Merge branch 'develop'

src/D3tensor.h

@@ -244,9 +244,9 @@ class D3tensor
 
   double norm2(const D3tensor& a) const
   {
-    return a_[0]*a_[0] + a_[1]*a_[1] + a_[2]*a_[2] +
-           a_[3]*a_[3] + a_[4]*a_[4] + a_[5]*a_[5] +
-           a_[6]*a_[6] + a_[7]*a_[7] + a_[8]*a_[8];
+    return a[0]*a[0] + a[1]*a[1] + a[2]*a[2] +
+           a[3]*a[3] + a[4]*a[4] + a[5]*a[5] +
+           a[6]*a[6] + a[7]*a[7] + a[8]*a[8];
   }
 
   double norm(const D3tensor& a) const

src/ExchangeOperator.C

@@ -356,7 +356,6 @@ void ExchangeOperator::apply_VXC_(double mix, Wavefunction& wf_ref,
 ////////////////////////////////////////////////////////////////////////////////
 void ExchangeOperator::apply_operator(Wavefunction& dwf)
 {
-  cout << "ExchangeOperator::apply_operator" << endl;
   // apply sigmaHF to s_.wf and store result in dwf
   // use the reference function wf0_ and reference sigma(wf) dwf0_
   apply_VXC_(1.0, wf0_, dwf0_, dwf);

src/Matrix.C

@@ -2025,6 +2025,7 @@ double DoubleMatrix::det_from_lu(valarray<int> ipiv)
 
     return det;
   }
+  return 0.0;
 }
 
 ////////////////////////////////////////////////////////////////////////////////
@@ -2041,6 +2042,7 @@ double DoubleMatrix::inverse_det(void)
     inverse_from_lu(ipiv);
     return det;
   }
+  return 0.0;
 }
 
 ////////////////////////////////////////////////////////////////////////////////
@@ -2131,6 +2133,7 @@ complex<double> ComplexMatrix::det_from_lu(valarray<int> ipiv)
 
     return det;
   }
+  return complex<double>(0.0,0.0);
 }
 
 ////////////////////////////////////////////////////////////////////////////////
@@ -2147,6 +2150,7 @@ complex<double> ComplexMatrix::inverse_det(void)
     inverse_from_lu(ipiv);
     return det;
   }
+  return complex<double>(0.0,0.0);
 }
 
 ////////////////////////////////////////////////////////////////////////////////
@@ -2814,7 +2818,7 @@ void DoubleMatrix::syev(char uplo, valarray<double>& w, DoubleMatrix& z)
             z.val, &ione, &ione, z.desc_, &tmpwork, &lwork,
             &info);
 
-    lwork = (int) (tmpwork + 0.1);
+    lwork = (int) (tmpwork + 1);
     double* work=new double[lwork];
     pdsyev(&jobz, &uplo, &m_, val, &ione, &ione, desc_, &w[0],
             z.val, &ione, &ione, z.desc_, work, &lwork,
@@ -2871,7 +2875,7 @@ void DoubleMatrix::syevd(char uplo, valarray<double>& w, DoubleMatrix& z)
             z.val, &ione, &ione, z.desc_, &tmpwork, &lwork,
             &tmpiwork, &liwork, &info);
 
-    lwork = (int) (tmpwork + 0.1);
+    lwork = (int) (tmpwork + 1);
     double* work=new double[lwork];
     liwork = tmpiwork;
     int* iwork = new int[liwork];
@@ -2943,7 +2947,7 @@ void DoubleMatrix::syevx(char uplo, valarray<double>& w, DoubleMatrix& z,
 
     assert(info==0);
 
-    lwork = (int) (tmpwork + 0.1);
+    lwork = (int) (tmpwork + 1);
     double* work=new double[lwork];
     liwork = tmpiwork;
     int* iwork = new int[liwork];
@@ -3061,7 +3065,7 @@ void DoubleMatrix::syevd(char uplo, valarray<double>& w)
             zval, &ione, &ione, descz, &tmpwork, &lwork,
             &tmpiwork, &liwork, &info);
 
-    lwork = (int) (tmpwork + 0.1);
+    lwork = (int) (tmpwork + 1);
     double* work=new double[lwork];
     liwork = tmpiwork;
     int* iwork = new int[liwork];

util/qbox_xyz.py

@@ -2,33 +2,33 @@
 # Copyright 2016 The Regents of the University of California
 # This file is part of Qbox
 #
-# qbox_xyz.py: extract first (or all) set(s) of atomic positions in xyz format
+# qbox_xyz.py: extract sets of atomic positions in xyz format
 # from a Qbox output file or from a Qbox sample file using SAX 
 # incremental parsing
 #
-# use: qbox_xyz.py [-all] {file|URL}
+# use: qbox_xyz.py [-first] {file|URL}
 import os.path
 import xml.sax
 import sys
 import urllib2
 
 def usage():
-  print "use: ",sys.argv[0]," [-all] {file|URL}"
+  print "use: ",sys.argv[0]," [-first] {file|URL}"
   sys.exit()
 
 argc=len(sys.argv)
 if ( argc < 2 or argc > 3 ):
   usage()
 
-# check if option "-all" is used
-# "-all" option: extract all atomsets
-# default: extract first atomset only
-first_only = True
+# check if option "-first" is used
+# "-first" option: extract first atomset only
+# default: extract all atomsets
+first_only = False
 input_source = sys.argv[1]
-if ( sys.argv[1] == "-all" ):
+if ( sys.argv[1] == "-first" ):
   if ( argc != 3 ):
     usage()
-  first_only = False
+  first_only = True
   input_source = sys.argv[2]
 
 # conversion from Bohr to Angstrom