RestWriter.cpp

/*
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 *    and/or other materials provided with the distribution.
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 *    contributors may be used to endorse or promote products derived from
 *    this software without specific prior written permission.
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 * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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 * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
 * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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 * POSSIBILITY OF SUCH DAMAGE.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the following paper when you publish your work:
 *
 * [1] Drisko et al., J. Open Source Softw. 9, 7004 (2024).
 *
 * Good starting points for code and simulation methodology are:
 *
 * [2] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
 * [3] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
 * [4] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
 * [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 * [6] Kuang & Gezelter, Mol. Phys., 110, 691-701 (2012).
 * [7] Lamichhane, Gezelter & Newman, J. Chem. Phys. 141, 134109 (2014).
 * [8] Bhattarai, Newman & Gezelter, Phys. Rev. B 99, 094106 (2019).
 * [9] Drisko & Gezelter, J. Chem. Theory Comput. 20, 4986-4997 (2024).
 */
 
#include "io/RestWriter.hpp"
 
#include <iostream>
#include <sstream>
#include <string>
 
#ifdef IS_MPI
#include <mpi.h>
#endif
 
#include "brains/SnapshotManager.hpp"
#include "utils/simError.h"
 
namespace OpenMD {
  RestWriter::RestWriter(SimInfo* info, const std::string& filename,
                         std::vector<Restraint*> restraints) :
      info_(info) {
    std::vector<Restraint*>::const_iterator resti;
 
    createRestFile_ = false;
 
#ifdef IS_MPI
    MPI_Status istatus;
#endif
 
    int printAny = 0;
    for (resti = restraints.begin(); resti != restraints.end(); ++resti) {
      if ((*resti)->getPrintRestraint()) { printAny = 1; }
    }
 
#ifdef IS_MPI
    MPI_Allreduce(MPI_IN_PLACE, &printAny, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
#endif
 
    if (printAny) createRestFile_ = true;
 
#ifdef IS_MPI
    if (worldRank == 0) {
#endif
 
      if (createRestFile_) {
        output_ = new std::ofstream(filename.c_str());
 
        if (!output_) {
          snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
                   "Could not open %s for restraint output.\n",
                   filename.c_str());
          painCave.isFatal = 1;
          simError();
        }
      }
 
#ifdef IS_MPI
    }
#endif  // is_mpi
 
#ifndef IS_MPI
 
    if (createRestFile_) (*output_) << "#time\t";
 
    for (resti = restraints.begin(); resti != restraints.end(); ++resti) {
      if ((*resti)->getPrintRestraint()) {
        std::string myName = (*resti)->getRestraintName();
        int myType         = (*resti)->getRestraintType();
 
        (*output_) << myName << ":";
 
        if (myType & Restraint::rtDisplacement)
          (*output_) << "\tPosition(angstroms)\tEnergy(kcal/mol)";
 
        if (myType & Restraint::rtAbsoluteZ)
          (*output_) << "\tPosition(angstroms)\tEnergy(kcal/mol)";
 
        if (myType & Restraint::rtTwist)
          (*output_) << "\tTwistAngle(radians)\tEnergy(kcal/mol)";
 
        if (myType & Restraint::rtSwingX)
          (*output_) << "\tSwingXAngle(radians)\tEnergy(kcal/mol)";
 
        if (myType & Restraint::rtSwingY)
          (*output_) << "\tSwingYAngle(radians)\tEnergy(kcal/mol)";
      }
    }
 
    if (createRestFile_) (*output_) << "\n";
    if (createRestFile_) (*output_).flush();
 
#else
 
    std::string buffer;
 
    for (resti = restraints.begin(); resti != restraints.end(); ++resti) {
      if ((*resti)->getPrintRestraint()) {
        std::string myName = (*resti)->getRestraintName();
        int myType         = (*resti)->getRestraintType();
 
        buffer += (myName + ":");
 
        if (myType & Restraint::rtDisplacement)
          buffer += "\tPosition(angstroms)\tEnergy(kcal/mol)";
 
        if (myType & Restraint::rtAbsoluteZ)
          buffer += "\tPosition(angstroms)\tEnergy(kcal/mol)";
 
        if (myType & Restraint::rtTwist)
          buffer += "\tTwistAngle(radians)\tEnergy(kcal/mol)";
 
        if (myType & Restraint::rtSwingX)
          buffer += "\tSwingXAngle(radians)\tEnergy(kcal/mol)";
 
        if (myType & Restraint::rtSwingY)
          buffer += "\tSwingYAngle(radians)\tEnergy(kcal/mol)";
 
        buffer += "\n";
      }
    }
 
    const int primaryNode = 0;
 
    if (worldRank == primaryNode) {
      if (createRestFile_) (*output_) << "#time\t";
      if (createRestFile_) (*output_) << buffer;
 
      int nProc;
      MPI_Comm_size(MPI_COMM_WORLD, &nProc);
 
      for (int i = 1; i < nProc; ++i) {
        // receive the length of the string buffer that was
        // prepared by processor i
 
        int recvLength;
        MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus);
        char* recvBuffer = new char[recvLength];
        if (recvBuffer == NULL) {
        } else {
          MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD,
                   &istatus);
          if (createRestFile_) (*output_) << recvBuffer;
          delete[] recvBuffer;
        }
      }
      if (createRestFile_) (*output_).flush();
    } else {
      int sendBufferLength = buffer.size() + 1;
      MPI_Send(&sendBufferLength, 1, MPI_INT, primaryNode, 0, MPI_COMM_WORLD);
      MPI_Send((void*)buffer.c_str(), sendBufferLength, MPI_CHAR, primaryNode,
               0, MPI_COMM_WORLD);
    }
 
#endif  // is_mpi
  }
 
  void RestWriter::writeRest(
      std::vector<std::map<int, Restraint::RealPair>> restInfo) {
#ifdef IS_MPI
    MPI_Status istatus;
#endif
 
#ifndef IS_MPI
    if (createRestFile_)
      (*output_)
          << info_->getSnapshotManager()->getCurrentSnapshot()->getTime();
 
    // output some information about the molecules
    std::vector<std::map<int, Restraint::RealPair>>::const_iterator i;
    std::map<int, Restraint::RealPair>::const_iterator j;
 
    if (createRestFile_) {
      for (i = restInfo.begin(); i != restInfo.end(); ++i) {
        for (j = (*i).begin(); j != (*i).end(); ++j) {
          (*output_) << "\t" << (j->second).first << "\t" << (j->second).second;
        }
        (*output_) << std::endl;
      }
      (*output_).flush();
    }
#else
    std::string buffer, first, second;
    std::stringstream ss;
 
    std::vector<std::map<int, Restraint::RealPair>>::const_iterator i;
    std::map<int, Restraint::RealPair>::const_iterator j;
 
    if (createRestFile_) {
      for (i = restInfo.begin(); i != restInfo.end(); ++i) {
        for (j = (*i).begin(); j != (*i).end(); ++j) {
          ss.clear();
          ss << (j->second).first;
          ss >> first;
          ss.clear();
          ss << (j->second).second;
          ss >> second;
          buffer += ("\t" + first + "\t" + second);
        }
        buffer += "\n";
      }
    }
 
    const int primaryNode = 0;
 
    if (createRestFile_) {
      if (worldRank == primaryNode) {
        (*output_)
            << info_->getSnapshotManager()->getCurrentSnapshot()->getTime();
        (*output_) << buffer;
 
        int nProc;
        MPI_Comm_size(MPI_COMM_WORLD, &nProc);
        for (int i = 1; i < nProc; ++i) {
          // receive the length of the string buffer that was
          // prepared by processor i
 
          int recvLength;
          MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus);
          char* recvBuffer = new char[recvLength];
          if (recvBuffer == NULL) {
          } else {
            MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD,
                     &istatus);
            if (createRestFile_) (*output_) << recvBuffer;
 
            delete[] recvBuffer;
          }
        }
        (*output_).flush();
      } else {
        int sendBufferLength = buffer.size() + 1;
        MPI_Send(&sendBufferLength, 1, MPI_INT, primaryNode, 0, MPI_COMM_WORLD);
        MPI_Send((void*)buffer.c_str(), sendBufferLength, MPI_CHAR, primaryNode,
                 0, MPI_COMM_WORLD);
      }
    }
#endif  // is_mpi
  }
 
  RestWriter::~RestWriter() {
#ifdef IS_MPI
 
    if (worldRank == 0) {
#endif  // is_mpi
      if (createRestFile_) {
        writeClosing(*output_);
        delete output_;
      }
#ifdef IS_MPI
    }
#endif  // is_mpi
  }
 
  void RestWriter::writeClosing(std::ostream& os) { os.flush(); }
 
}  // namespace OpenMD