mirror of https://github.com/QMCPACK/qmcpack.git
Merge branch 'develop' into cleanup_pseudopotentials
This commit is contained in:
Ye Luo
GitHub
commit
d8ed1e365f
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@ -49,7 +49,7 @@ SET(MOSRCS
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# create libmocommon
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ADD_LIBRARY(mocommon ${MOSRCS})
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set(QTOOLS convert4qmc MSDgenerator extract-eshdf-kvectors)
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set(QTOOLS convert4qmc extract-eshdf-kvectors)
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ADD_EXECUTABLE(getSupercell getSupercell.cpp)
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FOREACH(p ${QTOOLS})
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@ -21,7 +21,6 @@
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#include "Numerics/OneDimGridFunctor.h"
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#include "Numerics/OneDimCubicSpline.h"
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#include "QMCWaveFunctions/OrbitalBuilderBase.h"
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#include "QMCTools/MolecularOrbitalBasis.h"
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#include "QMCTools/RGFBuilderBase.h"
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namespace qmcplusplus
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@ -1,148 +0,0 @@
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//////////////////////////////////////////////////////////////////////////////////////
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// This file is distributed under the University of Illinois/NCSA Open Source License.
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// See LICENSE file in top directory for details.
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//
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// Copyright (c) 2016 Jeongnim Kim and QMCPACK developers.
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//
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// File developed by: Miguel Morales, moralessilva2@llnl.gov, Lawrence Livermore National Laboratory
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// Jeremy McMinnis, jmcminis@gmail.com, University of Illinois at Urbana-Champaign
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// Mark A. Berrill, berrillma@ornl.gov, Oak Ridge National Laboratory
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//
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// File created by: Miguel Morales, moralessilva2@llnl.gov, Lawrence Livermore National Laboratory
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//////////////////////////////////////////////////////////////////////////////////////
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#include <iostream>
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#include <cstdlib>
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#include <sstream>
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#include <iomanip>
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#include <vector>
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#include <map>
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#include "OhmmsData/OhmmsElementBase.h"
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#include "QMCTools/CasinoParser.h"
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#include "QMCTools/GaussianFCHKParser.h"
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#include "QMCTools/GamesXmlParser.h"
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#include "QMCTools/GamesAsciiParser.h"
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#include "QMCTools/BParser.h"
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#include "Message/Communicate.h"
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#include "OhmmsData/FileUtility.h"
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#include "Utilities/RandomGenerator.h"
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int main(int argc, char* argv[])
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{
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int nea=16,neb=16,nca=0,ncb=0,nstates=32;
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double wgt=0.00,thr=0.0;
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bool useCSF=true;
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std::string name = "dummy.xml";
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OHMMS::Controller->initialize(argc,argv);
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if (OHMMS::Controller->rank() != 0) {
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outputManager.shutOff();
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}
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Random.init(0,1,-1);
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std::cout.setf(std::ios::scientific, std::ios::floatfield);
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std::cout.setf(std::ios::right,std::ios::adjustfield);
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std::cout.precision(12);
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QMCGaussianParserBase::init();
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QMCGaussianParserBase *parser=0;
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parser = new GamesAsciiParser(argc,argv);
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parser->multideterminant = true;
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parser->SpinRestricted=true;
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parser->zeroCI=false;
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parser->orderByExcitation=false;
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parser->NumberOfEls=nca+ncb+nea+neb;
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parser->SpinMultiplicity=(parser->NumberOfEls-2*neb)+1;
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parser->NumberOfAlpha=nca+nea;
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parser->NumberOfBeta=ncb+neb;
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parser->ci_nca=nca;
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parser->ci_ncb=ncb;
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parser->ci_nea=nea;
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parser->ci_neb=neb;
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parser->ci_nstates=nstates;
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parser->ci_threshold=thr;
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parser->usingCSF=useCSF;
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std::vector<std::string> &CIalpha=parser->CIalpha;
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std::vector<std::string> &CIbeta=parser->CIbeta;
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std::vector<std::string> &CSFocc=parser->CSFocc;
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std::vector<std::vector<std::string> > &CSFalpha=parser->CSFalpha;
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std::vector<std::vector<std::string> > &CSFbeta=parser->CSFbeta;
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std::vector<std::vector<double> > &CSFexpansion=parser->CSFexpansion;
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std::vector<double> &CIcoeff=parser->CIcoeff;
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std::vector<std::pair<int,double> > &coeff2csf=parser->coeff2csf;
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if(useCSF)
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{
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// dummy for now
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std::string alpha0(nstates,'0'),beta0(nstates,'0'),occ0(nstates,'0');
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std::vector<std::string> dummy;
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for(int i=0; i<nea; i++)
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alpha0[i]='1';
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for(int i=0; i<neb; i++)
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beta0[i]='1';
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for(int i=0; i<neb; i++)
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occ0[i]='2';
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for(int i=neb; i<nea; i++)
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occ0[i]='1';
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std::vector<double> vec;
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std::pair<int,double> dum(1,0.95);
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// HF
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coeff2csf.push_back(dum);
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CSFocc.push_back(occ0);
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CSFexpansion.push_back(vec);
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CSFexpansion.back().push_back(1.0);
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CSFalpha.push_back(dummy);
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CSFalpha.back().push_back(alpha0);
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CSFbeta.push_back(dummy);
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CSFbeta.back().push_back(beta0);
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// singles, assume multiplicity of 1
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for(int i=0; i<nea; i++)
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{
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for(int v=0; v<nstates-nea; v++)
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{
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coeff2csf.push_back(dum);
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coeff2csf.back().second = wgt;
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CSFocc.push_back(occ0);
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CSFocc.back().at(i) = '1';
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CSFocc.back().at(nea+v) = '1';
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CSFexpansion.push_back(vec);
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CSFexpansion.back().push_back(1.0/std::sqrt(2.0));
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CSFexpansion.back().push_back(1.0/std::sqrt(2.0));
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CSFalpha.push_back(dummy);
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CSFalpha.back().push_back(alpha0);
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CSFalpha.back().back().at(i)='0';
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CSFalpha.back().back().at(nea+v)='1';
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CSFalpha.back().push_back(alpha0);
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CSFalpha.back().back().at(i)='1';
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CSFalpha.back().back().at(nea+v)='0';
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CSFbeta.push_back(dummy);
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CSFbeta.back().push_back(beta0);
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CSFbeta.back().back().at(i)='1';
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CSFbeta.back().back().at(nea+v)='0';
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CSFbeta.back().push_back(beta0);
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CSFbeta.back().back().at(i)='0';
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CSFbeta.back().back().at(nea+v)='1';
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}
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}
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}
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else
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{
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}
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if(useCSF)
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parser->ci_size = CSFocc.size();
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else
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parser->ci_size = CIcoeff.size();
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xmlDocPtr doc = xmlNewDoc((const xmlChar*)"1.0");
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xmlNodePtr qm_root = xmlNewNode(NULL, BAD_CAST "qmcsystem");
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xmlNodePtr multislaterdetPtr=NULL;
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multislaterdetPtr = parser->createMultiDeterminantSet();
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xmlAddChild(qm_root,multislaterdetPtr);
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xmlDocSetRootElement(doc, qm_root);
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xmlSaveFormatFile(name.c_str(),doc,1);
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xmlFreeDoc(doc);
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return 0;
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}
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@ -1,275 +0,0 @@
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//////////////////////////////////////////////////////////////////////////////////////
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// This file is distributed under the University of Illinois/NCSA Open Source License.
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// See LICENSE file in top directory for details.
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//
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// Copyright (c) 2016 Jeongnim Kim and QMCPACK developers.
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//
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// File developed by: Jeongnim Kim, jeongnim.kim@gmail.com, University of Illinois at Urbana-Champaign
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// Jeremy McMinnis, jmcminis@gmail.com, University of Illinois at Urbana-Champaign
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// Mark A. Berrill, berrillma@ornl.gov, Oak Ridge National Laboratory
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//
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// File created by: Jeongnim Kim, jeongnim.kim@gmail.com, University of Illinois at Urbana-Champaign
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//////////////////////////////////////////////////////////////////////////////////////
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#ifndef QMCPLUSPLUS_MOLECULARORBITALBASIS_H
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#define QMCPLUSPLUS_MOLECULARORBITALBASIS_H
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#include "OhmmsPETE/OhmmsMatrix.h"
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#include "Particle/DistanceTable.h"
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namespace qmcplusplus
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{
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class DistanceTableData;
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/** Class for a molecular orbital basis
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*
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*The molecular orbital \f$ \psi_i \f$ can be written as a linear
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*combination of basis functions \f$ \{\phi\} \f$ such that
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\f[
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\psi_i ({\bf r}_j) = \sum_I \sum_k C_{ikI} \phi_{ikI}({\bf r}_j-{\bf R}_I).
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\f]
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*This class performs the evaluation of the basis functions and their
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*derivatives for each of the N-particles in a configuration. All that
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*is required to generate the actual molecular orbitals is to multiply
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*by the coefficient matrix.
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*
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*The template (C)entered(O)rbital(T)ype should provide the fuctions
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<ul>
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<li> evaluate(int source, int first, int nptcl, int offset,
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VM& y, GM& dy, VM& d2y) {
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</ul>
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*An example being SphericalOrbitalSet
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*/
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template<class COT>
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class MolecularOrbitalBasis: public QMCTraits
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{
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public:
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const ParticleSet* IonConfig;
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///constructor
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MolecularOrbitalBasis(): NumWalkers(1),myTable(0), IonConfig(0) { }
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///constructor with ncenters
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explicit MolecularOrbitalBasis(int ncenters):NumWalkers(1), myTable(0), IonConfig(0)
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{
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for(int ic=0; ic<ncenters; ic++)
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AOs.push_back(0);
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}
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/**
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@param atable the distance table (ion-electron)
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@brief Assign the distance table (ion-electron) and
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*determine the total number of basis states.
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*/
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void setTable(DistanceTableData* atable)
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{
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IonConfig=&(atable->origin());
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myTable = atable;
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//first set up the center list
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const ParticleSet& ptcl_ref = myTable->origin();
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I.resize(myTable->centers());
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for(int ic=0; ic<I.size(); ic++)
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{
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I[ic] = ptcl_ref.GroupID[ic];
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}
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//reset the distance table for the atomic orbitals
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for(int i=0; i<AOs.size(); i++)
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AOs[i]->setTable(myTable);
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//evaluate the total basis dimension and offset for each center
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Basis.resize(I.size()+1);
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Basis[0] = 0;
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for(int c=0; c<I.size(); c++)
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{
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Basis[c+1] = Basis[c]+AOs[I[c]]->getBasisSetSize();
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}
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TotalBasis = Basis[I.size()];
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}
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void reset()
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{
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// DO NOTHING
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}
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void resetParameters(VarRegistry<RealType>& optVariables)
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{
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for(int i=0; i<AOs.size(); i++)
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AOs[i]->resetParameters(optVariables);
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}
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/** return the size of the basis set
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*/
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inline int size() const
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{
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return TotalBasis;
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}
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/** reset the distance table with a new target P
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*/
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void resetTargetParticleSet(ParticleSet& P)
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{
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LOGMSG("MolecularOrbitalBasis::resetTargetParticleSet")
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myTable = DistanceTable::add(*IonConfig,P,DT_AOS);
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for(int i=0; i<AOs.size(); i++)
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AOs[i]->setTable(myTable);
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}
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/**
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@param nptcl number of particles
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@brief resize the containers for data
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for nptcl particles and TotalBasis basis functions
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*/
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inline void resize(int nptcl)
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{
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NumPtcls = nptcl;
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Y.resize(nptcl,TotalBasis);
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dY.resize(nptcl,TotalBasis);
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d2Y.resize(nptcl,TotalBasis);
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}
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/** Evalaute the values of basis functions
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@param P input configuration containing N particles
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@brief For each center, evaluate all the Atomic Orbitals belonging to that center.
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*
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The data members contain
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- \f[ Y[i,j] = \phi_j(r_i-R_I) \f]
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- \f[ dY[i,j] = {\bf \nabla}_i \phi_j(r_i-R_I) \f]
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- \f[ d2Y[i,j] = \nabla^2_i \phi_j(r_i-R_I), \f]
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where \f$ {\bf R_I} \f$ is the correct center for the basis function \f$ \phi_j \f$
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*/
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inline void
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evaluate(const ParticleSet& P)
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{
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for(int c=0; c<I.size(); c++)
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{
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AOs[I[c]]->evaluate(c,0,P.getTotalNum(),Basis[c],Y,dY,d2Y);
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}
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}
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inline void
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evaluate(const ParticleSet& P, int iat)
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{
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for(int c=0; c<I.size(); c++)
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{
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AOs[I[c]]->evaluate(c,iat,Basis[c],Y);
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}
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}
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inline void
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evaluateAll(const ParticleSet& P, int iat)
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{
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for(int c=0; c<I.size(); c++)
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{
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AOs[I[c]]->evaluate(c,iat,Basis[c],Y,dY,d2Y);
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}
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}
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/** add a new set of Centered Atomic Orbitals
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*@param aos a set of Centered Atomic Orbitals
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*/
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inline void add(COT* aos)
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{
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ERRORMSG("!!!!!! this should not be used !!!!!! ")
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AOs.push_back(aos);
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}
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/** add a new set of Centered Atomic Orbitals
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* @param aos a set of Centered Atomic Orbitals
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* @param icenter the index of the center
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*/
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inline void add(COT* aos, int icenter)
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{
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AOs[icenter]=aos;
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}
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void print(std::ostream& os)
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{
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for(int i=0; i<Y.rows(); i++)
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{
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for(int j=0; j<Y.cols(); j++)
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{
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os << Y(i,j) << " " << dY(i,j) << " " << d2Y(i,j) << std::endl;
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}
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}
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}
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///row i of matrix Y
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||||
inline const ValueType* restrict y(int i)
|
||||
{
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return &Y(i,0);
|
||||
}
|
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///row i of vector matrix dY
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inline const GradType* restrict dy(int i)
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{
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return &dY(i,0);
|
||||
}
|
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///row i of matrix d2Y
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inline const ValueType* restrict d2y(int i)
|
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{
|
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return &d2Y(i,0);
|
||||
}
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|
||||
#ifdef USE_FASTWALKER
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inline const ValueType* restrict y(int iw, int ia)
|
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{
|
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return &Y(iw+NumWalkers*ia,0);
|
||||
}
|
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inline const GradType* restrict dy(int iw, int ia)
|
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{
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return &dY(iw+NumWalkers*ia,0);
|
||||
}
|
||||
inline const ValueType* restrict d2y(int iw, int ia)
|
||||
{
|
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return &d2Y(iw+NumWalkers*ia,0);
|
||||
}
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||||
#else
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inline const ValueType* restrict y(int iw, int ia)
|
||||
{
|
||||
return &Y(iw*NumPtcls+ia,0);
|
||||
}
|
||||
inline const GradType* restrict dy(int iw, int ia)
|
||||
{
|
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return &dY(iw*NumPtcls+ia,0);
|
||||
}
|
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inline const ValueType* restrict d2y(int iw, int ia)
|
||||
{
|
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return &d2Y(iw*NumPtcls+ia,0);
|
||||
}
|
||||
#endif
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||||
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||||
///the number of particles
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||||
int NumPtcls;
|
||||
///the number of walkers
|
||||
int NumWalkers;
|
||||
///total number of basis functions
|
||||
int TotalBasis;
|
||||
///container for the id's of the centers (ions),
|
||||
///several centers may share the same id
|
||||
std::vector<int> I;
|
||||
///container to store the offsets of the basis functions,
|
||||
///the number of basis states for center J is Basis[J+1]-Basis[J]
|
||||
std::vector<int> Basis;
|
||||
///container for the pointers to the Atomic Orbitals,
|
||||
///the size of this container being determined by the number
|
||||
///of unique centers
|
||||
std::vector<COT*> AOs;
|
||||
///matrix to store values \f$ Y[i,j] = \phi_j(r_i) \f$
|
||||
Matrix<ValueType> Y;
|
||||
///matrix to store gradients \f$ dY[i,j] = {\bf \nabla}_i \phi_j(r_i) \f$
|
||||
Matrix<GradType> dY;
|
||||
///matrix to store laplacians \f$ d2Y[i,j] = \nabla^2_i \phi_j(r_i) \f$
|
||||
Matrix<ValueType> d2Y;
|
||||
///the distance table (ion-electron)
|
||||
DistanceTableData* myTable;
|
||||
};
|
||||
|
||||
}
|
||||
#endif
|
||||
|
||||
|
||||
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