OOPSE-1.0/libmdtools/InitializeFromFile.cpp

#define _FILE_OFFSET_BITS 64
#include <iostream>
#include <math.h>

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <unistd.h>
#include <sys/types.h>
#include <sys/stat.h>

#include "ReadWrite.hpp"
#include "simError.h"
#include "GenericData.hpp"

#ifdef IS_MPI
#include <mpi.h>
#include "mpiSimulation.hpp"
#define TAKE_THIS_TAG_CHAR 3134
#define TAKE_THIS_TAG_INT 3135

namespace initFile{
  void nodeZeroError( void );
  void anonymousNodeDie( void );
}

using namespace initFile;

#endif // is_mpi

InitializeFromFile::InitializeFromFile( char *in_name ){

#ifdef IS_MPI
  if (worldRank == 0) {
#endif

  c_in_file = fopen(in_name, "r");
  if(c_in_file == NULL){
    sprintf(painCave.errMsg,
            "Cannot open file: %s\n", in_name);
    painCave.isFatal = 1;
    simError();
  }

  strcpy( c_in_name, in_name);
#ifdef IS_MPI
  }
  else{
          sprintf( c_in_name, "mpiNodeParser_%d", worldRank );
  }
  
  strcpy( checkPointMsg, "Infile opened for reading successfully." );
  MPIcheckPoint();
#endif
  return;
}

InitializeFromFile::~InitializeFromFile( ){
#ifdef IS_MPI
  if (worldRank == 0) {
#endif
  int error;
  error = fclose( c_in_file );
  if( error ){
    sprintf( painCave.errMsg,
             "Error closing %s\n", c_in_name );
    simError();
  }
#ifdef IS_MPI
  }
  strcpy( checkPointMsg, "Infile closed successfully." );
  MPIcheckPoint();
#endif

  return;
}


void InitializeFromFile :: readInit( SimInfo* the_simnfo ){

  int i, j;

#ifdef IS_MPI
  int done, which_node, which_atom; // loop counter
#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 *eof_test; // ptr to see when we reach the end of the file
  char *parseErr;

  vector<StuntDouble*> integrableObjects;

  simnfo = the_simnfo;


#ifndef IS_MPI
  eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
  if( eof_test == NULL ){
    sprintf( painCave.errMsg,
             "InitializeFromFile error: error reading 1st line of \"%s\"\n",
             c_in_name );
    painCave.isFatal = 1;
    simError();
  }

  nTotObjs = atoi( read_buffer );

  if( nTotObjs != simnfo->getTotIntegrableObjects() ){
    sprintf( painCave.errMsg,
             "Initialize from File error. %s n_atoms, %d, "
             "does not match the BASS file's n_atoms, %d.\n",
             c_in_name, nTotObjs, simnfo->getTotIntegrableObjects());
    painCave.isFatal = 1;
    simError();
  }

  //read the box mat from the comment line

  eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
  if(eof_test == NULL){
    sprintf( painCave.errMsg,
             "error in reading commment in %s\n", c_in_name);
    painCave.isFatal = 1;
    simError();
  }

  parseErr = parseCommentLine( read_buffer, simnfo);
  if( parseErr != NULL ){
    strcpy( painCave.errMsg, parseErr );
    painCave.isFatal = 1;
    simError();
  }

  //parse dump lines

  for( i=0; i < simnfo->n_mol; i++){

    integrableObjects = (simnfo->molecules[i]).getIntegrableObjects();

    for(j = 0; j < integrableObjects.size(); j++){

      eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
      if(eof_test == NULL){
        sprintf(painCave.errMsg,
              "error in reading file %s\n"
              "natoms  = %d; index = %d\n"
              "error reading the line from the file.\n",
              c_in_name, nTotObjs, i );
        painCave.isFatal = 1;
        simError();
      }
      
      parseErr = parseDumpLine( read_buffer, integrableObjects[j]);
      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 myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
  int haveError;

  MPI_Status istatus;
  int *MolToProcMap = mpiSim->getMolToProcMap();
  int localIndex;
  int nCurObj;
  int nItems;

  nTotObjs = simnfo->getTotIntegrableObjects();
  haveError = 0;
  if (worldRank == 0) {

    eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
    if( eof_test == NULL ){
      sprintf( painCave.errMsg,
               "Error reading 1st line of %s \n ",c_in_name);
      haveError = 1;
      simError();
    }

    nItems = atoi( read_buffer );

    // Check to see that the number of integrable objects  in the intial configuration file is the
    // same as declared in simBass.

    if( nTotObjs != nItems){
      sprintf( painCave.errMsg,
               "Initialize from File error. %s n_atoms, %d, "
               "does not match the BASS file's n_atoms, %d.\n",
               c_in_name, nTotObjs, simnfo->getTotIntegrableObjects());
      haveError= 1;
      simError();
    }

    //read the boxMat from the comment line

    eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
    if(eof_test == NULL){
      sprintf( painCave.errMsg,
               "error in reading commment in %s\n", c_in_name);
      haveError = 1;
      simError();
    }

    //Every single processor will parse the comment line by itself
    //By using this way, we might lose some efficiency, but if we want to add
    //more parameters into comment line, we only need to modify function
    //parseCommentLine

    MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD);


    parseErr = parseCommentLine( read_buffer, simnfo);

    if( parseErr != NULL ){
      strcpy( painCave.errMsg, parseErr );
      haveError = 1;
      simError();
    }

    for (i=0 ; i < mpiSim->getNMolGlobal(); i++) {
      which_node = MolToProcMap[i];
      if(which_node == 0){
       //molecules belong to master node

      localIndex = mpiSim->getGlobalToLocalMol(i);

      if(localIndex == -1) {
        strcpy(painCave.errMsg, "Molecule not found on node 0!");
        haveError = 1;
        simError();
      }

       integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();
       for(j=0; j < integrableObjects.size(); j++){
        
          eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
          if(eof_test == NULL){
                sprintf(painCave.errMsg,
                    "error in reading file %s\n"
                    "natoms  = %d; index = %d\n"
                    "error reading the line from the file.\n",
                    c_in_name, nTotObjs, i );
                haveError= 1;
                simError();
          }
          
          if(haveError) nodeZeroError();

          parseDumpLine(read_buffer, integrableObjects[j]);
           
       }


      }
      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++){
        
          eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
          if(eof_test == NULL){
                sprintf(painCave.errMsg,
                    "error in reading file %s\n"
                    "natoms  = %d; index = %d\n"
                    "error reading the line from the file.\n",
                    c_in_name, nTotObjs, i );
                haveError= 1;
                simError();
          }
          
          if(haveError) nodeZeroError();

            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, 0, MPI_COMM_WORLD);

    parseErr = parseCommentLine( read_buffer, simnfo);

    if( parseErr != NULL ){
      strcpy( painCave.errMsg, parseErr );
      haveError = 1;
      simError();
    }
  
    for (i=0 ; i < mpiSim->getNMolGlobal(); i++) {
      which_node = MolToProcMap[i];
      
      if(which_node == worldRank){
      //molecule with global index i belongs to this processor
      
        localIndex = mpiSim->getGlobalToLocalMol(i);

        if(localIndex == -1) {
          sprintf(painCave.errMsg, "Molecule not found on node %d\n", worldRank);
          haveError = 1;
          simError();
        }

        integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();        

        nCurObj = integrableObjects.size();
        
        MPI_Send(&nCurObj, 1, MPI_INT, 0,
                        TAKE_THIS_TAG_INT, MPI_COMM_WORLD);

        for(j = 0; j < integrableObjects.size(); j++){

          MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0,
                              TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);

          parseErr = parseDumpLine(read_buffer, integrableObjects[j]);

          if( parseErr != NULL ){
                strcpy( painCave.errMsg, parseErr );
                simError();
          }

        }
          
      }
      
    }

  }
#endif
}

char* InitializeFromFile::parseDumpLine(char* readLine, StuntDouble* sd){

  char *foo; // the pointer to the current string token

  double pos[3]; // position place holders
  double vel[3]; // velocity placeholders
  double q[4]; // the quaternions
  double ji[3]; // angular velocity placeholders;
  double qSqr, qLength; // needed to normalize the quaternion vector.


  // set the string tokenizer

  foo = strtok(readLine, " ,;\t");

  // check the atom name to the current atom

  if( strcmp( foo, sd->getType() ) ){
    sprintf( painCave.errMsg,
             "Initialize from file error.  Does not"
             " match the BASS atom %s.\n",
             sd->getType() );
    return strdup( painCave.errMsg );
  }

  // get the positions

  foo = strtok(NULL, " ,;\t");
  if(foo == NULL){
    sprintf( painCave.errMsg,
             "error in reading postition x from %s\n",
             c_in_name);
    return strdup( painCave.errMsg );
  }
  pos[0] = atof( foo );

  foo = strtok(NULL, " ,;\t");
  if(foo == NULL){
    sprintf( painCave.errMsg,
             "error in reading postition y from %s\n",
             c_in_name);
    return strdup( painCave.errMsg );
  }
  pos[1] = atof( foo );

  foo = strtok(NULL, " ,;\t");
  if(foo == NULL){
    sprintf( painCave.errMsg,
             "error in reading postition z from %s\n",
             c_in_name);
    return strdup( painCave.errMsg );
  }
  pos[2] = atof( foo );


  // get the velocities

  foo = strtok(NULL, " ,;\t");
  if(foo == NULL){
    sprintf( painCave.errMsg,
             "error in reading velocity x from %s\n",
             c_in_name );
    return strdup( painCave.errMsg );
  }
  vel[0] = atof( foo );

  foo = strtok(NULL, " ,;\t");
  if(foo == NULL){
    sprintf( painCave.errMsg,
             "error in reading velocity x from %s\n",
             c_in_name );
    return strdup( painCave.errMsg );
  }
  vel[1] = atof( foo );

  foo = strtok(NULL, " ,;\t");
  if(foo == NULL){
    sprintf( painCave.errMsg,
             "error in reading velocity x from %s\n",
             c_in_name );
    return strdup( painCave.errMsg );
  }
  vel[2] = atof( foo );


  // add the positions and velocities to the atom

  sd->setPos( pos );
  sd->setVel( vel );

  if (!sd->isDirectional())
    return NULL;

  // get the quaternions

  if( sd->isDirectional() ){

    foo = strtok(NULL, " ,;\t");
    if(foo == NULL){
      sprintf( painCave.errMsg,
                     "error in reading velocity x from %s\n",
                      c_in_name );
      return strdup( painCave.errMsg );
    }
    q[0] = atof( foo );

    foo = strtok(NULL, " ,;\t");
    if(foo == NULL){
      sprintf( painCave.errMsg,
                     "error in reading velocity x from %s\n",
                      c_in_name );
      return strdup( painCave.errMsg );
    }
    q[1] = atof( foo );

    foo = strtok(NULL, " ,;\t");
    if(foo == NULL){
      sprintf( painCave.errMsg,
                     "error in reading velocity x from %s\n",
                      c_in_name );
      return strdup( painCave.errMsg );
    }
    q[2] = atof( foo );

    foo = strtok(NULL, " ,;\t");
    if(foo == NULL){
      sprintf( painCave.errMsg,
                     "error in reading velocity x from %s\n",
                      c_in_name );
      return strdup( painCave.errMsg );
    }
    q[3] = atof( foo );

    // get the angular velocities

    foo = strtok(NULL, " ,;\t");
    if(foo == NULL){
      sprintf( painCave.errMsg,
                     "error in reading velocity x from %s\n",
                      c_in_name );
      return strdup( painCave.errMsg );
    }
    ji[0] = atof( foo );

    foo = strtok(NULL, " ,;\t");
    if(foo == NULL){
      sprintf( painCave.errMsg,
                     "error in reading velocity x from %s\n",
                      c_in_name );
      return strdup( painCave.errMsg );
    }
    ji[1] = atof(foo );

    foo = strtok(NULL, " ,;\t");
    if(foo == NULL){
      sprintf( painCave.errMsg,
                     "error in reading velocity x from %s\n",
                      c_in_name );
      return strdup( painCave.errMsg );
    }
    ji[2] = atof( foo );


    // check that the quaternion vector is normalized

    qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]);

    if (fabs(qSqr) < 1e-6) {
      sprintf(painCave.errMsg,
          "initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2 ~ 0).\n");
       return strdup(painCave.errMsg);
    }
    
    qLength = sqrt( qSqr );
    q[0] = q[0] / qLength;
    q[1] = q[1] / qLength;
    q[2] = q[2] / qLength;
    q[3] = q[3] / qLength;

    // add quaternion and angular velocities

    sd->setQ( q );
    sd->setJ( ji );
  }


  return NULL;
}


char* InitializeFromFile::parseCommentLine(char* readLine, SimInfo* entry_plug){

  double currTime;
  double boxMat[9];
  double theBoxMat3[3][3];
  double chi;
  double integralOfChidt;
  double eta[9];

  char *foo; // the pointer to the current string token

  // set the string tokenizer

  foo = strtok(readLine, " ,;\t");
  // set the timeToken.

  if(foo == NULL){
    sprintf( painCave.errMsg,
             "error in reading Time from %s\n",
             c_in_name );
    return strdup( painCave.errMsg );
  }

  currTime = atof( foo );
  entry_plug->setTime( currTime );

  //get H-Matrix

  for(int i = 0 ; i < 9; i++){
    foo = strtok(NULL, " ,;\t");
    if(foo == NULL){
      sprintf( painCave.errMsg,
               "error in reading H[%d] from %s\n", i, c_in_name );
      return strdup( painCave.errMsg );
    }
    boxMat[i] = atof( foo );
  }

  for(int i=0;i<3;i++)
    for(int j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i];

  //set H-Matrix
  entry_plug->setBoxM( theBoxMat3 );

  //get chi and integralOfChidt, they should appear by pair

  if( entry_plug->useInitXSstate ){
    foo = strtok(NULL, " ,;\t\n");
    if(foo != NULL){
      chi = atof(foo);
      
      foo = strtok(NULL, " ,;\t\n");
      if(foo == NULL){
        sprintf( painCave.errMsg,
                 "chi and integralOfChidt should appear by pair in %s\n", c_in_name );
        return strdup( painCave.errMsg );
      }
      integralOfChidt = atof( foo );
      
      //push chi and integralOfChidt into SimInfo::properties which can be
      //retrieved by integrator later
      DoubleData* chiValue = new DoubleData();
      chiValue->setID(CHIVALUE_ID);
      chiValue->setData(chi);
      entry_plug->addProperty(chiValue);
      
      DoubleData* integralOfChidtValue = new DoubleData();
      integralOfChidtValue->setID(INTEGRALOFCHIDT_ID);
      integralOfChidtValue->setData(integralOfChidt);
      entry_plug->addProperty(integralOfChidtValue);
      
    }
    else
      return NULL;
    
    //get eta
    foo = strtok(NULL, " ,;\t\n");
    if(foo != NULL ){
  
      for(int i = 0 ; i < 9; i++){
        
        if(foo == NULL){
          sprintf( painCave.errMsg,
                   "error in reading eta[%d] from %s\n", i, c_in_name );
          return strdup( painCave.errMsg );
        }
        eta[i] = atof( foo );
        foo = strtok(NULL, " ,;\t\n");
      }
    }
    else
      return NULL;
    
    //push eta into SimInfo::properties which can be
    //retrieved by integrator later
    
    DoubleArrayData* etaValue = new DoubleArrayData();
    etaValue->setID(ETAVALUE_ID);
    etaValue->setData(eta, 9);
    entry_plug->addProperty(etaValue);
  }

  return NULL;
}

#ifdef IS_MPI

// a couple of functions to let us escape the read loop

void initFile::nodeZeroError( void ){
  int j, myStatus;

  myStatus = 0;
  for (j = 0; j < mpiSim->getNProcessors(); j++) {
    MPI_Send( &myStatus, 1, MPI_INT, j,
              TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
  }


  MPI_Finalize();
  exit (0);

}

void initFile::anonymousNodeDie( void ){

  MPI_Finalize();
  exit (0);
}

#endif //is_mpi
Revision:	1334
Committed:	Fri Jul 16 18:58:03 2004 UTC (19 years, 11 months ago) by gezelter
File size:	16156 byte(s)
Log Message:	Initial import of OOPSE-1.0 source tree
#	Content
1	#define _FILE_OFFSET_BITS 64
2	#include <iostream>
3	#include <math.h>
4
5	#include <stdio.h>
6	#include <stdlib.h>
7	#include <string.h>
8	#include <unistd.h>
9	#include <sys/types.h>
10	#include <sys/stat.h>
11
12	#include "ReadWrite.hpp"
13	#include "simError.h"
14	#include "GenericData.hpp"
15
16	#ifdef IS_MPI
17	#include <mpi.h>
18	#include "mpiSimulation.hpp"
19	#define TAKE_THIS_TAG_CHAR 3134
20	#define TAKE_THIS_TAG_INT 3135
21
22	namespace initFile{
23	void nodeZeroError( void );
24	void anonymousNodeDie( void );
25	}
26
27	using namespace initFile;
28
29	#endif // is_mpi
30
31	InitializeFromFile::InitializeFromFile( char *in_name ){
32
33	#ifdef IS_MPI
34	if (worldRank == 0) {
35	#endif
36
37	c_in_file = fopen(in_name, "r");
38	if(c_in_file == NULL){
39	sprintf(painCave.errMsg,
40	"Cannot open file: %s\n", in_name);
41	painCave.isFatal = 1;
42	simError();
43	}
44
45	strcpy( c_in_name, in_name);
46	#ifdef IS_MPI
47	}
48	else{
49	sprintf( c_in_name, "mpiNodeParser_%d", worldRank );
50	}
51
52	strcpy( checkPointMsg, "Infile opened for reading successfully." );
53	MPIcheckPoint();
54	#endif
55	return;
56	}
57
58	InitializeFromFile::~InitializeFromFile( ){
59	#ifdef IS_MPI
60	if (worldRank == 0) {
61	#endif
62	int error;
63	error = fclose( c_in_file );
64	if( error ){
65	sprintf( painCave.errMsg,
66	"Error closing %s\n", c_in_name );
67	simError();
68	}
69	#ifdef IS_MPI
70	}
71	strcpy( checkPointMsg, "Infile closed successfully." );
72	MPIcheckPoint();
73	#endif
74
75	return;
76	}
77
78
79	void InitializeFromFile :: readInit( SimInfo* the_simnfo ){
80
81	int i, j;
82
83	#ifdef IS_MPI
84	int done, which_node, which_atom; // loop counter
85	#endif //is_mpi
86
87	const int BUFFERSIZE = 2000; // size of the read buffer
88	int nTotObjs; // the number of atoms
89	char read_buffer[BUFFERSIZE]; //the line buffer for reading
90
91	char *eof_test; // ptr to see when we reach the end of the file
92	char *parseErr;
93
94	vector<StuntDouble*> integrableObjects;
95
96	simnfo = the_simnfo;
97
98
99	#ifndef IS_MPI
100	eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
101	if( eof_test == NULL ){
102	sprintf( painCave.errMsg,
103	"InitializeFromFile error: error reading 1st line of \"%s\"\n",
104	c_in_name );
105	painCave.isFatal = 1;
106	simError();
107	}
108
109	nTotObjs = atoi( read_buffer );
110
111	if( nTotObjs != simnfo->getTotIntegrableObjects() ){
112	sprintf( painCave.errMsg,
113	"Initialize from File error. %s n_atoms, %d, "
114	"does not match the BASS file's n_atoms, %d.\n",
115	c_in_name, nTotObjs, simnfo->getTotIntegrableObjects());
116	painCave.isFatal = 1;
117	simError();
118	}
119
120	//read the box mat from the comment line
121
122	eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
123	if(eof_test == NULL){
124	sprintf( painCave.errMsg,
125	"error in reading commment in %s\n", c_in_name);
126	painCave.isFatal = 1;
127	simError();
128	}
129
130	parseErr = parseCommentLine( read_buffer, simnfo);
131	if( parseErr != NULL ){
132	strcpy( painCave.errMsg, parseErr );
133	painCave.isFatal = 1;
134	simError();
135	}
136
137	//parse dump lines
138
139	for( i=0; i < simnfo->n_mol; i++){
140
141	integrableObjects = (simnfo->molecules[i]).getIntegrableObjects();
142
143	for(j = 0; j < integrableObjects.size(); j++){
144
145	eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
146	if(eof_test == NULL){
147	sprintf(painCave.errMsg,
148	"error in reading file %s\n"
149	"natoms = %d; index = %d\n"
150	"error reading the line from the file.\n",
151	c_in_name, nTotObjs, i );
152	painCave.isFatal = 1;
153	simError();
154	}
155
156	parseErr = parseDumpLine( read_buffer, integrableObjects[j]);
157	if( parseErr != NULL ){
158	strcpy( painCave.errMsg, parseErr );
159	painCave.isFatal = 1;
160	simError();
161	}
162	}
163	}
164
165	// MPI Section of code..........
166	#else //IS_MPI
167
168	// first thing first, suspend fatalities.
169	painCave.isEventLoop = 1;
170
171	int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
172	int haveError;
173
174	MPI_Status istatus;
175	int *MolToProcMap = mpiSim->getMolToProcMap();
176	int localIndex;
177	int nCurObj;
178	int nItems;
179
180	nTotObjs = simnfo->getTotIntegrableObjects();
181	haveError = 0;
182	if (worldRank == 0) {
183
184	eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
185	if( eof_test == NULL ){
186	sprintf( painCave.errMsg,
187	"Error reading 1st line of %s \n ",c_in_name);
188	haveError = 1;
189	simError();
190	}
191
192	nItems = atoi( read_buffer );
193
194	// Check to see that the number of integrable objects in the intial configuration file is the
195	// same as declared in simBass.
196
197	if( nTotObjs != nItems){
198	sprintf( painCave.errMsg,
199	"Initialize from File error. %s n_atoms, %d, "
200	"does not match the BASS file's n_atoms, %d.\n",
201	c_in_name, nTotObjs, simnfo->getTotIntegrableObjects());
202	haveError= 1;
203	simError();
204	}
205
206	//read the boxMat from the comment line
207
208	eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
209	if(eof_test == NULL){
210	sprintf( painCave.errMsg,
211	"error in reading commment in %s\n", c_in_name);
212	haveError = 1;
213	simError();
214	}
215
216	//Every single processor will parse the comment line by itself
217	//By using this way, we might lose some efficiency, but if we want to add
218	//more parameters into comment line, we only need to modify function
219	//parseCommentLine
220
221	MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD);
222
223
224	parseErr = parseCommentLine( read_buffer, simnfo);
225
226	if( parseErr != NULL ){
227	strcpy( painCave.errMsg, parseErr );
228	haveError = 1;
229	simError();
230	}
231
232	for (i=0 ; i < mpiSim->getNMolGlobal(); i++) {
233	which_node = MolToProcMap[i];
234	if(which_node == 0){
235	//molecules belong to master node
236
237	localIndex = mpiSim->getGlobalToLocalMol(i);
238
239	if(localIndex == -1) {
240	strcpy(painCave.errMsg, "Molecule not found on node 0!");
241	haveError = 1;
242	simError();
243	}
244
245	integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();
246	for(j=0; j < integrableObjects.size(); j++){
247
248	eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
249	if(eof_test == NULL){
250	sprintf(painCave.errMsg,
251	"error in reading file %s\n"
252	"natoms = %d; index = %d\n"
253	"error reading the line from the file.\n",
254	c_in_name, nTotObjs, i );
255	haveError= 1;
256	simError();
257	}
258
259	if(haveError) nodeZeroError();
260
261	parseDumpLine(read_buffer, integrableObjects[j]);
262
263	}
264
265
266	}
267	else{
268	//molecule belongs to slave nodes
269
270	MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
271	TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
272
273	for(j=0; j < nCurObj; j++){
274
275	eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
276	if(eof_test == NULL){
277	sprintf(painCave.errMsg,
278	"error in reading file %s\n"
279	"natoms = %d; index = %d\n"
280	"error reading the line from the file.\n",
281	c_in_name, nTotObjs, i );
282	haveError= 1;
283	simError();
284	}
285
286	if(haveError) nodeZeroError();
287
288	MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
289	TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
290
291	}
292
293	}
294
295	}
296
297	}
298	else{
299	//actions taken at slave nodes
300
301	MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD);
302
303	parseErr = parseCommentLine( read_buffer, simnfo);
304
305	if( parseErr != NULL ){
306	strcpy( painCave.errMsg, parseErr );
307	haveError = 1;
308	simError();
309	}
310
311	for (i=0 ; i < mpiSim->getNMolGlobal(); i++) {
312	which_node = MolToProcMap[i];
313
314	if(which_node == worldRank){
315	//molecule with global index i belongs to this processor
316
317	localIndex = mpiSim->getGlobalToLocalMol(i);
318
319	if(localIndex == -1) {
320	sprintf(painCave.errMsg, "Molecule not found on node %d\n", worldRank);
321	haveError = 1;
322	simError();
323	}
324
325	integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();
326
327	nCurObj = integrableObjects.size();
328
329	MPI_Send(&nCurObj, 1, MPI_INT, 0,
330	TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
331
332	for(j = 0; j < integrableObjects.size(); j++){
333
334	MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0,
335	TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
336
337	parseErr = parseDumpLine(read_buffer, integrableObjects[j]);
338
339	if( parseErr != NULL ){
340	strcpy( painCave.errMsg, parseErr );
341	simError();
342	}
343
344	}
345
346	}
347
348	}
349
350	}
351	#endif
352	}
353
354	char* InitializeFromFile::parseDumpLine(char* readLine, StuntDouble* sd){
355
356	char *foo; // the pointer to the current string token
357
358	double pos[3]; // position place holders
359	double vel[3]; // velocity placeholders
360	double q[4]; // the quaternions
361	double ji[3]; // angular velocity placeholders;
362	double qSqr, qLength; // needed to normalize the quaternion vector.
363
364
365	// set the string tokenizer
366
367	foo = strtok(readLine, " ,;\t");
368
369	// check the atom name to the current atom
370
371	if( strcmp( foo, sd->getType() ) ){
372	sprintf( painCave.errMsg,
373	"Initialize from file error. Does not"
374	" match the BASS atom %s.\n",
375	sd->getType() );
376	return strdup( painCave.errMsg );
377	}
378
379	// get the positions
380
381	foo = strtok(NULL, " ,;\t");
382	if(foo == NULL){
383	sprintf( painCave.errMsg,
384	"error in reading postition x from %s\n",
385	c_in_name);
386	return strdup( painCave.errMsg );
387	}
388	pos[0] = atof( foo );
389
390	foo = strtok(NULL, " ,;\t");
391	if(foo == NULL){
392	sprintf( painCave.errMsg,
393	"error in reading postition y from %s\n",
394	c_in_name);
395	return strdup( painCave.errMsg );
396	}
397	pos[1] = atof( foo );
398
399	foo = strtok(NULL, " ,;\t");
400	if(foo == NULL){
401	sprintf( painCave.errMsg,
402	"error in reading postition z from %s\n",
403	c_in_name);
404	return strdup( painCave.errMsg );
405	}
406	pos[2] = atof( foo );
407
408
409	// get the velocities
410
411	foo = strtok(NULL, " ,;\t");
412	if(foo == NULL){
413	sprintf( painCave.errMsg,
414	"error in reading velocity x from %s\n",
415	c_in_name );
416	return strdup( painCave.errMsg );
417	}
418	vel[0] = atof( foo );
419
420	foo = strtok(NULL, " ,;\t");
421	if(foo == NULL){
422	sprintf( painCave.errMsg,
423	"error in reading velocity x from %s\n",
424	c_in_name );
425	return strdup( painCave.errMsg );
426	}
427	vel[1] = atof( foo );
428
429	foo = strtok(NULL, " ,;\t");
430	if(foo == NULL){
431	sprintf( painCave.errMsg,
432	"error in reading velocity x from %s\n",
433	c_in_name );
434	return strdup( painCave.errMsg );
435	}
436	vel[2] = atof( foo );
437
438
439	// add the positions and velocities to the atom
440
441	sd->setPos( pos );
442	sd->setVel( vel );
443
444	if (!sd->isDirectional())
445	return NULL;
446
447	// get the quaternions
448
449	if( sd->isDirectional() ){
450
451	foo = strtok(NULL, " ,;\t");
452	if(foo == NULL){
453	sprintf( painCave.errMsg,
454	"error in reading velocity x from %s\n",
455	c_in_name );
456	return strdup( painCave.errMsg );
457	}
458	q[0] = atof( foo );
459
460	foo = strtok(NULL, " ,;\t");
461	if(foo == NULL){
462	sprintf( painCave.errMsg,
463	"error in reading velocity x from %s\n",
464	c_in_name );
465	return strdup( painCave.errMsg );
466	}
467	q[1] = atof( foo );
468
469	foo = strtok(NULL, " ,;\t");
470	if(foo == NULL){
471	sprintf( painCave.errMsg,
472	"error in reading velocity x from %s\n",
473	c_in_name );
474	return strdup( painCave.errMsg );
475	}
476	q[2] = atof( foo );
477
478	foo = strtok(NULL, " ,;\t");
479	if(foo == NULL){
480	sprintf( painCave.errMsg,
481	"error in reading velocity x from %s\n",
482	c_in_name );
483	return strdup( painCave.errMsg );
484	}
485	q[3] = atof( foo );
486
487	// get the angular velocities
488
489	foo = strtok(NULL, " ,;\t");
490	if(foo == NULL){
491	sprintf( painCave.errMsg,
492	"error in reading velocity x from %s\n",
493	c_in_name );
494	return strdup( painCave.errMsg );
495	}
496	ji[0] = atof( foo );
497
498	foo = strtok(NULL, " ,;\t");
499	if(foo == NULL){
500	sprintf( painCave.errMsg,
501	"error in reading velocity x from %s\n",
502	c_in_name );
503	return strdup( painCave.errMsg );
504	}
505	ji[1] = atof(foo );
506
507	foo = strtok(NULL, " ,;\t");
508	if(foo == NULL){
509	sprintf( painCave.errMsg,
510	"error in reading velocity x from %s\n",
511	c_in_name );
512	return strdup( painCave.errMsg );
513	}
514	ji[2] = atof( foo );
515
516
517	// check that the quaternion vector is normalized
518
519	qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]);
520
521	if (fabs(qSqr) < 1e-6) {
522	sprintf(painCave.errMsg,
523	"initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2 ~ 0).\n");
524	return strdup(painCave.errMsg);
525	}
526
527	qLength = sqrt( qSqr );
528	q[0] = q[0] / qLength;
529	q[1] = q[1] / qLength;
530	q[2] = q[2] / qLength;
531	q[3] = q[3] / qLength;
532
533	// add quaternion and angular velocities
534
535	sd->setQ( q );
536	sd->setJ( ji );
537	}
538
539
540
541	return NULL;
542	}
543
544
545	char* InitializeFromFile::parseCommentLine(char* readLine, SimInfo* entry_plug){
546
547	double currTime;
548	double boxMat[9];
549	double theBoxMat3[3][3];
550	double chi;
551	double integralOfChidt;
552	double eta[9];
553
554	char *foo; // the pointer to the current string token
555
556	// set the string tokenizer
557
558	foo = strtok(readLine, " ,;\t");
559	// set the timeToken.
560
561	if(foo == NULL){
562	sprintf( painCave.errMsg,
563	"error in reading Time from %s\n",
564	c_in_name );
565	return strdup( painCave.errMsg );
566	}
567
568	currTime = atof( foo );
569	entry_plug->setTime( currTime );
570
571	//get H-Matrix
572
573	for(int i = 0 ; i < 9; i++){
574	foo = strtok(NULL, " ,;\t");
575	if(foo == NULL){
576	sprintf( painCave.errMsg,
577	"error in reading H[%d] from %s\n", i, c_in_name );
578	return strdup( painCave.errMsg );
579	}
580	boxMat[i] = atof( foo );
581	}
582
583	for(int i=0;i<3;i++)
584	for(int j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i];
585
586	//set H-Matrix
587	entry_plug->setBoxM( theBoxMat3 );
588
589	//get chi and integralOfChidt, they should appear by pair
590
591	if( entry_plug->useInitXSstate ){
592	foo = strtok(NULL, " ,;\t\n");
593	if(foo != NULL){
594	chi = atof(foo);
595
596	foo = strtok(NULL, " ,;\t\n");
597	if(foo == NULL){
598	sprintf( painCave.errMsg,
599	"chi and integralOfChidt should appear by pair in %s\n", c_in_name );
600	return strdup( painCave.errMsg );
601	}
602	integralOfChidt = atof( foo );
603
604	//push chi and integralOfChidt into SimInfo::properties which can be
605	//retrieved by integrator later
606	DoubleData* chiValue = new DoubleData();
607	chiValue->setID(CHIVALUE_ID);
608	chiValue->setData(chi);
609	entry_plug->addProperty(chiValue);
610
611	DoubleData* integralOfChidtValue = new DoubleData();
612	integralOfChidtValue->setID(INTEGRALOFCHIDT_ID);
613	integralOfChidtValue->setData(integralOfChidt);
614	entry_plug->addProperty(integralOfChidtValue);
615
616	}
617	else
618	return NULL;
619
620	//get eta
621	foo = strtok(NULL, " ,;\t\n");
622	if(foo != NULL ){
623
624	for(int i = 0 ; i < 9; i++){
625
626	if(foo == NULL){
627	sprintf( painCave.errMsg,
628	"error in reading eta[%d] from %s\n", i, c_in_name );
629	return strdup( painCave.errMsg );
630	}
631	eta[i] = atof( foo );
632	foo = strtok(NULL, " ,;\t\n");
633	}
634	}
635	else
636	return NULL;
637
638	//push eta into SimInfo::properties which can be
639	//retrieved by integrator later
640
641	DoubleArrayData* etaValue = new DoubleArrayData();
642	etaValue->setID(ETAVALUE_ID);
643	etaValue->setData(eta, 9);
644	entry_plug->addProperty(etaValue);
645	}
646
647	return NULL;
648	}
649
650	#ifdef IS_MPI
651
652	// a couple of functions to let us escape the read loop
653
654	void initFile::nodeZeroError( void ){
655	int j, myStatus;
656
657	myStatus = 0;
658	for (j = 0; j < mpiSim->getNProcessors(); j++) {
659	MPI_Send( &myStatus, 1, MPI_INT, j,
660	TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
661	}
662
663
664	MPI_Finalize();
665	exit (0);
666
667	}
668
669	void initFile::anonymousNodeDie( void ){
670
671	MPI_Finalize();
672	exit (0);
673	}
674
675	#endif //is_mpi