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"

#ifdef IS_MPI
#include "mpiSimulation.hpp"

#define TAKE_THIS_TAG 0
#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
  }
 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;
  int procIndex;

  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 != 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 <= 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 < mpiSim->getNumberProcessors();
         procIndex++){
    if (worldRank == 0) {

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

      mpiErr = MPI_Recv(&nodeAtomsEnd,1,MPI_INT,procIndex,TAKE_THIS_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,TAKE_THIS_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,TAKE_THIS_TAG,MPI_COMM_WORLD);
      
      for ( i = nodeAtomsStart; i <= nodeAtomsEnd; 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,TAKE_THIS_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,TAKE_THIS_TAG,MPI_COMM_WORLD);
        mpiErr = MPI_Recv(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG,MPI_COMM_WORLD,
                          istatus);
        if (sendError) MPIcheckPoint();

        masterIndex++;
      }
    }


    else if(worldRank == procIndex){
      nodeAtomsStart = mpiSim->getMyAtomStart();
      nodeAtomsEnd = mpiSim->getMyAtomEnd();
      mpiErr = MPI_Send(&nodeAtomsStart,1,MPI_INT,0,TAKE_THIS_TAG,MPI_COMM_WORLD);
      mpiErr = MPI_Send(&nodeAtomsEnd,1,MPI_INT,0,TAKE_THIS_TAG,MPI_COMM_WORLD);
      
      mpiErr = MPI_Recv(&sendError,1,MPI_INT,0,TAKE_THIS_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,TAKE_THIS_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,TAKE_THIS_TAG,MPI_COMM_WORLD);


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

#endif
}


char* InitializeFromFile::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 = mpiSim->getTotAtoms();
#else
  n_atoms = entry_plug->n_atoms;
#endif // 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:	260
Committed:	Fri Jan 31 21:04:27 2003 UTC (22 years, 8 months ago) by chuckv
File size:	13341 byte(s)
Log Message:	Fixed some bugs, made some more.
#	Content
1	#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	#include "simError.h"
13
14	#ifdef IS_MPI
15	#include "mpiSimulation.hpp"
16
17	#define TAKE_THIS_TAG 0
18	#endif // is_mpi
19
20	InitializeFromFile :: InitializeFromFile( char *in_name ){
21	#ifdef IS_MPI
22	if (worldRank == 0) {
23	#endif
24
25	c_in_file = fopen(in_name, "r");
26	if(c_in_file == NULL){
27	sprintf(painCave.errMsg,
28	"Cannot open file: %s\n", in_name);
29	painCave.isFatal = 1;
30	simError();
31	}
32
33	strcpy( c_in_name, in_name);
34	#ifdef IS_MPI
35	}
36	strcpy( checkPointMsg, "Infile opened for reading successfully." );
37	MPIcheckPoint();
38	#endif
39	return;
40	}
41
42	InitializeFromFile :: ~InitializeFromFile( ){
43	#ifdef IS_MPI
44	if (worldRank == 0) {
45	#endif
46	int error;
47	error = fclose( c_in_file );
48	if( error ){
49	sprintf( painCave.errMsg,
50	"Error closing %s\n", c_in_name );
51	simError();
52	}
53	#ifdef IS_MPI
54	}
55	strcpy( checkPointMsg, "Infile closed successfully." );
56	MPIcheckPoint();
57	#endif
58
59	return;
60	}
61
62
63	void InitializeFromFile :: read_xyz( SimInfo* the_entry_plug ){
64
65	int i; // loop counter
66
67	const int BUFFERSIZE = 2000; // size of the read buffer
68	int n_atoms; // the number of atoms
69	char read_buffer[BUFFERSIZE]; //the line buffer for reading
70	#ifdef IS_MPI
71	char send_buffer[BUFFERSIZE];
72	#endif
73
74	char *eof_test; // ptr to see when we reach the end of the file
75	char *parseErr;
76	int procIndex;
77
78	entry_plug = the_entry_plug;
79
80
81	#ifndef IS_MPI
82	eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
83	if( eof_test == NULL ){
84	sprintf( painCave.errMsg,
85	"InitializeFromFile error: error reading 1st line of \"%s\"\n",
86	c_in_name );
87	painCave.isFatal = 1;
88	simError();
89	}
90
91	n_atoms = atoi( read_buffer );
92
93	Atom **atoms = entry_plug->atoms;
94	DirectionalAtom* dAtom;
95
96	if( n_atoms != entry_plug->n_atoms ){
97	sprintf( painCave.errMsg,
98	"Initialize from File error. %s n_atoms, %d, "
99	"does not match the BASS file's n_atoms, %d.\n",
100	c_in_name, n_atoms, entry_plug->n_atoms );
101	painCave.isFatal = 1;
102	simError();
103	}
104
105	//read and toss the comment line
106
107	eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
108	if(eof_test == NULL){
109	sprintf( painCave.errMsg,
110	"error in reading commment in %s\n", c_in_name);
111	painCave.isFatal = 1;
112	simError();
113	}
114
115	for( i=0; i < n_atoms; i++){
116
117	eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
118	if(eof_test == NULL){
119	sprintf(painCave.errMsg,
120	"error in reading file %s\n"
121	"natoms = %d; index = %d\n"
122	"error reading the line from the file.\n",
123	c_in_name, n_atoms, i );
124	painCave.isFatal = 1;
125	simError();
126	}
127
128
129	parseErr = parseDumpLine( read_buffer, i );
130	if( parseErr != NULL ){
131	strcpy( painCave.errMsg, parseErr );
132	painCave.isFatal = 1;
133	simError();
134	}
135	}
136
137
138	// MPI Section of code..........
139	#else //IS_MPI
140
141	int masterIndex;
142	int nodeAtomsStart;
143	int nodeAtomsEnd;
144	int mpiErr;
145	int sendError;
146
147	MPI_Status istatus[MPI_STATUS_SIZE];
148
149	if (worldRank == 0) {
150	eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
151	if( eof_test == NULL ){
152	sprintf( painCave.errMsg,
153	"Error reading 1st line of %d \n ",c_in_name);
154	painCave.isFatal = 1;
155	simError();
156	}
157
158	n_atoms = atoi( read_buffer );
159
160	Atom **atoms = entry_plug->atoms;
161	DirectionalAtom* dAtom;
162
163	// Check to see that the number of atoms in the intial configuration file is the
164	// same as declared in simBass.
165
166	if( n_atoms != mpiSim->getTotAtoms() ){
167	sprintf( painCave.errMsg,
168	"Initialize from File error. %s n_atoms, %d, "
169	"does not match the BASS file's n_atoms, %d.\n",
170	c_in_name, n_atoms, entry_plug->n_atoms );
171	painCave.isFatal = 1;
172	simError();
173	}
174
175	//read and toss the comment line
176
177	eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
178	if(eof_test == NULL){
179	sprintf( painCave.errMsg,
180	"error in reading commment in %s\n", c_in_name);
181	painCave.isFatal = 1;
182	simError();
183	}
184
185	// Read Proc 0 share of the xyz file...
186	masterIndex = 0;
187	for( i=0; i <= mpiSim->getMyAtomEnd(); i++){
188
189	eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
190	if(eof_test == NULL){
191	sprintf(painCave.errMsg,
192	"error in reading file %s\n"
193	"natoms = %d; index = %d\n"
194	"error reading the line from the file.\n",
195	c_in_name, n_atoms, i );
196	painCave.isFatal = 1;
197	simError();
198	}
199
200	parseErr = parseDumpLine( read_buffer, i );
201	if( parseErr != NULL ){
202	strcpy( painCave.errMsg, parseErr );
203	painCave.isFatal = 1;
204	simError();
205	}
206	masterIndex++;
207	}
208	}
209
210	sprintf(checkPointMsg,
211	"Node 0 has successfully read positions from input file.");
212	MPIcheckPoint();
213
214	for (procIndex = 1; procIndex < mpiSim->getNumberProcessors();
215	procIndex++){
216	if (worldRank == 0) {
217
218	mpiErr = MPI_Recv(&nodeAtomsStart,1,MPI_INT,procIndex,TAKE_THIS_TAG,MPI_COMM_WORLD,
219	istatus);
220
221	mpiErr = MPI_Recv(&nodeAtomsEnd,1,MPI_INT,procIndex,TAKE_THIS_TAG,MPI_COMM_WORLD,
222	istatus);
223	// Make sure where node 0 is reading from, matches where the receiving node
224	// expects it to be.
225
226	if (masterIndex != nodeAtomsStart){
227	sendError = 1;
228	mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG,MPI_COMM_WORLD);
229	sprintf(painCave.errMsg,
230	"Initialize from file error: atoms start index (%d) for "
231	"node %d not equal to master index (%d)",nodeAtomsStart,procIndex,masterIndex );
232	painCave.isFatal = 1;
233	simError();
234	}
235	sendError = 0;
236	mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG,MPI_COMM_WORLD);
237
238	for ( i = nodeAtomsStart; i <= nodeAtomsEnd; i++){
239	eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
240	if(eof_test == NULL){
241
242	sprintf(read_buffer,"ERROR");
243	mpiErr = MPI_Send(read_buffer,BUFFERSIZE,MPI_CHAR,procIndex,TAKE_THIS_TAG,MPI_COMM_WORLD);
244
245	sprintf(painCave.errMsg,
246	"error in reading file %s\n"
247	"natoms = %d; index = %d\n"
248	"error reading the line from the file.\n",
249	c_in_name, n_atoms, i );
250	painCave.isFatal = 1;
251	simError();
252	}
253
254	mpiErr = MPI_Send(read_buffer,BUFFERSIZE,MPI_CHAR,procIndex,TAKE_THIS_TAG,MPI_COMM_WORLD);
255	mpiErr = MPI_Recv(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG,MPI_COMM_WORLD,
256	istatus);
257	if (sendError) MPIcheckPoint();
258
259	masterIndex++;
260	}
261	}
262
263
264	else if(worldRank == procIndex){
265	nodeAtomsStart = mpiSim->getMyAtomStart();
266	nodeAtomsEnd = mpiSim->getMyAtomEnd();
267	mpiErr = MPI_Send(&nodeAtomsStart,1,MPI_INT,0,TAKE_THIS_TAG,MPI_COMM_WORLD);
268	mpiErr = MPI_Send(&nodeAtomsEnd,1,MPI_INT,0,TAKE_THIS_TAG,MPI_COMM_WORLD);
269
270	mpiErr = MPI_Recv(&sendError,1,MPI_INT,0,TAKE_THIS_TAG,MPI_COMM_WORLD,
271	istatus);
272	if (sendError) MPIcheckPoint();
273
274	for ( i = 0; i < entry_plug->n_atoms; i++){
275
276	mpiErr = MPI_Recv(&read_buffer,BUFFERSIZE,MPI_CHAR,0,TAKE_THIS_TAG,MPI_COMM_WORLD,
277	istatus);
278
279	if(!strcmp(read_buffer, "ERROR")) MPIcheckPoint();
280
281	parseErr = parseDumpLine( read_buffer, i );
282	if( parseErr != NULL ){
283	sendError = 1;
284	mpiErr = MPI_Send(&sendError,1,MPI_INT,0,TAKE_THIS_TAG,MPI_COMM_WORLD);
285
286
287	strcpy( painCave.errMsg, parseErr );
288	painCave.isFatal = 1;
289	simError();
290	}
291	sendError = 0;
292	mpiErr = MPI_Send(&sendError,1,MPI_INT,0,TAKE_THIS_TAG,MPI_COMM_WORLD);
293	}
294	}
295	sprintf(checkPointMsg,"Node %d received initial configuration.",procIndex);
296	MPIcheckPoint();
297	}
298
299	#endif
300	}
301
302
303	char* InitializeFromFile::parseDumpLine(char* readLine, int atomIndex){
304
305	char *foo; // the pointer to the current string token
306
307	double rx, ry, rz; // position place holders
308	double vx, vy, vz; // velocity placeholders
309	double q[4]; // the quaternions
310	double jx, jy, jz; // angular velocity placeholders;
311	double qSqr, qLength; // needed to normalize the quaternion vector.
312
313	Atom **atoms = entry_plug->atoms;
314	DirectionalAtom* dAtom;
315
316	int n_atoms;
317
318	#ifdef IS_MPI
319	n_atoms = mpiSim->getTotAtoms();
320	#else
321	n_atoms = entry_plug->n_atoms;
322	#endif // is_mpi
323
324
325	// set the string tokenizer
326
327	foo = strtok(readLine, " ,;\t");
328
329	// check the atom name to the current atom
330
331	if( strcmp( foo, atoms[atomIndex]->getType() ) ){
332	sprintf( painCave.errMsg,
333	"Initialize from file error. Atom %s at index %d "
334	"in file %s does not"
335	" match the BASS atom %s.\n",
336	foo, atomIndex, c_in_name, atoms[atomIndex]->getType() );
337	return strdup( painCave.errMsg );
338	}
339
340	// get the positions
341
342	foo = strtok(NULL, " ,;\t");
343	if(foo == NULL){
344	sprintf( painCave.errMsg,
345	"error in reading postition x from %s\n"
346	"natoms = %d, index = %d\n",
347	c_in_name, n_atoms, atomIndex );
348	return strdup( painCave.errMsg );
349	}
350	rx = atof( foo );
351
352	foo = strtok(NULL, " ,;\t");
353	if(foo == NULL){
354	sprintf( painCave.errMsg,
355	"error in reading postition y from %s\n"
356	"natoms = %d, index = %d\n",
357	c_in_name, n_atoms, atomIndex );
358	return strdup( painCave.errMsg );
359	}
360	ry = atof( foo );
361
362	foo = strtok(NULL, " ,;\t");
363	if(foo == NULL){
364	sprintf( painCave.errMsg,
365	"error in reading postition z from %s\n"
366	"natoms = %d, index = %d\n",
367	c_in_name, n_atoms, atomIndex );
368	return strdup( painCave.errMsg );
369	}
370	rz = atof( foo );
371
372
373	// get the velocities
374
375	foo = strtok(NULL, " ,;\t");
376	if(foo == NULL){
377	sprintf( painCave.errMsg,
378	"error in reading velocity x from %s\n"
379	"natoms = %d, index = %d\n",
380	c_in_name, n_atoms, atomIndex );
381	return strdup( painCave.errMsg );
382	}
383	vx = atof( foo );
384
385	foo = strtok(NULL, " ,;\t");
386	if(foo == NULL){
387	sprintf( painCave.errMsg,
388	"error in reading velocity y from %s\n"
389	"natoms = %d, index = %d\n",
390	c_in_name, n_atoms, atomIndex );
391	return strdup( painCave.errMsg );
392	}
393	vy = atof( foo );
394
395	foo = strtok(NULL, " ,;\t");
396	if(foo == NULL){
397	sprintf( painCave.errMsg,
398	"error in reading velocity z from %s\n"
399	"natoms = %d, index = %d\n",
400	c_in_name, n_atoms, atomIndex );
401	return strdup( painCave.errMsg );
402	}
403	vz = atof( foo );
404
405
406	// get the quaternions
407
408	if( atoms[atomIndex]->isDirectional() ){
409
410	foo = strtok(NULL, " ,;\t");
411	if(foo == NULL){
412	sprintf(painCave.errMsg,
413	"error in reading quaternion 0 from %s\n"
414	"natoms = %d, index = %d\n",
415	c_in_name, n_atoms, atomIndex );
416	return strdup( painCave.errMsg );
417	}
418	q[0] = atof( foo );
419
420	foo = strtok(NULL, " ,;\t");
421	if(foo == NULL){
422	sprintf( painCave.errMsg,
423	"error in reading quaternion 1 from %s\n"
424	"natoms = %d, index = %d\n",
425	c_in_name, n_atoms, atomIndex );
426	return strdup( painCave.errMsg );
427	}
428	q[1] = atof( foo );
429
430	foo = strtok(NULL, " ,;\t");
431	if(foo == NULL){
432	sprintf( painCave.errMsg,
433	"error in reading quaternion 2 from %s\n"
434	"natoms = %d, index = %d\n",
435	c_in_name, n_atoms, atomIndex );
436	return strdup( painCave.errMsg );
437	}
438	q[2] = atof( foo );
439
440	foo = strtok(NULL, " ,;\t");
441	if(foo == NULL){
442	sprintf( painCave.errMsg,
443	"error in reading quaternion 3 from %s\n"
444	"natoms = %d, index = %d\n",
445	c_in_name, n_atoms, atomIndex );
446	return strdup( painCave.errMsg );
447	}
448	q[3] = atof( foo );
449
450	// get the angular velocities
451
452	foo = strtok(NULL, " ,;\t");
453	if(foo == NULL){
454	sprintf( painCave.errMsg,
455	"error in reading angular momentum jx from %s\n"
456	"natoms = %d, index = %d\n",
457	c_in_name, n_atoms, atomIndex );
458	return strdup( painCave.errMsg );
459	}
460	jx = atof( foo );
461
462	foo = strtok(NULL, " ,;\t");
463	if(foo == NULL){
464	sprintf( painCave.errMsg,
465	"error in reading angular momentum jy from %s\n"
466	"natoms = %d, index = %d\n",
467	c_in_name, n_atoms, atomIndex );
468	return strdup( painCave.errMsg );
469	}
470	jy = atof(foo );
471
472	foo = strtok(NULL, " ,;\t");
473	if(foo == NULL){
474	sprintf( painCave.errMsg,
475	"error in reading angular momentum jz from %s\n"
476	"natoms = %d, index = %d\n",
477	c_in_name, n_atoms, atomIndex );
478	return strdup( painCave.errMsg );
479	}
480	jz = atof( foo );
481
482	dAtom = ( DirectionalAtom* )atoms[atomIndex];
483
484	// check that the quaternion vector is normalized
485
486	qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]);
487
488	qLength = sqrt( qSqr );
489	q[0] = q[0] / qLength;
490	q[1] = q[1] / qLength;
491	q[2] = q[2] / qLength;
492	q[3] = q[3] / qLength;
493
494	dAtom->setQ( q );
495
496	// add the angular velocities
497
498	dAtom->setJx( jx );
499	dAtom->setJy( jy );
500	dAtom->setJz( jz );
501	}
502
503	// add the positions and velocities to the atom
504
505	atoms[atomIndex]->setX( rx );
506	atoms[atomIndex]->setY( ry );
507	atoms[atomIndex]->setZ( rz );
508
509	atoms[atomIndex]->set_vx( vx );
510	atoms[atomIndex]->set_vy( vy );
511	atoms[atomIndex]->set_vz( vz );
512
513	return NULL;
514	}