diff options
| -rw-r--r-- | src/compression/bwt.c | 14 | ||||
| -rw-r--r-- | src/compression/coder.c | 25 | ||||
| -rw-r--r-- | src/compression/dict.c | 16 | ||||
| -rw-r--r-- | src/compression/mtf.c | 20 | ||||
| -rw-r--r-- | src/compression/widemuldiv.c | 49 | ||||
| -rw-r--r-- | src/compression/xtc2.c | 120 | ||||
| -rw-r--r-- | src/compression/xtc3.c | 48 | ||||
| -rw-r--r-- | src/tests/CMakeLists.txt | 7 |
8 files changed, 174 insertions, 125 deletions
diff --git a/src/compression/bwt.c b/src/compression/bwt.c index 66d3ecf..681d66b 100644 --- a/src/compression/bwt.c +++ b/src/compression/bwt.c @@ -1,7 +1,7 @@ /* This code is part of the tng compression routines. * - * Written by Daniel Spangberg - * Copyright (c) 2010, 2013, The GROMACS development team. + * Written by Daniel Spangberg and Magnus Lundborg + * Copyright (c) 2010, 2013-2014 The GROMACS development team. * * * This program is free software; you can redistribute it and/or @@ -162,8 +162,9 @@ void Ptngc_comp_to_bwt(unsigned int *vals, int nvals, indices[i]=i; /* Find the length of the initial repeating pattern for the strings. */ /* First mark that the index does not have a found repeating string. */ - for (i=0; i<nvals; i++) - nrepeat[i]=0U; + + memset(nrepeat, 0U, sizeof(unsigned int) * nvals); + #ifdef SHOWIT printf("nvals is %d\n",nvals); #endif @@ -312,8 +313,9 @@ void Ptngc_comp_from_bwt(unsigned int *input, int nvals, int index, unsigned int *c=warnmalloc(0x10000*sizeof *c); unsigned int *p=warnmalloc(nvals*sizeof *p); unsigned int sum=0; - for (i=0; i<0x10000; i++) - c[i]=0; + + memset(c, 0, sizeof(unsigned int) * 0x10000); + for (i=0; i<nvals; i++) { p[i]=c[input[i]]; diff --git a/src/compression/coder.c b/src/compression/coder.c index cf89140..d51e8cd 100644 --- a/src/compression/coder.c +++ b/src/compression/coder.c @@ -1,7 +1,7 @@ /* This code is part of the tng compression routines. * - * Written by Daniel Spangberg - * Copyright (c) 2010, 2013, The GROMACS development team. + * Written by Daniel Spangberg and Magnus Lundborg + * Copyright (c) 2010, 2013-2014 The GROMACS development team. * * * This program is free software; you can redistribute it and/or @@ -44,19 +44,17 @@ void DECLSPECDLLEXPORT Ptngc_coder_deinit(struct coder *coder_inst) TNG_INLINE void DECLSPECDLLEXPORT Ptngc_out8bits(struct coder *coder_inst, unsigned char **output) { - int pack_temporary_bits=coder_inst->pack_temporary_bits; - unsigned int pack_temporary=coder_inst->pack_temporary; - while (pack_temporary_bits>=8) + while (coder_inst->pack_temporary_bits>=8) { - unsigned int mask=~(0xFFU<<(pack_temporary_bits-8)); - unsigned char out=(unsigned char)(pack_temporary>>(pack_temporary_bits-8)); + unsigned int mask; + unsigned char out; + coder_inst->pack_temporary_bits-=8; + mask=~(0xFFU<<(coder_inst->pack_temporary_bits)); + out=(unsigned char)(coder_inst->pack_temporary>>(coder_inst->pack_temporary_bits)); **output=out; (*output)++; - pack_temporary_bits-=8; - pack_temporary&=mask; + coder_inst->pack_temporary&=mask; } - coder_inst->pack_temporary_bits=pack_temporary_bits; - coder_inst->pack_temporary=pack_temporary; } void DECLSPECDLLEXPORT Ptngc_write_pattern(struct coder *coder_inst, unsigned int pattern, @@ -102,11 +100,11 @@ void DECLSPECDLLEXPORT Ptngc_write32bits(struct coder *coder_inst,unsigned int v while (nbits>8) { /* Make room for the bits. */ + nbits-=8; coder_inst->pack_temporary<<=8; coder_inst->pack_temporary_bits+=8; - coder_inst->pack_temporary|=(value&mask)>>(nbits-8); + coder_inst->pack_temporary|=(value&mask)>>(nbits); Ptngc_out8bits(coder_inst,output_ptr); - nbits-=8; mask>>=8; } if (nbits) @@ -246,7 +244,6 @@ unsigned char DECLSPECDLLEXPORT *Ptngc_pack_array(struct coder *coder_inst, { int item=input[k*3*natoms+i*3+j]; pval[cnt++]=(unsigned int)(item+most_negative); - } if (speed>=5) bwlzh_compress(pval,n,output+4,length); diff --git a/src/compression/dict.c b/src/compression/dict.c index 24e6ae7..fdfe7a0 100644 --- a/src/compression/dict.c +++ b/src/compression/dict.c @@ -1,7 +1,7 @@ /* This code is part of the tng compression routines. * - * Written by Daniel Spangberg - * Copyright (c) 2010, 2013, The GROMACS development team. + * Written by Daniel Spangberg and Magnus Lundborg + * Copyright (c) 2010, 2013-2014 The GROMACS development team. * * * This program is free software; you can redistribute it and/or @@ -17,6 +17,7 @@ void Ptngc_comp_canonical_dict(unsigned int *dict, int *ndict) int i; for (i=0; i<0x20004; i++) dict[i]=i; + *ndict=0x20004; } @@ -26,18 +27,19 @@ void Ptngc_comp_make_dict_hist(unsigned int *vals, int nvals, { int i; int j=0; - for (i=0; i<0x20004; i++) - hist[i]=0; - for (i=0; i<0x20004; i++) - dict[i]=i; + + memset(hist, 0, sizeof(unsigned int)*0x20004); + for (i=0; i<nvals; i++) hist[vals[i]]++; for (i=0; i<0x20004; i++) if (hist[i]!=0) { hist[j]=hist[i]; - dict[j]=dict[i]; + dict[j]=i; j++; + if(j==nvals) + break; } *ndict=j; } diff --git a/src/compression/mtf.c b/src/compression/mtf.c index d6eaf30..bfb0e19 100644 --- a/src/compression/mtf.c +++ b/src/compression/mtf.c @@ -1,7 +1,7 @@ /* This code is part of the tng compression routines. * - * Written by Daniel Spangberg - * Copyright (c) 2010, 2013, The GROMACS development team. + * Written by Daniel Spangberg and Magnus Lundborg + * Copyright (c) 2010, 2013-2014 The GROMACS development team. * * * This program is free software; you can redistribute it and/or @@ -10,6 +10,7 @@ #include <stdlib.h> +#include <string.h> #include "../../include/compression/warnmalloc.h" #include "../../include/compression/mtf.h" @@ -63,8 +64,9 @@ void Ptngc_comp_conv_to_mtf_partial(unsigned int *vals, int nvals, { unsigned char *tmp=warnmalloc(nvals*2); int i, j; - for (i=0; i<nvals; i++) - valsmtf[i]=0U; + + memset(valsmtf, 0U, sizeof(unsigned int) * nvals); + for (j=0; j<3; j++) { for (i=0; i<nvals; i++) @@ -138,8 +140,9 @@ void Ptngc_comp_conv_from_mtf_partial(unsigned int *valsmtf, int nvals, { unsigned char *tmp=warnmalloc(nvals*2); int i, j; - for (i=0; i<nvals; i++) - vals[i]=0U; + + memset(vals, 0U, sizeof(unsigned int) * nvals); + for (j=0; j<3; j++) { for (i=0; i<nvals; i++) @@ -156,8 +159,9 @@ void Ptngc_comp_conv_from_mtf_partial3(unsigned char *valsmtf, int nvals, { unsigned char *tmp=warnmalloc(nvals); int i, j; - for (i=0; i<nvals; i++) - vals[i]=0U; + + memset(vals, 0U, sizeof(unsigned int) * nvals); + for (j=0; j<3; j++) { comp_conv_from_mtf_byte(valsmtf+j*nvals,nvals,tmp); diff --git a/src/compression/widemuldiv.c b/src/compression/widemuldiv.c index 7d03c57..63056f9 100644 --- a/src/compression/widemuldiv.c +++ b/src/compression/widemuldiv.c @@ -1,7 +1,7 @@ /* This code is part of the tng compression routines. * - * Written by Daniel Spangberg - * Copyright (c) 2010, 2013, The GROMACS development team. + * Written by Daniel Spangberg and Magnus Lundborg + * Copyright (c) 2010, 2013-2014 The GROMACS development team. * * * This program is free software; you can redistribute it and/or @@ -11,6 +11,7 @@ #include <stdio.h> #include <stdlib.h> +#include <string.h> #include "../../include/compression/tng_compress.h" @@ -31,8 +32,14 @@ #endif /* gcc & x86_64 */ #endif /* TRAJNG X86 GCC INLINE MULDIV */ +#ifdef USE_WINDOWS +#define TNG_INLINE __inline +#else +#define TNG_INLINE inline +#endif + /* Multiply two 32 bit unsigned integers returning a 64 bit unsigned value (in two integers) */ -void Ptngc_widemul(unsigned int i1, unsigned int i2, unsigned int *ohi, unsigned int *olo) +TNG_INLINE void Ptngc_widemul(unsigned int i1, unsigned int i2, unsigned int *ohi, unsigned int *olo) { #if defined(TRAJNG_X86_GCC_INLINE_MULDIV) __asm__ __volatile__ ("mull %%edx\n\t" @@ -99,7 +106,7 @@ void Ptngc_widemul(unsigned int i1, unsigned int i2, unsigned int *ohi, unsigned /* Divide a 64 bit unsigned value in hi:lo with the 32 bit value i and return the result in result and the remainder in remainder */ -void Ptngc_widediv(unsigned int hi, unsigned int lo, unsigned int i, unsigned int *result, unsigned int *remainder) +TNG_INLINE void Ptngc_widediv(unsigned int hi, unsigned int lo, unsigned int i, unsigned int *result, unsigned int *remainder) { #if defined(TRAJNG_X86_GCC_INLINE_MULDIV) __asm__ __volatile__ ("divl %%ecx\n\t" @@ -163,7 +170,7 @@ void Ptngc_widediv(unsigned int hi, unsigned int lo, unsigned int i, unsigned in /* Add a unsigned int to a largeint. j determines which value in the largeint to add v1 to. */ -static void largeint_add_gen(unsigned int v1, unsigned int *largeint, int n, int j) +TNG_INLINE static void largeint_add_gen(const unsigned int v1, unsigned int *largeint, const int n, int j) { /* Add with carry. unsigned ints in C wrap modulo 2**bits when "overflowed". */ unsigned int v2=(v1+largeint[j])&0xFFFFFFFFU; /* Add and cap at 32 bits */ @@ -184,46 +191,50 @@ static void largeint_add_gen(unsigned int v1, unsigned int *largeint, int n, int } /* Add a unsigned int to a largeint. */ -void Ptngc_largeint_add(unsigned int v1, unsigned int *largeint, int n) +void Ptngc_largeint_add(const unsigned int v1, unsigned int *largeint, const int n) { largeint_add_gen(v1,largeint,n,0); } /* Multiply v1 with largeint_in and return result in largeint_out */ -void Ptngc_largeint_mul(unsigned int v1, unsigned int *largeint_in, unsigned int *largeint_out, int n) +TNG_INLINE void Ptngc_largeint_mul(const unsigned int v1, unsigned int *largeint_in, unsigned int *largeint_out, const int n) { int i; - for (i=0; i<n; i++) - largeint_out[i]=0U; - for (i=0; i<n; i++) + unsigned int lo,hi; + + memset(largeint_out, 0U, sizeof(unsigned int) * n); + + for (i=0; i<n-1; i++) { if (largeint_in[i]!=0U) { - unsigned int lo,hi; Ptngc_widemul(v1,largeint_in[i],&hi,&lo); /* 32x32->64 mul */ largeint_add_gen(lo,largeint_out,n,i); - if (i+1<n) - largeint_add_gen(hi,largeint_out,n,i+1); + largeint_add_gen(hi,largeint_out,n,i+1); } } + if (largeint_in[i]!=0U) + { + Ptngc_widemul(v1,largeint_in[i],&hi,&lo); /* 32x32->64 mul */ + largeint_add_gen(lo,largeint_out,n,i); + } } /* Return the remainder from dividing largeint_in with v1. Result of the division is returned in largeint_out */ -unsigned int Ptngc_largeint_div(unsigned int v1, unsigned int *largeint_in, unsigned int *largeint_out, int n) +TNG_INLINE unsigned int Ptngc_largeint_div(const unsigned int v1, unsigned int *largeint_in, unsigned int *largeint_out, const int n) { unsigned int result,remainder=0; int i; - unsigned int hi, lo; + unsigned int hi; /* Boot */ hi=0U; i=n; while (i) { - lo=largeint_in[i-1]; - Ptngc_widediv(hi,lo,v1,&result,&remainder); - largeint_out[i-1]=result; - hi=remainder; i--; + Ptngc_widediv(hi,largeint_in[i],v1,&result,&remainder); + largeint_out[i]=result; + hi=remainder; } return remainder; } diff --git a/src/compression/xtc2.c b/src/compression/xtc2.c index bbd45e9..e5b688a 100644 --- a/src/compression/xtc2.c +++ b/src/compression/xtc2.c @@ -1,7 +1,7 @@ /* This code is part of the tng compression routines. * - * Written by Daniel Spangberg - * Copyright (c) 2010, 2013, The GROMACS development team. + * Written by Daniel Spangberg and Magnus Lundborg + * Copyright (c) 2010, 2013-2014 The GROMACS development team. * * * This program is free software; you can redistribute it and/or @@ -26,6 +26,12 @@ /* Generated by gen_magic.py */ #define MAX_MAGIC 92 +#ifdef USE_WINDOWS +#define TNG_INLINE __inline +#else +#define TNG_INLINE inline +#endif + static unsigned int magic[MAX_MAGIC]={ 2U, 3U, 4U, 5U, 6U, 8U, 10U, 12U, @@ -159,20 +165,43 @@ static const double iflipgaincheck=0.89089871814033927; /* 1./(2**(1./6)) */ #define SHOWIT #endif +#ifdef USE_WINDOWS +#define TNG_INLINE __inline +#else +#define TNG_INLINE inline +#endif + int Ptngc_magic(unsigned int i) { return magic[i]; } -int Ptngc_find_magic_index(unsigned int maxval) +TNG_INLINE int Ptngc_find_magic_index(const unsigned int maxval) { - int i=0; + int i; + + if(maxval > magic[MAX_MAGIC/4]) + { + if(maxval > magic[MAX_MAGIC/2]) + { + i = MAX_MAGIC/2 + 1; + } + else + { + i = MAX_MAGIC/4 + 1; + } + } + else + { + i = 0; + } + while (magic[i]<=maxval) i++; return i; } -static unsigned int positive_int(int item) +TNG_INLINE static unsigned int positive_int(const int item) { int s=0; if (item>0) @@ -182,7 +211,7 @@ static unsigned int positive_int(int item) return s; } -static int unpositive_int(int val) +TNG_INLINE static int unpositive_int(const int val) { int s=(val+1)/2; if ((val%2)==0) @@ -438,23 +467,26 @@ static int compute_magic_bits(int *index) /* Convert a sequence of (hopefully) small positive integers using the base pointed to by index (x base, y base and z base can be different). The largest number of integers supported is 18 (29 to handle/detect overflow) */ -static void trajcoder_base_compress(int *input, int n, int *index, unsigned char *result) +static void trajcoder_base_compress(int *input, const int n, int *index, unsigned char *result) { unsigned int largeint[19]; unsigned int largeint_tmp[19]; - int i,j; - for (i=0; i<19; i++) - largeint[i]=0U; + int i, j; + + memset(largeint, 0U, sizeof(unsigned int) * 19); - for (i=0; i<n; i++) + if(n > 0) { - if (i!=0) - { - /* We must do the multiplication of the largeint with the integer base */ - Ptngc_largeint_mul(magic[index[i%3]],largeint,largeint_tmp,19); - for (j=0; j<19; j++) - largeint[j]=largeint_tmp[j]; - } + Ptngc_largeint_add(input[0],largeint,19); + } + + for (i=1; i<n; i++) + { + /* We must do the multiplication of the largeint with the integer base */ + Ptngc_largeint_mul(magic[index[i%3]],largeint,largeint_tmp,19); + + memcpy(largeint,largeint_tmp,19*sizeof *largeint); + Ptngc_largeint_add(input[i],largeint,19); } if (largeint[18]) @@ -481,7 +513,7 @@ static void trajcoder_base_compress(int *input, int n, int *index, unsigned char } /* The opposite of base_compress. */ -static void trajcoder_base_decompress(unsigned char *input, int n, int *index, int *output) +static void trajcoder_base_decompress(unsigned char *input, const int n, int *index, int *output) { unsigned int largeint[19]; unsigned int largeint_tmp[19]; @@ -524,7 +556,7 @@ static void trajcoder_base_decompress(unsigned char *input, int n, int *index, i /* It is "large" if we have to increase the small index quite a bit. Not so much to be rejected by the not very large check later. */ -static int is_quite_large(int *input, int small_index, int max_large_index) +static int is_quite_large(int *input, const int small_index, const int max_large_index) { int is=0; int i; @@ -547,7 +579,7 @@ int nbits_sum; int nvalues_sum; #endif -static void write_three_large(struct coder *coder, int *encode_ints, int *large_index, int nbits, unsigned char *compress_buffer, unsigned char **output_ptr) +static void write_three_large(struct coder *coder, int *encode_ints, int *large_index, const int nbits, unsigned char *compress_buffer, unsigned char **output_ptr) { trajcoder_base_compress(encode_ints,3,large_index,compress_buffer); Ptngc_writemanybits(coder,compress_buffer,nbits,output_ptr); @@ -559,7 +591,7 @@ static void write_three_large(struct coder *coder, int *encode_ints, int *large_ #endif } -static void insert_batch(int *input_ptr, int ntriplets_left, int *prevcoord,int *minint, int *encode_ints, int startenc, int *nenc) +static void insert_batch(int *input_ptr, int ntriplets_left, const int *prevcoord,int *minint, int *encode_ints, const int startenc, int *nenc) { int nencode=startenc*3; int tmp_prevcoord[3]; @@ -617,8 +649,8 @@ static void insert_batch(int *input_ptr, int ntriplets_left, int *prevcoord,int *nenc=nencode; } -static void flush_large(struct coder *coder, int *has_large, int *has_large_ints, int n, - int *large_index, int large_nbits, unsigned char *compress_buffer, +static void flush_large(struct coder *coder, int *has_large, int *has_large_ints, const int n, + int *large_index, const int large_nbits, unsigned char *compress_buffer, unsigned char **output_ptr) { int i; @@ -651,7 +683,7 @@ static void flush_large(struct coder *coder, int *has_large, int *has_large_ints } static void buffer_large(struct coder *coder, int *has_large, int *has_large_ints, int *new_large_ints, - int *large_index, int large_nbits, unsigned char *compress_buffer, + int *large_index, const int large_nbits, unsigned char *compress_buffer, unsigned char **output_ptr) { /* If it is full we must write them all. */ @@ -669,7 +701,7 @@ unsigned char *Ptngc_pack_array_xtc2(struct coder *coder,int *input, int *length { unsigned char *output=NULL; unsigned char *output_ptr=NULL; - int i,ienc,j; + int i,ienc,j,imult; int output_length=0; /* Pack triplets. */ int ntriplets=*length/3; @@ -709,13 +741,15 @@ unsigned char *Ptngc_pack_array_xtc2(struct coder *coder,int *input, int *length maxint[2]=minint[2]=input[2]; for (i=1; i<ntriplets; i++) - for (j=0; j<3; j++) - { - if (input[i*3+j]>maxint[j]) - maxint[j]=input[i*3+j]; - if (input[i*3+j]<minint[j]) - minint[j]=input[i*3+j]; - } + { + for (j=0; j<3; j++) + { + if (input[i*3+j]>maxint[j]) + maxint[j]=input[i*3+j]; + if (input[i*3+j]<minint[j]) + minint[j]=input[i*3+j]; + } + } large_index[0]=Ptngc_find_magic_index(maxint[0]-minint[0]+1); large_index[1]=Ptngc_find_magic_index(maxint[1]-minint[1]+1); @@ -794,9 +828,7 @@ unsigned char *Ptngc_pack_array_xtc2(struct coder *coder,int *input, int *length #endif /* Initial prevcoord is the minimum integers. */ - prevcoord[0]=minint[0]; - prevcoord[1]=minint[1]; - prevcoord[2]=minint[2]; + memcpy(prevcoord, minint, 3*sizeof *prevcoord); while (ntriplets_left) { @@ -1304,9 +1336,7 @@ int Ptngc_unpack_array_xtc2(struct coder *coder,unsigned char *packed,int *outpu #endif /* Initial prevcoord is the minimum integers. */ - prevcoord[0]=minint[0]; - prevcoord[1]=minint[1]; - prevcoord[2]=minint[2]; + memcpy(prevcoord, minint, 3*sizeof *prevcoord); while (ntriplets_left) { @@ -1329,9 +1359,7 @@ int Ptngc_unpack_array_xtc2(struct coder *coder,unsigned char *packed,int *outpu /* Get the large value. */ readmanybits(&ptr,&bitptr,large_nbits,compress_buffer); trajcoder_base_decompress(compress_buffer,3,large_index,encode_ints); - large_ints[0]=encode_ints[0]; - large_ints[1]=encode_ints[1]; - large_ints[2]=encode_ints[2]; + memcpy(large_ints, encode_ints, 3*sizeof *large_ints); #ifdef SHOWIT fprintf(stderr,"large ints: %d %d %d\n",large_ints[0],large_ints[1],large_ints[2]); #endif @@ -1444,16 +1472,12 @@ int Ptngc_unpack_array_xtc2(struct coder *coder,unsigned char *packed,int *outpu /* Get the large value. */ readmanybits(&ptr,&bitptr,large_nbits,compress_buffer); trajcoder_base_decompress(compress_buffer,3,large_index,encode_ints); - large_ints[0]=encode_ints[0]; - large_ints[1]=encode_ints[1]; - large_ints[2]=encode_ints[2]; + memcpy(large_ints, encode_ints, 3*sizeof *large_ints); /* Output large value */ *output++=large_ints[0]+minint[0]; *output++=large_ints[1]+minint[1]; *output++=large_ints[2]+minint[2]; - prevcoord[0]=large_ints[0]; - prevcoord[1]=large_ints[1]; - prevcoord[2]=large_ints[2]; + memcpy(prevcoord, large_ints, 3*sizeof *prevcoord); } ntriplets_left-=n; } diff --git a/src/compression/xtc3.c b/src/compression/xtc3.c index 95483b3..673b321 100644 --- a/src/compression/xtc3.c +++ b/src/compression/xtc3.c @@ -1,7 +1,7 @@ /* This code is part of the tng compression routines. * - * Written by Daniel Spangberg - * Copyright (c) 2010, 2013, The GROMACS development team. + * Written by Daniel Spangberg and Magnus Lundborg + * Copyright (c) 2010, 2013-2014 The GROMACS development team. * * * This program is free software; you can redistribute it and/or @@ -60,11 +60,17 @@ static const double iflipgaincheck=0.89089871814033927; /* 1./(2**(1./6)) */ #define SHOWIT_LIGHT #endif +#ifdef USE_WINDOWS +#define TNG_INLINE __inline +#else +#define TNG_INLINE inline +#endif + /* These routines are in xtc2.c */ int Ptngc_magic(unsigned int i); int Ptngc_find_magic_index(unsigned int maxval); -static unsigned int positive_int(int item) +TNG_INLINE static unsigned int positive_int(int item) { int s=0; if (item>0) @@ -74,7 +80,7 @@ static unsigned int positive_int(int item) return s; } -static int unpositive_int(int val) +TNG_INLINE static int unpositive_int(int val) { int s=(val+1)/2; if ((val%2)==0) @@ -574,15 +580,15 @@ static int base_bytes(unsigned int base, int n) unsigned int largeint[MAXMAXBASEVALS+1]; unsigned int largeint_tmp[MAXMAXBASEVALS+1]; int numbytes=0; - for (i=0; i<n+1; i++) - largeint[i]=0U; + + memset(largeint, 0U, sizeof(unsigned int) * (n+1)); + for (i=0; i<n; i++) { if (i!=0) { Ptngc_largeint_mul(base,largeint,largeint_tmp,n+1); - for (j=0; j<n+1; j++) - largeint[j]=largeint_tmp[j]; + memcpy(largeint, largeint_tmp, (n+1)*sizeof *largeint); } Ptngc_largeint_add(base-1U,largeint,n+1); } @@ -612,8 +618,9 @@ static void base_compress(unsigned int *data, int len, unsigned char *output, in unsigned int base=0U; int nvals=0; int basegiven=0; - for (j=0; j<MAXBASEVALS+1; j++) - largeint[j]=0U; + + memset(largeint, 0U, sizeof(unsigned int) * (MAXBASEVALS+1)); + for (i=ixyz; i<len; i+=3) { if (nvals==0) @@ -679,8 +686,8 @@ static void base_compress(unsigned int *data, int len, unsigned char *output, in fprintf(stderr,"\n"); #endif nvals=0; - for (j=0; j<MAXBASEVALS+1; j++) - largeint[j]=0U; + + memset(largeint, 0U, sizeof(unsigned int) * (MAXBASEVALS+1)); } } if (nvals) @@ -747,8 +754,7 @@ static void base_decompress(unsigned char *input, int len, unsigned int *output) fprintf(stderr,"Base for %d is %u. I need %d bytes for %d values.\n",ixyz,base,numbytes,nvals_left); #endif } - for (j=0; j<maxbasevals+1; j++) - largeint[j]=0U; + memset(largeint, 0U, sizeof(unsigned int) * (maxbasevals+1)); #ifdef SHOWIT fprintf(stderr,"Reading largeint: "); #endif @@ -840,9 +846,8 @@ unsigned char *Ptngc_pack_array_xtc3(int *input, int *length, int natoms, int sp struct xtc3_context xtc3_context; init_xtc3_context(&xtc3_context); - xtc3_context.maxint[0]=xtc3_context.minint[0]=input[0]; - xtc3_context.maxint[1]=xtc3_context.minint[1]=input[1]; - xtc3_context.maxint[2]=xtc3_context.minint[2]=input[2]; + memcpy(xtc3_context.maxint, input, 3*sizeof *xtc3_context.maxint); + memcpy(xtc3_context.minint, input, 3*sizeof *xtc3_context.maxint); /* Values of speed should be sane. */ if (speed<1) @@ -923,6 +928,7 @@ unsigned char *Ptngc_pack_array_xtc3(int *input, int *length, int natoms, int sp #endif /* Initial prevcoord is the minimum integers. */ + memcpy(prevcoord, xtc3_context.minint, 3*sizeof *prevcoord); prevcoord[0]=xtc3_context.minint[0]; prevcoord[1]=xtc3_context.minint[1]; prevcoord[2]=xtc3_context.minint[2]; @@ -1722,9 +1728,7 @@ static void unpack_one_large(struct xtc3_context *xtc3_context, +output[outdata-natoms*3+2+didswap*3]; (*ilargeinter)+=3; } - prevcoord[0]=large_ints[0]; - prevcoord[1]=large_ints[1]; - prevcoord[2]=large_ints[2]; + memcpy(prevcoord, large_ints, 3*sizeof *prevcoord); output[outdata]=large_ints[0]; output[outdata+1]=large_ints[1]; output[outdata+2]=large_ints[2]; @@ -1833,9 +1837,7 @@ int Ptngc_unpack_array_xtc3(unsigned char *packed,int *output, int length, int n } /* Initial prevcoord is the minimum integers. */ - prevcoord[0]=minint[0]; - prevcoord[1]=minint[1]; - prevcoord[2]=minint[2]; + memcpy(prevcoord, minint, 3*sizeof *prevcoord); while (ntriplets_left>0 && iinstr<xtc3_context.ninstr) { diff --git a/src/tests/CMakeLists.txt b/src/tests/CMakeLists.txt index f465b6b..cd2d7fd 100644 --- a/src/tests/CMakeLists.txt +++ b/src/tests/CMakeLists.txt @@ -74,6 +74,13 @@ if(TNG_BUILD_EXAMPLES) endif() set_property(TARGET tng_io_read_pos_util PROPERTY RUNTIME_OUTPUT_DIRECTORY ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/examples) + add_executable(tng_io_gen_versioned_output tng_io_gen_versioned_output.c) + target_link_libraries(tng_io_gen_versioned_output tng_io) + if(HAVE_INTTYPES_H) + set_property(TARGET tng_io_gen_versioned_output APPEND PROPERTY COMPILE_DEFINITIONS USE_STD_INTTYPES_H=1) + endif() + set_property(TARGET tng_io_gen_versioned_output PROPERTY RUNTIME_OUTPUT_DIRECTORY ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/examples) + if(TNG_BUILD_FORTRAN) # This does not work due to a bug in CMake. Remove lines below if no fortran compiler is found. enable_language(Fortran OPTIONAL) |