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/********************************************************************** |
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|
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This basic Periodic Table class was originally taken from the data.cpp |
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file in OpenBabel. The code has been modified to match the OpenMD coding style. |
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|
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We have retained the OpenBabel copyright and GPL license on this class: |
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|
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Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc. |
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Some portions Copyright (C) 2001-2005 by Geoffrey R. Hutchison |
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|
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This file is part of the Open Babel project. |
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For more information, see <http://openbabel.sourceforge.net/> |
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|
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This program is free software; you can redistribute it and/or modify |
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it under the terms of the GNU General Public License as published by |
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the Free Software Foundation version 2 of the License. |
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|
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This program is distributed in the hope that it will be useful, |
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but WITHOUT ANY WARRANTY; without even the implied warranty of |
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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GNU General Public License for more details. |
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***********************************************************************/ |
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|
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/** |
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* @file ElementsTable.cpp |
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* @author gezelter |
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* @date 12/21/2007 |
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* @time 11:30am |
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* @version 1.0 |
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*/ |
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|
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#include <iostream> |
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#include "config.h" |
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#include <cstdlib> |
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#include <string> |
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#include <fstream> |
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#include <cstdlib> |
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#include "utils/ElementsTable.hpp" |
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#include "utils/simError.h" |
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#include "io/basic_ifstrstream.hpp" |
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|
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#if !HAVE_STRNCASECMP |
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extern "C" int strncasecmp(const char *s1, const char *s2, size_t n); |
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#endif |
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|
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#ifdef WIN32 |
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#define FILE_SEP_CHAR "\\" |
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#else |
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#define FILE_SEP_CHAR "/" |
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#endif |
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|
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#ifndef BUFF_SIZE |
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#define BUFF_SIZE 32768 |
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#endif |
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|
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namespace OpenMD { |
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|
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ElementsTable etab; |
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|
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ElementsTable::ElementsTable() { |
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init_ = false; |
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STR_DEFINE(dir_, FRC_PATH ); |
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envvar_ = "FORCE_PARAM_PATH"; |
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filename_ = "element.txt"; |
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} |
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|
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ElementsTable::~ElementsTable() { |
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std::vector<Element*>::iterator i; |
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for (i = elements_.begin(); i != elements_.end(); i++) |
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delete *i; |
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} |
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|
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void ElementsTable::ParseLine(const char *line) { |
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int num, maxbonds; |
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char symbol[5]; |
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char name[256]; |
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RealType Rcov,Rvdw,mass, elNeg, ionize, elAffin; |
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RealType red, green, blue; |
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|
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// skip comment line (at the top) |
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if (line[0] != '#') { |
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sscanf(line,"%d %5s %lf %*f %lf %d %lf %lf %lf %lf %lf %lf %lf %255s", |
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&num, |
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symbol, |
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&Rcov, |
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&Rvdw, |
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&maxbonds, |
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&mass, |
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&elNeg, |
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&ionize, |
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&elAffin, |
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&red, |
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&green, |
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&blue, |
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name); |
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|
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Element *ele = new Element(num, symbol, Rcov, Rvdw, maxbonds, mass, |
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elNeg, ionize, elAffin, red, green, blue, |
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name); |
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elements_.push_back(ele); |
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|
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} |
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} |
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|
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unsigned int ElementsTable::GetNumberOfElements() { |
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if (!init_) |
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Init(); |
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|
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return elements_.size(); |
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} |
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|
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const char *ElementsTable::GetSymbol(int atomicnum) { |
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if (!init_) |
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Init(); |
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|
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if (atomicnum < 0 || atomicnum > static_cast<int>(elements_.size())) |
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return("\0"); |
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|
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return(elements_[atomicnum]->GetSymbol()); |
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} |
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|
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int ElementsTable::GetMaxBonds(int atomicnum) { |
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if (!init_) |
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Init(); |
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|
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if (atomicnum < 0 || atomicnum > static_cast<int>(elements_.size())) |
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return(0); |
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|
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return(elements_[atomicnum]->GetMaxBonds()); |
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} |
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|
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RealType ElementsTable::GetElectroNeg(int atomicnum) { |
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if (!init_) |
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Init(); |
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|
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if (atomicnum < 0 || atomicnum > static_cast<int>(elements_.size())) |
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return(0.0); |
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|
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return(elements_[atomicnum]->GetElectroNeg()); |
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} |
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|
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RealType ElementsTable::GetIonization(int atomicnum) { |
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if (!init_) |
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Init(); |
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|
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if (atomicnum < 0 || atomicnum > static_cast<int>(elements_.size())) |
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return(0.0); |
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|
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return(elements_[atomicnum]->GetIonization()); |
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} |
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|
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|
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RealType ElementsTable::GetElectronAffinity(int atomicnum) { |
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if (!init_) |
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Init(); |
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|
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if (atomicnum < 0 || atomicnum > static_cast<int>(elements_.size())) |
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return(0.0); |
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|
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return(elements_[atomicnum]->GetElectronAffinity()); |
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} |
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|
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std::vector<RealType> ElementsTable::GetRGB(int atomicnum) { |
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if (!init_) |
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Init(); |
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|
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std::vector <RealType> colors; |
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colors.reserve(3); |
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|
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if (atomicnum < 0 || atomicnum > static_cast<int>(elements_.size())) { |
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colors.push_back(0.0); |
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colors.push_back(0.0); |
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colors.push_back(0.0); |
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return(colors); |
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} |
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|
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colors.push_back(elements_[atomicnum]->GetRed()); |
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colors.push_back(elements_[atomicnum]->GetGreen()); |
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colors.push_back(elements_[atomicnum]->GetBlue()); |
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|
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return (colors); |
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} |
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|
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std::string ElementsTable::GetName(int atomicnum) { |
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if (!init_) |
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Init(); |
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|
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if (atomicnum < 0 || atomicnum > static_cast<int>(elements_.size())) |
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return("Unknown"); |
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|
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return(elements_[atomicnum]->GetName()); |
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} |
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|
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RealType ElementsTable::GetVdwRad(int atomicnum) { |
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if (!init_) |
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Init(); |
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|
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if (atomicnum < 0 || atomicnum > static_cast<int>(elements_.size())) |
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return(0.0); |
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|
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return(elements_[atomicnum]->GetVdwRad()); |
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} |
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|
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RealType ElementsTable::CorrectedBondRad(int atomicnum, int hyb) { |
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RealType rad; |
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if (!init_) |
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Init(); |
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|
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if (atomicnum < 0 || atomicnum > static_cast<int>(elements_.size())) |
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return(1.0); |
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|
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rad = elements_[atomicnum]->GetCovalentRad(); |
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|
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if (hyb == 2) |
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rad *= 0.95; |
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else if (hyb == 1) |
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rad *= 0.90; |
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|
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return(rad); |
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} |
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|
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RealType ElementsTable::CorrectedVdwRad(int atomicnum, int hyb) { |
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RealType rad; |
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if (!init_) |
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Init(); |
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|
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if (atomicnum < 0 || atomicnum > static_cast<int>(elements_.size())) |
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return(1.95); |
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|
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rad = elements_[atomicnum]->GetVdwRad(); |
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|
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if (hyb == 2) |
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rad *= 0.95; |
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else if (hyb == 1) |
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rad *= 0.90; |
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|
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return(rad); |
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} |
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|
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RealType ElementsTable::GetCovalentRad(int atomicnum) { |
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if (!init_) |
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Init(); |
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|
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if (atomicnum < 0 || atomicnum > static_cast<int>(elements_.size())) |
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return(0.0); |
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|
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return(elements_[atomicnum]->GetCovalentRad()); |
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} |
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|
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RealType ElementsTable::GetMass(int atomicnum) { |
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if (!init_) |
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Init(); |
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|
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if (atomicnum < 0 || atomicnum > static_cast<int>(elements_.size())) |
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return(0.0); |
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|
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return(elements_[atomicnum]->GetMass()); |
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} |
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|
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int ElementsTable::GetAtomicNum(const char *sym) { |
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int temp; |
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return GetAtomicNum(sym, temp); |
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} |
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|
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int ElementsTable::GetAtomicNum(const char *sym, int &iso) { |
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if (!init_) |
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Init(); |
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|
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std::vector<Element*>::iterator i; |
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for (i = elements_.begin();i != elements_.end();i++) |
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if (!strncasecmp(sym,(*i)->GetSymbol(),2)) |
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return((*i)->GetAtomicNum()); |
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|
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if (strcasecmp(sym, "D") == 0) { |
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iso = 2; |
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return(1); |
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} else if (strcasecmp(sym, "T") == 0) { |
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iso = 3; |
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return(1); |
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} else |
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iso = 0; |
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return(0); |
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} |
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|
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void ElementsTable::Init() { |
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if (init_) |
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return; |
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init_ = true; |
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|
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std::string buffer, subbuffer; |
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ifstrstream ifs1, ifs2, ifs3, ifs4, *ifsP; |
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// First, look for an environment variable |
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if (getenv(envvar_.c_str()) != NULL) { |
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buffer = getenv(envvar_.c_str()); |
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buffer += FILE_SEP_CHAR; |
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|
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|
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|
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|
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if (!subdir_.empty()) { |
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subbuffer = buffer; |
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subbuffer += subdir_; |
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subbuffer += FILE_SEP_CHAR; |
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} |
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|
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|
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|
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buffer += filename_; |
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subbuffer += filename_; |
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|
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|
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ifs1.open(subbuffer.c_str()); |
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ifsP= &ifs1; |
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if (!(ifsP->is_open())) { |
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ifs2.open(buffer.c_str()); |
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ifsP = &ifs2; |
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} |
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|
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} else { |
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sprintf( painCave.errMsg, |
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"ElementsTable error.\n" |
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"\tunable to open datafile %s \n", filename_.c_str()); |
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painCave.isFatal = 0; |
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simError(); |
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} |
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|
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char charBuffer[BUFF_SIZE]; |
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if ((*ifsP)) { |
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while(ifsP->getline(charBuffer,BUFF_SIZE)) |
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ParseLine(charBuffer); |
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|
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if (ifs1) |
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ifs1.close(); |
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if (ifs2) |
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ifs2.close(); |
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if (ifs3) |
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ifs3.close(); |
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if (ifs4) |
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ifs4.close(); |
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|
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if (GetSize() == 0) { |
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sprintf( painCave.errMsg, |
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"ElementsTable error.\n" |
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"\tCannot initialize database %s \n", filename_.c_str()); |
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painCave.isFatal = 0; |
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simError(); |
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} |
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|
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} |
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|
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} |
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} |
