OOPSE/libmdtools/LJ_FF.cpp

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

#include <iostream>
using namespace std;

#ifdef IS_MPI
#include <mpi.h>
#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 LinkedType();
        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 LinkedType;
    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;
  }
      
#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;
  }
  
  entry_plug->useLJ = 1;

#ifdef IS_MPI
  sprintf( checkPointMsg, "LJ_FF atoms initialized succesfully" );
  MPIcheckPoint();
#endif // is_mpi

}

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();
    }
#ifdef IS_MPI
  MPIcheckPoint();
#endif // is_mpi

}

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();
    }
#ifdef IS_MPI
  MPIcheckPoint();
#endif // is_mpi

}

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();
    }
#ifdef IS_MPI
  MPIcheckPoint();
#endif // is_mpi

}

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:	420
Committed:	Thu Mar 27 17:32:03 2003 UTC (21 years, 3 months ago) by mmeineke
File size:	12331 byte(s)
Log Message:	LJ_FF has been converted to the new Molecule model. TraPPE_Ex is currently being updated. SimSetups routines are writtten, but not yet called.
#	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			#include <mpi++.h>
11			#endif //is_mpi
12
13			#include "ForceFields.hpp"
14			#include "SRI.hpp"
15			#include "simError.h"
16
17			#include "fortranWrappers.hpp"
18
19			#ifdef IS_MPI
20			#include "mpiForceField.h"
21			#endif // is_mpi
22
23
24
25			namespace LJ_NS{
26
27			// Declare the structures that will be passed by the parser and MPI
28
29			typedef struct{
30			char name[15];
31			double mass;
32			double epslon;
33			double sigma;
34			int ident;
35			int last; // 0 -> default
36			// 1 -> in MPI: tells nodes to stop listening
37			} atomStruct;
38
39			int parseAtom( char *lineBuffer, int lineNum, atomStruct &info );
40
41			#ifdef IS_MPI
42
43			MPI_Datatype mpiAtomStructType;
44
45			#endif
46	mmeineke	420
47			class LinkedAtomType {
48			public:
49			LinkedAtomType(){
50			next = NULL;
51			name[0] = '\0';
52			}
53			~LinkedAtomType(){ if( next != NULL ) delete next; }
54
55			LinkedAtomType* find(char* key){
56			if( !strcmp(name, key) ) return this;
57			if( next != NULL ) return next->find(key);
58			return NULL;
59			}
60
61
62			void add( atomStruct &info ){
63
64			// check for duplicates
65
66			if( !strcmp( info.name, name ) ){
67			sprintf( painCave.errMsg,
68			"Duplicate LJ atom type \"%s\" found in "
69			"the LJ_FF param file./n",
70			name );
71			painCave.isFatal = 1;
72			simError();
73			}
74
75			if( next != NULL ) next->add(info);
76			else{
77			next = new LinkedType();
78			strcpy(next->name, info.name);
79			next->mass = info.mass;
80			next->epslon = info.epslon;
81			next->sigma = info.sigma;
82			next->ident = info.ident;
83			}
84			}
85
86
87			#ifdef IS_MPI
88
89			void duplicate( atomStruct &info ){
90			strcpy(info.name, name);
91			info.mass = mass;
92			info.epslon = epslon;
93			info.sigma = sigma;
94			info.ident = ident;
95			info.last = 0;
96			}
97
98
99			#endif
100
101			char name[15];
102			double mass;
103			double epslon;
104			double sigma;
105			int ident;
106			LinkedAtomType* next;
107			};
108
109			LinkedAtomType* headAtomType;
110			LinkedAtomType* currentAtomType;
111
112	mmeineke	377	}
113
114			using namespace LJ_NS;
115
116			//****************************************************************
117			// begins the actual forcefield stuff.
118			//****************************************************************
119
120
121			LJ_FF::LJ_FF(){
122
123			char fileName[200];
124			char* ffPath_env = "FORCE_PARAM_PATH";
125			char* ffPath;
126			char temp[200];
127			char errMsg[1000];
128
129	mmeineke	420	headAtomType = NULL;
130			currentAtomType = NULL;
131
132	mmeineke	377	// do the funtion wrapping
133			wrapMeFF( this );
134
135			#ifdef IS_MPI
136			int i;
137
138			// **********************************************************************
139			// Init the atomStruct mpi type
140
141			atomStruct atomProto; // mpiPrototype
142			int atomBC[3] = {15,3,2}; // block counts
143			MPI_Aint atomDspls[3]; // displacements
144			MPI_Datatype atomMbrTypes[3]; // member mpi types
145
146			MPI_Address(&atomProto.name, &atomDspls[0]);
147			MPI_Address(&atomProto.mass, &atomDspls[1]);
148			MPI_Address(&atomProto.ident, &atomDspls[2]);
149
150			atomMbrTypes[0] = MPI_CHAR;
151			atomMbrTypes[1] = MPI_DOUBLE;
152			atomMbrTypes[2] = MPI_INT;
153
154			for (i=2; i >= 0; i--) atomDspls[i] -= atomDspls[0];
155
156			MPI_Type_struct(3, atomBC, atomDspls, atomMbrTypes, &mpiAtomStructType);
157			MPI_Type_commit(&mpiAtomStructType);
158
159			// ***********************************************************************
160
161			if( worldRank == 0 ){
162			#endif
163
164			// generate the force file name
165
166			strcpy( fileName, "LJ_FF.frc" );
167			// fprintf( stderr,"Trying to open %s\n", fileName );
168
169			// attempt to open the file in the current directory first.
170
171			frcFile = fopen( fileName, "r" );
172
173			if( frcFile == NULL ){
174
175			// next see if the force path enviorment variable is set
176
177			ffPath = getenv( ffPath_env );
178			if( ffPath == NULL ) {
179			STR_DEFINE(ffPath, FRC_PATH );
180			}
181
182
183			strcpy( temp, ffPath );
184			strcat( temp, "/" );
185			strcat( temp, fileName );
186			strcpy( fileName, temp );
187
188			frcFile = fopen( fileName, "r" );
189
190			if( frcFile == NULL ){
191
192			sprintf( painCave.errMsg,
193			"Error opening the force field parameter file: %s\n"
194			"Have you tried setting the FORCE_PARAM_PATH environment "
195			"vairable?\n",
196			fileName );
197			painCave.isFatal = 1;
198			simError();
199			}
200			}
201
202			#ifdef IS_MPI
203			}
204
205			sprintf( checkPointMsg, "LJ_FF file opened sucessfully." );
206			MPIcheckPoint();
207
208			#endif // is_mpi
209			}
210
211
212			LJ_FF::~LJ_FF(){
213
214	mmeineke	420	if( headAtomType != NULL ) delete headAtomType;
215
216	mmeineke	377	#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 LJ_FF::initForceField( int ljMixRule ){
228
229			initFortran( ljMixRule, 0 );
230			}
231
232	mmeineke	420	void LJ_FF::cleanMe( void ){
233	mmeineke	377
234	mmeineke	420	#ifdef IS_MPI
235	mmeineke	377
236	mmeineke	420	// keep the linked list in the mpi version
237	mmeineke	377
238	mmeineke	420	#else // is_mpi
239	mmeineke	377
240	mmeineke	420	// delete the linked list in the single processor version
241	mmeineke	377
242	mmeineke	420	if( headAtomType != NULL ) delete headAtomType;
243	mmeineke	377
244	mmeineke	420	#endif // is_mpi
245			}
246	mmeineke	377
247	mmeineke	420	void LJ_FF::readParams( void ){
248	mmeineke	377
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 i;
254			int identNum;
255
256	mmeineke	420
257			bigSigma = 0.0;
258	mmeineke	377	#ifdef IS_MPI
259			if( worldRank == 0 ){
260			#endif
261
262			// read in the atom types.
263
264	mmeineke	420	headAtomType = new LinkedAtomType;
265	mmeineke	377
266			fastForward( "AtomTypes", "initializeAtoms" );
267
268			// we are now at the AtomTypes section.
269
270			eof_test = fgets( readLine, sizeof(readLine), frcFile );
271			lineNum++;
272
273
274			// read a line, and start parseing out the atom types
275
276			if( eof_test == NULL ){
277			sprintf( painCave.errMsg,
278			"Error in reading Atoms from force file at line %d.\n",
279			lineNum );
280			painCave.isFatal = 1;
281			simError();
282			}
283
284			identNum = 1;
285			// stop reading at end of file, or at next section
286			while( readLine[0] != '#' && eof_test != NULL ){
287
288			// toss comment lines
289			if( readLine[0] != '!' ){
290
291			// the parser returns 0 if the line was blank
292			if( parseAtom( readLine, lineNum, info ) ){
293			info.ident = identNum;
294			headAtomType->add( info );;
295			identNum++;
296			}
297			}
298			eof_test = fgets( readLine, sizeof(readLine), frcFile );
299			lineNum++;
300			}
301
302			#ifdef IS_MPI
303
304			// send out the linked list to all the other processes
305
306			sprintf( checkPointMsg,
307			"LJ_FF atom structures read successfully." );
308			MPIcheckPoint();
309
310			currentAtomType = headAtomType->next; //skip the first element who is a place holder.
311			while( currentAtomType != NULL ){
312			currentAtomType->duplicate( info );
313
314
315
316			sendFrcStruct( &info, mpiAtomStructType );
317
318			sprintf( checkPointMsg,
319			"successfully sent lJ force type: \"%s\"\n",
320			info.name );
321			MPIcheckPoint();
322
323			currentAtomType = currentAtomType->next;
324			}
325			info.last = 1;
326			sendFrcStruct( &info, mpiAtomStructType );
327
328			}
329
330			else{
331
332			// listen for node 0 to send out the force params
333
334			MPIcheckPoint();
335
336			headAtomType = new LinkedType;
337			recieveFrcStruct( &info, mpiAtomStructType );
338
339			while( !info.last ){
340
341
342
343			headAtomType->add( info );
344
345			MPIcheckPoint();
346
347			recieveFrcStruct( &info, mpiAtomStructType );
348			}
349			}
350			#endif // is_mpi
351
352			// call new A_types in fortran
353
354			int isError;
355
356			// dummy variables
357			int isLJ = 1;
358			int isDipole = 0;
359			int isSSD = 0;
360			int isGB = 0;
361			double w0 = 0.0;
362			double v0 = 0.0;
363			double dipole = 0.0;
364			double GB_dummy = 0.0;
365
366
367			currentAtomType = headAtomType;
368			while( currentAtomType != NULL ){
369
370			if( currentAtomType->name[0] != '\0' ){
371			isError = 0;
372			makeAtype( &(currentAtomType->ident),
373			&isLJ,
374			&isSSD,
375			&isDipole,
376			&isGB,
377			&(currentAtomType->epslon),
378			&(currentAtomType->sigma),
379			&dipole,
380			&w0,
381			&v0,
382			&GB_dummy,
383			&GB_dummy,
384			&GB_dummy,
385			&GB_dummy,
386			&GB_dummy,
387			&GB_dummy,
388			&isError );
389			if( isError ){
390			sprintf( painCave.errMsg,
391			"Error initializing the \"%s\" atom type in fortran\n",
392			currentAtomType->name );
393			painCave.isFatal = 1;
394			simError();
395			}
396			}
397			currentAtomType = currentAtomType->next;
398			}
399
400			#ifdef IS_MPI
401			sprintf( checkPointMsg,
402			"LJ_FF atom structures successfully sent to fortran\n" );
403			MPIcheckPoint();
404			#endif // is_mpi
405
406	mmeineke	420	}
407
408
409			void LJ_FF::initializeAtoms( int nAtoms, Atom** the_atoms ){
410	mmeineke	377
411	mmeineke	420	int i;
412	mmeineke	377
413			// initialize the atoms
414
415	mmeineke	420
416	mmeineke	377	Atom* thisAtom;
417
418			for( i=0; i<nAtoms; i++ ){
419
420			currentAtomType = headAtomType->find( the_atoms[i]->getType() );
421			if( currentAtomType == NULL ){
422			sprintf( painCave.errMsg,
423			"AtomType error, %s not found in force file.\n",
424			the_atoms[i]->getType() );
425			painCave.isFatal = 1;
426			simError();
427			}
428
429			the_atoms[i]->setMass( currentAtomType->mass );
430			the_atoms[i]->setEpslon( currentAtomType->epslon );
431			the_atoms[i]->setSigma( currentAtomType->sigma );
432			the_atoms[i]->setIdent( currentAtomType->ident );
433			the_atoms[i]->setLJ();
434
435			if( bigSigma < currentAtomType->sigma ) bigSigma = currentAtomType->sigma;
436			}
437
438			entry_plug->useLJ = 1;
439
440			#ifdef IS_MPI
441			sprintf( checkPointMsg, "LJ_FF atoms initialized succesfully" );
442			MPIcheckPoint();
443			#endif // is_mpi
444
445			}
446
447	mmeineke	420	void LJ_FF::initializeBonds( int nBonds, Bond** BondArray,
448			bond_pair* the_bonds ){
449	mmeineke	377
450	mmeineke	420	if( nBonds ){
451	mmeineke	377	sprintf( painCave.errMsg,
452			"LJ_FF does not support bonds.\n" );
453			painCave.isFatal = 1;
454			simError();
455			}
456			#ifdef IS_MPI
457			MPIcheckPoint();
458			#endif // is_mpi
459
460			}
461
462	mmeineke	420	void LJ_FF::initializeBends( int nBends, Bend** bendArray,
463			bend_set* the_bends ){
464	mmeineke	377
465	mmeineke	420	if( nBends ){
466	mmeineke	377	sprintf( painCave.errMsg,
467			"LJ_FF does not support bends.\n" );
468			painCave.isFatal = 1;
469			simError();
470			}
471			#ifdef IS_MPI
472			MPIcheckPoint();
473			#endif // is_mpi
474
475			}
476
477	mmeineke	420	void LJ_FF::initializeTorsions( int nTorsions, Torsion** torsionArray,
478			torsion_set* the_torsions ){
479	mmeineke	377
480	mmeineke	420	if( nTorsions ){
481	mmeineke	377	sprintf( painCave.errMsg,
482			"LJ_FF does not support torsions.\n" );
483			painCave.isFatal = 1;
484			simError();
485			}
486			#ifdef IS_MPI
487			MPIcheckPoint();
488			#endif // is_mpi
489
490			}
491
492			void LJ_FF::fastForward( char* stopText, char* searchOwner ){
493
494			int foundText = 0;
495			char* the_token;
496
497			rewind( frcFile );
498			lineNum = 0;
499
500			eof_test = fgets( readLine, sizeof(readLine), frcFile );
501			lineNum++;
502			if( eof_test == NULL ){
503			sprintf( painCave.errMsg, "Error fast forwarding force file for %s: "
504			" file is empty.\n",
505			searchOwner );
506			painCave.isFatal = 1;
507			simError();
508			}
509
510
511			while( !foundText ){
512			while( eof_test != NULL && readLine[0] != '#' ){
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			the_token = strtok( readLine, " ,;\t#\n" );
527			foundText = !strcmp( stopText, the_token );
528
529			if( !foundText ){
530			eof_test = fgets( readLine, sizeof(readLine), frcFile );
531			lineNum++;
532
533			if( eof_test == NULL ){
534			sprintf( painCave.errMsg,
535			"Error fast forwarding force file for %s at "
536			"line %d: file ended unexpectedly.\n",
537			searchOwner,
538			lineNum );
539			painCave.isFatal = 1;
540			simError();
541			}
542			}
543			}
544			}
545
546
547
548			int LJ_NS::parseAtom( char *lineBuffer, int lineNum, atomStruct &info ){
549
550			char* the_token;
551
552			the_token = strtok( lineBuffer, " \n\t,;" );
553			if( the_token != NULL ){
554
555			strcpy( info.name, the_token );
556
557			if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
558			sprintf( painCave.errMsg,
559			"Error parseing AtomTypes: line %d\n", lineNum );
560			painCave.isFatal = 1;
561			simError();
562			}
563
564			info.mass = atof( the_token );
565
566			if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
567			sprintf( painCave.errMsg,
568			"Error parseing AtomTypes: line %d\n", lineNum );
569			painCave.isFatal = 1;
570			simError();
571			}
572
573			info.epslon = atof( the_token );
574
575			if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
576			sprintf( painCave.errMsg,
577			"Error parseing AtomTypes: line %d\n", lineNum );
578			painCave.isFatal = 1;
579			simError();
580			}
581
582			info.sigma = atof( the_token );
583
584			return 1;
585			}
586			else return 0;
587			}