diff options
Diffstat (limited to 'src/compression/xtc3.c')
| -rw-r--r-- | src/compression/xtc3.c | 91 |
1 files changed, 47 insertions, 44 deletions
diff --git a/src/compression/xtc3.c b/src/compression/xtc3.c index 8c742a2..c26d7aa 100644 --- a/src/compression/xtc3.c +++ b/src/compression/xtc3.c @@ -10,9 +10,9 @@ * of the License, or (at your option) any later version. */ -/* This code is heavily influenced by +/* This code is heavily influenced by http://hpcv100.rc.rug.nl/xdrf.html - Based on coordinate compression (c) by Frans van Hoesel. + Based on coordinate compression (c) by Frans van Hoesel. and GROMACS xtc files (http://www.gromacs.org) (c) Copyright (c) Erik Lindahl, David van der Spoel */ @@ -101,9 +101,9 @@ static int unpositive_int(int val) struct xtc3_context { unsigned int *instructions; - int ninstr, ninstr_alloc; + int ninstr, ninstr_alloc; unsigned int *rle; - int nrle, nrle_alloc; + int nrle, nrle_alloc; unsigned int *large_direct; int nlargedir, nlargedir_alloc; unsigned int *large_intra_delta; @@ -117,17 +117,17 @@ struct xtc3_context int has_large_ints[MAX_LARGE_RLE*3]; /* Large cache. */ int has_large_type[MAX_LARGE_RLE]; /* What kind of type this large int is. */ - int current_large_type; + int current_large_type; }; static void init_xtc3_context(struct xtc3_context *xtc3_context) { xtc3_context->instructions=NULL; xtc3_context->ninstr=0; - xtc3_context->ninstr_alloc=0; + xtc3_context->ninstr_alloc=0; xtc3_context->rle=NULL; xtc3_context->nrle=0; - xtc3_context->nrle_alloc=0; + xtc3_context->nrle_alloc=0; xtc3_context->large_direct=NULL; xtc3_context->nlargedir=0; xtc3_context->nlargedir_alloc=0; @@ -208,7 +208,7 @@ static void insert_value_in_array(unsigned int **ptr, int *nele, int *nele_alloc allocate_enough_memory(ptr,nele,nele_alloc); #ifdef SHOWIT fprintf(stderr,"Inserting value %u into array %s @ %d\n",value,arrayname,(*nele)-1); -#endif +#endif (*ptr)[(*nele)-1]=value; } @@ -228,7 +228,7 @@ static void swapdecide(struct xtc3_context *xtc3_context, int *input,int *swapat */ #ifdef SHOWIT fprintf(stderr,"Trying Flip: %g %g\n",(double)swapped/normal, (double)normal/swapped); -#endif +#endif if (((swapped<normal) && (fabs((double)swapped/normal)<iflipgaincheck)) || ((normal<swapped) && (fabs((double)normal/swapped)<iflipgaincheck))) { @@ -291,7 +291,7 @@ static void insert_batch(int *input_ptr, int ntriplets_left, int *prevcoord, int { int nencode=startenc*3; int tmp_prevcoord[3]; - + tmp_prevcoord[0]=prevcoord[0]; tmp_prevcoord[1]=prevcoord[1]; tmp_prevcoord[2]=prevcoord[2]; @@ -313,13 +313,13 @@ static void insert_batch(int *input_ptr, int ntriplets_left, int *prevcoord, int positive_int(encode_ints[i*3]), positive_int(encode_ints[i*3+1]), positive_int(encode_ints[i*3+2])); -#endif +#endif } } #ifdef SHOWIT fprintf(stderr,"New batch\n"); -#endif +#endif while ((nencode<3+MAX_SMALL_RLE*3) && (nencode<ntriplets_left*3)) { encode_ints[nencode]=input_ptr[nencode]-tmp_prevcoord[0]; @@ -336,7 +336,7 @@ static void insert_batch(int *input_ptr, int ntriplets_left, int *prevcoord, int positive_int(encode_ints[nencode]), positive_int(encode_ints[nencode+1]), positive_int(encode_ints[nencode+2])); -#endif +#endif tmp_prevcoord[0]=input_ptr[nencode]; tmp_prevcoord[1]=input_ptr[nencode+1]; tmp_prevcoord[2]=input_ptr[nencode+2]; @@ -663,7 +663,7 @@ static void base_compress(unsigned int *data, int len, unsigned char *output, in { #ifdef SHOWIT fprintf(stderr,"Writing largeint: "); -#endif +#endif for (j=0; j<numbytes; j++) { int ilarge=j/4; @@ -671,11 +671,11 @@ static void base_compress(unsigned int *data, int len, unsigned char *output, in output[nwrittenout++]=(unsigned char)((largeint[ilarge]>>(ibyte*8))&(0xFFU)); #ifdef SHOWIT fprintf(stderr,"%02x",(unsigned int)output[nwrittenout-1]); -#endif +#endif } #ifdef SHOWIT fprintf(stderr,"\n"); -#endif +#endif nvals=0; for (j=0; j<MAXBASEVALS+1; j++) largeint[j]=0U; @@ -692,7 +692,7 @@ static void base_compress(unsigned int *data, int len, unsigned char *output, in int ilarge=j/4; int ibyte=j%4; output[nwrittenout++]=(unsigned char)((largeint[ilarge]>>(ibyte*8))&(0xFFU)); - } + } } } *outlen=nwrittenout; @@ -750,7 +750,7 @@ static void base_decompress(unsigned char *input, int len, unsigned int *output) largeint[j]=0U; #ifdef SHOWIT fprintf(stderr,"Reading largeint: "); -#endif +#endif for (j=0; j<numbytes; j++) { int ilarge=j/4; @@ -758,11 +758,11 @@ static void base_decompress(unsigned char *input, int len, unsigned int *output) largeint[ilarge]|=((unsigned int)input[j])<<(ibyte*8); #ifdef SHOWIT fprintf(stderr,"%02x",(unsigned int)input[j]); -#endif +#endif } #ifdef SHOWIT fprintf(stderr,"\n"); -#endif +#endif input+=numbytes; /* Do the long division required to get the output values. */ n=maxbasevals; @@ -800,10 +800,10 @@ static int heuristic_bwlzh(unsigned int *ints, int nints) } /* Speed selects how careful to try to find the most efficient compression. The BWLZH algo is expensive! - Speed <=2 always avoids BWLZH everywhere it is possible. + Speed <=2 always avoids BWLZH everywhere it is possible. Speed 3 and 4 and 5 use heuristics (check proportion of large value). This should mostly be safe. Speed 5 enables the LZ77 component of BWLZH. - Speed 6 always tests if BWLZH is better and if it is uses it. This can be very slow. + Speed 6 always tests if BWLZH is better and if it is uses it. This can be very slow. */ unsigned char *Ptngc_pack_array_xtc3(int *input, int *length, int natoms, int speed) { @@ -833,7 +833,7 @@ unsigned char *Ptngc_pack_array_xtc3(int *input, int *length, int natoms, int sp int bwlzh_buf_len; unsigned char *base_buf=NULL; int base_buf_len; - + struct xtc3_context xtc3_context; init_xtc3_context(&xtc3_context); @@ -852,7 +852,10 @@ unsigned char *Ptngc_pack_array_xtc3(int *input, int *length, int natoms, int sp nvalues_sum=0; #endif /* Allocate enough memory for output */ - output=warnmalloc(8* *length*sizeof *output); + if (*length < 48) + output=warnmalloc(8*48*sizeof *output); + else + output=warnmalloc(8* *length*sizeof *output); for (i=1; i<ntriplets; i++) @@ -955,7 +958,7 @@ unsigned char *Ptngc_pack_array_xtc3(int *input, int *length, int natoms, int sp /* Insert the next batch of integers to be encoded into the buffer */ #ifdef SHOWIT fprintf(stderr,"Initial batch\n"); -#endif +#endif insert_batch(input+inpdata,ntriplets_left,prevcoord,encode_ints,0,&nencode); /* First we must decide if the next value is large (does not reasonably fit in current small encoding) @@ -1044,8 +1047,8 @@ unsigned char *Ptngc_pack_array_xtc3(int *input, int *length, int natoms, int sp positive_int(encode_ints[i*3]), positive_int(encode_ints[i*3+1]), positive_int(encode_ints[i*3+2])); - -#endif + +#endif min_runlength=2; } } @@ -1076,11 +1079,11 @@ unsigned char *Ptngc_pack_array_xtc3(int *input, int *length, int natoms, int sp ntriplets_left--; refused=0; - + /* Insert the next batch of integers to be encoded into the buffer */ #ifdef SHOWIT fprintf(stderr,"Update batch due to large int.\n"); -#endif +#endif if ((swapatoms) && (didswap)) { /* Keep swapped values. */ @@ -1139,7 +1142,7 @@ unsigned char *Ptngc_pack_array_xtc3(int *input, int *length, int natoms, int sp new_runlength=1; new_small_index=small_index; } - + iter_runlength=new_runlength; iter_small_index=new_small_index; @@ -1152,7 +1155,7 @@ unsigned char *Ptngc_pack_array_xtc3(int *input, int *length, int natoms, int sp do { new_runlength=iter_runlength; new_small_index=iter_small_index; - + #ifdef SHOWIT fprintf(stderr,"Test new_small_index=%d Base=%d\n",new_small_index,Ptngc_magic(new_small_index)); #endif @@ -1205,7 +1208,7 @@ unsigned char *Ptngc_pack_array_xtc3(int *input, int *length, int natoms, int sp else if (new_runlength<6) rle_index_dep=QUITE_LARGE; if ((min_runlength) - || ((new_small_index<small_index+IS_LARGE) && (new_small_index+rle_index_dep<max_large_index)) + || ((new_small_index<small_index+IS_LARGE) && (new_small_index+rle_index_dep<max_large_index)) #if 1 || (new_small_index+IS_LARGE<max_large_index) #endif @@ -1254,7 +1257,7 @@ unsigned char *Ptngc_pack_array_xtc3(int *input, int *length, int natoms, int sp if ((new_runlength!=runlength) || (new_small_index!=small_index)) { int change=new_small_index-small_index; - + if (new_small_index<=0) change=0; @@ -1276,12 +1279,12 @@ unsigned char *Ptngc_pack_array_xtc3(int *input, int *length, int natoms, int sp rejected=0; #ifdef SHOWIT fprintf(stderr,"Tested decrease %d of index: %g>=%g?\n",change,isum,(double)Ptngc_magic(small_index+change)*(double)Ptngc_magic(small_index+change)); -#endif +#endif if (isum>(double)Ptngc_magic(small_index+change)*(double)Ptngc_magic(small_index+change)) { #ifdef SHOWIT fprintf(stderr,"Rejected decrease %d of index due to length of vector: %g>=%g\n",change,isum,(double)Ptngc_magic(small_index+change)*(double)Ptngc_magic(small_index+change)); -#endif +#endif rejected=1; change++; } @@ -1308,7 +1311,7 @@ unsigned char *Ptngc_pack_array_xtc3(int *input, int *length, int natoms, int sp } #ifdef SHOWIT fprintf(stderr,"Current small index: %d Base=%d\n",small_index,Ptngc_magic(small_index)); -#endif +#endif } /* If we have a large previous integer we can combine it with a sequence of small ints. */ if (xtc3_context.has_large) @@ -1336,14 +1339,14 @@ unsigned char *Ptngc_pack_array_xtc3(int *input, int *length, int natoms, int sp } else { - + #ifdef SHOWIT fprintf(stderr,"Sequence of one large and small integers (good compression).\n"); #endif /* Flush all large atoms but one! */ if (xtc3_context.has_large>1) flush_large(&xtc3_context,xtc3_context.has_large-1); - + /* Here we must check if we should emit a large type change instruction. */ large_instruction_change(&xtc3_context,0); @@ -1352,7 +1355,7 @@ unsigned char *Ptngc_pack_array_xtc3(int *input, int *length, int natoms, int sp &xtc3_context.ninstr, &xtc3_context.ninstr_alloc, INSTR_DEFAULT,"instr"); - + write_three_large(&xtc3_context,0); xtc3_context.has_large=0; } @@ -1396,7 +1399,7 @@ unsigned char *Ptngc_pack_array_xtc3(int *input, int *length, int natoms, int sp fprintf(stderr,"Prevcoord in packing: %d %d %d\n", prevcoord[0],prevcoord[1],prevcoord[2]); #endif - + inpdata+=3*runlength; ntriplets_left-=runlength; #if 1 @@ -1408,13 +1411,13 @@ unsigned char *Ptngc_pack_array_xtc3(int *input, int *length, int natoms, int sp #ifdef SHOWIT fprintf(stderr,"Refused value: %d old is %d max is %d\n",new_small_index,small_index,max_large_index); fflush(stderr); -#endif +#endif refused=1; } } #ifdef SHOWIT fprintf(stderr,"Number of triplets left is %d\n",ntriplets_left); -#endif +#endif } /* If we have large previous integers we must flush them now. */ @@ -1726,7 +1729,7 @@ static void unpack_one_large(struct xtc3_context *xtc3_context, fprintf(stderr,"Unpack one large: %d %d %d\n",prevcoord[0],prevcoord[1],prevcoord[2]); #endif } - + int Ptngc_unpack_array_xtc3(unsigned char *packed,int *output, int length, int natoms) { @@ -1812,7 +1815,7 @@ int Ptngc_unpack_array_xtc3(unsigned char *packed,int *output, int length, int n else decompress_base_block(&ptr,xtc3_context.nlargeinter,&xtc3_context.large_inter_delta); } - + xtc3_context.nsmallintra=(int)(((unsigned int)ptr[0]) | (((unsigned int)ptr[1])<<8) | (((unsigned int)ptr[2])<<16) | |