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[Mpqc-commits] SF.net SVN: mpqc:[9263] trunk/mpqc/src/lib/chemistry/molecule/molecule.cc

From: <evaleev@us...> - 2009-10-07 17:51

Revision: 9263
          http://mpqc.svn.sourceforge.net/mpqc/?rev=9263&view=rev
Author:   evaleev
Date:     2009-10-07 17:51:22 +0000 (Wed, 07 Oct 2009)

Log Message:
-----------
fixed bug in Molecule::symmetrize() caused by exception thrown when trying to construct a std::string by providing a null pointer.

Modified Paths:
--------------
    trunk/mpqc/src/lib/chemistry/molecule/molecule.cc

Modified: trunk/mpqc/src/lib/chemistry/molecule/molecule.cc
===================================================================
--- trunk/mpqc/src/lib/chemistry/molecule/molecule.cc	2009-10-07 15:45:42 UTC (rev 9262)
+++ trunk/mpqc/src/lib/chemistry/molecule/molecule.cc	2009-10-07 17:51:22 UTC (rev 9263)
@@ -957,7 +957,9 @@
 
       int atom = newmol->atom_at_position(np.data(), tol);
       if (atom < 0) {
-        newmol->add_atom(Z_[i],np[0],np[1],np[2],label(i));
+        const char* c_lbl = label(i);
+        const std::string lbl = (c_lbl ? c_lbl : "");
+        newmol->add_atom(Z_[i],np[0],np[1],np[2],lbl);
       }
       else {
         if (Z(i) != newmol->Z(atom)


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Thread	Author	Date
[Mpqc-commits] SF.net SVN: mpqc:[9263] trunk/mpqc/src/lib/chemistry/molecule/molecule.cc	<evaleev@us...>

[Mpqc-commits] SF.net SVN: mpqc:[9301] trunk/mpqc/src/lib/chemistry/molecule/molecule.cc

From: <evaleev@us...> - 2009-11-12 23:46

Revision: 9301
          http://mpqc.svn.sourceforge.net/mpqc/?rev=9301&view=rev
Author:   evaleev
Date:     2009-11-12 23:46:47 +0000 (Thu, 12 Nov 2009)

Log Message:
-----------
origin keyword now specifies the origin in the same units as declared by unit keyword.

Modified Paths:
--------------
    trunk/mpqc/src/lib/chemistry/molecule/molecule.cc

Modified: trunk/mpqc/src/lib/chemistry/molecule/molecule.cc
===================================================================
--- trunk/mpqc/src/lib/chemistry/molecule/molecule.cc	2009-10-28 21:03:00 UTC (rev 9300)
+++ trunk/mpqc/src/lib/chemistry/molecule/molecule.cc	2009-11-12 23:46:47 UTC (rev 9301)
@@ -208,10 +208,11 @@
   else {
       pg_ = new PointGroup(input);
 
+      const double conv = geometry_units_->to_atomic_units();
       // translate to the origin of the symmetry frame
       double r[3];
       for (int i=0; i<3; i++) {
-          r[i] = -pg_->origin()[i];
+          r[i] = -pg_->origin()[i] * conv;
           pg_->origin()[i] = 0;
         }
       translate(r);


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[Mpqc-commits] SF.net SVN: mpqc:[9405] trunk/mpqc/src/lib/chemistry/molecule/molecule.cc

From: <cljanss@us...> - 2010-04-08 17:27

Revision: 9405
          http://mpqc.svn.sourceforge.net/mpqc/?rev=9405&view=rev
Author:   cljanss
Date:     2010-04-08 17:27:25 +0000 (Thu, 08 Apr 2010)

Log Message:
-----------
fixed a bug kindly pointed out by Jeff Hammond

Modified Paths:
--------------
    trunk/mpqc/src/lib/chemistry/molecule/molecule.cc

Modified: trunk/mpqc/src/lib/chemistry/molecule/molecule.cc
===================================================================
--- trunk/mpqc/src/lib/chemistry/molecule/molecule.cc	2010-04-06 23:19:58 UTC (rev 9404)
+++ trunk/mpqc/src/lib/chemistry/molecule/molecule.cc	2010-04-08 17:27:25 UTC (rev 9405)
@@ -1339,7 +1339,7 @@
           char name[5];
           strncpy(name,&line[12],4); name[4] = '\0';
           char resSeq[5];
-          strncpy(resSeq,&line[23],4); resSeq[5] = '\0';
+          strncpy(resSeq,&line[23],4); resSeq[4] = '\0';
 
           if (element[0]==' '&&element[1]==' ') {
               // no element was given so get the element from the atom name


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