NesObject::NesObject( NesInstrument * nes, const sample_rate_t samplerate, NotePlayHandle * nph, fpp_t frames ) :
m_parent( nes ),
m_samplerate( samplerate ),
m_nph( nph ),
m_fpp( frames )
{
m_pitchUpdateCounter = 0;
m_pitchUpdateFreq = wavelength( 60.0f );
m_LFSR = LFSR_INIT;
m_ch1Counter = 0;
m_ch2Counter = 0;
m_ch3Counter = 0;
m_ch4Counter = 0;
m_ch1EnvCounter = 0;
m_ch2EnvCounter = 0;
m_ch4EnvCounter = 0;
m_ch1EnvValue = 15;
m_ch2EnvValue = 15;
m_ch4EnvValue = 15;
m_ch1SweepCounter = 0;
m_ch2SweepCounter = 0;
m_ch4SweepCounter = 0;
m_12Last = 0.0f;
m_34Last = 0.0f;
m_maxWlen = wavelength( MIN_FREQ );
m_nsf = NES_SIMPLE_FILTER * ( m_samplerate / 44100.0 );
m_lastNoteFreq = 0;
m_lastNoiseFreq = -1.0f; // value that is always different than noisefreq so it gets updated at start
m_vibratoPhase = 0;
updatePitch();
}
/*------------------------ main() ---------------------*/
int main()
{
char fileout[NCMAX], cline[NCMAX];
const char version[] = "06-apr-2013 (ejk)";
int ix, iy, nx, ny, ixmid, iymid, i, ismoth, npixels, ns,
done, status, multiMode, NPARAM;
float rmin, rmax, aimin, aimax, p2;
float *param, pixr, pixi, **pixsq;
double k2max, keV, wavlen, ax, by, rx, ry,
rx2, ry2, pi, dx, dy, scale, scale2, pixel,
Cs3, Cs5, df, sum, time, apert;
double x;
cfpix cpix;
floatTIFF myFile;
/* Echo version date etc. */
printf( "probe version dated %s\n", version );
printf("Copyright (C) 1998-2013 Earl J. Kirkland\n" );
printf( "This program is provided AS-IS with ABSOLUTELY NO WARRANTY\n "
" under the GNU general public license\n\n" );
#ifdef MANY_ABERR
printf( "calculate a focused probe wave function including multiple aberr.\n\n");
#else
printf( "calculate a focused probe wave function\n\n");
#endif
pi = 4.0 * atan( 1.0 );
/* memory to store parameters */
NPARAM = myFile.maxParam();
param = (float*) malloc1D( NPARAM, sizeof(float), "probe-param" );
for( i=0; i<NPARAM; i++) param[i] = 0.0F;
/* ---- Get desired image size, parameters etc. ------------- */
printf("Name of file to get focused probe wave function:\n");
ns = scanf("%s", fileout );
printf("Desired size of output image in pixels Nx,Ny:\n");
ns = scanf("%d %d", &nx, &ny );
printf("Size of output image in Angstroms ax,by:\n");
ns = scanf("%lf %lf", &ax, &by );
printf("Probe parameters, V0(kv), Cs3(mm), Cs5(mm),"
" df(Angstroms), apert(mrad):\n");
ns = scanf("%lg %lg %lg %lg %lg",
&keV, &Cs3, &Cs5, &df, &apert );
param[pDEFOCUS] = (float) df;
param[pCS] = (float) ( Cs3*1.0e7 );
param[pCS5] = (float) ( Cs5*1.0e7 );
printf("Type 1 for smooth aperture:\n");
ns = scanf("%d", &ismoth );
printf("Probe position x,y in Ang.:\n");
ns = scanf("%lf %lf", &dx, &dy );
#ifdef MANY_ABERR
/* get higher order aberrations if necessary */
printf("type higher order aber. name (as C32a, etc.) followed\n"
" by a value in mm. (END to end)\n");
done = multiMode = 0;
do{
ns = scanf( "%20s", cline );
if( strstr( cline, "END" ) != NULL ) {
done = 1;
} else {
ns = scanf( "%lg", &x );
/* printf("%s, %f\n", cline, x ); testing */
status = readCnm( cline, param, x );
if( status < 0 ) {
printf( "unrecognized aberration, exit...\n");
exit( EXIT_SUCCESS );
} else multiMode = 1;
}
} while( !done );
#endif
/* ------- Calculate misc constants ------------ */
time = cputim( );
rx = 1.0/ax;
rx2 = rx * rx;
ry = 1.0/by;
ry2 = ry * ry;
ixmid = nx/2;
iymid = ny/2;
wavlen = wavelength( keV );
printf("electron wavelength = %g Angstroms\n", wavlen);
k2max = apert*0.001/wavlen;
k2max = k2max * k2max;
/* ------- allocate memory ------------ */
pixsq = (float**) malloc2D( nx, ny, sizeof(float), "pixsq" );
kx = (float*) malloc1D( nx, sizeof(float), "kx" );
kx2 = (float*) malloc1D( nx, sizeof(float), "kx2" );
xpos = (float*) malloc1D( nx, sizeof(float), "xpos" );
freqn( kx, kx2, xpos, nx, ax );
ky = (float*) malloc1D( ny, sizeof(float), "ky" );
ky2 = (float*) malloc1D( ny, sizeof(float), "ky2" );
ypos = (float*) malloc1D( ny, sizeof(float), "ypos" );
freqn( ky, ky2, ypos, ny, by );
cpix.resize( nx, ny );
cpix.init( 1 ); // only fast init and slow execution needed here
/* --------- calculate probe wavefunction -------- */
pixel = ( rx2 + ry2 );
npixels = makeProbe( cpix, nx, ny, dx, dy,
param, wavlen, k2max, pixel, multiMode, ismoth );
printf("there were %d pixels inside the aperture\n", npixels );
/* ----- copy back for output ----- */
sum = 0.0;
myFile.resize( 2*nx, ny);
myFile.setnpix( 2 );
for( ix=0; ix<nx; ix++)
for( iy=0; iy<ny; iy++) {
myFile(ix,iy) = pixr = cpix.re(ix,iy); // real
myFile(ix+nx,iy) = pixi = cpix.im(ix,iy); // imag
pixsq[ix][iy] = p2 = pixr*pixr + pixi*pixi;
sum += p2;
}
/* ----- Normalize probe intensity to unity ------------ */
scale = 1.0 / sum;
scale = scale * ((double)nx) * ((double)ny);
scale = (double) sqrt( scale );
scale2 = scale*scale;
for( ix=0; ix<nx; ix++)
for( iy=0; iy<ny; iy++) {
myFile(ix,iy) *= (float) scale;
myFile(ix+nx,iy) *= (float) scale;
pixsq[ix][iy] *= (float) scale2;
}
/*------- Output results and find min and max to echo ---------------
*/
rmin = myFile.min(0); // real part
rmax = myFile.max(0);
aimin = myFile.min(1); // imaginary
aimax = myFile.max(1);
param[pRMAX] = rmax;
param[pIMAX] = aimax;
param[pRMIN] = rmin;
param[pIMIN] = aimin;
param[pDEFOCUS]= (float) df;
param[pDX]= (float) (ax / nx);
param[pDY]= (float) (by / ny);
param[pENERGY]= (float) keV;
param[pWAVEL]= (float) ( sqrt(k2max) * wavlen);
param[pCS]= (float) Cs3;
param[pPPOSX]= (float) dx;
param[pPPOSX]= (float) dy;
for( i=0; i<NPARAM; i++) myFile.setParam( i, param[i] ); // not very efficient
if( myFile.write( fileout, rmin, rmax, aimin, aimax, param[pDX], param[pDY] ) != 1 )
printf( "probe cannot write an output file.\n");
printf( "Pix range %15.7g to %15.7g real,\n"
" and %15.7g to %15.7g imaginary\n",
rmin, rmax, aimin, aimax );
/*------- calculate probe size ---------------*/
x = prbSize( pixsq, nx, ny, dx, dy, ax, by );
printf("probe size (FWHM-II) = %g Ang.\n", x);
/*------- exit ---------------*/
time = cputim() - time;
printf("\nCPU time = %f sec\n", time );
return EXIT_SUCCESS;
} /* end main() */
void NesObject::renderOutput( sampleFrame * buf, fpp_t frames )
{
////////////////////////////////
// //
// variables for processing //
// //
////////////////////////////////
bool ch1Enabled = m_parent->m_ch1Enabled.value();
bool ch2Enabled = m_parent->m_ch2Enabled.value();
bool ch3Enabled = m_parent->m_ch3Enabled.value();
bool ch4Enabled = m_parent->m_ch4Enabled.value();
float ch1DutyCycle = DUTY_CYCLE[ m_parent->m_ch1DutyCycle.value() ];
int ch1EnvLen = wavelength( floorf( 240.0 / ( m_parent->m_ch1EnvLen.value() + 1 ) ) );
bool ch1EnvLoop = m_parent->m_ch1EnvLooped.value();
float ch2DutyCycle = DUTY_CYCLE[ m_parent->m_ch2DutyCycle.value() ];
int ch2EnvLen = wavelength( floorf( 240.0 / ( m_parent->m_ch2EnvLen.value() + 1 ) ) );
bool ch2EnvLoop = m_parent->m_ch2EnvLooped.value();
int ch4EnvLen = wavelength( floorf( 240.0 / ( m_parent->m_ch4EnvLen.value() + 1 ) ) );
bool ch4EnvLoop = m_parent->m_ch4EnvLooped.value();
// processing variables for operators
int ch1;
int ch2;
int ch3;
int ch4;
// levels for generators (used for dc offset compensation)
int ch1Level;
int ch2Level;
int ch3Level;
int ch4Level;
int ch1SweepRate = wavelength( floorf( 120.0 / ( m_parent->m_ch1SweepRate.value() + 1 ) ) );
int ch2SweepRate = wavelength( floorf( 120.0 / ( m_parent->m_ch2SweepRate.value() + 1 ) ) );
int ch4SweepRate = wavelength( floorf( 60.0f / ( 8.0f - qAbs( m_parent->m_ch4Sweep.value() ) ) ) );
int ch1Sweep = static_cast<int>( m_parent->m_ch1SweepAmt.value() * -1.0 );
int ch2Sweep = static_cast<int>( m_parent->m_ch2SweepAmt.value() * -1.0 );
int ch4Sweep = 0;
if( m_parent->m_ch4Sweep.value() != 0.0f )
{
ch4Sweep = m_parent->m_ch4Sweep.value() > 0.0f
? -1
: 1;
}
// the amounts are inverted so we correct them here
if( ch1Sweep > 0 )
{
ch1Sweep = 8 - ch1Sweep;
}
if( ch1Sweep < 0 )
{
ch1Sweep = -8 - ch1Sweep;
}
if( ch2Sweep > 0 )
{
ch2Sweep = 8 - ch2Sweep;
}
if( ch2Sweep < 0 )
{
ch2Sweep = -8 - ch2Sweep;
}
// start framebuffer loop
for( f_cnt_t f = 0; f < frames; f++ )
{
////////////////////////////////
// //
// pitch update //
// //
////////////////////////////////
m_pitchUpdateCounter++;
if( m_pitchUpdateCounter >= m_pitchUpdateFreq )
{
updatePitch();
m_pitchUpdateCounter = 0;
}
////////////////////////////////
// //
// channel 1 //
// //
////////////////////////////////
// render pulse wave
if( m_wlen1 <= m_maxWlen && m_wlen1 >= MIN_WLEN && ch1Enabled )
{
ch1Level = m_parent->m_ch1EnvEnabled.value()
? static_cast<int>( ( m_parent->m_ch1Volume.value() * m_ch1EnvValue ) / 15.0 )
: static_cast<int>( m_parent->m_ch1Volume.value() );
ch1 = m_ch1Counter > m_wlen1 * ch1DutyCycle
? 0
: ch1Level;
}
else ch1 = ch1Level = 0;
// update sweep
m_ch1SweepCounter++;
if( m_ch1SweepCounter >= ch1SweepRate )
{
m_ch1SweepCounter = 0;
if( m_parent->m_ch1SweepEnabled.value() && m_wlen1 <= m_maxWlen && m_wlen1 >= MIN_WLEN )
{
// check if the sweep goes up or down
if( ch1Sweep > 0 )
{
m_wlen1 += m_wlen1 >> qAbs( ch1Sweep );
}
if( ch1Sweep < 0 )
{
m_wlen1 -= m_wlen1 >> qAbs( ch1Sweep );
m_wlen1--; // additional minus 1 for ch1 only
}
}
int main()
{
char filein[NCMAX], fileout[NCMAX], filestart[NCMAX],
filebeam[NCMAX], description[NCMAX],
filecross[NCMAX], cline[NCMAX];
const char version[] = "21-nov-2012 (ejk)";
int lstart=0, lpartl=0, lbeams=0, lwobble=0, lcross=0, nwobble=1;
int ix, iy, iz, nx, ny, nz, nzout, ixmid, iymid, i, nslic0, islice,
nacx,nacy, iqx, iqy, iwobble, ndf, idf, nbout, ib,
ncellx, ncelly, ncellz, iycross, ns, NPARAM;
int *hbeam, *kbeam;
int natom, *Znum, *Znum2, istart, na, done, status, multiMode;
long nbeams, nillum;
long ltime;
unsigned long iseed;
long32 nxl, nyl; /* tiffsubs 32 bit integer type */
float *x, *y, *z, *occ, *wobble;
float *x2, *y2, *z2, *occ2;
float wmin, wmax, xmin,xmax, ymin, ymax, zmin, zmax;
float *kx, *ky, *xpos, *ypos, *param, *sparam;
float k2, k2max, scale, v0, mm0, wavlen, rx, ry,
ax, by, cz, pi, rmin, rmax, aimin, aimax,
rx2,ry2, ctiltx, ctilty, tctx, tcty,
acmin, acmax, Cs3, Cs5, df, df0, sigmaf, dfdelt, aobj,
qx, qy, qy2, q2, q2min, q2max, sumdf, pdf, k2maxo,
temperature, ycross, dx, dy;
float tr, ti, wr, wi;
float **wave0r, **wave0i, **pix, **depthpix,
*propxr, *propxi, *propyr, *propyi;
cfpix wave; /* complex probe wave functions */
cfpix trans; /* complex transmission functions */
cfpix temp ; /* complex scratch wavefunction */
double sum, timer, xdf, chi0, chi1, chi2, chi3, t, zslice,
deltaz, phirms, rsq, vz, alx, aly;
FILE *fp1;
floatTIFF myFile;
/* echo version date and get input file name */
printf("autoslic(e) version dated %s\n", version);
printf("Copyright (C) 1998-2012 Earl J. Kirkland\n" );
printf( "This program is provided AS-IS with ABSOLUTELY NO WARRANTY\n "
" under the GNU general public license\n\n" );
printf("perform CTEM multislice with automatic slicing and FFTW\n");
#ifdef USE_OPENMP
printf( "and multithreaded using openMP\n");
#endif
printf( "\n" );
pi = (float) (4.0 * atan( 1.0 ));
NPARAM = myFile.maxParam();
param = (float*) malloc1D( NPARAM, sizeof(float), "param" );
sparam = (float*) malloc1D( NPARAM, sizeof(float), "sparam" );
for( ix=0; ix<NPARAM; ix++ ) param[ix] = 0.0F;
printf("Name of file with input atomic "
"potential in x,y,z format:\n");
ns = scanf("%s", filein );
/* get simulation options */
printf("Replicate unit cell by NCELLX,NCELLY,NCELLZ :\n");
ns = scanf("%d %d %d", &ncellx, &ncelly, &ncellz);
if( ncellx < 1 ) ncellx = 1;
if( ncelly < 1 ) ncelly = 1;
if( ncellz < 1 ) ncellz = 1;
printf("Name of file to get binary output of multislice result:\n");
ns = scanf("%s", fileout );
lpartl = askYN("Do you want to include partial coherence");
if( lpartl == 1 ) {
printf("Illumination angle min, max in mrad:\n");
ns = scanf("%f %f", &acmin, &acmax);
acmin = acmin * 0.001F;
acmax = acmax * 0.001F;
printf("Spherical aberration Cs3, Cs5(in mm.):\n");
ns = scanf("%g %g", &Cs3, &Cs5);
param[pCS] = (float) ( Cs3*1.0e7 );
param[pCS5] = (float) ( Cs5*1.0e7 );
printf("Defocus, mean, standard deviation, and"
" sampling size (in Angstroms) =\n");
ns = scanf("%f %f %f", &df0, &sigmaf, &dfdelt);
param[pDEFOCUS] = (float) df0;
printf("Objective aperture (in mrad) =\n");
ns = scanf("%f", &aobj);
aobj = aobj * 0.001F;
#ifdef MANY_ABERR
/* get higher order aberrations if necessary */
printf("type higher order aber. name (as C32a, etc.) followed\n"
" by a value in mm. (END to end)\n");
done = multiMode = 0;
do{
ns = scanf( "%20s", cline );
if( strstr( cline, "END" ) != NULL ) {
done = 1;
} else {
ns = scanf( "%lg", &vz );
status = readCnm( cline, param, vz );
if( status < 0 ) {
printf( "unrecognized aberration, exit...\n");
exit( EXIT_SUCCESS );
} else multiMode = 1;
}
} while( !done );
#endif
lstart = 0;
} else {
printf("NOTE, the program image must also be run.\n");
lstart = askYN("Do you want to start from previous result");
}
if ( lstart == 1 ) {
printf("Name of file to start from:\n");
ns = scanf("%s", filestart);
} else {
printf("Incident beam energy in kev:\n");
ns = scanf("%g", &v0);
printf("Wavefunction size in pixels, Nx,Ny:\n");
ns = scanf("%d %d", &nx, &ny );
}
printf("Crystal tilt x,y in mrad.:\n");
ns = scanf("%f %f", &ctiltx, &ctilty);
ctiltx = ctiltx /1000;
ctilty = ctilty /1000;
/* remember that the slice thickness must be > atom size
to use projected atomic potential */
printf("Slice thickness (in Angstroms):\n");
ns = scanf("%lf", &deltaz );
if( deltaz < 1.0 ) {
printf("WARNING: this slice thickness is probably too thin"
" for autoslice to work properly.\n");
}
if( lpartl == 0 ) {
lbeams = askYN("Do you want to record the (real,imag) value\n"
" of selected beams vs. thickness");
if( lbeams == 1 ) {
printf("Name of file for beams info:\n");
ns = scanf("%s", filebeam );
printf("Number of beams:\n");
ns = scanf("%d", &nbout);
if( nbout<1 ) nbout = 1;
hbeam = (int*) malloc1D( nbout, sizeof(int), "hbeam" );
kbeam = (int*) malloc1D( nbout, sizeof(int), "kbeam" );
for( ib=0; ib<nbout; ib++) {
printf("Beam %d, h,k=\n", ib+1);
ns = scanf("%d %d", &hbeam[ib], &kbeam[ib] );
}
}
}
lwobble = askYN("Do you want to include thermal vibrations");
if( lwobble == 1 ) {
printf( "Type the temperature in degrees K:\n");
ns = scanf( "%g", &temperature );
printf( "Type number of configurations to average over:\n");
ns = scanf( "%d", &nwobble );
if( nwobble < 1 ) nwobble = 1;
/* get random number seed from time if available
otherwise ask for a seed */
ltime = (long) time( NULL );
iseed = (unsigned) ltime;
if( ltime == -1 ) {
printf("Type initial seed for random number generator:\n");
ns = scanf("%ld", &iseed);
} else
printf( "Random number seed initialized to %ld\n", iseed );
} else temperature = 0.0F;
if( lpartl == 0 ) {
lcross = askYN("Do you want to output intensity vs. depth cross section");
if( lcross == 1 ){
printf( "Type name of file to get depth profile image:\n");
ns = scanf("%s", filecross );
printf( "Type y position of depth cross section (in Ang.):\n");
ns = scanf("%f", &ycross );
}
}
/* start timing the actual computation just for fun */
timer = cputim();
#ifdef USE_OPENMP
walltimer = walltim(); /* wall time for opneMP */
#endif
/* get starting value of transmitted wavefunction if required
(this can only be used in coherent mode)
remember to save params for final output pix */
if ( lstart == 1 ) {
if( myFile.read( filestart ) != 1 ) {
printf("Cannot open input file: %s .\n", filestart );
exit( 0 );
}
if( myFile.getnpix() != 2 ) {
printf("Input file %s must be complex, can't continue.\n",
filestart );
exit( 0 );
}
nx = myFile.nx();
ny = myFile.ny();
wave0r = (float**) malloc2D( nx, ny, sizeof(float), "waver" );
nx = nx/2;
wave0i = wave0r + nx;
// save starting pix for later
for( ix=0; ix<nx; ix++) for( iy=0; iy<ny; iy++) {
wave0r[ix][iy] = myFile(ix,iy);
wave0i[ix][iy] = myFile(ix+nx,iy);
}
// save parameters to verify successive images are same size etc.
for( i=0; i<NPARAM; i++) sparam[i] = myFile.getParam( i );
ax = sparam[pDX] * nx;
by = sparam[pDY] * ny;
v0 = sparam[pENERGY];
nslic0 = (int) sparam[pNSLICES];
printf("Starting pix range %g to %g real\n"
" %g to %g imag\n",
sparam[pRMIN], sparam[pRMAX], sparam[pIMIN], sparam[pIMAX] );
printf("Beam voltage = %g kV\n", v0);
printf("Old crystal tilt x,y = %g, %g mrad\n", 1000.*sparam[pXCTILT],
1000.*sparam[pYCTILT]);
} else nslic0 = 0; /* end if( lstart...) */
/* calculate relativistic factor and electron wavelength */
mm0 = 1.0F + v0/511.0F;
wavlen = (float) wavelength( v0 );
printf("electron wavelength = %g Angstroms\n", wavlen);
/* read in specimen coordinates and scattering factors */
natom = ReadXYZcoord( filein, ncellx, ncelly, ncellz,
&ax, &by, &cz, &Znum, &x, &y, &z, &occ, &wobble,
description, NCMAX );
printf("%d atomic coordinates read in\n", natom );
printf("%s", description );
printf("Size in pixels Nx, Ny= %d x %d = %d beams\n",
nx,ny, nx*ny);
printf("Lattice constant a,b = %12.4f, %12.4f\n", ax,by);
/* calculate the total specimen volume and echo */
xmin = xmax = x[0];
ymin = ymax = y[0];
zmin = zmax = z[0];
wmin = wmax = wobble[0];
for( i=0; i<natom; i++) {
if( x[i] < xmin ) xmin = x[i];
if( x[i] > xmax ) xmax = x[i];
if( y[i] < ymin ) ymin = y[i];
if( y[i] > ymax ) ymax = y[i];
if( z[i] < zmin ) zmin = z[i];
if( z[i] > zmax ) zmax = z[i];
if( wobble[i] < wmin ) wmin = wobble[i];
if( wobble[i] > wmax ) wmax = wobble[i];
}
printf("Total specimen range is\n %g to %g in x\n"
" %g to %g in y\n %g to %g in z\n", xmin, xmax,
ymin, ymax, zmin, zmax );
if( lwobble == 1 )
printf("Range of thermal rms displacements (300K) = %g to %g\n",
wmin, wmax );
#ifdef USE_OPENMP
/* force LUT init. to avoid redundant init in parallel form */
rsq = 0.5; /* arbitrary position */
for( i=0; i<natom; i++) vz = vzatomLUT( Znum[i], rsq );
#endif
/* calculate spatial frequencies and positions for future use */
rx = 1.0F/ax;
rx2= rx*rx;
ry = 1.0F/by;
ry2= ry*ry;
ixmid = nx/2;
iymid = ny/2;
nxl = nx;
nyl = ny;
kx = (float*) malloc1D( nx, sizeof(float), "kx" );
kx2 = (float*) malloc1D( nx, sizeof(float), "kx2" );
xpos = (float*) malloc1D( nx, sizeof(float), "xpos" );
freqn( kx, kx2, xpos, nx, ax );
ky = (float*) malloc1D( ny, sizeof(float), "ky" );
ky2 = (float*) malloc1D( ny, sizeof(float), "ky2" );
ypos = (float*) malloc1D( ny, sizeof(float), "ypos" );
freqn( ky, ky2, ypos, ny, by );
/* allocate some more arrays and initialize wavefunction */
trans.resize( nx, ny );
trans.init();
wave.resize( nx, ny );
wave.copyInit( trans );
if( lstart == 0 ) {
for( ix=0; ix<nx; ix++)
for( iy=0; iy<ny; iy++) {
wave.re(ix,iy) = 1.0F; /* real part */
wave.im(ix,iy) = 1.0F; /* imag part */
}
} else {
for( ix=0; ix<nx; ix++)
for( iy=0; iy<ny; iy++) {
wave.re(ix,iy) = wave0r[ix][iy]; /* real part */
wave.im(ix,iy) = wave0i[ix][iy]; /* imag part */
}
}
if( lcross == 1 ) {
/* nz may be too small with thermal vibrations so add a few extra */
nz = (int) ( (zmax-zmin)/ deltaz + 3.5);
depthpix = (float**) malloc2D( nx, nz,
sizeof(float), "depthpix" );
for( ix=0; ix<nx; ix++)
for( iz=0; iz<nz; iz++) depthpix[ix][iz] = 0.0F;
iycross = (int) ( 0.5 + (ny * ycross / by));
while( iycross < 0 ) iycross += ny;
iycross = iycross%ny; /* make periodic in ny */
printf("save xz cross section at iy= %d pixels\n", iycross );
}
/* calculate propagator function */
k2max = nx/(2.0F*ax);
tctx = ny/(2.0F*by);
if( tctx < k2max ) k2max = tctx;
k2max = BW * k2max;
printf("Bandwidth limited to a real space resolution of %f Angstroms\n",
1.0F/k2max);
printf(" (= %.2f mrad) for symmetrical anti-aliasing.\n",
wavlen*k2max*1000.0F);
k2max = k2max*k2max;
tctx = (float) (2.0 * tan(ctiltx));
tcty = (float) (2.0 * tan(ctilty));
propxr = (float*) malloc1D( nx, sizeof(float), "propxr" );
propxi = (float*) malloc1D( nx, sizeof(float), "propxi" );
propyr = (float*) malloc1D( ny, sizeof(float), "propyr" );
propyi = (float*) malloc1D( ny, sizeof(float), "propyi" );
scale = pi * ((float)deltaz);
for( ix=0; ix<nx; ix++) {
t = scale * ( kx2[ix]*wavlen - kx[ix]*tctx );
propxr[ix] = (float) cos(t);
propxi[ix] = (float) -sin(t);
}
for( iy=0; iy<ny; iy++) {
t = scale * ( ky2[iy]*wavlen - ky[iy]*tcty );
propyr[iy] = (float) cos(t);
propyi[iy] = (float) -sin(t);
}
/* iterate the multislice algorithm proper
NOTE: zero freg is in the bottom left corner and
expands into all other corners - not in the center
this is required for the FFT - don't waste time rearranging
partial coherence method
force the integrals to include the origin and to be symmetric
about the origin and to have the same periodic boundary
conditions as the sampling grid
*/
if( lpartl == 1 ) {
printf("Illumination angle sampling (in mrad) = %f, %f\n\n",
1000.*rx*wavlen, 1000.*ry*wavlen);
pix = (float**) malloc2D( nx, ny, sizeof(float), "pix" );
for( ix=0; ix<nx; ix++)
for( iy=0; iy<ny; iy++) pix[ix][iy] = 0.0F;
temp.resize( nx, ny );
temp.copyInit( trans );
ndf = (int) ( ( 2.5F * sigmaf ) / dfdelt );
nacx = (int) ( ( acmax / ( wavlen * rx ) ) + 1.5F );
nacy = (int) ( ( acmax / ( wavlen * ry ) ) + 1.5F );
q2max = acmax / wavlen;
q2max = q2max*q2max;
q2min = acmin / wavlen;
q2min = q2min*q2min;
k2maxo = aobj / wavlen;
k2maxo = k2maxo*k2maxo;
chi1 = pi * wavlen;
chi2 = 0.5 * Cs3 * wavlen *wavlen;
chi3 = Cs5 * wavlen*wavlen*wavlen*wavlen /3.0;
nillum = 0;
/* for Monte Carlo stuff */
x2 = (float*) malloc1D( natom, sizeof(float), "x2" );
y2 = (float*) malloc1D( natom, sizeof(float), "y2" );
z2 = (float*) malloc1D( natom, sizeof(float), "z2" );
occ2 = (float*) malloc1D( natom, sizeof(float), "occ2" );
Znum2 = (int*) malloc1D( natom, sizeof(int), "Znum2" );
if( lwobble == 0 )
sortByZ( x, y, z, occ, Znum, natom );
/* integrate over the illumination angles */
for( iwobble=0; iwobble<nwobble; iwobble++) {
if( lwobble == 1 ) printf("configuration # %d\n", iwobble+1 );
for( iqy= -nacy; iqy<=nacy; iqy++) {
qy = iqy * ry;
qy2 = qy * qy;
for( iqx= -nacx; iqx<=nacx; iqx++) {
qx = iqx * rx;
q2 = qx*qx + qy2;
if( (q2 <= q2max) && (q2 >= q2min) ) {
nillum += 1;
for( ix=0; ix<nx; ix++) {
for( iy=0; iy<ny; iy++) {
t = 2.0*pi*( qx*xpos[ix] + qy*ypos[iy] );
wave.re(ix,iy) = (float) cos(t); /* real */
wave.im(ix,iy) = (float) sin(t); /* imag */
}
}
/* add random thermal displacements scaled by temperature
if requested
remember that initial wobble is at 300K for each direction */
if( lwobble == 1 ){
scale = (float) sqrt(temperature/300.0) ;
for( i=0; i<natom; i++) {
x2[i] = x[i] + (float)(wobble[i]*rangauss(&iseed)*scale);
y2[i] = y[i] + (float)(wobble[i]*rangauss(&iseed)*scale);
z2[i] = z[i] + (float)(wobble[i]*rangauss(&iseed)*scale);
occ2[i] = occ[i];
Znum2[i] = Znum[i];
}
printf( "Sorting atoms by depth...\n");
sortByZ( x2, y2, z2, occ2, Znum2, natom );
zmin = z2[0]; /* reset zmin/max after wobble */
zmax = z2[natom-1];
printf("Thickness range with thermal displacements"
" is %g to %g (in z)\n", zmin, zmax );
} else for( i=0; i<natom; i++) {
x2[i] = x[i];
y2[i] = y[i];
z2[i] = z[i];
occ2[i] = occ[i];
Znum2[i] = Znum[i];
}
zslice = 0.75*deltaz; /* start a little before top of unit cell */
istart = 0;
while( istart < natom ) {
/* find range of atoms for current slice */
na = 0;
for(i=istart; i<natom; i++)
if( z2[i] < zslice ) na++; else break;
/* calculate transmission function, skip if layer empty */
if( na > 0 ) {
trlayer( &x2[istart], &y2[istart], &occ2[istart],
&Znum2[istart],na, ax, by, v0,
trans, nxl, nyl, &phirms, &nbeams, k2max );
wave *= trans; // transmit
}
/* remember: prop needed here to get anti-aliasing
right */
wave.fft();
propagate( wave, propxr, propxi,
propyr, propyi,
kx2, ky2, k2max, nx, ny );
wave.ifft();
zslice += deltaz;
istart += na;
} /* end while(zslice<=..) */
scale = 1.0F / ( ((float)nx) * ((float)ny) );
sum = 0.0;
for( ix=0; ix<nx; ix++) {
for( iy=0; iy<ny; iy++)
sum += wave.re(ix,iy)*wave.re(ix,iy)
+ wave.im(ix,iy)*wave.im(ix,iy);
}
sum = sum * scale;
printf("Illumination angle = %7.3f, %7.3f mrad",
1000.*qx*wavlen, 1000.*qy*wavlen);
printf(", integrated intensity= %f\n", sum );
/*-------- integrate over +/- 2.5 sigma of defocus ------------ */
wave.fft();
sumdf = 0.0F;
for( idf= -ndf; idf<=ndf; idf++) {
param[pDEFOCUS] = df = df0 + idf*dfdelt;
for( ix=0; ix<nx; ix++) {
alx = wavlen * kx[ix]; /* x component of angle alpha */
for( iy=0; iy<ny; iy++) {
aly = wavlen * ky[iy]; /* y component of angle alpha */
k2 = kx2[ix] + ky2[iy];
if( k2 <= k2maxo ) {
chi0 = (2.0*pi/wavlen) * chi( param,
alx, aly, multiMode );
tr = (float) cos(chi0);
ti = (float) -sin(chi0);
wr = wave.re(ix,iy);
wi = wave.im(ix,iy);
temp.re(ix,iy) = wr*tr - wi*ti;
temp.im(ix,iy) = wr*ti + wi*tr;
} else {
temp.re(ix,iy) = 0.0F; /* real */
temp.im(ix,iy) = 0.0F; /* imag */
}
} /* end for( iy=0... ) */
} /* end for( ix=0... ) */
temp.ifft();
xdf = (double) ( (df - df0) /sigmaf );
pdf = (float) exp( -0.5F * xdf*xdf );
sumdf += pdf;
for( ix=0; ix<nx; ix++) {
for( iy=0; iy<ny; iy++) {
wr = temp.re(ix,iy);
wi = temp.im(ix,iy);
pix[ix][iy] += pdf* ( wr*wr + wi*wi );
}
}
}/* end for(idf..) */
}/* end if( q2...) */
} /* end for( iqx..) */
} /* end for( iqy..) */
} /* end for( iwobble...) */
printf("Total number of illumination angle = %ld\n",
nillum);
printf("Total number of defocus values = %d\n", 2*ndf+1);
/* remember that nillum already includes nwobble so don't
divide by nwobble! */
scale = 1.0F / ( ((float)nillum) * sumdf );
rmin = pix[0][0] * scale;
rmax = rmin;
aimin = 0.0F;
aimax = 0.0F;
for( ix=0; ix<nx; ix++)
for( iy=0; iy<ny; iy++) {
pix[ix][iy] = pix[ix][iy] * scale;
if( pix[ix][iy] < rmin ) rmin = pix[ix][iy];
if( pix[ix][iy] > rmax ) rmax = pix[ix][iy];
}
/* ---- start coherent method below ----------------
(remember that waver,i[][] was initialize above) */
} else {
if( lbeams ==1 ) {
fp1 = fopen( filebeam, "w" );
if( NULL == fp1 ) {
printf("can't open file %s\n", filebeam);
exit(0);
}
fprintf( fp1, " (h,k) = " );
for(ib=0; ib<nbout; ib++)
fprintf(fp1," (%d,%d)", hbeam[ib], kbeam[ib]);
fprintf( fp1, "\n" );
fprintf( fp1, "nslice, (real,imag) (real,imag) ...\n\n");
for( ib=0; ib<nbout; ib++) {
if( hbeam[ib] < 0 ) hbeam[ib] = nx + hbeam[ib];
if( kbeam[ib] < 0 ) kbeam[ib] = ny + kbeam[ib];
if( hbeam[ib] < 0 ) hbeam[ib] = 0;
if( kbeam[ib] < 0 ) kbeam[ib] = 0;
if( hbeam[ib] > nx-1 ) hbeam[ib] = nx-1;
if( kbeam[ib] > ny-1 ) kbeam[ib] = ny-1;
}
}
/* add random thermal displacements scaled by temperature if requested
remember that initial wobble is at 300K for each direction */
if( lwobble == 1 ){
scale = (float) sqrt(temperature/300.0) ;
for( i=0; i<natom; i++) {
x[i] += (float) (wobble[i] * rangauss( &iseed ) * scale);
y[i] += (float) (wobble[i] * rangauss( &iseed ) * scale);
z[i] += (float) (wobble[i] * rangauss( &iseed ) * scale);
}
}
printf( "Sorting atoms by depth...\n");
sortByZ( x, y, z, occ, Znum, natom );
if( lwobble == 1 ){
zmin = z[0]; /* reset zmin/max after wobble */
zmax = z[natom-1];
printf("Thickness range with thermal displacements"
" is %g to %g (in z)\n", zmin, zmax );
}
scale = 1.0F / ( ((float)nx) * ((float)ny) );
zslice = 0.75*deltaz; /* start a little before top of unit cell */
istart = 0;
islice = 1;
while( (istart < natom) && ( zslice < (zmax+deltaz) ) ) {
/* find range of atoms for current slice */
na = 0;
for(i=istart; i<natom; i++)
if( z[i] < zslice ) na++; else break;
/* calculate transmission function, skip if layer empty */
if( na > 0 ) {
trlayer( &x[istart], &y[istart], &occ[istart],
&Znum[istart], na, ax, by, v0, trans,
nxl, nyl, &phirms, &nbeams, k2max );
/*??? printf("average atompot comparison = %g\n",
phirms/(wavlen*mm0) ); */
wave *= trans; // transmit
}
/* bandwidth limit */
wave.fft();
if( lbeams== 1 ) {
fprintf( fp1, "%5d", islice);
for( ib=0; ib<nbout; ib++)
fprintf(fp1, "%10.6f %10.6f",
scale*wave.re(hbeam[ib],kbeam[ib]), /* real */
scale*wave.im(hbeam[ib],kbeam[ib]) ); /* imag */
fprintf( fp1, "\n");
}
/* remember: prop needed here to get anti-aliasing right */
propagate( wave, propxr, propxi,
propyr, propyi, kx2, ky2, k2max, nx, ny );
wave.ifft();
/* save depth cross section if requested */
if( (lcross == 1) && (islice<=nz) ) {
for( ix=0; ix<nx; ix++) {
depthpix[ix][islice-1] =
wave.re(ix,iycross)*wave.re(ix,iycross)
+ wave.im(ix,iycross)*wave.im(ix,iycross);
}
nzout = islice;
}
sum = 0.0;
for( ix=0; ix<nx; ix++) {
for( iy=0; iy<ny; iy++)
sum += wave.re(ix,iy)*wave.re(ix,iy) +
wave.im(ix,iy)*wave.im(ix,iy);
}
sum = sum * scale;
printf("z= %f A, %ld beams, %d coord., \n"
" aver. phase= %f, total intensity = %f\n",
zslice, nbeams, na, phirms, sum );
zslice += deltaz;
istart += na;
islice++;
} /* end while(istart<natom..) */
rmin = wave.re(0,0);
rmax = rmin;
aimin = wave.im(0,0);
aimax = aimin;
for( ix=0; ix<nx; ix++) {
for( iy=0; iy<ny; iy++) {
wr = wave.re(ix,iy);
wi = wave.im(ix,iy);
if( wr < rmin ) rmin = wr;
if( wr > rmax ) rmax = wr;
if( wi < aimin ) aimin = wi;
if( wi > aimax ) aimax = wi;
}
}
} /* end else .. coherent section */
/* output results and find min and max to echo
remember that complex pix are stored in the file in FORTRAN
order for compatibility */
if( lstart == 1 )
for( ix=0; ix<NPARAM; ix++ ) param[ix] = sparam[ix];
param[pRMAX] = rmax;
param[pIMAX] = aimax;
param[pRMIN] = rmin;
param[pIMIN] = aimin;
param[pXCTILT] = ctiltx;
param[pYCTILT] = ctilty;
param[pENERGY] = v0;
param[pDX] = dx = (float) ( ax/((float)nx) );
param[pDY] = dy = (float) ( by/((float)ny) );
param[pWAVEL] = wavlen;
param[pNSLICES] = 0.0F; /* ??? */
if ( lpartl == 1 ) {
param[pDEFOCUS] = df0;
param[pOAPERT] = aobj;
param[pCAPERT] = acmax;
param[pDDF] = sigmaf;
}
for( ix=0; ix<NPARAM; ix++ ) myFile.setParam( ix, param[ix] );
if ( lpartl == 1 ) {
myFile.resize( nx, ny );
myFile.setnpix( 1 );
for( ix=0; ix<nx; ix++) for( iy=0; iy<ny; iy++)
myFile(ix,iy) = pix[ix][iy];
i = myFile.write( fileout, rmin, rmax, aimin, aimax, dx, dy );
} else {
myFile.resize( 2*nx, ny );
myFile.setnpix( 2 );
for( ix=0; ix<nx; ix++) for( iy=0; iy<ny; iy++) {
myFile(ix,iy) = wave.re(ix,iy);
myFile(ix+nx,iy) = wave.im(ix,iy);
}
i = myFile.write( fileout, rmin, rmax, aimin, aimax, dx, dy );
}
if( i != 1 ) printf( "autoslice cannot write TIF file %s\n",
fileout );
printf( "pix range %g to %g real,\n"
" %g to %g imag\n", rmin,rmax,aimin,aimax );
/* output depth cross section if requested */
if( lcross == 1 ){
rmin = depthpix[0][0];
rmax = rmin;
for( ix=0; ix<nx; ix++)
for( iz=0; iz<nzout; iz++) {
wr = depthpix[ix][iz];
if( wr < rmin ) rmin = wr;
if( wr > rmax ) rmax = wr;
}
myFile.setParam( pRMAX, rmax );
myFile.setParam( pIMAX, 0.0F );
myFile.setParam( pRMIN, rmin );
myFile.setParam( pIMIN, 0.0F );
myFile.setParam( pDY, dy = (float) ( deltaz ) );
myFile.resize( nx, nzout );
myFile.setnpix( 1 );
for( ix=0; ix<nx; ix++) for( iz=0; iz<nzout; iz++) {
myFile(ix,iz) = depthpix[ix][iz];
}
i = myFile.write( filecross, rmin, rmax, aimin, aimax, dx, dy );
if( i != 1 ) printf( "autoslice cannot write TIF file %s\n",
filecross );
printf( "depth pix range %g to %g real,\n", rmin,rmax );
}
printf("Total CPU time = %f sec.\n", cputim()-timer );
#ifdef USE_OPENMP
printf("wall time = %g sec.\n", walltim() - walltimer);
#endif
return 0;
} /* end main() */
