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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* Copyright (c) 2009 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
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* [4] Vardeman & Gezelter, in progress (2009). |
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*/ |
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|
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#include "io/DumpReader.hpp" |
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< |
#include "io/RestReader.hpp" |
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#include "primitives/Molecule.hpp" |
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|
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|
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#include <sys/types.h> |
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#include <sys/stat.h> |
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|
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#include <math.h> |
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#include <string> |
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#include <sstream> |
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#include <iostream> |
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#include <stdio.h> |
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#include <stdlib.h> |
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#include <string.h> |
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|
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#include "io/RestReader.hpp" |
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#include "primitives/Molecule.hpp" |
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#include "utils/simError.h" |
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> |
#include "utils/MemoryUtils.hpp" |
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> |
#include "utils/StringTokenizer.hpp" |
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#include "restraints/ObjectRestraint.hpp" |
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#include "restraints/MolecularRestraint.hpp" |
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> |
#include "restraints/MolecularRestraint.hpp" |
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|
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#ifdef IS_MPI |
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|
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#include <mpi.h> |
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#endif |
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|
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namespace OpenMD { |
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+ |
|
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void RestReader::scanFile(){ |
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int lineNo = 0; |
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std::streampos prevPos; |
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std::streampos currPos; |
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|
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#ifdef IS_MPI |
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|
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if (worldRank == 0) { |
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#endif // is_mpi |
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|
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inFile_->clear(); |
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currPos = inFile_->tellg(); |
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prevPos = currPos; |
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|
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void RestReader::readReferenceStructure() { |
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> |
bool foundOpenSnapshotTag = false; |
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|
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while(!foundOpenSnapshotTag && inFile_->getline(buffer, bufferSize)) { |
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++lineNo; |
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|
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std::string line = buffer; |
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currPos = inFile_->tellg(); |
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if (line.find("<Snapshot>")!= std::string::npos) { |
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foundOpenSnapshotTag = true; |
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framePos_ = prevPos; |
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} |
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prevPos = currPos; |
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} |
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|
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#ifdef IS_MPI |
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} |
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MPI_Bcast(&framePos_, 1, MPI_INT, 0, MPI_COMM_WORLD); |
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#endif // is_mpi |
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} |
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|
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// some of this comes directly from DumpReader. |
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|
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if (!isScanned_) |
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scanFile(); |
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|
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int storageLayout = info_->getSnapshotManager()->getStorageLayout(); |
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|
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if (storageLayout & DataStorage::dslPosition) { |
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needPos_ = true; |
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void RestReader::readSet(){ |
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std::string line; |
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|
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#ifndef IS_MPI |
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|
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inFile_->clear(); |
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inFile_->seekg(framePos_); |
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|
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std::istream& inputStream = *inFile_; |
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#else |
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|
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int masterNode = 0; |
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std::stringstream sstream; |
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if (worldRank == masterNode) { |
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std::string sendBuffer; |
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|
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inFile_->clear(); |
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inFile_->seekg(framePos_); |
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|
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while (inFile_->getline(buffer, bufferSize)) { |
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|
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line = buffer; |
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sendBuffer += line; |
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sendBuffer += '\n'; |
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if (line.find("</Snapshot>") != std::string::npos) { |
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break; |
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} |
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} |
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|
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int sendBufferSize = sendBuffer.size(); |
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MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD); |
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MPI_Bcast((void *)sendBuffer.c_str(), sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); |
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|
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sstream.str(sendBuffer); |
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} else { |
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needPos_ = false; |
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int sendBufferSize; |
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MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD); |
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char * recvBuffer = new char[sendBufferSize+1]; |
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assert(recvBuffer); |
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recvBuffer[sendBufferSize] = '\0'; |
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MPI_Bcast(recvBuffer, sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); |
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sstream.str(recvBuffer); |
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delete [] recvBuffer; |
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} |
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|
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std::istream& inputStream = sstream; |
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#endif |
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|
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inputStream.getline(buffer, bufferSize); |
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|
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line = buffer; |
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if (line.find("<Snapshot>") == std::string::npos) { |
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sprintf(painCave.errMsg, |
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"RestReader Error: can not find <Snapshot>\n"); |
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painCave.isFatal = 1; |
| 159 |
> |
simError(); |
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} |
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|
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needVel_ = false; |
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|
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if (storageLayout & DataStorage::dslAmat || storageLayout & DataStorage::dslElectroFrame) { |
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needQuaternion_ = true; |
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} else { |
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needQuaternion_ = false; |
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< |
} |
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|
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//read frameData |
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readFrameProperties(inputStream); |
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|
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//read StuntDoubles |
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readStuntDoubles(inputStream); |
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|
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> |
inputStream.getline(buffer, bufferSize); |
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> |
line = buffer; |
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> |
if (line.find("</Snapshot>") == std::string::npos) { |
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> |
sprintf(painCave.errMsg, |
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> |
"RestReader Error: can not find </Snapshot>\n"); |
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> |
painCave.isFatal = 1; |
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> |
simError(); |
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> |
} |
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> |
} |
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> |
|
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> |
void RestReader::readReferenceStructure() { |
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|
|
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needAngMom_ = false; |
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– |
|
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|
// We need temporary storage to keep track of all StuntDouble positions |
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// in case some of the restraints are molecular (i.e. if they use |
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// multiple SD positions to determine restrained orientations or positions: |
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|
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all_pos_.clear(); |
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< |
all_pos_.resize(info_->getNGlobalIntegrableObjects() ); |
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< |
|
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< |
|
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> |
all_pos_.resize(info_->getNGlobalIntegrableObjects()) ; |
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> |
|
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// Restraint files are just standard dump files, but with the reference |
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// structure stored in the first frame (frame 0). |
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// RestReader overloads readSet and explicitly handles all of the |
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// ObjectRestraints in that method: |
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|
|
| 192 |
< |
readSet(0); |
| 193 |
< |
|
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> |
scanFile(); |
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> |
|
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> |
|
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> |
readSet(); |
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> |
|
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> |
|
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|
// all ObjectRestraints have been handled, now we have to worry about |
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// molecular restraints: |
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|
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|
Molecule::IntegrableObjectIterator j; |
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Molecule* mol; |
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StuntDouble* sd; |
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< |
|
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> |
|
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// no need to worry about parallel molecules, as molecules are not |
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// split across processor boundaries. Just loop over all molecules |
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// we know about: |
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|
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> |
|
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|
for (mol = info_->beginMolecule(i); mol != NULL; |
| 211 |
|
mol = info_->nextMolecule(i)) { |
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< |
|
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> |
|
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|
// is this molecule restrained? |
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|
GenericData* data = mol->getPropertyByName("Restraint"); |
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|
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|
if (data != NULL) { |
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< |
|
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> |
|
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|
// make sure we can reinterpret the generic data as restraint data: |
| 219 |
< |
|
| 219 |
> |
|
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|
RestraintData* restData= dynamic_cast<RestraintData*>(data); |
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< |
|
| 221 |
> |
|
| 222 |
|
if (restData != NULL) { |
| 223 |
< |
|
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> |
|
| 224 |
|
// make sure we can reinterpet the restraint data as a |
| 225 |
|
// pointer to a MolecularRestraint: |
| 226 |
< |
|
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> |
|
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|
MolecularRestraint* mRest = dynamic_cast<MolecularRestraint*>(restData->getData()); |
| 228 |
< |
|
| 228 |
> |
|
| 229 |
|
if (mRest != NULL) { |
| 230 |
< |
|
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> |
|
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|
// now we need to pack the stunt doubles for the reference |
| 232 |
|
// structure: |
| 233 |
< |
|
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> |
|
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|
std::vector<Vector3d> ref; |
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|
int count = 0; |
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|
RealType mass, mTot; |
| 248 |
|
// doubles from the *globally* sorted array of |
| 249 |
|
// positions: |
| 250 |
|
|
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< |
ref.push_back( all_pos_[sd->getGlobalIndex()] ); |
| 252 |
< |
|
| 145 |
< |
mass = sd->getMass(); |
| 146 |
< |
|
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> |
ref.push_back( all_pos_[sd->getGlobalIntegrableObjectIndex()] ); |
| 252 |
> |
mass = sd->getMass(); |
| 253 |
|
COM = COM + mass * ref[count]; |
| 254 |
|
mTot = mTot + mass; |
| 255 |
|
count = count + 1; |
| 256 |
|
} |
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– |
|
| 257 |
|
COM /= mTot; |
| 153 |
– |
|
| 258 |
|
mRest->setReferenceStructure(ref, COM); |
| 155 |
– |
|
| 259 |
|
} |
| 260 |
|
} |
| 261 |
|
} |
| 265 |
|
|
| 266 |
|
|
| 267 |
|
void RestReader::parseDumpLine(const std::string& line) { |
| 268 |
+ |
|
| 269 |
|
StringTokenizer tokenizer(line); |
| 270 |
|
int nTokens; |
| 271 |
|
|
| 273 |
|
|
| 274 |
|
if (nTokens < 2) { |
| 275 |
|
sprintf(painCave.errMsg, |
| 276 |
< |
"DumpReader Error: Not enough Tokens.\n%s\n", line.c_str()); |
| 276 |
> |
"RestReader Error: Not enough Tokens.\n%s\n", line.c_str()); |
| 277 |
|
painCave.isFatal = 1; |
| 278 |
|
simError(); |
| 279 |
|
} |
| 280 |
|
|
| 281 |
|
int index = tokenizer.nextTokenAsInt(); |
| 178 |
– |
|
| 179 |
– |
StuntDouble* integrableObject = info_->getIOIndexToIntegrableObject(index); |
| 282 |
|
|
| 283 |
< |
if (integrableObject == NULL) { |
| 284 |
< |
return; |
| 285 |
< |
} |
| 286 |
< |
|
| 287 |
< |
std::string type = tokenizer.nextToken(); |
| 288 |
< |
int size = type.size(); |
| 289 |
< |
Vector3d pos; |
| 290 |
< |
Vector3d vel; |
| 291 |
< |
Quat4d q; |
| 292 |
< |
Vector3d ji; |
| 293 |
< |
Vector3d force; |
| 294 |
< |
Vector3d torque; |
| 295 |
< |
|
| 296 |
< |
for(int i = 0; i < size; ++i) { |
| 297 |
< |
switch(type[i]) { |
| 283 |
> |
|
| 284 |
> |
if (index < 1116){ |
| 285 |
> |
std::string type = tokenizer.nextToken(); |
| 286 |
> |
|
| 287 |
> |
Vector3d pos; |
| 288 |
> |
|
| 289 |
> |
pos[0] = tokenizer.nextTokenAsDouble(); |
| 290 |
> |
pos[1] = tokenizer.nextTokenAsDouble(); |
| 291 |
> |
pos[2] = tokenizer.nextTokenAsDouble(); |
| 292 |
> |
|
| 293 |
> |
all_pos_[index] = pos; |
| 294 |
> |
}else{ |
| 295 |
> |
|
| 296 |
> |
bool exist = false; |
| 297 |
> |
int indexCount = 0; |
| 298 |
> |
|
| 299 |
> |
while ( (!exist) && (indexCount < stuntDoubleIndex_.size())){ |
| 300 |
> |
if (index == stuntDoubleIndex_[indexCount]) |
| 301 |
> |
exist = true; |
| 302 |
> |
indexCount++; |
| 303 |
> |
} |
| 304 |
> |
|
| 305 |
> |
StuntDouble* integrableObject; |
| 306 |
> |
|
| 307 |
> |
if (exist){ |
| 308 |
|
|
| 309 |
< |
case 'p': { |
| 310 |
< |
pos[0] = tokenizer.nextTokenAsDouble(); |
| 311 |
< |
pos[1] = tokenizer.nextTokenAsDouble(); |
| 312 |
< |
pos[2] = tokenizer.nextTokenAsDouble(); |
| 313 |
< |
break; |
| 314 |
< |
} |
| 315 |
< |
case 'v' : { |
| 316 |
< |
vel[0] = tokenizer.nextTokenAsDouble(); |
| 317 |
< |
vel[1] = tokenizer.nextTokenAsDouble(); |
| 318 |
< |
vel[2] = tokenizer.nextTokenAsDouble(); |
| 319 |
< |
break; |
| 320 |
< |
} |
| 321 |
< |
|
| 322 |
< |
case 'q' : { |
| 323 |
< |
if (integrableObject->isDirectional()) { |
| 324 |
< |
|
| 325 |
< |
q[0] = tokenizer.nextTokenAsDouble(); |
| 326 |
< |
q[1] = tokenizer.nextTokenAsDouble(); |
| 327 |
< |
q[2] = tokenizer.nextTokenAsDouble(); |
| 328 |
< |
q[3] = tokenizer.nextTokenAsDouble(); |
| 329 |
< |
|
| 330 |
< |
RealType qlen = q.length(); |
| 331 |
< |
if (qlen < OpenMD::epsilon) { //check quaternion is not equal to 0 |
| 332 |
< |
|
| 333 |
< |
sprintf(painCave.errMsg, |
| 334 |
< |
"DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2) ~ 0\n"); |
| 335 |
< |
painCave.isFatal = 1; |
| 336 |
< |
simError(); |
| 337 |
< |
|
| 226 |
< |
} |
| 227 |
< |
|
| 228 |
< |
q.normalize(); |
| 229 |
< |
} |
| 230 |
< |
break; |
| 309 |
> |
integrableObject = info_->getIOIndexToIntegrableObject(index); |
| 310 |
> |
|
| 311 |
> |
int compareindex = integrableObject->getGlobalIntegrableObjectIndex(); |
| 312 |
> |
|
| 313 |
> |
if (integrableObject == NULL) { |
| 314 |
> |
return; |
| 315 |
> |
} |
| 316 |
> |
|
| 317 |
> |
std::string type = tokenizer.nextToken(); |
| 318 |
> |
|
| 319 |
> |
Vector3d pos; |
| 320 |
> |
|
| 321 |
> |
pos[0] = tokenizer.nextTokenAsDouble(); |
| 322 |
> |
pos[1] = tokenizer.nextTokenAsDouble(); |
| 323 |
> |
pos[2] = tokenizer.nextTokenAsDouble(); |
| 324 |
> |
|
| 325 |
> |
Vector3d vel; |
| 326 |
> |
vel[0] = tokenizer.nextTokenAsDouble(); |
| 327 |
> |
vel[1] = tokenizer.nextTokenAsDouble(); |
| 328 |
> |
vel[2] = tokenizer.nextTokenAsDouble(); |
| 329 |
> |
|
| 330 |
> |
|
| 331 |
> |
Quat4d q; |
| 332 |
> |
if (integrableObject->isDirectional()) { |
| 333 |
> |
|
| 334 |
> |
q[0] = tokenizer.nextTokenAsDouble(); |
| 335 |
> |
q[1] = tokenizer.nextTokenAsDouble(); |
| 336 |
> |
q[2] = tokenizer.nextTokenAsDouble(); |
| 337 |
> |
q[3] = tokenizer.nextTokenAsDouble(); |
| 338 |
|
} |
| 339 |
< |
case 'j' : { |
| 340 |
< |
if (integrableObject->isDirectional()) { |
| 341 |
< |
ji[0] = tokenizer.nextTokenAsDouble(); |
| 342 |
< |
ji[1] = tokenizer.nextTokenAsDouble(); |
| 343 |
< |
ji[2] = tokenizer.nextTokenAsDouble(); |
| 339 |
> |
// keep the position in case we need it for a molecular restraint: |
| 340 |
> |
|
| 341 |
> |
all_pos_[index] = pos; |
| 342 |
> |
|
| 343 |
> |
// is this io restrained? |
| 344 |
> |
GenericData* data = integrableObject->getPropertyByName("Restraint"); |
| 345 |
> |
ObjectRestraint* oRest; |
| 346 |
> |
|
| 347 |
> |
if (data != NULL) { |
| 348 |
> |
// make sure we can reinterpret the generic data as restraint data: |
| 349 |
> |
RestraintData* restData= dynamic_cast<RestraintData*>(data); |
| 350 |
> |
if (restData != NULL) { |
| 351 |
> |
// make sure we can reinterpet the restraint data as a pointer to |
| 352 |
> |
// an ObjectRestraint: |
| 353 |
> |
oRest = dynamic_cast<ObjectRestraint*>(restData->getData()); |
| 354 |
> |
if (oRest != NULL) { |
| 355 |
> |
if (integrableObject->isDirectional()) { |
| 356 |
> |
oRest->setReferenceStructure(pos, q.toRotationMatrix3()); |
| 357 |
> |
} else { |
| 358 |
> |
oRest->setReferenceStructure(pos); |
| 359 |
> |
} |
| 360 |
> |
} |
| 361 |
|
} |
| 238 |
– |
break; |
| 239 |
– |
} |
| 240 |
– |
case 'f': { |
| 241 |
– |
force[0] = tokenizer.nextTokenAsDouble(); |
| 242 |
– |
force[1] = tokenizer.nextTokenAsDouble(); |
| 243 |
– |
force[2] = tokenizer.nextTokenAsDouble(); |
| 244 |
– |
|
| 245 |
– |
break; |
| 362 |
|
} |
| 247 |
– |
case 't' : { |
| 248 |
– |
torque[0] = tokenizer.nextTokenAsDouble(); |
| 249 |
– |
torque[1] = tokenizer.nextTokenAsDouble(); |
| 250 |
– |
torque[2] = tokenizer.nextTokenAsDouble(); |
| 251 |
– |
|
| 252 |
– |
break; |
| 253 |
– |
} |
| 254 |
– |
default: { |
| 255 |
– |
sprintf(painCave.errMsg, |
| 256 |
– |
"DumpReader Error: %s is an unrecognized type\n", type.c_str()); |
| 257 |
– |
painCave.isFatal = 1; |
| 258 |
– |
simError(); |
| 259 |
– |
break; |
| 260 |
– |
} |
| 261 |
– |
|
| 363 |
|
} |
| 364 |
|
} |
| 365 |
< |
|
| 366 |
< |
// keep the position in case we need it for a molecular restraint: |
| 365 |
> |
} |
| 366 |
> |
|
| 367 |
> |
void RestReader::readStuntDoubles(std::istream& inputStream) { |
| 368 |
|
|
| 369 |
< |
all_pos_[index] = pos; |
| 370 |
< |
|
| 371 |
< |
// is this io restrained? |
| 372 |
< |
GenericData* data = integrableObject->getPropertyByName("Restraint"); |
| 373 |
< |
ObjectRestraint* oRest; |
| 374 |
< |
|
| 375 |
< |
if (data != NULL) { |
| 376 |
< |
// make sure we can reinterpret the generic data as restraint data: |
| 377 |
< |
RestraintData* restData= dynamic_cast<RestraintData*>(data); |
| 378 |
< |
if (restData != NULL) { |
| 379 |
< |
// make sure we can reinterpet the restraint data as a pointer to |
| 380 |
< |
// an ObjectRestraint: |
| 381 |
< |
oRest = dynamic_cast<ObjectRestraint*>(restData->getData()); |
| 382 |
< |
if (oRest != NULL) { |
| 383 |
< |
if (integrableObject->isDirectional()) { |
| 282 |
< |
oRest->setReferenceStructure(pos, q.toRotationMatrix3()); |
| 283 |
< |
} else { |
| 284 |
< |
oRest->setReferenceStructure(pos); |
| 285 |
< |
} |
| 286 |
< |
} |
| 369 |
> |
inputStream.getline(buffer, bufferSize); |
| 370 |
> |
std::string line(buffer); |
| 371 |
> |
|
| 372 |
> |
if (line.find("<StuntDoubles>") == std::string::npos) { |
| 373 |
> |
sprintf(painCave.errMsg, |
| 374 |
> |
"RestReader Error: Missing <StuntDoubles>\n"); |
| 375 |
> |
painCave.isFatal = 1; |
| 376 |
> |
simError(); |
| 377 |
> |
} |
| 378 |
> |
|
| 379 |
> |
while(inputStream.getline(buffer, bufferSize)) { |
| 380 |
> |
line = buffer; |
| 381 |
> |
|
| 382 |
> |
if(line.find("</StuntDoubles>") != std::string::npos) { |
| 383 |
> |
break; |
| 384 |
|
} |
| 385 |
+ |
|
| 386 |
+ |
parseDumpLine(line); |
| 387 |
|
} |
| 388 |
< |
|
| 388 |
> |
|
| 389 |
|
} |
| 291 |
– |
|
| 390 |
|
|
| 391 |
< |
|
| 391 |
> |
|
| 392 |
|
void RestReader::readFrameProperties(std::istream& inputStream) { |
| 393 |
|
inputStream.getline(buffer, bufferSize); |
| 394 |
|
std::string line(buffer); |
| 395 |
|
|
| 396 |
|
if (line.find("<FrameData>") == std::string::npos) { |
| 397 |
|
sprintf(painCave.errMsg, |
| 398 |
< |
"DumpReader Error: Missing <FrameData>\n"); |
| 398 |
> |
"RestReader Error: Missing <FrameData>\n"); |
| 399 |
|
painCave.isFatal = 1; |
| 400 |
|
simError(); |
| 401 |
|
} |
| 412 |
|
} |
| 413 |
|
|
| 414 |
|
} |
| 415 |
< |
|
| 415 |
> |
|
| 416 |
|
} |
| 417 |
|
|
| 418 |
|
|
