OOPSE/libmdtools/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 <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
  }
 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, j, done, which_node, which_atom; // 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

  // first thing first, suspend fatalities.
  painCave.isEventLoop = 1;

  int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
  int haveError;
  
  MPI_Status istatus;
  int *AtomToProcMap = mpiSim->getAtomToProcMap();

  
  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 %d \n ",c_in_name);
      haveError = 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 );
      haveError= 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);
      haveError= 1;
      simError();
    }
  
    if(haveError) nodeZeroError();

    for (i=0 ; i < mpiSim->getTotAtoms(); 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 );
        haveError= 1;
        simError();
      }
    
      if(haveError) nodeZeroError();

      // Get the Node number which wants this atom:
      which_node = AtomToProcMap[i];     
      if (which_node == 0) {
        parseErr = parseDumpLine( read_buffer, i );
        if( parseErr != NULL ){
          strcpy( painCave.errMsg, parseErr );
          haveError = 1;
          simError();
        }    
        if(haveError) nodeZeroError();
      } 
      
      else {
       
        myStatus = 1;
        MPI_Send(&myStatus, 1, MPI_INT, which_node, 
                 TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
        MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node, 
                 TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
        MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
                 MPI_COMM_WORLD);
        MPI_Recv(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, 
                 MPI_COMM_WORLD, &istatus);
        
        if(!myStatus) nodeZeroError();
      }
    }
    myStatus = -1;
    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
      MPI_Send( &myStatus, 1, MPI_INT, j, 
                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
    }
    
  } else {
    
    done = 0;
    while (!done) {

      MPI_Recv(&myStatus, 1, MPI_INT, 0, 
               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
      
      if(!myStatus) anonymousNodeDie();
      
      if(myStatus < 0) break;

      MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0, 
               TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
      MPI_Recv(&which_atom, 1, MPI_INT, 0, 
               TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
      
      myStatus = 1;
      parseErr = parseDumpLine( read_buffer, which_atom );
      if( parseErr != NULL ){
        strcpy( painCave.errMsg, parseErr );
        myStatus = 0;;
        simError();
      }
      
      MPI_Send( &myStatus, 1, MPI_INT, 0, 
                TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
      
    }
  }
     
 // last  thing last, enable  fatalities.
  painCave.isEventLoop = 0;
   
#endif
}

char* InitializeFromFile::parseDumpLine(char* readLine, int globalIndex){

  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 j, n_atoms, atomIndex;

#ifdef IS_MPI
  n_atoms = mpiSim->getTotAtoms();
  atomIndex=-1;        
  for (j=0; j < mpiSim->getMyNlocal(); j++) {
    if (atoms[j]->getGlobalIndex() == globalIndex) atomIndex = j;
  }
  if (atomIndex == -1) {
    sprintf( painCave.errMsg,
             "Initialize from file error. Atom at index %d "
             "in file %s does not exist on processor %d .\n",
             globalIndex, c_in_name, mpiSim->getMyNode() );
    return strdup( painCave.errMsg );
  }  
#else
  n_atoms = entry_plug->n_atoms;
  atomIndex = globalIndex;
#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;
}


#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:	447
Committed:	Thu Apr 3 20:21:54 2003 UTC (21 years, 3 months ago) by mmeineke
File size:	13274 byte(s)
Log Message:	fixed some small things with simError.h
#	User	Rev	Content
1	mmeineke	377	#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	gezelter	417	#include <mpi.h>
16	mmeineke	377	#include "mpiSimulation.hpp"
17	chuckv	436	#define TAKE_THIS_TAG_CHAR 0
18			#define TAKE_THIS_TAG_INT 1
19
20	mmeineke	440	namespace initFile{
21			void nodeZeroError( void );
22			void anonymousNodeDie( void );
23			}
24	chuckv	436
25	mmeineke	440	using namespace initFile;
26
27	mmeineke	377	#endif // is_mpi
28
29			InitializeFromFile :: InitializeFromFile( char *in_name ){
30			#ifdef IS_MPI
31			if (worldRank == 0) {
32			#endif
33
34			c_in_file = fopen(in_name, "r");
35			if(c_in_file == NULL){
36			sprintf(painCave.errMsg,
37			"Cannot open file: %s\n", in_name);
38			painCave.isFatal = 1;
39			simError();
40			}
41
42			strcpy( c_in_name, in_name);
43			#ifdef IS_MPI
44			}
45			strcpy( checkPointMsg, "Infile opened for reading successfully." );
46			MPIcheckPoint();
47			#endif
48			return;
49			}
50
51			InitializeFromFile :: ~InitializeFromFile( ){
52			#ifdef IS_MPI
53			if (worldRank == 0) {
54			#endif
55			int error;
56			error = fclose( c_in_file );
57			if( error ){
58			sprintf( painCave.errMsg,
59			"Error closing %s\n", c_in_name );
60			simError();
61			}
62			#ifdef IS_MPI
63			}
64			strcpy( checkPointMsg, "Infile closed successfully." );
65			MPIcheckPoint();
66			#endif
67
68			return;
69			}
70
71
72			void InitializeFromFile :: read_xyz( SimInfo* the_entry_plug ){
73
74	gezelter	417	int i, j, done, which_node, which_atom; // loop counter
75	mmeineke	377
76			const int BUFFERSIZE = 2000; // size of the read buffer
77			int n_atoms; // the number of atoms
78			char read_buffer[BUFFERSIZE]; //the line buffer for reading
79			#ifdef IS_MPI
80			char send_buffer[BUFFERSIZE];
81			#endif
82
83			char *eof_test; // ptr to see when we reach the end of the file
84			char *parseErr;
85			int procIndex;
86
87			entry_plug = the_entry_plug;
88
89
90			#ifndef IS_MPI
91			eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
92			if( eof_test == NULL ){
93			sprintf( painCave.errMsg,
94			"InitializeFromFile error: error reading 1st line of \"%s\"\n",
95			c_in_name );
96			painCave.isFatal = 1;
97			simError();
98			}
99
100			n_atoms = atoi( read_buffer );
101
102			Atom **atoms = entry_plug->atoms;
103			DirectionalAtom* dAtom;
104
105			if( n_atoms != entry_plug->n_atoms ){
106			sprintf( painCave.errMsg,
107			"Initialize from File error. %s n_atoms, %d, "
108			"does not match the BASS file's n_atoms, %d.\n",
109			c_in_name, n_atoms, entry_plug->n_atoms );
110			painCave.isFatal = 1;
111			simError();
112			}
113
114			//read and toss the comment line
115
116			eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
117			if(eof_test == NULL){
118			sprintf( painCave.errMsg,
119			"error in reading commment in %s\n", c_in_name);
120			painCave.isFatal = 1;
121			simError();
122			}
123
124			for( i=0; i < n_atoms; i++){
125
126			eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
127			if(eof_test == NULL){
128			sprintf(painCave.errMsg,
129			"error in reading file %s\n"
130			"natoms = %d; index = %d\n"
131			"error reading the line from the file.\n",
132			c_in_name, n_atoms, i );
133			painCave.isFatal = 1;
134			simError();
135			}
136
137
138			parseErr = parseDumpLine( read_buffer, i );
139			if( parseErr != NULL ){
140			strcpy( painCave.errMsg, parseErr );
141			painCave.isFatal = 1;
142			simError();
143			}
144			}
145
146
147			// MPI Section of code..........
148			#else //IS_MPI
149
150	chuckv	436	// first thing first, suspend fatalities.
151			painCave.isEventLoop = 1;
152
153			int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone
154			int haveError;
155
156	mmeineke	447	MPI_Status istatus;
157	gezelter	417	int *AtomToProcMap = mpiSim->getAtomToProcMap();
158	mmeineke	377
159	chuckv	436
160			haveError = 0;
161	mmeineke	377	if (worldRank == 0) {
162	chuckv	436
163	mmeineke	377	eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
164			if( eof_test == NULL ){
165			sprintf( painCave.errMsg,
166			"Error reading 1st line of %d \n ",c_in_name);
167	chuckv	436	haveError = 1;
168	mmeineke	377	simError();
169			}
170
171			n_atoms = atoi( read_buffer );
172
173			Atom **atoms = entry_plug->atoms;
174			DirectionalAtom* dAtom;
175
176			// Check to see that the number of atoms in the intial configuration file is the
177			// same as declared in simBass.
178
179			if( n_atoms != mpiSim->getTotAtoms() ){
180			sprintf( painCave.errMsg,
181			"Initialize from File error. %s n_atoms, %d, "
182			"does not match the BASS file's n_atoms, %d.\n",
183			c_in_name, n_atoms, entry_plug->n_atoms );
184	chuckv	436	haveError= 1;
185	mmeineke	377	simError();
186			}
187
188			//read and toss the comment line
189
190			eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
191			if(eof_test == NULL){
192			sprintf( painCave.errMsg,
193			"error in reading commment in %s\n", c_in_name);
194	chuckv	436	haveError= 1;
195	mmeineke	377	simError();
196			}
197
198	chuckv	436	if(haveError) nodeZeroError();
199	gezelter	417
200			for (i=0 ; i < mpiSim->getTotAtoms(); i++) {
201
202	mmeineke	377	eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
203			if(eof_test == NULL){
204			sprintf(painCave.errMsg,
205			"error in reading file %s\n"
206			"natoms = %d; index = %d\n"
207			"error reading the line from the file.\n",
208			c_in_name, n_atoms, i );
209	chuckv	436	haveError= 1;
210	mmeineke	377	simError();
211			}
212
213	chuckv	436	if(haveError) nodeZeroError();
214
215	gezelter	417	// Get the Node number which wants this atom:
216			which_node = AtomToProcMap[i];
217	chuckv	436	if (which_node == 0) {
218	gezelter	417	parseErr = parseDumpLine( read_buffer, i );
219			if( parseErr != NULL ){
220			strcpy( painCave.errMsg, parseErr );
221	chuckv	436	haveError = 1;
222	gezelter	417	simError();
223			}
224	chuckv	436	if(haveError) nodeZeroError();
225			}
226
227			else {
228
229			myStatus = 1;
230	mmeineke	447	MPI_Send(&myStatus, 1, MPI_INT, which_node,
231			TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
232			MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node,
233			TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD);
234			MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
235			MPI_COMM_WORLD);
236			MPI_Recv(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT,
237			MPI_COMM_WORLD, &istatus);
238	chuckv	436
239			if(!myStatus) nodeZeroError();
240	mmeineke	377	}
241			}
242	chuckv	436	myStatus = -1;
243	gezelter	417	for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
244	mmeineke	447	MPI_Send( &myStatus, 1, MPI_INT, j,
245			TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
246	gezelter	417	}
247	gezelter	419
248	gezelter	417	} else {
249	gezelter	419
250	gezelter	417	done = 0;
251			while (!done) {
252	chuckv	436
253	mmeineke	447	MPI_Recv(&myStatus, 1, MPI_INT, 0,
254			TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
255	chuckv	436
256			if(!myStatus) anonymousNodeDie();
257
258			if(myStatus < 0) break;
259
260	mmeineke	447	MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0,
261			TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus);
262			MPI_Recv(&which_atom, 1, MPI_INT, 0,
263			TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
264	chuckv	436
265			myStatus = 1;
266			parseErr = parseDumpLine( read_buffer, which_atom );
267			if( parseErr != NULL ){
268			strcpy( painCave.errMsg, parseErr );
269			myStatus = 0;;
270			simError();
271	mmeineke	377	}
272	chuckv	436
273	mmeineke	447	MPI_Send( &myStatus, 1, MPI_INT, 0,
274			TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
275	chuckv	436
276	mmeineke	377	}
277			}
278	chuckv	436
279			// last thing last, enable fatalities.
280			painCave.isEventLoop = 0;
281
282	mmeineke	377	#endif
283			}
284
285	gezelter	419	char* InitializeFromFile::parseDumpLine(char* readLine, int globalIndex){
286	mmeineke	377
287			char *foo; // the pointer to the current string token
288
289			double rx, ry, rz; // position place holders
290			double vx, vy, vz; // velocity placeholders
291			double q[4]; // the quaternions
292			double jx, jy, jz; // angular velocity placeholders;
293			double qSqr, qLength; // needed to normalize the quaternion vector.
294
295			Atom **atoms = entry_plug->atoms;
296			DirectionalAtom* dAtom;
297
298	gezelter	419	int j, n_atoms, atomIndex;
299	mmeineke	377
300			#ifdef IS_MPI
301			n_atoms = mpiSim->getTotAtoms();
302	gezelter	419	atomIndex=-1;
303			for (j=0; j < mpiSim->getMyNlocal(); j++) {
304			if (atoms[j]->getGlobalIndex() == globalIndex) atomIndex = j;
305			}
306			if (atomIndex == -1) {
307			sprintf( painCave.errMsg,
308			"Initialize from file error. Atom at index %d "
309			"in file %s does not exist on processor %d .\n",
310			globalIndex, c_in_name, mpiSim->getMyNode() );
311			return strdup( painCave.errMsg );
312			}
313	mmeineke	377	#else
314			n_atoms = entry_plug->n_atoms;
315	gezelter	419	atomIndex = globalIndex;
316	mmeineke	377	#endif // is_mpi
317
318			// set the string tokenizer
319
320			foo = strtok(readLine, " ,;\t");
321
322			// check the atom name to the current atom
323
324			if( strcmp( foo, atoms[atomIndex]->getType() ) ){
325			sprintf( painCave.errMsg,
326			"Initialize from file error. Atom %s at index %d "
327			"in file %s does not"
328			" match the BASS atom %s.\n",
329			foo, atomIndex, c_in_name, atoms[atomIndex]->getType() );
330			return strdup( painCave.errMsg );
331			}
332
333			// get the positions
334
335			foo = strtok(NULL, " ,;\t");
336			if(foo == NULL){
337			sprintf( painCave.errMsg,
338			"error in reading postition x from %s\n"
339			"natoms = %d, index = %d\n",
340			c_in_name, n_atoms, atomIndex );
341			return strdup( painCave.errMsg );
342			}
343			rx = atof( foo );
344
345			foo = strtok(NULL, " ,;\t");
346			if(foo == NULL){
347			sprintf( painCave.errMsg,
348			"error in reading postition y from %s\n"
349			"natoms = %d, index = %d\n",
350			c_in_name, n_atoms, atomIndex );
351			return strdup( painCave.errMsg );
352			}
353			ry = atof( foo );
354
355			foo = strtok(NULL, " ,;\t");
356			if(foo == NULL){
357			sprintf( painCave.errMsg,
358			"error in reading postition z from %s\n"
359			"natoms = %d, index = %d\n",
360			c_in_name, n_atoms, atomIndex );
361			return strdup( painCave.errMsg );
362			}
363			rz = atof( foo );
364
365
366			// get the velocities
367
368			foo = strtok(NULL, " ,;\t");
369			if(foo == NULL){
370			sprintf( painCave.errMsg,
371			"error in reading velocity x from %s\n"
372			"natoms = %d, index = %d\n",
373			c_in_name, n_atoms, atomIndex );
374			return strdup( painCave.errMsg );
375			}
376			vx = atof( foo );
377
378			foo = strtok(NULL, " ,;\t");
379			if(foo == NULL){
380			sprintf( painCave.errMsg,
381			"error in reading velocity y from %s\n"
382			"natoms = %d, index = %d\n",
383			c_in_name, n_atoms, atomIndex );
384			return strdup( painCave.errMsg );
385			}
386			vy = atof( foo );
387
388			foo = strtok(NULL, " ,;\t");
389			if(foo == NULL){
390			sprintf( painCave.errMsg,
391			"error in reading velocity z from %s\n"
392			"natoms = %d, index = %d\n",
393			c_in_name, n_atoms, atomIndex );
394			return strdup( painCave.errMsg );
395			}
396			vz = atof( foo );
397
398
399			// get the quaternions
400
401			if( atoms[atomIndex]->isDirectional() ){
402
403			foo = strtok(NULL, " ,;\t");
404			if(foo == NULL){
405			sprintf(painCave.errMsg,
406			"error in reading quaternion 0 from %s\n"
407			"natoms = %d, index = %d\n",
408			c_in_name, n_atoms, atomIndex );
409			return strdup( painCave.errMsg );
410			}
411			q[0] = atof( foo );
412
413			foo = strtok(NULL, " ,;\t");
414			if(foo == NULL){
415			sprintf( painCave.errMsg,
416			"error in reading quaternion 1 from %s\n"
417			"natoms = %d, index = %d\n",
418			c_in_name, n_atoms, atomIndex );
419			return strdup( painCave.errMsg );
420			}
421			q[1] = atof( foo );
422
423			foo = strtok(NULL, " ,;\t");
424			if(foo == NULL){
425			sprintf( painCave.errMsg,
426			"error in reading quaternion 2 from %s\n"
427			"natoms = %d, index = %d\n",
428			c_in_name, n_atoms, atomIndex );
429			return strdup( painCave.errMsg );
430			}
431			q[2] = atof( foo );
432
433			foo = strtok(NULL, " ,;\t");
434			if(foo == NULL){
435			sprintf( painCave.errMsg,
436			"error in reading quaternion 3 from %s\n"
437			"natoms = %d, index = %d\n",
438			c_in_name, n_atoms, atomIndex );
439			return strdup( painCave.errMsg );
440			}
441			q[3] = atof( foo );
442
443			// get the angular velocities
444
445			foo = strtok(NULL, " ,;\t");
446			if(foo == NULL){
447			sprintf( painCave.errMsg,
448			"error in reading angular momentum jx from %s\n"
449			"natoms = %d, index = %d\n",
450			c_in_name, n_atoms, atomIndex );
451			return strdup( painCave.errMsg );
452			}
453			jx = atof( foo );
454
455			foo = strtok(NULL, " ,;\t");
456			if(foo == NULL){
457			sprintf( painCave.errMsg,
458			"error in reading angular momentum jy from %s\n"
459			"natoms = %d, index = %d\n",
460			c_in_name, n_atoms, atomIndex );
461			return strdup( painCave.errMsg );
462			}
463			jy = atof(foo );
464
465			foo = strtok(NULL, " ,;\t");
466			if(foo == NULL){
467			sprintf( painCave.errMsg,
468			"error in reading angular momentum jz from %s\n"
469			"natoms = %d, index = %d\n",
470			c_in_name, n_atoms, atomIndex );
471			return strdup( painCave.errMsg );
472			}
473			jz = atof( foo );
474
475			dAtom = ( DirectionalAtom* )atoms[atomIndex];
476
477			// check that the quaternion vector is normalized
478
479			qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]);
480
481			qLength = sqrt( qSqr );
482			q[0] = q[0] / qLength;
483			q[1] = q[1] / qLength;
484			q[2] = q[2] / qLength;
485			q[3] = q[3] / qLength;
486
487			dAtom->setQ( q );
488
489			// add the angular velocities
490
491			dAtom->setJx( jx );
492			dAtom->setJy( jy );
493			dAtom->setJz( jz );
494			}
495
496			// add the positions and velocities to the atom
497
498			atoms[atomIndex]->setX( rx );
499			atoms[atomIndex]->setY( ry );
500			atoms[atomIndex]->setZ( rz );
501
502			atoms[atomIndex]->set_vx( vx );
503			atoms[atomIndex]->set_vy( vy );
504			atoms[atomIndex]->set_vz( vz );
505
506			return NULL;
507			}
508	chuckv	436
509
510			#ifdef IS_MPI
511
512			// a couple of functions to let us escape the read loop
513
514	mmeineke	440	void initFile::nodeZeroError( void ){
515	chuckv	436	int j, myStatus;
516
517			myStatus = 0;
518			for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
519	mmeineke	447	MPI_Send( &myStatus, 1, MPI_INT, j,
520			TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
521	chuckv	436	}
522
523
524			MPI_Finalize();
525			exit (0);
526
527			}
528
529	mmeineke	440	void initFile::anonymousNodeDie( void ){
530	chuckv	436
531			MPI_Finalize();
532			exit (0);
533			}
534
535			#endif //is_mpi