biod.pnpi.spb.ru
/
alexxy
/
gromacs.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
Merge release-5-0 into master
[alexxy/gromacs.git]
/
src
/
gromacs
/
gmxpreprocess
/
readir.c
diff --git
a/src/gromacs/gmxpreprocess/readir.c
b/src/gromacs/gmxpreprocess/readir.c
index 763b6d8e5da1001ebcde6dc9a9b4af91f2971788..b86bbef806e7f0a6317fe8900035573c4612b2d3 100644
(file)
--- a/
src/gromacs/gmxpreprocess/readir.c
+++ b/
src/gromacs/gmxpreprocess/readir.c
@@
-34,36
+34,35
@@
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <ctype.h>
#include <ctype.h>
-#include <stdlib.h>
#include <limits.h>
#include <limits.h>
-#include "sysstuff.h"
-#include "gromacs/utility/smalloc.h"
-#include "typedefs.h"
-#include "physics.h"
-#include "names.h"
-#include "gmx_fatal.h"
-#include "macros.h"
-#include "index.h"
-#include "symtab.h"
+#include <stdlib.h>
+
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/units.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/topology/index.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/cstringutil.h"
-#include "readinp.h"
-#include "warninp.h"
+#include "
gromacs/legacyheaders/
readinp.h"
+#include "
gromacs/legacyheaders/
warninp.h"
#include "readir.h"
#include "toputil.h"
#include "readir.h"
#include "toputil.h"
-#include "index.h"
-#include "network.h"
-#include "vec.h"
-#include "pbc.h"
-#include "mtop_util.h"
-#include "chargegroup.h"
-#include "inputrec.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/legacyheaders/chargegroup.h"
+#include "gromacs/legacyheaders/inputrec.h"
#include "calc_verletbuf.h"
#include "calc_verletbuf.h"
+#include "gromacs/topology/block.h"
+#include "gromacs/topology/symtab.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
+
#define MAXPTR 254
#define NOGID 255
#define MAXPTR 254
#define NOGID 255
@@
-1426,7
+1425,7
@@
int str_nelem(const char *str, int maxptr, char *ptr[])
int np = 0;
char *copy0, *copy;
int np = 0;
char *copy0, *copy;
- copy0 = strdup(str);
+ copy0 =
gmx_
strdup(str);
copy = copy0;
ltrim(copy);
while (*copy != '\0')
copy = copy0;
ltrim(copy);
while (*copy != '\0')
@@
-1681,7
+1680,7
@@
static void do_wall_params(t_inputrec *ir,
}
for (i = 0; i < ir->nwall; i++)
{
}
for (i = 0; i < ir->nwall; i++)
{
- opts->wall_atomtype[i] = strdup(names[i]);
+ opts->wall_atomtype[i] =
gmx_
strdup(names[i]);
}
if (ir->wall_type == ewt93 || ir->wall_type == ewt104)
}
if (ir->wall_type == ewt93 || ir->wall_type == ewt104)
@@
-2344,7
+2343,7
@@
void get_ir(const char *mdparin, const char *mdparout,
{
if (ir->efep != efepNO)
{
{
if (ir->efep != efepNO)
{
- opts->couple_moltype = strdup(is->couple_moltype);
+ opts->couple_moltype =
gmx_
strdup(is->couple_moltype);
if (opts->couple_lam0 == opts->couple_lam1)
{
warning(wi, "The lambda=0 and lambda=1 states for coupling are identical");
if (opts->couple_lam0 == opts->couple_lam1)
{
warning(wi, "The lambda=0 and lambda=1 states for coupling are identical");
@@
-2936,7
+2935,7
@@
static void decode_cos(char *s, t_cosines *cosine)
double a, phi;
int i;
double a, phi;
int i;
- t = strdup(s);
+ t =
gmx_
strdup(s);
trim(t);
cosine->n = 0;
trim(t);
cosine->n = 0;
@@
-3117,7
+3116,7
@@
static void make_swap_groups(
void make_IMD_group(t_IMD *IMDgroup, char *IMDgname, t_blocka *grps, char **gnames)
{
void make_IMD_group(t_IMD *IMDgroup, char *IMDgname, t_blocka *grps, char **gnames)
{
- int ig
= -1
, i;
+ int ig, i;
ig = search_string(IMDgname, grps->nr, gnames);
ig = search_string(IMDgname, grps->nr, gnames);