--- trunk/src/io/ZConsReader.cpp 2004/09/24 16:27:58 3
+++ trunk/src/io/ZConsReader.cpp 2005/12/02 15:38:03 770
@@ -1,183 +1,108 @@
+/*
+ * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
+ *
+ * The University of Notre Dame grants you ("Licensee") a
+ * non-exclusive, royalty free, license to use, modify and
+ * redistribute this software in source and binary code form, provided
+ * that the following conditions are met:
+ *
+ * 1. Acknowledgement of the program authors must be made in any
+ * publication of scientific results based in part on use of the
+ * program. An acceptable form of acknowledgement is citation of
+ * the article in which the program was described (Matthew
+ * A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
+ * J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
+ * Parallel Simulation Engine for Molecular Dynamics,"
+ * J. Comput. Chem. 26, pp. 252-271 (2005))
+ *
+ * 2. Redistributions of source code must retain the above copyright
+ * notice, this list of conditions and the following disclaimer.
+ *
+ * 3. Redistributions in binary form must reproduce the above copyright
+ * notice, this list of conditions and the following disclaimer in the
+ * documentation and/or other materials provided with the
+ * distribution.
+ *
+ * This software is provided "AS IS," without a warranty of any
+ * kind. All express or implied conditions, representations and
+ * warranties, including any implied warranty of merchantability,
+ * fitness for a particular purpose or non-infringement, are hereby
+ * excluded. The University of Notre Dame and its licensors shall not
+ * be liable for any damages suffered by licensee as a result of
+ * using, modifying or distributing the software or its
+ * derivatives. In no event will the University of Notre Dame or its
+ * licensors be liable for any lost revenue, profit or data, or for
+ * direct, indirect, special, consequential, incidental or punitive
+ * damages, however caused and regardless of the theory of liability,
+ * arising out of the use of or inability to use software, even if the
+ * University of Notre Dame has been advised of the possibility of
+ * such damages.
+ */
+
#include "io/ZConsReader.hpp"
#include "utils/simError.h"
+#include "utils/StringUtils.hpp"
+namespace oopse {
-ZConsReader::ZConsReader(SimInfo* info)
- :istream(NULL){
+ ZConsReader::ZConsReader(SimInfo* info) : info_(info){
- GenericData* data;
- StringData* filename;
- this->info = info;
+ std::string zconsFileName_ = getPrefix(info_->getFinalConfigFileName()) + ".fz";
+ istream_.open(zconsFileName_.c_str());
- //retrieve output filename of z force
- data = info->getProperty(ZCONSFILENAME_ID);
- if(!data) {
-
-
- sprintf( painCave.errMsg,
- "ZConsReader error: If you use an ZConstraint\n"
- " , you must set output filename of z-force.\n");
- painCave.isFatal = 1;
- simError();
-
- }
- else{
-
- filename = dynamic_cast<StringData*>(data);
-
- if(!filename){
-
- sprintf( painCave.errMsg,
- "ZConsReader error: Can not get property from SimInfo\n");
- painCave.isFatal = 1;
- simError();
-
+ if (!istream_){
+ std::cerr << "open " << zconsFileName_ << "error" << std::endl;
+ exit(1);
}
- else{
- zconsFileName = filename->getData();
- }
-
- }
- istream = new ifstream(zconsFileName.c_str());
-
- if (!istream){
- cerr << "open " << filename << "error" << endl;
- exit(1);
+ Globals* simParam = info_->getSimParams();
+ int nZconstraints = simParam->getNZconsStamps();
+ std::vector<ZConsStamp*> stamp = simParam->getZconsStamps();
+ for (int i = 0; i < nZconstraints; i++){
+ allZmols_.push_back(stamp[i]->getMolIndex());
+ }
}
-
- readHeader();
-}
-ZConsReader::ZConsReader(const string& filename){
- istream = new ifstream(zconsFileName.c_str());
-
- if (!istream){
- cerr << "open " << filename << "error" << endl;
- exit(1);
+ ZConsReader::~ZConsReader(){
+ istream_.close();
}
-
- readHeader();
-}
-ZConsReader::~ZConsReader(){
- istream->close();
-}
+ void ZConsReader::readNextFrame(){
+ char line[MAXBUFFERSIZE];
+ int nFixedZmol;
+ int sscanfCount;
-int ZConsReader::getNumZMol(){
- return nZMol;
-}
+ fixedZmolData_.clear();
-vector<int> ZConsReader::getZConsIndex(){
- return index;
-}
+ while(istream_.getline(line, MAXBUFFERSIZE) && line[0] == '/' && line[1] == '/');
+ sscanfCount = sscanf(line, "%lf", &curTime_);
+ if (sscanfCount != 1){
+ std::cerr << "ZConsReader Error : reading file error" << std::endl;
+ exit(1);
+ }
-vector<double> ZConsReader::getZConsPos(){
- return zconsPos;
-}
+ istream_.getline(line, MAXBUFFERSIZE);
+ sscanfCount = sscanf(line, "%d", &nFixedZmol);
+ if (sscanfCount != 1){
+ std::cerr << "ZConsReader Error : reading file error" << std::endl;
+ exit(1);
+ }
-//double ZConsReader::getKRatio(){
-// return kRatio;
-//}
-
-double ZConsReader::getCurTime(){
- return curTime;
-}
+ ZconsData data;
+ for(int i = 0; i < nFixedZmol; i++){
+ istream_.getline(line, MAXBUFFERSIZE);
+ sscanfCount = sscanf(line, "%d\t%lf\t%lf\t%lf", &data.zmolIndex, &data.zforce, &data.zpos,&data.zconsPos);
+ if (sscanfCount != 4){
+ std::cerr << "ZConsReader Error : reading file error" << std::endl;
+ exit(1);
+ }
-vector<double> ZConsReader::getCurZPos(){
- return curZPos;
-}
-
-vector<double> ZConsReader::getCurFZ(){
- return curFZ;
-}
-
-void ZConsReader::readHeader(){
- const int MAXBUFFERSIZE = 2000;
- char line[MAXBUFFERSIZE];
- int zmolIndex;
- float zmolPos;
- int sscanfCount;
-
- istream->getline(line, MAXBUFFERSIZE);
-
- cout << line << endl;
- //skip the comment lines
- while(line[0] == '#')
- istream->getline(line, MAXBUFFERSIZE);
-
- sscanfCount = sscanf(line, "%d", &nZMol);
-
- if (sscanfCount != 1){
- cerr << "ZConsReader Error : reading file error" << endl;
- exit(1);
- }
-
- for(int i = 0 ; i < nZMol; i++){
-
- istream->getline(line, MAXBUFFERSIZE);
-
- sscanfCount = sscanf(line, "%d\t%f", &zmolIndex, &zmolPos);
- if (sscanfCount != 2){
- cerr << "ZConsReader Error : reading file error" << endl;
- exit(1);
+ fixedZmolData_.push_back(data);
}
-
- index.push_back(zmolIndex);
- zconsPos.push_back(zmolPos);
- }
- curZPos.resize(nZMol);
- curFZ.resize(nZMol);
-}
-
-void ZConsReader::readNextFrame(){
- const int MAXBUFFERSIZE = 2000;
- char line[MAXBUFFERSIZE];
- int tempNZMol;
- int sscanfCount;
- int tempIndex;
- float tempCurTime;
- float tempFZ;
- float tempCurZPos;
- float tempZconsPos;
-
- istream->getline(line, MAXBUFFERSIZE);
- sscanfCount = sscanf(line, "%f", &tempCurTime);
- if (sscanfCount != 1){
- cerr << "ZConsReader Error : reading file error" << endl;
- exit(1);
}
- curTime = tempCurTime;
-
- istream->getline(line, MAXBUFFERSIZE);
- sscanfCount = sscanf(line, "%d", &tempNZMol);
- if (sscanfCount != 1){
- cerr << "ZConsReader Error : reading file error" << endl;
- exit(1);
- }
-
- if (tempNZMol != nZMol){
- cerr << "ZConsReader Error: reading file error" << endl;
- exit(1);
- }
- for(int i = 0; i < nZMol; i++){
- istream->getline(line, MAXBUFFERSIZE);
- sscanfCount = sscanf(line, "%d\t%f\t%f\t%f", &tempIndex, &tempFZ, &tempCurZPos,&tempZconsPos);
- if (sscanfCount != 4){
- cerr << "ZConsReader Error : reading file error" << endl;
- exit(1);
- }
-
- index[i] = tempIndex;
- curFZ[i] = tempFZ;
- curZPos[i]= tempCurZPos;
- zconsPos[i] = tempZconsPos;
+ bool ZConsReader::hasNextFrame(){
+ return istream_.peek() != EOF ? true : false;
}
}
-
-bool ZConsReader::hasNextFrame(){
- return istream->peek() != EOF ? true : false;
-}
-