libhoomd/analyzers/MOL2DumpWriter.cc

   1 /*
   2 Highly Optimized Object-oriented Many-particle Dynamics -- Blue Edition
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  49
  50 // Maintainer: joaander
  51
  52 /*! \file MOL2DumpWriter.cc
  53     \brief Defines the MOL2DumpWriter class
  54 */
  55
  56 #ifdef WIN32
  57 #pragma warning( push )
  58 #pragma warning( disable : 4244 )
  59 #endif
  60
  61 #include <boost/python.hpp>
  62 using namespace boost::python;
  63
  64 #include <iomanip>
  65 #include <fstream>
  66 #include <stdexcept>
  67 #include <boost/shared_ptr.hpp>
  68
  69 #include "MOL2DumpWriter.h"
  70 #include "BondedGroupData.h"
  71
  72 using namespace std;
  73
  74 /*! \param sysdef SystemDefinition containing the ParticleData to dump
  75     \param fname_base The base file name to write the output to
  76 */
  77 MOL2DumpWriter::MOL2DumpWriter(boost::shared_ptr<SystemDefinition> sysdef, std::string fname_base)
  78         : Analyzer(sysdef), m_base_fname(fname_base)
  79     {
  80     m_exec_conf->msg->notice(5) << "Constructing MOL2DumpWriter: " << fname_base << endl;
  81     }
  82
  83 MOL2DumpWriter::~MOL2DumpWriter()
  84     {
  85     m_exec_conf->msg->notice(5) << "Destroying PDBDumpWriter" << endl;
  86     }
  87
  88 /*! \param timestep Current time step of the simulation
  89     Writes a snapshot of the current state of the ParticleData to a mol2 file
  90 */
  91 void MOL2DumpWriter::analyze(unsigned int timestep)
  92     {
  93     if (m_prof)
  94         m_prof->push("Dump MOL2");
  95
  96     ostringstream full_fname;
  97     string filetype = ".mol2";
  98
  99     // Generate a filename with the timestep padded to ten zeros
 100     full_fname << m_base_fname << "." << setfill('0') << setw(10) << timestep << filetype;
 101     writeFile(full_fname.str());
 102
 103     if (m_prof)
 104         m_prof->pop();
 105     }
 106
 107 /*! \param fname File name to write
 108 */
 109 void MOL2DumpWriter::writeFile(std::string fname)
 110     {
 111     // open the file for writing
 112     ofstream f(fname.c_str());
 113
 114     if (!f.good())
 115         {
 116         m_exec_conf->msg->error() << "dump.mol2: Unable to open dump file for writing: " << fname << endl;
 117         throw runtime_error("Error writting mol2 dump file");
 118         }
 119
 120     // acquire the particle data
 121     ArrayHandle<Scalar4> h_pos(m_pdata->getPositions(), access_location::host, access_mode::read);
 122     ArrayHandle<unsigned int> h_rtag(m_pdata->getRTags(), access_location::host, access_mode::read);
 123
 124     // write the header
 125     f << "@<TRIPOS>MOLECULE" << "\n";
 126     f << "Generated by HOOMD" << "\n";
 127     int num_bonds = 1;
 128     boost::shared_ptr<BondData> bond_data = m_sysdef->getBondData();
 129     if (bond_data && bond_data->getN() > 0)
 130         num_bonds = bond_data->getN();
 131
 132     f << m_pdata->getN() << " " << num_bonds << "\n";
 133     f << "NO_CHARGES" << "\n";
 134
 135     f << "@<TRIPOS>ATOM" << "\n";
 136     for (unsigned int j = 0; j < m_pdata->getN(); j++)
 137         {
 138         // use the rtag data to output the particles in the order they were read in
 139         int i;
 140         i= h_rtag.data[j];
 141
 142         // get the coordinates
 143         Scalar x = (h_pos.data[i].x);
 144         Scalar y = (h_pos.data[i].y);
 145         Scalar z = (h_pos.data[i].z);
 146
 147         // get the type by name
 148         unsigned int type_id = __scalar_as_int(h_pos.data[i].w);
 149         string type_name = m_pdata->getNameByType(type_id);
 150
 151         // this is intended to go to VMD, so limit the type name to 15 characters
 152         if (type_name.size() > 15)
 153             {
 154             m_exec_conf->msg->error() << "dump.mol2: Type name <" << type_name << "> too long: please limit to 15 characters" << endl;
 155             throw runtime_error("Error writting mol2 dump file");
 156             }
 157
 158         f << j+1 << " " << type_name << " " << x << " " << y << " "<< z << " " << type_name << "\n";
 159
 160         if (!f.good())
 161             {
 162             m_exec_conf->msg->error() << "dump.mol2: I/O error while writing MOL2 dump file" << endl;
 163             throw runtime_error("Error writting mol2 dump file");
 164             }
 165         }
 166
 167     f << "@<TRIPOS>BOND" << "\n";
 168     if (bond_data && bond_data->getN() > 0)
 169         {
 170         for (unsigned int i = 0; i < bond_data->getN(); i++)
 171             {
 172             BondData::members_t b = bond_data->getMembersByIndex(i);
 173             f << i+1 << " " << b.tag[0]+1 << " " << b.tag[1]+1 << " 1" << "\n";
 174             }
 175         }
 176     else
 177         {
 178         // write a dummy bond since VMD doesn't like loading mol2 files without bonds
 179         f << "1 1 2 1" << "\n";
 180         }
 181
 182     if (!f.good())
 183         {
 184         m_exec_conf->msg->error() << "dump.mol2: I/O error while writing file" << endl;
 185         throw runtime_error("Error writting mol2 dump file");
 186         }
 187
 188     f.close();
 189     }
 190
 191 void export_MOL2DumpWriter()
 192     {
 193     class_<MOL2DumpWriter, boost::shared_ptr<MOL2DumpWriter>, bases<Analyzer>, boost::noncopyable>
 194     ("MOL2DumpWriter", init< boost::shared_ptr<SystemDefinition>, std::string >())
 195     .def("writeFile", &MOL2DumpWriter::writeFile)
 196     ;
 197
 198     }
 199
 200 #ifdef WIN32
 201 #pragma warning( pop )
 202 #endif