Fix some MSVC and Inter C Compiler warnings.

7 files changed, 149 insertions, 136 deletions

diff --git a/src/compression/coder.c b/src/compression/coder.c
index 8d8b5bd..c12042c 100644
--- a/src/compression/coder.c
+++ b/src/compression/coder.c
@@ -61,7 +61,8 @@ TNG_INLINE void Ptngc_out8bits(struct coder *coder_inst, unsigned char **output)
   coder_inst->pack_temporary=pack_temporary;
 }
 
-void Ptngc_write_pattern(struct coder *coder_inst,unsigned int pattern, int nbits, unsigned char **output)
+void Ptngc_write_pattern(struct coder *coder_inst, unsigned int pattern,
+                         int nbits, unsigned char **output)
 {
     unsigned int mask1,mask2;
     mask1=1;
@@ -80,7 +81,9 @@ void Ptngc_write_pattern(struct coder *coder_inst,unsigned int pattern, int nbit
 }
 
 /* Write up to 24 bits */
-TNG_INLINE void Ptngc_writebits(struct coder *coder_inst,unsigned int value,int nbits, unsigned char **output_ptr)
+TNG_INLINE void Ptngc_writebits(struct coder *coder_inst,
+                                unsigned int value, int nbits,
+                                unsigned char **output_ptr)
 {
   /* Make room for the bits. */
   coder_inst->pack_temporary<<=nbits;
@@ -90,7 +93,8 @@ TNG_INLINE void Ptngc_writebits(struct coder *coder_inst,unsigned int value,int
 }
 
 /* Write up to 32 bits */
-void Ptngc_write32bits(struct coder *coder_inst,unsigned int value,int nbits, unsigned char **output_ptr)
+void Ptngc_write32bits(struct coder *coder_inst,unsigned int value,
+                       int nbits, unsigned char **output_ptr)
 {
   unsigned int mask;
   if (nbits>=8)
@@ -112,7 +116,8 @@ void Ptngc_write32bits(struct coder *coder_inst,unsigned int value,int nbits, un
 }
 
 /* Write "arbitrary" number of bits */
-void Ptngc_writemanybits(struct coder *coder_inst,unsigned char *value,int nbits, unsigned char **output_ptr)
+void Ptngc_writemanybits(struct coder *coder_inst, unsigned char *value,
+                         int nbits, unsigned char **output_ptr)
 {
   int vptr=0;
   while (nbits>=24)
@@ -136,7 +141,9 @@ void Ptngc_writemanybits(struct coder *coder_inst,unsigned char *value,int nbits
     }
 }
 
-static int write_stop_bit_code(struct coder *coder_inst, unsigned int s,unsigned int coding_parameter, unsigned char **output)
+static int write_stop_bit_code(struct coder *coder_inst, unsigned int s,
+                               unsigned int coding_parameter,
+                               unsigned char **output)
 {
   do {
     unsigned int extract=~(0xffffffffU<<coding_parameter);
@@ -162,7 +169,8 @@ static int write_stop_bit_code(struct coder *coder_inst, unsigned int s,unsigned
   return 0;
 }
 
-static int pack_stopbits_item(struct coder *coder_inst,int item, unsigned char **output, int coding_parameter)
+static int pack_stopbits_item(struct coder *coder_inst,int item,
+                              unsigned char **output, int coding_parameter)
 {
     /* Find this symbol in table. */
     int s=0;
@@ -173,7 +181,8 @@ static int pack_stopbits_item(struct coder *coder_inst,int item, unsigned char *
     return write_stop_bit_code(coder_inst,s,coding_parameter,output);
 }
 
-static int pack_triplet(struct coder *coder_inst,unsigned int *s, unsigned char **output, int coding_parameter,
+static int pack_triplet(struct coder *coder_inst, unsigned int *s,
+                        unsigned char **output, int coding_parameter,
 			unsigned int max_base, int maxbits)
 {
   /* Determine base for this triplet. */
@@ -213,7 +222,9 @@ void Ptngc_pack_flush(struct coder *coder_inst,unsigned char **output)
     Ptngc_write_pattern(coder_inst,0,8-coder_inst->pack_temporary_bits,output);
 }
 
-unsigned char *Ptngc_pack_array(struct coder *coder_inst,int *input, int *length, int coding, int coding_parameter,int natoms, int speed)
+unsigned char *Ptngc_pack_array(struct coder *coder_inst,
+                                int *input, int *length, int coding,
+                                int coding_parameter, int natoms, int speed)
 {
   if ((coding==TNG_COMPRESS_ALGO_BWLZH1) || (coding==TNG_COMPRESS_ALGO_BWLZH2))
     {
@@ -307,7 +318,8 @@ unsigned char *Ptngc_pack_array(struct coder *coder_inst,int *input, int *length
 		  else if (item<0)
 		    s[j]=2+(-item-1)*2;
 		}
-	      if (pack_triplet(coder_inst,s,&output_ptr,coding_parameter,max_base,maxbits))
+	      if (pack_triplet(coder_inst, s, &output_ptr,
+                               coding_parameter, max_base,maxbits))
 		{
 		  free(output);
 		  return NULL;
@@ -332,10 +344,10 @@ static int unpack_array_stop_bits(struct coder *coder_inst,
                                   unsigned char *packed,int *output,
                                   int length, int coding_parameter)
 {
-  (void) coder_inst;
   int i,j;
   unsigned int extract_mask=0x80;
   unsigned char *ptr=packed;
+  (void) coder_inst;
   for (i=0; i<length; i++)
     {
       unsigned int pattern=0;
@@ -387,7 +399,6 @@ static int unpack_array_triplet(struct coder *coder_inst,
                                 unsigned char *packed, int *output,
                                 int length, int coding_parameter)
 {
-  (void) coder_inst;
   int i,j;
   unsigned int extract_mask=0x80;
   unsigned char *ptr=packed;
@@ -396,6 +407,7 @@ static int unpack_array_triplet(struct coder *coder_inst,
   unsigned int maxbits=coding_parameter;
   unsigned int intmax;
   /* Get intmax */
+  (void) coder_inst;
   intmax=((unsigned int)ptr[0])<<24|
     ((unsigned int)ptr[1])<<16|
     ((unsigned int)ptr[2])<<8|
@@ -461,7 +473,6 @@ static int unpack_array_bwlzh(struct coder *coder_inst,
                               unsigned char *packed, int *output,
                               int length, int natoms)
 {
-  (void) coder_inst;
   int i,j,k,n=length;
   unsigned int *pval=warnmalloc(n*sizeof *pval);
   int nframes=n/natoms/3;
@@ -470,6 +481,7 @@ static int unpack_array_bwlzh(struct coder *coder_inst,
 			  (((unsigned int)packed[1])<<8) |
 			  (((unsigned int)packed[2])<<16) |
 			  (((unsigned int)packed[3])<<24));
+  (void) coder_inst;
   bwlzh_decompress(packed+4,length,pval);
   for (i=0; i<natoms; i++)
     for (j=0; j<3; j++)
diff --git a/src/compression/huffman.c b/src/compression/huffman.c
index bdcd5a0..bd0a15c 100644
--- a/src/compression/huffman.c
+++ b/src/compression/huffman.c
@@ -56,10 +56,10 @@ struct codelength
 
 static int comp_htree(const void *leafptr1, const void *leafptr2, const void *private)
 {
-  (void)private;
   const union htree_nodeleaf *leaf1=(union htree_nodeleaf *)leafptr1;
   const union htree_nodeleaf *leaf2=(union htree_nodeleaf *)leafptr2;
-  
+  (void)private;
+
   int rval=0;
   if (leaf1->leaf.prob<leaf2->leaf.prob)
     rval=1;
@@ -71,7 +71,7 @@ static int comp_htree(const void *leafptr1, const void *leafptr2, const void *pr
 static void assign_codes(union htree_nodeleaf *htree,
 			 struct codelength *codelength,
 			 unsigned int code,
-			 int length, 
+			 int length,
 			 int top)
 {
 #if 0
@@ -130,7 +130,7 @@ static void flush_8bits(unsigned int *combine, unsigned char **output, int *bitp
       (*output)++;
       (*bitptr)-=8;
       (*combine)&=mask;
-    }  
+    }
 }
 
 static void writebits(unsigned int value,int length, unsigned char **output, int *bitptr)
@@ -186,10 +186,10 @@ static unsigned int readbits(int length, unsigned char **input, int *bitptr)
 
 static int comp_codes(const void *codeptr1, const void *codeptr2, const void *private)
 {
-  (void)private;
   const struct codelength *code1=(struct codelength *)codeptr1;
   const struct codelength *code2=(struct codelength *)codeptr2;
-  
+  (void)private;
+
   int rval=0; /* It shouldn't be possible to get equal here, though. */
   if (code1->length>code2->length)
     rval=1;
@@ -204,11 +204,11 @@ static int comp_codes(const void *codeptr1, const void *codeptr2, const void *pr
 
 static int comp_codes_value(const void *codeptr1, const void *codeptr2, const void *private)
 {
-  (void)private;
   const struct codelength *code1=(struct codelength *)codeptr1;
   const struct codelength *code2=(struct codelength *)codeptr2;
-  
+
   int rval=0; /* It shouldn't be possible to get equal here, though. */
+  (void)private;
   if (code1->dict>code2->dict)
     rval=1;
   else
@@ -253,7 +253,7 @@ void Ptngc_comp_conv_to_huffman(unsigned int *vals, int nvals,
 	}
       /* Sort the leafs wrt probability. */
       Ptngc_merge_sort(htree,ndict,sizeof *htree,comp_htree,NULL);
-  
+
 #if 0
       for (i=0; i<ndict; i++)
 	{
@@ -271,7 +271,7 @@ void Ptngc_comp_conv_to_huffman(unsigned int *vals, int nvals,
 	{
 	  /* Nodes and leafs left. */
 	  nleft=ndict;
-  
+
 	  /* Take the two least probable symbols (which are at the end of the
 	     array and combine them until there is nothing left. */
 	  while (nleft>1)
@@ -473,14 +473,14 @@ void Ptngc_comp_conv_from_huffman(unsigned char *huffman,
 			    unsigned int *huffman_dict_unpacked,
 			    int huffman_dict_unpackedlen)
 {
-  (void)huffman_dictlen;
-  (void)huffman_dict_unpackedlen;
   struct codelength *codelength=warnmalloc(ndict*sizeof *codelength);
   int i,j;
   int maxdict;
   int code;
   unsigned char *huffman_ptr;
   int bitptr;
+  (void)huffman_dictlen;
+  (void)huffman_dict_unpackedlen;
   if (huffman_dict_unpacked)
     {
       maxdict=huffman_dict_unpacked[0]|(huffman_dict_unpacked[1]<<8)|(huffman_dict_unpacked[2]<<16);
diff --git a/src/compression/huffmem.c b/src/compression/huffmem.c
index eec8646..2232b7e 100644
--- a/src/compression/huffmem.c
+++ b/src/compression/huffmem.c
@@ -72,7 +72,7 @@ void Ptngc_comp_huff_compress_verbose(unsigned int *vals, int nvals,
 		       huffdict,&nhuffdict,
 		       huffdictunpack,&nhuffdictunpack);
   *huffdatalen=nhuff;
-  
+
   /* Algorithm 0 stores the huffman dictionary directly (+ a code for
      the algorithm) + lengths of the huffman buffer (4) and the huffman dictionary (3). */
   huffman_lengths[0]=nhuff+nhuffdict+1*2+3*4+3+3;
@@ -92,7 +92,7 @@ void Ptngc_comp_huff_compress_verbose(unsigned int *vals, int nvals,
   /* ... and rle + huffman coding ... (algorithm 2) Pack any repetetitive patterns. */
   Ptngc_comp_conv_to_rle(huffdictunpack,nhuffdictunpack,
 		   huffdictrle,&nhuffrle,1);
-  
+
   /* Determine probabilities. */
   Ptngc_comp_make_dict_hist(huffdictrle,nhuffrle,dict,&ndict2,hist);
   /* Pack huffman dictionary */
@@ -102,10 +102,10 @@ void Ptngc_comp_huff_compress_verbose(unsigned int *vals, int nvals,
 		       huffdict2,&nhuffdict2,
 		       huffdictunpack2,&nhuffdictunpack2);
   huffman_lengths[2]=nhuff+nhuff2+nhuffdict2+1*2+3*4+3+3+3+3+3+3;
-  
+
   /* Choose the best algorithm and output the data. */
   if ((*chosen_algo==0) || ((*chosen_algo==-1) &&
-			    (((huffman_lengths[0]<huffman_lengths[1]) && 
+			    (((huffman_lengths[0]<huffman_lengths[1]) &&
 			      (huffman_lengths[0]<huffman_lengths[2])))))
     {
       *chosen_algo=0;
@@ -242,7 +242,6 @@ void Ptngc_comp_huff_compress(unsigned int *vals, int nvals,
 void Ptngc_comp_huff_decompress(unsigned char *huffman, int huffman_len,
 			  unsigned int *vals)
 {
-  (void)huffman_len;
   int isvals16=(int)huffman[0];
   unsigned int *vals16=NULL;
   int algo=(int)huffman[1];
@@ -261,6 +260,7 @@ void Ptngc_comp_huff_decompress(unsigned char *huffman, int huffman_len,
   int ndict=(int)((unsigned int)huffman[17+nhuff]|
 		  (((unsigned int)huffman[18+nhuff])<<8)|
 		  (((unsigned int)huffman[19+nhuff])<<16));
+  (void)huffman_len;
   if (!isvals16)
     vals16=warnmalloc(nvals16*sizeof *vals16);
   else
diff --git a/src/compression/lz77.c b/src/compression/lz77.c
index 77a17cf..5ea63cf 100644
--- a/src/compression/lz77.c
+++ b/src/compression/lz77.c
@@ -125,7 +125,7 @@ static void sort_strings(unsigned int *vals, int nvals,
 	      nrepeat[i+m]=((unsigned int) (good_k)) | (((unsigned int) (repeat))<<8);
 	    }
 	  /* If no repetition was found for this value signal that here. */
-	  if (!nrepeat[i]) 
+	  if (!nrepeat[i])
 	    nrepeat[i+m]=257U; /* This is 1<<8 | 1 */
 	}
     }
@@ -138,7 +138,7 @@ static void sort_strings(unsigned int *vals, int nvals,
     {
       output[i*2]=indices[i];
       output[indices[i]*2+1]=i;
-    }  
+    }
   free(nrepeat);
   free(indices);
 }
@@ -313,13 +313,13 @@ void Ptngc_comp_from_lz77(unsigned int *data, int ndata,
 		    unsigned int *offsets, int noffsets,
 		    unsigned int *vals, int nvals)
 {
-  (void)ndata;
-  (void)nlens;
-  (void)noffsets;
   int i=0;
   int joff=0;
   int jdat=0;
   int jlen=0;
+  (void)ndata;
+  (void)nlens;
+  (void)noffsets;
   while (i<nvals)
     {
       unsigned int v=data[jdat++];
diff --git a/src/compression/xtc2.c b/src/compression/xtc2.c
index be12d1c..2c46cb7 100644
--- a/src/compression/xtc2.c
+++ b/src/compression/xtc2.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
 */
@@ -29,29 +29,29 @@
 #define MAX_MAGIC  92
 
 static unsigned int magic[MAX_MAGIC]={
-2U,  3U,  4U,  5U,  
-6U,  8U,  10U,  12U,  
-16U,  20U,  25U,  32U,  
-40U,  50U,  64U,  80U,  
-101U,  128U,  161U,  203U,  
-256U,  322U,  406U,  512U,  
-645U,  812U,  1024U,  1290U,  
-1625U,  2048U,  2580U,  3250U,  
-4096U,  5160U,  6501U,  8192U,  
-10321U,  13003U,  16384U,  20642U,  
-26007U,  32768U,  41285U,  52015U,  
-65536U,  82570U,  104031U,  131072U,  
-165140U,  208063U,  262144U,  330280U,  
-416127U,  524288U,  660561U,  832255U,  
-1048576U,  1321122U,  1664510U,  2097152U,  
-2642245U,  3329021U,  4194304U,  5284491U,  
-6658042U,  8388608U,  10568983U,  13316085U,  
-16777216U,  21137967U,  26632170U,  33554432U,  
-42275935U,  53264340U,  67108864U,  84551870U,  
-106528681U,  134217728U,  169103740U,  213057362U,  
-268435456U,  338207481U,  426114725U,  536870912U,  
-676414963U,  852229450U,  1073741824U,  1352829926U,  
-1704458900U,  2147483648U,  2705659852U,  3408917801U,  
+2U,  3U,  4U,  5U,
+6U,  8U,  10U,  12U,
+16U,  20U,  25U,  32U,
+40U,  50U,  64U,  80U,
+101U,  128U,  161U,  203U,
+256U,  322U,  406U,  512U,
+645U,  812U,  1024U,  1290U,
+1625U,  2048U,  2580U,  3250U,
+4096U,  5160U,  6501U,  8192U,
+10321U,  13003U,  16384U,  20642U,
+26007U,  32768U,  41285U,  52015U,
+65536U,  82570U,  104031U,  131072U,
+165140U,  208063U,  262144U,  330280U,
+416127U,  524288U,  660561U,  832255U,
+1048576U,  1321122U,  1664510U,  2097152U,
+2642245U,  3329021U,  4194304U,  5284491U,
+6658042U,  8388608U,  10568983U,  13316085U,
+16777216U,  21137967U,  26632170U,  33554432U,
+42275935U,  53264340U,  67108864U,  84551870U,
+106528681U,  134217728U,  169103740U,  213057362U,
+268435456U,  338207481U,  426114725U,  536870912U,
+676414963U,  852229450U,  1073741824U,  1352829926U,
+1704458900U,  2147483648U,  2705659852U,  3408917801U,
 };
 
 static unsigned int magic_bits[MAX_MAGIC][8]={
@@ -219,9 +219,9 @@ static char *instrnames[MAXINSTR]={
 /* Bit patterns in the compressed code stream: */
 
 static const int seq_instr[MAXINSTR][2]=
-  {     
+  {
     { 1,1 }, /* 1 : one large atom + runlength encoded small integers. Use same settings as before. */
-    { 0,2 }, /* 00 : set base and runlength in next four bits (x). base (increase/keep/decrease)=x%3-1. runlength=1+x/3. 
+    { 0,2 }, /* 00 : set base and runlength in next four bits (x). base (increase/keep/decrease)=x%3-1. runlength=1+x/3.
 	              The special value 1111 in the four bits means runlength=6 and base change=0 */
     { 4,4 }, /* 0100 : next only a large atom comes. */
     { 5,4 }, /* 0101 : next only runlength encoded small integers. Use same settings as before. */
@@ -363,9 +363,9 @@ static void swap_is_better(int *input, int *minint, int *sum_normal, int *sum_sw
 
 static void swapdecide(struct coder *coder, int *input,int *swapatoms, int *large_index, int *minint, unsigned char **output_ptr)
 {
-  (void)large_index;
   int didswap=0;
   int normal,swapped;
+  (void)large_index;
   swap_is_better(input,minint,&normal,&swapped);
   /* We have to determine if it is worth to change the behaviour.
      If diff is positive it means that it is worth something to
@@ -376,7 +376,7 @@ static void swapdecide(struct coder *coder, int *input,int *swapatoms, int *larg
   */
 #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)))
     {
@@ -447,7 +447,7 @@ static void trajcoder_base_compress(int *input, int n, int *index, unsigned char
   int i,j;
   for (i=0; i<19; i++)
     largeint[i]=0U;
-  
+
   for (i=0; i<n; i++)
     {
       if (i!=0)
@@ -468,7 +468,7 @@ static void trajcoder_base_compress(int *input, int n, int *index, unsigned char
 #ifdef SHOWIT
   for (i=0; i<19; i++)
     fprintf(stderr,"Largeint[%d]=0x%x\n",i,largeint[i]);
-#endif  
+#endif
 #endif
   /* Convert the largeint to a sequence of bytes. */
   for (i=0; i<18; i++)
@@ -504,7 +504,7 @@ static void trajcoder_base_decompress(unsigned char *input, int n, int *index, i
 #ifdef SHOWIT
   for (i=0; i<19; i++)
     fprintf(stderr,"Largeint[%d]=0x%x\n",i,largeint[i]);
-#endif  
+#endif
 #endif
   for (i=n-1; i>=0; i--)
     {
@@ -514,7 +514,7 @@ static void trajcoder_base_decompress(unsigned char *input, int n, int *index, i
       fprintf(stderr,"Remainder: %u\n",remainder);
 #endif
 #endif
-#if 0      
+#if 0
       for (j=0; j<19; j++)
 	largeint[j]=largeint_tmp[j];
 #endif
@@ -552,7 +552,7 @@ int nvalues_sum;
 static void write_three_large(struct coder *coder, int *encode_ints, int *large_index, 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);      
+  Ptngc_writemanybits(coder,compress_buffer,nbits,output_ptr);
 #ifdef SHOWIT
   fprintf(stderr,"nbits=%d (%g)\n",nbits,nbits/3.);
   nbits_sum+=nbits;
@@ -565,7 +565,7 @@ 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];
@@ -587,13 +587,13 @@ 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<21) && (nencode<ntriplets_left*3))
     {
       encode_ints[nencode]=input_ptr[nencode]-minint[0]-tmp_prevcoord[0];
@@ -610,7 +610,7 @@ 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]-minint[0];
       tmp_prevcoord[1]=input_ptr[nencode+1]-minint[1];
       tmp_prevcoord[2]=input_ptr[nencode+2]-minint[2];
@@ -837,7 +837,7 @@ unsigned char *Ptngc_pack_array_xtc2(struct coder *coder,int *input, int *length
 	  /* Insert the next batch of integers to be encoded into the buffer */
 #ifdef SHOWIT
 	  fprintf(stderr,"Initial batch\n");
-#endif	  
+#endif
 	  insert_batch(input_ptr,ntriplets_left,prevcoord,minint,encode_ints,0,&nencode);
 
 	  /* First we must decide if the next value is large (does not reasonably fit in current small encoding)
@@ -883,8 +883,8 @@ unsigned char *Ptngc_pack_array_xtc2(struct coder *coder,int *input, int *length
 				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;
 		    }
 		}
@@ -911,11 +911,11 @@ unsigned char *Ptngc_pack_array_xtc2(struct coder *coder,int *input, int *length
 	      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. */
@@ -974,7 +974,7 @@ unsigned char *Ptngc_pack_array_xtc2(struct coder *coder,int *input, int *length
 	      new_runlength=1;
 	      new_small_index=small_index;
 	    }
-	  
+
 	  iter_runlength=new_runlength;
 	  iter_small_index=new_small_index;
 
@@ -987,7 +987,7 @@ unsigned char *Ptngc_pack_array_xtc2(struct coder *coder,int *input, int *length
 	  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,magic[new_small_index]);
 #endif
@@ -1040,7 +1040,7 @@ unsigned char *Ptngc_pack_array_xtc2(struct coder *coder,int *input, int *length
 	  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
@@ -1050,7 +1050,7 @@ unsigned char *Ptngc_pack_array_xtc2(struct coder *coder,int *input, int *length
 	      if ((new_runlength!=runlength) || (new_small_index!=small_index))
 		{
 		  int change=new_small_index-small_index;
-		  
+
 		  if (new_small_index<=0)
 		    change=0;
 
@@ -1072,12 +1072,12 @@ unsigned char *Ptngc_pack_array_xtc2(struct coder *coder,int *input, int *length
 			    rejected=0;
 #ifdef SHOWIT
 			    fprintf(stderr,"Tested decrease %d of index: %g>=%g?\n",change,isum,(double)magic[small_index+change]*(double)magic[small_index+change]);
-#endif			      
+#endif
 			    if (isum>(double)magic[small_index+change]*(double)magic[small_index+change])
 			      {
 #ifdef SHOWIT
 				fprintf(stderr,"Rejected decrease %d of index due to length of vector: %g>=%g\n",change,isum,(double)magic[small_index+change]*(double)magic[small_index+change]);
-#endif			      
+#endif
 				rejected=1;
 				change++;
 			      }
@@ -1155,10 +1155,10 @@ unsigned char *Ptngc_pack_array_xtc2(struct coder *coder,int *input, int *length
 #ifdef SHOWIT
 		  else
 		    fprintf(stderr,"Rejected base change due to only change==-1\n");
-#endif		  
+#endif
 #ifdef SHOWIT
 		  fprintf(stderr,"Current small index: %d Base=%d\n",small_index,magic[small_index]);
-#endif		  
+#endif
 		}
 	      /* If we have a large previous integer we can combine it with a sequence of small ints. */
 	      if (has_large)
@@ -1183,7 +1183,7 @@ unsigned char *Ptngc_pack_array_xtc2(struct coder *coder,int *input, int *length
 		    }
 		  else
 		    {
-		      
+
 #ifdef SHOWIT
 		      fprintf(stderr,"Sequence of one large and small integers (good compression).\n");
 #endif
@@ -1239,7 +1239,7 @@ unsigned char *Ptngc_pack_array_xtc2(struct coder *coder,int *input, int *length
 	      fprintf(stderr,"Prevcoord in packing: %d %d %d\n",
 		      prevcoord[0],prevcoord[1],prevcoord[2]);
 #endif
-	  
+
 	      input_ptr+=3*runlength;
 	      ntriplets_left-=runlength;
 	    }
@@ -1248,13 +1248,13 @@ unsigned char *Ptngc_pack_array_xtc2(struct coder *coder,int *input, int *length
 #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. */
   if (has_large)
@@ -1271,7 +1271,6 @@ unsigned char *Ptngc_pack_array_xtc2(struct coder *coder,int *input, int *length
 
 int Ptngc_unpack_array_xtc2(struct coder *coder,unsigned char *packed,int *output, int length)
 {
-  (void)coder;
   unsigned char *ptr=packed;
   int bitptr=0;
   int minint[3];
@@ -1284,6 +1283,7 @@ int Ptngc_unpack_array_xtc2(struct coder *coder,unsigned char *packed,int *outpu
   int large_nbits;
   unsigned char compress_buffer[18*4]; /* Holds compressed result for 3 large ints or up to 18 small ints. */
   int encode_ints[21]; /* Up to 3 large + 18 small ints can be encoded at once */
+  (void)coder;
 
   /* Read min integers. */
   minint[0]=unpositive_int(readbits(&ptr,&bitptr,32));
@@ -1297,7 +1297,7 @@ int Ptngc_unpack_array_xtc2(struct coder *coder,unsigned char *packed,int *outpu
   small_index=readbits(&ptr,&bitptr,8);
 
   large_nbits=compute_magic_bits(large_index);
-  
+
 #ifdef SHOWIT
   fprintf(stderr,"Minimum integers: %d %d %d\n",minint[0],minint[1],minint[2]);
   fprintf(stderr,"Large indices: %d %d %d\n",large_index[0],large_index[1],large_index[2]);
@@ -1316,7 +1316,7 @@ int Ptngc_unpack_array_xtc2(struct coder *coder,unsigned char *packed,int *outpu
 #ifdef SHOWIT
       if ((instr>=0) && (instr<MAXINSTR))
 	fprintf(stderr,"Decoded instruction %s\n",instrnames[instr]);
-#endif      
+#endif
       if ((instr==INSTR_DEFAULT) /* large+small */
 	  || (instr==INSTR_ONLY_LARGE) /* only large */
 	  || (instr==INSTR_ONLY_SMALL)) /* only small */
@@ -1336,7 +1336,7 @@ int Ptngc_unpack_array_xtc2(struct coder *coder,unsigned char *packed,int *outpu
 	      large_ints[2]=encode_ints[2];
 #ifdef SHOWIT
 	      fprintf(stderr,"large ints: %d %d %d\n",large_ints[0],large_ints[1],large_ints[2]);
-#endif	      
+#endif
 	    }
 	  if (instr!=INSTR_ONLY_LARGE)
 	    {
@@ -1355,7 +1355,7 @@ int Ptngc_unpack_array_xtc2(struct coder *coder,unsigned char *packed,int *outpu
 #ifdef SHOWIT
 	      for (i=0; i<runlength; i++)
 		fprintf(stderr,"small ints: %d %d %d\n",encode_ints[i*3+0],encode_ints[i*3+1],encode_ints[i*3+2]);
-#endif	      
+#endif
 	    }
 	  if (instr==INSTR_DEFAULT)
 	    {
@@ -1495,7 +1495,7 @@ int Ptngc_unpack_array_xtc2(struct coder *coder,unsigned char *packed,int *outpu
 	}
 #ifdef SHOWIT
       fprintf(stderr,"Number of triplets left is %d\n",ntriplets_left);
-#endif      
+#endif
     }
   return 0;
 }
diff --git a/src/compression/xtc3.c b/src/compression/xtc3.c
index f7bab63..834def0 100644
--- a/src/compression/xtc3.c
+++ b/src/compression/xtc3.c
@@ -219,9 +219,9 @@ static void insert_value_in_array(unsigned int **ptr, int *nele, int *nele_alloc
 
 static void swapdecide(struct xtc3_context *xtc3_context, int *input,int *swapatoms, int *large_index, int *minint)
 {
-  (void)large_index;
   int didswap=0;
   int normal,swapped;
+  (void)large_index;
   swap_is_better(input,minint,&normal,&swapped);
   /* We have to determine if it is worth to change the behaviour.
      If diff is positive it means that it is worth something to
diff --git a/src/lib/tng_io.c b/src/lib/tng_io.c
index db44e30..35ed5eb 100644
--- a/src/lib/tng_io.c
+++ b/src/lib/tng_io.c
@@ -3978,11 +3978,11 @@ static tng_function_status tng_uncompress(tng_trajectory_t tng_data,
                                           void *start_pos,
                                           const unsigned long uncompressed_len)
 {
-    (void)tng_data;
     char *temp;
     double *d_dest = 0;
     float *f_dest = 0;
     int offset, result;
+    (void)tng_data;
 
     if(block->id != TNG_TRAJ_POSITIONS &&
        block->id != TNG_TRAJ_VELOCITIES)
@@ -4027,7 +4027,7 @@ static tng_function_status tng_uncompress(tng_trajectory_t tng_data,
         return(TNG_FAILURE);
     }
 
-    offset = start_pos - (void *)block->block_contents;
+    offset = (char *)start_pos - (char *)block->block_contents;
 
 
     block->block_contents_size = uncompressed_len + offset;
@@ -4076,10 +4076,10 @@ static tng_function_status tng_gzip_compress(tng_trajectory_t tng_data,
                                              tng_gen_block_t block,
                                              void *start_pos, const int len)
 {
-    (void)tng_data;
     Bytef *dest;
     char *temp;
     uLong max_len, stat;
+    (void)tng_data;
 
     max_len = compressBound(len);
     dest = malloc(max_len);
@@ -4125,11 +4125,11 @@ static tng_function_status tng_gzip_uncompress(tng_trajectory_t tng_data,
                                                void *start_pos,
                                                unsigned long uncompressed_len)
 {
-    (void)tng_data;
     Bytef *dest;
     char *temp;
     unsigned long stat;
     int offset;
+    (void)tng_data;
 
     offset = start_pos - (void *)block->block_contents;
 
@@ -4200,9 +4200,9 @@ static tng_function_status tng_allocate_particle_data_mem
                  const int64_t n_particles,
                  const int64_t n_values_per_frame)
 {
-    (void)tng_data;
     void ***values;
     int64_t i, j, k, size, frame_alloc;
+    (void)tng_data;
 
     if(n_particles == 0 || n_values_per_frame == 0)
     {
@@ -4629,7 +4629,8 @@ static tng_function_status tng_particle_data_read
     }
     else
     {
-        memcpy(data->values + n_frames_div * size * n_values * num_first_particle,
+        memcpy((char *)data->values + n_frames_div * size * n_values *
+               num_first_particle,
                block->block_contents + *offset,
                block->block_contents_size - *offset);
         switch(datatype)
@@ -4640,7 +4641,7 @@ static tng_function_status tng_particle_data_read
                 for(i = 0; i < (block->block_contents_size - *offset); i+=size)
                 {
                     if(tng_data->input_endianness_swap_func_32(tng_data,
-                        (int32_t *)(data->values + i))
+                        (int32_t *)((char *)data->values + i))
                         != TNG_SUCCESS)
                     {
                         printf("Cannot swap byte order. %s: %d\n",
@@ -4656,7 +4657,7 @@ static tng_function_status tng_particle_data_read
                 for(i = 0; i < (block->block_contents_size - *offset); i+=size)
                 {
                     if(tng_data->input_endianness_swap_func_64(tng_data,
-                        (int64_t *)(data->values + i))
+                        (int64_t *)((char *)data->values + i))
                         != TNG_SUCCESS)
                     {
                         printf("Cannot swap byte order. %s: %d\n",
@@ -5246,9 +5247,9 @@ static tng_function_status tng_allocate_data_mem
                  int64_t stride_length,
                  const int64_t n_values_per_frame)
 {
-    (void)tng_data;
     void **values;
     int64_t i, j, size, frame_alloc;
+    (void)tng_data;
 
     if(data->strings && data->datatype == TNG_CHAR_DATA)
     {
@@ -5507,7 +5508,7 @@ static tng_function_status tng_data_read(tng_trajectory_t tng_data,
                 for(i = 0; i < (block->block_contents_size - *offset); i+=size)
                 {
                     if(tng_data->input_endianness_swap_func_32(tng_data,
-                        (int32_t *)(data->values + i))
+                        (int32_t *)((char *)data->values + i))
                         != TNG_SUCCESS)
                     {
                         printf("Cannot swap byte order. %s: %d\n",
@@ -5523,7 +5524,7 @@ static tng_function_status tng_data_read(tng_trajectory_t tng_data,
                 for(i = 0; i < (block->block_contents_size - *offset); i+=size)
                 {
                     if(tng_data->input_endianness_swap_func_64(tng_data,
-                        (int64_t *)(data->values + i))
+                        (int64_t *)((char *)data->values + i))
                         != TNG_SUCCESS)
                     {
                         printf("Cannot swap byte order. %s: %d\n",
@@ -6732,8 +6733,8 @@ tng_function_status tng_atom_name_set(tng_trajectory_t tng_data,
                                       tng_atom_t atom,
                                       const char *new_name)
 {
-    (void)tng_data;
     int len;
+    (void)tng_data;
 
     len = tng_min(strlen(new_name) + 1, TNG_MAX_STR_LEN);
 
@@ -6764,8 +6765,8 @@ tng_function_status tng_atom_type_set(tng_trajectory_t tng_data,
                                       tng_atom_t atom,
                                       const char *new_type)
 {
-    (void)tng_data;
     int len;
+    (void)tng_data;
 
     len = tng_min(strlen(new_type) + 1, TNG_MAX_STR_LEN);
 
@@ -6924,8 +6925,8 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_name_set
                  tng_molecule_t molecule,
                  const char *new_name)
 {
-    (void)tng_data;
     int len;
+    (void)tng_data;
 
     len = tng_min(strlen(new_name) + 1, TNG_MAX_STR_LEN);
 
@@ -7038,8 +7039,8 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_chain_find
                  int64_t nr,
                  tng_chain_t *chain)
 {
-    (void)tng_data;
     int i, n_chains;
+    (void)tng_data;
 
     n_chains = molecule->n_chains;
 
@@ -7128,8 +7129,8 @@ tng_function_status DECLSPECDLLEXPORT tng_chain_name_set
                  tng_chain_t chain,
                  const char *new_name)
 {
-    (void)tng_data;
     int len;
+    (void)tng_data;
 
     len = tng_min(strlen(new_name) + 1, TNG_MAX_STR_LEN);
 
@@ -7163,8 +7164,8 @@ tng_function_status DECLSPECDLLEXPORT tng_chain_residue_find
                  int64_t id,
                  tng_residue_t *residue)
 {
-    (void)tng_data;
     int i, n_residues;
+    (void)tng_data;
 
     n_residues = chain->n_residues;
 
@@ -7291,8 +7292,8 @@ tng_function_status DECLSPECDLLEXPORT tng_residue_name_set(tng_trajectory_t tng_
                                                            tng_residue_t residue,
                                                            const char *new_name)
 {
-    (void)tng_data;
     int len;
+    (void)tng_data;
 
     len = tng_min(strlen(new_name) + 1, TNG_MAX_STR_LEN);
 
@@ -7411,8 +7412,8 @@ tng_function_status DECLSPECDLLEXPORT tng_molecule_init(const tng_trajectory_t t
 tng_function_status DECLSPECDLLEXPORT tng_molecule_destroy(const tng_trajectory_t tng_data,
                                                            tng_molecule_t molecule)
 {
-    (void)tng_data;
     int i;
+    (void)tng_data;
 
     if(molecule->name)
     {
@@ -12024,8 +12025,8 @@ tng_function_status DECLSPECDLLEXPORT tng_data_values_free
                  const int64_t n_values_per_frame,
                  const char type)
 {
-    (void)tng_data;
     int i, j;
+    (void)tng_data;
 
     if(values)
     {
@@ -12134,8 +12135,8 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_values_free
                  const int64_t n_values_per_frame,
                  const char type)
 {
-    (void)tng_data;
     int i, j, k;
+    (void)tng_data;
 
     if(values)
     {
@@ -12269,7 +12270,7 @@ tng_function_status DECLSPECDLLEXPORT tng_data_get
         {
             for(j=*n_values_per_frame; j--;)
             {
-                (*values)[i][j].i = *(int *)(data->values + size *
+                (*values)[i][j].i = *(int *)((char *)data->values + size *
                                              (i*(*n_values_per_frame) + j));
             }
         }
@@ -12280,7 +12281,7 @@ tng_function_status DECLSPECDLLEXPORT tng_data_get
         {
             for(j=*n_values_per_frame; j--;)
             {
-                (*values)[i][j].f = *(float *)(data->values + size *
+                (*values)[i][j].f = *(float *)((char *)data->values + size *
                                                (i*(*n_values_per_frame) + j));
             }
         }
@@ -12292,7 +12293,7 @@ tng_function_status DECLSPECDLLEXPORT tng_data_get
         {
             for(j=*n_values_per_frame; j--;)
             {
-                (*values)[i][j].d = *(double *)(data->values + size *
+                (*values)[i][j].d = *(double *)((char *)data->values + size *
                                                 (i*(*n_values_per_frame) + j));
             }
         }
@@ -12546,9 +12547,9 @@ tng_function_status DECLSPECDLLEXPORT tng_data_interval_get
             }
             for(j=*n_values_per_frame; j--;)
             {
-                (*values)[i][j].i = *(int *)(data->values + size *
-                                             (current_frame_pos *
-                                              (*n_values_per_frame) + j));
+                (*values)[i][j].i = *(int *)((char *)data->values + size *
+                                            (current_frame_pos *
+                                             (*n_values_per_frame) + j));
             }
             current_frame_pos++;
         }
@@ -12568,7 +12569,7 @@ tng_function_status DECLSPECDLLEXPORT tng_data_interval_get
             }
             for(j=*n_values_per_frame; j--;)
             {
-                (*values)[i][j].f = *(float *)(data->values + size *
+                (*values)[i][j].f = *(float *)((char *)data->values + size *
                                                (current_frame_pos *
                                                 (*n_values_per_frame) + j));
             }
@@ -12591,7 +12592,7 @@ tng_function_status DECLSPECDLLEXPORT tng_data_interval_get
             }
             for(j=*n_values_per_frame; j--;)
             {
-                (*values)[i][j].d = *(double *)(data->values + size *
+                (*values)[i][j].d = *(double *)((char *)data->values + size *
                                                 (current_frame_pos *
                                                  (*n_values_per_frame) + j));
             }
@@ -12735,7 +12736,7 @@ tng_function_status DECLSPECDLLEXPORT tng_data_vector_interval_get
                        last_frame_pos / *stride_length;
         n_frames_div_2 = tng_max(1, n_frames_div_2);
 
-        memcpy(*values, current_values + n_frames_div * frame_size,
+        memcpy(*values, (char *)current_values + n_frames_div * frame_size,
                n_frames_div_2 * frame_size);
 
         current_frame_pos += n_frames - frame_set->first_frame -
@@ -12940,7 +12941,7 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_get
                 for(k=*n_values_per_frame; k--;)
                 {
                     (*values)[i][mapping][k].i = *(int *)
-                                                 (data->values + size *
+                                                 ((char *)data->values + size *
                                                  (i * i_step + j *
                                                   (*n_values_per_frame) + k));
                 }
@@ -12958,7 +12959,7 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_get
                 for(k=*n_values_per_frame; k--;)
                 {
                     (*values)[i][mapping][k].f = *(float *)
-                                                 (data->values + size *
+                                                 ((char *)data->values + size *
                                                  (i * i_step + j *
                                                   (*n_values_per_frame) + k));
                 }
@@ -12977,7 +12978,7 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_get
                 for(k=*n_values_per_frame; k--;)
                 {
                     (*values)[i][mapping][k].d = *(double *)
-                                                 (data->values + size *
+                                                 ((char *)data->values + size *
                                                  (i * i_step + j *
                                                   (*n_values_per_frame) + k));
                 }
@@ -13298,7 +13299,7 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_interval_get
                 for(k=*n_values_per_frame; k--;)
                 {
                     (*values)[i][mapping][k].i = *(int *)
-                                                 (data->values + size *
+                                                 ((char *)data->values + size *
                                                   (current_frame_pos *
                                                    i_step + j *
                                                    (*n_values_per_frame) + k));
@@ -13327,7 +13328,7 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_interval_get
                 for(k=*n_values_per_frame; k--;)
                 {
                     (*values)[i][mapping][k].f = *(float *)
-                                                 (data->values + size *
+                                                 ((char *)data->values + size *
                                                   (current_frame_pos *
                                                    i_step + j *
                                                    (*n_values_per_frame) + k));
@@ -13357,7 +13358,7 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_interval_get
                 for(k=*n_values_per_frame; k--;)
                 {
                     (*values)[i][mapping][k].d = *(double *)
-                                                 (data->values + size *
+                                                 ((char *)data->values + size *
                                                   (current_frame_pos *
                                                    i_step + j *
                                                    (*n_values_per_frame) + k));
@@ -13506,7 +13507,7 @@ tng_function_status DECLSPECDLLEXPORT tng_particle_data_vector_interval_get
                        last_frame_pos / *stride_length;
         n_frames_div_2 = tng_max(1, n_frames_div_2);
 
-        memcpy(*values, current_values + n_frames_div * frame_size,
+        memcpy(*values, (char *)current_values + n_frames_div * frame_size,
                n_frames_div_2 * frame_size);
 
         current_frame_pos += n_frames - frame_set->first_frame -
@@ -13676,11 +13677,11 @@ tng_function_status DECLSPECDLLEXPORT tng_util_molecule_particles_get
                  char ***chain_names,
                  int64_t **chain_ids)
 {
-    (void)tng_data;
     tng_atom_t atom;
     tng_residue_t res;
     tng_chain_t chain;
     int64_t i;
+    (void)tng_data;
 
     *n_particles = mol->n_atoms;
 
@@ -14207,7 +14208,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_generic_write
 
             frame_pos = (frame_nr - frame_set->first_frame) / stride_length;
 
-            memcpy(p_data->values + sizeof(float) * frame_pos * n_particles *
+            memcpy((char *)p_data->values + sizeof(float) * frame_pos * n_particles *
                    n_values_per_frame, values, sizeof(float) *
                    n_particles * n_values_per_frame);
         }
@@ -14257,7 +14258,7 @@ tng_function_status DECLSPECDLLEXPORT tng_util_generic_write
 
             frame_pos = (frame_nr - frame_set->first_frame) / stride_length;
 
-            memcpy(np_data->values + sizeof(float) * frame_pos *
+            memcpy((char *)np_data->values + sizeof(float) * frame_pos *
                    n_values_per_frame, values, sizeof(float) *
                    n_values_per_frame);
         }