Fixing many llvm clang warnings.

4 files changed, 34 insertions, 42 deletions

diff --git a/src/compression/bwt.c b/src/compression/bwt.c
index ea75199..e5cb5ce 100644
--- a/src/compression/bwt.c
+++ b/src/compression/bwt.c
@@ -37,8 +37,8 @@ static int compare_index(int i1,int i2,int nvals,unsigned int *vals,unsigned int
       int k1=(int)(nrepeat[i1]&0xFFU);
       int repeat2=(int)(nrepeat[i2]>>8);
       int k2=(int)(nrepeat[i2]&0xFFU);
-      
-      if ((repeat1>1) && (repeat1>1) && (k1==k2))
+
+      if ((repeat1>1) && (repeat2>1) && (k1==k2))
 	{
 	  int maxskip=0;
 	  /* Yes. Compare the repeating patterns. */
@@ -88,7 +88,7 @@ void Ptngc_bwt_merge_sort_inner(int *indices, int nvals,unsigned int *vals,
       middle=start+(end-start)/2;
 #if 0
       printf("For start %d end %d obtained new middle: %d\n",start,end,middle);
-#endif      
+#endif
       Ptngc_bwt_merge_sort_inner(indices,nvals,vals,
 			   start,middle,
 			   nrepeat,
@@ -126,7 +126,7 @@ void Ptngc_bwt_merge_sort_inner(int *indices, int nvals,unsigned int *vals,
 		  if (compare_index(indices[ileft],indices[iright],nvals,vals,nrepeat)>0)
 		    {
 		      workarray[i]=indices[iright];
-		      iright++;		      
+		      iright++;
 		    }
 		  else
 		    {
@@ -221,7 +221,7 @@ void Ptngc_comp_to_bwt(unsigned int *vals, int nvals,
 						  pattern. */
 #ifdef SHOWIT
 			      printf("Best j and k is now %d and %d\n",good_j,good_k);
-#endif			      
+#endif
 			    }
 			}
 		      else
@@ -257,7 +257,7 @@ void Ptngc_comp_to_bwt(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 */
 	}
     }
@@ -334,4 +334,4 @@ void Ptngc_comp_from_bwt(unsigned int *input, int nvals, int index,
   free(p);
   free(c);
 }
-		   
+
diff --git a/src/compression/coder.c b/src/compression/coder.c
index 270e4d3..ca3de86 100644
--- a/src/compression/coder.c
+++ b/src/compression/coder.c
@@ -171,7 +171,6 @@ static int pack_stopbits_item(struct coder *coder_inst,int item, unsigned char *
     else if (item<0)
 	s=2+(-item-1)*2;
     return write_stop_bit_code(coder_inst,s,coding_parameter,output);
-    return 0;
 }
 
 static int pack_triplet(struct coder *coder_inst,unsigned int *s, unsigned char **output, int coding_parameter,
@@ -194,7 +193,6 @@ static int pack_triplet(struct coder *coder_inst,unsigned int *s, unsigned char
     {
       if (this_base>max_base)
 	return 1;
-      this_base=max_base;
       bits_per_value=maxbits;
       jbase=3;
     }
@@ -332,7 +330,7 @@ unsigned char *Ptngc_pack_array(struct coder *coder_inst,int *input, int *length
 
 static int unpack_array_stop_bits(struct coder *coder_inst,unsigned char *packed,int *output, int length, int coding_parameter)
 {
-  (void)coder_inst;
+  (void) coder_inst;
   int i,j;
   unsigned int extract_mask=0x80;
   unsigned char *ptr=packed;
@@ -385,7 +383,7 @@ static int unpack_array_stop_bits(struct coder *coder_inst,unsigned char *packed
 
 static int unpack_array_triplet(struct coder *coder_inst,unsigned char *packed,int *output, int length, int coding_parameter)
 {
-  (void)coder_inst;
+  (void) coder_inst;
   int i,j;
   unsigned int extract_mask=0x80;
   unsigned char *ptr=packed;
@@ -457,7 +455,7 @@ static int unpack_array_triplet(struct coder *coder_inst,unsigned char *packed,i
 
 static int unpack_array_bwlzh(struct coder *coder_inst,unsigned char *packed,int *output, int length, int natoms)
 {
-  (void)coder_inst;
+  (void) coder_inst;
   int i,j,k,n=length;
   unsigned int *pval=warnmalloc(n*sizeof *pval);
   int nframes=n/natoms/3;
diff --git a/src/compression/tng_compress.c b/src/compression/tng_compress.c
index ebd495b..2578336 100644
--- a/src/compression/tng_compress.c
+++ b/src/compression/tng_compress.c
@@ -481,13 +481,14 @@ static void compress_quantized_vel(int *quant, int *quant_inter,
   if (data)
     bufferfix((unsigned char*)data+bufloc,prec_hi,4);
   bufloc+=4;
+
+  length=natoms*3;
   /* The initial frame */
   if ((initial_coding==TNG_COMPRESS_ALGO_VEL_STOPBIT_ONETOONE) ||
       (initial_coding==TNG_COMPRESS_ALGO_VEL_TRIPLET_ONETOONE) ||
       (initial_coding==TNG_COMPRESS_ALGO_VEL_BWLZH_ONETOONE))
     {
       struct coder *coder=Ptngc_coder_init();
-      length=natoms*3;
       datablock=(char*)Ptngc_pack_array(coder,quant,&length,
 					    initial_coding,initial_coding_parameter,natoms,speed);
       Ptngc_coder_deinit(coder);
@@ -497,10 +498,12 @@ static void compress_quantized_vel(int *quant, int *quant_inter,
     bufferfix((unsigned char*)data+bufloc,(fix_t)length,4);
   bufloc+=4;
   /* The actual data block. */
-  if (data)
-    memcpy(data+bufloc,datablock,length);
-  free(datablock);
-  bufloc+=length;
+  if (data && datablock)
+    {
+      memcpy(data+bufloc,datablock,length);
+      free(datablock);
+      bufloc+=length;
+    }
   /* The remaining frames */
   if (nframes>1)
     {
@@ -683,7 +686,6 @@ static void determine_best_pos_initial_coding(int *quant, int *quant_intra, int
 	    {
 	      best_coding=current_coding;
 	      best_coding_parameter=current_coding_parameter;
-	      best_code_size=current_code_size;
 	    }
 	}
       *initial_coding=best_coding;
@@ -846,7 +848,6 @@ static void determine_best_pos_coding(int *quant, int *quant_inter, int *quant_i
 	    {
 	      best_coding=current_coding;
 	      best_coding_parameter=current_coding_parameter;
-	      best_code_size=current_code_size;
 	    }
 	}
       *coding=best_coding;
@@ -950,7 +951,6 @@ static void determine_best_vel_initial_coding(int *quant, int natoms, int speed,
 	    {
 	      best_coding=current_coding;
 	      best_coding_parameter=current_coding_parameter;
-	      best_code_size=current_code_size;
 	    }
 	}
       *initial_coding=best_coding;
@@ -1090,7 +1090,6 @@ static void determine_best_vel_coding(int *quant, int *quant_inter, int natoms,
 	  if (current_code_size<best_code_size)
 	    {
 	      best_coding=current_coding;
-	      best_code_size=current_code_size;
 	      best_coding_parameter=current_coding_parameter;
 	    }
 	}
@@ -1492,7 +1491,6 @@ int DECLSPECDLLEXPORT tng_compress_inquire(char *data,int *vel, int *natoms,
   prec_lo=readbufferfix((unsigned char *)data+bufloc,4);
   bufloc+=4;
   prec_hi=readbufferfix((unsigned char *)data+bufloc,4);
-  bufloc+=4;
   *precision=PRECISION(prec_hi, prec_lo);
   algo[0]=initial_coding;
   algo[1]=initial_coding_parameter;
@@ -1583,8 +1581,6 @@ static int tng_compress_uncompress_pos_gen(char *data,double *posd,float *posf,i
   /* The remaining frames. */
   if (nframes>1)
     {
-      /* The data block length. */
-      length=(int)readbufferfix((unsigned char *)data+bufloc,4);
       bufloc+=4;
       coder=Ptngc_coder_init();
       rval=Ptngc_unpack_array(coder,(unsigned char *)data+bufloc,quant+natoms*3,(nframes-1)*natoms*3,
@@ -1721,8 +1717,6 @@ static int tng_compress_uncompress_vel_gen(char *data,double *veld,float *velf,i
   /* The remaining frames. */
   if (nframes>1)
     {
-      /* The data block length. */
-      length=(int)readbufferfix((unsigned char *)data+bufloc,4);
       bufloc+=4;
       coder=Ptngc_coder_init();
       rval=Ptngc_unpack_array(coder,(unsigned char *)data+bufloc,quant+natoms*3,(nframes-1)*natoms*3,
diff --git a/src/compression/xtc3.c b/src/compression/xtc3.c
index 197cc12..297e948 100644
--- a/src/compression/xtc3.c
+++ b/src/compression/xtc3.c
@@ -512,7 +512,6 @@ static void buffer_large(struct xtc3_context *xtc3_context, int *input, int inpd
       thislen=compute_intlen(interdelta);
       if (thislen*TRESHOLD_INTRA_INTER_DIRECT<minlen)
 	{
-	  minlen=thislen;
 	  best_type=2; /* Inter delta */
 	}
     }
@@ -730,7 +729,6 @@ static void base_decompress(unsigned char *input, int len, unsigned int *output)
       while (nvals_left)
 	{
 	  int n;
-	  int numints;
 	  if (basegiven==0)
 	    {
 	      base=(unsigned int)(input[0])|
@@ -755,24 +753,26 @@ static void base_decompress(unsigned char *input, int len, unsigned int *output)
 #ifdef SHOWIT
 	  fprintf(stderr,"Reading largeint: ");
 #endif
-	  for (j=0; j<numbytes; j++)
-	    {
-	      int ilarge=j/4;
-	      int ibyte=j%4;
-	      largeint[ilarge]|=((unsigned int)input[j])<<(ibyte*8);
+          if (numbytes/4 < maxbasevals+1)
+            {
+	      for (j=0; j<numbytes; j++)
+	        {
+	          int ilarge=j/4;
+	          int ibyte=j%4;
+	          largeint[ilarge]|=((unsigned int)input[j])<<(ibyte*8);
 #ifdef SHOWIT
-	      fprintf(stderr,"%02x",(unsigned int)input[j]);
+	          fprintf(stderr,"%02x",(unsigned int)input[j]);
 #endif
+                }
 	    }
 #ifdef SHOWIT
-	      fprintf(stderr,"\n");
+	  fprintf(stderr,"\n");
 #endif
 	  input+=numbytes;
 	  /* Do the long division required to get the output values. */
 	  n=maxbasevals;
 	  if (n>nvals_left)
 	    n=nvals_left;
-	  numints=(numbytes+3)/4;
 	  for (i=n-1; i>=0; i--)
 	    {
 	      output[outvals+i*3]=Ptngc_largeint_div(base,largeint,largeint_tmp,maxbasevals+1);
@@ -1699,21 +1699,21 @@ static void unpack_one_large(struct xtc3_context *xtc3_context,
 			     int natoms, int current_large_type)
 {
   int large_ints[3]={0,0,0};
-  if (current_large_type==0)
+  if (current_large_type==0 && xtc3_context->large_direct)
     {
       large_ints[0]=(int)xtc3_context->large_direct[(*ilargedir)]+minint[0];
       large_ints[1]=(int)xtc3_context->large_direct[(*ilargedir)+1]+minint[1];
       large_ints[2]=(int)xtc3_context->large_direct[(*ilargedir)+2]+minint[2];
       (*ilargedir)+=3;
     }
-  else if (current_large_type==1)
+  else if (current_large_type==1 && xtc3_context->large_intra_delta)
     {
       large_ints[0]=unpositive_int(xtc3_context->large_intra_delta[(*ilargeintra)])+prevcoord[0];
       large_ints[1]=unpositive_int(xtc3_context->large_intra_delta[(*ilargeintra)+1])+prevcoord[1];
       large_ints[2]=unpositive_int(xtc3_context->large_intra_delta[(*ilargeintra)+2])+prevcoord[2];
       (*ilargeintra)+=3;
     }
-  else
+  else if (xtc3_context->large_inter_delta)
     {
       large_ints[0]=unpositive_int(xtc3_context->large_inter_delta[(*ilargeinter)])
 	+output[outdata-natoms*3+didswap*3];
@@ -1838,7 +1838,7 @@ int Ptngc_unpack_array_xtc3(unsigned char *packed,int *output, int length, int n
   prevcoord[1]=minint[1];
   prevcoord[2]=minint[2];
 
-  while (ntriplets_left>0)
+  while (ntriplets_left>0 && iinstr<xtc3_context.ninstr)
     {
       int instr=xtc3_context.instructions[iinstr++];
 #ifdef SHOWIT
@@ -1895,7 +1895,7 @@ int Ptngc_unpack_array_xtc3(unsigned char *packed,int *output, int length, int n
 	      outdata+=runlength*3;
 	    }
 	}
-      else if (instr==INSTR_LARGE_RLE)
+      else if (instr==INSTR_LARGE_RLE && irle<xtc3_context.nrle)
 	{
 	  int large_rle=xtc3_context.rle[irle++];
 #ifdef SHOWIT
@@ -1910,7 +1910,7 @@ int Ptngc_unpack_array_xtc3(unsigned char *packed,int *output, int length, int n
 	      outdata+=3;
 	    }
 	}
-      else if (instr==INSTR_SMALL_RUNLENGTH)
+      else if (instr==INSTR_SMALL_RUNLENGTH && irle<xtc3_context.nrle)
 	{
 	  runlength=xtc3_context.rle[irle++];
 #ifdef SHOWIT