- Added another missing file
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koennecke
286
simindex.c
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286
simindex.c
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/**
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* This is the SICS driver for the simple indexing algorithm in simidx.c
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*
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* copyright: GPL
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*
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* Mark Koennecke, August 2008
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*/
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#include <stdlib.h>
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#include <math.h>
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#include <sics.h>
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#include <sicshipadaba.h>
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#include <sicsobj.h>
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#include "simidx.h"
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#include "singlex.h"
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#include "matrix/matrix.h"
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#include "ubfour.h"
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extern double nintd(double d);
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/*----------------------------------------------------------------------*/
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static void SicsOutFunc(void *data, char *text)
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{
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SConnection *pCon = (SConnection *) data;
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if (pCon != NULL) {
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SCWrite(pCon, text, eWarning);
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}
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}
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/*-----------------------------------------------------------------------*/
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static hdbCallbackReturn SetSttLim(pHdb node, void *userData,
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pHdbMessage mm)
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{
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pHdbDataMessage set = NULL;
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SConnection *pCon = NULL;
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hdbValue v;
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if ((set = GetHdbSetMessage(mm)) != NULL) {
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SimIdxSetSttLim(set->v->v.doubleValue);
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return hdbContinue;
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}
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return hdbContinue;
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}
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/*-----------------------------------------------------------------------*/
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static hdbCallbackReturn SetAngLim(pHdb node, void *userData,
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pHdbMessage mm)
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{
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pHdbDataMessage set = NULL;
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SConnection *pCon = NULL;
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hdbValue v;
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if ((set = GetHdbSetMessage(mm)) != NULL) {
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SimIdxSetAngLim(set->v->v.doubleValue);
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return hdbContinue;
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}
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return hdbContinue;
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}
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/*-------------------------------------------------------------------------*/
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static int RunIndexCmd(pSICSOBJ self, SConnection * pCon, pHdb commandNode,
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pHdb par[], int nPar)
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{
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int i, j, status;
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pSingleDiff diffi;
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pSICSOBJ reflist;
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double ang[4], z1[3];
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IndexSolution is;
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SimIdxSetLambda(SXGetLambda());
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SimIdxSetCell((double *) SXGetCell());
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SimIdxSetSpacegroup(SXGetSpaceGroup());
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SimIdxOutput(pCon, SicsOutFunc, 10);
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reflist = SXGetReflectionList();
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diffi = SXGetDiffractometer();
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SimIdxClearReflection();
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for (i = 0; i < ReflectionListCount(reflist); i++) {
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GetRefAngles(reflist, i, ang);
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diffi->calcZ1(diffi, GetRefName(reflist, i), z1);
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SimIdxAddReflection(z1);
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}
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status = SimIdxRun();
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if (status == 1) {
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if (SimIdxGetNSolutions() < 1) {
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SCWrite(pCon, "No solutions were found", eWarning);
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return 0;
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}
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SCWrite(pCon, "Indexing Suggestions:", eWarning);
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for (i = 0; i < SimIdxGetNSolutions(); i++) {
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is = SimIdxGetSolution(i);
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SCPrintf(pCon, eWarning, "Solution No : %d, GOF = %6.3f", i,
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is.diff * 100);
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for (j = 0; j < 3; j++) {
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if (is.originalID[j] != 999) {
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SCPrintf(pCon, eWarning, " Ref = %2d, HKL = %4d %4d %4d ",
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is.originalID[j], is.h[j], is.k[j], is.l[j]);
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}
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}
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}
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}
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return status;
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}
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/*-----------------------------------------------------------------------*/
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static int ChooseCmd(pSICSOBJ self, SConnection * pCon, pHdb commandNode,
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pHdb par[], int nPar)
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{
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MATRIX UB;
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int err, solution, i;
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IndexSolution is;
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double hkl[3], ub[9];
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pSICSOBJ reflist;
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pSingleDiff diffi;
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if (nPar < 1) {
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SCWrite(pCon, "ERROR: need the solution number as argument", eError);
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return 0;
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}
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solution = par[0]->value.v.intValue;
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if (solution < 0 || solution >= SimIdxGetNSolutions()) {
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SCWrite(pCon, "ERROR: solution number out of range", eError);
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return 0;
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}
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is = SimIdxGetSolution(i);
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reflist = SXGetReflectionList();
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diffi = SXGetDiffractometer();
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assert(reflist != NULL);
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assert(diffi != NULL);
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for (i = 0; i < 3; i++) {
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if (is.originalID[i] != 999) {
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hkl[0] = (double) is.h[i];
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hkl[1] = (double) is.k[i];
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hkl[2] = (double) is.l[i];
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SetRefIndex(reflist, is.originalID[i], hkl);
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}
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}
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if (is.originalID[2] == 999) {
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UB = diffi->calcUBFromTwo(diffi, GetRefName(reflist, is.originalID[0]),
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GetRefName(reflist, is.originalID[1]), &err);
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} else {
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UB = diffi->calcUBFromThree(diffi,
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GetRefName(reflist, is.originalID[0]),
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GetRefName(reflist, is.originalID[1]),
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GetRefName(reflist, is.originalID[2]),
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&err);
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}
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if (UB == NULL) {
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switch (err) {
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case REFERR:
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SCWrite(pCon, "ERROR: one of reflections ID's is invalid", eError);
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return 0;
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break;
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case UBNOMEMORY:
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SCWrite(pCon, "ERROR: out of memory calculating UB", eError);
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break;
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case INVALID_LAMBDA:
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SCWrite(pCon, "ERROR: bad value for wavelength", eError);
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break;
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case NOTRIGHTHANDED:
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SCWrite(pCon,
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"ERROR: reflections are coplanar or do not form a right handed system",
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eError);
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break;
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default:
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SCWrite(pCon, "ERROR: unknown error code from UB calculation",
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eError);
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break;
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}
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return 0;
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}
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for (i = 0; i < 3; i++) {
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ub[i] = UB[0][i];
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ub[i + 3] = UB[1][i];
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ub[i + 6] = UB[2][i];
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}
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SXSetUB(ub);
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mat_free(UB);
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SCSendOK(pCon);
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return 1;
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}
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/*-----------------------------------------------------------------------*/
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static int DiraxCmd(pSICSOBJ self, SConnection * pCon, pHdb commandNode,
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pHdb par[], int nPar)
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{
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FILE *fd = NULL;
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int i;
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double uvw[3];
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pSICSOBJ reflist = NULL;
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pSingleDiff diffi = NULL;
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if (nPar < 1) {
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SCWrite(pCon, "ERROR: need filename parameter", eError);
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return 0;
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}
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reflist = SXGetReflectionList();
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assert(reflist != NULL);
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diffi = SXGetDiffractometer();
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assert(diffi != NULL);
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fd = fopen(par[0]->value.v.text, "w");
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if (fd == NULL) {
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SCWrite(pCon, "ERROR: failed to open dirax file", eError);
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return 0;
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}
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fprintf(fd, " %f\n", SXGetLambda());
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for (i = 0; i < ReflectionListCount(reflist); i++) {
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diffi->calcZ1(diffi, GetRefName(reflist, i), uvw);
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fprintf(fd, " %f %f %f\n", uvw[0], uvw[1], uvw[2]);
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}
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fclose(fd);
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SCSendOK(pCon);
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return 1;
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}
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/*-----------------------------------------------------------------------*/
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static int IndexCmd(pSICSOBJ self, SConnection * pCon, pHdb commandNode,
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pHdb par[], int nPar)
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{
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int i, j;
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double ang[4], hkl[3];
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const double *ub;
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pSICSOBJ reflist = NULL;
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pSingleDiff diffi = NULL;
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reflist = SXGetReflectionList();
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assert(reflist != NULL);
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diffi = SXGetDiffractometer();
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assert(diffi != NULL);
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for (i = 0; i < ReflectionListCount(reflist); i++) {
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GetRefAngles(reflist, i, ang);
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diffi->hklFromAnglesGiven(diffi, ang, hkl);
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for (j = 0; j < 3; j++) {
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hkl[j] = nintd(hkl[j]);
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}
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SetRefIndex(reflist, i, hkl);
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}
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SCSendOK(pCon);
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return 1;
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}
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/*-----------------------------------------------------------------------*/
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void InitSimpleIndex(SConnection * pCon, SicsInterp * pSics)
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{
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pSICSOBJ pNew = NULL;
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pHdb cmd;
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pNew = MakeSICSOBJ("simidx", "SimpleIndexer");
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if (!pNew) {
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return;
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}
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SimIdxInit();
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cmd = AddSICSHdbPar(pNew->objectNode, "sttlim", usUser,
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MakeHdbFloat(.2));
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AppendHipadabaCallback(cmd, MakeHipadabaCallback(SetSttLim, NULL, NULL));
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SetHdbProperty(cmd, "__save", "true");
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cmd = AddSICSHdbPar(pNew->objectNode, "anglim", usUser,
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MakeHdbFloat(.5));
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AppendHipadabaCallback(cmd, MakeHipadabaCallback(SetAngLim, NULL, NULL));
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SetHdbProperty(cmd, "__save", "true");
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cmd = AddSICSHdbPar(pNew->objectNode, "run", usUser,
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MakeSICSFunc(RunIndexCmd));
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cmd = AddSICSHdbPar(pNew->objectNode, "choose", usUser,
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MakeSICSFunc(ChooseCmd));
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cmd = AddSICSHdbPar(cmd, "solution", usUser, MakeHdbInt(0));
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cmd = AddSICSHdbPar(pNew->objectNode, "dirax", usUser,
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MakeSICSFunc(ChooseCmd));
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cmd = AddSICSHdbPar(cmd, "name", usUser, MakeHdbText("sics.drx"));
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cmd = AddSICSHdbPar(pNew->objectNode, "idxref", usUser,
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MakeSICSFunc(IndexCmd));
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AddCommand(pSics, "simidx", InterInvokeSICSOBJ, KillSICSOBJ, pNew);
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}
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15
singelbi.h
Normal file
15
singelbi.h
Normal file
@ -0,0 +1,15 @@
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/**
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* This is an implementation of the polymorphic single crystal calculation
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* system defined in singlediff.h for a bisecting four circle diffractometer with
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* an eulerian cradle.
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*
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* copyright: see file COPYRIGHT
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*
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* Mark Koennecke, August 2008
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*/
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#ifndef SINGELBI_H_
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#define SINGELBI_H_
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#include "singlediff.h"
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void initializeSingleBisecting(pSingleDiff diff);
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#endif /*SINGELBI_H_ */
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