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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 OOPSE coding style. |
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file in OpenBabel. The code has been modified to match the OpenMD coding style. |
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We have retained the OpenBabel copyright and GPL license on this class: |
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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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#include "config.h" |
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#include <iostream> |
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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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#include "io/ifstrstream.hpp" |
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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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#ifdef _MSC_VER |
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#define strncasecmp _strnicmp |
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#define strcasecmp _stricmp |
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#endif |
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#ifdef WIN32 |
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#define FILE_SEP_CHAR "\\" |
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#else |
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#define BUFF_SIZE 32768 |
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#endif |
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namespace oopse { |
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namespace OpenMD { |
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ElementsTable etab; |
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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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dir_ = std::string("TO_STRING(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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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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for (i = elements_.begin(); i != elements_.end(); ++i) |
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delete *i; |
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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 symbol[6]; |
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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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// 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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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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return elements_.size(); |
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} |
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char *ElementsTable::GetSymbol(int atomicnum) { |
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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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Init(); |
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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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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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buffer = getenv(envvar_.c_str()); |
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buffer += FILE_SEP_CHAR; |
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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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buffer += filename_; |
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subbuffer += filename_; |
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ifs1.open(subbuffer.c_str()); |
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ifsP= &ifs1; |
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if (!(*ifsP)) { |
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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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} else { |
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sprintf( painCave.errMsg, |
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"ElementsTable error.\n" |
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simError(); |
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} |
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char charBuffer[BUFF_SIZE]; |
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if ((*ifsP)) { |
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char charBuffer[BUFF_SIZE]; |
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while(ifsP->getline(charBuffer,BUFF_SIZE)) |
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ParseLine(charBuffer); |
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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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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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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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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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} |
