mdtools/md_code/InitializeFromFile.cpp

#include <iostream>
#include <cmath>

#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"


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
  }
 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 :: read_xyz( SimInfo* the_entry_plug ){

  int i; // loop counter

  const int BUFFERSIZE = 2000; // size of the read buffer
  int n_atoms; // the number of atoms
  char read_buffer[BUFFERSIZE]; //the line buffer for reading 
#ifdef IS_MPI
  char send_buffer[BUFFERSIZE];
#endif

  char *eof_test; // ptr to see when we reach the end of the file 
  char *parseErr;


  entry_plug = the_entry_plug


#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();
  }

  n_atoms = atoi( read_buffer );

  Atom **atoms = entry_plug->atoms;
  DirectionalAtom* dAtom;

  if( n_atoms != entry_plug->n_atoms ){
    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, n_atoms, entry_plug->n_atoms );
    painCave.isFatal = 1;
    simError();
  }
  
  //read and toss 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();
  }

  for( i=0; i < n_atoms; i++){
    
    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, n_atoms, i );
      painCave.isFatal = 1;
      simError();
    }

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


  // MPI Section of code..........
#else //IS_MPI

  int masterIndex;
  int nodeAtomsStart;
  int nodeAtomsEnd;
  int mpiErr;
  int sendError;

  MPI_Status istatus[MPI_STATUS_SIZE];

  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 %d \n ",c_in_name);
      painCave.isFatal = 1;
      simError();
    }
    
    n_atoms = atoi( read_buffer );
    
    Atom **atoms = entry_plug->atoms;
    DirectionalAtom* dAtom;
 
    // Check to see that the number of atoms in the intial configuration file is the
    // same as declared in simBass.
    
    if( n_atoms != entry_plug->mpiSim->getTotAtoms() ){
      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, n_atoms, entry_plug->n_atoms );
      painCave.isFatal = 1;
      simError();
    }
    
    //read and toss 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();
    }
  
    // Read Proc 0 share of the xyz file...
    masterIndex = 0;
    for( i=0; i <= entry_plug->mpiSim->getMyAtomEnd(); i++){
    
      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, n_atoms, i );
        painCave.isFatal = 1;
        simError();
      }
    
      parseErr = parseDumpLine( read_buffer, i );
      if( parseErr != NULL ){
        strcpy( painCave.errMsg, parseErr );
        painCave.isFatal = 1;
        simError();
      }    
      masterIndex++;
    }
  }

  sprintf(checkPointMsg,
          "Node 0 has successfully read positions from input file.");
  mpiCheckPoint();

  for (procIndex = 1; procIndex < entryPlug->mpiSim->getNumberProcessors();
         procIndex++){
    if (worldRank == 0) {

      mpiErr = MPI_Recv(&nodeAtomsStart,1,MPI_INT,procIndex,MPI_ANY_TAG,MPI_COMM_WORLD,
               istatus);

      mpiErr = MPI_Recv(&nodeAtomsEnd,1,MPI_INT,procIndex,MPI_ANY_TAG,MPI_COMM_WORLD,
               istatus);
      // Make sure where node 0 is reading from, matches where the receiving node
      // expects it to be.

      if (masterIndex != nodeAtomsStart){
        sendError = 1;
        mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,MPI_ANY_TAG,MPI_COMM_WORLD);
        sprintf(painCave.errMsg,
                "Initialize from file error: atoms start index (%d) for "
                "node %d not equal to master index (%d)",nodeAtomsStart,procIndex,masterIndex );
        painCave.isFatal = 1;
        simError();
      }
      sendError = 0;
      mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,MPI_ANY_TAG,MPI_COMM_WORLD);
      
      for ( i = nodeAtomStart; i <= nodeAtomEnd, i++){
        eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
        if(eof_test == NULL){
          
          sprintf(read_buffer,"ERROR");
          mpiErr = MPI_Send(read_buffer,BUFFERSIZE,MPI_CHAR,procIndex,MPI_ANY_TAG,MPI_COMM_WORLD);
          
          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, n_atoms, i );
          painCave.isFatal = 1;
          simError();
        }
        
        mpiErr = MPI_Send(read_buffer,BUFFERSIZE,MPI_CHAR,procIndex,MPI_ANY_TAG,MPI_COMM_WORLD);
        mpiErr = MPI_Recv(&sendError,1,MPI_INT,procIndex,MPI_ANY_TAG,MPI_COMM_WORLD,
                          istatus);
        if (sendError) mpiCheckpoint();

        masterIndex++;
      }
    }


    else if(worldRank == procIndex){
      nodeAtomStart = entry_plug->mpiSim->getMyAtomStart();
      nodeAtomEnd = entry_plug->mpiSim->getMyAtomEnd();
      mpiErr = MPI_Send(&nodeAtomsStart,1,MPI_INT,0,MPI_ANY_TAG,MPI_COMM_WORLD);
      mpiErr = MPI_Send(&nodeAtomsEnd,1,MPI_INT,0,MPI_ANY_TAG,MPI_COMM_WORLD);
      
      mpiErr = MPI_Recv(&sendError,1,MPI_INT,0,MPI_ANY_TAG,MPI_COMM_WORLD,
               istatus);
      if (sendError) mpiCheckpoint();

      for ( i = 0; i < entry_plug->n_atoms, i++){

        mpiErr = MPI_Recv(&read_buffer,BUFFERSIZE,MPI_CHAR,0,MPI_ANY_TAG,MPI_COMM_WORLD,
                          istatus);
        
        if(!strcmp(read_buffer, "ERROR")) mpiCheckPoint();
        
        parseErr = parseDumpLine( read_buffer, i );
        if( parseErr != NULL ){
          sendError = 1;
          mpiErr = MPI_Send(&sendError,1,MPI_INT,0,MPI_ANY_TAG,MPI_COMM_WORLD);


          strcpy( painCave.errMsg, parseErr );
          painCave.isFatal = 1;
          simError();
        }
        sendError = 0;
        mpiErr = MPI_Send(&sendError,1,MPI_INT,0,MPI_ANY_TAG,MPI_COMM_WORLD);
      }
    }
    sprintf(checkPointMsg,"Node %d received initial configuration.",procIndex);
    mpiCheckPoint();
  }

#endif
}


char* IntitializeFromFile::parseDumpLine(char* readLine, int atomIndex){

  char *foo; // the pointer to the current string token 
  
  double rx, ry, rz; // position place holders
  double vx, vy, vz; // velocity placeholders
  double q[4]; // the quaternions
  double jx, jy, jz; // angular velocity placeholders;
  double qSqr, qLength; // needed to normalize the quaternion vector.
  
  Atom **atoms = entry_plug->atoms;
  DirectionalAtom* dAtom;
  
  int n_atoms;

#ifdef IS_MPI
  n_atoms = entry_plug->mpiSim->getTotAtoms();
#else
  n_atoms = entry_plug->n_atoms;
#endi // is_mpi


  // set the string tokenizer
  
  foo = strtok(readLine, " ,;\t");
  
  // check the atom name to the current atom
  
  if( strcmp( foo, atoms[atomIndex]->getType() ) ){
    sprintf( painCave.errMsg,
             "Initialize from file error. Atom %s at index %d "
             "in file %s does not"
             " match the BASS atom %s.\n",
             foo, atomIndex, c_in_name, atoms[atomIndex]->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"
             "natoms  = %d, index = %d\n",
             c_in_name, n_atoms, atomIndex );
    return strdup( painCave.errMsg );
  }
  rx = atof( foo );
   
  foo = strtok(NULL, " ,;\t");
  if(foo == NULL){
    sprintf( painCave.errMsg,
             "error in reading postition y from %s\n"
             "natoms  = %d, index = %d\n",
             c_in_name, n_atoms, atomIndex );
    return strdup( painCave.errMsg );
  }
  ry = atof( foo );
     
  foo = strtok(NULL, " ,;\t");
  if(foo == NULL){
    sprintf( painCave.errMsg,
             "error in reading postition z from %s\n"
             "natoms  = %d, index = %d\n",
             c_in_name, n_atoms, atomIndex );
    return strdup( painCave.errMsg );
  }
  rz = atof( foo );    


  // get the velocities

  foo = strtok(NULL, " ,;\t");
  if(foo == NULL){
    sprintf( painCave.errMsg,
             "error in reading velocity x from %s\n"
             "natoms  = %d, index = %d\n",
             c_in_name, n_atoms, atomIndex );
    return strdup( painCave.errMsg );
  }
  vx = atof( foo );
    
  foo = strtok(NULL, " ,;\t");
  if(foo == NULL){
    sprintf( painCave.errMsg,
             "error in reading velocity y from %s\n"
             "natoms  = %d, index = %d\n",
             c_in_name, n_atoms, atomIndex );
    return strdup( painCave.errMsg );
  }
  vy = atof( foo );
    
  foo = strtok(NULL, " ,;\t");
  if(foo == NULL){
    sprintf( painCave.errMsg,
             "error in reading velocity z from %s\n"
             "natoms  = %d, index = %d\n",
             c_in_name, n_atoms, atomIndex );
    return strdup( painCave.errMsg );
  }
  vz = atof( foo );
    
    
  // get the quaternions
    
  if( atoms[atomIndex]->isDirectional() ){
      
    foo = strtok(NULL, " ,;\t");
    if(foo == NULL){
      sprintf(painCave.errMsg,
              "error in reading quaternion 0 from %s\n"
              "natoms  = %d, index = %d\n",
              c_in_name, n_atoms, atomIndex );
      return strdup( painCave.errMsg );
    }
    q[0] = atof( foo );
      
    foo = strtok(NULL, " ,;\t");
    if(foo == NULL){
      sprintf( painCave.errMsg,
               "error in reading quaternion 1 from %s\n"
               "natoms  = %d, index = %d\n",
               c_in_name, n_atoms, atomIndex );
      return strdup( painCave.errMsg );
    }
    q[1] = atof( foo );
      
    foo = strtok(NULL, " ,;\t");
    if(foo == NULL){
      sprintf( painCave.errMsg,
               "error in reading quaternion 2 from %s\n"
               "natoms  = %d, index = %d\n",
               c_in_name, n_atoms, atomIndex );
      return strdup( painCave.errMsg );
    }
    q[2] = atof( foo );
      
    foo = strtok(NULL, " ,;\t");
    if(foo == NULL){
      sprintf( painCave.errMsg,
               "error in reading quaternion 3 from %s\n"
               "natoms  = %d, index = %d\n",
               c_in_name, n_atoms, atomIndex );
      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 angular momentum jx from %s\n"
               "natoms  = %d, index = %d\n",
               c_in_name, n_atoms, atomIndex );
      return strdup( painCave.errMsg );
    }
    jx = atof( foo );
      
    foo = strtok(NULL, " ,;\t");
    if(foo == NULL){
      sprintf( painCave.errMsg,
               "error in reading angular momentum jy from %s\n"
               "natoms  = %d, index = %d\n",
               c_in_name, n_atoms, atomIndex );
      return strdup( painCave.errMsg );
    }
    jy = atof(foo );
      
    foo = strtok(NULL, " ,;\t");
    if(foo == NULL){
      sprintf( painCave.errMsg,
               "error in reading angular momentum jz from %s\n"
               "natoms  = %d, index = %d\n",
               c_in_name, n_atoms, atomIndex );
      return strdup( painCave.errMsg );
    }
    jz = atof( foo );
      
    dAtom = ( DirectionalAtom* )atoms[atomIndex];

    // 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;
      
    dAtom->setQ( q );
      
    // add the angular velocities

    dAtom->setJx( jx );
    dAtom->setJy( jy );
    dAtom->setJz( jz );
  }
    
  // add the positions and velocities to the atom
    
  atoms[atomIndex]->setX( rx );
  atoms[atomIndex]->setY( ry );
  atoms[atomIndex]->setZ( rz );
    
  atoms[atomIndex]->set_vx( vx );
  atoms[atomIndex]->set_vy( vy );
  atoms[atomIndex]->set_vz( vz );

  return NULL;
}
Revision:	212
Committed:	Fri Dec 13 21:17:00 2002 UTC (21 years, 8 months ago) by chuckv
File size:	13280 byte(s)
Log Message:	Added mpi to InitializeFromFile read in.
#	User	Rev	Content
1	mmeineke	10	#include <iostream>
2			#include <cmath>
3
4			#include <stdio.h>
5			#include <stdlib.h>
6			#include <string.h>
7			#include <unistd.h>
8			#include <sys/types.h>
9			#include <sys/stat.h>
10
11			#include "ReadWrite.hpp"
12	mmeineke	162	#include "simError.h"
13	mmeineke	10
14
15			InitializeFromFile :: InitializeFromFile( char *in_name ){
16	chuckv	206	#ifdef IS_MPI
17			if (worldRank == 0) {
18			#endif
19	mmeineke	10
20			c_in_file = fopen(in_name, "r");
21			if(c_in_file == NULL){
22	mmeineke	162	sprintf(painCave.errMsg,
23			"Cannot open file: %s\n", in_name);
24			painCave.isFatal = 1;
25			simError();
26	mmeineke	10	}
27
28			strcpy( c_in_name, in_name);
29	chuckv	206	#ifdef IS_MPI
30			}
31			strcpy( checkPointMsg, "Infile opened for reading successfully." );
32			MPIcheckPoint();
33			#endif
34	mmeineke	10	return;
35			}
36
37			InitializeFromFile :: ~InitializeFromFile( ){
38	chuckv	206	#ifdef IS_MPI
39			if (worldRank == 0) {
40			#endif
41	mmeineke	10	int error;
42			error = fclose( c_in_file );
43			if( error ){
44	mmeineke	162	sprintf( painCave.errMsg,
45			"Error closing %s\n", c_in_name );
46			simError();
47	mmeineke	10	}
48	chuckv	206	#ifdef IS_MPI
49			}
50			strcpy( checkPointMsg, "Infile closed successfully." );
51			MPIcheckPoint();
52			#endif
53
54	mmeineke	10	return;
55			}
56
57
58	chuckv	206	void InitializeFromFile :: read_xyz( SimInfo* the_entry_plug ){
59	mmeineke	10
60			int i; // loop counter
61
62	mmeineke	209	const int BUFFERSIZE = 2000; // size of the read buffer
63	mmeineke	10	int n_atoms; // the number of atoms
64	mmeineke	209	char read_buffer[BUFFERSIZE]; //the line buffer for reading
65	chuckv	206	#ifdef IS_MPI
66	mmeineke	209	char send_buffer[BUFFERSIZE];
67	chuckv	206	#endif
68
69	mmeineke	10	char *eof_test; // ptr to see when we reach the end of the file
70	mmeineke	209	char *parseErr;
71	mmeineke	10
72
73	chuckv	206	entry_plug = the_entry_plug
74
75
76			#ifndef IS_MPI
77	mmeineke	10	eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
78			if( eof_test == NULL ){
79	mmeineke	209	sprintf( painCave.errMsg,
80			"InitializeFromFile error: error reading 1st line of \"%s\"\n",
81			c_in_name );
82			painCave.isFatal = 1;
83			simError();
84	mmeineke	10	}
85
86	mmeineke	209	n_atoms = atoi( read_buffer );
87	mmeineke	10
88			Atom **atoms = entry_plug->atoms;
89			DirectionalAtom* dAtom;
90
91			if( n_atoms != entry_plug->n_atoms ){
92	mmeineke	162	sprintf( painCave.errMsg,
93	mmeineke	10	"Initialize from File error. %s n_atoms, %d, "
94			"does not match the BASS file's n_atoms, %d.\n",
95			c_in_name, n_atoms, entry_plug->n_atoms );
96	mmeineke	162	painCave.isFatal = 1;
97			simError();
98	mmeineke	10	}
99
100			//read and toss the comment line
101
102			eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
103			if(eof_test == NULL){
104	mmeineke	162	sprintf( painCave.errMsg,
105			"error in reading commment in %s\n", c_in_name);
106			painCave.isFatal = 1;
107			simError();
108	mmeineke	10	}
109
110			for( i=0; i < n_atoms; i++){
111
112			eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
113			if(eof_test == NULL){
114	mmeineke	162	sprintf(painCave.errMsg,
115			"error in reading file %s\n"
116			"natoms = %d; index = %d\n"
117			"error reading the line from the file.\n",
118			c_in_name, n_atoms, i );
119			painCave.isFatal = 1;
120			simError();
121	mmeineke	10	}
122
123
124	mmeineke	209	parseErr = parseDumpLine( read_buffer, i );
125			if( parseErr != NULL ){
126			strcpy( painCave.errMsg, parseErr );
127	mmeineke	162	painCave.isFatal = 1;
128			simError();
129	mmeineke	209	}
130	mmeineke	10	}
131	chuckv	206
132
133			// MPI Section of code..........
134			#else //IS_MPI
135
136	chuckv	212	int masterIndex;
137			int nodeAtomsStart;
138			int nodeAtomsEnd;
139			int mpiErr;
140			int sendError;
141	chuckv	206
142	chuckv	212	MPI_Status istatus[MPI_STATUS_SIZE];
143	chuckv	206
144			if (worldRank == 0) {
145			eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
146			if( eof_test == NULL ){
147			sprintf( painCave.errMsg,
148			"Error reading 1st line of %d \n ",c_in_name);
149			painCave.isFatal = 1;
150			simError();
151			}
152
153	mmeineke	209	n_atoms = atoi( read_buffer );
154	chuckv	206
155			Atom **atoms = entry_plug->atoms;
156			DirectionalAtom* dAtom;
157	chuckv	212
158			// Check to see that the number of atoms in the intial configuration file is the
159			// same as declared in simBass.
160	chuckv	206
161	mmeineke	209	if( n_atoms != entry_plug->mpiSim->getTotAtoms() ){
162	chuckv	206	sprintf( painCave.errMsg,
163			"Initialize from File error. %s n_atoms, %d, "
164			"does not match the BASS file's n_atoms, %d.\n",
165			c_in_name, n_atoms, entry_plug->n_atoms );
166			painCave.isFatal = 1;
167			simError();
168			}
169
170			//read and toss the comment line
171
172			eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
173			if(eof_test == NULL){
174			sprintf( painCave.errMsg,
175			"error in reading commment in %s\n", c_in_name);
176			painCave.isFatal = 1;
177			simError();
178			}
179	chuckv	212
180			// Read Proc 0 share of the xyz file...
181			masterIndex = 0;
182			for( i=0; i <= entry_plug->mpiSim->getMyAtomEnd(); i++){
183
184			eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
185			if(eof_test == NULL){
186			sprintf(painCave.errMsg,
187			"error in reading file %s\n"
188			"natoms = %d; index = %d\n"
189			"error reading the line from the file.\n",
190			c_in_name, n_atoms, i );
191			painCave.isFatal = 1;
192			simError();
193			}
194
195			parseErr = parseDumpLine( read_buffer, i );
196			if( parseErr != NULL ){
197			strcpy( painCave.errMsg, parseErr );
198			painCave.isFatal = 1;
199			simError();
200			}
201			masterIndex++;
202			}
203	chuckv	206	}
204	mmeineke	209
205	chuckv	212	sprintf(checkPointMsg,
206			"Node 0 has successfully read positions from input file.");
207			mpiCheckPoint();
208
209			for (procIndex = 1; procIndex < entryPlug->mpiSim->getNumberProcessors();
210			procIndex++){
211			if (worldRank == 0) {
212
213			mpiErr = MPI_Recv(&nodeAtomsStart,1,MPI_INT,procIndex,MPI_ANY_TAG,MPI_COMM_WORLD,
214			istatus);
215
216			mpiErr = MPI_Recv(&nodeAtomsEnd,1,MPI_INT,procIndex,MPI_ANY_TAG,MPI_COMM_WORLD,
217			istatus);
218			// Make sure where node 0 is reading from, matches where the receiving node
219			// expects it to be.
220
221			if (masterIndex != nodeAtomsStart){
222			sendError = 1;
223			mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,MPI_ANY_TAG,MPI_COMM_WORLD);
224			sprintf(painCave.errMsg,
225			"Initialize from file error: atoms start index (%d) for "
226			"node %d not equal to master index (%d)",nodeAtomsStart,procIndex,masterIndex );
227			painCave.isFatal = 1;
228			simError();
229			}
230			sendError = 0;
231			mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,MPI_ANY_TAG,MPI_COMM_WORLD);
232
233			for ( i = nodeAtomStart; i <= nodeAtomEnd, i++){
234			eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
235			if(eof_test == NULL){
236
237			sprintf(read_buffer,"ERROR");
238			mpiErr = MPI_Send(read_buffer,BUFFERSIZE,MPI_CHAR,procIndex,MPI_ANY_TAG,MPI_COMM_WORLD);
239
240			sprintf(painCave.errMsg,
241			"error in reading file %s\n"
242			"natoms = %d; index = %d\n"
243			"error reading the line from the file.\n",
244			c_in_name, n_atoms, i );
245			painCave.isFatal = 1;
246			simError();
247			}
248
249			mpiErr = MPI_Send(read_buffer,BUFFERSIZE,MPI_CHAR,procIndex,MPI_ANY_TAG,MPI_COMM_WORLD);
250			mpiErr = MPI_Recv(&sendError,1,MPI_INT,procIndex,MPI_ANY_TAG,MPI_COMM_WORLD,
251			istatus);
252			if (sendError) mpiCheckpoint();
253
254			masterIndex++;
255			}
256	chuckv	206	}
257	chuckv	212
258
259			else if(worldRank == procIndex){
260			nodeAtomStart = entry_plug->mpiSim->getMyAtomStart();
261			nodeAtomEnd = entry_plug->mpiSim->getMyAtomEnd();
262			mpiErr = MPI_Send(&nodeAtomsStart,1,MPI_INT,0,MPI_ANY_TAG,MPI_COMM_WORLD);
263			mpiErr = MPI_Send(&nodeAtomsEnd,1,MPI_INT,0,MPI_ANY_TAG,MPI_COMM_WORLD);
264
265			mpiErr = MPI_Recv(&sendError,1,MPI_INT,0,MPI_ANY_TAG,MPI_COMM_WORLD,
266			istatus);
267			if (sendError) mpiCheckpoint();
268
269			for ( i = 0; i < entry_plug->n_atoms, i++){
270
271			mpiErr = MPI_Recv(&read_buffer,BUFFERSIZE,MPI_CHAR,0,MPI_ANY_TAG,MPI_COMM_WORLD,
272			istatus);
273
274			if(!strcmp(read_buffer, "ERROR")) mpiCheckPoint();
275
276			parseErr = parseDumpLine( read_buffer, i );
277			if( parseErr != NULL ){
278			sendError = 1;
279			mpiErr = MPI_Send(&sendError,1,MPI_INT,0,MPI_ANY_TAG,MPI_COMM_WORLD);
280
281
282			strcpy( painCave.errMsg, parseErr );
283			painCave.isFatal = 1;
284			simError();
285			}
286			sendError = 0;
287			mpiErr = MPI_Send(&sendError,1,MPI_INT,0,MPI_ANY_TAG,MPI_COMM_WORLD);
288			}
289			}
290			sprintf(checkPointMsg,"Node %d received initial configuration.",procIndex);
291			mpiCheckPoint();
292	mmeineke	209	}
293	chuckv	212
294	mmeineke	209	#endif
295			}
296
297
298			char* IntitializeFromFile::parseDumpLine(char* readLine, int atomIndex){
299
300			char *foo; // the pointer to the current string token
301
302			double rx, ry, rz; // position place holders
303			double vx, vy, vz; // velocity placeholders
304			double q[4]; // the quaternions
305			double jx, jy, jz; // angular velocity placeholders;
306			double qSqr, qLength; // needed to normalize the quaternion vector.
307
308			Atom **atoms = entry_plug->atoms;
309			DirectionalAtom* dAtom;
310
311			int n_atoms;
312
313			#ifdef IS_MPI
314			n_atoms = entry_plug->mpiSim->getTotAtoms();
315			#else
316			n_atoms = entry_plug->n_atoms;
317			#endi // is_mpi
318
319
320			// set the string tokenizer
321
322			foo = strtok(readLine, " ,;\t");
323
324			// check the atom name to the current atom
325
326			if( strcmp( foo, atoms[atomIndex]->getType() ) ){
327			sprintf( painCave.errMsg,
328			"Initialize from file error. Atom %s at index %d "
329			"in file %s does not"
330			" match the BASS atom %s.\n",
331			foo, atomIndex, c_in_name, atoms[atomIndex]->getType() );
332			return strdup( painCave.errMsg );
333			}
334	chuckv	206
335	mmeineke	209	// get the positions
336	chuckv	206
337	mmeineke	209	foo = strtok(NULL, " ,;\t");
338			if(foo == NULL){
339			sprintf( painCave.errMsg,
340			"error in reading postition x from %s\n"
341			"natoms = %d, index = %d\n",
342			c_in_name, n_atoms, atomIndex );
343			return strdup( painCave.errMsg );
344			}
345			rx = atof( foo );
346
347			foo = strtok(NULL, " ,;\t");
348			if(foo == NULL){
349			sprintf( painCave.errMsg,
350			"error in reading postition y from %s\n"
351			"natoms = %d, index = %d\n",
352			c_in_name, n_atoms, atomIndex );
353			return strdup( painCave.errMsg );
354			}
355			ry = atof( foo );
356
357			foo = strtok(NULL, " ,;\t");
358			if(foo == NULL){
359			sprintf( painCave.errMsg,
360			"error in reading postition z from %s\n"
361			"natoms = %d, index = %d\n",
362			c_in_name, n_atoms, atomIndex );
363			return strdup( painCave.errMsg );
364			}
365			rz = atof( foo );
366
367
368			// get the velocities
369
370			foo = strtok(NULL, " ,;\t");
371			if(foo == NULL){
372			sprintf( painCave.errMsg,
373			"error in reading velocity x from %s\n"
374			"natoms = %d, index = %d\n",
375			c_in_name, n_atoms, atomIndex );
376			return strdup( painCave.errMsg );
377			}
378			vx = atof( foo );
379
380			foo = strtok(NULL, " ,;\t");
381			if(foo == NULL){
382			sprintf( painCave.errMsg,
383			"error in reading velocity y from %s\n"
384			"natoms = %d, index = %d\n",
385			c_in_name, n_atoms, atomIndex );
386			return strdup( painCave.errMsg );
387			}
388			vy = atof( foo );
389
390			foo = strtok(NULL, " ,;\t");
391			if(foo == NULL){
392			sprintf( painCave.errMsg,
393			"error in reading velocity z from %s\n"
394			"natoms = %d, index = %d\n",
395			c_in_name, n_atoms, atomIndex );
396			return strdup( painCave.errMsg );
397			}
398			vz = atof( foo );
399
400
401			// get the quaternions
402
403			if( atoms[atomIndex]->isDirectional() ){
404
405	chuckv	206	foo = strtok(NULL, " ,;\t");
406			if(foo == NULL){
407	mmeineke	209	sprintf(painCave.errMsg,
408			"error in reading quaternion 0 from %s\n"
409			"natoms = %d, index = %d\n",
410			c_in_name, n_atoms, atomIndex );
411			return strdup( painCave.errMsg );
412			}
413			q[0] = atof( foo );
414
415			foo = strtok(NULL, " ,;\t");
416			if(foo == NULL){
417	chuckv	206	sprintf( painCave.errMsg,
418	mmeineke	209	"error in reading quaternion 1 from %s\n"
419	chuckv	206	"natoms = %d, index = %d\n",
420	mmeineke	209	c_in_name, n_atoms, atomIndex );
421			return strdup( painCave.errMsg );
422	chuckv	206	}
423	mmeineke	209	q[1] = atof( foo );
424
425	chuckv	206	foo = strtok(NULL, " ,;\t");
426			if(foo == NULL){
427			sprintf( painCave.errMsg,
428	mmeineke	209	"error in reading quaternion 2 from %s\n"
429	chuckv	206	"natoms = %d, index = %d\n",
430	mmeineke	209	c_in_name, n_atoms, atomIndex );
431			return strdup( painCave.errMsg );
432	chuckv	206	}
433	mmeineke	209	q[2] = atof( foo );
434
435	chuckv	206	foo = strtok(NULL, " ,;\t");
436			if(foo == NULL){
437			sprintf( painCave.errMsg,
438	mmeineke	209	"error in reading quaternion 3 from %s\n"
439	chuckv	206	"natoms = %d, index = %d\n",
440	mmeineke	209	c_in_name, n_atoms, atomIndex );
441			return strdup( painCave.errMsg );
442	chuckv	206	}
443	mmeineke	209	q[3] = atof( foo );
444
445			// get the angular velocities
446
447	chuckv	206	foo = strtok(NULL, " ,;\t");
448			if(foo == NULL){
449			sprintf( painCave.errMsg,
450	mmeineke	209	"error in reading angular momentum jx from %s\n"
451	chuckv	206	"natoms = %d, index = %d\n",
452	mmeineke	209	c_in_name, n_atoms, atomIndex );
453			return strdup( painCave.errMsg );
454	chuckv	206	}
455	mmeineke	209	jx = atof( foo );
456
457	chuckv	206	foo = strtok(NULL, " ,;\t");
458			if(foo == NULL){
459			sprintf( painCave.errMsg,
460	mmeineke	209	"error in reading angular momentum jy from %s\n"
461	chuckv	206	"natoms = %d, index = %d\n",
462	mmeineke	209	c_in_name, n_atoms, atomIndex );
463			return strdup( painCave.errMsg );
464	chuckv	206	}
465	mmeineke	209	jy = atof(foo );
466
467	chuckv	206	foo = strtok(NULL, " ,;\t");
468			if(foo == NULL){
469			sprintf( painCave.errMsg,
470	mmeineke	209	"error in reading angular momentum jz from %s\n"
471	chuckv	206	"natoms = %d, index = %d\n",
472	mmeineke	209	c_in_name, n_atoms, atomIndex );
473			return strdup( painCave.errMsg );
474	chuckv	206	}
475	mmeineke	209	jz = atof( foo );
476	chuckv	206
477	mmeineke	209	dAtom = ( DirectionalAtom* )atoms[atomIndex];
478	chuckv	206
479	mmeineke	209	// check that the quaternion vector is normalized
480	chuckv	206
481	mmeineke	209	qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]);
482	chuckv	206
483	mmeineke	209	qLength = sqrt( qSqr );
484			q[0] = q[0] / qLength;
485			q[1] = q[1] / qLength;
486			q[2] = q[2] / qLength;
487			q[3] = q[3] / qLength;
488	chuckv	206
489	mmeineke	209	dAtom->setQ( q );
490	chuckv	206
491	mmeineke	209	// add the angular velocities
492	chuckv	206
493	mmeineke	209	dAtom->setJx( jx );
494			dAtom->setJy( jy );
495			dAtom->setJz( jz );
496			}
497	chuckv	206
498	mmeineke	209	// add the positions and velocities to the atom
499	chuckv	206
500	mmeineke	209	atoms[atomIndex]->setX( rx );
501			atoms[atomIndex]->setY( ry );
502			atoms[atomIndex]->setZ( rz );
503	chuckv	206
504	mmeineke	209	atoms[atomIndex]->set_vx( vx );
505			atoms[atomIndex]->set_vy( vy );
506			atoms[atomIndex]->set_vz( vz );
507
508			return NULL;
509	mmeineke	10	}