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Fixed BBNBI not compiling
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@miekkasarki
miekkasarki committed Jul 25, 2024
1 parent 2a09dca commit 46023f1
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Showing 3 changed files with 173 additions and 172 deletions.
4 changes: 2 additions & 2 deletions src/Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -131,7 +131,7 @@ HEADERS=ascot5.h math.h consts.h list.h octree.h physlib.h error.h \
neutral.h plasma.h particle.h endcond.h B_field.h gctransform.h \
E_field.h wall.h simulate.h diag.h offload.h boozer.h mhd.h \
random.h print.h hdf5_interface.h suzuki.h nbi.h biosaw.h \
asigma.h boschhale.h mpi_interface.h
asigma.h boschhale.h mpi_interface.h bbnbi5.h

OBJS= math.o list.o octree.o error.c \
$(DIAGOBJS) $(BFOBJS) $(EFOBJS) $(WALLOBJS) \
Expand All @@ -141,7 +141,7 @@ OBJS= math.o list.o octree.o error.c \
neutral.o plasma.o particle.o endcond.o B_field.o gctransform.o \
E_field.o wall.o simulate.o diag.o offload.o boozer.o mhd.o \
random.o print.o hdf5_interface.o suzuki.o nbi.o biosaw.o \
asigma.o mpi_interface.o boschhale.o
asigma.o mpi_interface.o boschhale.o bbnbi5.o

BINS=test_math test_nbi test_bsearch \
test_wall_2d test_plasma test_random \
Expand Down
169 changes: 0 additions & 169 deletions src/bbnbi5.c
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Original file line number Diff line number Diff line change
Expand Up @@ -37,8 +37,6 @@
#include "diag.h"
#include "bbnbi5.h"

int bbnbi_read_arguments(int argc, char** argv, sim_offload_data* sim,
int* nprt, real* t1, real* t2);
void bbnbi_trace_markers(particle_queue *pq, sim_data* sim);
void bbnbi_inject_markers(particle_state* p, int nprt, int ngenerated, real t0,
real t1, nbi_injector* inj, sim_data* sim);
Expand Down Expand Up @@ -421,170 +419,3 @@ void bbnbi_trace_markers(particle_queue *pq, sim_data* sim) {
n_running = particle_cycle_fo(pq, &p, &sim->B_data, cycle);
}
}

/**
* @brief Read command line arguments
*
* Read in command line arguments, input and output names and mpi parameters
* are stored in sim structure as with ascot5, number of markers is passed
* as an argument.
*
* If the arguments could not be parsed, this function returns a non-zero exit
* value.
*
* @param argc argument count as given to main()
* @param argv argument vector as given to main()
* @param sim pointer to offload data struct
* @param nprt pointer to integer where number of markers is stored
* @param t1 pointer to store beginning of time interval
* @param t2 pointer to store end of the time interval
*
* @return Zero if success
*/
int bbnbi_read_arguments(int argc, char** argv, sim_offload_data* sim,
int* nprt, real* t1, real* t2) {
struct option longopts[] = {
{"in", required_argument, 0, 1},
{"out", required_argument, 0, 2},
{"mpi_size", required_argument, 0, 3},
{"mpi_rank", required_argument, 0, 4},
{"d", required_argument, 0, 5},
{"bfield", required_argument, 0, 6},
{"wall", required_argument, 0, 7},
{"plasma", required_argument, 0, 8},
{"nbi", required_argument, 0, 9},
{"n", required_argument, 0, 10},
{"t1", required_argument, 0, 11},
{"t2", required_argument, 0, 12},
{0, 0, 0, 0}
};

/* Initialize default values */
sim->hdf5_in[0] = '\0';
sim->hdf5_out[0] = '\0';
sim->qid_options[0] = '\0';
sim->qid_bfield[0] = '\0';
sim->qid_efield[0] = '\0';
sim->qid_marker[0] = '\0';
sim->qid_wall[0] = '\0';
sim->qid_plasma[0] = '\0';
sim->qid_neutral[0] = '\0';
sim->qid_boozer[0] = '\0';
sim->qid_mhd[0] = '\0';
sim->qid_asigma[0] = '\0';
sim->qid_nbi[0] = '\0';
sim->mpi_rank = 0;
sim->mpi_size = 0;
*nprt = 10000;
*t1 = 0.0;
*t2 = 0.0;
strcpy(sim->description, "TAG");

/* Read user input */
int c;
int slen;
while((c = getopt_long(argc, argv, "", longopts, NULL)) != -1) {
switch(c) {
case 1:
/* The .hdf5 filename can be specified with or without the
* trailing .h5 */
slen = strlen(optarg);
if ( slen > 3 && !strcmp(optarg+slen-3, ".h5") ) {
strcpy(sim->hdf5_in, optarg);
(sim->hdf5_in)[slen-3]='\0';
}
else {
strcpy(sim->hdf5_in, optarg);
}
break;
case 2:
/* The .hdf5 filename can be specified with or without the
* trailing .h5 */
slen = strlen(optarg);
if ( slen > 3 && !strcmp(optarg+slen-3, ".h5") ) {
strcpy(sim->hdf5_out, optarg);
(sim->hdf5_out)[slen-3]='\0';
}
else {
strcpy(sim->hdf5_out, optarg);
}
break;
case 3:
sim->mpi_size = atoi(optarg);
break;
case 4:
sim->mpi_rank = atoi(optarg);
break;
case 5:
strcpy(sim->description, optarg);
break;
case 6:
strcpy(sim->qid_bfield, optarg);
break;
case 7:
strcpy(sim->qid_wall, optarg);
break;
case 8:
strcpy(sim->qid_plasma, optarg);
break;
case 9:
strcpy(sim->qid_nbi, optarg);
break;
case 10:
*nprt = atoi(optarg);
break;
case 11:
*t1 = atof(optarg);
break;
case 12:
*t2 = atof(optarg);
break;
default:
// Unregonizable argument(s). Tell user how to run ascot5_main
print_out(VERBOSE_MINIMAL,
"\nUnrecognized argument. The valid arguments are:\n");
print_out(VERBOSE_MINIMAL,
"--in input file (default: ascot.h5)\n");
print_out(VERBOSE_MINIMAL,
"--out output file (default: same as input)\n");
print_out(VERBOSE_MINIMAL,
"--mpi_size number of independent processes\n");
print_out(VERBOSE_MINIMAL,
"--mpi_rank rank of independent process\n");
print_out(VERBOSE_MINIMAL,
"--d run description maximum of 250 characters\n");
print_out(VERBOSE_MINIMAL,
"--n number of markers to generate (default: 10000)\n");
print_out(VERBOSE_MINIMAL,
"--t1 time when injectors are turned on (default: 0.0 s)\n");
print_out(VERBOSE_MINIMAL,
"--t2 time when injectors are turned off (default: 0.0 s)\n");
return 1;
}
}

/* Default value for input file is ascot.h5, and for output same as input
* file. Adujust hdf5_in and hdf5_out accordingly. For output file, we don't
* add the .h5 extension here. */
if(sim->hdf5_in[0] == '\0' && sim->hdf5_out[0] == '\0') {
/* No input, use default values for both */
strcpy(sim->hdf5_in, "ascot.h5");
strcpy(sim->hdf5_out, "ascot.h5");
}
else if(sim->hdf5_in[0] == '\0' && sim->hdf5_out[0] != '\0') {
/* Output file is given but the input file is not */
strcpy(sim->hdf5_in, "ascot.h5");
strcat(sim->hdf5_out, ".h5");
}
else if(sim->hdf5_in[0] != '\0' && sim->hdf5_out[0] == '\0') {
/* Input file is given but the output is not */
strcat(sim->hdf5_in, ".h5");
strcpy(sim->hdf5_out, sim->hdf5_in);
}
else {
/* Both input and output files are given */
strcat(sim->hdf5_in, ".h5");
strcat(sim->hdf5_out, ".h5");
}
return 0;
}
172 changes: 171 additions & 1 deletion src/bbnbi5_main.c
View file
Original file line number Diff line number Diff line change
Expand Up @@ -28,6 +28,9 @@
#include "diag.h"
#include "bbnbi5.h"

int bbnbi_read_arguments(int argc, char** argv, sim_offload_data* sim,
int* nprt, real* t1, real* t2);

/**
* @brief Main function for BBNBI5
*
Expand Down Expand Up @@ -141,4 +144,171 @@ int main(int argc, char** argv) {
print_out0(VERBOSE_MINIMAL, sim.mpi_rank, sim.mpi_root, "\nDone\n");

return 0;
}
}

/**
* @brief Read command line arguments
*
* Read in command line arguments, input and output names and mpi parameters
* are stored in sim structure as with ascot5, number of markers is passed
* as an argument.
*
* If the arguments could not be parsed, this function returns a non-zero exit
* value.
*
* @param argc argument count as given to main()
* @param argv argument vector as given to main()
* @param sim pointer to offload data struct
* @param nprt pointer to integer where number of markers is stored
* @param t1 pointer to store beginning of time interval
* @param t2 pointer to store end of the time interval
*
* @return Zero if success
*/
int bbnbi_read_arguments(int argc, char** argv, sim_offload_data* sim,
int* nprt, real* t1, real* t2) {
struct option longopts[] = {
{"in", required_argument, 0, 1},
{"out", required_argument, 0, 2},
{"mpi_size", required_argument, 0, 3},
{"mpi_rank", required_argument, 0, 4},
{"d", required_argument, 0, 5},
{"bfield", required_argument, 0, 6},
{"wall", required_argument, 0, 7},
{"plasma", required_argument, 0, 8},
{"nbi", required_argument, 0, 9},
{"n", required_argument, 0, 10},
{"t1", required_argument, 0, 11},
{"t2", required_argument, 0, 12},
{0, 0, 0, 0}
};

/* Initialize default values */
sim->hdf5_in[0] = '\0';
sim->hdf5_out[0] = '\0';
sim->qid_options[0] = '\0';
sim->qid_bfield[0] = '\0';
sim->qid_efield[0] = '\0';
sim->qid_marker[0] = '\0';
sim->qid_wall[0] = '\0';
sim->qid_plasma[0] = '\0';
sim->qid_neutral[0] = '\0';
sim->qid_boozer[0] = '\0';
sim->qid_mhd[0] = '\0';
sim->qid_asigma[0] = '\0';
sim->qid_nbi[0] = '\0';
sim->mpi_rank = 0;
sim->mpi_size = 0;
*nprt = 10000;
*t1 = 0.0;
*t2 = 0.0;
strcpy(sim->description, "TAG");

/* Read user input */
int c;
int slen;
while((c = getopt_long(argc, argv, "", longopts, NULL)) != -1) {
switch(c) {
case 1:
/* The .hdf5 filename can be specified with or without the
* trailing .h5 */
slen = strlen(optarg);
if ( slen > 3 && !strcmp(optarg+slen-3, ".h5") ) {
strcpy(sim->hdf5_in, optarg);
(sim->hdf5_in)[slen-3]='\0';
}
else {
strcpy(sim->hdf5_in, optarg);
}
break;
case 2:
/* The .hdf5 filename can be specified with or without the
* trailing .h5 */
slen = strlen(optarg);
if ( slen > 3 && !strcmp(optarg+slen-3, ".h5") ) {
strcpy(sim->hdf5_out, optarg);
(sim->hdf5_out)[slen-3]='\0';
}
else {
strcpy(sim->hdf5_out, optarg);
}
break;
case 3:
sim->mpi_size = atoi(optarg);
break;
case 4:
sim->mpi_rank = atoi(optarg);
break;
case 5:
strcpy(sim->description, optarg);
break;
case 6:
strcpy(sim->qid_bfield, optarg);
break;
case 7:
strcpy(sim->qid_wall, optarg);
break;
case 8:
strcpy(sim->qid_plasma, optarg);
break;
case 9:
strcpy(sim->qid_nbi, optarg);
break;
case 10:
*nprt = atoi(optarg);
break;
case 11:
*t1 = atof(optarg);
break;
case 12:
*t2 = atof(optarg);
break;
default:
// Unregonizable argument(s). Tell user how to run ascot5_main
print_out(VERBOSE_MINIMAL,
"\nUnrecognized argument. The valid arguments are:\n");
print_out(VERBOSE_MINIMAL,
"--in input file (default: ascot.h5)\n");
print_out(VERBOSE_MINIMAL,
"--out output file (default: same as input)\n");
print_out(VERBOSE_MINIMAL,
"--mpi_size number of independent processes\n");
print_out(VERBOSE_MINIMAL,
"--mpi_rank rank of independent process\n");
print_out(VERBOSE_MINIMAL,
"--d run description maximum of 250 characters\n");
print_out(VERBOSE_MINIMAL,
"--n number of markers to generate (default: 10000)\n");
print_out(VERBOSE_MINIMAL,
"--t1 time when injectors are turned on (default: 0.0 s)\n");
print_out(VERBOSE_MINIMAL,
"--t2 time when injectors are turned off (default: 0.0 s)\n");
return 1;
}
}

/* Default value for input file is ascot.h5, and for output same as input
* file. Adujust hdf5_in and hdf5_out accordingly. For output file, we don't
* add the .h5 extension here. */
if(sim->hdf5_in[0] == '\0' && sim->hdf5_out[0] == '\0') {
/* No input, use default values for both */
strcpy(sim->hdf5_in, "ascot.h5");
strcpy(sim->hdf5_out, "ascot.h5");
}
else if(sim->hdf5_in[0] == '\0' && sim->hdf5_out[0] != '\0') {
/* Output file is given but the input file is not */
strcpy(sim->hdf5_in, "ascot.h5");
strcat(sim->hdf5_out, ".h5");
}
else if(sim->hdf5_in[0] != '\0' && sim->hdf5_out[0] == '\0') {
/* Input file is given but the output is not */
strcat(sim->hdf5_in, ".h5");
strcpy(sim->hdf5_out, sim->hdf5_in);
}
else {
/* Both input and output files are given */
strcat(sim->hdf5_in, ".h5");
strcat(sim->hdf5_out, ".h5");
}
return 0;
}

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