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xjw040金蟲 (正式寫手)
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[求助]
在Lammps中安裝xmovie工具時(shí)，Makefile文件怎么修改X庫(kù)路徑
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| 在Lammps中安裝xmovie工具時(shí)，Makefile文件怎么修改X庫(kù)路徑，謝謝 |
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xjw040
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送鮮花一朵 |
不好意思，又要麻煩你了。 xuejunwei@xuejunwei-VirtualBox:~/software/lammps-11Jan12/tools/xmovie$ make gcc -c -O2 -finline-functions -g -DMISSINGDEFS -D_POSIX_SOURCE -DUSEPRIVATE -DINCL_FLOAT -Wimplicit -Wunused -Wmissing-prototypes version.c gcc -o xmovie -O2 -finline-functions -g version.o xmovie.o control.o scene.o read.o hpsort.o -L/usr/X11R6/lib -lX11 -lXaw -lXt -lXext -lXmu -lXpm read.o: In function `get_positions': /home/xuejunwei/software/lammps-11Jan12/tools/xmovie/read.c:533: undefined reference to `fmod' /home/xuejunwei/software/lammps-11Jan12/tools/xmovie/read.c:526: undefined reference to `fmod' /home/xuejunwei/software/lammps-11Jan12/tools/xmovie/read.c:535: undefined reference to `fmod' /home/xuejunwei/software/lammps-11Jan12/tools/xmovie/read.c:528: undefined reference to `fmod' /home/xuejunwei/software/lammps-11Jan12/tools/xmovie/read.c:524: undefined reference to `fmod' read.o:/home/xuejunwei/software/lammps-11Jan12/tools/xmovie/read.c:530: more undefined references to `fmod' follow collect2: ld 返回 1 make: *** [xmovie] 錯(cuò)誤 1 改了Makefile之后出現(xiàn)這樣的問(wèn)題。 |
3樓2012-03-08 13:43:53
chaonie
銅蟲 (初入文壇)
- 應(yīng)助: 2 (幼兒園)
- 金幣: 59.5
- 帖子: 11
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- 蟲號(hào): 1638734
- 注冊(cè): 2012-02-24
【答案】應(yīng)助回帖
★ ★ ★ ★ ★ ★ ★ ★
感謝參與，應(yīng)助指數(shù) +1
jiaoyixiong(金幣+3): 鼓勵(lì)交流 2012-03-07 07:56:37
xjw040(金幣+5): ★有幫助 謝謝您的熱情幫助！ 2012-03-08 13:42:12
感謝參與，應(yīng)助指數(shù) +1
jiaoyixiong(金幣+3): 鼓勵(lì)交流 2012-03-07 07:56:37
xjw040(金幣+5): ★有幫助 謝謝您的熱情幫助！ 2012-03-08 13:42:12
|
我大概記得我當(dāng)初是把Makefile離得什么東西給改了，然后就可以make了， 這是我的Makefile， 貌似是出事文件某一個(gè)地方?jīng)]有寫全，所以沒(méi)辦法運(yùn)行。 CC = gcc LN = gcc OPTIM = -O2 -finline-functions -g XLIBDIR = -L/usr/X11R6/lib XINCLUDE = DEFINES = -DMISSINGDEFS -D_POSIX_SOURCE -DUSEPRIVATE -DINCL_FLOAT WARNS = -Wimplicit -Wunused -Wmissing-prototypes CCOPTS = -c $(OPTIM) $(DEFINES) $(WARNS) $(XINCLUDE) LNOPTS = $(OPTIM) #LIBS = $(XLIBDIR) -lX11 -lXaw -lm # try this version on a Mac LIBS = $(XLIBDIR) -lX11 -lXaw -lXt -lXext -lXmu -lXpm OBJS = xmovie.o \ control.o \ scene.o \ read.o \ hpsort.o EXES = xmovie dummy tobinary toascii .c.o: $(CC) $(CCOPTS) $*.c xmovie: $(OBJS) $(CC) $(CCOPTS) version.c $(LN) -o xmovie $(LNOPTS) version.o $(OBJS) $(LIBS) xmovie.o: xmovie.h resource.h xmovie.c control.o: xmovie.h control.c scene.o: xmovie.h scene.c read.o: xmovie.h read.c hpsort.o: hpsort.c clean: rm -f *.o *~ $(EXES) tar: tar cvf xmovie.tar Makefile *.c *.h compress xmovie.tar uuencode xmovie.tar.Z xmovie.tar.Z > xmovie.tar.Z.uu clean_obj: rm -f *.o all: $(EXES) dummy: dummy.o $(LN) $(LNOPTS) -o dummy dummy.o -lm dummy.o: dummy.c toascii: toascii.o $(LN) $(LNOPTS) -o toascii toascii.o toascii.o: toascii.c tobinary: tobinary.o $(LN) $(LNOPTS) -o tobinary tobinary.o tobinary.o: tobinary.c |
2樓2012-03-07 01:32:44
chaonie
銅蟲 (初入文壇)
- 應(yīng)助: 2 (幼兒園)
- 金幣: 59.5
- 帖子: 11
- 在線: 3.4小時(shí)
- 蟲號(hào): 1638734
- 注冊(cè): 2012-02-24
【答案】應(yīng)助回帖
★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★ ★
jiaoyixiong(金幣+3): 鼓勵(lì)交流 2012-03-09 07:48:34
xjw040(金幣+15): ★★★很有幫助 太感謝了�。�！ 2012-03-09 11:39:35
jiaoyixiong(金幣+3): 鼓勵(lì)交流 2012-03-09 07:48:34
xjw040(金幣+15): ★★★很有幫助 太感謝了�。�！ 2012-03-09 11:39:35
|
/* **************************************************************** */ /* functions to read data from files */ #include #include #include #include #include /* commented this out for SGI gcc compiler #ifdef INCL_FLOAT double strtod(char *s, char **t); long strtol(char *s, char **t, int base); #endif */ #include extern FILE *popen(const char *, const char *); extern int pclose(FILE *); #include "xmovie.h" #define LINELEN 256 #define WHITESPACE " \f\n\r\t\v" #define SEPARATORS ",;:" WHITESPACE #define NPRINT 500 #define NREAD 50 #define NBREAD 2000 #define ERROR -1 #define END_OF_FILE 1 #define BEING_NICE 2 #define READ_OK 3 #define LOOK_FOR_ITEM 10 #define LOOK_FOR_BOUNDS 11 #define LOOK_FOR_POSITIONS 12 #define LOOK_FOR_TIME 13 #define LOOK_FOR_BONDS 14 #define BAD_STATE -2 #define ALL_DONE TRUE #define MORE_TO_READ FALSE /* **************************************************************** */ /* local typedefs */ typedef struct { char *string; int state; } PARSETABLE; #define NPARSE(x) (sizeof(x)/sizeof(PARSETABLE)) typedef struct { int nfiles; char **fnames; FILE *file; int in_read; int is_compressed; int is_binary; } READDATA; typedef int (*PFI)(); typedef struct { RECORD record_id; PFI reader; } READER; /* **************************************************************** */ /* local prototypes */ PRIVATE int DoSomeReading(void); PRIVATE int ReadSomeBinary(void); PRIVATE int parser(char *token, PARSETABLE *table, int cnt); PRIVATE int get_bounds(FILE *file, char *line); PRIVATE int get_positions(FILE *file, char *line); PRIVATE int get_time(FILE *file, char *line); PRIVATE int get_bonds(FILE *file, char *line); PRIVATE int copy_bonds(void); PRIVATE void add_point(int index, int type, float x, float y, float z); PRIVATE void add_bond(int type, int index1, int index2); PRIVATE void NewData(void); PRIVATE void ShowStatus(void); PRIVATE char *RemoveNL(char *s); PRIVATE int getline(FILE *file, char *line); PRIVATE int get_float(char **s, float *f); PRIVATE int get_int(char **s, int *i); PRIVATE void ungetline(void); PRIVATE int LineIsBlank(char *s); PRIVATE void SortData(DATA *dptr); PRIVATE int compare_atypes(POSITION *a, POSITION *b); PRIVATE int compare_btypes(BOND *a, BOND *b); PRIVATE int IsCompressed(char *s); PRIVATE int IsBinary(char *s); PRIVATE int TestBinary(FILE *f, int rewind); PRIVATE FILE *GetCompressed(char *s); PRIVATE FILE *OpenFile(char *s, int compressed, int binary); PRIVATE READER *GetReader(RECORD record_id); PRIVATE int ReadTime(FILE *f, LENGTH length); PRIVATE int ReadBound(FILE *f, LENGTH length); PRIVATE int ReadPosition(FILE *f, LENGTH length); PRIVATE int ReadBond(FILE *f, LENGTH length); PRIVATE int CopyBond(FILE *f, LENGTH length); PRIVATE int ReadRecordHeader(FILE *f, RECORD *record, LENGTH *length); /* **************************************************************** */ /* local data */ /* include last 3 out-of-date item names in PARSETABLE for compatability */ static PARSETABLE parse_table[] = { { "TIMESTEP", LOOK_FOR_TIME }, { "BOX BOUNDS", LOOK_FOR_BOUNDS }, { "ATOMS", LOOK_FOR_POSITIONS }, { "BONDS", LOOK_FOR_BONDS }, { "TIME", LOOK_FOR_TIME }, { "BOUNDS", LOOK_FOR_BOUNDS }, { "POSITIONS", LOOK_FOR_POSITIONS }, }; static DATA *current_data = (DATA *) NULL; static int seen_time = 0; static int npositions = 0; static int nlines = 0; static int nbonds = 0; static int read_this_time = 0; static READDATA ReadData = { 0, /* nfiles */ NULL, /* filenames */ NULL, /* file pointer */ 0, /* not in read */ 0, /* not compressed */ 0, /* not binary */ }; static READER read_table[] = { { TimeID, ReadTime }, { BoundID, ReadBound }, { PositionID, ReadPosition }, { BondID, ReadBond }, { CopyBondID, CopyBond }, }; /* **************************************************************** */ void InitRead(int nfiles, char **fnames) { static char *Stdin = "stdin"; if (nfiles > 0) { ReadData.nfiles = nfiles; ReadData.fnames = fnames; return; } if (isatty(fileno(stdin))) { Usage(); exit(0); } ReadData.nfiles = 1; ReadData.fnames = &Stdin; ReadData.file = stdin; ReadData.in_read = 1; ReadData.is_binary = TestBinary(stdin, TRUE); if (ReadData.is_binary) fseek(stdin, 2*sizeof(INT4), SEEK_CUR); /* skip header */ } Boolean ReadProc(XtPointer client_data) { char err_msg[512]; char *file_type; if (ReadData.in_read) goto do_read; next_file: if (ReadData.nfiles <= 0) { ShowStatus(); SortData(current_data); return(ALL_DONE); } ReadData.is_compressed = FALSE; ReadData.is_binary = FALSE; ReadData.is_compressed = IsCompressed(*ReadData.fnames); if (ReadData.is_compressed) { file_type = "compressed"; goto open_file; } ReadData.is_binary = IsBinary(*ReadData.fnames); if (ReadData.is_binary) { file_type = "binary"; goto open_file; } file_type = "ascii"; goto open_file; open_file: ReadData.file = OpenFile(*ReadData.fnames, ReadData.is_compressed, ReadData.is_binary); if (ReadData.file == (FILE *) NULL) { sprintf(err_msg, "Frames: %i Positions: %i Bonds: %i\n" "Error: unable to open %s file \"%s\".\n" "Read aborted.", Common.ndata, npositions, nbonds, file_type, *ReadData.fnames); SetReadString(err_msg); SortData(current_data); return(ALL_DONE); } ReadData.in_read = 1; nlines = 0; ShowStatus(); do_read: switch(DoSomeReading()) { case END_OF_FILE: if (ReadData.is_compressed) pclose(ReadData.file); else if (strcmp("stdin",*ReadData.fnames)) fclose(ReadData.file); ReadData.in_read = 0; ReadData.nfiles--; ReadData.fnames++; goto next_file; case ERROR: SortData(current_data); return(ALL_DONE); case BEING_NICE: break; default: fprintf(stderr,"Don't know how I got here: ReadProc.\n"  ;exit(0); } return(MORE_TO_READ); } PRIVATE int IsCompressed(char *s) { register char *t; t = s + strlen(s) - 3; if (t < s) return(FALSE); return(!strcmp(t,".gz" );} PRIVATE int IsBinary(char *s) { FILE *f; int ok; if ((FILE *) NULL == (f = fopen(s, "r" )) return(FALSE);ok = TestBinary(f, FALSE); fclose(f); return(ok); } PRIVATE int TestBinary(FILE *f, int rewind) { union { INT4 magic; char c[sizeof(INT4)]; } u; int i; if (1 != fread(&u.magic, sizeof(u.magic), 1, f)) return(FALSE); if (rewind) for(i = sizeof(u); i; i--) ungetc(u.c[i-1], f); return(u.magic == MagicNumber); } PRIVATE FILE *GetCompressed(char *name) { char cmd[256]; sprintf(cmd, "gunzip -c %s", name); return(popen(cmd,"r" );} PRIVATE FILE *OpenFile(char *name, int compressed, int binary) { FILE *f; if (compressed) return(GetCompressed(name)); f = fopen(name, "r" ;if (f == (FILE *) NULL) return(f); if (binary) fseek(f, 2*sizeof(INT4), SEEK_CUR); return(f); } PRIVATE int DoSomeReading(void) { static int state = LOOK_FOR_ITEM; static char line[LINELEN]; static char token[LINELEN]; static char *t; int ntries; int newstate; char err_msg[512]; if (ReadData.is_binary) return(ReadSomeBinary()); read_this_time = 0; begin: switch(state) { case LOOK_FOR_ITEM: ntries = 0; while(1) { ntries++; if (ntries > 100) return(BEING_NICE); if (!getline(ReadData.file, line)) return(END_OF_FILE); t = strtok(line, WHITESPACE); if (!t) continue; if (strcmp(t, "ITEM:" ) continue;t = strtok(NULL, WHITESPACE); if (!t) continue; sprintf(token,"%s",t); t = strtok(NULL, WHITESPACE); while (t != NULL) { sprintf(token,"%s %s",token,t); t = strtok(NULL, WHITESPACE); } newstate = parser(token, parse_table,NPARSE(parse_table)); if (newstate == BAD_STATE) continue; state = newstate; goto begin; } case LOOK_FOR_TIME: if (!get_time(ReadData.file, line)) goto print_error; state = LOOK_FOR_ITEM; goto begin; case LOOK_FOR_BOUNDS: if (!get_bounds(ReadData.file, line)) goto print_error; state = LOOK_FOR_ITEM; goto begin; case LOOK_FOR_POSITIONS: case LOOK_FOR_BONDS: switch((state == LOOK_FOR_POSITIONS) ? get_positions(ReadData.file, line) : get_bonds(ReadData.file, line)) { case END_OF_FILE: state = LOOK_FOR_ITEM; return(END_OF_FILE); case BEING_NICE: return(BEING_NICE); case LOOK_FOR_ITEM: state = LOOK_FOR_ITEM; return(BEING_NICE); case ERROR: default: goto print_error; } case BAD_STATE: default: fprintf(stderr,"Error: read state corrupted: %i\n", state); exit(0); } print_error: sprintf(err_msg,"Frames: %i Positions: %i Bonds: %i\n" "Error occurred at line %i\n" "Processing ITEM: %s\n" "Line = \"%s\"\n" "Read aborted.", Common.ndata, npositions, nbonds, nlines, token, RemoveNL(line)); SetReadString(err_msg); return(ERROR); /* exit(0); */ } /* **************************************************************** */ PRIVATE int parser(char *token, PARSETABLE *table, int cnt) { PARSETABLE *t; int i; for(i = cnt, t = table; i; i--, t++) if (strstr(token,t->string) == token) return t->state; return(BAD_STATE); } /* **************************************************************** */ PRIVATE int get_bounds(FILE *file, char *line) { int i, n, changed; char *t; BOUND *b, *cb; if (!current_data) NewData(); n = (Common.two_d) ? 2 : 3; for(i = 0; i < n; i++){ if (!getline(file, line)) return(0); t = line; if (!get_float(&t, &(current_data->bounds.low))) return(0); if (!get_float(&t, &(current_data->bounds.high))) return(0); } if (Common.two_d) { current_data->bounds[2].low = -0.01; current_data->bounds[2].high = 0.01; } changed = 0; for(b=current_data->bounds,cb=Common.bounds,i=3; i;i--,b++,cb++){ if (b->low < cb->low) { cb->low = b->low; changed = 1; } if (b->high > cb->high) { cb->high = b->high; changed = 1; } } if (changed) NewDataSetup(); return(1); } PRIVATE int get_positions(FILE *file, char *line) { char *t; float x, y, z; float xlow,xhigh,ylow,yhigh,zlow,zhigh,dx,dy,dz; int index, type; if (!current_data) NewData(); if (Common.copy_bond) copy_bonds(); if (Common.remap || Common.scaleflag) { xlow = current_data->bounds[0].low; xhigh = current_data->bounds[0].high; dx = xhigh - xlow; ylow = current_data->bounds[1].low; yhigh = current_data->bounds[1].high; dy = yhigh - ylow; if (!Common.two_d) { zlow = current_data->bounds[2].low; zhigh = current_data->bounds[2].high; dz = zhigh - zlow; } } z = 0.0; while(1) { if (read_this_time++ > NREAD) return(BEING_NICE); if (!getline(file, line)) return(END_OF_FILE); t = line; if (!get_int(&t, &index)){ ungetline(); return(LOOK_FOR_ITEM); } if (!get_int(&t, &type)) return(ERROR); if (!get_float(&t, &x)) return(ERROR); if (!get_float(&t, &y)) return(ERROR); if (!Common.two_d) if (!get_float(&t, &z)) return(ERROR); if (type < 1 || type > Common.natomcolors) type = 1; if (Common.remap) { if (x-xlow >= 0.0) x = fmod(x-xlow,dx) + xlow; else x = xhigh + fmod(x-xlow,dx); if (y-ylow >= 0.0) y = fmod(y-ylow,dy) + ylow; else y = yhigh + fmod(y-ylow,dy); if (!Common.two_d) { if (z-zlow >= 0.0) z = fmod(z-zlow,dz) + zlow; else z = zhigh + fmod(z-zlow,dz); } } if (Common.scaleflag) { x = xlow + x*dx; y = ylow + y*dy; if (!Common.two_d) z = zlow + z*dz; } add_point(index, type, x, y, z); npositions++; if ((nbonds + npositions) % NPRINT == 0) ShowStatus(); } return(1); } PRIVATE int get_bonds(FILE *file, char *line) { char *t; int type, index1, index2; if (!current_data) NewData(); while(1) { if (read_this_time++ > NREAD) return(BEING_NICE); if (!getline(file, line)) return(END_OF_FILE); t = line; if (!get_int(&t, &type)){ ungetline(); return(LOOK_FOR_ITEM); } if (!get_int(&t, &index1)) return(ERROR); if (!get_int(&t, &index2)) return(ERROR); if (type < 1 || type > Common.nbondcolors) type = 1; add_bond(type, index1, index2); nbonds++; if ((nbonds + npositions) % NPRINT == 0) ShowStatus(); } return(1); } PRIVATE int get_time(FILE *file, char *line) { char *t; if (!current_data || seen_time) NewData(); seen_time = 1; if (!getline(file, line)) return(0); t = line; if (!get_float(&t, &(current_data->time))) return(0); return(1); } PRIVATE int copy_bonds() { DATA *last_data; int i; BOND *b1, *b2; if (Common.ndata < 2) return(0); last_data = current_data-1; current_data->nbonds = last_data->nbonds; current_data->maxbonds = last_data->maxbonds; current_data->bonds = (BOND *) XtMalloc(current_data->maxbonds * sizeof(BOND)); b1 = current_data->bonds; b2 = last_data->bonds; for(i = current_data->nbonds; i ; i--, b1++, b2++) *b1 = *b2; return(1); } /* **************************************************************** */ PRIVATE char *RemoveNL(char *s) { register char *t; if (!s) return(s); if ((t = s + strlen(s) - 1) < s) return(s); if (*t == '\n') *t = '\0'; return(s); } static int got_line = 0; PRIVATE int getline(FILE *file, char *line) { int result; if (got_line) { got_line = 0; return(1); } do { nlines++; result = (fgets(line, LINELEN, file) != NULL); } while( result && LineIsBlank(line) ); return(result); } PRIVATE void ungetline(void) { got_line = 1; } PRIVATE int LineIsBlank(char *s) { register char *t; t = s + strspn(s, WHITESPACE); return( *t == '\0' ); } PRIVATE int get_int(char **s, int *i) { register char *t; t = *s + strspn(*s, SEPARATORS); *i = strtol(t, s, 10); return(t != *s); } PRIVATE int get_float(char **s, float *f) { register char *t; t = *s + strspn(*s, SEPARATORS); *f = strtod(t, s); return(t != *s); } /* **************************************************************** */ PRIVATE void NewData(void) { int i; DATA *last_data,*olddataptr; olddataptr = Common.dataptr; last_data = current_data; if (Common.ndata >= Common.maxdata) { /* need to realloc */ Common.maxdata += 256; Common.dataptr = (DATA *) XtMalloc(Common.maxdata * sizeof(DATA)); memcpy(Common.dataptr,olddataptr,Common.ndata*sizeof(DATA)); } current_data = Common.dataptr + Common.ndata; Common.ndata++; current_data->natypes = (INT4 *) XtMalloc(Common.natomcolors * sizeof(INT4)); for(i = 0; i < Common.natomcolors; i++) current_data->natypes = 0; current_data->nbtypes = (INT4 *) XtMalloc(Common.nbondcolors * sizeof(INT4)); for(i = 0; i < Common.nbondcolors; i++) current_data->nbtypes = 0; if (Common.ndata > 1) { current_data->time = last_data->time; for(i = 0; i < 3; i++) current_data->bounds = last_data->bounds; current_data->maxatoms = last_data->natoms; current_data->positions = (POSITION *) XtMalloc(last_data->natoms * sizeof(POSITION)); current_data->natoms = 0; current_data->maxbonds = last_data->nbonds; current_data->bonds = (BOND *) XtMalloc(last_data->nbonds * sizeof(BOND)); current_data->nbonds = 0; SortData(last_data); } else { current_data->time = 0.0; for(i = 0; i < 3; i++) { current_data->bounds.low = -1.0; current_data->bounds.high = 1.0; } current_data->natoms = 0; current_data->positions = NULL; current_data->maxatoms = 0; current_data->nbonds = 0; current_data->bonds = NULL; current_data->maxbonds = 0; } if (olddataptr != Common.dataptr) XtFree((char *) olddataptr); } PRIVATE void add_point(int index, int type, float x, float y, float z) { POSITION *p; if (current_data->natoms >= current_data->maxatoms) { current_data->maxatoms += 16; current_data->positions = (POSITION *) XtRealloc((char *) current_data->positions, current_data->maxatoms * sizeof(POSITION)); } p = &(current_data->positions[current_data->natoms]); p->index = index; p->type = type; p->x = x; p->y = y; p->z = z; current_data->natoms++; } PRIVATE void add_bond(int type, int index1, int index2) { BOND *b; if (current_data->nbonds >= current_data->maxbonds) { current_data->maxbonds += 16; current_data->bonds = (BOND *) XtRealloc((char *) current_data->bonds, current_data->maxbonds * sizeof(BOND)); } b = &(current_data->bonds[current_data->nbonds]); b->type = type; b->index1 = index1; b->index2 = index2; b->atom1 = NULL; b->atom2 = NULL; current_data->nbonds++; } PRIVATE void ShowStatus(void) { static char buffer[256]; if (ReadData.in_read) sprintf(buffer, "Reading file: %s\n" "Frames: %i Positions: %i Bonds: %i", *ReadData.fnames, Common.ndata, npositions, nbonds); else sprintf(buffer, "Reading done.\n" "Frames: %i Positions: %i Bonds %i", Common.ndata, npositions, nbonds); SetReadString(buffer); } /* **************************************************************** */ PRIVATE void SortData(DATA *dptr) { POSITION *p, **p_by_index, **pp; register int i, j; int maxindex, minindex, nindex, n; register BOND *b, *b2; float bond_length, shortest, dx, dy, dz; /* add hpsort in place of standard C qsort, which is very slow when atoms or bonds are already in order (N^2 instead of NlnN) calling syntax does not change except for first argument becomes arg-1, qsort -> hpsort in 2 places */ void hpsort(POSITION *, int, int, int (*)(POSITION *, POSITION *)); if (!dptr) return; /* sort by type */ hpsort((dptr->positions)-1, dptr->natoms, sizeof(POSITION), compare_atypes); /* find out how many of each type */ for(i = dptr->natoms, p = dptr->positions; i ;i--, p++) dptr->natypes[p->type-1]++; if (dptr->nbonds < 1) return; /* find max, min indicies */ minindex = 1000000000; maxindex = -minindex; for(i = dptr->natoms, p = dptr->positions; i; i--, p++) { if (p->index > maxindex) maxindex = p->index; if (p->index < minindex) minindex = p->index; } nindex = maxindex - minindex + 1; if (nindex < 0) { dptr->nbonds = 0; return; } if (nindex < 1000000) { p_by_index = (POSITION **) XtMalloc(nindex*sizeof(POSITION *)); for(pp = p_by_index, i = nindex; i; i--, pp++) *pp = (POSITION *) NULL; for(p = dptr->positions, i = dptr->natoms; i; i--, p++){ pp = p_by_index + p->index - minindex; if (*pp != (POSITION *) NULL) { fprintf(stderr, "Error: atom %i has more than one position at time %g.\n", p->index, dptr->time); exit(EXIT_FAILURE); } *pp = p; } for(b = dptr->bonds, i = dptr->nbonds; i ; i--, b++) { b->atom1 = p_by_index[b->index1 - minindex]; b->atom2 = p_by_index[b->index2 - minindex]; if (b->atom1 == (POSITION *) NULL) { fprintf(stderr, "Error: atom %d has no position at time %g.\n", b->index1, dptr->time); exit(EXIT_FAILURE); } if (b->atom2 == (POSITION *) NULL) { fprintf(stderr, "Error: atom %d has no position at time %g.\n", b->index2, dptr->time); exit(EXIT_FAILURE); } } XtFree((char *) p_by_index); } else { for(b = dptr->bonds, i = dptr->nbonds; i; i--, b++) { for(p = dptr->positions, j = dptr->natoms; j; j--, p++) if (b->index1 == p->index) { b->atom1 = p; break; } if (j < 1) { fprintf(stderr, "Error: atom %i has no position at time %g.\n", b->index1, dptr->time); exit(EXIT_FAILURE); } for(p = dptr->positions, j = dptr->natoms; j; j--, p++) if (b->index2 == p->index) { b->atom2 = p; break; } if (j < 1) { fprintf(stderr, "Error: atom %i has no position at time %g.\n", b->index2, dptr->time); exit(EXIT_FAILURE); } } } /* throw out bonds longer than half the shortest cell size */ /* only do if periodic-bond switch is set */ if (Common.pbc_bond) { n = (Common.two_d) ? 2 : 3; shortest = 1e30; for(i = 0; i < n; i++){ bond_length = dptr->bounds.high - dptr->bounds.low; if (bond_length < shortest) shortest = bond_length; } shortest *= 0.5; shortest *= shortest; b = dptr->bonds; b2 = b; for(i = dptr->nbonds; i; i--, b++) { dx = b->atom1->x - b->atom2->x; dy = b->atom1->y - b->atom2->y; dz = b->atom1->z - b->atom2->z; bond_length = dx*dx + dy*dy + dz*dz; if (bond_length < shortest) { if (b2 != b) *b2 = *b; b2++; } } dptr->nbonds -= b - b2; } /* sort by type */ hpsort((dptr->bonds)-1, dptr->nbonds, sizeof(BOND), compare_btypes); /* find out how many of each type */ for(b = dptr->bonds, i = dptr->nbonds; i; i--, b++) dptr->nbtypes[b->type-1]++; } PRIVATE int compare_atypes(POSITION *a, POSITION *b) { if (a->type > b->type) return(1); if (a->type == b->type) return(0); if (a->type < b->type) return(-1); } PRIVATE int compare_btypes(BOND *a, BOND *b) { if (a->type > b->type) return(1); if (a->type == b->type) return(0); if (a->type < b->type) return(-1); } /* routine to print out all data for debugging */ #if 0 print_them(void) { int i; for(i = 0; i < Common.ndata; i++) print_data(Common.dataptr); } print_data(DATA *data) { int i; POSITION *p; fprintf(stderr,"Time: %f\n", data->time); for(i = 0; i < 3; i++) fprintf(stderr,"Bounds %i: %f %f\n", i, data->bounds.low, data->bounds.high); for(i = 0; i < data->natoms; i++) { p = &(data->positions); fprintf(stderr,"Atom: %i %i %f %f %f\n", p->index, p->type, p->x, p->y, p->z); } } #endif /* **************************************************************** */ PRIVATE int ReadSomeBinary(void) { RECORD record_id; LENGTH length; READER *r; char err_msg[256]; int state; int old_positions, old_bonds; old_positions = npositions; old_bonds = nbonds; while(1) { if (!ReadRecordHeader(ReadData.file, &record_id, &length)) return(END_OF_FILE); r = GetReader(record_id); if (r == (READER *) NULL) { /* dont recognize */ fseek(ReadData.file, length, SEEK_CUR); continue; } switch(state = (*r->reader)(ReadData.file, length)) { case BEING_NICE: if (old_positions + old_bonds + NBREAD > nbonds + npositions) continue; return(state); case END_OF_FILE: return(state); case READ_OK: continue; case ERROR: default: sprintf(err_msg,"Frames: %i Positions: %i Bonds: %i\n" "Error occurred during binary read.\n" "Read aborted.", Common.ndata, npositions, nbonds); SetReadString(err_msg); return(ERROR); } } } PRIVATE READER *GetReader(RECORD record_id) { register int i; register READER *r; i = sizeof(read_table)/sizeof(read_table[0]); for(r = read_table; i; i--, r++) if (r->record_id == record_id) return(r); return((READER *) NULL); } PRIVATE int ReadRecordHeader(FILE *f, RECORD *record, LENGTH *length) { if (1 != fread(record, sizeof(*record), 1, f)) return(FALSE); if (1 != fread(length, sizeof(*length), 1, f)) return(FALSE); return(TRUE); } /*ARGSUSED*/ PRIVATE int ReadBound(FILE *file, LENGTH length) { int i, changed; BOUND *b, *cb; if (!current_data) NewData(); for(b = current_data->bounds, i = 3; i; i--, b++){ if (1 != fread(&(b->low), sizeof(b->low), 1, file)) return(ERROR); if (1 != fread(&(b->high), sizeof(b->high), 1, file)) return(ERROR); } changed = 0; for(b=current_data->bounds,cb=Common.bounds,i=3; i;i--,b++,cb++){ if (b->low < cb->low) { cb->low = b->low; changed = 1; } if (b->high > cb->high) { cb->high = b->high; changed = 1; } } if (changed) NewDataSetup(); return(READ_OK); } PRIVATE int ReadPosition(FILE *file, LENGTH length) { POSITION *p; int n; int i; if (!current_data) NewData(); n = length / (sizeof(p->index) + sizeof(p->type) + 3*sizeof(p->x)); if (current_data->maxatoms < n) { free(current_data->positions); current_data->maxatoms = n; current_data->positions = (POSITION *) XtMalloc(n * sizeof(POSITION)); } current_data->natoms = 0; p = current_data->positions; i = 0; for(; i < n; i++, p++) { if (1 != fread(&(p->index), sizeof(p->index), 1, file)) return(ERROR); if (1 != fread(&(p->type), sizeof(p->type), 1, file)) return(ERROR); if (1 != fread(&(p->x), sizeof(p->x), 1, file)) return(ERROR); if (1 != fread(&(p->y), sizeof(p->y), 1, file)) return(ERROR); if (1 != fread(&(p->z), sizeof(p->z), 1, file)) return(ERROR); if (p->type < 1 || p->type > Common.natomcolors) p->type = 1; npositions++; current_data->natoms++; if ((npositions + nbonds)% NPRINT == 0) ShowStatus(); } return(BEING_NICE); } PRIVATE int ReadBond(FILE *file, LENGTH length) { BOND *b; int n; int i; if (!current_data) NewData(); n = length / (sizeof(b->type) + sizeof(b->index1) + sizeof(b->index2)); if (current_data->maxbonds < n) { free(current_data->bonds); current_data->maxbonds = n; current_data->bonds = (BOND *) XtMalloc(n * sizeof(BOND)); } current_data->nbonds = 0; b = current_data->bonds; i = 0; for(; i < n; i++, b++) { if (1 != fread(&(b->type), sizeof(b->type), 1, file)) return(ERROR); if (1 != fread(&(b->index1), sizeof(b->index1), 1, file)) return(ERROR); if (1 != fread(&(b->index2), sizeof(b->index2), 1, file)) return(ERROR); if (b->type < 1 || b->type > Common.nbondcolors) b->type = 1; nbonds++; current_data->nbonds++; if ((npositions + nbonds)% NPRINT == 0) ShowStatus(); } return(BEING_NICE); } /*ARGSUSED*/ PRIVATE int CopyBond(FILE *file, LENGTH length) { return( (copy_bonds()) ? READ_OK : ERROR ); } /*ARGSUSED*/ PRIVATE int ReadTime(FILE *file, LENGTH length) { if (!current_data || seen_time) NewData(); seen_time = 1; if (1 != fread(&(current_data->time), sizeof(current_data->time), 1, file)) return(ERROR); return(READ_OK); } 這是我的read.c文件，你看看和你的有什么區(qū)別吧，呵呵，我沒(méi)有仔細(xì)研究過(guò)xmovie, 我都用vmd的， xmovie能辦到的vmd都可以，而且使用更方便，更美觀， 所以你如果還是弄不好xmovie， 那就別糾結(jié)了，換vmd吧 |
4樓2012-03-09 03:00:23
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