--- trunk/src/io/RestReader.cpp 2006/06/28 14:35:14 996
+++ trunk/src/io/RestReader.cpp 2009/11/25 20:02:06 1390
@@ -1,24 +1,15 @@
-/*
- * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
- *
+/*
+ * 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
+ * 1. 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
+ * 2. 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.
@@ -37,762 +28,294 @@
* 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.
- */
-
-#define _LARGEFILE_SOURCE64
-#define _FILE_OFFSET_BITS 64
-
-#include <sys/types.h>
-#include <sys/stat.h>
-
-#include <iostream>
-#include <math.h>
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-
-#include "primitives/Molecule.hpp"
-#include "utils/MemoryUtils.hpp"
-#include "utils/StringTokenizer.hpp"
+ *
+ * SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
+ * research, please cite the appropriate papers when you publish your
+ * work. Good starting points are:
+ *
+ * [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
+ * [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
+ * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
+ * [4] Vardeman & Gezelter, in progress (2009).
+ */
+
+#include "io/DumpReader.hpp"
#include "io/RestReader.hpp"
-#include "utils/simError.h"
+#include "primitives/Molecule.hpp"
+#include "restraints/ObjectRestraint.hpp"
+#include "restraints/MolecularRestraint.hpp"
-#ifdef IS_MPI
-#include <mpi.h>
-#define TAKE_THIS_TAG_CHAR 0
-#define TAKE_THIS_TAG_INT 1
-#define TAKE_THIS_TAG_DOUBLE 2
-#endif // is_mpi
+namespace OpenMD {
+
+ void RestReader::readReferenceStructure() {
-namespace oopse {
-
- RestReader::RestReader( SimInfo* info ) : info_(info){
-
- idealName = "idealCrystal.in";
+ // some of this comes directly from DumpReader.
+
+ if (!isScanned_)
+ scanFile();
+
+ int storageLayout = info_->getSnapshotManager()->getStorageLayout();
-#ifdef IS_MPI
- if (worldRank == 0) {
-#endif
+ if (storageLayout & DataStorage::dslPosition) {
+ needPos_ = true;
+ } else {
+ needPos_ = false;
+ }
+
+ needVel_ = false;
+
+ if (storageLayout & DataStorage::dslAmat || storageLayout & DataStorage::dslElectroFrame) {
+ needQuaternion_ = true;
+ } else {
+ needQuaternion_ = false;
+ }
- inIdealFile = new std::ifstream(idealName.c_str());
+ needAngMom_ = false;
- if(inIdealFile->fail()){
- sprintf(painCave.errMsg,
- "RestReader: Cannot open file: %s\n",
- idealName.c_str());
- painCave.isFatal = 1;
- simError();
- }
-
-#ifdef IS_MPI
- }
- strcpy( checkPointMsg,
- "File \"idealCrystal.in\" opened successfully for reading." );
- MPIcheckPoint();
-#endif
+ // We need temporary storage to keep track of all StuntDouble positions
+ // in case some of the restraints are molecular (i.e. if they use
+ // multiple SD positions to determine restrained orientations or positions:
- return;
- }
-
- RestReader :: ~RestReader( ){
-#ifdef IS_MPI
- if (worldRank == 0) {
-#endif
+ all_pos_.clear();
+ all_pos_.resize(info_->getNGlobalIntegrableObjects() );
- delete inIdealFile;
- delete inAngFile;
-#ifdef IS_MPI
- }
- strcpy( checkPointMsg,
- "File idealCrystal.in (and .zang0 if present) closed successfully." );
- MPIcheckPoint();
-#endif
+ // Restraint files are just standard dump files, but with the reference
+ // structure stored in the first frame (frame 0).
+ // RestReader overloads readSet and explicitly handles all of the
+ // ObjectRestraints in that method:
+
+ readSet(0);
- return;
- }
-
-
- void RestReader :: readIdealCrystal(){
-
-#ifdef IS_MPI
- int which_node;
- int i, j;
-#endif //is_mpi
-
- const int BUFFERSIZE = 2000; // size of the read buffer
- int nTotObjs; // the number of atoms
- char read_buffer[BUFFERSIZE]; //the line buffer for reading
-
- char *parseErr;
-
- std::vector<StuntDouble*> integrableObjects;
-
+ // all ObjectRestraints have been handled, now we have to worry about
+ // molecular restraints:
+
+ SimInfo::MoleculeIterator i;
+ Molecule::IntegrableObjectIterator j;
Molecule* mol;
- StuntDouble* integrableObject;
- SimInfo::MoleculeIterator mi;
- Molecule::IntegrableObjectIterator ii;
-
-#ifndef IS_MPI
-
- inIdealFile->getline(read_buffer, sizeof(read_buffer));
+ StuntDouble* sd;
- if( inIdealFile->eof() ){
- sprintf( painCave.errMsg,
- "RestraintReader error: error reading 1st line of \"%s\"\n",
- idealName.c_str() );
- painCave.isFatal = 1;
- simError();
- }
-
- nTotObjs = atoi( read_buffer );
-
- if( nTotObjs != info_->getNGlobalIntegrableObjects() ){
- sprintf( painCave.errMsg,
- "RestraintReader error. %s nIntegrable, %d, "
- "does not match the meta-data file's nIntegrable, %d.\n",
- idealName.c_str(),
- nTotObjs,
- info_->getNGlobalIntegrableObjects());
- painCave.isFatal = 1;
- simError();
- }
-
- // skip over the comment line
- inIdealFile->getline(read_buffer, sizeof(read_buffer));
+ // no need to worry about parallel molecules, as molecules are not
+ // split across processor boundaries. Just loop over all molecules
+ // we know about:
- if( inIdealFile->eof() ){
- sprintf( painCave.errMsg,
- "error in reading commment in %s\n",
- idealName.c_str());
- painCave.isFatal = 1;
- simError();
- }
-
- // parse the ideal crystal lines
- /*
- * Note: we assume that there is a one-to-one correspondence between
- * integrable objects and lines in the idealCrystal.in file. Thermodynamic
- * integration is only supported for simple rigid bodies.
- */
- for (mol = info_->beginMolecule(mi); mol != NULL;
- mol = info_->nextMolecule(mi)) {
+ for (mol = info_->beginMolecule(i); mol != NULL;
+ mol = info_->nextMolecule(i)) {
+
+ // is this molecule restrained?
+ GenericData* data = mol->getPropertyByName("Restraint");
- for (integrableObject = mol->beginIntegrableObject(ii);
- integrableObject != NULL;
- integrableObject = mol->nextIntegrableObject(ii)) {
+ if (data != NULL) {
- inIdealFile->getline(read_buffer, sizeof(read_buffer));
+ // make sure we can reinterpret the generic data as restraint data:
- if( inIdealFile->eof() ){
- sprintf(painCave.errMsg,
- "RestReader Error: error in reading file %s\n"
- "natoms = %d; index = %d\n"
- "error reading the line from the file.\n",
- idealName.c_str(), nTotObjs,
- integrableObject->getGlobalIndex() );
- painCave.isFatal = 1;
- simError();
- }
-
- parseErr = parseIdealLine( read_buffer, integrableObject);
- if( parseErr != NULL ){
- strcpy( painCave.errMsg, parseErr );
- painCave.isFatal = 1;
- simError();
- }
- }
- }
-
- // MPI Section of code..........
-#else //IS_MPI
-
- // first thing first, suspend fatalities.
- painCave.isEventLoop = 1;
-
- int masterNode = 0;
-
- MPI_Status istatus;
- int nCurObj;
- int nitems;
- int haveError;
+ RestraintData* restData= dynamic_cast<RestraintData*>(data);
- nTotObjs = info_->getNGlobalIntegrableObjects();
- haveError = 0;
+ if (restData != NULL) {
- if (worldRank == masterNode) {
- inIdealFile->getline(read_buffer, sizeof(read_buffer));
+ // make sure we can reinterpet the restraint data as a
+ // pointer to a MolecularRestraint:
- if( inIdealFile->eof() ){
- sprintf( painCave.errMsg,
- "Error reading 1st line of %s \n ",idealName.c_str());
- painCave.isFatal = 1;
- simError();
- }
-
- nitems = atoi( read_buffer );
-
- // Check to see that the number of integrable objects in the
- // intial configuration file is the same as derived from the
- // meta-data file.
- if( nTotObjs != nitems){
- sprintf( painCave.errMsg,
- "RestraintReader Error. %s nIntegrable, %d, "
- "does not match the meta-data file's nIntegrable, %d.\n",
- idealName.c_str(), nTotObjs,
- info_->getNGlobalIntegrableObjects());
- painCave.isFatal = 1;
- simError();
- }
-
- // skip over the comment line
- inIdealFile->getline(read_buffer, sizeof(read_buffer));
+ MolecularRestraint* mRest = dynamic_cast<MolecularRestraint*>(restData->getData());
- if( inIdealFile->eof() ){
- sprintf( painCave.errMsg,
- "error in reading commment in %s\n", idealName.c_str());
- painCave.isFatal = 1;
- simError();
- }
+ if (mRest != NULL) {
- MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, masterNode, MPI_COMM_WORLD);
+ // now we need to pack the stunt doubles for the reference
+ // structure:
- for (i=0 ; i < info_->getNGlobalMolecules(); i++) {
- which_node = info_->getMolToProc(i);
-
- if(which_node == masterNode){
- //molecules belong to master node
-
- mol = info_->getMoleculeByGlobalIndex(i);
-
- if(mol == NULL) {
- sprintf(painCave.errMsg,
- "RestReader Error: Molecule not found on node %d!\n",
- worldRank);
- painCave.isFatal = 1;
- simError();
- }
-
- for (integrableObject = mol->beginIntegrableObject(ii);
- integrableObject != NULL;
- integrableObject = mol->nextIntegrableObject(ii)){
+ std::vector<Vector3d> ref;
+ int count = 0;
+ RealType mass, mTot;
+ Vector3d COM(0.0);
- inIdealFile->getline(read_buffer, sizeof(read_buffer));
+ mTot = 0.0;
- if( inIdealFile->eof() ){
- sprintf(painCave.errMsg,
- "RestReader Error: error in reading file %s\n"
- "natoms = %d; index = %d\n"
- "error reading the line from the file.\n",
- idealName.c_str(), nTotObjs, i );
- painCave.isFatal = 1;
- simError();
+ // loop over the stunt doubles in this molecule in the order we
+ // will be looping them in the restraint code:
+
+ for (sd = mol->beginIntegrableObject(j); sd != NULL;
+ sd = mol->nextIntegrableObject(j)) {
+
+ // push back the reference positions of the stunt
+ // doubles from the *globally* sorted array of
+ // positions:
+
+ ref.push_back( all_pos_[sd->getGlobalIndex()] );
+
+ mass = sd->getMass();
+
+ COM = COM + mass * ref[count];
+ mTot = mTot + mass;
+ count = count + 1;
}
-
- parseIdealLine(read_buffer, integrableObject);
-
- }
-
- } else {
- //molecule belongs to slave nodes
-
- MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
- TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
-
- for(j = 0; j < nCurObj; j++){
- inIdealFile->getline(read_buffer, sizeof(read_buffer));
-
- if( inIdealFile->eof() ){
- sprintf(painCave.errMsg,
- "RestReader Error: error in reading file %s\n"
- "natoms = %d; index = %d\n"
- "error reading the line from the file.\n",
- idealName.c_str(), nTotObjs, i );
- painCave.isFatal = 1;
- simError();
- }
- MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
- TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
- }
- }
- }
- } else {
- //actions taken at slave nodes
- MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, masterNode, MPI_COMM_WORLD);
+ COM /= mTot;
- for (i=0 ; i < info_->getNGlobalMolecules(); i++) {
- int which_node = info_->getMolToProc(i);
+ mRest->setReferenceStructure(ref, COM);
- if(which_node == worldRank){
- //molecule with global index i belongs to this processor
-
- mol = info_->getMoleculeByGlobalIndex(i);
-
- if(mol == NULL) {
- sprintf(painCave.errMsg,
- "RestReader Error: molecule not found on node %d\n",
- worldRank);
- painCave.isFatal = 1;
- simError();
}
-
- nCurObj = mol->getNIntegrableObjects();
-
- MPI_Send(&nCurObj, 1, MPI_INT, masterNode,
- TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
-
- for (integrableObject = mol->beginIntegrableObject(ii);
- integrableObject != NULL;
- integrableObject = mol->nextIntegrableObject(ii)){
-
- MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, masterNode,
- TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
-
- parseErr = parseIdealLine(read_buffer, integrableObject);
-
- if( parseErr != NULL ){
- strcpy( painCave.errMsg, parseErr );
- simError();
- }
- }
}
}
}
-#endif
}
-
- char* RestReader::parseIdealLine(char* readLine, StuntDouble* sd){
-
- RealType pos[3]; // position place holders
- RealType q[4]; // the quaternions
- RealType RfromQ[3][3]; // the rotation matrix
- RealType normalize; // to normalize the reference unit vector
- RealType uX, uY, uZ; // reference unit vector place holders
- RealType uselessToken;
- StringTokenizer tokenizer(readLine);
- int nTokens;
-
- nTokens = tokenizer.countTokens();
- if (nTokens < 14) {
- sprintf(painCave.errMsg,
- "RestReader Error: Not enough Tokens.\n");
- painCave.isFatal = 1;
- simError();
- }
-
- std::string name = tokenizer.nextToken();
+
+
+ void RestReader::parseDumpLine(const std::string& line) {
+ StringTokenizer tokenizer(line);
+ int nTokens;
+
+ nTokens = tokenizer.countTokens();
+
+ if (nTokens < 2) {
+ sprintf(painCave.errMsg,
+ "DumpReader Error: Not enough Tokens.\n%s\n", line.c_str());
+ painCave.isFatal = 1;
+ simError();
+ }
- if (name != sd->getType()) {
-
- sprintf(painCave.errMsg,
- "RestReader Error: Atom type [%s] in %s does not "
- "match Atom Type [%s] in .md file.\n",
- name.c_str(), idealName.c_str(),
- sd->getType().c_str());
- painCave.isFatal = 1;
- simError();
- }
-
- pos[0] = tokenizer.nextTokenAsDouble();
- pos[1] = tokenizer.nextTokenAsDouble();
- pos[2] = tokenizer.nextTokenAsDouble();
+ int index = tokenizer.nextTokenAsInt();
+
+ StuntDouble* integrableObject = info_->getIOIndexToIntegrableObject(index);
- // store the positions in the stuntdouble as generic data doubles
- DoubleGenericData* refPosX = new DoubleGenericData();
- refPosX->setID("refPosX");
- refPosX->setData(pos[0]);
- sd->addProperty(refPosX);
+ if (integrableObject == NULL) {
+ return;
+ }
- DoubleGenericData* refPosY = new DoubleGenericData();
- refPosY->setID("refPosY");
- refPosY->setData(pos[1]);
- sd->addProperty(refPosY);
-
- DoubleGenericData* refPosZ = new DoubleGenericData();
- refPosZ->setID("refPosZ");
- refPosZ->setData(pos[2]);
- sd->addProperty(refPosZ);
-
- // we don't need the velocities
- uselessToken = tokenizer.nextTokenAsDouble();
- uselessToken = tokenizer.nextTokenAsDouble();
- uselessToken = tokenizer.nextTokenAsDouble();
-
- if (sd->isDirectional()) {
-
- q[0] = tokenizer.nextTokenAsDouble();
- q[1] = tokenizer.nextTokenAsDouble();
- q[2] = tokenizer.nextTokenAsDouble();
- q[3] = tokenizer.nextTokenAsDouble();
-
- // now build the rotation matrix and find the unit vectors
- RfromQ[0][0] = q[0]*q[0] + q[1]*q[1] - q[2]*q[2] - q[3]*q[3];
- RfromQ[0][1] = 2*(q[1]*q[2] + q[0]*q[3]);
- RfromQ[0][2] = 2*(q[1]*q[3] - q[0]*q[2]);
- RfromQ[1][0] = 2*(q[1]*q[2] - q[0]*q[3]);
- RfromQ[1][1] = q[0]*q[0] - q[1]*q[1] + q[2]*q[2] - q[3]*q[3];
- RfromQ[1][2] = 2*(q[2]*q[3] + q[0]*q[1]);
- RfromQ[2][0] = 2*(q[1]*q[3] + q[0]*q[2]);
- RfromQ[2][1] = 2*(q[2]*q[3] - q[0]*q[1]);
- RfromQ[2][2] = q[0]*q[0] - q[1]*q[1] - q[2]*q[2] + q[3]*q[3];
-
- normalize = sqrt(RfromQ[2][0]*RfromQ[2][0] + RfromQ[2][1]*RfromQ[2][1]
- + RfromQ[2][2]*RfromQ[2][2]);
- uX = RfromQ[2][0]/normalize;
- uY = RfromQ[2][1]/normalize;
- uZ = RfromQ[2][2]/normalize;
-
- // store reference unit vectors as generic data in the stuntdouble
- DoubleGenericData* refVectorX = new DoubleGenericData();
- refVectorX->setID("refVectorX");
- refVectorX->setData(uX);
- sd->addProperty(refVectorX);
-
- DoubleGenericData* refVectorY = new DoubleGenericData();
- refVectorY->setID("refVectorY");
- refVectorY->setData(uY);
- sd->addProperty(refVectorY);
-
- DoubleGenericData* refVectorZ = new DoubleGenericData();
- refVectorZ->setID("refVectorZ");
- refVectorZ->setData(uZ);
- sd->addProperty(refVectorZ);
- }
-
- // we don't need the angular velocities, so let's exit the line
- return NULL;
- }
-
- void RestReader::readZangle(){
-
- int i;
- int isPresent;
-
- Molecule* mol;
- StuntDouble* integrableObject;
- SimInfo::MoleculeIterator mi;
- Molecule::IntegrableObjectIterator ii;
-
-#ifdef IS_MPI
- int which_node;
- MPI_Status istatus;
-#endif //is_mpi
-
- const int BUFFERSIZE = 2000; // size of the read buffer
- unsigned int nTotObjs; // the number of atoms
- char read_buffer[BUFFERSIZE]; //the line buffer for reading
-
- std::vector<StuntDouble*> vecParticles;
- std::vector<RealType> tempZangs;
-
- angFile = info_->getRestFileName();
-
- angFile += "0";
-
- // open the omega value file for reading
-#ifdef IS_MPI
- if (worldRank == 0) {
-#endif
- isPresent = 1;
-
- inAngFile = new std::ifstream(angFile.c_str());
-
- if(inAngFile->fail()){
- sprintf(painCave.errMsg,
- "Restraints Warning: %s file is not present\n"
- "\tAll omega values will be initialized to zero. If the\n"
- "\tsimulation is starting from the idealCrystal.in reference\n"
- "\tconfiguration, this is the desired action. If this is not\n"
- "\tthe case, the energy calculations will be incorrect.\n",
- angFile.c_str());
- painCave.severity = OOPSE_WARNING;
- painCave.isFatal = 0;
- simError();
- isPresent = 0;
- }
-
-#ifdef IS_MPI
- // let the other nodes know the status of the file search
- MPI_Bcast(&isPresent, 1, MPI_INT, 0, MPI_COMM_WORLD);
-#endif // is_mpi
-
- if (!isPresent) {
- zeroZangle();
- return;
- }
-
-#ifdef IS_MPI
- if (!isPresent) {
- // master node zeroes out its zAngles if .zang0 isn't present
- zeroZangle();
- return;
- }
+ std::string type = tokenizer.nextToken();
+ int size = type.size();
+ Vector3d pos;
+ Vector3d vel;
+ Quat4d q;
+ Vector3d ji;
+ Vector3d force;
+ Vector3d torque;
+
+ for(int i = 0; i < size; ++i) {
+ switch(type[i]) {
+
+ case 'p': {
+ pos[0] = tokenizer.nextTokenAsDouble();
+ pos[1] = tokenizer.nextTokenAsDouble();
+ pos[2] = tokenizer.nextTokenAsDouble();
+ break;
+ }
+ case 'v' : {
+ vel[0] = tokenizer.nextTokenAsDouble();
+ vel[1] = tokenizer.nextTokenAsDouble();
+ vel[2] = tokenizer.nextTokenAsDouble();
+ break;
+ }
- }
-
- // listen to node 0 to see if we should exit this function
- if (worldRank != 0) {
- MPI_Bcast(&isPresent, 1, MPI_INT, 0, MPI_COMM_WORLD);
- if (!isPresent) {
- zeroZangle();
- return;
- }
- }
-
- strcpy( checkPointMsg, "zAngle file opened successfully for reading." );
- MPIcheckPoint();
-#endif
-
-#ifndef IS_MPI
-
- // read the first line and die if there is a failure
- inAngFile->getline(read_buffer, sizeof(read_buffer));
+ case 'q' : {
+ if (integrableObject->isDirectional()) {
+
+ q[0] = tokenizer.nextTokenAsDouble();
+ q[1] = tokenizer.nextTokenAsDouble();
+ q[2] = tokenizer.nextTokenAsDouble();
+ q[3] = tokenizer.nextTokenAsDouble();
+
+ RealType qlen = q.length();
+ if (qlen < OpenMD::epsilon) { //check quaternion is not equal to 0
+
+ sprintf(painCave.errMsg,
+ "DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2) ~ 0\n");
+ painCave.isFatal = 1;
+ simError();
+
+ }
+
+ q.normalize();
+ }
+ break;
+ }
+ case 'j' : {
+ if (integrableObject->isDirectional()) {
+ ji[0] = tokenizer.nextTokenAsDouble();
+ ji[1] = tokenizer.nextTokenAsDouble();
+ ji[2] = tokenizer.nextTokenAsDouble();
+ }
+ break;
+ }
+ case 'f': {
+ force[0] = tokenizer.nextTokenAsDouble();
+ force[1] = tokenizer.nextTokenAsDouble();
+ force[2] = tokenizer.nextTokenAsDouble();
- if( inAngFile->eof() ){
- sprintf( painCave.errMsg,
- "RestraintReader error: error reading 1st line of \"%s\"\n",
- angFile.c_str() );
- painCave.isFatal = 1;
- simError();
- }
+ break;
+ }
+ case 't' : {
+ torque[0] = tokenizer.nextTokenAsDouble();
+ torque[1] = tokenizer.nextTokenAsDouble();
+ torque[2] = tokenizer.nextTokenAsDouble();
- // read the file and load the values into a vector
- inAngFile->getline(read_buffer, sizeof(read_buffer));
-
- while ( !inAngFile->eof() ) {
- // check for and ignore blank lines
- if ( read_buffer != NULL )
- tempZangs.push_back( atof(read_buffer) );
-
- inAngFile->getline(read_buffer, sizeof(read_buffer));
- }
-
- nTotObjs = info_->getNGlobalIntegrableObjects();
-
- if( nTotObjs != tempZangs.size() ){
- sprintf( painCave.errMsg,
- "RestraintReader zAngle reading error. %s nIntegrable, %d, "
- "does not match the meta-data file's nIntegrable, %i.\n",
- angFile.c_str(),
- tempZangs.size(),
- nTotObjs );
- painCave.isFatal = 1;
- simError();
- }
-
- // load the zAngles into the integrable objects
- i = 0;
- for (mol = info_->beginMolecule(mi); mol != NULL;
- mol = info_->nextMolecule(mi)) {
-
- for (integrableObject = mol->beginIntegrableObject(ii);
- integrableObject != NULL;
- integrableObject = mol->nextIntegrableObject(ii)) {
-
- integrableObject->setZangle(tempZangs[i]);
- i++;
+ break;
+ }
+ default: {
+ sprintf(painCave.errMsg,
+ "DumpReader Error: %s is an unrecognized type\n", type.c_str());
+ painCave.isFatal = 1;
+ simError();
+ break;
+ }
+
}
}
+
+ // keep the position in case we need it for a molecular restraint:
- // MPI Section of code..........
-#else //IS_MPI
-
- // first thing first, suspend fatalities.
- painCave.isEventLoop = 1;
+ all_pos_[index] = pos;
- int masterNode = 0;
+ // is this io restrained?
+ GenericData* data = integrableObject->getPropertyByName("Restraint");
+ ObjectRestraint* oRest;
- int haveError;
- int intObjIndex;
- int intObjIndexTransfer;
-
- int j;
- int nCurObj;
- RealType angleTransfer;
-
- nTotObjs = info_->getNGlobalIntegrableObjects();
- haveError = 0;
-
- if (worldRank == masterNode) {
-
- inAngFile->getline(read_buffer, sizeof(read_buffer));
-
- if( inAngFile->eof() ){
- sprintf( painCave.errMsg,
- "Error reading 1st line of %s \n ",angFile.c_str());
- haveError = 1;
- simError();
+ if (data != NULL) {
+ // make sure we can reinterpret the generic data as restraint data:
+ RestraintData* restData= dynamic_cast<RestraintData*>(data);
+ if (restData != NULL) {
+ // make sure we can reinterpet the restraint data as a pointer to
+ // an ObjectRestraint:
+ oRest = dynamic_cast<ObjectRestraint*>(restData->getData());
+ if (oRest != NULL) {
+ if (integrableObject->isDirectional()) {
+ oRest->setReferenceStructure(pos, q.toRotationMatrix3());
+ } else {
+ oRest->setReferenceStructure(pos);
+ }
+ }
}
-
- // let the master node read the file and load the temporary angle vector
- inAngFile->getline(read_buffer, sizeof(read_buffer));
+ }
- while ( !inAngFile->eof() ) {
- // check for and ignore blank lines
- if ( read_buffer != NULL )
- tempZangs.push_back( atof(read_buffer) );
+ }
+
- inAngFile->getline(read_buffer, sizeof(read_buffer));
- }
- // Check to see that the number of integrable objects in the
- // intial configuration file is the same as derived from the
- // meta-data file.
- if( nTotObjs != tempZangs.size() ){
- sprintf( painCave.errMsg,
- "RestraintReader zAngle reading Error. %s nIntegrable, %d, "
- "does not match the meta-data file's nIntegrable, %d.\n",
- angFile.c_str(),
- tempZangs.size(),
- nTotObjs);
- haveError= 1;
- simError();
- }
-
- // At this point, node 0 has a tempZangs vector completed, and
- // everyone else has nada
-
- for (i=0 ; i < info_->getNGlobalMolecules(); i++) {
- // Get the Node number which has this atom
- which_node = info_->getMolToProc(i);
-
- if (which_node == masterNode) {
- mol = info_->getMoleculeByGlobalIndex(i);
+ void RestReader::readFrameProperties(std::istream& inputStream) {
+ inputStream.getline(buffer, bufferSize);
+ std::string line(buffer);
- if(mol == NULL) {
- strcpy(painCave.errMsg, "Molecule not found on node 0!");
- haveError = 1;
- simError();
- }
+ if (line.find("<FrameData>") == std::string::npos) {
+ sprintf(painCave.errMsg,
+ "DumpReader Error: Missing <FrameData>\n");
+ painCave.isFatal = 1;
+ simError();
+ }
- for (integrableObject = mol->beginIntegrableObject(ii);
- integrableObject != NULL;
- integrableObject = mol->nextIntegrableObject(ii)){
- intObjIndex = integrableObject->getGlobalIndex();
- integrableObject->setZangle(tempZangs[intObjIndex]);
- }
-
- } else {
- // I am MASTER OF THE UNIVERSE, but I don't own this molecule
- // listen for the number of integrableObjects in the molecule
- MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
- TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
-
- for(j=0; j < nCurObj; j++){
- // listen for which integrableObject we need to send the value for
- MPI_Recv(&intObjIndexTransfer, 1, MPI_INT, which_node,
- TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
- angleTransfer = tempZangs[intObjIndexTransfer];
- // send the value to the node so it can initialize the object
- MPI_Send(&angleTransfer, 1, MPI_REALTYPE, which_node,
- TAKE_THIS_TAG_DOUBLE, MPI_COMM_WORLD);
- }
- }
- }
- } else {
- // I am SLAVE TO THE MASTER
- for (i=0 ; i < info_->getNGlobalMolecules(); i++) {
- which_node = info_->getMolToProc(i);
+ // restraints don't care about frame data (unless we need to wrap
+ // coordinates, but we'll worry about that later), so
+ // we'll just scan ahead until the end of the frame data:
- if (which_node == worldRank) {
-
- // BUT I OWN THIS MOLECULE!!!
-
- mol = info_->getMoleculeByGlobalIndex(i);
-
- if(mol == NULL) {
- sprintf(painCave.errMsg,
- "RestReader Error: molecule not found on node %d\n",
- worldRank);
- painCave.isFatal = 1;
- simError();
- }
-
- nCurObj = mol->getNIntegrableObjects();
- // send the number of integrableObjects in the molecule
- MPI_Send(&nCurObj, 1, MPI_INT, 0,
- TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
-
- for (integrableObject = mol->beginIntegrableObject(ii);
- integrableObject != NULL;
- integrableObject = mol->nextIntegrableObject(ii)){
- intObjIndexTransfer = integrableObject->getGlobalIndex();
- // send the global index of the integrableObject
- MPI_Send(&intObjIndexTransfer, 1, MPI_INT, 0,
- TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
- // listen for the value we want to set locally
- MPI_Recv(&angleTransfer, 1, MPI_REALTYPE, 0,
- TAKE_THIS_TAG_DOUBLE, MPI_COMM_WORLD, &istatus);
-
- integrableObject->setZangle(angleTransfer);
- }
- }
- }
- }
-#endif
- }
-
- void RestReader :: zeroZangle(){
-
- Molecule* mol;
- StuntDouble* integrableObject;
- SimInfo::MoleculeIterator mi;
- Molecule::IntegrableObjectIterator ii;
-
-#ifndef IS_MPI
- // set all zAngles to 0.0
- for (mol = info_->beginMolecule(mi); mol != NULL;
- mol = info_->nextMolecule(mi))
+ while(inputStream.getline(buffer, bufferSize)) {
+ line = buffer;
- for (integrableObject = mol->beginIntegrableObject(ii);
- integrableObject != NULL;
- integrableObject = mol->nextIntegrableObject(ii))
- integrableObject->setZangle( 0.0 );
-
-
- // MPI Section of code..........
-#else //IS_MPI
-
- // first thing first, suspend fatalities.
- painCave.isEventLoop = 1;
-
- int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
- int haveError;
- int which_node;
-
- haveError = 0;
-
- for (int i=0 ; i < info_->getNGlobalMolecules(); i++) {
-
- // Get the Node number which has this atom
- which_node = info_->getMolToProc(i);
-
- // each processor zeroes its own integrable objects
- if (which_node == worldRank) {
- mol = info_->getMoleculeByGlobalIndex(i);
-
- if(mol == NULL) {
- sprintf( painCave.errMsg,
- "Molecule not found on node %i!",
- which_node );
- haveError = 1;
- simError();
- }
-
- for (integrableObject = mol->beginIntegrableObject(ii);
- integrableObject != NULL;
- integrableObject = mol->nextIntegrableObject(ii)){
-
- integrableObject->setZangle( 0.0 );
-
- }
+ if(line.find("</FrameData>") != std::string::npos) {
+ break;
}
+
}
-
-#endif
+
}
-
-} // end namespace oopse
+
+
+}//end namespace OpenMD