OOPSE/libmdtools/LJFF.cpp

#include <cstdlib>
#include <cstdio>
#include <cstring>

#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: %s\n"
                 "Have you tried setting the FORCE_PARAM_PATH environment "
                 "vairable?\n",
                 fileName );
        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;
    recieveFrcStruct( &info, mpiAtomStructType );
    
    while( !info.last ){


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

      recieveFrcStruct( &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;
  double dipole = 0.0;
  
  currentAtomType = headAtomType;
  while( currentAtomType != NULL ){
    
    if( currentAtomType->name[0] != '\0' ){
      isError = 0;
      makeAtype( &(currentAtomType->ident),
                 &isLJ,
                 &isSSD,
                 &isDipole,
                 &isGB,
                 &isEAM,
                 &(currentAtomType->epslon),
                 &(currentAtomType->sigma),
                 &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

}


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]->setEpslon( currentAtomType->epslon );
    the_atoms[i]->setSigma( currentAtomType->sigma );
    the_atoms[i]->setIdent( currentAtomType->ident );
    the_atoms[i]->setLJ();

    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:	787
Committed:	Thu Sep 25 19:27:15 2003 UTC (20 years, 9 months ago) by mmeineke
File size:	11833 byte(s)
Log Message:	cleaned things with gcc -Wall and g++ -Wall
#	User	Rev	Content
1	mmeineke	559	#include <cstdlib>
2			#include <cstdio>
3			#include <cstring>
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	mmeineke	561	"the LJFF param file./n",
69	mmeineke	559	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	mmeineke	561	LJFF::LJFF(){
121	mmeineke	559
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	mmeineke	561	strcpy( fileName, "LJFF.frc" );
165			fprintf( stderr,"Trying to open %s\n", fileName );
166	mmeineke	559
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: %s\n"
192			"Have you tried setting the FORCE_PARAM_PATH environment "
193			"vairable?\n",
194			fileName );
195			painCave.isFatal = 1;
196			simError();
197			}
198			}
199
200			#ifdef IS_MPI
201			}
202
203	mmeineke	561	sprintf( checkPointMsg, "LJFF file opened sucessfully." );
204	mmeineke	559	MPIcheckPoint();
205
206			#endif // is_mpi
207			}
208
209
210	mmeineke	561	LJFF::~LJFF(){
211	mmeineke	559
212			if( headAtomType != NULL ) delete headAtomType;
213
214			#ifdef IS_MPI
215			if( worldRank == 0 ){
216			#endif // is_mpi
217
218			fclose( frcFile );
219
220			#ifdef IS_MPI
221			}
222			#endif // is_mpi
223			}
224
225	mmeineke	561	void LJFF::initForceField( int ljMixRule ){
226	mmeineke	559
227			initFortran( ljMixRule, 0 );
228			}
229
230	mmeineke	561	void LJFF::cleanMe( void ){
231	mmeineke	559
232			#ifdef IS_MPI
233
234			// keep the linked list in the mpi version
235
236			#else // is_mpi
237
238			// delete the linked list in the single processor version
239
240			if( headAtomType != NULL ) delete headAtomType;
241
242			#endif // is_mpi
243			}
244
245	mmeineke	561	void LJFF::readParams( void ){
246	mmeineke	559
247			atomStruct info;
248			info.last = 1; // initialize last to have the last set.
249			// if things go well, last will be set to 0
250
251			int identNum;
252
253
254			bigSigma = 0.0;
255			#ifdef IS_MPI
256			if( worldRank == 0 ){
257			#endif
258
259			// read in the atom types.
260
261			headAtomType = new LinkedAtomType;
262
263			fastForward( "AtomTypes", "initializeAtoms" );
264
265			// we are now at the AtomTypes section.
266
267			eof_test = fgets( readLine, sizeof(readLine), frcFile );
268			lineNum++;
269
270
271			// read a line, and start parseing out the atom types
272
273			if( eof_test == NULL ){
274			sprintf( painCave.errMsg,
275			"Error in reading Atoms from force file at line %d.\n",
276			lineNum );
277			painCave.isFatal = 1;
278			simError();
279			}
280
281			identNum = 1;
282			// stop reading at end of file, or at next section
283			while( readLine[0] != '#' && eof_test != NULL ){
284
285			// toss comment lines
286			if( readLine[0] != '!' ){
287
288			// the parser returns 0 if the line was blank
289			if( parseAtom( readLine, lineNum, info ) ){
290			info.ident = identNum;
291			headAtomType->add( info );;
292			identNum++;
293			}
294			}
295			eof_test = fgets( readLine, sizeof(readLine), frcFile );
296			lineNum++;
297			}
298
299			#ifdef IS_MPI
300
301			// send out the linked list to all the other processes
302
303			sprintf( checkPointMsg,
304	mmeineke	561	"LJFF atom structures read successfully." );
305	mmeineke	559	MPIcheckPoint();
306
307			currentAtomType = headAtomType->next; //skip the first element who is a place holder.
308			while( currentAtomType != NULL ){
309			currentAtomType->duplicate( info );
310
311
312
313			sendFrcStruct( &info, mpiAtomStructType );
314
315			sprintf( checkPointMsg,
316			"successfully sent lJ force type: \"%s\"\n",
317			info.name );
318			MPIcheckPoint();
319
320			currentAtomType = currentAtomType->next;
321			}
322			info.last = 1;
323			sendFrcStruct( &info, mpiAtomStructType );
324
325			}
326
327			else{
328
329			// listen for node 0 to send out the force params
330
331			MPIcheckPoint();
332
333			headAtomType = new LinkedAtomType;
334			recieveFrcStruct( &info, mpiAtomStructType );
335
336			while( !info.last ){
337
338
339
340			headAtomType->add( info );
341
342			MPIcheckPoint();
343
344			recieveFrcStruct( &info, mpiAtomStructType );
345			}
346			}
347			#endif // is_mpi
348
349			// call new A_types in fortran
350
351			int isError;
352
353			// dummy variables
354			int isLJ = 1;
355			int isDipole = 0;
356			int isSSD = 0;
357			int isGB = 0;
358	chuckv	631	int isEAM = 0;
359	mmeineke	559	double dipole = 0.0;
360
361			currentAtomType = headAtomType;
362			while( currentAtomType != NULL ){
363
364			if( currentAtomType->name[0] != '\0' ){
365			isError = 0;
366			makeAtype( &(currentAtomType->ident),
367			&isLJ,
368			&isSSD,
369			&isDipole,
370			&isGB,
371	chuckv	631	&isEAM,
372	mmeineke	559	&(currentAtomType->epslon),
373			&(currentAtomType->sigma),
374			&dipole,
375			&isError );
376			if( isError ){
377			sprintf( painCave.errMsg,
378			"Error initializing the \"%s\" atom type in fortran\n",
379			currentAtomType->name );
380			painCave.isFatal = 1;
381			simError();
382			}
383			}
384			currentAtomType = currentAtomType->next;
385			}
386
387			entry_plug->useLJ = 1;
388
389			#ifdef IS_MPI
390			sprintf( checkPointMsg,
391	mmeineke	561	"LJFF atom structures successfully sent to fortran\n" );
392	mmeineke	559	MPIcheckPoint();
393			#endif // is_mpi
394
395			}
396
397
398	mmeineke	561	void LJFF::initializeAtoms( int nAtoms, Atom** the_atoms ){
399	mmeineke	559
400			int i;
401
402			// initialize the atoms
403
404
405			for( i=0; i<nAtoms; i++ ){
406
407			currentAtomType = headAtomType->find( the_atoms[i]->getType() );
408			if( currentAtomType == NULL ){
409			sprintf( painCave.errMsg,
410			"AtomType error, %s not found in force file.\n",
411			the_atoms[i]->getType() );
412			painCave.isFatal = 1;
413			simError();
414			}
415
416			the_atoms[i]->setMass( currentAtomType->mass );
417			the_atoms[i]->setEpslon( currentAtomType->epslon );
418			the_atoms[i]->setSigma( currentAtomType->sigma );
419			the_atoms[i]->setIdent( currentAtomType->ident );
420			the_atoms[i]->setLJ();
421
422			if( bigSigma < currentAtomType->sigma ) bigSigma = currentAtomType->sigma;
423			}
424			}
425
426	mmeineke	561	void LJFF::initializeBonds( int nBonds, Bond** BondArray,
427	mmeineke	559	bond_pair* the_bonds ){
428
429			if( nBonds ){
430			sprintf( painCave.errMsg,
431	mmeineke	561	"LJFF does not support bonds.\n" );
432	mmeineke	559	painCave.isFatal = 1;
433			simError();
434			}
435			}
436
437	mmeineke	561	void LJFF::initializeBends( int nBends, Bend** bendArray,
438	mmeineke	559	bend_set* the_bends ){
439
440			if( nBends ){
441			sprintf( painCave.errMsg,
442	mmeineke	561	"LJFF does not support bends.\n" );
443	mmeineke	559	painCave.isFatal = 1;
444			simError();
445			}
446			}
447
448	mmeineke	561	void LJFF::initializeTorsions( int nTorsions, Torsion** torsionArray,
449	mmeineke	559	torsion_set* the_torsions ){
450
451			if( nTorsions ){
452			sprintf( painCave.errMsg,
453	mmeineke	561	"LJFF does not support torsions.\n" );
454	mmeineke	559	painCave.isFatal = 1;
455			simError();
456			}
457			}
458
459	mmeineke	561	void LJFF::fastForward( char* stopText, char* searchOwner ){
460	mmeineke	559
461			int foundText = 0;
462			char* the_token;
463
464			rewind( frcFile );
465			lineNum = 0;
466
467			eof_test = fgets( readLine, sizeof(readLine), frcFile );
468			lineNum++;
469			if( eof_test == NULL ){
470			sprintf( painCave.errMsg, "Error fast forwarding force file for %s: "
471			" file is empty.\n",
472			searchOwner );
473			painCave.isFatal = 1;
474			simError();
475			}
476
477
478			while( !foundText ){
479			while( eof_test != NULL && readLine[0] != '#' ){
480			eof_test = fgets( readLine, sizeof(readLine), frcFile );
481			lineNum++;
482			}
483			if( eof_test == NULL ){
484			sprintf( painCave.errMsg,
485			"Error fast forwarding force file for %s at "
486			"line %d: file ended unexpectedly.\n",
487			searchOwner,
488			lineNum );
489			painCave.isFatal = 1;
490			simError();
491			}
492
493			the_token = strtok( readLine, " ,;\t#\n" );
494			foundText = !strcmp( stopText, the_token );
495
496			if( !foundText ){
497			eof_test = fgets( readLine, sizeof(readLine), frcFile );
498			lineNum++;
499
500			if( eof_test == NULL ){
501			sprintf( painCave.errMsg,
502			"Error fast forwarding force file for %s at "
503			"line %d: file ended unexpectedly.\n",
504			searchOwner,
505			lineNum );
506			painCave.isFatal = 1;
507			simError();
508			}
509			}
510			}
511			}
512
513
514
515			int LJ_NS::parseAtom( char *lineBuffer, int lineNum, atomStruct &info ){
516
517			char* the_token;
518
519			the_token = strtok( lineBuffer, " \n\t,;" );
520			if( the_token != NULL ){
521
522			strcpy( info.name, the_token );
523
524			if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
525			sprintf( painCave.errMsg,
526			"Error parseing AtomTypes: line %d\n", lineNum );
527			painCave.isFatal = 1;
528			simError();
529			}
530
531			info.mass = atof( the_token );
532
533			if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
534			sprintf( painCave.errMsg,
535			"Error parseing AtomTypes: line %d\n", lineNum );
536			painCave.isFatal = 1;
537			simError();
538			}
539
540			info.epslon = atof( the_token );
541
542			if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
543			sprintf( painCave.errMsg,
544			"Error parseing AtomTypes: line %d\n", lineNum );
545			painCave.isFatal = 1;
546			simError();
547			}
548
549			info.sigma = atof( the_token );
550
551			return 1;
552			}
553			else return 0;
554			}