OOPSE/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 0
#define TAKE_THIS_TAG_INT 1

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;
  vector<StuntDouble*>::iterator iter;

  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(iter = integrableObjects.begin(); iter!= integrableObjects.end(); iter++)

      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, *iter);
      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;

  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();
    }

    nTotObjs = 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 != 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());
      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->getTotNmol(); 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[i]);
           
       }


      }
      else{
      //molecule belongs to slave nodes

        MPI_Recv(&nCurObj, 1, MPI_INT, 0,
               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
      
       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();

            MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
                      TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
           
       }

      }
      
    }
    
  }
  else{
  //actions taken at slave nodes
    for (i=0 ; i < mpiSim->getTotNmol(); 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_Recv(&nCurObj, 1, MPI_INT, 0,
                        TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);

        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]);

    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
    //entry_plug->setBoxM( theBoxMat3 );
    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->getNumberProcessors(); 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:	1108
Committed:	Wed Apr 14 15:37:41 2004 UTC (20 years, 2 months ago) by tim
File size:	15806 byte(s)
Log Message:	Change DumpWriter and InitFromFile
#	User	Rev	Content
1	gezelter	830	#define _FILE_OFFSET_BITS 64
2	mmeineke	377	#include <iostream>
3	gezelter	829	#include <math.h>
4	mmeineke	377
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	tim	837	#include "GenericData.hpp"
15	mmeineke	377
16			#ifdef IS_MPI
17	gezelter	417	#include <mpi.h>
18	mmeineke	377	#include "mpiSimulation.hpp"
19	chuckv	436	#define TAKE_THIS_TAG_CHAR 0
20			#define TAKE_THIS_TAG_INT 1
21
22	mmeineke	440	namespace initFile{
23			void nodeZeroError( void );
24			void anonymousNodeDie( void );
25			}
26	chuckv	436
27	mmeineke	440	using namespace initFile;
28
29	mmeineke	377	#endif // is_mpi
30
31	tim	689	InitializeFromFile::InitializeFromFile( char *in_name ){
32
33	mmeineke	377	#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	tim	837
45	mmeineke	377	strcpy( c_in_name, in_name);
46			#ifdef IS_MPI
47			}
48	mmeineke	874	else{
49			sprintf( c_in_name, "mpiNodeParser_%d", worldRank );
50			}
51
52			strcpy( checkPointMsg, "Infile opened for reading successfully." );
53	mmeineke	377	MPIcheckPoint();
54			#endif
55	tim	837	return;
56	mmeineke	377	}
57
58	tim	689	InitializeFromFile::~InitializeFromFile( ){
59	mmeineke	377	#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	mmeineke	641	void InitializeFromFile :: readInit( SimInfo* the_simnfo ){
80	mmeineke	377
81	mmeineke	787	int i, j;
82	tim	837
83	mmeineke	787	#ifdef IS_MPI
84			int done, which_node, which_atom; // loop counter
85			#endif //is_mpi
86	mmeineke	377
87			const int BUFFERSIZE = 2000; // size of the read buffer
88	tim	1108	int nTotObjs; // the number of atoms
89	tim	837	char read_buffer[BUFFERSIZE]; //the line buffer for reading
90	mmeineke	377
91	tim	837	char *eof_test; // ptr to see when we reach the end of the file
92	mmeineke	377	char *parseErr;
93	mmeineke	787
94	tim	1108	vector<StuntDouble*> integrableObjects;
95			vector<StuntDouble*>::iterator iter;
96
97	mmeineke	586	simnfo = the_simnfo;
98	mmeineke	377
99
100			#ifndef IS_MPI
101			eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
102			if( eof_test == NULL ){
103			sprintf( painCave.errMsg,
104			"InitializeFromFile error: error reading 1st line of \"%s\"\n",
105			c_in_name );
106			painCave.isFatal = 1;
107			simError();
108			}
109
110	tim	1108	nTotObjs = atoi( read_buffer );
111	mmeineke	377
112	tim	1108	if( nTotObjs != simnfo->getTotIntegrableObjects() ){
113	mmeineke	377	sprintf( painCave.errMsg,
114			"Initialize from File error. %s n_atoms, %d, "
115			"does not match the BASS file's n_atoms, %d.\n",
116	tim	1108	c_in_name, nTotObjs, simnfo->getTotIntegrableObjects());
117	mmeineke	377	painCave.isFatal = 1;
118			simError();
119			}
120	tim	837
121			//read the box mat from the comment line
122
123	mmeineke	377	eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
124			if(eof_test == NULL){
125			sprintf( painCave.errMsg,
126			"error in reading commment in %s\n", c_in_name);
127			painCave.isFatal = 1;
128			simError();
129			}
130
131	tim	837	parseErr = parseCommentLine( read_buffer, simnfo);
132	mmeineke	586	if( parseErr != NULL ){
133			strcpy( painCave.errMsg, parseErr );
134			painCave.isFatal = 1;
135			simError();
136			}
137
138	tim	837	//parse dump lines
139	mmeineke	586
140	tim	1108	for( i=0; i < simnfo->n_mol; i++){
141	mmeineke	586
142	tim	1108	integrableObjects = (simnfo->molecules[i]).getIntegrableObjects();
143	mmeineke	377
144	tim	1108	for(iter = integrableObjects.begin(); iter!= integrableObjects.end(); iter++)
145	tim	837
146	tim	1108	eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
147			if(eof_test == NULL){
148			sprintf(painCave.errMsg,
149			"error in reading file %s\n"
150			"natoms = %d; index = %d\n"
151			"error reading the line from the file.\n",
152			c_in_name, nTotObjs, i );
153			painCave.isFatal = 1;
154			simError();
155			}
156
157			parseErr = parseDumpLine( read_buffer, *iter);
158			if( parseErr != NULL ){
159			strcpy( painCave.errMsg, parseErr );
160			painCave.isFatal = 1;
161			simError();
162			}
163	mmeineke	377	}
164
165
166			// MPI Section of code..........
167			#else //IS_MPI
168
169	chuckv	436	// first thing first, suspend fatalities.
170			painCave.isEventLoop = 1;
171
172			int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
173			int haveError;
174	tim	837
175	mmeineke	447	MPI_Status istatus;
176	tim	1108	int *MolToProcMap = mpiSim->getMolToProcMap();
177			int localIndex;
178			int nCurObj;
179	mmeineke	377
180	chuckv	436	haveError = 0;
181	mmeineke	377	if (worldRank == 0) {
182	chuckv	436
183	mmeineke	377	eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
184			if( eof_test == NULL ){
185			sprintf( painCave.errMsg,
186	mmeineke	787	"Error reading 1st line of %s \n ",c_in_name);
187	chuckv	436	haveError = 1;
188	mmeineke	377	simError();
189			}
190	tim	837
191	tim	1108	nTotObjs = atoi( read_buffer );
192	tim	837
193	tim	1108	// Check to see that the number of integrable objects in the intial configuration file is the
194	mmeineke	377	// same as declared in simBass.
195	tim	837
196	tim	1108	if( nTotObjs != simnfo->getTotIntegrableObjects()){
197	mmeineke	377	sprintf( painCave.errMsg,
198			"Initialize from File error. %s n_atoms, %d, "
199			"does not match the BASS file's n_atoms, %d.\n",
200	tim	1108	c_in_name, nTotObjs, simnfo->getTotIntegrableObjects());
201	chuckv	436	haveError= 1;
202	mmeineke	377	simError();
203			}
204	tim	837
205			//read the boxMat from the comment line
206
207	mmeineke	377	eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
208			if(eof_test == NULL){
209			sprintf( painCave.errMsg,
210			"error in reading commment in %s\n", c_in_name);
211	mmeineke	586	haveError = 1;
212	mmeineke	377	simError();
213			}
214	tim	837
215			//Every single processor will parse the comment line by itself
216			//By using this way, we might lose some efficiency, but if we want to add
217			//more parameters into comment line, we only need to modify function
218			//parseCommentLine
219
220			MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD);
221
222			parseErr = parseCommentLine( read_buffer, simnfo);
223
224	mmeineke	586	if( parseErr != NULL ){
225			strcpy( painCave.errMsg, parseErr );
226			haveError = 1;
227			simError();
228			}
229
230	tim	1108	for (i=0 ; i < mpiSim->getTotNmol(); i++) {
231			which_node = MolToProcMap[i];
232			if(which_node == 0){
233			//molecules belong to master node
234	gezelter	417
235	tim	1108	localIndex = mpiSim->getGlobalToLocalMol(i);
236
237			if(localIndex == -1) {
238			strcpy(painCave.errMsg, "Molecule not found on node 0!");
239			haveError = 1;
240			simError();
241	mmeineke	377	}
242	tim	837
243	tim	1108	integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();
244			for(j=0; j < integrableObjects.size(); j++){
245
246			eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
247			if(eof_test == NULL){
248			sprintf(painCave.errMsg,
249			"error in reading file %s\n"
250			"natoms = %d; index = %d\n"
251			"error reading the line from the file.\n",
252			c_in_name, nTotObjs, i );
253			haveError= 1;
254			simError();
255			}
256
257			if(haveError) nodeZeroError();
258	chuckv	436
259	tim	1108	parseDumpLine(read_buffer, integrableObjects[i]);
260
261			}
262
263
264	tim	837	}
265	tim	1108	else{
266			//molecule belongs to slave nodes
267	tim	837
268	tim	1108	MPI_Recv(&nCurObj, 1, MPI_INT, 0,
269			TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
270
271			for(j=0; j < integrableObjects.size(); j++){
272
273			eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
274			if(eof_test == NULL){
275			sprintf(painCave.errMsg,
276			"error in reading file %s\n"
277			"natoms = %d; index = %d\n"
278			"error reading the line from the file.\n",
279			c_in_name, nTotObjs, i );
280			haveError= 1;
281			simError();
282			}
283
284			if(haveError) nodeZeroError();
285	tim	837
286	tim	1108	MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
287			TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
288
289			}
290	tim	837
291	mmeineke	377	}
292	tim	1108
293	mmeineke	377	}
294	tim	1108
295			}
296			else{
297			//actions taken at slave nodes
298			for (i=0 ; i < mpiSim->getTotNmol(); i++) {
299			which_node = MolToProcMap[i];
300
301			if(which_node == worldRank){
302			//molecule with global index i belongs to this processor
303
304			localIndex = mpiSim->getGlobalToLocalMol(i);
305	tim	837
306	tim	1108	if(localIndex == -1) {
307			sprintf(painCave.errMsg, "Molecule not found on node %d\n", worldRank);
308			haveError = 1;
309			simError();
310			}
311	mmeineke	586
312	tim	1108	integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();
313	tim	837
314	tim	1108	nCurObj = integrableObjects.size();
315
316			MPI_Recv(&nCurObj, 1, MPI_INT, 0,
317			TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
318	tim	837
319	tim	1108	for(j = 0; j < integrableObjects.size(); j++){
320	tim	837
321	tim	1108	MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0,
322			TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
323	tim	837
324	tim	1108	parseErr = parseDumpLine(read_buffer, integrableObjects[j]);
325	chuckv	436
326	tim	1108	if( parseErr != NULL ){
327			strcpy( painCave.errMsg, parseErr );
328			simError();
329			}
330	tim	837
331	tim	1108	}
332
333	mmeineke	377	}
334	tim	1108
335			}
336	tim	837
337	mmeineke	377	}
338			#endif
339			}
340
341	tim	1108	char* InitializeFromFile::parseDumpLine(char* readLine, StuntDouble* sd){
342	mmeineke	377
343	tim	837	char *foo; // the pointer to the current string token
344
345	mmeineke	670	double pos[3]; // position place holders
346			double vel[3]; // velocity placeholders
347	mmeineke	377	double q[4]; // the quaternions
348	gezelter	1097	double ji[3]; // angular velocity placeholders;
349	mmeineke	377	double qSqr, qLength; // needed to normalize the quaternion vector.
350	tim	837
351
352	mmeineke	377	// set the string tokenizer
353	tim	837
354	mmeineke	377	foo = strtok(readLine, " ,;\t");
355	tim	837
356	mmeineke	377	// check the atom name to the current atom
357	tim	837
358	tim	1108	if( strcmp( foo, sd->getType() ) ){
359	mmeineke	377	sprintf( painCave.errMsg,
360	tim	1108	"Initialize from file error. Does not"
361	mmeineke	377	" match the BASS atom %s.\n",
362	tim	1108	sd->getType() );
363	mmeineke	377	return strdup( painCave.errMsg );
364			}
365	tim	837
366	mmeineke	377	// get the positions
367
368			foo = strtok(NULL, " ,;\t");
369			if(foo == NULL){
370			sprintf( painCave.errMsg,
371	tim	1108	"error in reading postition x from %s\n",
372			c_in_name);
373	mmeineke	377	return strdup( painCave.errMsg );
374			}
375	mmeineke	670	pos[0] = atof( foo );
376	tim	837
377	mmeineke	377	foo = strtok(NULL, " ,;\t");
378			if(foo == NULL){
379			sprintf( painCave.errMsg,
380	tim	1108	"error in reading postition y from %s\n",
381			c_in_name);
382	mmeineke	377	return strdup( painCave.errMsg );
383			}
384	mmeineke	670	pos[1] = atof( foo );
385	tim	837
386	mmeineke	377	foo = strtok(NULL, " ,;\t");
387			if(foo == NULL){
388			sprintf( painCave.errMsg,
389	tim	1108	"error in reading postition z from %s\n",
390			c_in_name);
391	mmeineke	377	return strdup( painCave.errMsg );
392			}
393	tim	837	pos[2] = atof( foo );
394	mmeineke	377
395
396			// get the velocities
397
398			foo = strtok(NULL, " ,;\t");
399			if(foo == NULL){
400			sprintf( painCave.errMsg,
401	tim	1108	"error in reading velocity x from %s\n",
402			c_in_name );
403	mmeineke	377	return strdup( painCave.errMsg );
404			}
405	mmeineke	670	vel[0] = atof( foo );
406	tim	837
407	mmeineke	377	foo = strtok(NULL, " ,;\t");
408			if(foo == NULL){
409			sprintf( painCave.errMsg,
410	tim	1108	"error in reading velocity x from %s\n",
411			c_in_name );
412	mmeineke	377	return strdup( painCave.errMsg );
413			}
414	mmeineke	670	vel[1] = atof( foo );
415	tim	837
416	mmeineke	377	foo = strtok(NULL, " ,;\t");
417			if(foo == NULL){
418			sprintf( painCave.errMsg,
419	tim	1108	"error in reading velocity x from %s\n",
420			c_in_name );
421	mmeineke	377	return strdup( painCave.errMsg );
422			}
423	mmeineke	670	vel[2] = atof( foo );
424	tim	837
425
426	tim	1108	// add the positions and velocities to the atom
427
428			sd->setPos( pos );
429			sd->setVel( vel );
430
431			if (!sd->isDirectional())
432			return NULL;
433
434	mmeineke	377	// get the quaternions
435	tim	837
436	tim	1108	if( sd->isDirectional() ){
437	tim	837
438	mmeineke	377	foo = strtok(NULL, " ,;\t");
439			if(foo == NULL){
440	tim	1108	sprintf( painCave.errMsg,
441			"error in reading velocity x from %s\n",
442			c_in_name );
443	mmeineke	377	return strdup( painCave.errMsg );
444			}
445			q[0] = atof( foo );
446	tim	837
447	mmeineke	377	foo = strtok(NULL, " ,;\t");
448			if(foo == NULL){
449			sprintf( painCave.errMsg,
450	tim	1108	"error in reading velocity x from %s\n",
451			c_in_name );
452	mmeineke	377	return strdup( painCave.errMsg );
453			}
454			q[1] = atof( foo );
455	tim	837
456	mmeineke	377	foo = strtok(NULL, " ,;\t");
457			if(foo == NULL){
458			sprintf( painCave.errMsg,
459	tim	1108	"error in reading velocity x from %s\n",
460			c_in_name );
461	mmeineke	377	return strdup( painCave.errMsg );
462			}
463			q[2] = atof( foo );
464	tim	837
465	mmeineke	377	foo = strtok(NULL, " ,;\t");
466			if(foo == NULL){
467			sprintf( painCave.errMsg,
468	tim	1108	"error in reading velocity x from %s\n",
469			c_in_name );
470	mmeineke	377	return strdup( painCave.errMsg );
471			}
472			q[3] = atof( foo );
473	tim	837
474	mmeineke	377	// get the angular velocities
475	tim	837
476	mmeineke	377	foo = strtok(NULL, " ,;\t");
477			if(foo == NULL){
478			sprintf( painCave.errMsg,
479	tim	1108	"error in reading velocity x from %s\n",
480			c_in_name );
481	mmeineke	377	return strdup( painCave.errMsg );
482			}
483	gezelter	1097	ji[0] = atof( foo );
484	tim	837
485	mmeineke	377	foo = strtok(NULL, " ,;\t");
486			if(foo == NULL){
487			sprintf( painCave.errMsg,
488	tim	1108	"error in reading velocity x from %s\n",
489			c_in_name );
490	mmeineke	377	return strdup( painCave.errMsg );
491			}
492	gezelter	1097	ji[1] = atof(foo );
493	tim	837
494	mmeineke	377	foo = strtok(NULL, " ,;\t");
495			if(foo == NULL){
496			sprintf( painCave.errMsg,
497	tim	1108	"error in reading velocity x from %s\n",
498			c_in_name );
499	mmeineke	377	return strdup( painCave.errMsg );
500			}
501	gezelter	1097	ji[2] = atof( foo );
502	tim	837
503	mmeineke	377
504			// check that the quaternion vector is normalized
505
506			qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]);
507	tim	837
508	mmeineke	377	qLength = sqrt( qSqr );
509			q[0] = q[0] / qLength;
510			q[1] = q[1] / qLength;
511			q[2] = q[2] / qLength;
512			q[3] = q[3] / qLength;
513	tim	837
514	tim	1108	// add quaternion and angular velocities
515	tim	837
516	tim	1108	sd->setQ( q );
517			sd->setJ( ji );
518	mmeineke	377	}
519	tim	837
520
521	mmeineke	377
522			return NULL;
523			}
524	chuckv	436
525
526	tim	837	char* InitializeFromFile::parseCommentLine(char* readLine, SimInfo* entry_plug){
527	mmeineke	586
528	tim	837	double currTime;
529			double boxMat[9];
530			double theBoxMat3[3][3];
531			double chi;
532			double integralOfChidt;
533			double eta[9];
534	mmeineke	586
535	tim	837	char *foo; // the pointer to the current string token
536
537	mmeineke	586	// set the string tokenizer
538	tim	837
539	mmeineke	586	foo = strtok(readLine, " ,;\t");
540	mmeineke	641	// set the timeToken.
541	mmeineke	586
542	mmeineke	641	if(foo == NULL){
543			sprintf( painCave.errMsg,
544			"error in reading Time from %s\n",
545			c_in_name );
546			return strdup( painCave.errMsg );
547			}
548	mmeineke	586
549	tim	837	currTime = atof( foo );
550			entry_plug->setTime( currTime );
551	mmeineke	586
552	tim	837	//get H-Matrix
553
554			for(int i = 0 ; i < 9; i++){
555			foo = strtok(NULL, " ,;\t");
556			if(foo == NULL){
557			sprintf( painCave.errMsg,
558			"error in reading H[%d] from %s\n", i, c_in_name );
559			return strdup( painCave.errMsg );
560			}
561			boxMat[i] = atof( foo );
562	mmeineke	586	}
563
564	tim	837	for(int i=0;i<3;i++)
565			for(int j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i];
566	mmeineke	586
567	tim	837	//set H-Matrix
568			entry_plug->setBoxM( theBoxMat3 );
569	mmeineke	586
570	tim	837	//get chi and integralOfChidt, they should appear by pair
571	mmeineke	586
572	mmeineke	906	if( entry_plug->useInitXSstate ){
573	tim	837	foo = strtok(NULL, " ,;\t\n");
574	mmeineke	906	if(foo != NULL){
575			chi = atof(foo);
576
577			foo = strtok(NULL, " ,;\t\n");
578			if(foo == NULL){
579			sprintf( painCave.errMsg,
580			"chi and integralOfChidt should appear by pair in %s\n", c_in_name );
581			return strdup( painCave.errMsg );
582			}
583			integralOfChidt = atof( foo );
584
585			//push chi and integralOfChidt into SimInfo::properties which can be
586			//retrieved by integrator later
587			DoubleData* chiValue = new DoubleData();
588			chiValue->setID(CHIVALUE_ID);
589			chiValue->setData(chi);
590			entry_plug->addProperty(chiValue);
591
592			DoubleData* integralOfChidtValue = new DoubleData();
593			integralOfChidtValue->setID(INTEGRALOFCHIDT_ID);
594			integralOfChidtValue->setData(integralOfChidt);
595			entry_plug->addProperty(integralOfChidtValue);
596
597	tim	837	}
598	mmeineke	906	else
599			return NULL;
600
601			//get eta
602	mmeineke	911	foo = strtok(NULL, " ,;\t\n");
603	mmeineke	909	if(foo != NULL ){
604	mmeineke	911
605	mmeineke	909	for(int i = 0 ; i < 9; i++){
606
607			if(foo == NULL){
608			sprintf( painCave.errMsg,
609			"error in reading eta[%d] from %s\n", i, c_in_name );
610			return strdup( painCave.errMsg );
611			}
612			eta[i] = atof( foo );
613	mmeineke	911	foo = strtok(NULL, " ,;\t\n");
614	mmeineke	906	}
615			}
616	mmeineke	909	else
617			return NULL;
618	mmeineke	906
619			//push eta into SimInfo::properties which can be
620	tim	837	//retrieved by integrator later
621	mmeineke	906	//entry_plug->setBoxM( theBoxMat3 );
622			DoubleArrayData* etaValue = new DoubleArrayData();
623			etaValue->setID(ETAVALUE_ID);
624			etaValue->setData(eta, 9);
625			entry_plug->addProperty(etaValue);
626	mmeineke	586	}
627	tim	837
628	mmeineke	586	return NULL;
629			}
630
631	chuckv	436	#ifdef IS_MPI
632
633			// a couple of functions to let us escape the read loop
634
635	mmeineke	440	void initFile::nodeZeroError( void ){
636	chuckv	436	int j, myStatus;
637	tim	837
638	chuckv	436	myStatus = 0;
639	tim	837	for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
640			MPI_Send( &myStatus, 1, MPI_INT, j,
641	mmeineke	447	TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
642	tim	837	}
643	chuckv	436
644	tim	837
645	chuckv	436	MPI_Finalize();
646			exit (0);
647	tim	837
648	chuckv	436	}
649
650	mmeineke	440	void initFile::anonymousNodeDie( void ){
651	chuckv	436
652			MPI_Finalize();
653			exit (0);
654			}
655
656			#endif //is_mpi