/// Returns signed 2 theta (signed scattering angle w.r.t. to beam direction).
double
DetectorInfo::signedTwoTheta(const std::pair<size_t, size_t> &index) const {
if (isMonitor(index))
throw std::logic_error(
"Two theta (scattering angle) is not defined for monitors.");
const auto samplePos = samplePosition();
const auto beamLine = samplePos - sourcePosition();
if (beamLine.nullVector()) {
throw Kernel::Exception::InstrumentDefinitionError(
"Source and sample are at same position!");
}
// Get the axis defining the sign
const auto &instrumentUpAxis =
m_instrument->getReferenceFrame()->vecThetaSign();
const auto sampleDetVec = position(index) - samplePos;
double angle = sampleDetVec.angle(beamLine);
const auto cross = beamLine.cross_prod(sampleDetVec);
const auto normToSurface = beamLine.cross_prod(instrumentUpAxis);
if (normToSurface.scalar_prod(cross) < 0) {
angle *= -1;
}
return angle;
}
void InstrumentRenderer::drawSingleDetector(size_t detIndex, bool picking) {
const auto &compInfo = m_actor.componentInfo();
if (picking)
m_pickColors[detIndex].paint();
else
m_colors[detIndex].paint();
glPushMatrix();
// Translate
auto pos = compInfo.position(detIndex);
if (!pos.nullVector())
glTranslated(pos[0], pos[1], pos[2]);
// Rotate
auto rot = compInfo.rotation(detIndex);
if (!rot.isNull()) {
double deg, ax0, ax1, ax2;
rot.getAngleAxis(deg, ax0, ax1, ax2);
glRotated(deg, ax0, ax1, ax2);
}
// Scale
auto scale = compInfo.scaleFactor(detIndex);
if (scale != Mantid::Kernel::V3D(1, 1, 1))
glScaled(scale[0], scale[1], scale[2]);
compInfo.shape(detIndex).draw();
glPopMatrix();
}
/// Returns 2 theta (scattering angle w.r.t. to beam direction).
double DetectorInfo::twoTheta(const std::pair<size_t, size_t> &index) const {
if (isMonitor(index))
throw std::logic_error(
"Two theta (scattering angle) is not defined for monitors.");
const auto samplePos = samplePosition();
const auto beamLine = samplePos - sourcePosition();
if (beamLine.nullVector()) {
throw Kernel::Exception::InstrumentDefinitionError(
"Source and sample are at same position!");
}
const auto sampleDetVec = position(index) - samplePos;
return sampleDetVec.angle(beamLine);
}
static void leaveBootloader()
{
statusLedOff();
cli();
boot_rww_enable();
USB_INTR_ENABLE = 0;
USB_INTR_CFG = 0; /* also reset config bits */
GICR = (1 << IVCE); /* enable change of interrupt vectors */
GICR = (0 << IVSEL); /* move interrupts to application flash section */
/* We must go through a global function pointer variable instead of writing
* ((void (*)(void))0)();
* because the compiler optimizes a constant 0 to "rcall 0" which is not
* handled correctly by the assembler.
*/
nullVector();
}
static inline __attribute__((noreturn)) void leaveBootloader(void)
{
DBG1(0x01, 0, 0);
bootLoaderExit();
cli();
USB_INTR_ENABLE = 0;
USB_INTR_CFG = 0; /* also reset config bits */
#ifdef TINY85MODE
// make sure remainder of flash is erased and write checksum and application reset vectors
if(appWriteComplete)
{
CURRENT_ADDRESS = writeSize;
while(CURRENT_ADDRESS < BOOTLOADER_ADDRESS)
{
fillFlashWithVectors();
}
}
#else
GICR = (1 << IVCE); /* enable change of interrupt vectors */
GICR = (0 << IVSEL); /* move interrupts to application flash section */
#endif
// TODO: watchdog reset instead to reset registers?
#ifdef APPCHECKSUM
if(!testForValidApplication())
asm volatile ("rjmp __vectors");
#endif
#ifdef TINY85MODE
// clear magic word from bottom of stack before jumping to the app
*(uint8_t*)(RAMEND) = 0x00;
*(uint8_t*)(RAMEND-1) = 0x00;
// jump to application reset vector at end of flash
asm volatile ("rjmp __vectors - 4");
#else
/* We must go through a global function pointer variable instead of writing
* ((void (*)(void))0)();
* because the compiler optimizes a constant 0 to "rcall 0" which is not
* handled correctly by the assembler.
*/
nullVector();
#endif
}
static void leaveBootloader()
{
uint8_t gicr;
DBG1(0x01, 0, 0);
cli();
boot_rww_enable();
USB_INTR_ENABLE = 0;
USB_INTR_CFG = 0; /* also reset config bits */
#if F_CPU == 12800000
TCCR0 = 0; /* default value */
#endif
gicr = GICR;
GICR = gicr | (1 << IVCE); /* enable change of interrupt vectors */
GICR = gicr & ~(1 << IVSEL); /* move interrupts to application flash section */
bootLoaderShut();
/* We must go through a global function pointer variable instead of writing
* ((void (*)(void))0)();
* because the compiler optimizes a constant 0 to "rcall 0" which is not
* handled correctly by the assembler.
*/
nullVector();
}
inline void computeSphereStress(){
printf("Computing sphere stress tensor...\n");
int atom, id1, id2, j;
Vector atomDistance, atomForce;
double r, r2;
double atomArea, atomVolume;
double sp_1, sp_2, sp_3;
for (atom = 0; atom < pdbData.atomCount; atom++){
atomSphereStress[atom].x = 0.0;
atomSphereStress[atom].y = 0.0;
atomSphereStress[atom].z = 0.0;
atomSphereStress[atom].value = 0.0;
}
for (atom = 0; atom < pdbData.atomCount; atom++){
r = 0.0;
r2 = 0.0;
copyVector(&atomDistance, nullVector());
copyVector(&atomForce, nullVector());
copyVector(&ePhi, DCDtoEphi(X[atom], Y[atom], Z[atom]));
copyVector(&eTheta, DCDtoEtheta(X[atom], Y[atom], Z[atom]));
copyVector(&eRad, DCDtoErad(X[atom], Y[atom], Z[atom]));
for (j = 0; j < bondsCount[atom]; j++){
id1 = atom, id2 = bonds[atom * MAX_BONDS + j];
funcParam.refDist = bondsR0[atom * MAX_BONDS + j];
copyVector(&atomDistance, DCDtoVector(X[id1] - X[id2], Y[id1] - Y[id2], Z[id1] - Z[id2]));
copyVector(&atomForce, getFENEDerivative_1(atomDistance));
sp_1 = eTheta.x * atomDistance.x + eTheta.y * atomDistance.y + eTheta.z * atomDistance.z;
sp_2 = ePhi.x * atomDistance.x + ePhi.y * atomDistance.y + ePhi.z * atomDistance.z;
sp_3 = eRad.x * atomDistance.x + eRad.y * atomDistance.y + eRad.z * atomDistance.z;
atomSphereStress[atom].x += 0.5 * atomForce.value/atomDistance.value * (sp_1 * sp_1 + sp_2 * sp_2); //lateral
atomSphereStress[atom].y += atomForce.value/atomDistance.value * sp_1 * sp_2; //45-shear
atomSphereStress[atom].z += atomForce.value/atomDistance.value * sp_3 * sp_3; //radial
r += 1.0/atomDistance.value;
r2 += 1.0/(atomDistance.value * atomDistance.value);
}
for (j = 0; j < nativeCount[atom]; j++){
id1 = atom; id2 = native[atom * MAX_NATIVE + j];
funcParam.refDist = nativeR0[atom * MAX_NATIVE + j];
funcParam.Eh = nativeEh[atom * MAX_NATIVE + j];
copyVector(&atomDistance, DCDtoVector(X[id1] - X[id2], Y[id1] - Y[id2], Z[id1] - Z[id2]));
copyVector(&atomForce, getNativeDerivative_1(atomDistance));
sp_1 = eTheta.x * atomDistance.x + eTheta.y * atomDistance.y + eTheta.z * atomDistance.z;
sp_2 = ePhi.x * atomDistance.x + ePhi.y * atomDistance.y + ePhi.z * atomDistance.z;
sp_3 = eRad.x * atomDistance.x + eRad.y * atomDistance.y + eRad.z * atomDistance.z;
atomSphereStress[atom].x += 0.5 * atomForce.value/atomDistance.value * (sp_1 * sp_1 + sp_2 * sp_2); //lateral
atomSphereStress[atom].y += atomForce.value/atomDistance.value * sp_1 * sp_2; //45-shear
atomSphereStress[atom].z += atomForce.value/atomDistance.value * sp_3 * sp_3; //radial
r += 1.0/atomDistance.value;
r2 += 1.0/(atomDistance.value * atomDistance.value);
}
for (j = 0; j < pairsCount[atom]; j++){
id1 = atom; id2 = pairs[atom * MAX_PAIRS + j];
copyVector(&atomDistance, DCDtoVector(X[id1] - X[id2], Y[id1] - Y[id2], Z[id1] - Z[id2]));
if (atomDistance.value < pairs_cutoff && id1 != id2 ){
copyVector(&atomDistance, DCDtoVector(X[id1] - X[id2], Y[id1] - Y[id2], Z[id1] - Z[id2]));
copyVector(&atomForce, getRepulsiveDerivative_1(atomDistance));
sp_1 = eTheta.x * atomDistance.x + eTheta.y * atomDistance.y + eTheta.z * atomDistance.z;
sp_2 = ePhi.x * atomDistance.x + ePhi.y * atomDistance.y + ePhi.z * atomDistance.z;
sp_3 = eRad.x * atomDistance.x + eRad.y * atomDistance.y + eRad.z * atomDistance.z;
atomSphereStress[atom].x += 0.5 * atomForce.value/atomDistance.value * (sp_1 * sp_1 + sp_2 * sp_2); //lateral
atomSphereStress[atom].y += atomForce.value/atomDistance.value * sp_1 * sp_2; //45-shear
atomSphereStress[atom].z += atomForce.value/atomDistance.value * sp_3 * sp_3; //radial
r += 1.0/atomDistance.value;
r2 += 1.0/(atomDistance.value * atomDistance.value);
}
}
atomArea = Pi * (0.5*r/r2) * (0.5*r/r2);
atomVolume = 4.0/3.0 * Pi * (0.5*r/r2) * (0.5*r/r2) * (0.5*r/r2);
atomSphereStress[atom].x /= atomArea;
atomSphereStress[atom].y /= atomArea;
atomSphereStress[atom].z /= atomVolume;
}
}
