Fix bilayer and dna benchmarks. Add NaN support for checking sim box boundaries in PuReMD.

puremd_rc_1003/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));

puremd_rc_1003/PuReMD/src/geo_tools.c

@@ -176,7 +176,7 @@ int Read_Box_Info( reax_system *system, FILE *geo, int geo_format )
 		&s_a[0], &s_b[0], &s_c[0],
 		&s_alpha[0], &s_beta[0], &s_gamma[0],
 		&s_group[0], &s_zValue[0] );
-      
+
       /* compute full volume tensor from the angles */
       Setup_Big_Box( atof(s_a),  atof(s_b), atof(s_c), 
 		     atof(s_alpha), atof(s_beta), atof(s_gamma), 

puremd_rc_1003/PuReMD/src/reax_types.h

@@ -54,6 +54,15 @@
 #define REAX_MAX_ATOM_TYPES     25
 #define REAX_MAX_MOLECULE_SIZE  20
 
+/* 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
+
 /********************** TYPE DEFINITIONS ********************/
 typedef int  ivec[3];
 typedef double real;

puremd_rc_1003/data/benchmarks/dna/dna_19733.pdb

 REMARK     Created by ReaxFF
-CRYST1   44.80000   44.80000  103.60000   90.00000   90.00000   90.00000
+CRYST1   44.80000 44.80000 103.6000090.000090.000090.00000           0
 ATOM      1 'HO5  DA S   1      18.338  31.595  15.144  1.00  2.20           H
 ATOM      2  O5'  DA S   1      18.062  30.912  15.797  1.00  2.20           O
 ATOM      3  O3'  DA S   1      16.044  28.806  17.723  1.00  2.20           O