OOPSE/libmdtools/LJ_FF.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 LJ_FF 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.  
//****************************************************************


LJ_FF::LJ_FF(){

  char fileName[200];
  char* ffPath_env = "FORCE_PARAM_PATH";
  char* ffPath;
  char temp[200];
  char errMsg[1000];

  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, "LJ_FF.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, "LJ_FF file opened sucessfully." );
  MPIcheckPoint();
  
#endif // is_mpi
}


LJ_FF::~LJ_FF(){

  if( headAtomType != NULL ) delete headAtomType;

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

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

void LJ_FF::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 LJ_FF::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 i;
  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,
             "LJ_FF 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;
  double w0 = 0.0;
  double v0 = 0.0;
  double dipole = 0.0;
  double GB_dummy = 0.0;
  
  
  currentAtomType = headAtomType;
  while( currentAtomType != NULL ){
    
    if( currentAtomType->name[0] != '\0' ){
      isError = 0;
      makeAtype( &(currentAtomType->ident),
                 &isLJ,
                 &isSSD,
                 &isDipole,
                 &isGB,
                 &(currentAtomType->epslon),
                 &(currentAtomType->sigma),
                 &dipole,
                 &w0,
                 &v0,
                 &GB_dummy,
                 &GB_dummy,
                 &GB_dummy,
                 &GB_dummy,
                 &GB_dummy,
                 &GB_dummy,
                 &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,
           "LJ_FF atom structures successfully sent to fortran\n" );
  MPIcheckPoint();
#endif // is_mpi

}


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

  // initialize the atoms
  

  Atom* thisAtom;

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

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

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

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

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

void LJ_FF::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:	447
Committed:	Thu Apr 3 20:21:54 2003 UTC (21 years, 3 months ago) by mmeineke
File size:	12046 byte(s)
Log Message:	fixed some small things with simError.h
#	User	Rev	Content
1	mmeineke	377	#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	mmeineke	420
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 LJ_FF param file./n",
69			name );
70			painCave.isFatal = 1;
71			simError();
72			}
73
74			if( next != NULL ) next->add(info);
75			else{
76	mmeineke	424	next = new LinkedAtomType();
77	mmeineke	420	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	mmeineke	377	}
112
113			using namespace LJ_NS;
114
115			//****************************************************************
116			// begins the actual forcefield stuff.
117			//****************************************************************
118
119
120			LJ_FF::LJ_FF(){
121
122			char fileName[200];
123			char* ffPath_env = "FORCE_PARAM_PATH";
124			char* ffPath;
125			char temp[200];
126			char errMsg[1000];
127
128	mmeineke	420	headAtomType = NULL;
129			currentAtomType = NULL;
130
131	mmeineke	377	// do the funtion wrapping
132			wrapMeFF( this );
133
134			#ifdef IS_MPI
135			int i;
136
137			// **********************************************************************
138			// Init the atomStruct mpi type
139
140			atomStruct atomProto; // mpiPrototype
141			int atomBC[3] = {15,3,2}; // block counts
142			MPI_Aint atomDspls[3]; // displacements
143			MPI_Datatype atomMbrTypes[3]; // member mpi types
144
145			MPI_Address(&atomProto.name, &atomDspls[0]);
146			MPI_Address(&atomProto.mass, &atomDspls[1]);
147			MPI_Address(&atomProto.ident, &atomDspls[2]);
148
149			atomMbrTypes[0] = MPI_CHAR;
150			atomMbrTypes[1] = MPI_DOUBLE;
151			atomMbrTypes[2] = MPI_INT;
152
153			for (i=2; i >= 0; i--) atomDspls[i] -= atomDspls[0];
154
155			MPI_Type_struct(3, atomBC, atomDspls, atomMbrTypes, &mpiAtomStructType);
156			MPI_Type_commit(&mpiAtomStructType);
157
158			// ***********************************************************************
159
160			if( worldRank == 0 ){
161			#endif
162
163			// generate the force file name
164
165			strcpy( fileName, "LJ_FF.frc" );
166			// fprintf( stderr,"Trying to open %s\n", fileName );
167
168			// attempt to open the file in the current directory first.
169
170			frcFile = fopen( fileName, "r" );
171
172			if( frcFile == NULL ){
173
174			// next see if the force path enviorment variable is set
175
176			ffPath = getenv( ffPath_env );
177			if( ffPath == NULL ) {
178			STR_DEFINE(ffPath, FRC_PATH );
179			}
180
181
182			strcpy( temp, ffPath );
183			strcat( temp, "/" );
184			strcat( temp, fileName );
185			strcpy( fileName, temp );
186
187			frcFile = fopen( fileName, "r" );
188
189			if( frcFile == NULL ){
190
191			sprintf( painCave.errMsg,
192			"Error opening the force field parameter file: %s\n"
193			"Have you tried setting the FORCE_PARAM_PATH environment "
194			"vairable?\n",
195			fileName );
196			painCave.isFatal = 1;
197			simError();
198			}
199			}
200
201			#ifdef IS_MPI
202			}
203
204			sprintf( checkPointMsg, "LJ_FF file opened sucessfully." );
205			MPIcheckPoint();
206
207			#endif // is_mpi
208			}
209
210
211			LJ_FF::~LJ_FF(){
212
213	mmeineke	420	if( headAtomType != NULL ) delete headAtomType;
214
215	mmeineke	377	#ifdef IS_MPI
216			if( worldRank == 0 ){
217			#endif // is_mpi
218
219			fclose( frcFile );
220
221			#ifdef IS_MPI
222			}
223			#endif // is_mpi
224			}
225
226			void LJ_FF::initForceField( int ljMixRule ){
227
228			initFortran( ljMixRule, 0 );
229			}
230
231	mmeineke	420	void LJ_FF::cleanMe( void ){
232	mmeineke	377
233	mmeineke	420	#ifdef IS_MPI
234	mmeineke	377
235	mmeineke	420	// keep the linked list in the mpi version
236	mmeineke	377
237	mmeineke	420	#else // is_mpi
238	mmeineke	377
239	mmeineke	420	// delete the linked list in the single processor version
240	mmeineke	377
241	mmeineke	420	if( headAtomType != NULL ) delete headAtomType;
242	mmeineke	377
243	mmeineke	420	#endif // is_mpi
244			}
245	mmeineke	377
246	mmeineke	420	void LJ_FF::readParams( void ){
247	mmeineke	377
248			atomStruct info;
249			info.last = 1; // initialize last to have the last set.
250			// if things go well, last will be set to 0
251
252			int i;
253			int identNum;
254
255	mmeineke	420
256			bigSigma = 0.0;
257	mmeineke	377	#ifdef IS_MPI
258			if( worldRank == 0 ){
259			#endif
260
261			// read in the atom types.
262
263	mmeineke	420	headAtomType = new LinkedAtomType;
264	mmeineke	377
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			"LJ_FF 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	mmeineke	428	headAtomType = new LinkedAtomType;
336	mmeineke	377	recieveFrcStruct( &info, mpiAtomStructType );
337
338			while( !info.last ){
339
340
341
342			headAtomType->add( info );
343
344			MPIcheckPoint();
345
346			recieveFrcStruct( &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			double w0 = 0.0;
361			double v0 = 0.0;
362			double dipole = 0.0;
363			double GB_dummy = 0.0;
364
365
366			currentAtomType = headAtomType;
367			while( currentAtomType != NULL ){
368
369			if( currentAtomType->name[0] != '\0' ){
370			isError = 0;
371			makeAtype( &(currentAtomType->ident),
372			&isLJ,
373			&isSSD,
374			&isDipole,
375			&isGB,
376			&(currentAtomType->epslon),
377			&(currentAtomType->sigma),
378			&dipole,
379			&w0,
380			&v0,
381			&GB_dummy,
382			&GB_dummy,
383			&GB_dummy,
384			&GB_dummy,
385			&GB_dummy,
386			&GB_dummy,
387			&isError );
388			if( isError ){
389			sprintf( painCave.errMsg,
390			"Error initializing the \"%s\" atom type in fortran\n",
391			currentAtomType->name );
392			painCave.isFatal = 1;
393			simError();
394			}
395			}
396			currentAtomType = currentAtomType->next;
397			}
398
399	mmeineke	433	entry_plug->useLJ = 1;
400
401	mmeineke	377	#ifdef IS_MPI
402			sprintf( checkPointMsg,
403			"LJ_FF atom structures successfully sent to fortran\n" );
404			MPIcheckPoint();
405			#endif // is_mpi
406
407	mmeineke	420	}
408
409
410			void LJ_FF::initializeAtoms( int nAtoms, Atom** the_atoms ){
411	mmeineke	377
412	mmeineke	420	int i;
413	mmeineke	377
414			// initialize the atoms
415
416	mmeineke	420
417	mmeineke	377	Atom* thisAtom;
418
419			for( i=0; i<nAtoms; i++ ){
420
421			currentAtomType = headAtomType->find( the_atoms[i]->getType() );
422			if( currentAtomType == NULL ){
423			sprintf( painCave.errMsg,
424			"AtomType error, %s not found in force file.\n",
425			the_atoms[i]->getType() );
426			painCave.isFatal = 1;
427			simError();
428			}
429
430			the_atoms[i]->setMass( currentAtomType->mass );
431			the_atoms[i]->setEpslon( currentAtomType->epslon );
432			the_atoms[i]->setSigma( currentAtomType->sigma );
433			the_atoms[i]->setIdent( currentAtomType->ident );
434			the_atoms[i]->setLJ();
435
436			if( bigSigma < currentAtomType->sigma ) bigSigma = currentAtomType->sigma;
437			}
438			}
439
440	mmeineke	420	void LJ_FF::initializeBonds( int nBonds, Bond** BondArray,
441			bond_pair* the_bonds ){
442	mmeineke	377
443	mmeineke	420	if( nBonds ){
444	mmeineke	377	sprintf( painCave.errMsg,
445			"LJ_FF does not support bonds.\n" );
446			painCave.isFatal = 1;
447			simError();
448			}
449			}
450
451	mmeineke	420	void LJ_FF::initializeBends( int nBends, Bend** bendArray,
452			bend_set* the_bends ){
453	mmeineke	377
454	mmeineke	420	if( nBends ){
455	mmeineke	377	sprintf( painCave.errMsg,
456			"LJ_FF does not support bends.\n" );
457			painCave.isFatal = 1;
458			simError();
459			}
460			}
461
462	mmeineke	420	void LJ_FF::initializeTorsions( int nTorsions, Torsion** torsionArray,
463			torsion_set* the_torsions ){
464	mmeineke	377
465	mmeineke	420	if( nTorsions ){
466	mmeineke	377	sprintf( painCave.errMsg,
467			"LJ_FF does not support torsions.\n" );
468			painCave.isFatal = 1;
469			simError();
470			}
471			}
472
473			void LJ_FF::fastForward( char* stopText, char* searchOwner ){
474
475			int foundText = 0;
476			char* the_token;
477
478			rewind( frcFile );
479			lineNum = 0;
480
481			eof_test = fgets( readLine, sizeof(readLine), frcFile );
482			lineNum++;
483			if( eof_test == NULL ){
484			sprintf( painCave.errMsg, "Error fast forwarding force file for %s: "
485			" file is empty.\n",
486			searchOwner );
487			painCave.isFatal = 1;
488			simError();
489			}
490
491
492			while( !foundText ){
493			while( eof_test != NULL && readLine[0] != '#' ){
494			eof_test = fgets( readLine, sizeof(readLine), frcFile );
495			lineNum++;
496			}
497			if( eof_test == NULL ){
498			sprintf( painCave.errMsg,
499			"Error fast forwarding force file for %s at "
500			"line %d: file ended unexpectedly.\n",
501			searchOwner,
502			lineNum );
503			painCave.isFatal = 1;
504			simError();
505			}
506
507			the_token = strtok( readLine, " ,;\t#\n" );
508			foundText = !strcmp( stopText, the_token );
509
510			if( !foundText ){
511			eof_test = fgets( readLine, sizeof(readLine), frcFile );
512			lineNum++;
513
514			if( eof_test == NULL ){
515			sprintf( painCave.errMsg,
516			"Error fast forwarding force file for %s at "
517			"line %d: file ended unexpectedly.\n",
518			searchOwner,
519			lineNum );
520			painCave.isFatal = 1;
521			simError();
522			}
523			}
524			}
525			}
526
527
528
529			int LJ_NS::parseAtom( char *lineBuffer, int lineNum, atomStruct &info ){
530
531			char* the_token;
532
533			the_token = strtok( lineBuffer, " \n\t,;" );
534			if( the_token != NULL ){
535
536			strcpy( info.name, the_token );
537
538			if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
539			sprintf( painCave.errMsg,
540			"Error parseing AtomTypes: line %d\n", lineNum );
541			painCave.isFatal = 1;
542			simError();
543			}
544
545			info.mass = atof( the_token );
546
547			if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
548			sprintf( painCave.errMsg,
549			"Error parseing AtomTypes: line %d\n", lineNum );
550			painCave.isFatal = 1;
551			simError();
552			}
553
554			info.epslon = atof( the_token );
555
556			if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
557			sprintf( painCave.errMsg,
558			"Error parseing AtomTypes: line %d\n", lineNum );
559			painCave.isFatal = 1;
560			simError();
561			}
562
563			info.sigma = atof( the_token );
564
565			return 1;
566			}
567			else return 0;
568			}