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Commit 9fc89eea authored by hchou10's avatar hchou10
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add some new kernel of functions and fix some bugs

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GridDxFormat/grid_reader.c
+ 85
− 0
View file @ 9fc89eea
......@@ -243,10 +243,12 @@ int gridformat_writer(char* name, void* src)
bytes_write = write(fildes, "#OpenDx file generated from grids reader/writer program\n",56);
if(bytes_write < -1)
{
perror("Error in writing");
return errno;
}
else if(bytes_write < 56)
{
fprintf(stderr, "less bytes written");
return 9999;
}
......@@ -258,10 +260,12 @@ int gridformat_writer(char* name, void* src)
if(bytes_write < -1)
{
perror("Error in writing");
return errno;
}
else if(bytes_write < len)
{
fprintf(stderr, "less bytes written");
return 9999;
}
......@@ -271,10 +275,12 @@ int gridformat_writer(char* name, void* src)
if(bytes_write < -1)
{
perror("Error in writing");
return errno;
}
else if(bytes_write < len)
{
fprintf(stderr, "less bytes written");
return 9999;
}
......@@ -285,10 +291,12 @@ int gridformat_writer(char* name, void* src)
bytes_write = write(fildes, buff, len);
if(bytes_write < -1)
{
perror("Error in writing");
return errno;
}
else if(bytes_write < len)
{
fprintf(stderr, "less bytes written");
return 9999;
}
......@@ -299,10 +307,12 @@ int gridformat_writer(char* name, void* src)
bytes_write = write(fildes, buff, len);
if(bytes_write < -1)
{
perror("Error in writing");
return errno;
}
else if(bytes_write < len)
{
fprintf(stderr, "less bytes written");
return 9999;
}
......@@ -311,10 +321,12 @@ int gridformat_writer(char* name, void* src)
bytes_write = write(fildes, buff, len);
if(bytes_write < -1)
{
perror("Error in writing");
return errno;
}
else if(bytes_write < len)
{
fprintf(stderr, "less bytes written");
return 9999;
}
......@@ -326,10 +338,12 @@ int gridformat_writer(char* name, void* src)
bytes_write = write(fildes, buff, len);
if(bytes_write < -1)
{
perror("Error in writing");
return errno;
}
else if(bytes_write < len)
{
fprintf(stderr, "less bytes written");
return 9999;
}
}
......@@ -340,10 +354,12 @@ int gridformat_writer(char* name, void* src)
bytes_write = write(fildes, buff, len);
if(bytes_write < -1)
{
perror("Error in writing");
return errno;
}
else if(bytes_write < len)
{
fprintf(stderr, "less bytes written");
return 9999;
}
}
......@@ -354,10 +370,12 @@ int gridformat_writer(char* name, void* src)
bytes_write = write(fildes, buff, len);
if(bytes_write < -1)
{
perror("Error in writing");
return errno;
}
else if(bytes_write < len)
{
fprintf(stderr, "less bytes written");
return 9999;
}
}
......@@ -583,3 +601,70 @@ void sum_grids(void* dest, int num, void** src)
out->data[idx] += in[i]->data[idx];
}
}
void pad_grid(void** g, int nx, int ny, int nz)
{
grid* src = (grid*)(*g);
int old_nx = get_nx(src);
int old_ny = get_ny(src);
int old_nz = get_nz(src);
if(nx < old_nx || ny < old_ny || nz < old_nz)
{
fprintf(stderr, "New grid dimension is smaller than old one, use slice function\n");
return;
}
grid* dest = create_new_grid(nx, ny, nz, get_grid_origin(src), get_grid_basis(src));
for(int i = 0; i < old_nx; ++i)
{
for(int j = 0; j < old_ny; ++j)
{
for(int k = 0; k < old_nz; ++k)
{
int old = k + old_nz * ( j + old_ny * i);
int new = k+(nz-old_nz)/2 + nz * ( j + (ny-old_ny)/2 + ny * (i +(nx-old_nx)/2));
(get_grid_data(dest))[new] = (get_grid_data(src))[old];
}
}
}
grid_destroy(src);
*g = dest;
}
void slice_grid(void** g, int nx, int ny, int nz)
{
grid* src = (grid*)(*g);
int old_nx = get_nx(src);
int old_ny = get_ny(src);
int old_nz = get_nz(src);
if(nx > old_nx || ny > old_ny || nz > old_nz)
{
fprintf(stderr, "New grid dimension is bigger than old one, use pad function\n");
return;
}
grid* dest = create_new_grid(nx, ny, nz, get_grid_origin(src), get_grid_basis(src));
int i0 = (old_nx-nx)/2;
int i1 = i0 + nx;
int j0 = (old_ny-ny)/2;
int j1 = j0 + ny;
int k0 = (old_nz-nz)/2;
int k1 = k0 + nz;
for(int i = i0; i < i1; ++i)
{
for(int j = j0; j < j1; ++j)
{
for(int k = k0; k < k1; ++k)
{
int old = k + old_nz * ( j + old_ny * i);
int new = k+(nz-old_nz)/2 + nz * ( j + (ny-old_ny)/2 + ny * (i +(nx-old_nx)/2));
(get_grid_data(dest))[new] = (get_grid_data(src))[old];
}
}
}
grid_destroy(src);
*g = dest;
}
Makefile
+ 19
− 7
View file @ 9fc89eea
CC=gcc
INC=-I/usr/include -I./inc
ifeq ($(dbg),1)
CFLAGS=-std=c99 -g -Og -Wall -Wextra
CFLAGS= -std=c99 -D_GNU_SOURCE -g -Og -Wall -Wextra -lm
else
CFLAGS=-std=c99 -O3 -Wall -Wextra
CFLAGS= -std=c99 -D_GNU_SOURCE -O3 -Wall -Wextra -lm
endif
CLIB=-lfftw3 -lm
OBJ=main.o GridDxFormat/grid_reader.o Kernel/debye_huckel_kernel.o LinkList/link_list.o fftw/fftw.o Kernel/lenard_jones_kernel.o
CLIB=-lfftw3
OBJ=main.o GridDxFormat/grid_reader.o Kernel/debye_huckel_kernel.o Kernel/lenard_jones_repulsion_kernel.o Kernel/lenard_jones_trunc_kernel.o LinkList/link_list.o fftw/fftw.o Kernel/lenard_jones_kernel.o
ifeq ($(dbg),1)
EXE=gen_pot-dbg
else
EXE=gen_pot
endif
all: ${EXE}
EXE_SUM=sum_grid
all: ${EXE} ${EXE_SUM}
${EXE}:${OBJ}
${CC} ${CFLAGS} ${INC} ${OBJ} -o ${EXE} ${CLIB}
${EXE_SUM}: sum.o GridDxFormat/grid_reader.o
${CC} ${CFLAGS} ${INC} sum.o GridDxFormat/grid_reader.o -o ${EXE_SUM}
main.o: main.c
${CC} ${CFLAGS} ${INC} -c main.c -o main.o
sum.o: sum.c
${CC} ${CFLAGS} ${INC} -c sum.c -o sum.o
GridDxFormat/grid_reader.o: GridDxFormat/grid_reader.c
${CC} ${CFLAGS} ${INC} -c GridDxFormat/grid_reader.c -o GridDxFormat/grid_reader.o
......@@ -30,6 +36,12 @@ Kernel/debye_huckel_kernel.o:Kernel/debye_huckel_kernel.c
Kernel/lenard_jones_kernel.o:Kernel/lenard_jones_kernel.c
${CC} ${CFLAGS} ${INC} -c Kernel/lenard_jones_kernel.c -o Kernel/lenard_jones_kernel.o
Kernel/lenard_jones_trunc_kernel.o:Kernel/lenard_jones_trunc_kernel.c
${CC} ${CFLAGS} ${INC} -c Kernel/lenard_jones_trunc_kernel.c -o Kernel/lenard_jones_trunc_kernel.o
Kernel/lenard_jones_repulsion_kernel.o:Kernel/lenard_jones_repulsion_kernel.c
${CC} ${CFLAGS} ${INC} -c Kernel/lenard_jones_repulsion_kernel.c -o Kernel/lenard_jones_repulsion_kernel.o
LinkList/link_list.o:LinkList/link_list.c
${CC} ${CFLAGS} ${INC} -c LinkList/link_list.c -o LinkList/link_list.o
......@@ -37,4 +49,4 @@ fftw/fftw.o:fftw/fftw.c
${CC} ${CFLAGS} ${INC} -c fftw/fftw.c -o fftw/fftw.o
clean:
rm -f ${OBJ} ${EXE}
rm -f ${OBJ} ${EXE} ${EXE_SUM}
inc/grid_reader.h
+ 2
− 0
View file @ 9fc89eea
......@@ -18,4 +18,6 @@ typedef double (*compute_type)(size_t,size_t,size_t,double*,double**, void*);
void set_grid_data(void* src, compute_type compute, void* kernel);
void* resample_grid_data(void* src);
void sum_grids(void* dest, int num, void** src);
void pad_grid(void** g, int nx, int ny, int nz);
void slice_grid(void** g, int nx, int ny, int nz);
#endif
inc/kernel.h
+ 2
− 0
View file @ 9fc89eea
......@@ -5,3 +5,5 @@ typedef void (*destroy_type)(char*);
#endif
#include "debye_huckel_kernel.h"
#include "lenard_jones_kernel.h"
#include "lenard_jones_trunc_kernel.h"
#include "lenard_jones_repulsion_kernel.h"
main.c
+ 0
− 3
View file @ 9fc89eea
......@@ -91,9 +91,6 @@ int main(int argc, char** argv)
compute_type functor = find_list(compute_map, kernel_name);
set_grid_data(potential, functor, kernel);
//gridformat_writer("kernel.dx", potential);
//shift_zero_frequency(get_nx(density), get_ny(density), get_nz(density), get_grid_data(density));
//shift_zero_frequency(get_nx(potential), get_ny(potential), get_nz(potential), get_grid_data(potential));
fftw_complex* density_out, *potential_out;
fftw_plan plan1, plan2;
......
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