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make_particle.c
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make_particle.c
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/* This module initializes the dipole set, either using predefined shapes or reading from a file;
* includes granule generator
*
* Copyright (C) ADDA contributors
* This file is part of ADDA.
*
* ADDA is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as
* published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
* ADDA is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with ADDA. If not, see
* <http://www.gnu.org/licenses/>.
*/
#include "const.h" // keep this first
// project headers
#include "cmplx.h"
#include "comm.h"
#include "debug.h"
#include "io.h"
#include "memory.h"
#include "param.h"
#include "timing.h"
#include "types.h"
#include "vars.h"
// 3rd party headers
#include "mt19937ar.h"
// system headers
#include <float.h> // for DBL_MAX
#include <limits.h>
#include <math.h>
#include <stdint.h>
#include <stdlib.h>
#include <string.h>
#include <time.h> // for time and clock (used for random seed)
// SEMI-GLOBAL VARIABLES
// defined and initialized in param.c
extern const enum sh shape;
extern const double lambda;
extern double sizeX,dpl,a_eq;
extern const int jagged;
extern const char *shape_fname;
extern const char *shapename;
extern const bool volcor,save_geom;
extern const opt_index opt_sh;
#ifndef SPARSE
extern const int sh_Npars;
extern const double sh_pars[];
extern const char *save_geom_fname;
extern const double gr_vf;
extern double gr_d;
extern const int gr_mat;
extern enum shform sg_format;
extern const bool store_grans;
#endif
// defined and initialized in timing.c
extern TIME_TYPE Timing_Particle;
#ifndef SPARSE
extern TIME_TYPE Timing_Granul,Timing_GranulComm;
#endif
// used in interaction.c
double ZsumShift; // real distance between the lowest (in Z) dipoles and its image, must be positive
// used in param.c
bool volcor_used; // volume correction was actually employed
const char *sh_form_str1,*sh_form_str2; // strings for log file with shape parameters (first one should end with :)
size_t gr_N; // number of granules
double gr_vf_real; // actual granules volume fraction
size_t mat_count[MAX_NMAT+1]; // number of dipoles in each domain
// LOCAL VARIABLES
#define GEOM_FORMAT "%d %d %d" // format of the geom file
#define GEOM_FORMAT_EXT "%d %d %d %d" // extended format of the geom file
/* DDSCAT shape formats; several format are used, since first variable is unpredictable and last two are not actually
* used (only to produce warnings)
*/
static const char ddscat_format_read1[]="%*s %d %d %d %d %d %d";
static const char ddscat_format_read2[]="%*s %d %d %d %d";
#ifndef SPARSE
static const char ddscat_format_write[]="%zu %d %d %d %d %d %d\n";
#endif
// ratio of scatterer volume to sizeX^3; used for dpl correction and initialization by a_eq
static double volume_ratio;
static double Ndip; // total number of dipoles (in a circumscribing cube); has limited use in sparse mode
static double dpl_def; // default value of dpl
static int minX,minY,minZ; // minimum values of dipole positions in dipole file
static FILE * restrict dipfile; // handle of dipole file
static enum shform read_format; // format of dipole file, which is read
static double cX,cY,cZ; // center for DipoleCoord in units of dipoles (counted from 0)
static double drelX,drelY,drelZ; // ratios of dipole sizes to the maximal one (dsX/dsMax...)
static double yx_ratio,zx_ratio; // ratios of particle dimensions along different axes
#ifndef SPARSE
// shape parameters
static double coat_x,coat_y,coat_z,coat_r2;
static double shell_r2,core_r2; // for coated2
static double ad2,egnu,egeps; // for egg
static double chebeps,r0_2; // for Chebyshev
static int chebn; // for Chebyshev
static double hdratio,invsqY,invsqY2,invsqZ,invsqZ2,haspY,haspZ;
static double xcenter,zcenter; // coordinates of natural particle center (in units of Dx)
static double rc_2,ri_2; // squares of circumscribed and inscribed spheres (circles) in units of Dx
static double boundZ,zcenter1,zcenter2,ell_rsq1,ell_rsq2,ell_x1,ell_x2;
static double * restrict onion_r2; //for onion
static int nlayers; // for onion
static double rbcP,rbcQ,rbcR,rbcS; // for RBC
static double prang; // for prism
static double seE,seN,seT,seR,seToverR,seInvR; // for superellipsoid
// for axisymmetric; all coordinates defined here are relative
static double * restrict contSegRoMin,* restrict contSegRoMax,* restrict contRo,* restrict contZ;
static double contCurRo,contCurZ;
static int contNseg;
struct segment {
bool single; // whether segment consists of a single joint
int first; // index of the first point in the segment
int last; // index of the last point in the segment
double zmin; // minimum z-coordinate of the segment points
double zmax; // maximum z-coordinate of the segment points
double romid; // ro-coordinate of the point in the middle
struct segment *left; // pointer to left subsegment
struct segment *right; // pointer to right subsegment
double slope; // only for single; (z[i+1]-z[i])/(ro[i+1]-ro[i])
double add; // only for single; ro[i](1-slope);
};
struct segment * restrict contSeg;
/* TO ADD NEW SHAPE
* Add here all internal variables (aspect ratios, etc.), which you initialize in InitShape() and use in MakeParticle()
* afterwards. If you need local, intermediate variables, put them into the beginning of the corresponding function. Add
* descriptive comments, use 'static'.
*/
// temporary arrays before their real counterparts are allocated
static unsigned char * restrict material_tmp;
static unsigned short * restrict position_tmp;
#endif // !SPARSE
#ifndef SPARSE //much of the functionality here is disabled in sparse mode
// EXTERNAL FUNCTIONS
// chebyshev.c
void ChebyshevParams(double eps_in,int n_in,double *dx,double *dz,double *sz,double *vr);
//======================================================================================================================
static void SaveGeometry(void)
// saves dipole configuration to a file
{
char fname[MAX_FNAME];
FILE * restrict geom;
size_t i,j;
int mat;
/* TO ADD NEW FORMAT OF SHAPE FILE
* Add code to this function to save geometry in new format. It should consist of:
* 1) definition of default filename (by supplying an appropriate extension);
* 2) writing header to the beginning of the file;
* 3) writing a single line for each dipole (this is done in parallel).
* Each part is done in corresponding switch-case sequence
*/
TIME_TYPE tstart=GET_TIME();
// create save_geom_fname if not specified, by adding extension to the shapename
if (save_geom_fname[0]==0) {
const char *ext;
// choose extension
switch (sg_format) {
case SF_TEXT:
case SF_TEXT_EXT: ext="geom"; break;
case SF_DDSCAT6:
case SF_DDSCAT7: ext="dat"; break;
default: LogError(ONE_POS,"Unknown format for saved geometry file (%d)",(int)sg_format);
// no break
}
save_geom_fname=dyn_sprintf("%s.%s",shapename,ext);
}
// automatically change format if needed
if (sg_format==SF_TEXT && Nmat>1) sg_format=SF_TEXT_EXT;
// choose filename
#ifdef PARALLEL
SnprintfErr(ALL_POS,fname,MAX_FNAME,"%s/"F_GEOM_TMP,directory,ringid);
#else
SnprintfErr(ALL_POS,fname,MAX_FNAME,"%s/%s",directory,save_geom_fname);
#endif
geom=FOpenErr(fname,"w",ALL_POS);
// print head of file
#ifdef PARALLEL
if (ringid==0) { // this condition can be different from being root
#endif
switch (sg_format) {
case SF_TEXT:
case SF_TEXT_EXT:
fprintf(geom,"#generated by ADDA v."ADDA_VERSION"\n"
"#shape: '%s'\n"
"#box size: %dx%dx%d\n"
"#lattice spacings: %g %g %g\n",shapename,boxX,boxY,boxZ,rectScaleX,rectScaleY,rectScaleZ);
if (sg_format==SF_TEXT_EXT) fprintf(geom,"Nmat=%d\n",Nmat);
break;
case SF_DDSCAT6:
case SF_DDSCAT7:
fprintf(geom,"shape: '%s'; box size: %dx%dx%d; generated by ADDA v."ADDA_VERSION"\n"
"%zu = NAT\n"
"1 0 0 = A_1 vector\n"
"0 1 0 = A_2 vector\n"
"%g %g %g = lattice spacings (dx,dy,dz)/d\n",
shapename,boxX,boxY,boxZ,nvoid_Ndip,rectScaleX,rectScaleY,rectScaleZ);
if (sg_format==SF_DDSCAT7) fprintf(geom,"%g %g %g = coordinates (x0/dx,y0/dy,z0/dz) of the zero dipole "
"(IX=IY=IZ=0)\n",(1-boxX)/2.0,(1-boxY)/2.0,(1-boxZ)/2.0);
fprintf(geom,"JA IX IY IZ ICOMP(x,y,z)\n");
break;
}
#ifdef PARALLEL
} // end of if
#endif
// save geometry
for(i=0;i<local_nvoid_Ndip;i++) {
j=3*i;
switch (sg_format) {
case SF_TEXT:
fprintf(geom,GEOM_FORMAT"\n",position[j],position[j+1],position[j+2]);
break;
case SF_TEXT_EXT:
fprintf(geom,GEOM_FORMAT_EXT"\n",position[j],position[j+1],position[j+2],material[i]+1);
break;
case SF_DDSCAT6:
case SF_DDSCAT7:
mat=material[i]+1;
fprintf(geom,ddscat_format_write,i+local_nvoid_d0+1,position[j],position[j+1],position[j+2],mat,mat,
mat);
break;
}
}
FCloseErr(geom,fname,ALL_POS);
#ifdef PARALLEL
// wait for all processes to save their part of geometry
Synchronize();
// combine all files into one and clean
if (IFROOT) CatNFiles(directory,F_GEOM_TMP,save_geom_fname);
#endif
if (IFROOT) PRINTFB("Geometry saved to file\n");
Timing_FileIO+=GET_TIME()-tstart;
}
//======================================================================================================================
#define ALLOCATE_SEGMENTS(N) (struct segment *)voidVector((N)*sizeof(struct segment),ALL_POS,"contour segment");
void InitContourSegment(struct segment * restrict seg,const bool increasing)
/* recursively initialize a segment of a contour: allocates memory and calculates all elements. Some elements are
* calculated during the forward sweep (from long segments to short), others - during the backward sweep.
* Recursive function calls incurs certain overhead, however here it is not critical.
*/
{
int i;
struct segment * restrict s1,* restrict s2;
/* Remove constant parts in the beginning and end of segment, if present. After this procedure 'first' is guaranteed
* to be less than 'last' by definition of the segment
*/
while (contRo[seg->first]==contRo[seg->first+1]) {
(seg->first)++;
if (seg->first == seg->last) LogError(ONE_POS,"Bug in InitContour: One of the segments (ending at index %d) "
"has constant ro",seg->last);
}
while (contRo[seg->last-1]==contRo[seg->last]) (seg->last)--; // here above error checks are not needed
if (seg->first+1 == seg->last) { // segment with a single fragment
seg->single=true;
seg->zmin=MIN(contZ[seg->first],contZ[seg->last]);
seg->zmax=MAX(contZ[seg->first],contZ[seg->last]);
seg->slope=(contZ[seg->last]-contZ[seg->first])/(contRo[seg->last]-contRo[seg->first]);
seg->add=contZ[seg->first]-contRo[seg->first]*seg->slope;
}
else { // divide segment into two, and initialize each of them
seg->single=false;
i=(seg->first+seg->last)/2;
seg->romid=contRo[i];
// construct subsegments
s1=ALLOCATE_SEGMENTS(1);
s2=ALLOCATE_SEGMENTS(1);
s1->first=seg->first;
s1->last=s2->first=i;
s2->last=seg->last;
// initialize subsegments
InitContourSegment(s1,increasing);
InitContourSegment(s2,increasing);
// calculate zmax and zmin
seg->zmax=MAX(s1->zmax,s2->zmax);
seg->zmin=MIN(s1->zmin,s2->zmin);
// assign new segments to left and right based on 'increasing' - only weak monotonicity is assumed
if (increasing) {
seg->left=s1;
seg->right=s2;
}
else {
seg->left=s2;
seg->right=s1;
}
}
}
//======================================================================================================================
#define CHUNK_SIZE 128 // how many numbers are allocated at once for adjustable arrays
static void InitContour(const char *fname,double *ratio,double *shSize)
/* Reads a contour from the file, rotates it so that it starts from a local minimum in ro, then divides it into
* monotonic (over ro) segments. It produces data, which are later used to test each dipole for being inside the
* contour. Segments are either weakly increasing or weakly decreasing (i.e. can contain constant parts).
*/
{
size_t line; // current line number
int nr; // number of contour points read from the file
int size; // current size of the allocated memory for contour
int i,j,scanned;
double *bufRo,*bufZ; // temporary buffers
int *index;
double ro,z,romin,romax,zmin,zmax,mult,zmid;
FILE* file;
bool increasing;
char linebuf[BUF_LINE];
D("InitContour has started");
// Read contour from file
TIME_TYPE tstart=GET_TIME();
file=FOpenErr(fname,"r",ALL_POS);
line=SkipComments(file);
size=CHUNK_SIZE;
MALLOC_VECTOR(bufRo,double,size,ALL);
MALLOC_VECTOR(bufZ,double,size,ALL);
nr=0;
// this depends on variables been declared double
romin=zmin=DBL_MAX;
romax=zmax=-DBL_MAX;
// reading is performed in lines
while (FGetsError(file,fname,&line,linebuf,BUF_LINE,ONE_POS)!=NULL) {
// scan numbers in a line
scanned=sscanf(linebuf,"%lf %lf",&ro,&z);
// if sscanf returns EOF, that is a blank line -> just skip
if (scanned!=EOF) {
if (scanned!=2) // this in most cases indicates wrong format
LogError(ONE_POS,"Error occurred during scanning of line %zu in contour file %s",line,fname);
// check for consistency of input
if (ro<0) LogError(ONE_POS,"Negative ro-coordinate is found on line %zu in contour file %s",line,fname);
// update extreme values
if (z>zmax) zmax=z;
if (z<zmin) zmin=z;
if (ro>romax) romax=ro;
if (ro<romin) romin=ro;
// add allocated memory to buf, if needed
if (nr >= size) {
size+=CHUNK_SIZE;
REALLOC_VECTOR(bufRo,double,size,ALL);
REALLOC_VECTOR(bufZ,double,size,ALL);
}
bufRo[nr]=ro;
bufZ[nr]=z;
nr++;
}
}
FCloseErr(file,fname,ALL_POS);
Timing_FileIO+=GET_TIME()-tstart;
// Check number of points read
if (nr<3) LogError(ONE_POS,"Contour from file %s contains less than three points",fname);
// Determine initial point with local minimum ro[i-j]>ro[i-j+1]=...=ro[i]<ro[i+1]
i=0;
while (i<nr-1 && bufRo[i]>=bufRo[i+1]) i++;
if (i==0) { // first point is a minimum candidate
if (bufRo[0]>=bufRo[nr-1]) { // if required, search backwards; guaranteed to converge, since bufRo[1]>bufRo[0]
i=nr-1;
while (bufRo[i]>=bufRo[i-1]) i--;
}
}
// if the whole contour is non-decreasing, check for constancy
else if (i==nr-1 && bufRo[nr-1]==bufRo[0])
LogError(ONE_POS,"Contour from file %s has zero area. Hence the scatterer is void",fname);
/* Construct working contour so that its first point = last and is a local minimum. It is done by rotating buf and
* adding one extra point. Then free the buffer.
*/
MALLOC_VECTOR(contRo,double,nr+1,ALL);
memcpy(contRo,bufRo+i,(nr-i)*sizeof(double));
memcpy(contRo+nr-i,bufRo,i*sizeof(double));
contRo[nr]=contRo[0];
Free_general(bufRo);
// same for Z vectors
MALLOC_VECTOR(contZ,double,nr+1,ALL);
memcpy(contZ,bufZ+i,(nr-i)*sizeof(double));
memcpy(contZ+nr-i,bufZ,i*sizeof(double));
contZ[nr]=contZ[0];
Free_general(bufZ);
// scale coordinates to be relative to total diameter, and centered (by z) around 0
mult=1/(2*romax);
zmid=(zmax+zmin)/2;
*ratio=(zmax-zmin)*mult;
*shSize=2*romax;
ri_2=romin*romin*mult*mult;
for (i=0;i<=nr;i++) {
contRo[i]*=mult;
contZ[i]=(contZ[i]-zmid)*mult;
}
// divide the contour into the segments; actually only the index is constructed marking end points of the segments
MALLOC_VECTOR(index,int,nr+1,ALL); // this is enough, even if all segments are of one joint
index[0]=0;
i=j=1;
increasing=true;
while (i<nr) { // uses greedy algorithm for weak monotonicity
while (i<nr && (increasing ? (contRo[i]<=contRo[i+1]) : (contRo[i]>=contRo[i+1]))) i++;
index[j]=i;
j++;
increasing=!increasing;
}
contNseg=j-1;
if (IS_ODD(contNseg)) LogError(ONE_POS,"Bug in InitContour: Resulting number of monotonic (in values of ro) "
"segments (%d) is odd",contNseg);
/* Calculate maximum and minimum ro for segments; We implicitly use that first segment is increasing, second -
* decreasing, and so on.
*/
MALLOC_VECTOR(contSegRoMin,double,contNseg,ALL);
MALLOC_VECTOR(contSegRoMax,double,contNseg,ALL);
for (j=0;j<contNseg;j++) {
if (IS_EVEN(j)) {
contSegRoMin[j]=contRo[index[j]];
contSegRoMax[j]=contRo[index[j+1]];
}
else {
contSegRoMin[j]=contRo[index[j+1]];
contSegRoMax[j]=contRo[index[j]];
}
}
// Construct a tree of segments
contSeg=ALLOCATE_SEGMENTS(contNseg);
for (j=0;j<contNseg;j++) {
contSeg[j].first=index[j];
contSeg[j].last=index[j+1];
InitContourSegment(contSeg+j,IS_EVEN(j));
}
Free_general(index);
Free_general(contRo);
Free_general(contZ);
D("InitContour has finished");
D("Nseg=%d",contNseg);
D("minroSq="GFORM_DEBUG,ri_2);
}
#undef CHUNK_SIZE
#undef ALLOCATE_SEGMENTS
//======================================================================================================================
bool CheckContourSegment(struct segment * restrict seg)
/* Checks, whether point is under or above the segment, by traversing the tree of segments. It returns true, if
* intersecting z value is larger than given z, and false otherwise. Point is defined by local variables contCurRo and
* contCurZ.
*/
{
while (true) {
if (contCurZ < seg->zmin) return true;
else if (contCurZ > seg->zmax) return false;
else if (seg->single) return (contCurZ < seg->add + contCurRo*seg->slope);
else seg=(contCurRo<seg->romid ? seg->left : seg->right);
}
}
//======================================================================================================================
void FreeContourSegment(struct segment * restrict seg)
/* recursively frees memory allocated for contour segments;
* Recursive function calls incurs certain overhead, however here it is not critical.
*/
{
if (!(seg->single)) {
FreeContourSegment(seg->left);
FreeContourSegment(seg->right);
}
}
//======================================================================================================================
#define KEY_LENGTH 2 // length of key for initialization of random generator
#define MAX_ZERO_FITS 1E4 // maximum number of zero fits in a row (each - many granules)
#define MAX_FALSE_SKIP 10 // number of false skips in granule placement to complete the set
#define MAX_FALSE_SKIP_SMALL 10 // the same for small granules
#define MAX_GR_SET USHRT_MAX // maximum size of granule set
#define MIN_CELL_SIZE 4.0 // minimum cell size for small granules
#define CHECK_CELL(a) CheckCell(gr,vgran,tree_index,Di2,occup[a],&fits) // macro for simplicity
#define CHECK_CELL_TEST(a) (CHECK_CELL(a),fits) // ... combined with test for 'fits'
static inline int CheckCell(const double * restrict gr,const double * restrict vgran,
const unsigned short * restrict tree_index,const double Di2,const int start,bool * restrict fits)
// function that checks whether granule intersects anything in the cell
{
int index,last,index1;
double t1,t2,t3;
last=index=start;
while (index!=MAX_GR_SET && (*fits)) {
last=index;
index1=3*index;
t1=gr[0]-vgran[index1];
t2=gr[1]-vgran[index1+1];
t3=gr[2]-vgran[index1+2];
if ((t1*t1+t2*t2+t3*t3)<Di2) *fits=false;
index=tree_index[index];
}
return last;
}
//======================================================================================================================
static size_t PlaceGranules(void)
/* Randomly places granules inside the specified domain; Mersenne Twister is used for generating random numbers
*
* A simplest algorithm is used: to place randomly a sphere, and see if it overlaps with any dipoles (more exactly:
* centers of dipoles) of not correct domain; if not, accept it and fill all this dipoles with granules' domain.
* Optimized to perform in two steps: First it places of set of not-intersecting granules and do only a quick check
* against the "domain pattern" - coarse representation of the domain. On the second step granules of the whole set are
* thoroughly checked against the whole domain on each processor. When small granules are used, no domain pattern is
* used - makes it simpler. Intersection of two granules between the sets is checked only through dipoles, which is not
* exact, however it allows considering arbitrary complex domains, which is described only by a set of occupied dipoles.
*
* This algorithm is unsuitable for high volume fractions, it becomes very slow and for some volume fractions may fail
* at all (Metropolis algorithm should be more suitable, however it is hard to code for arbitrary domains). Moreover,
* statistical properties of the obtained granules distribution may be not perfect, however it seems good enough for our
* applications.
*
* Currently it is not working with jagged. That should be improved, by rewriting the jagged calculation throughout the
* program
*/
{
int i,j,k,zerofit,last;
size_t n,count,count_gr,false_count,ui;
size_t nd; // number of dipoles occupied by granules
int index,index1,index2; // indices for dipole grid
int dom_index,dom_index1,dom_index2; // indices for auxiliary grid
int gX,gY,gZ; // auxiliary grid dimensions
size_t gXY,gr_gN; // ... and their products
size_t avail; // number of available (free) domain cells
int gX2,gY2,gZ2,locgZ2;
int i0,i1,j0,j1,k0,k1;
bool fits;
int cur_Ngr,ig,max_Ngr; // number of granules in a current set, index, and maximum set size
double gdX,gdY,gdZ,gdXh,gdYh,gdZh; // auxiliary grid cell sizes and their halfs (h)
int locz0,locz1,locgZ,gr_locgN;
double R,R2,Di,Di2; // radius and diameter of granule, and their squares
double x0,x1,y0,y1,z0,z1; // where to put random number (inner box)
int id0,id1,jd0,jd1,kd0,kd1; // dipoles limit that fall inside inner box
int Nfit; // number of successfully placed granules in a current set
double overhead; // estimate of the overhead needed to have exactly needed N of granules
double tmp1,tmp2,t1,t2,t3;
// maximum shifts for checks of neighboring cells in auxiliary grid; for 'small' it is the shift in index
int sx,sy,sz;
unsigned long key[KEY_LENGTH]; // key to initialize random number generator
unsigned char * restrict dom; // information about the domain on a granule grid
unsigned short * restrict occup; // information about the occupied cells
int sm_gr; // whether granules are small (then simpler algorithm is used)
unsigned short * restrict tree_index; // index for traversing granules inside one cell (small)
double * restrict vgran; // coordinates of a set of granules
bool * restrict vfit; // results of granule fitting on the grid (boolean)
int * restrict ginX,* restrict ginY,* restrict ginZ; // indices to find dipoles inside auxiliary grid
int indX,indY,indZ; // indices for doubled auxiliary grid
int bit; // bit position in char of 'dom'
double gr[3]; // coordinates of a single granule
FILE * restrict file; // file for saving granule positions
char fname[MAX_FNAME]; // filename of file
double minval; // minimum size of auxiliary grid
// next line should never happen
if (rectDip) LogError(ONE_POS,"Incompatibility error in PlaceGranules");
/* redundant initialization to remove warnings; most of this is due to the fact that code for small and large
* granules is largely independent (although there are some common parts, which motivates against complete
* separation of them into two functions).
*/
zerofit=gX2=gY2=gZ2=locgZ2=id0=id1=jd0=jd1=kd0=kd1=indZ=locgZ=gr_locgN=sx=sy=sz=0;
gdXh=gdYh=gdZh=0;
ginX=ginY=ginZ=NULL;
dom=NULL;
tree_index=occup=NULL;
file=NULL;
// prepare granule file for saving if needed
if (store_grans && IFROOT) {
SnprintfErr(ONE_POS,fname,MAX_FNAME,"%s/"F_GRANS,directory);
file=FOpenErr(fname,"w",ONE_POS);
fprintf(file,"#generated by ADDA v."ADDA_VERSION"\n"
"#granule diameter = "GFORM"\n",gr_d);
}
// set variables; consider jagged
Di=gr_d/(gridspace*jagged);
if (Di<1) LogWarning(EC_WARN,ONE_POS,
"Granule diameter is smaller than dipole size. It is recommended to increase resolution");
R=Di/2;
R2=R*R;
Di2=4*R2;
// inner box
D("gr_N=%zu, Di="GFORMDEF,gr_N,Di);
x0=R-0.5;
x1=boxX-R-0.5;
y0=R-0.5;
y1=boxY-R-0.5;
z0=R-0.5;
z1=boxZ-R-0.5;
minval=MIN(x1-x0,MIN(y1-y0,z1-z0));
if (minval<=0) LogError(ONE_POS,"Granule size must be smaller than minimum particle dimension");
/* initialize auxiliary grid; grid size is chosen to be always <= D/sqrt(3). Thus we can be sure that each cell
* contain no more than 1 granule.
*/
CheckOverflow(MAX(boxX,MAX(boxY,boxZ))*10/Di,ONE_POS_FUNC);
tmp1=sqrt(3)/Di;
gX=(int)ceil((x1-x0)*tmp1);
gY=(int)ceil((y1-y0)*tmp1);
gZ=(int)ceil((z1-z0)*tmp1);
// this should occur only as a consequence of float inaccuracy in error check above
if (gX==0 || gY==0 || gZ==0) LogError(ONE_POS,"Granule size is too close to minimum particle dimension");
gdX=(x1-x0)/gX;
gdY=(y1-y0)/gY;
gdZ=(z1-z0)/gZ;
tmp1=MAX(2*Di,MIN_CELL_SIZE);
/* sets the discrimination for small or large granules; it should guarantee that no divisions by zero occur
* afterwards in the code for small granules
*/
sm_gr=minval>tmp1 && (gdX<2 || gdY<2 || gdZ<2);
if (sm_gr) {
if (IFROOT) PRINTFB("Using algorithm for small granules\n");
/* redefine auxiliary grid; now the grid size is chosen to be always >= 2*D. Thus we can be sure that granule
* can intersect with granule in either left or right (x=+-1) cell but not both (and analogously with other
* coordinates).
*/
tmp1=1/tmp1;
gX=(int)floor((x1-x0)*tmp1);
gdX=(x1-x0)/gX;
gY=(int)floor((y1-y0)*tmp1);
gdY=(y1-y0)/gY;
gZ=(int)floor((z1-z0)*tmp1);
gdZ=(z1-z0)/gZ;
}
else { // large granules
if (IFROOT) PRINTFB("Using algorithm for large granules\n");
gX2=2*gX;
gdXh=gdX/2;
gY2=2*gY;
gdYh=gdY/2;
gZ2=2*gZ;
gdZh=gdZ/2;
/* this sets maximum distance of neighboring cells to check; condition gdX<R can only occur if gX<=7, which is
* quite rare, so no optimization is performed. sx>3 can only occur if gX<=2 and then it doesn't make sense to
* take bigger sx. Absolutely analogous for y, z.
*/
if (gdX<R) sx=3;
else sx=2;
if (gdY<R) sy=3;
else sy=2;
if (gdZ<R) sz=3;
else sz=2;
}
gXY=MultOverflow(gX,gY,ONE_POS_FUNC);
gr_gN=MultOverflow(gXY,gZ,ONE_POS_FUNC);
// calculate maximum number of granules in a grid; crude estimate
tmp2=(ceil((x1-x0)/Di)+1)*(ceil((y1-y0)/Di)+1)*(ceil((z1-z0)/Di)+1);
max_Ngr=MIN(MAX_GR_SET,tmp2);
// local z grid + initialize communications
D("gr_gN=%zu, max_Ngr=%d",gr_gN,max_Ngr);
SetGranulComm(z0,z1,gdZ,gZ,gXY,max_Ngr,&locz0,&locz1,sm_gr);
if (!sm_gr) {
locgZ=locz1-locz0;
locgZ2=2*locgZ;
gr_locgN=gXY*locgZ;
}
if (IFROOT) {
// initialize random generator
key[0]=(unsigned long)time(NULL);
key[1]=(unsigned long)(clock());
init_by_array(key,KEY_LENGTH);
// allocate memory
MALLOC_VECTOR(occup,ushort,gr_gN,ONE);
if (sm_gr) MALLOC_VECTOR(tree_index,ushort,max_Ngr,ONE);
else MALLOC_VECTOR(dom,uchar,gr_gN,ALL);
}
else if (!sm_gr && locgZ!=0) MALLOC_VECTOR(dom,uchar,gr_locgN,ALL);
MALLOC_VECTOR(vgran,double,3*max_Ngr,ALL);
MALLOC_VECTOR(vfit,bool,max_Ngr,ALL);
if (!sm_gr && locgZ!=0) {
// build some more indices
MALLOC_VECTOR(ginX,int,gX2+1,ALL);
MALLOC_VECTOR(ginY,int,gY2+1,ALL);
MALLOC_VECTOR(ginZ,int,locgZ2+1,ALL);
for (i=0;i<=gX2;i++) ginX[i]=(int)ceil(x0+i*gdXh);
id0=ginX[0];
id1=ginX[gX2];
for (i=0;i<=gY2;i++) ginY[i]=(int)ceil(y0+i*gdYh);
jd0=ginY[0];
jd1=ginY[gY2];
for (i=0;i<=locgZ2;i++) ginZ[i]=(int)ceil(z0+(i+2*locz0)*gdZh);
kd0=MAX(ginZ[0],local_z0);
indZ=1;
if (kd0>=ginZ[1]) indZ++;
kd1=MIN(ginZ[locgZ2],local_z1_coer);
}
n=count=count_gr=false_count=0;
nd=0;
// crude estimate of the probability to place a small granule into domain
if (sm_gr) overhead=Ndip/mat_count[gr_mat];
else overhead=1;
// main cycle
D("Starting main iteration cycle");
while (n<gr_N) {
if (sm_gr) { // small granules
// just generate granules
if (IFROOT) {
cur_Ngr=MIN(ceil((gr_N-n)*overhead),max_Ngr);
// generate points and quick check
ig=false_count=0;
for (ui=0;ui<gr_gN;ui++) occup[ui]=MAX_GR_SET; // used as undefined
while (ig<cur_Ngr) {
count++;
false_count++;
fits=true;
// random position in a grid
gr[0]=genrand(0,gX);
gr[1]=genrand(0,gY);
gr[2]=genrand(0,gZ);
// coordinates in a grid
t1=floor(gr[0]);
t2=floor(gr[1]);
t3=floor(gr[2]);
indX=(int)t1;
indY=(int)t2;
indZ=(int)t3;
t1=gr[0]-t1; // t_i are distances to the edges
t2=gr[1]-t2;
t3=gr[2]-t3;
// convert to usual coordinates (in dipole grid)
gr[0]=gr[0]*gdX+x0;
gr[1]=gr[1]*gdY+y0;
gr[2]=gr[2]*gdZ+z0;
index=indZ*gXY+indY*gX+indX;
// 'last' is used only if fits, so when this test actually reaches last element
last=CHECK_CELL(index);
// weird construction (7-level nested 'ifs') but should be fast
if (fits) {
t1*=gdX; // transform shifts to usual coordinates; done only when needed
sx=0;
if (t1<Di) {
if (indX!=0) sx=-1;
}
else if ((t1=gdX-t1)<Di && indX!=gX-1) sx=1;
if (sx==0 || CHECK_CELL_TEST(index+sx)) { // test for x-neighbor
t2*=gdY;
sy=0;
if (t2<Di) {
if (indY!=0) sy=-gX;
}
else if ((t2=gdY-t2)<Di && indY!=gY-1) sy=gX;
if (sy==0 || CHECK_CELL_TEST(index+sy)) { // test for y-neighbor
t3*=gdZ;
sz=0;
if (t3<Di) {
if (indZ!=0) sz=-(int)gXY;
}
else if ((t3=gdZ-t3)<Di && indZ!=gZ-1) sz=gXY;
if (sz!=0) {
if (CHECK_CELL_TEST(index+sz)) { // test for z-neighbor
if (sy!=0) {
tmp1=Di2-t2*t2-t3*t3;
// test for yz- and xyz-neighbors
if (tmp1>0 && CHECK_CELL_TEST(index+sy+sz )&& sx!=0 && t1*t1<tmp1)
CHECK_CELL(index+sx+sy+sz);
}
else if (sx!= 0 && t1*t1+t3*t3<Di2) CHECK_CELL(index+sx+sz);
}
}
// test for xy-neighbor
else if (sx!=0 && sy!=0 && t1*t1+t2*t2<Di2) CHECK_CELL(index+sx+sy);
}
}
}
if (fits) {
memcpy(vgran+3*ig,gr,3*sizeof(double));
tree_index[ig]=MAX_GR_SET;
if (last==MAX_GR_SET) occup[index]=(unsigned short)ig;
else tree_index[last]=(unsigned short)ig;
ig++;
false_count=0;
}
if (false_count>MAX_FALSE_SKIP_SMALL) break;
}
// real number of placed granules for this set
cur_Ngr=ig;
}
}
else { // large granules
// generate domain pattern
if (locgZ!=0) {
for (i=0;i<gr_locgN;i++) dom[i]=0;
/* indices 'index' and 'dom_index' are build up gradually for optimization. Finally,
* index=(k-local_z0)*boxXY + j*boxX +i.
* TODO: ??? final formula for dom_index is unclear, moreover indZ seems to be not always initialized
*/
dom_index2=0;
index2=(kd0-local_z0)*boxXY;
bit=((indZ&1)^1)<<2;
for (k=kd0;k<kd1;k++,index2+=boxXY) {
index1=index2+jd0*boxX;
dom_index1=dom_index2;
indY=1;
bit&=~2;
for (j=jd0;j<jd1;j++,index1+=boxX) {
index=index1+id0;
dom_index=dom_index1;
indX=1;
bit&=~1;
for (i=id0;i<id1;i++,index++) {
if (material_tmp[index]!=gr_mat) dom[dom_index]|=(unsigned char)(1<<bit);
if (i+1==ginX[indX]) {
indX++;
bit^=1;
if (indX&1) dom_index++;
}
}
if (j+1==ginY[indY]) {
indY++;
bit^=2;
if (indY&1) dom_index1+=gX;
}
}
if (k+1==ginZ[indZ]) {
indZ++;
bit^=4;
if (indZ&1) dom_index2+=gXY;
}
}
}
D("Domain pattern generated");
// send/collect domain pattern
CollectDomainGranul(dom,gXY,locz0,locgZ,&Timing_GranulComm);
if (IFROOT) {
// analyze domain pattern
avail=0;
for (ui=0;ui<gr_gN;ui++) if (dom[ui]!=0xFF) avail++;
cur_Ngr=MIN(avail,(size_t)max_Ngr);
tmp1=(gr_N-n)*overhead;
if (cur_Ngr>tmp1) cur_Ngr=(int)ceil(tmp1);
// generate points and quick check
ig=false_count=0;
for (ui=0;ui<gr_gN;ui++) occup[ui]=MAX_GR_SET; // used as undefined
while (ig<cur_Ngr) {
count++;
// random position in a double grid
gr[0]=genrand(0,gX2);
gr[1]=genrand(0,gY2);
gr[2]=genrand(0,gZ2);
// coordinates in doubled grid
indX=(int)floor(gr[0]);
indY=(int)floor(gr[1]);
indZ=(int)floor(gr[2]);
bit=1<<((indX&1)+((indY&1)<<1)+((indZ&1)<<2)); // position bit inside one cell
// coordinates in usual grid
indX/=2;
indY/=2;
indZ/=2;
index=indZ*gXY+indY*gX+indX;
// two simple checks
if (!(dom[index]&bit) && occup[index]==MAX_GR_SET) {
// convert to usual coordinates (in dipole grid)
gr[0]=gr[0]*gdXh+x0;
gr[1]=gr[1]*gdYh+y0;
gr[2]=gr[2]*gdZh+z0;
fits=true;
false_count++;
if ((i0=indX-sx)<0) i0=0;
if ((i1=indX+sx+1)>gX) i1=gX;
if ((j0=indY-sy)<0) j0=0;
if ((j1=indY+sy+1)>gY) j1=gY;
if ((k0=indZ-sz)<0) k0=0;
if ((k1=indZ+sz+1)>gZ) k1=gZ;
dom_index2=k0*gXY;
for (k=k0;k<k1;k++,dom_index2+=gXY) {
dom_index1=dom_index2+j0*gX;
for (j=j0;j<j1;j++,dom_index1+=gX) {
dom_index=dom_index1+i0;
for (i=i0;i<i1;i++,dom_index++) if (occup[dom_index]!=MAX_GR_SET) {
index1=3*occup[dom_index];
t1=gr[0]-vgran[index1];
t2=gr[1]-vgran[index1+1];
t3=gr[2]-vgran[index1+2];
if ((t1*t1+t2*t2+t3*t3)<Di2) {
fits=false;
break;
}
}
if (!fits) break;
}
if (!fits) break;
}
if (fits) {
memcpy(vgran+3*ig,gr,3*sizeof(double));
occup[index]=(unsigned short)ig;
ig++;
false_count=0;
/* Here it is possible to correct the domain pattern because of the presence of a new
* granule. However it probably will be useful only for large volume fractions
*/
}
if (false_count>MAX_FALSE_SKIP) break;
}
}
// real number of placed granules for this set
cur_Ngr=ig;
}
} // end of large granules
D("Set of possible granules produced");
// cast to all processors
MyBcast(&cur_Ngr,int_type,1,&Timing_GranulComm);
MyBcast(vgran,double_type,3*cur_Ngr,&Timing_GranulComm);
count_gr+=cur_Ngr;
// final check if granules belong to the domain
for (ig=0;ig<cur_Ngr;ig++) {
memcpy(gr,vgran+3*ig,3*sizeof(double));
k0=MAX((int)ceil(gr[2]-R),local_z0);
k1=MIN((int)floor(gr[2]+R),local_z1_coer-1);
fits=true;
index2=(k0-local_z0)*boxXY;
for (k=k0;k<=k1;k++,index2+=boxXY) {
tmp1=R2-(gr[2]-k)*(gr[2]-k);
tmp2=sqrt(tmp1);
j0=(int)ceil(gr[1]-tmp2);
j1=(int)floor(gr[1]+tmp2);
index1=index2+j0*boxX;
for (j=j0;j<=j1;j++,index1+=boxX) {
tmp2=sqrt(tmp1-(gr[1]-j)*(gr[1]-j));
i0=(int)ceil(gr[0]-tmp2);
i1=(int)floor(gr[0]+tmp2);
index=index1+i0;
for (i=i0;i<=i1;i++,index++) {
if (material_tmp[index]!=gr_mat) {
fits=false;
break;
}
}
if (!fits) break;
}
if (!fits) break;
}
vfit[ig]=fits;
}
// collect fits
ExchangeFits(vfit,cur_Ngr,&Timing_GranulComm);
// fit dipole grid with successive granules
Nfit=n;
for (ig=0;ig<cur_Ngr && n<gr_N;ig++) {
if (vfit[ig]) { // a successful granule
n++;
// fill dipoles in the sphere with granule material
memcpy(gr,vgran+3*ig,3*sizeof(double));
k0=MAX((int)ceil(gr[2]-R),local_z0);
k1=MIN((int)floor(gr[2]+R),local_z1_coer-1);
index2=(k0-local_z0)*boxXY;
for (k=k0;k<=k1;k++,index2+=boxXY) {
tmp1=R2-(gr[2]-k)*(gr[2]-k);
tmp2=sqrt(tmp1);
j0=(int)ceil(gr[1]-tmp2);
j1=(int)floor(gr[1]+tmp2);
index1=index2+j0*boxX;
for (j=j0;j<=j1;j++,index1+=boxX) {
tmp2=sqrt(tmp1-(gr[1]-j)*(gr[1]-j));
i0=(int)ceil(gr[0]-tmp2);
i1=(int)floor(gr[0]+tmp2);
index=index1+i0;
for (i=i0;i<=i1;i++,index++) {
material_tmp[index]=(unsigned char)(Nmat-1);
nd++;
}
}
}
}
}
cur_Ngr=ig; // this is non-trivial only if n=gr_N occurred above
// save correct granule positions to file
if (store_grans && IFROOT) for (ig=0;ig<cur_Ngr;ig++) if (vfit[ig]) fprintf(file,GFORM3L"\n",
gridspace*(vgran[3*ig]-cX),gridspace*(vgran[3*ig+1]-cY),gridspace*(vgran[3*ig+2]-cZ));
Nfit=n-Nfit;
/* overhead is estimated based on the estimation of mean value - 1*standard deviation for the probability of
* fitting one granule. It is estimated from the Bernoulli statistics: k out of n successful hits.
* M(p)=(k+1)/(n+2); s^2(p)=(k+1)(n-k+1)/(n+3)(n+2)^2; M(p)-s(p)=[(k+1)/(n+2)]*[1-sqrt((n-k+1)/(k+1)(n+3))];
* overhead=1/latter.
*/
overhead=(cur_Ngr+2)/((1-sqrt((cur_Ngr-Nfit+1)/(double)((Nfit+1)*(cur_Ngr+3))))*(Nfit+1));
if (Nfit!=0) zerofit=0;
else {
zerofit++;
// check if taking too long
if (zerofit>MAX_ZERO_FITS) {
MyInnerProduct(&nd,sizet_type,1,&Timing_GranulComm);
LogError(ONE_POS,"The granule generator failed to reach required volume fraction ("GFORMDEF") of "
"granules. %zu granules were successfully placed up to a volume fraction of "GFORMDEF".",