/* 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
#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);
+int Ptngc_find_magic_index(const unsigned int maxval);
-static unsigned int positive_int(int item)
+static TNG_INLINE unsigned int positive_int(const int item)
{
int s=0;
if (item>0)
return s;
}
-static int unpositive_int(int val)
+static TNG_INLINE int unpositive_int(const int val)
{
int s=(val+1)/2;
if ((val%2)==0)
}
/* Modifies three integer values for better compression of water */
-static void swap_ints(int *in, int *out)
+static void swap_ints(const int *in, int *out)
{
out[0]=in[0]+in[1];
out[1]=-in[1];
out[2]=in[1]+in[2];
}
-static void swap_is_better(int *input, int *minint, int *sum_normal, int *sum_swapped)
+static void swap_is_better(const int *input, const int *minint, int *sum_normal, int *sum_swapped)
{
int normal_max=0;
int swapped_max=0;
}
static void insert_value_in_array(unsigned int **ptr, int *nele, int *nele_alloc,
- unsigned int value,
+ const unsigned int value,
char *arrayname)
{
#ifndef SHOWIT
/* 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(const int *input, const int small_index, const int max_large_index)
{
int is=0;
int i;
int nvalues_sum;
#endif
-static void insert_batch(int *input_ptr, int ntriplets_left, int *prevcoord, int *encode_ints, int startenc, int *nenc)
+static void insert_batch(const int *input_ptr, const int ntriplets_left, const int *prevcoord, int *encode_ints, const int startenc, int *nenc)
{
int nencode=startenc*3;
int tmp_prevcoord[3];
*nenc=nencode;
}
-static void large_instruction_change(struct xtc3_context *xtc3_context, int i)
+static void large_instruction_change(struct xtc3_context *xtc3_context, const int i)
{
/* If the first large is of a different kind than the currently used we must
emit an "instruction" to change the large type. */
}
static void write_three_large(struct xtc3_context *xtc3_context,
- int i)
+ const int i)
{
int m;
if (xtc3_context->current_large_type==0)
}
static void flush_large(struct xtc3_context *xtc3_context,
- int n) /* How many to flush. */
+ const int n) /* How many to flush. */
{
int i;
i=0;
return (double)m;
}
-static void buffer_large(struct xtc3_context *xtc3_context, int *input, int inpdata,
- int natoms, int intradelta_ok)
+static void buffer_large(struct xtc3_context *xtc3_context, int *input, const int inpdata,
+ const int natoms, const int intradelta_ok)
{
unsigned int direct[3], intradelta[3]={0,}, interdelta[3]={0,};
double minlen;
xtc3_context->has_large++;
}
-static void output_int(unsigned char *output,int *outdata, unsigned int n)
+static void output_int(unsigned char *output,int *outdata, const unsigned int n)
{
output[(*outdata)++]=((unsigned int)n)&0xFFU;
output[(*outdata)++]=(((unsigned int)n)>>8)&0xFFU;
#define BASEINTERVAL 8
/* How many bytes are needed to store n values in base base */
-static int base_bytes(unsigned int base, int n)
+static int base_bytes(const unsigned int base, const int n)
{
int i,j;
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);
}
return numbytes;
}
-static void base_compress(unsigned int *data, int len, unsigned char *output, int *outlen)
+static void base_compress(unsigned int *data, const int len, unsigned char *output, int *outlen)
{
unsigned int largeint[MAXBASEVALS+1];
unsigned int largeint_tmp[MAXBASEVALS+1];
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)
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)
*outlen=nwrittenout;
}
-static void base_decompress(unsigned char *input, int len, unsigned int *output)
+static void base_decompress(unsigned char *input, const int len, unsigned int *output)
{
unsigned int largeint[MAXMAXBASEVALS+1];
unsigned int largeint_tmp[MAXMAXBASEVALS+1];
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
}
/* If a large proportion of the integers are large (More than 10\% are >14 bits) we return 0, otherwise 1 */
-static int heuristic_bwlzh(unsigned int *ints, int nints)
+static int heuristic_bwlzh(unsigned int *ints, const int nints)
{
int i,num;
num=0;
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.
*/
-unsigned char *Ptngc_pack_array_xtc3(int *input, int *length, int natoms, int speed)
+unsigned char *Ptngc_pack_array_xtc3(int *input, int *length, const int natoms, int speed)
{
unsigned char *output=NULL;
int i,ienc,j;
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)
#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];
}
static void decompress_bwlzh_block(unsigned char **ptr,
- int nvals,
+ const int nvals,
unsigned int **vals)
{
int bwlzh_buf_len=(int)(((unsigned int)(*ptr)[0]) |
}
static void decompress_base_block(unsigned char **ptr,
- int nvals,
+ const int nvals,
unsigned int **vals)
{
int base_buf_len=(int)(((unsigned int)(*ptr)[0]) |
int *ilargedir, int *ilargeintra,
int *ilargeinter, int *prevcoord,
int *minint, int *output,
- int outdata, int didswap,
- int natoms, int current_large_type)
+ const int outdata, const int didswap,
+ const int natoms, const int current_large_type)
{
int large_ints[3]={0,0,0};
if (current_large_type==0 && xtc3_context->large_direct)
+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];
}
-int Ptngc_unpack_array_xtc3(unsigned char *packed,int *output, int length, int natoms)
+int Ptngc_unpack_array_xtc3(unsigned char *packed,int *output, const int length, const int natoms)
{
int i;
int minint[3];
}
/* 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)
{
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff