--- /dev/null
+/*
+This source code file is part of thread_mpi.
+Written by Sander Pronk, Erik Lindahl, and possibly others.
+
+Copyright (c) 2009, Sander Pronk, Erik Lindahl.
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+1) Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+2) Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions and the following disclaimer in the
+ documentation and/or other materials provided with the distribution.
+3) Neither the name of the copyright holders nor the
+ names of its contributors may be used to endorse or promote products
+ derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY US ''AS IS'' AND ANY
+EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL WE BE LIABLE FOR ANY
+DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+If you want to redistribute modifications, please consider that
+scientific software is very special. Version control is crucial -
+bugs must be traceable. We will be happy to consider code for
+inclusion in the official distribution, but derived work should not
+be called official thread_mpi. Details are found in the README & COPYING
+files.
+*/
+
+
+/* File contributed by Sergey Klyaus */
+
+#include <atomic.h>
+
+/* this is for newer versions of gcc that have built-in intrinsics,
+ on platforms not explicitly supported with inline assembly. */
+
+#define tMPI_Atomic_memory_barrier() do { membar_consumer(); membar_producer(); } while (0)
+
+/* Only gcc and Intel support this check, otherwise set it to true (skip doc) */
+#if (!defined(__GNUC__) && !defined(__INTEL_COMPILER) && !defined DOXYGEN)
+#define __builtin_constant_p(i) (1)
+#endif
+
+
+typedef struct tMPI_Atomic
+{
+ volatile uint_t value;
+}
+tMPI_Atomic_t;
+
+typedef struct tMPI_Atomic_ptr
+{
+ void* volatile value;
+}
+tMPI_Atomic_ptr_t;
+
+
+
+#define TMPI_SPINLOCK_INITIALIZER { 0 }
+
+
+/* for now we simply assume that int and void* assignments are atomic */
+#define tMPI_Atomic_get(a) ((int)( (a)->value) )
+#define tMPI_Atomic_set(a,i) (((a)->value) = (i))
+
+
+#define tMPI_Atomic_ptr_get(a) ((void*)((a)->value) )
+#define tMPI_Atomic_ptr_set(a,i) (((a)->value) = (void*)(i))
+
+static inline int tMPI_Atomic_add_return(tMPI_Atomic_t *a, volatile int i)
+{
+ return (int) atomic_add_int_nv(&a->value, i);
+}
+
+static inline int tMPI_Atomic_fetch_add(tMPI_Atomic_t *a, volatile int i)
+{
+ return (int) atomic_add_int_nv(&a->value, i) - i;
+}
+
+
+static inline int tMPI_Atomic_cas(tMPI_Atomic_t *a, int oldval, int newval)
+{
+ return (int)atomic_cas_uint(&a->value, (uint_t)oldval, (uint_t)newval);
+}
+
+
+static inline int tMPI_Atomic_ptr_cas(tMPI_Atomic_ptr_t* a, void *oldval,
+ void *newval)
+{
+ /*atomic_cas_ptr always returns value stored in a, so*/
+ return atomic_cas_ptr(&(a->value), oldval, newval) == oldval;
+}
+
+
+
+typedef struct tMPI_Spinlock
+{
+ volatile unsigned long lock;
+} tMPI_Spinlock_t;
+
+#define TMPI_SPINLOCK_INITIALIZER { 0 }
+
+static inline unsigned long tas(volatile unsigned long *ptr)
+{
+ unsigned long result;
+ __asm__ __volatile__(" \
+ ldstub [%1], %0 "
+ : "=r"(result)
+ : "r"(ptr)
+ : "memory");
+ return result;
+}
+
+
+static inline void tMPI_Spinlock_init(tMPI_Spinlock_t *x)
+{
+ x->lock = 0;
+}
+
+
+static inline void tMPI_Spinlock_lock(tMPI_Spinlock_t *x)
+{
+ do
+ {
+ } while (tas(&(x->lock)) == 1);
+}
+
+
+static inline int tMPI_Spinlock_trylock(tMPI_Spinlock_t *x)
+{
+ return tas(&(x->lock));
+}
+
+
+static inline void tMPI_Spinlock_unlock(tMPI_Spinlock_t * x)
+{
+ x->lock = 0;
+}
+
+static inline int tMPI_Spinlock_islocked(const tMPI_Spinlock_t * x)
+{
+ tMPI_Atomic_memory_barrier();
+ return ( x->lock == 1 );
+}
+
+static inline void tMPI_Spinlock_wait(tMPI_Spinlock_t * x)
+{
+ do
+ {
+ } while (x->lock == 1);
+ tMPI_Atomic_memory_barrier();
+}
+
int *mol;
int *block;
int nr;
-} rm_t;
+} rmm_t;
int search_string(char *s,int ng,char ***gn)
{
}
}
-int gen_rm_list(rm_t *rm_p,t_block *ins_at,t_block *rest_at,t_pbc *pbc, gmx_mtop_t *mtop,
+int gen_rm_list(rmm_t *rm_p,t_block *ins_at,t_block *rest_at,t_pbc *pbc, gmx_mtop_t *mtop,
rvec *r, rvec *r_ins, mem_t *mem_p, pos_ins_t *pos_ins, real probe_rad, int low_up_rm, gmx_bool bALLOW_ASYMMETRY)
{
int i,j,k,l,at,at2,mol_id;
return nupper+nlower;
}
-void rm_group(t_inputrec *ir, gmx_groups_t *groups, gmx_mtop_t *mtop, rm_t *rm_p, t_state *state, t_block *ins_at, pos_ins_t *pos_ins)
+void rm_group(t_inputrec *ir, gmx_groups_t *groups, gmx_mtop_t *mtop, rmm_t *rm_p, t_state *state, t_block *ins_at, pos_ins_t *pos_ins)
{
int i,j,k,n,rm,mol_id,at,block;
rvec *x_tmp,*v_tmp;
return rm_at;
}
-void top_update(const char *topfile, char *ins, rm_t *rm_p, gmx_mtop_t *mtop)
+void top_update(const char *topfile, char *ins, rmm_t *rm_p, gmx_mtop_t *mtop)
{
#define TEMP_FILENM "temp.top"
int bMolecules=0;
t_block *ins_at,*rest_at;
pos_ins_t *pos_ins;
mem_t *mem_p;
- rm_t *rm_p;
+ rmm_t *rm_p;
gmx_groups_t *groups;
gmx_bool bExcl=FALSE;
t_atoms atoms;
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff