src/UseTheForce/LJFF.cpp

#include <stdlib.h>
#include <stdio.h>
#include <string.h>

#include <iostream>
using namespace std;

#ifdef IS_MPI
#include <mpi.h>
#endif //is_mpi

#include "ForceFields.hpp"
#include "SRI.hpp"
#include "simError.h"

#include "fortranWrappers.hpp"

#ifdef IS_MPI
#include "mpiForceField.h"
#endif // is_mpi


namespace LJ_NS{

  // Declare the structures that will be passed by the parser and  MPI
  
  typedef struct{
    char name[15];
    double mass;
    double epslon;
    double sigma;
    int ident;
    int last;      //  0  -> default
                   //  1  -> in MPI: tells nodes to stop listening
  } atomStruct;

  int parseAtom( char *lineBuffer, int lineNum, atomStruct &info );
  
#ifdef IS_MPI
  
  MPI_Datatype mpiAtomStructType;
  
#endif

  class LinkedAtomType {
  public:
    LinkedAtomType(){ 
      next = NULL;
      name[0] = '\0';
    }
    ~LinkedAtomType(){ if( next != NULL ) delete next; }

    LinkedAtomType* find(char* key){ 
      if( !strcmp(name, key) ) return this;
      if( next != NULL ) return next->find(key);
      return NULL;
    }
    

    void add( atomStruct &info ){
    
      // check for duplicates
      
      if( !strcmp( info.name, name ) ){
        sprintf( painCave.errMsg,
                 "Duplicate LJ atom type \"%s\" found in "
                 "the LJFF param file./n",
                 name );
        painCave.isFatal = 1;
        simError();
      }
      
      if( next != NULL ) next->add(info);
      else{
        next = new LinkedAtomType();
        strcpy(next->name, info.name);
        next->mass     = info.mass;
        next->epslon   = info.epslon;
        next->sigma    = info.sigma;
        next->ident    = info.ident;
      }
    }
    

#ifdef IS_MPI
    
    void duplicate( atomStruct &info ){
      strcpy(info.name, name);
      info.mass     = mass;
      info.epslon   = epslon;
      info.sigma    = sigma;
      info.ident    = ident;
      info.last     = 0;
    }


#endif

    char name[15];
    double mass;
    double epslon;
    double sigma;
    int ident;
    LinkedAtomType* next;
  };

  LinkedAtomType* headAtomType; 
  LinkedAtomType* currentAtomType;

}

using namespace LJ_NS;

//****************************************************************
// begins the actual forcefield stuff.  
//****************************************************************


LJFF::LJFF(){

  char fileName[200];
  char* ffPath_env = "FORCE_PARAM_PATH";
  char* ffPath;
  char temp[200];

  headAtomType = NULL;
  currentAtomType = NULL;

  // do the funtion wrapping
  wrapMeFF( this );

#ifdef IS_MPI
  int i;
  
   // **********************************************************************
  // Init the atomStruct mpi type

  atomStruct atomProto; // mpiPrototype
  int atomBC[3] = {15,3,2};  // block counts
  MPI_Aint atomDspls[3];           // displacements
  MPI_Datatype atomMbrTypes[3];    // member mpi types

  MPI_Address(&atomProto.name, &atomDspls[0]);
  MPI_Address(&atomProto.mass, &atomDspls[1]);
  MPI_Address(&atomProto.ident, &atomDspls[2]);
  
  atomMbrTypes[0] = MPI_CHAR;
  atomMbrTypes[1] = MPI_DOUBLE;
  atomMbrTypes[2] = MPI_INT;
  
  for (i=2; i >= 0; i--) atomDspls[i] -= atomDspls[0];
  
  MPI_Type_struct(3, atomBC, atomDspls, atomMbrTypes, &mpiAtomStructType);
  MPI_Type_commit(&mpiAtomStructType);

  // ***********************************************************************
  
  if( worldRank == 0 ){
#endif
    
    // generate the force file name
    
    strcpy( fileName, "LJFF.frc" ); 
    // fprintf( stderr,"Trying to open %s\n", fileName );
    
    // attempt to open the file in the current directory first.
    
    frcFile = fopen( fileName, "r" );
    
    if( frcFile == NULL ){
      
      // next see if the force path enviorment variable is set
      
      ffPath = getenv( ffPath_env );
      if( ffPath == NULL ) {
        STR_DEFINE(ffPath, FRC_PATH );
      }
      
      
      strcpy( temp, ffPath );
      strcat( temp, "/" );
      strcat( temp, fileName );
      strcpy( fileName, temp );
      
      frcFile = fopen( fileName, "r" );
      
      if( frcFile == NULL ){

        sprintf( painCave.errMsg,
                 "Error opening the force field parameter file:\n"
                 "\t%s\n"
                 "\tHave you tried setting the FORCE_PARAM_PATH environment "
                 "variable?\n",
                 fileName );
        painCave.severity = OOPSE_ERROR;
        painCave.isFatal = 1;
        simError();
      }
    }
    
#ifdef IS_MPI
  }
  
  sprintf( checkPointMsg, "LJFF file opened sucessfully." );
  MPIcheckPoint();
  
#endif // is_mpi
}


LJFF::~LJFF(){

  if( headAtomType != NULL ) delete headAtomType;

#ifdef IS_MPI
  if( worldRank == 0 ){
#endif // is_mpi
    
    fclose( frcFile );
    
#ifdef IS_MPI
  }
#endif // is_mpi
}

void LJFF::initForceField( int ljMixRule ){
  
  initFortran( ljMixRule, 0 );
}

void LJFF::cleanMe( void ){

#ifdef IS_MPI
  
  // keep the linked list in the mpi version

#else // is_mpi

  // delete the linked list in the single processor version

  if( headAtomType != NULL ) delete headAtomType;

#endif // is_mpi
}

void LJFF::readParams( void ){

  atomStruct info;
  info.last = 1; // initialize last to have the last set. 
                 // if things go well, last will be set to 0

  int identNum;
  

  bigSigma = 0.0;
#ifdef IS_MPI
  if( worldRank == 0 ){
#endif
    
    // read in the atom types.

    headAtomType = new LinkedAtomType;
    
    fastForward( "AtomTypes", "initializeAtoms" );

    // we are now at the AtomTypes section.
    
    eof_test = fgets( readLine, sizeof(readLine), frcFile );
    lineNum++;
    
    
    // read a line, and start parseing out the atom types 

    if( eof_test == NULL ){
      sprintf( painCave.errMsg, 
               "Error in reading Atoms from force file at line %d.\n",
               lineNum );
      painCave.isFatal = 1;
      simError();
    }
    
    identNum = 1;
    // stop reading at end of file, or at next section
    while( readLine[0] != '#' && eof_test != NULL ){

      // toss comment lines
      if( readLine[0] != '!' ){
        
        // the parser returns 0 if the line was blank
        if( parseAtom( readLine, lineNum, info ) ){
          info.ident = identNum;
          headAtomType->add( info );;
          identNum++;
        }
      }
      eof_test = fgets( readLine, sizeof(readLine), frcFile );
      lineNum++;
    }

#ifdef IS_MPI
    
    // send out the linked list to all the other processes

    sprintf( checkPointMsg,
             "LJFF atom structures read successfully." );
    MPIcheckPoint();

    currentAtomType = headAtomType->next; //skip the first element who is a place holder.
    while( currentAtomType != NULL ){
      currentAtomType->duplicate( info );

 
      sendFrcStruct( &info, mpiAtomStructType );

      sprintf( checkPointMsg,
               "successfully sent lJ force type: \"%s\"\n",
               info.name );
      MPIcheckPoint();

      currentAtomType = currentAtomType->next;
    }
    info.last = 1;
    sendFrcStruct( &info, mpiAtomStructType );
    
  }

  else{
    
    // listen for node 0 to send out the force params
    
    MPIcheckPoint();

    headAtomType = new LinkedAtomType;
    receiveFrcStruct( &info, mpiAtomStructType );
    
    while( !info.last ){


      headAtomType->add( info );
      
      MPIcheckPoint();

      receiveFrcStruct( &info, mpiAtomStructType );
    }
  }
#endif // is_mpi

  // call new A_types in fortran
  
  int isError;

  // dummy variables
  int isLJ = 1;
  int isDipole = 0;
  int isSSD = 0;
  int isGB = 0;
  int isEAM = 0;
  int isCharge = 0;
  double charge = 0.0;
  double dipole = 0.0;
  
  currentAtomType = headAtomType;
  while( currentAtomType != NULL ){
    
    if( currentAtomType->name[0] != '\0' ){
      isError = 0;
      makeAtype( &(currentAtomType->ident),
                 &isLJ,
                 &isSSD,
                 &isDipole,
                 &isGB,
                 &isEAM,
                 &isCharge,
                 &(currentAtomType->epslon),
                 &(currentAtomType->sigma),
                 &charge,
                 &dipole,
                 &isError );
      if( isError ){
        sprintf( painCave.errMsg,
                 "Error initializing the \"%s\" atom type in fortran\n",
                 currentAtomType->name );
        painCave.isFatal = 1;
        simError();
      }
    }
    currentAtomType = currentAtomType->next;
  }
      
  entry_plug->useLJ = 1;

#ifdef IS_MPI
  sprintf( checkPointMsg,
           "LJFF atom structures successfully sent to fortran\n" );
  MPIcheckPoint();
#endif // is_mpi

}

double LJFF::getAtomTypeMass (char* atomType) {

  currentAtomType = headAtomType->find( atomType );
  if( currentAtomType == NULL ){
    sprintf( painCave.errMsg,
            "AtomType error, %s not found in force file.\n",
             atomType );
    painCave.isFatal = 1;
    simError();
  }

  return currentAtomType->mass;
}

void LJFF::initializeAtoms( int nAtoms, Atom** the_atoms ){
  
  int i;

  // initialize the atoms
  

  for( i=0; i<nAtoms; i++ ){
    
    currentAtomType = headAtomType->find( the_atoms[i]->getType() );
    if( currentAtomType == NULL ){
      sprintf( painCave.errMsg, 
               "AtomType error, %s not found in force file.\n",
               the_atoms[i]->getType() );
      painCave.isFatal = 1;
      simError();
    }
    
    the_atoms[i]->setMass( currentAtomType->mass );
    the_atoms[i]->setIdent( currentAtomType->ident );

    if( bigSigma < currentAtomType->sigma ) bigSigma = currentAtomType->sigma;
  }
}

void LJFF::initializeBonds( int nBonds, Bond** BondArray,
                             bond_pair* the_bonds ){
  
    if( nBonds ){
      sprintf( painCave.errMsg,
               "LJFF does not support bonds.\n" );
      painCave.isFatal = 1;
      simError();
    }
}

void LJFF::initializeBends( int nBends, Bend** bendArray,
                             bend_set* the_bends ){

    if( nBends ){
      sprintf( painCave.errMsg,
               "LJFF does not support bends.\n" );
      painCave.isFatal = 1;
      simError();
    }
}

void LJFF::initializeTorsions( int nTorsions, Torsion** torsionArray,
                                torsion_set* the_torsions ){

    if( nTorsions ){
      sprintf( painCave.errMsg,
               "LJFF does not support torsions.\n" );
      painCave.isFatal = 1;
      simError();
    }
}

void LJFF::fastForward( char* stopText, char* searchOwner ){

  int foundText = 0;
  char* the_token;

  rewind( frcFile );
  lineNum = 0;

  eof_test = fgets( readLine, sizeof(readLine), frcFile );
  lineNum++;
  if( eof_test == NULL ){
    sprintf( painCave.errMsg, "Error fast forwarding force file for %s: "
             " file is empty.\n",
             searchOwner );
    painCave.isFatal = 1;
    simError();
  }
  
  
  while( !foundText ){
    while( eof_test != NULL && readLine[0] != '#' ){
      eof_test = fgets( readLine, sizeof(readLine), frcFile );
      lineNum++;
    }
    if( eof_test == NULL ){
      sprintf( painCave.errMsg,
               "Error fast forwarding force file for %s at "
               "line %d: file ended unexpectedly.\n",
               searchOwner,
               lineNum );
      painCave.isFatal = 1;
      simError();
    }
    
    the_token = strtok( readLine, " ,;\t#\n" );
    foundText = !strcmp( stopText, the_token );
    
    if( !foundText ){
      eof_test = fgets( readLine, sizeof(readLine), frcFile );
      lineNum++;
      
      if( eof_test == NULL ){
        sprintf( painCave.errMsg, 
                 "Error fast forwarding force file for %s at "
                 "line %d: file ended unexpectedly.\n",
                 searchOwner,
                 lineNum );
        painCave.isFatal = 1;
        simError();
      } 
    }
  }  
}


int LJ_NS::parseAtom( char *lineBuffer, int lineNum,  atomStruct &info ){

  char* the_token;
  
  the_token = strtok( lineBuffer, " \n\t,;" );
  if( the_token != NULL ){
    
    strcpy( info.name, the_token );
          
    if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
      sprintf( painCave.errMsg, 
               "Error parseing AtomTypes: line %d\n", lineNum );
      painCave.isFatal = 1;
      simError();
    }
    
    info.mass = atof( the_token );
    
    if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
      sprintf( painCave.errMsg, 
               "Error parseing AtomTypes: line %d\n", lineNum );
      painCave.isFatal = 1;
      simError();
    }
        
    info.epslon = atof( the_token );
          
    if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
      sprintf( painCave.errMsg, 
               "Error parseing AtomTypes: line %d\n", lineNum );
      painCave.isFatal = 1;
      simError();
    }
        
    info.sigma = atof( the_token );
    
    return 1;
  }
  else return 0;
}


Revision:	2
Committed:	Fri Sep 24 04:16:43 2004 UTC (20 years, 7 months ago) by gezelter
File size:	12197 byte(s)
Log Message:	Import of OOPSE v. 2.0
#	User	Rev	Content
1	gezelter	2	#include <stdlib.h>
2			#include <stdio.h>
3			#include <string.h>
4
5			#include <iostream>
6			using namespace std;
7
8			#ifdef IS_MPI
9			#include <mpi.h>
10			#endif //is_mpi
11
12			#include "ForceFields.hpp"
13			#include "SRI.hpp"
14			#include "simError.h"
15
16			#include "fortranWrappers.hpp"
17
18			#ifdef IS_MPI
19			#include "mpiForceField.h"
20			#endif // is_mpi
21
22
23
24			namespace LJ_NS{
25
26			// Declare the structures that will be passed by the parser and MPI
27
28			typedef struct{
29			char name[15];
30			double mass;
31			double epslon;
32			double sigma;
33			int ident;
34			int last; // 0 -> default
35			// 1 -> in MPI: tells nodes to stop listening
36			} atomStruct;
37
38			int parseAtom( char *lineBuffer, int lineNum, atomStruct &info );
39
40			#ifdef IS_MPI
41
42			MPI_Datatype mpiAtomStructType;
43
44			#endif
45
46			class LinkedAtomType {
47			public:
48			LinkedAtomType(){
49			next = NULL;
50			name[0] = '\0';
51			}
52			~LinkedAtomType(){ if( next != NULL ) delete next; }
53
54			LinkedAtomType* find(char* key){
55			if( !strcmp(name, key) ) return this;
56			if( next != NULL ) return next->find(key);
57			return NULL;
58			}
59
60
61			void add( atomStruct &info ){
62
63			// check for duplicates
64
65			if( !strcmp( info.name, name ) ){
66			sprintf( painCave.errMsg,
67			"Duplicate LJ atom type \"%s\" found in "
68			"the LJFF param file./n",
69			name );
70			painCave.isFatal = 1;
71			simError();
72			}
73
74			if( next != NULL ) next->add(info);
75			else{
76			next = new LinkedAtomType();
77			strcpy(next->name, info.name);
78			next->mass = info.mass;
79			next->epslon = info.epslon;
80			next->sigma = info.sigma;
81			next->ident = info.ident;
82			}
83			}
84
85
86			#ifdef IS_MPI
87
88			void duplicate( atomStruct &info ){
89			strcpy(info.name, name);
90			info.mass = mass;
91			info.epslon = epslon;
92			info.sigma = sigma;
93			info.ident = ident;
94			info.last = 0;
95			}
96
97
98			#endif
99
100			char name[15];
101			double mass;
102			double epslon;
103			double sigma;
104			int ident;
105			LinkedAtomType* next;
106			};
107
108			LinkedAtomType* headAtomType;
109			LinkedAtomType* currentAtomType;
110
111			}
112
113			using namespace LJ_NS;
114
115			//****************************************************************
116			// begins the actual forcefield stuff.
117			//****************************************************************
118
119
120			LJFF::LJFF(){
121
122			char fileName[200];
123			char* ffPath_env = "FORCE_PARAM_PATH";
124			char* ffPath;
125			char temp[200];
126
127			headAtomType = NULL;
128			currentAtomType = NULL;
129
130			// do the funtion wrapping
131			wrapMeFF( this );
132
133			#ifdef IS_MPI
134			int i;
135
136			// **********************************************************************
137			// Init the atomStruct mpi type
138
139			atomStruct atomProto; // mpiPrototype
140			int atomBC[3] = {15,3,2}; // block counts
141			MPI_Aint atomDspls[3]; // displacements
142			MPI_Datatype atomMbrTypes[3]; // member mpi types
143
144			MPI_Address(&atomProto.name, &atomDspls[0]);
145			MPI_Address(&atomProto.mass, &atomDspls[1]);
146			MPI_Address(&atomProto.ident, &atomDspls[2]);
147
148			atomMbrTypes[0] = MPI_CHAR;
149			atomMbrTypes[1] = MPI_DOUBLE;
150			atomMbrTypes[2] = MPI_INT;
151
152			for (i=2; i >= 0; i--) atomDspls[i] -= atomDspls[0];
153
154			MPI_Type_struct(3, atomBC, atomDspls, atomMbrTypes, &mpiAtomStructType);
155			MPI_Type_commit(&mpiAtomStructType);
156
157			// ***********************************************************************
158
159			if( worldRank == 0 ){
160			#endif
161
162			// generate the force file name
163
164			strcpy( fileName, "LJFF.frc" );
165			// fprintf( stderr,"Trying to open %s\n", fileName );
166
167			// attempt to open the file in the current directory first.
168
169			frcFile = fopen( fileName, "r" );
170
171			if( frcFile == NULL ){
172
173			// next see if the force path enviorment variable is set
174
175			ffPath = getenv( ffPath_env );
176			if( ffPath == NULL ) {
177			STR_DEFINE(ffPath, FRC_PATH );
178			}
179
180
181			strcpy( temp, ffPath );
182			strcat( temp, "/" );
183			strcat( temp, fileName );
184			strcpy( fileName, temp );
185
186			frcFile = fopen( fileName, "r" );
187
188			if( frcFile == NULL ){
189
190			sprintf( painCave.errMsg,
191			"Error opening the force field parameter file:\n"
192			"\t%s\n"
193			"\tHave you tried setting the FORCE_PARAM_PATH environment "
194			"variable?\n",
195			fileName );
196			painCave.severity = OOPSE_ERROR;
197			painCave.isFatal = 1;
198			simError();
199			}
200			}
201
202			#ifdef IS_MPI
203			}
204
205			sprintf( checkPointMsg, "LJFF file opened sucessfully." );
206			MPIcheckPoint();
207
208			#endif // is_mpi
209			}
210
211
212			LJFF::~LJFF(){
213
214			if( headAtomType != NULL ) delete headAtomType;
215
216			#ifdef IS_MPI
217			if( worldRank == 0 ){
218			#endif // is_mpi
219
220			fclose( frcFile );
221
222			#ifdef IS_MPI
223			}
224			#endif // is_mpi
225			}
226
227			void LJFF::initForceField( int ljMixRule ){
228
229			initFortran( ljMixRule, 0 );
230			}
231
232			void LJFF::cleanMe( void ){
233
234			#ifdef IS_MPI
235
236			// keep the linked list in the mpi version
237
238			#else // is_mpi
239
240			// delete the linked list in the single processor version
241
242			if( headAtomType != NULL ) delete headAtomType;
243
244			#endif // is_mpi
245			}
246
247			void LJFF::readParams( void ){
248
249			atomStruct info;
250			info.last = 1; // initialize last to have the last set.
251			// if things go well, last will be set to 0
252
253			int identNum;
254
255
256			bigSigma = 0.0;
257			#ifdef IS_MPI
258			if( worldRank == 0 ){
259			#endif
260
261			// read in the atom types.
262
263			headAtomType = new LinkedAtomType;
264
265			fastForward( "AtomTypes", "initializeAtoms" );
266
267			// we are now at the AtomTypes section.
268
269			eof_test = fgets( readLine, sizeof(readLine), frcFile );
270			lineNum++;
271
272
273			// read a line, and start parseing out the atom types
274
275			if( eof_test == NULL ){
276			sprintf( painCave.errMsg,
277			"Error in reading Atoms from force file at line %d.\n",
278			lineNum );
279			painCave.isFatal = 1;
280			simError();
281			}
282
283			identNum = 1;
284			// stop reading at end of file, or at next section
285			while( readLine[0] != '#' && eof_test != NULL ){
286
287			// toss comment lines
288			if( readLine[0] != '!' ){
289
290			// the parser returns 0 if the line was blank
291			if( parseAtom( readLine, lineNum, info ) ){
292			info.ident = identNum;
293			headAtomType->add( info );;
294			identNum++;
295			}
296			}
297			eof_test = fgets( readLine, sizeof(readLine), frcFile );
298			lineNum++;
299			}
300
301			#ifdef IS_MPI
302
303			// send out the linked list to all the other processes
304
305			sprintf( checkPointMsg,
306			"LJFF atom structures read successfully." );
307			MPIcheckPoint();
308
309			currentAtomType = headAtomType->next; //skip the first element who is a place holder.
310			while( currentAtomType != NULL ){
311			currentAtomType->duplicate( info );
312
313
314
315			sendFrcStruct( &info, mpiAtomStructType );
316
317			sprintf( checkPointMsg,
318			"successfully sent lJ force type: \"%s\"\n",
319			info.name );
320			MPIcheckPoint();
321
322			currentAtomType = currentAtomType->next;
323			}
324			info.last = 1;
325			sendFrcStruct( &info, mpiAtomStructType );
326
327			}
328
329			else{
330
331			// listen for node 0 to send out the force params
332
333			MPIcheckPoint();
334
335			headAtomType = new LinkedAtomType;
336			receiveFrcStruct( &info, mpiAtomStructType );
337
338			while( !info.last ){
339
340
341
342			headAtomType->add( info );
343
344			MPIcheckPoint();
345
346			receiveFrcStruct( &info, mpiAtomStructType );
347			}
348			}
349			#endif // is_mpi
350
351			// call new A_types in fortran
352
353			int isError;
354
355			// dummy variables
356			int isLJ = 1;
357			int isDipole = 0;
358			int isSSD = 0;
359			int isGB = 0;
360			int isEAM = 0;
361			int isCharge = 0;
362			double charge = 0.0;
363			double dipole = 0.0;
364
365			currentAtomType = headAtomType;
366			while( currentAtomType != NULL ){
367
368			if( currentAtomType->name[0] != '\0' ){
369			isError = 0;
370			makeAtype( &(currentAtomType->ident),
371			&isLJ,
372			&isSSD,
373			&isDipole,
374			&isGB,
375			&isEAM,
376			&isCharge,
377			&(currentAtomType->epslon),
378			&(currentAtomType->sigma),
379			&charge,
380			&dipole,
381			&isError );
382			if( isError ){
383			sprintf( painCave.errMsg,
384			"Error initializing the \"%s\" atom type in fortran\n",
385			currentAtomType->name );
386			painCave.isFatal = 1;
387			simError();
388			}
389			}
390			currentAtomType = currentAtomType->next;
391			}
392
393			entry_plug->useLJ = 1;
394
395			#ifdef IS_MPI
396			sprintf( checkPointMsg,
397			"LJFF atom structures successfully sent to fortran\n" );
398			MPIcheckPoint();
399			#endif // is_mpi
400
401			}
402
403			double LJFF::getAtomTypeMass (char* atomType) {
404
405			currentAtomType = headAtomType->find( atomType );
406			if( currentAtomType == NULL ){
407			sprintf( painCave.errMsg,
408			"AtomType error, %s not found in force file.\n",
409			atomType );
410			painCave.isFatal = 1;
411			simError();
412			}
413
414			return currentAtomType->mass;
415			}
416
417			void LJFF::initializeAtoms( int nAtoms, Atom** the_atoms ){
418
419			int i;
420
421			// initialize the atoms
422
423
424			for( i=0; i<nAtoms; i++ ){
425
426			currentAtomType = headAtomType->find( the_atoms[i]->getType() );
427			if( currentAtomType == NULL ){
428			sprintf( painCave.errMsg,
429			"AtomType error, %s not found in force file.\n",
430			the_atoms[i]->getType() );
431			painCave.isFatal = 1;
432			simError();
433			}
434
435			the_atoms[i]->setMass( currentAtomType->mass );
436			the_atoms[i]->setIdent( currentAtomType->ident );
437
438			if( bigSigma < currentAtomType->sigma ) bigSigma = currentAtomType->sigma;
439			}
440			}
441
442			void LJFF::initializeBonds( int nBonds, Bond** BondArray,
443			bond_pair* the_bonds ){
444
445			if( nBonds ){
446			sprintf( painCave.errMsg,
447			"LJFF does not support bonds.\n" );
448			painCave.isFatal = 1;
449			simError();
450			}
451			}
452
453			void LJFF::initializeBends( int nBends, Bend** bendArray,
454			bend_set* the_bends ){
455
456			if( nBends ){
457			sprintf( painCave.errMsg,
458			"LJFF does not support bends.\n" );
459			painCave.isFatal = 1;
460			simError();
461			}
462			}
463
464			void LJFF::initializeTorsions( int nTorsions, Torsion** torsionArray,
465			torsion_set* the_torsions ){
466
467			if( nTorsions ){
468			sprintf( painCave.errMsg,
469			"LJFF does not support torsions.\n" );
470			painCave.isFatal = 1;
471			simError();
472			}
473			}
474
475			void LJFF::fastForward( char* stopText, char* searchOwner ){
476
477			int foundText = 0;
478			char* the_token;
479
480			rewind( frcFile );
481			lineNum = 0;
482
483			eof_test = fgets( readLine, sizeof(readLine), frcFile );
484			lineNum++;
485			if( eof_test == NULL ){
486			sprintf( painCave.errMsg, "Error fast forwarding force file for %s: "
487			" file is empty.\n",
488			searchOwner );
489			painCave.isFatal = 1;
490			simError();
491			}
492
493
494			while( !foundText ){
495			while( eof_test != NULL && readLine[0] != '#' ){
496			eof_test = fgets( readLine, sizeof(readLine), frcFile );
497			lineNum++;
498			}
499			if( eof_test == NULL ){
500			sprintf( painCave.errMsg,
501			"Error fast forwarding force file for %s at "
502			"line %d: file ended unexpectedly.\n",
503			searchOwner,
504			lineNum );
505			painCave.isFatal = 1;
506			simError();
507			}
508
509			the_token = strtok( readLine, " ,;\t#\n" );
510			foundText = !strcmp( stopText, the_token );
511
512			if( !foundText ){
513			eof_test = fgets( readLine, sizeof(readLine), frcFile );
514			lineNum++;
515
516			if( eof_test == NULL ){
517			sprintf( painCave.errMsg,
518			"Error fast forwarding force file for %s at "
519			"line %d: file ended unexpectedly.\n",
520			searchOwner,
521			lineNum );
522			painCave.isFatal = 1;
523			simError();
524			}
525			}
526			}
527			}
528
529
530
531			int LJ_NS::parseAtom( char *lineBuffer, int lineNum, atomStruct &info ){
532
533			char* the_token;
534
535			the_token = strtok( lineBuffer, " \n\t,;" );
536			if( the_token != NULL ){
537
538			strcpy( info.name, the_token );
539
540			if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
541			sprintf( painCave.errMsg,
542			"Error parseing AtomTypes: line %d\n", lineNum );
543			painCave.isFatal = 1;
544			simError();
545			}
546
547			info.mass = atof( the_token );
548
549			if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
550			sprintf( painCave.errMsg,
551			"Error parseing AtomTypes: line %d\n", lineNum );
552			painCave.isFatal = 1;
553			simError();
554			}
555
556			info.epslon = atof( the_token );
557
558			if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
559			sprintf( painCave.errMsg,
560			"Error parseing AtomTypes: line %d\n", lineNum );
561			painCave.isFatal = 1;
562			simError();
563			}
564
565			info.sigma = atof( the_token );
566
567			return 1;
568			}
569			else return 0;
570			}
571
572