,z1);
u3 = vectorToMatrix(z1);
HCHI = buildHCHIMatrix(u1, u2, u3);
HI = buildIndexMatrix(r1, r2, r3);
if (HCHI == NULL || HI == NULL) {
*errCode = UBNOMEMORY;
killVector(u1);
killVector(u2);
killVector(u3);
return NULL;
}
HIINV = mat_inv(HI);
if (HIINV == NULL) {
*errCode = NOTRIGHTHANDED;
killVector(u1);
killVector(u2);
killVector(u3);
mat_free(HI);
mat_free(HCHI);
return NULL;
}
UB = mat_mul(HCHI, HIINV);
det = mat_det(UB);
if (det < .0) {
mat_free(UB);
UB = NULL;
*errCode = NOTRIGHTHANDED;
}
killVector(u1);
killVector(u2);
killVector(u3);
mat_free(HI);
mat_free(HCHI);
mat_free(HIINV);
return UB;
}
/*---------------------------------------------------------------------------------*/
static int copyReflections(int list, refIndex index[], int maxIndex)
{
int count = 0, status;
refIndex ri;
status = LLDnodePtr2First(list);
while (status == 1 && count < maxIndex) {
LLDnodeDataTo(list, &ri);
index[count] = ri;
status = LLDnodePtr2Next(list);
count++;
}
return count;
}
/*-----------------------------------------------------------------------------------
- matching reflections will be entered in to a list in a sorted way. This list
is copied into the index array.
- There is some waste here in allocating and deallocating the HC vector in the
inner loop. I'am to lazy to resolve this.... May be I'am spared.....
-----------------------------------------------------------------------------------*/
int searchIndex(lattice direct, double lambda, double two_theta,
double max_deviation, int limit, refIndex index[],
int maxIndex)
{
int status, i, j, k, list;
MATRIX B, HC;
double theta, d;
reflection r;
B = mat_creat(3, 3, UNIT_MATRIX);
if (B == NULL) {
return UBNOMEMORY;
}
status = calculateBMatrix(direct, B);
if (status < 0) {
return status;
}
list = LLDcreate(sizeof(refIndex));
if (list < 0) {
return UBNOMEMORY;
}
for (i = -limit; i < limit; i++) {
r.h = (double) i;
for (j = -limit; j < limit; j++) {
r.k = (double) j;
for (k = -limit; k < limit; k++) {
r.l = (double) k;
HC = reflectionToHC(r, B);
status = calcTheta(lambda, HC, &d, &theta);
if (status == 1) {
if (ABS(two_theta - 2. * theta) <= max_deviation) {
storeReflection(r, two_theta, theta * 2., list);
}
}
killVector(HC);
}
}
}
mat_free(B);
status = copyReflections(list, index, maxIndex);
LLDdelete(list);
return status;
}
/*-------------------------------------------------------------------------*/
double angleBetweenReflections(MATRIX B, reflection r1, reflection r2)
{
MATRIX chi1, chi2, h1, h2;
double angle = .0;
h1 = makeVector();
if (h1 == NULL) {
return -9999.99;
}
h1[0][0] = r1.h;
h1[1][0] = r1.k;
h1[2][0] = r1.l;
h2 = makeVector();
if (h2 == NULL) {
return -999.99;
}
h2[0][0] = r2.h;
h2[1][0] = r2.k;
h2[2][0] = r2.l;
chi1 = mat_mul(B, h1);
chi2 = mat_mul(B, h2);
if (chi1 != NULL && chi2 != NULL) {
angle = angleBetween(chi1, chi2);
killVector(chi1);
killVector(chi2);
}
killVector(h1);
killVector(h2);
return angle;
}
/*---------------------------------------------------------------------------*/
MATRIX makeInstToConeVectorMatrix(reflection r, double lambda)
{
double z1[3], alpha, beta;
MATRIX mAlpha = NULL, mBeta = NULL, inst2CS = NULL;
z1FromAngles(lambda, r.s2t, r.om, r.chi, r.phi, z1);
alpha = atan2(z1[1], z1[0]);
beta = -atan2(z1[0], z1[2]);
/* printf("alpha = %f, beta = %f\n", alpha*57.57, beta*57.57);*/
mAlpha = mat_creat(3, 3, ZERO_MATRIX);
mBeta = mat_creat(3, 3, ZERO_MATRIX);
if (mAlpha == NULL || mBeta == NULL) {
return NULL;
}
mAlpha[0][0] = cos(alpha);
mAlpha[0][1] = sin(alpha);
mAlpha[1][0] = -sin(alpha);
mAlpha[1][1] = cos(alpha);
mAlpha[2][2] = 1.;
mBeta[0][0] = cos(beta);
mBeta[0][2] = sin(beta);
mBeta[1][1] = 1.;
mBeta[2][0] = -sin(beta);
mBeta[2][2] = cos(beta);
inst2CS = mat_mul(mBeta, mAlpha);
mat_free(mAlpha);
mat_free(mBeta);
return inst2CS;
}
/*--------------------------------------------------------------------------*/
MATRIX calcConeVector(double openingAngle, double coneAngle,
double length, MATRIX coneToPsi)
{
MATRIX coneRot = NULL, nullVector = NULL, coneVector = NULL;
MATRIX coneVectorScatter = NULL;
double testAngle;
MATRIX z;
z = makeVector();
z[2][0] = 1.;
coneRot = mat_creat(3, 3, ZERO_MATRIX);
if (coneRot == NULL) {
return NULL;
}
coneRot[0][0] = Cosd(coneAngle);
coneRot[0][1] = -Sind(coneAngle);
coneRot[1][0] = Sind(coneAngle);
coneRot[1][1] = Cosd(coneAngle);
coneRot[2][2] = 1.0;
nullVector = makeVector();
if (nullVector == NULL) {
return NULL;
}
nullVector[0][0] = Sind(openingAngle);
nullVector[1][0] = .0;
nullVector[2][0] = Cosd(openingAngle);
normalizeVector(nullVector);
scaleVector(nullVector, length);
testAngle = angleBetween(z, nullVector);
coneVector = mat_mul(coneRot, nullVector);
if (coneVector == NULL) {
return NULL;
}
testAngle = angleBetween(z, coneVector);
coneVectorScatter = mat_mul(coneToPsi, coneVector);
mat_free(coneRot);
killVector(nullVector);
killVector(coneVector);
return coneVectorScatter;
}
/*---------------------------------------------------------------------------*/
double scatteringVectorLength(MATRIX B, reflection r)
{
MATRIX h = NULL, psi = NULL;
double length;
h = makeVector();
if (h == NULL) {
return -9999.9;
}
h[0][0] = r.h;
h[1][0] = r.k;
h[2][0] = r.l;
psi = mat_mul(B, h);
length = vectorLength(psi);
killVector(h);
killVector(psi);
return length;
}