int main(){
/*--- message ---*/
printf("*********************************\n");
printf("*** Use SGESV to solve Ax = B ***\n");
printf("*********************************\n");
printf("\n");
/*--- open files that store data ---*/
OPEN_FILE();
/*--- read data ---*/
GET_DATA();
/*--- call lapack subroutine SGESV, note: ---*/
/*--- (1) all the arguments must be pointers ---*/
/*--- (2) add an underscore to the routine name ---*/
/*--- (3) matrices must be transformed into their Fortran vector formats ---*/
SGESV_(&n, &nrhs, AT, &lda, IPIV, BT, &ldb, &info);
/*--- print the solution ---*/
PRINT_SOLUTION();
/*--- close files ---*/
fclose(fptA);
fclose(fptB);
return 0;
}
stream::inout_sptr FATArchive::open(const EntryPtr id)
{
// TESTED BY: fmt_grp_duke3d_open
// Make sure we're not trying to open a folder as a file
//assert((id->fAttr & EA_FOLDER) == 0);
// We can't do this because some folder formats have their FAT and
// everything stored as a "file" in the parent archive, so the subfolder
// code opens this file (even though it's flagged as a folder) and then
// passes the data to the Archive.
// We are casting away const here, but that's because we need to maintain
// access to the EntryPtr, which we may need to "change" later (to update the
// offset if another file gets inserted before it, i.e. any change would not
// be visible externally.)
FATEntryPtr pFAT = boost::dynamic_pointer_cast<FATEntry>(id);
stream::sub_sptr psSub(new stream::sub());
stream::fn_truncate fnTrunc = boost::bind(&FATArchive::resizeSubstream, this, pFAT, _1);
psSub->open(
this->psArchive,
pFAT->iOffset + pFAT->lenHeader,
pFAT->storedSize,
fnTrunc
);
// Add it to the list of open files, in case we need to shift the substream
// around later on as files are added/removed/resized.
this->openFiles.insert(OPEN_FILE(
pFAT,
psSub
));
return psSub;
}
partition load_partition_info(char *bin_data_dir, int num, char *spec, double *time){
//loads partitioning information
partition p;
int i, n, id;
FILE *fp;
char fn[STRLEN], tmp[MAXSTRLEN];
float tm;
sprintf(fn, "%s%s_%06d.txt", bin_data_dir, spec, num);
if(!strcmp(spec, "sys")){
OPEN_FILE(fp, fn, "rt");
fscanf(fp, "@ %e", &tm);
*time = (double)tm;
fgets(tmp, MAXSTRLEN, fp); //skip the remainder of the line
fscanf(fp, "@ %d", &n);
fgets(tmp, MAXSTRLEN, fp); //skip the remainder of the line
fscanf(fp, "@ %d", &id);
fclose(fp);
}
else if(!strcmp(spec, "tec")){
OPEN_FILE(fp, fn, "rb");
fread(time, sizeof(double), 1, fp);
fread(&n, sizeof(int), 1, fp);
fread(&id, sizeof(int), 1, fp);
fclose(fp);
}
else error(FUNCTION, "unknown spec = \"%s\"", spec);
p.N = n;
p.nodes = calloc(n, sizeof(cpudmn));
sprintf(fn, "%sfileMap_%06d.txt", bin_data_dir, id);
OPEN_FILE(fp, fn, "rt");
fgets(tmp, MAXSTRLEN, fp); //skip first line
for(i = 0; i < p.N; i++){
fgets(tmp, MAXSTRLEN, fp);
if(strlen(tmp) < 2) error(FUNCTION, "inconsistent structure of file %s", fn);
sscanf(tmp, "%d: (%d %d %d) - (%d %d %d)", &n, &(p.nodes[i].imin), &(p.nodes[i].jmin), &(p.nodes[i].kmin), &(p.nodes[i].imax), &(p.nodes[i].jmax), &(p.nodes[i].kmax));
//printf("cpu %d: (%d %d %d) - (%d %d %d)\n", n, p.nodes[i].imin, p.nodes[i].jmin, p.nodes[i].kmin, p.nodes[i].imax, p.nodes[i].jmax, p.nodes[i].kmax);
}
fclose(fp);
return p;
}
void load_domain_info(domain *dmn, char *bin_data_dir){
//loads domain information
FILE *fp;
char fn[STRLEN];
sprintf(fn, "%s/domain.bin", bin_data_dir);
OPEN_FILE(fp, fn, "rb");
fread(&(dmn->h1), sizeof(double), 1, fp);
fread(&(dmn->h2), sizeof(double), 1, fp);
fread(&(dmn->h3), sizeof(double), 1, fp);
fread(&(dmn->Lx), sizeof(double), 1, fp);
fread(&(dmn->Ly), sizeof(double), 1, fp);
fread(&(dmn->Lz), sizeof(double), 1, fp);
fread(&(dmn->tau), sizeof(double), 1, fp);
fread(&(dmn->imin), sizeof(int), 1, fp);
fread(&(dmn->jmin), sizeof(int), 1, fp);
fread(&(dmn->kmin), sizeof(int), 1, fp);
fread(&(dmn->imax), sizeof(int), 1, fp);
fread(&(dmn->jmax), sizeof(int), 1, fp);
fread(&(dmn->kmax), sizeof(int), 1, fp);
fclose(fp);
if( (dmn->imin != dmn->imax)&&(dmn->jmin != dmn->jmax)&&(dmn->kmin != dmn->kmax) ){
dmn->dim = 3;
dmn->mp_2D = 0;
dmn->aa_1D = 0;
}
else if( (dmn->imin == dmn->imax)&&(dmn->jmin != dmn->jmax)&&(dmn->kmin != dmn->kmax) ){
dmn->dim = 2;
dmn->mp_2D = 2;
dmn->aa_1D = 0;
}
else if( (dmn->imin != dmn->imax)&&(dmn->jmin == dmn->jmax)&&(dmn->kmin != dmn->kmax) ){
dmn->dim = 2;
dmn->mp_2D = 3;
dmn->aa_1D = 0;
}
else if( (dmn->imin != dmn->imax)&&(dmn->jmin != dmn->jmax)&&(dmn->kmin == dmn->kmax) ){
dmn->dim = 2;
dmn->mp_2D = 1;
dmn->aa_1D = 0;
}
else if( (dmn->imin == dmn->imax)&&(dmn->jmin == dmn->jmax)&&(dmn->kmin != dmn->kmax) ){
dmn->dim = 1;
dmn->mp_2D = 0;
dmn->aa_1D = 3;
}
else if( (dmn->imin == dmn->imax)&&(dmn->jmin != dmn->jmax)&&(dmn->kmin == dmn->kmax) ){
dmn->dim = 1;
dmn->mp_2D = 0;
dmn->aa_1D = 2;
}
else{
dmn->dim = 1;
dmn->mp_2D = 0;
dmn->aa_1D = 1;
}
}
void load_plasma(marker *m, char *bin_data_dir, int num, int cpu){
//loads the plasma from checpoint for the current cpu
long int N;
char fn[STRLEN];
FILE *fp;
sprintf(fn, "%splasma_%06d_%03d.bin", bin_data_dir, num, cpu);
OPEN_FILE(fp, fn, "rb");
fread(&N, sizeof(long int), 1, fp);
fread(m, sizeof(marker), (size_t)N, fp);
fclose(fp);
}
abstract_fstream::abstract_fstream(
const char *filename,
stream_mode mode)
{
switch(mode) {
case io::in:
_data = OPEN_FILE(filename, READ_MODE);
break;
case io::out:
_data = OPEN_FILE(filename, WRITE_MODE);
break;
default:
throw "Invalid mode";
}
if(_data == INV_FILE) {
#ifdef _DEBUG
printf("abstract_fstream: Can not open file '%s' for %s\n", filename, mode == io::in ? "input" : "output");
#endif
throw "Can not open file";
}
}
int get_checkpoints_num(char *bin_data_dir, char *suffix){
//reads the number of saved checkpoints
FILE *fp;
char fn[STRLEN];
int num;
sprintf(fn, "%s%s.N", bin_data_dir, suffix);
OPEN_FILE(fp, fn, "r");
fscanf(fp, "@ %d", &num);
fclose(fp);
return num;
}
void open_mesh_binary_files(char *bin_data_dir, char *source_spec, char *target_spec, int num, FILE **fs, int N){
//opens the binary files containing meshed data and positions heads at the beginning of useful data
char fn[STRLEN];
int cpu;
#if CPU_64_BIT == 1
#define HEADER_SIZE 112
#else
#define HEADER_SIZE 108
#endif
for(cpu = 0; cpu < N; cpu++){
sprintf(fn, "%s%s_%s_%06d(%03d).bin", bin_data_dir, source_spec, target_spec, num, cpu);
OPEN_FILE(fs[cpu], fn, "rb");
fseek(fs[cpu], HEADER_SIZE, SEEK_SET);
}
}
int main(){
/*--- message ---*/
printf("******************************************\n");
printf("*** Use SGEEQU to equilibrate matrix A ***\n");
printf("******************************************\n");
printf("\n");
/*--- open files that store data ---*/
OPEN_FILE();
/*--- read data ---*/
GET_DATA();
/*--- compute smallest/largest safe numbers ---*/
SMLNUM = SLAMCH(&CMACH);
BIGNUM = 1.0/SMLNUM;
printf("SMLNUM = %e\n", SMLNUM);
printf("BIGNUM = %e\n\n", BIGNUM);
/*--- call lapack subroutine SGEEQU, note: ---*/
/*--- (1) all the arguments must be pointers ---*/
/*--- (2) add an underscore to the routine name ---*/
/*--- (3) matrices must be transformed into Fortran vector format ---*/
SGEEQU_(&m, &n, AT, &lda, R, C, &rowcnd, &colcnd, &amax, &info);
/*--- print the solution ---*/
PRINT_SOLUTION();
/*--- write scaled matrix if there is one ---*/
SCALED_MATRIX();
/*--- close files ---*/
fclose(fptA);
return 0;
}
int plot_init(FILE **plt, int hor_pic_size, domain dmn, subdomain subdmn, int mmain_plane){
//initializes .plt file
int vert_pic_size = 0;
OPEN_FILE(*plt, "plot.plt", "wt");
fprintf(*plt, "#gnuplot plot file\n");
if(dmn.dim == 1) vert_pic_size = hor_pic_size*0.75;
if(dmn.dim == 2){
if(dmn.mp_2D == 1) vert_pic_size = (hor_pic_size*(subdmn.jmax - subdmn.jmin)*dmn.h2)/((subdmn.imax - subdmn.imin)*dmn.h1) + VERT_EXTRA;
if(dmn.mp_2D == 2) vert_pic_size = (hor_pic_size*(subdmn.kmax - subdmn.kmin)*dmn.h3)/((subdmn.jmax - subdmn.jmin)*dmn.h2) + VERT_EXTRA;
if(dmn.mp_2D == 3) vert_pic_size = (hor_pic_size*(subdmn.kmax - subdmn.kmin)*dmn.h3)/((subdmn.imax - subdmn.imin)*dmn.h1) + VERT_EXTRA;
}
if(dmn.dim == 3){
if(mmain_plane == 1) vert_pic_size = (hor_pic_size*(subdmn.jmax - subdmn.jmin)*dmn.h2)/((subdmn.imax - subdmn.imin)*dmn.h1) + VERT_EXTRA;
if(mmain_plane == 2) vert_pic_size = (hor_pic_size*(subdmn.kmax - subdmn.kmin)*dmn.h3)/((subdmn.jmax - subdmn.jmin)*dmn.h2) + VERT_EXTRA;
if(mmain_plane == 3) vert_pic_size = (hor_pic_size*(subdmn.kmax - subdmn.kmin)*dmn.h3)/((subdmn.imax - subdmn.imin)*dmn.h1) + VERT_EXTRA;
}
fprintf(*plt, "set term png large size %d,%d\n", hor_pic_size, vert_pic_size);
return vert_pic_size;
}
static void init_data(args_t *args)
{
int i;
if ( args->nflt )
{
if ( args->nflt > 1 && args->nflt!=args->files->nreaders )
error("Error: expected either one -i/-e option or as many as there are input files\n");
if ( args->nflt < args->files->nreaders )
{
if ( !args->flt_expr[0] ) error("Error: useless use of -i/-e\n");
args->nflt = args->files->nreaders;
args->flt_expr = (char**) realloc(args->flt_expr,sizeof(char*)*args->nflt);
args->flt_logic = (int*) realloc(args->flt_logic,sizeof(int)*args->nflt);
args->flt = (filter_t**) realloc(args->flt,sizeof(filter_t*)*args->nflt);
for (i=1; i<args->nflt; i++)
{
args->flt_expr[i] = args->flt_expr[0];
args->flt_logic[i] = args->flt_logic[0];
args->flt[i] = filter_init(args->files->readers[i].header,args->flt_expr[i]);
}
args->flt[0] = filter_init(args->files->readers[0].header,args->flt_expr[0]);
}
else
{
for (i=0; i<args->files->nreaders; i++)
{
if ( !args->flt_expr[i] ) continue;
args->flt[i] = filter_init(args->files->readers[i].header,args->flt_expr[i]);
}
}
}
if ( args->isec_op==OP_EXACT )
{
if ( strlen(args->isec_exact)!=args->files->nreaders )
error("The number of files does not match the bitmask: %d vs %s\n", args->files->nreaders,args->isec_exact);
for (i=0; i<args->files->nreaders; i++)
if ( args->isec_exact[i]!='0' && args->isec_exact[i]!='1' ) error("Unexpected bitmask: %s\n",args->isec_exact);
for (i=0; i<args->files->nreaders; i++)
args->isec_exact[i] -= '0';
}
// Which files to write: parse the string passed with -w
char *p = args->write_files;
while (p && *p)
{
if ( !args->write ) args->write = (int*) calloc(args->files->nreaders,sizeof(int));
if ( sscanf(p,"%d",&i)!=1 ) error("Could not parse --write %s\n", args->write_files);
if ( i<0 || i>args->files->nreaders ) error("The index is out of range: %d (%s)\n", i, args->write_files);
args->write[i-1] = 1;
args->iwrite = i-1;
args->nwrite++;
while (*p && *p!=',') p++;
if ( *p==',' ) p++;
}
if ( args->nwrite>1 && !args->prefix ) error("Expected -p when mutliple output files given: --write %s\n", args->write_files);
if ( args->isec_op==OP_COMPLEMENT && args->nwrite )
{
if ( args->nwrite>1 ) error("Multiple files to -w make no sense with -C\n");
if ( !args->write[0] ) error("Only -w1 makes sense with -C\n");
}
if ( args->prefix )
{
// Init output directory and create the readme file
args->fh_log = open_file(NULL,"w","%s/README.txt", args->prefix);
if ( !args->fh_log ) error("%s/README.txt: %s\n", args->prefix, strerror(errno));
fprintf(args->fh_log,"This file was produced by vcfisec.\n");
fprintf(args->fh_log,"The command line was:\tbcftools %s ", args->argv[0]);
int i;
for (i=1; i<args->argc; i++) fprintf(args->fh_log," %s",args->argv[i]);
fprintf(args->fh_log,"\n\nUsing the following file names:\n");
const char *suffix = "vcf";
if ( args->output_type & FT_BCF ) suffix = "bcf";
else if ( args->output_type & FT_GZ ) suffix = "vcf.gz";
// Open output files and write the legend
if ( args->isec_op==OP_VENN )
{
args->fh_out = (htsFile**) malloc(sizeof(htsFile*)*4);
args->fnames = (char**) calloc(4,sizeof(char*));
#define OPEN_FILE(i,j) { \
open_file(&args->fnames[i], NULL, "%s/%04d.%s", args->prefix, i, suffix); \
args->fh_out[i] = hts_open(args->fnames[i], hts_bcf_wmode(args->output_type)); \
if ( !args->fh_out[i] ) error("Could not open %s\n", args->fnames[i]); \
if ( args->n_threads ) hts_set_threads(args->fh_out[i], args->n_threads); \
if (args->record_cmd_line) bcf_hdr_append_version(args->files->readers[j].header,args->argc,args->argv,"bcftools_isec"); \
bcf_hdr_write(args->fh_out[i], args->files->readers[j].header); \
}
if ( !args->nwrite || args->write[0] )
{
OPEN_FILE(0,0);
fprintf(args->fh_log,"%s\tfor records private to\t%s\n", args->fnames[0], args->files->readers[0].fname);
}
if ( !args->nwrite || args->write[1] )
{
OPEN_FILE(1,1);
fprintf(args->fh_log,"%s\tfor records private to\t%s\n", args->fnames[1], args->files->readers[1].fname);
}
if ( !args->nwrite || args->write[0] )
{
OPEN_FILE(2,0);
fprintf(args->fh_log,"%s\tfor records from %s shared by both\t%s %s\n", args->fnames[2], args->files->readers[0].fname, args->files->readers[0].fname, args->files->readers[1].fname);
}
if ( !args->nwrite || args->write[1] )
{
OPEN_FILE(3,1);
fprintf(args->fh_log,"%s\tfor records from %s shared by both\t%s %s\n", args->fnames[3], args->files->readers[1].fname, args->files->readers[0].fname, args->files->readers[1].fname);
}
}
else
{
// Init one output file for each reader
args->fh_out = (htsFile**) calloc(args->files->nreaders, sizeof(htsFile*));
args->fnames = (char**) calloc(args->files->nreaders, sizeof(char*));
for (i=0; i<args->files->nreaders; i++)
{
if ( args->write && !args->write[i] ) continue;
if ( args->isec_op==OP_COMPLEMENT && i>0 ) break;
OPEN_FILE(i,i);
fprintf(args->fh_log,"%s\tfor stripped\t%s\n", args->fnames[i], args->files->readers[i].fname);
}
#undef OPEN_FILE
args->fh_sites = open_file(NULL, "w", "%s/sites.txt", args->prefix);
if ( !args->fh_sites ) error("%s/sites.txt: %s\n", args->prefix, strerror(errno));
}
}
else {
if (args->output_fname) {
args->fh_sites = fopen(args->output_fname, "w");
if ( args->fh_sites == NULL ) error("Can't write to \"%s\": %s\n", args->output_fname, strerror(errno));
}
else
args->fh_sites = pysam_stdout;
}
}
static void init_data(args_t *args)
{
// Which files to write: parse the string passed with -w
char *p = args->write_files;
while (p && *p)
{
int i;
if ( !args->write ) args->write = (int*) calloc(args->files->nreaders,sizeof(int));
if ( sscanf(p,"%d",&i)!=1 ) error("Could not parse --write %s\n", args->write_files);
if ( i<0 || i>args->files->nreaders ) error("The index is out of range: %d (%s)\n", i, args->write_files);
args->write[i-1] = 1;
args->iwrite = i-1;
args->nwrite++;
while (*p && *p!=',') p++;
if ( *p==',' ) p++;
}
if ( args->nwrite>1 && !args->prefix ) error("Expected -p when mutliple output files given: --write %s\n", args->write_files);
if ( args->isec_op==OP_COMPLEMENT && args->nwrite )
{
if ( args->nwrite>1 ) error("Multiple files to -w make no sense with -C\n");
if ( !args->write[0] ) error("Only -w1 makes sense with -C\n");
}
if ( args->prefix )
{
// Init output directory and create the readme file
args->fh_log = open_file(NULL,"w","%s/README.txt", args->prefix);
if ( !args->fh_log ) error("%s/README.txt: %s\n", args->prefix, strerror(errno));
fprintf(args->fh_log,"This file was produced by vcfisec.\n");
fprintf(args->fh_log,"The command line was:\tbcftools %s ", args->argv[0]);
int i;
for (i=1; i<args->argc; i++) fprintf(args->fh_log," %s",args->argv[i]);
fprintf(args->fh_log,"\n\nUsing the following file names:\n");
const char *suffix = "vcf";
if ( args->output_type & FT_BCF ) suffix = "bcf";
else if ( args->output_type & FT_GZ ) suffix = "vcf.gz";
// Open output files and write the legend
if ( args->isec_op==OP_VENN )
{
args->fh_out = (htsFile**) malloc(sizeof(htsFile*)*3);
args->fnames = (char**) malloc(sizeof(char*)*3);
#define OPEN_FILE(i,j) { \
open_file(&args->fnames[i], NULL, "%s/%04d.%s", args->prefix, i, suffix); \
args->fh_out[i] = hts_open(args->fnames[i], hts_bcf_wmode(args->output_type)); \
if ( !args->fh_out[i] ) error("Could not open %s\n", args->fnames[i]); \
bcf_hdr_append_version(args->files->readers[j].header,args->argc,args->argv,"bcftools_isec"); \
bcf_hdr_write(args->fh_out[i], args->files->readers[j].header); \
}
OPEN_FILE(0,0);
fprintf(args->fh_log,"%s\tfor records private to\t%s\n", args->fnames[0], args->files->readers[0].fname);
OPEN_FILE(1,1);
fprintf(args->fh_log,"%s\tfor records private to\t%s\n", args->fnames[1], args->files->readers[1].fname);
OPEN_FILE(2,0);
fprintf(args->fh_log,"%s\tfor records shared by both\t%s %s\n", args->fnames[2], args->files->readers[0].fname, args->files->readers[1].fname);
}
else
{
// Init one output file for each reader
args->fh_out = (htsFile**) calloc(args->files->nreaders, sizeof(htsFile*));
args->fnames = (char**) calloc(args->files->nreaders, sizeof(char*));
for (i=0; i<args->files->nreaders; i++)
{
if ( args->write && !args->write[i] ) continue;
if ( args->isec_op==OP_COMPLEMENT && i>0 ) break;
OPEN_FILE(i,i);
fprintf(args->fh_log,"%s\tfor stripped\t%s\n", args->fnames[i], args->files->readers[i].fname);
}
#undef OPEN_FILE
args->fh_sites = open_file(NULL, "w", "%s/sites.txt", args->prefix);
if ( !args->fh_sites ) error("%s/sites.txt: %s\n", args->prefix, strerror(errno));
}
}
else
args->fh_sites = stdout;
}
int main(int argn, char **argv)
{
/* Initialize QT application */
QApplication app(argn, argv);
/* Handle signals, sent by program by
* telling about them to user and
* ending the execution
*/
LLCCEP_exec::cAttachSignalsHandler();
try {
/* Windows, created by the executing program */
::std::vector<LLCCEP_exec::window *> windows;
;
/* Command-line parameters */
LLCCEP_tools::commandLineParametersParser clpp;
clpp.addFlag(LLCCEP_tools::commandLineFlag{{"--help", "-h"},
"help", false});
clpp.setHelpText("LLCCEP debugger help:\n"
"-h/--help | show help(this text)\n"
"The single free parameter will be input "
"program");
clpp.setMaxFreeParams(1);
/* Parse command-line parameters */
clpp.parse(argn, argv);
/* If needed to show help, show it
* and end the execution
*/
if (clpp.getParam("help") == "1" ||
!clpp.getFreeParams().size()) {
if (!clpp.getFreeParams().size())
::std::cerr << "No input!" << ::std::endl;
clpp.showHelp();
return 0;
}
/* Soft-processor */
LLCCEP_exec::softcore sc;
/* Memeory manager */
LLCCEP_exec::memoryManager mm;
/* Program reader */
LLCCEP::codeReader cr;
::std::FILE *in;
OPEN_FILE(in, clpp.getFreeParams()[0].c_str(), "r");
/* Read program's common information */
cr.initializeInputFile(in);
cr.readProgramHeader();
/* Initialize soft-processor data */
sc.setMm(&mm);
sc.setCodeReader(&cr);
/* Execute program */
sc.executeProgram();
/* Close input */
::std::fclose(in);
} catch (LLCCEP::runtime_exception &exc) {
/* Spawn message box in case of
* internal exception
*/
LLCCEP_exec::messageBox("Program was interrupted by an exception",
exc.msg(),
QMessageBox::Close,
QMessageBox::Close,
QMessageBox::Critical).spawn();
/* Dump to console error information */
QUITE_ERROR(yes, "Program was interrupted by an exception:\n"
"%s", exc.msg());
} catch (::std::exception &exc) {
/* Spawn message box in case of
* internal exception
*/
LLCCEP_exec::messageBox("Program was interrupted by an exception",
exc.what(),
QMessageBox::Close,
QMessageBox::Close,
QMessageBox::Critical).spawn();
/* Dump to console error information and exit */
QUITE_ERROR(yes, "Program was interrupted by an exception:\n"
"%s", exc.what());
} catch (::std::string &err) {
/* Dump to console error information and exit */
QUITE_ERROR(yes, "%s", err.c_str());
} catch (int64_t id) {
/* Dump to console error information and exit */
QUITE_ERROR(yes, "Error " int64_t_pf, id);
} catch (...) {
/* Dump to console error information and exit */
QUITE_ERROR(yes, "Unknown exception");
}
return 0;
}
void plot_fourier_transform(domain dmn, special_task st, int mmain_plane, int_array mcuts, arr2d A, int i_slice, int num, FILE *plt, int hor_pic_size, int vert_pic_size, double time){
//saves a number of cuts for fourier components into dat-files using procedures save_dat_file
int i, j, flag;
double kxmin = 0, kymin = 0, kxmax = 0, kymax = 0, kx, ky, kxmin_bound = 0, kxmax_bound = 0, kymin_bound = 0, kymax_bound = 0;
double z = 0;
char str[STRLEN];
char xlabel[16], ylabel[16], zlabel[2];
FILE *fp;
#define BOUNDS_F(kxmin_, kxmax_, kymin_, kymax_, hx_, hy_, hz_, xlabel_, ylabel_, zlabel_){ \
kxmin = -1./(2*hx_); \
kxmax = 1./(2*hx_); \
kymin = -1./(2*hy_); \
kymax = 1./(2*hy_); \
if(st.enable_intervals){ \
kxmin_bound = kxmin_; \
kxmax_bound = kxmax_; \
kymin_bound = kymin_; \
kymax_bound = kymax_; \
} \
else{ \
kxmin_bound = kxmin; \
kxmax_bound = kxmax; \
kymin_bound = kymin; \
kymax_bound = kymax; \
} \
z = hz_*mcuts.data[i_slice]; \
sprintf(xlabel, "%s", xlabel_); \
sprintf(ylabel, "%s", ylabel_); \
sprintf(zlabel, "%s", zlabel_); \
}
if(dmn.dim == 3){
if(mmain_plane == 1) BOUNDS_F(st.ix.min, st.ix.max, st.iy.min, st.iy.max, dmn.h1, dmn.h2, dmn.h3, "lambda k_x", "lambda k_y", "z");
if(mmain_plane == 2) BOUNDS_F(st.iy.min, st.iy.max, st.iz.min, st.iz.max, dmn.h2, dmn.h3, dmn.h1, "lambda k_y", "lambda k_z", "x");
if(mmain_plane == 3) BOUNDS_F(st.ix.min, st.ix.max, st.iz.min, st.iz.max, dmn.h1, dmn.h3, dmn.h2, "lambda k_x", "lambda k_z", "y");
}
else if(dmn.dim == 2){
if(dmn.mp_2D == 1) BOUNDS_F(st.ix.min, st.ix.max, st.iy.min, st.iy.max, dmn.h1, dmn.h2, 0, "lambda k_x", "lambda k_y", "");
if(dmn.mp_2D == 2) BOUNDS_F(st.iy.min, st.iy.max, st.iz.min, st.iz.max, dmn.h2, dmn.h3, 0, "lambda k_y", "lambda k_z", "");
if(dmn.mp_2D == 3) BOUNDS_F(st.ix.min, st.ix.max, st.iz.min, st.iz.max, dmn.h1, dmn.h3, 0, "lambda k_x", "lambda k_z", "");
}
else{
if(dmn.aa_1D == 1) BOUNDS_F(st.ix.min, st.ix.max, 0, 1, dmn.h1, 1, 0, "lambda k_x", "", "");
if(dmn.aa_1D == 2) BOUNDS_F(st.iy.min, st.iy.max, 0, 1, dmn.h2, 1, 0, "lambda k_y", "", "");
if(dmn.aa_1D == 3) BOUNDS_F(st.iz.min, st.iz.max, 0, 1, dmn.h3, 1, 0, "lambda k_z", "", "");
}
sprintf(str, "dat/spectr_%06d(%03d).dat", num, i_slice);
OPEN_FILE(fp, str, "w");
if(dmn. dim > 1){
flag = 0;
for(i = 0; i < A.nx; i++){
for(j = 0; j < A.ny; j++){
kx = kxmax*(i+0.5-A.nx/2)*2/A.nx;
ky = kymax*(j+0.5-A.ny/2)*2/A.ny;
if(in(kx, kxmin_bound, kxmax_bound) && in(ky, kymin_bound, kymax_bound)){
if(flag == 0){
flag = 1;
arr2d_set_ij(arr2d_ij(A, i, j) + VERY_SMALL_VALUE, &A, i, j); //for gnuplot
}
fprintf(fp, "%e %e %e\n", kx, ky, arr2d_ij(A, i, j));
}
}
fprintf(fp, "\n");
}
}
else{
for(i = 0; i < A.nx; i++){
kx = kxmax*(i+0.5-A.nx/2)*2/A.nx;
if(in(kx, kxmin_bound, kxmax_bound)) fprintf(fp, "%e %e\n", kx, arr2d_ij(A, i, 0));
}
}
fclose(fp);
fprintf(plt, "set output 'pics/spectr_%06d(%03d).png'\n", num, i_slice);
if(dmn.dim == 3) fprintf(plt, "set title 'energy spectral density: cut at %s = %.2f lambdas, time = %.2f waveperiods'\n", zlabel, z, time);
else fprintf(plt, "set title 'energy spectral density: time = %.2f waveperiods'\n", time);
fprintf(plt, "set xlabel '%s'\n", xlabel);
fprintf(plt, "set ylabel '%s'\n", ylabel);
if(dmn.dim > 1){
fprintf(plt, "set term png large size %d,%d\n", hor_pic_size, (int)((hor_pic_size*kymax_bound)/kxmax_bound + VERT_EXTRA));
fprintf(plt, "set pm3d map\n");
fprintf(plt, "splot 'dat/spectr_%06d(%03d).dat' notitle\n", num, i_slice);
}
else{
fprintf(plt, "set term png large size %d,%d\n", hor_pic_size, (int)(hor_pic_size*0.75));
fprintf(plt, "set grid\n");
fprintf(plt, "plot 'dat/spectr_%06d(%03d).dat' w l notitle\n", num, i_slice);
fprintf(plt, "unset grid\n");
}
fprintf(plt, "set term png large size %d,%d\n", hor_pic_size, vert_pic_size);
}
void df_plot(distrib_function_task dt, arr2d df, int hor_pic_size, int vert_pic_size, int num, double time, FILE *plt){
//saves distribution function data and updates plot file
FILE *fp;
char str[STRLEN], xlabel[32], ylabel[32];
int i, j, sum = 0;
double x, y;
sprintf(str, "dat/df_%06d.dat", num);
OPEN_FILE(fp, str, "w");
if((df.nx > 1)&&(df.ny > 1)) arr2d_set_ij(arr2d_ij(df, 0, 0) + 1, &df, 0, 0);
for(i = 0; i < dt.nhist1; i++){
x = dt.i1.min + (i+0.5)*(dt.i1.max-dt.i1.min)/dt.nhist1;
if(dt.sum == 2){
for(j = 0; j < dt.nhist2; j++){
y = dt.i2.min + (j+0.5)*(dt.i2.max-dt.i2.min)/dt.nhist2;
if(!dt.log_distr) fprintf(fp, "%e %e %.0f\n", x, y, arr2d_ij(df, i, j));
else fprintf(fp, "%e %e %e\n", x, y, log(1 + arr2d_ij(df, i, j)));
}
fprintf(fp, "\n");
}
else{
if(!dt.log_distr) fprintf(fp, "%e %.0f\n", x, arr2d_ij(df, i, 0));
else fprintf(fp, "%e %e\n", x, log(1 + arr2d_ij(df, i, 0)));
}
}
fclose(fp);
fprintf(plt, "set term png large size %d,%d\n", hor_pic_size, (int)(hor_pic_size*0.75));
#define MKLABEL(label_) { \
if(sum == 0) sprintf(xlabel, "%s", label_); \
else sprintf(ylabel, "%s", label_); \
sum++; \
}
if(dt.x) MKLABEL("x/lambda");
if(dt.y) MKLABEL("y/lambda");
if(dt.z) MKLABEL("z/lambda");
if(dt.px) MKLABEL("p_x/mc");
if(dt.py) MKLABEL("p_y/mc");
if(dt.pz) MKLABEL("p_z/mc");
if(dt.gamma) MKLABEL("particles gamma factor");
if(dt.theta_pos_x) MKLABEL("theta_pos_x");
if(dt.theta_pos_y) MKLABEL("theta_pos_y");
if(dt.theta_pos_z) MKLABEL("theta_pos_z");
if(dt.theta_mom_x) MKLABEL("theta_mom_x");
if(dt.theta_mom_y) MKLABEL("theta_mom_y");
if(dt.theta_mom_z) MKLABEL("theta_mom_z");
if(dt.phi_pos_xy) MKLABEL("phi_pos_xy");
if(dt.phi_pos_yz) MKLABEL("phi_pos_yz");
if(dt.phi_pos_xz) MKLABEL("phi_pos_xz");
if(dt.phi_mom_xy) MKLABEL("phi_mom_xy");
if(dt.phi_mom_yz) MKLABEL("phi_mom_yz");
if(dt.phi_mom_xz) MKLABEL("phi_mom_xz");
if(dt.sum == 1){
if(!dt.log_distr) sprintf(ylabel, "delta N");
else sprintf(ylabel, "ln ( 1 + delta N )");
}
fprintf(plt, "set output 'pics/df_%06d.png'\n", num);
sprintf(str, "q/m = %f", dt.q_div_m);
fprintf(plt, "set title 'Particle %shistogram", dt.log_distr?"logarithmic ":"");
if((dt.q_div_m <= MAX_Q_DIV_M)||(dt.energy_filter)) fprintf(plt, " for particles having ");
fprintf(plt, "%s", (dt.q_div_m > MAX_Q_DIV_M)?"":str);
sprintf(str, "gamma in [%.3e, %.3e]", dt.ef.min, dt.ef.max);
fprintf(plt, "%s%s", ((dt.q_div_m <= MAX_Q_DIV_M)?" and ":""), (dt.energy_filter?str:""));
fprintf(plt, ": t = %.2f'\n", time);
fprintf(plt, "set xlabel '%s'\n", xlabel);
fprintf(plt, "set ylabel '%s'\n", ylabel);
if(dt.sum == 2){
fprintf(plt, "set pm3d map\n");
fprintf(plt, "splot 'dat/df_%06d.dat' using 1:2:3 notitle\n", num);
fprintf(plt, "unset pm3d\n");
}
else{
fprintf(plt, "set grid\n");
fprintf(plt, "plot 'dat/df_%06d.dat' w l notitle\n", num);
fprintf(plt, "unset grid\n");
}
fprintf(plt, "set term png large size %d,%d\n", hor_pic_size, vert_pic_size);
}
INPUT_INFO* parse_input(const char* file_name)
{
/*
hf 6-31g*
0 1
N 7 0.0000000000 0.0000000000 0.0000000000
N 7 0.0000000000 0.0000000000 1.0980000000
*/
int i = 0, j;
FILE *f;
INPUT_INFO *inputFile;
char BasisFile[20] = "EMSL/"; // save the name of basis file
char method[5], basisName[10];
ATOM_INFO *atomList;
COORD *coord;
int gCount = 0, basisCount;
// initial allocate 100 basis function, 300 GTO;
inputFile = calloc(sizeof(INPUT_INFO), 1);
atomList = inputFile->atomList =
malloc(sizeof(ATOM_INFO)*INITIAL_ATOM_COUNT);
coord = inputFile->gXYZ = malloc(sizeof(COORD) * INITIAL_ATOM_COUNT);
OPEN_FILE(f, file_name);
// read the control parameter like Gaussian 09
fscanf(f, "%s%s", method, basisName);
// Get the electronic count and multidegree of the system
fscanf(f, "%d%u", &inputFile->icharge, &inputFile->imult);
#if DEBUG_OUTPUT_INPUTFILE
fprintf(stdout, "%s %s\n\n%d %u\n",
method, basisName, inputFile->icharge, inputFile->imult);
#endif
// read the atom information include atom Number and coordination
while (fscanf(f, "%s%d%lf%lf%lf", atomList[i].symbol, &atomList[i].n,
&coord[i].x, &coord[i].y, &coord[i].z) != EOF) {
// tranverse ANGS to BOHR
coord[i].x *= ANGS_2_BOHR;
coord[i].y *= ANGS_2_BOHR;
coord[i].z *= ANGS_2_BOHR;
#if DEBUG_OUTPUT_INPUTFILE
fprintf(stdout, "%s %d %lf %lf %lf\n",
atomList[i].symbol,
atomList[i].n,
coord[i].x,
coord[i].y,
coord[i].z);
#endif
// connect the coordination
inputFile->atomList[i].cid = i;
inputFile->atomCount++;
i++;
}
fclose(f);
// release redundant memory
REALLOC(inputFile->atomList, inputFile->atomCount * sizeof(ATOM_INFO));
// ----------------------------------------------------------------
// Read Basis information from the basis function database
// ----------------------------------------------------------------
inputFile->basisSet = malloc(sizeof(BASIS)* INITIAL_BASIS_COUNT);
inputFile->gp = malloc(sizeof(GTO_PARTIAL)* INDEPENDENT_GTO_COUNT);
inputFile->gtoSet = malloc(sizeof(GTO)* INDEPENDENT_GTO_COUNT);
Get_Basis_File(basisName, BasisFile);
OPEN_FILE(f, BasisFile);
readbasis(f, inputFile);
fclose(f);
/* ----------------------------------------------------------------
* allocate memory for store P, K, gamma
* ----------------------------------------------------------------
*/
gCount = inputFile->gCount;
basisCount = inputFile->basisCount;
#if DEBUG_INPUT
fprintf(stdout, "%d %d %d\n", gCount, inputFile->gtoCount, basisCount);
for (i = 0; i < gCount; i++)
fprintf(stdout, "%d %lf %lf\n", i, inputFile->gp[i].alpha,
inputFile->gp[i].coeff);
#endif
inputFile->K = (double **)malloc(sizeof(double *) * gCount);
inputFile->zeta = (double **)malloc(sizeof(double *) * gCount);
inputFile->P = (COORD **)malloc(sizeof(COORD *) * gCount);
for (i = 0; i < gCount; i ++) {
MALLOC(inputFile->K[i], sizeof(double) * gCount);
MALLOC(inputFile->zeta[i], sizeof(double) * gCount);
MALLOC(inputFile->P[i], sizeof(COORD) * gCount);
}
for (i = 0; i < gCount; i++) {
for (j = 0; j <= i; j++) {
// compute \zeta = \alpha_1 + \alpha_2
inputFile->zeta[i][j] = inputFile->zeta[j][i] =
inputFile->gp[i].alpha + inputFile->gp[j].alpha;
// compute K = f(\alpha_1, \alpha_2, AB)
inputFile->K[i][j] = inputFile->K[j][i] = K_OS(&inputFile->gp[i],
&inputFile->gp[j],
inputFile->gXYZ);
// compute P
Gaussian_product_center(&inputFile->gp[i], &inputFile->gp[j],
inputFile->gXYZ,
&inputFile->P[i][j]);
inputFile->P[j][i] = inputFile->P[i][j];
#if DEBUG_ZETA_K_P
fprintf(stdout, "i, j: %d %d\nzeta = %lf\tK = %lf\tP: %lf %lf %lf\n",
i, j,
inputFile->zeta[i][j],
inputFile->K[i][j],
inputFile->P[i][j].x,
inputFile->P[i][j].y,
inputFile->P[i][j].z);
#endif
}
}
return inputFile;
}
