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;

  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;

  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:	1113
Committed:	Thu Apr 15 16:18:26 2004 UTC (20 years, 2 months ago) by tim
File size:	15756 byte(s)
Log Message:	fix whole bunch of bugs :-)
#	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
96	mmeineke	586	simnfo = the_simnfo;
97	mmeineke	377
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	tim	1108	nTotObjs = atoi( read_buffer );
110	mmeineke	377
111	tim	1108	if( nTotObjs != simnfo->getTotIntegrableObjects() ){
112	mmeineke	377	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	tim	1108	c_in_name, nTotObjs, simnfo->getTotIntegrableObjects());
116	mmeineke	377	painCave.isFatal = 1;
117			simError();
118			}
119	tim	837
120			//read the box mat from the comment line
121
122	mmeineke	377	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	tim	837	parseErr = parseCommentLine( read_buffer, simnfo);
131	mmeineke	586	if( parseErr != NULL ){
132			strcpy( painCave.errMsg, parseErr );
133			painCave.isFatal = 1;
134			simError();
135			}
136
137	tim	837	//parse dump lines
138	mmeineke	586
139	tim	1108	for( i=0; i < simnfo->n_mol; i++){
140	mmeineke	586
141	tim	1108	integrableObjects = (simnfo->molecules[i]).getIntegrableObjects();
142	mmeineke	377
143	tim	1113	for(j = 0; j < integrableObjects.size(); j++){
144	tim	837
145	tim	1108	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	tim	1113	parseErr = parseDumpLine( read_buffer, integrableObjects[j]);
157	tim	1108	if( parseErr != NULL ){
158			strcpy( painCave.errMsg, parseErr );
159			painCave.isFatal = 1;
160			simError();
161			}
162	tim	1113	}
163	mmeineke	377	}
164
165			// MPI Section of code..........
166			#else //IS_MPI
167
168	chuckv	436	// first thing first, suspend fatalities.
169			painCave.isEventLoop = 1;
170
171			int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
172			int haveError;
173	tim	837
174	mmeineke	447	MPI_Status istatus;
175	tim	1108	int *MolToProcMap = mpiSim->getMolToProcMap();
176			int localIndex;
177			int nCurObj;
178	mmeineke	377
179	chuckv	436	haveError = 0;
180	mmeineke	377	if (worldRank == 0) {
181	chuckv	436
182	mmeineke	377	eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
183			if( eof_test == NULL ){
184			sprintf( painCave.errMsg,
185	mmeineke	787	"Error reading 1st line of %s \n ",c_in_name);
186	chuckv	436	haveError = 1;
187	mmeineke	377	simError();
188			}
189	tim	837
190	tim	1108	nTotObjs = atoi( read_buffer );
191	tim	837
192	tim	1108	// Check to see that the number of integrable objects in the intial configuration file is the
193	mmeineke	377	// same as declared in simBass.
194	tim	837
195	tim	1108	if( nTotObjs != simnfo->getTotIntegrableObjects()){
196	mmeineke	377	sprintf( painCave.errMsg,
197			"Initialize from File error. %s n_atoms, %d, "
198			"does not match the BASS file's n_atoms, %d.\n",
199	tim	1108	c_in_name, nTotObjs, simnfo->getTotIntegrableObjects());
200	chuckv	436	haveError= 1;
201	mmeineke	377	simError();
202			}
203	tim	837
204			//read the boxMat from the comment line
205
206	mmeineke	377	eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
207			if(eof_test == NULL){
208			sprintf( painCave.errMsg,
209			"error in reading commment in %s\n", c_in_name);
210	mmeineke	586	haveError = 1;
211	mmeineke	377	simError();
212			}
213	tim	837
214			//Every single processor will parse the comment line by itself
215			//By using this way, we might lose some efficiency, but if we want to add
216			//more parameters into comment line, we only need to modify function
217			//parseCommentLine
218
219			MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD);
220
221			parseErr = parseCommentLine( read_buffer, simnfo);
222
223	mmeineke	586	if( parseErr != NULL ){
224			strcpy( painCave.errMsg, parseErr );
225			haveError = 1;
226			simError();
227			}
228
229	tim	1108	for (i=0 ; i < mpiSim->getTotNmol(); i++) {
230			which_node = MolToProcMap[i];
231			if(which_node == 0){
232			//molecules belong to master node
233	gezelter	417
234	tim	1108	localIndex = mpiSim->getGlobalToLocalMol(i);
235
236			if(localIndex == -1) {
237			strcpy(painCave.errMsg, "Molecule not found on node 0!");
238			haveError = 1;
239			simError();
240	mmeineke	377	}
241	tim	837
242	tim	1108	integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();
243			for(j=0; j < integrableObjects.size(); j++){
244
245			eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
246			if(eof_test == NULL){
247			sprintf(painCave.errMsg,
248			"error in reading file %s\n"
249			"natoms = %d; index = %d\n"
250			"error reading the line from the file.\n",
251			c_in_name, nTotObjs, i );
252			haveError= 1;
253			simError();
254			}
255
256			if(haveError) nodeZeroError();
257	chuckv	436
258	tim	1108	parseDumpLine(read_buffer, integrableObjects[i]);
259
260			}
261
262
263	tim	837	}
264	tim	1108	else{
265			//molecule belongs to slave nodes
266	tim	837
267	tim	1108	MPI_Recv(&nCurObj, 1, MPI_INT, 0,
268			TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
269
270			for(j=0; j < integrableObjects.size(); j++){
271
272			eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
273			if(eof_test == NULL){
274			sprintf(painCave.errMsg,
275			"error in reading file %s\n"
276			"natoms = %d; index = %d\n"
277			"error reading the line from the file.\n",
278			c_in_name, nTotObjs, i );
279			haveError= 1;
280			simError();
281			}
282
283			if(haveError) nodeZeroError();
284	tim	837
285	tim	1108	MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
286			TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
287
288			}
289	tim	837
290	mmeineke	377	}
291	tim	1108
292	mmeineke	377	}
293	tim	1108
294			}
295			else{
296			//actions taken at slave nodes
297			for (i=0 ; i < mpiSim->getTotNmol(); i++) {
298			which_node = MolToProcMap[i];
299
300			if(which_node == worldRank){
301			//molecule with global index i belongs to this processor
302
303			localIndex = mpiSim->getGlobalToLocalMol(i);
304	tim	837
305	tim	1108	if(localIndex == -1) {
306			sprintf(painCave.errMsg, "Molecule not found on node %d\n", worldRank);
307			haveError = 1;
308			simError();
309			}
310	mmeineke	586
311	tim	1108	integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects();
312	tim	837
313	tim	1108	nCurObj = integrableObjects.size();
314
315			MPI_Recv(&nCurObj, 1, MPI_INT, 0,
316			TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
317	tim	837
318	tim	1108	for(j = 0; j < integrableObjects.size(); j++){
319	tim	837
320	tim	1108	MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0,
321			TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
322	tim	837
323	tim	1108	parseErr = parseDumpLine(read_buffer, integrableObjects[j]);
324	chuckv	436
325	tim	1108	if( parseErr != NULL ){
326			strcpy( painCave.errMsg, parseErr );
327			simError();
328			}
329	tim	837
330	tim	1108	}
331
332	mmeineke	377	}
333	tim	1108
334			}
335	tim	837
336	mmeineke	377	}
337			#endif
338			}
339
340	tim	1108	char* InitializeFromFile::parseDumpLine(char* readLine, StuntDouble* sd){
341	mmeineke	377
342	tim	837	char *foo; // the pointer to the current string token
343
344	mmeineke	670	double pos[3]; // position place holders
345			double vel[3]; // velocity placeholders
346	mmeineke	377	double q[4]; // the quaternions
347	gezelter	1097	double ji[3]; // angular velocity placeholders;
348	mmeineke	377	double qSqr, qLength; // needed to normalize the quaternion vector.
349	tim	837
350
351	mmeineke	377	// set the string tokenizer
352	tim	837
353	mmeineke	377	foo = strtok(readLine, " ,;\t");
354	tim	837
355	mmeineke	377	// check the atom name to the current atom
356	tim	837
357	tim	1108	if( strcmp( foo, sd->getType() ) ){
358	mmeineke	377	sprintf( painCave.errMsg,
359	tim	1108	"Initialize from file error. Does not"
360	mmeineke	377	" match the BASS atom %s.\n",
361	tim	1108	sd->getType() );
362	mmeineke	377	return strdup( painCave.errMsg );
363			}
364	tim	837
365	mmeineke	377	// get the positions
366
367			foo = strtok(NULL, " ,;\t");
368			if(foo == NULL){
369			sprintf( painCave.errMsg,
370	tim	1108	"error in reading postition x from %s\n",
371			c_in_name);
372	mmeineke	377	return strdup( painCave.errMsg );
373			}
374	mmeineke	670	pos[0] = atof( foo );
375	tim	837
376	mmeineke	377	foo = strtok(NULL, " ,;\t");
377			if(foo == NULL){
378			sprintf( painCave.errMsg,
379	tim	1108	"error in reading postition y from %s\n",
380			c_in_name);
381	mmeineke	377	return strdup( painCave.errMsg );
382			}
383	mmeineke	670	pos[1] = atof( foo );
384	tim	837
385	mmeineke	377	foo = strtok(NULL, " ,;\t");
386			if(foo == NULL){
387			sprintf( painCave.errMsg,
388	tim	1108	"error in reading postition z from %s\n",
389			c_in_name);
390	mmeineke	377	return strdup( painCave.errMsg );
391			}
392	tim	837	pos[2] = atof( foo );
393	mmeineke	377
394
395			// get the velocities
396
397			foo = strtok(NULL, " ,;\t");
398			if(foo == NULL){
399			sprintf( painCave.errMsg,
400	tim	1108	"error in reading velocity x from %s\n",
401			c_in_name );
402	mmeineke	377	return strdup( painCave.errMsg );
403			}
404	mmeineke	670	vel[0] = atof( foo );
405	tim	837
406	mmeineke	377	foo = strtok(NULL, " ,;\t");
407			if(foo == NULL){
408			sprintf( painCave.errMsg,
409	tim	1108	"error in reading velocity x from %s\n",
410			c_in_name );
411	mmeineke	377	return strdup( painCave.errMsg );
412			}
413	mmeineke	670	vel[1] = atof( foo );
414	tim	837
415	mmeineke	377	foo = strtok(NULL, " ,;\t");
416			if(foo == NULL){
417			sprintf( painCave.errMsg,
418	tim	1108	"error in reading velocity x from %s\n",
419			c_in_name );
420	mmeineke	377	return strdup( painCave.errMsg );
421			}
422	mmeineke	670	vel[2] = atof( foo );
423	tim	837
424
425	tim	1108	// add the positions and velocities to the atom
426
427			sd->setPos( pos );
428			sd->setVel( vel );
429
430			if (!sd->isDirectional())
431			return NULL;
432
433	mmeineke	377	// get the quaternions
434	tim	837
435	tim	1108	if( sd->isDirectional() ){
436	tim	837
437	mmeineke	377	foo = strtok(NULL, " ,;\t");
438			if(foo == NULL){
439	tim	1108	sprintf( painCave.errMsg,
440			"error in reading velocity x from %s\n",
441			c_in_name );
442	mmeineke	377	return strdup( painCave.errMsg );
443			}
444			q[0] = atof( foo );
445	tim	837
446	mmeineke	377	foo = strtok(NULL, " ,;\t");
447			if(foo == NULL){
448			sprintf( painCave.errMsg,
449	tim	1108	"error in reading velocity x from %s\n",
450			c_in_name );
451	mmeineke	377	return strdup( painCave.errMsg );
452			}
453			q[1] = atof( foo );
454	tim	837
455	mmeineke	377	foo = strtok(NULL, " ,;\t");
456			if(foo == NULL){
457			sprintf( painCave.errMsg,
458	tim	1108	"error in reading velocity x from %s\n",
459			c_in_name );
460	mmeineke	377	return strdup( painCave.errMsg );
461			}
462			q[2] = atof( foo );
463	tim	837
464	mmeineke	377	foo = strtok(NULL, " ,;\t");
465			if(foo == NULL){
466			sprintf( painCave.errMsg,
467	tim	1108	"error in reading velocity x from %s\n",
468			c_in_name );
469	mmeineke	377	return strdup( painCave.errMsg );
470			}
471			q[3] = atof( foo );
472	tim	837
473	mmeineke	377	// get the angular velocities
474	tim	837
475	mmeineke	377	foo = strtok(NULL, " ,;\t");
476			if(foo == NULL){
477			sprintf( painCave.errMsg,
478	tim	1108	"error in reading velocity x from %s\n",
479			c_in_name );
480	mmeineke	377	return strdup( painCave.errMsg );
481			}
482	gezelter	1097	ji[0] = atof( foo );
483	tim	837
484	mmeineke	377	foo = strtok(NULL, " ,;\t");
485			if(foo == NULL){
486			sprintf( painCave.errMsg,
487	tim	1108	"error in reading velocity x from %s\n",
488			c_in_name );
489	mmeineke	377	return strdup( painCave.errMsg );
490			}
491	gezelter	1097	ji[1] = atof(foo );
492	tim	837
493	mmeineke	377	foo = strtok(NULL, " ,;\t");
494			if(foo == NULL){
495			sprintf( painCave.errMsg,
496	tim	1108	"error in reading velocity x from %s\n",
497			c_in_name );
498	mmeineke	377	return strdup( painCave.errMsg );
499			}
500	gezelter	1097	ji[2] = atof( foo );
501	tim	837
502	mmeineke	377
503			// check that the quaternion vector is normalized
504
505			qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]);
506	tim	837
507	mmeineke	377	qLength = sqrt( qSqr );
508			q[0] = q[0] / qLength;
509			q[1] = q[1] / qLength;
510			q[2] = q[2] / qLength;
511			q[3] = q[3] / qLength;
512	tim	837
513	tim	1108	// add quaternion and angular velocities
514	tim	837
515	tim	1108	sd->setQ( q );
516			sd->setJ( ji );
517	mmeineke	377	}
518	tim	837
519
520	mmeineke	377
521			return NULL;
522			}
523	chuckv	436
524
525	tim	837	char* InitializeFromFile::parseCommentLine(char* readLine, SimInfo* entry_plug){
526	mmeineke	586
527	tim	837	double currTime;
528			double boxMat[9];
529			double theBoxMat3[3][3];
530			double chi;
531			double integralOfChidt;
532			double eta[9];
533	mmeineke	586
534	tim	837	char *foo; // the pointer to the current string token
535
536	mmeineke	586	// set the string tokenizer
537	tim	837
538	mmeineke	586	foo = strtok(readLine, " ,;\t");
539	mmeineke	641	// set the timeToken.
540	mmeineke	586
541	mmeineke	641	if(foo == NULL){
542			sprintf( painCave.errMsg,
543			"error in reading Time from %s\n",
544			c_in_name );
545			return strdup( painCave.errMsg );
546			}
547	mmeineke	586
548	tim	837	currTime = atof( foo );
549			entry_plug->setTime( currTime );
550	mmeineke	586
551	tim	837	//get H-Matrix
552
553			for(int i = 0 ; i < 9; i++){
554			foo = strtok(NULL, " ,;\t");
555			if(foo == NULL){
556			sprintf( painCave.errMsg,
557			"error in reading H[%d] from %s\n", i, c_in_name );
558			return strdup( painCave.errMsg );
559			}
560			boxMat[i] = atof( foo );
561	mmeineke	586	}
562
563	tim	837	for(int i=0;i<3;i++)
564			for(int j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i];
565	mmeineke	586
566	tim	837	//set H-Matrix
567			entry_plug->setBoxM( theBoxMat3 );
568	mmeineke	586
569	tim	837	//get chi and integralOfChidt, they should appear by pair
570	mmeineke	586
571	mmeineke	906	if( entry_plug->useInitXSstate ){
572	tim	837	foo = strtok(NULL, " ,;\t\n");
573	mmeineke	906	if(foo != NULL){
574			chi = atof(foo);
575
576			foo = strtok(NULL, " ,;\t\n");
577			if(foo == NULL){
578			sprintf( painCave.errMsg,
579			"chi and integralOfChidt should appear by pair in %s\n", c_in_name );
580			return strdup( painCave.errMsg );
581			}
582			integralOfChidt = atof( foo );
583
584			//push chi and integralOfChidt into SimInfo::properties which can be
585			//retrieved by integrator later
586			DoubleData* chiValue = new DoubleData();
587			chiValue->setID(CHIVALUE_ID);
588			chiValue->setData(chi);
589			entry_plug->addProperty(chiValue);
590
591			DoubleData* integralOfChidtValue = new DoubleData();
592			integralOfChidtValue->setID(INTEGRALOFCHIDT_ID);
593			integralOfChidtValue->setData(integralOfChidt);
594			entry_plug->addProperty(integralOfChidtValue);
595
596	tim	837	}
597	mmeineke	906	else
598			return NULL;
599
600			//get eta
601	mmeineke	911	foo = strtok(NULL, " ,;\t\n");
602	mmeineke	909	if(foo != NULL ){
603	mmeineke	911
604	mmeineke	909	for(int i = 0 ; i < 9; i++){
605
606			if(foo == NULL){
607			sprintf( painCave.errMsg,
608			"error in reading eta[%d] from %s\n", i, c_in_name );
609			return strdup( painCave.errMsg );
610			}
611			eta[i] = atof( foo );
612	mmeineke	911	foo = strtok(NULL, " ,;\t\n");
613	mmeineke	906	}
614			}
615	mmeineke	909	else
616			return NULL;
617	mmeineke	906
618			//push eta into SimInfo::properties which can be
619	tim	837	//retrieved by integrator later
620	mmeineke	906	//entry_plug->setBoxM( theBoxMat3 );
621			DoubleArrayData* etaValue = new DoubleArrayData();
622			etaValue->setID(ETAVALUE_ID);
623			etaValue->setData(eta, 9);
624			entry_plug->addProperty(etaValue);
625	mmeineke	586	}
626	tim	837
627	mmeineke	586	return NULL;
628			}
629
630	chuckv	436	#ifdef IS_MPI
631
632			// a couple of functions to let us escape the read loop
633
634	mmeineke	440	void initFile::nodeZeroError( void ){
635	chuckv	436	int j, myStatus;
636	tim	837
637	chuckv	436	myStatus = 0;
638	tim	837	for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
639			MPI_Send( &myStatus, 1, MPI_INT, j,
640	mmeineke	447	TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
641	tim	837	}
642	chuckv	436
643	tim	837
644	chuckv	436	MPI_Finalize();
645			exit (0);
646	tim	837
647	chuckv	436	}
648
649	mmeineke	440	void initFile::anonymousNodeDie( void ){
650	chuckv	436
651			MPI_Finalize();
652			exit (0);
653			}
654
655			#endif //is_mpi