Made changes to ctests infrastructure and added appropriate changes i…

…n src folder

include/PeriodicTable.h

@@ -0,0 +1,60 @@
+// ---------------------------------------------------------------------
+//
+// Copyright (c) 2017 The Regents of the University of Michigan and DFT-FE authors.
+//
+// This file is part of the DFT-FE code.
+//
+// The DFT-FE code is free software; you can use it, redistribute
+// it, and/or modify it under the terms of the GNU Lesser General
+// Public License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+// The full text of the license can be found in the file LICENSE at
+// the top level of the DFT-FE distribution.
+//
+// ---------------------------------------------------------------------
+//
+// @author Phani Motamarri (2018)
+//
+
+#ifndef PERIODICTABLE_H
+#define PERIODICTABLE_H
+
+#include <map>
+#include <vector>
+#include <string>
+
+namespace dftfe
+{
+ namespace pseudoUtils
+ {
+ struct Element
+ {
+ int z;
+ std::string symbol;
+ std::string config;
+ double mass;
+ Element(int zz, std::string s, std::string c, double m) : z(zz), symbol(s), config(c),mass(m) {}
+ };
+
+ class PeriodicTable
+ {
+ private:
+
+ std::vector<Element> ptable;
+ std::map<std::string,int> zmap;
+
+ public:
+
+ PeriodicTable(void);
+ int z(std::string symbol) const;
+ std::string symbol(int zval) const;
+ std::string configuration(int zval) const;
+ std::string configuration(std::string symbol) const;
+ double mass(int zval) const;
+ double mass(std::string symbol) const;
+ int size(void) const;
+
+ };
+ }
+}
+#endif

include/dftParameters.h

@@ -35,13 +35,13 @@ namespace dftfe {
  namespace dftParameters
  {
 
- extern unsigned int finiteElementPolynomialOrder,n_refinement_steps,numberEigenValues,xc_id, spinPolarized, nkx,nky,nkz, pseudoProjector;
+ extern unsigned int finiteElementPolynomialOrder,n_refinement_steps,numberEigenValues,xc_id, spinPolarized, nkx,nky,nkz;
  extern unsigned int chebyshevOrder,numPass,numSCFIterations,maxLinearSolverIterations, mixingHistory, npool;
 
  extern double radiusAtomBall, mixingParameter, dkx, dky, dkz;
  extern double lowerEndWantedSpectrum,relLinearSolverTolerance,selfConsistentSolverTolerance,TVal, start_magnetization;
 
- extern bool isPseudopotential, periodicX, periodicY, periodicZ, useSymm, timeReversal;
+ extern bool isPseudopotential, periodicX, periodicY, periodicZ, useSymm, timeReversal,pseudoTestsFlag;
  extern std::string meshFileName,coordinatesFile,domainBoundingVectorsFile,kPointDataFile, ionRelaxFlagsFile, orthogType,pseudoPotentialFile;
 
  extern double outerAtomBallRadius, meshSizeOuterDomain;

include/pseudoConverter.h

@@ -0,0 +1,30 @@
+// ---------------------------------------------------------------------
+//
+// Copyright (c) 2017 The Regents of the University of Michigan and DFT-FE authors.
+//
+// This file is part of the DFT-FE code.
+//
+// The DFT-FE code is free software; you can use it, redistribute
+// it, and/or modify it under the terms of the GNU Lesser General
+// Public License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+// The full text of the license can be found in the file LICENSE at
+// the top level of the DFT-FE distribution.
+//
+// ---------------------------------------------------------------------
+//
+// @author Phani Motamarri (2018)
+//
+
+#ifndef converter_h
+#define converter_h
+#include <string>
+#include "string.h"
+namespace dftfe
+{
+ namespace pseudoUtils
+ {
+ void convert(std::string & file);
+ }
+}
+#endif 

include/upfToxml.h

@@ -0,0 +1,34 @@
+// ---------------------------------------------------------------------
+//
+// Copyright (c) 2017 The Regents of the University of Michigan and DFT-FE authors.
+//
+// This file is part of the DFT-FE code.
+//
+// The DFT-FE code is free software; you can use it, redistribute
+// it, and/or modify it under the terms of the GNU Lesser General
+// Public License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+// The full text of the license can be found in the file LICENSE at
+// the top level of the DFT-FE distribution.
+//
+// ---------------------------------------------------------------------
+//
+// @author Phani Motamarri (2018)
+//
+
+#ifndef upfToxml_h
+#define upfToxml_h
+#include <string>
+#include "string.h"
+#include <headers.h>
+#include <dftParameters.h>
+
+namespace dftfe
+{
+ namespace pseudoUtils
+ {
+ int upfToxml(std::string &inputFile,
+ std::string &outputFile);
+ }
+}
+#endif 

include/xmlTodftfeParser.h

@@ -0,0 +1,94 @@
+// ---------------------------------------------------------------------
+//
+// Copyright (c) 2017-2018 The Regents of the University of Michigan and DFT-FE authors.
+//
+// This file is part of the DFT-FE code.
+//
+// The DFT-FE code is free software; you can use it, redistribute
+// it, and/or modify it under the terms of the GNU Lesser General
+// Public License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+// The full text of the license can be found in the file LICENSE at
+// the top level of the DFT-FE distribution.
+//
+// ---------------------------------------------------------------------
+//
+// @author Shukan Parekh, Phani Motamarri
+//
+
+#include <vector>
+#include <string>
+#include <string.h>
+#include <stdio.h>
+#include <iostream>
+#include <cstring>
+#include <sstream>
+#include <fstream>
+#include <tuple>
+#include <stack>
+#include <libxml/parser.h>
+#include <libxml/tree.h>
+#include <fstream>
+
+#ifndef xmlTodftfeParser_h
+#define xmlTodftfeParser_h
+
+namespace dftfe{
+ //
+ //Declare pseudoUtils function
+ //
+namespace pseudoUtils
+{
+
+class xmlTodftfeParser{
+
+private:
+ xmlDoc *doc;
+ xmlNode *root;
+ double mesh_spacing;
+ std::vector<std::string> local_potential;
+ std::vector<std::string> density;
+ std::vector<std::string> mesh;
+ std::vector<std::tuple<size_t, size_t, std::vector<std::string>>> projectors;
+ std::vector<std::tuple<size_t, size_t, size_t, double>> d_ij;
+
+ std::ofstream loc_pot;
+ std::ofstream dense;
+ std::ofstream denom;
+ std::ofstream l1;
+ std::ofstream l2;
+ std::ofstream l3;
+ std::ofstream ad_file;
+ std::ofstream pseudo;
+
+public:
+ /**
+ * class constructor
+ */
+ xmlTodftfeParser();
+
+ /**
+ * class destructor
+ */
+ ~xmlTodftfeParser();
+
+ /**
+ * @brief parse a given xml pseudopotential file 
+ * 
+ * @param filePath location of the xml file
+ */
+ bool parseFile(std::string & filePath);
+
+ /**
+ * @brief output the parsed xml pseudopotential file into dat files required by dftfe code
+ * 
+ * @param filePath location to write the data
+ */
+ bool outputData(std::string & filePath);
+
+};
+
+}
+
+}
+#endif /* parser_h */

src/dft/initPseudo-OV.cc

@@ -326,7 +326,8 @@ void dftClass<FEOrder>::initNonLocalPseudoPotential_OV()
 
  unsigned int atomicNumber = *it;
 
- pcout<<"Reading data from file: "<<pseudoAtomDataFile<<std::endl;
+ if(dftParameters::verbosity >= 2)
+ pcout<<"Reading data from file: "<<pseudoAtomDataFile<<std::endl;
 
  //
  // open the testFunctionFileName

src/dft/initPseudo.cc

@@ -43,7 +43,7 @@ void dftClass<FEOrder>::initLocalPseudoPotential()
  //else
  //sprintf(pseudoFile,"%s/data/electronicStructure/pseudoPotential/z%u/pseudoAtomData/locPot.dat", DFT_PATH,*it);
 
- if (!dftParameters::reproducible_output)
+ if (dftParameters::verbosity>=2)
  pcout<<"Reading Local Pseudo-potential data from: " <<pseudoFile<<std::endl;
  dftUtils::readFile(2, pseudoPotentialData[*it], pseudoFile);
  unsigned int numRows = pseudoPotentialData[*it].size()-1;
@@ -59,9 +59,9 @@ void dftClass<FEOrder>::initLocalPseudoPotential()
  x.setcontent(numRows,&xData[0]);
  alglib::real_1d_array y;
  y.setcontent(numRows,&yData[0]);
- alglib::ae_int_t bound_type_l = 2;
+ alglib::ae_int_t bound_type_l = 0;
  alglib::ae_int_t bound_type_r = 1;
- const double slopeL= 0;//(pseudoPotentialData[*it][1][1]-pseudoPotentialData[*it][0][1])/(pseudoPotentialData[*it][1][0]-pseudoPotentialData[*it][0][0]);
+ const double slopeL= (pseudoPotentialData[*it][1][1]-pseudoPotentialData[*it][0][1])/(pseudoPotentialData[*it][1][0]-pseudoPotentialData[*it][0][0]);
  const double slopeR=-pseudoPotentialData[*it][numRows-1][1]/pseudoPotentialData[*it][numRows-1][0];
  spline1dbuildcubic(x, y, numRows, bound_type_l, slopeL, bound_type_r, slopeR, pseudoSpline[*it]);
  outerMostPointPseudo[*it]= xData[numRows-1];

src/dft/initRho.cc

@@ -54,9 +54,9 @@ void dftClass<FEOrder>::initRho()
  char densityFile[256];
  if(dftParameters::isPseudopotential)
  {
- if(dftParameters::pseudoProjector==1)
-   sprintf(densityFile, "%s/data/electronicStructure/pseudoPotential/z%u/singleAtomData/density.inp", DFT_PATH, *it);
- else
+ //if(dftParameters::pseudoProjector==1)
+ // sprintf(densityFile, "%s/data/electronicStructure/pseudoPotential/z%u/singleAtomData/density.inp", DFT_PATH, *it);
+ //else
  sprintf(densityFile,"temp/z%u/density.inp",*it);
  //sprintf(densityFile, "%s/data/electronicStructure/pseudoPotential/z%u/oncv/singleAtomData/density.inp", DFT_PATH, *it);