From a545435260689902bf67da97d049a6156e645912 Mon Sep 17 00:00:00 2001
From: "Kurt A. O'Hearn" <ohearnku@cse.msu.edu>
Date: Fri, 29 Jul 2016 14:32:22 -0400
Subject: [PATCH] Begin merging PuReMD and PG-PuReMD codes to enable MPI-only
in PG-PuReMD.
---
PG-PuReMD/src/box.c | 7 ++++
PG-PuReMD/src/reax_types.h | 69 ++++++++++++++++++++++++++++++++++++++
PuReMD/src/reax_types.h | 4 +--
3 files changed, 78 insertions(+), 2 deletions(-)
diff --git a/PG-PuReMD/src/box.c b/PG-PuReMD/src/box.c
index f9aabadc..7d1782c9 100644
--- a/PG-PuReMD/src/box.c
+++ b/PG-PuReMD/src/box.c
@@ -141,6 +141,13 @@ void Setup_Big_Box( real a, real b, real c, real alpha, real beta, real gamma,
{
double c_alpha, c_beta, c_gamma, s_gamma, zi;
+ if ( IS_NAN_REAL(a) || IS_NAN_REAL(b) || IS_NAN_REAL(c)
+ || IS_NAN_REAL(alpha) || IS_NAN_REAL(beta) || IS_NAN_REAL(gamma) )
+ {
+ fprintf( stderr, "Invalid simulation box boundaries for big box (NaN). Terminating...\n" );
+ exit( INVALID_INPUT );
+ }
+
c_alpha = cos(DEG2RAD(alpha));
c_beta = cos(DEG2RAD(beta));
c_gamma = cos(DEG2RAD(gamma));
diff --git a/PG-PuReMD/src/reax_types.h b/PG-PuReMD/src/reax_types.h
index eaf75641..b75d9139 100644
--- a/PG-PuReMD/src/reax_types.h
+++ b/PG-PuReMD/src/reax_types.h
@@ -164,6 +164,15 @@
#define MAX_ITR 10
#define RESTART 30
+/* NaN IEEE 754 representation for C99 in math.h
+ * Note: function choice must match REAL typedef below */
+#ifdef NAN
+#define IS_NAN_REAL(a) (isnan(a))
+#else
+#warn "No support for NaN"
+#define NAN_REAL(a) (0)
+#endif
+
/**************** RESOURCE CONSTANTS **********************/
#ifdef HAVE_CUDA
//#define CUDA_BLOCK_SIZE 256
@@ -567,6 +576,14 @@ typedef struct
{
int num_atom_types;
+#ifndef HAVE_CUDA
+ global_parameters gp;
+ single_body_parameters *sbp;
+ two_body_parameters **tbp;
+ three_body_header ***thbp;
+ hbond_parameters ***hbp;
+ four_body_header ****fbp;
+#else
global_parameters gp;
global_parameters d_gp;
@@ -584,6 +601,7 @@ typedef struct
four_body_header *fbp; //changed
four_body_header *d_fbp; //changed
+#endif
} reax_interaction;
@@ -626,6 +644,21 @@ typedef struct
struct grid_cell
{
+#ifndef HAVE_CUDA
+ real cutoff;
+ rvec min, max;
+ ivec rel_box;
+
+ int mark;
+ int type;
+ int str;
+ int end;
+ int top;
+ int* atoms;
+ struct grid_cell** nbrs;
+ ivec* nbrs_x;
+ rvec* nbrs_cp;
+#else
//real cutoff;
rvec min, max;
//ivec rel_box;
@@ -639,6 +672,7 @@ struct grid_cell
//struct grid_cell** nbrs; //changed
//ivec* nbrs_x;
//rvec* nbrs_cp;
+#endif
};
typedef struct grid_cell grid_cell;
@@ -665,6 +699,10 @@ typedef struct
ivec ghost_hbond_span;
ivec ghost_bond_span;
+#ifndef HAVE_CUDA
+ grid_cell*** cells;
+ ivec *order;
+#else
grid_cell* cells; //changed
ivec *order;
@@ -676,6 +714,7 @@ typedef struct
rvec *nbrs_cp;
ivec *rel_box;
+#endif
} grid;
@@ -1066,7 +1105,11 @@ typedef struct
int *bond_mark, *done_after;
/* QEq storage */
+#ifndef HAVE_CUDA
+ sparse_matrix *H, *L, *U;
+#else
sparse_matrix H, L, U; //CHANGED
+#endif
real *Hdia_inv, *b_s, *b_t, *b_prc, *b_prm, *s, *t;
real *droptol;
rvec2 *b, *x;
@@ -1074,7 +1117,11 @@ typedef struct
/* GMRES storage */
real *y, *z, *g;
real *hc, *hs;
+#ifndef HAVE_CUDA
+ real **h, **v;
+#else
real *h, *v; //changed
+#endif
/* CG storage */
real *r, *d, *q, *p;
rvec2 *r2, *d2, *q2, *p2;
@@ -1088,7 +1135,11 @@ typedef struct
/* storage space for bond restrictions */
int *restricted;
+#ifndef HAVE_CUDA
+ int **restricted_list;
+#else
int *restricted_list; //changed
+#endif
/* integrator */
rvec *v_const;
@@ -1132,6 +1183,7 @@ typedef struct
typedef union
{
+#ifdef HAVE_CUDA
void *v;
three_body_interaction_data *three_body_list;
bond_data *bond_list;
@@ -1139,6 +1191,7 @@ typedef union
dDelta_data *dDelta_list;
far_neighbor_data *far_nbr_list;
hbond_data *hbond_list;
+#endif
} list_type;
@@ -1154,12 +1207,24 @@ typedef struct
int type;
list_type select;
+
+#ifndef HAVE_CUDA
+ void *v;
+ three_body_interaction_data *three_body_list;
+ bond_data *bond_list;
+ dbond_data *dbo_list;
+ dDelta_data *dDelta_list;
+ far_neighbor_data *far_nbr_list;
+ hbond_data *hbond_list;
+#endif
} reax_list;
typedef struct
{
+#if defined(PURE_REAX)
MPI_File trj;
+#endif
FILE *strj;
int trj_offset;
int atom_line_len;
@@ -1260,7 +1325,11 @@ typedef struct
cubic_spline_coef *ele, *CEclmb;
} LR_lookup_table;
+#ifndef HAVE_CUDA
+extern LR_lookup_table **LR;
+#else
extern LR_lookup_table *LR; //changed
+#endif
/* function pointer defs */
typedef void (*evolve_function)(reax_system*, control_params*,
diff --git a/PuReMD/src/reax_types.h b/PuReMD/src/reax_types.h
index 497abed4..073918c4 100644
--- a/PuReMD/src/reax_types.h
+++ b/PuReMD/src/reax_types.h
@@ -42,8 +42,8 @@
//#define TEST_ENERGY
//#define TEST_FORCES
//#define CG_PERFORMANCE
-//#define LOG_PERFORMANCE
-//#define STANDARD_BOUNDARIES
+#define LOG_PERFORMANCE
+#define STANDARD_BOUNDARIES
//#define OLD_BOUNDARIES
//#define MIDPOINT_BOUNDARIES
--
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