mdtools/interface_implementation/LJ_FF.cpp

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

#include <iostream>
using namespace std;

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


// 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 parseAtomLJ( char *lineBuffer, int lineNum, atomStruct &info );

#ifdef IS_MPI

#include "mpiForceField.h"

MPI_Datatype mpiAtomStructType;

#endif


// declaration of functions needed to wrap the fortran module

extern "C" {
  void forcefactory_( char* forceName,
                      int* status,
                      void (*wrapFunction)( void (*p1)( int* ident, 
                                                        double* mass, 
                                                        double* epslon, 
                                                        double* sigma, 
                                                        int* status ),
                                            void (*p2)( void ),
                                            void (*p3)( double* positionArray,
                                                        double* forceArray,
                                                        double* potentialEnergy,
                                                        short int* doPotentialCalc )),
                      int forceNameLength );
}


void LJfunctionWrapper( void (*p1)( int* ident, double* mass, double* epslon, 
                                   double* sigma, int* status ),
                        void (*p2)( void ),
                        void (*p3)( double* positionArray,double* forceArray,
                                    double* potentialEnergy,
                                    short int* doPotentialCalc ) );

void (*newLJtype)( int* ident, double* mass, double* epslon, double* sigma,
                   int* status );

void (*initLJfortran)( void );

LJ_FF* currentLJwrap;


//****************************************************************
// 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];

  // do the funtion wrapping
  currentLJwrap = this;
  wrapMe();

#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 ) {
        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();
      }
      
      
      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(){

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


void LJ_FF::wrapMe( void ){
  
  char* currentFF = "LJ";
  int isError = 0;
  
  forcefactory_( currentFF, &isError, LJfunctionWrapper, strlen(currentFF) );

  if( isError ){
    
    sprintf( painCave.errMsg,
             "LJ_FF error: an error was returned from fortran when the "
             "the functions were being wrapped.\n" );
    painCave.isFatal = 1;
    simError();
  }

#ifdef IS_MPI
  sprintf( checkPointMsg, "LJ_FF functions succesfully wrapped." );
  MPIcheckPoint();
#endif // is_mpi
}
  

void LJfunctionWrapper( void (*p1)( int* ident, double* mass, double* epslon, 
                                   double* sigma, int* status ),
                        void (*p2)( void ),
                        void (*p3)( double* positionArray,double* forceArray,
                                    double* potentialEnergy,
                                    short int* doPotentialCalc ) ){
  
  
  p1 = newLJtype;
  p2 = initLJfortran;
  this->setLJfortran( p3 );
}


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

    LinkedType* 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( simError.painCave,
                 "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;
    LinkedType* next;
  };
  
  LinkedType* headAtomType; 
  LinkedType* currentAtomType;
  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;
  
  Atom** the_atoms;
  int nAtoms;
  the_atoms = entry_plug->atoms;
  nAtoms = entry_plug->n_atoms;
  
  
#ifdef IS_MPI
  if( worldRank == 0 ){
#endif
    
    // read in the atom types.

    headAtomType = new LinkedType;
    
    fastFoward( "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( parseAtomLJ( 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;
    while( currentAtomType != NULL ){
      currentAtomType->duplicate( info );
      sendFrcStruct( &info, mpiAtomStructType );
      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 );
      recieveFrcStruct( &info, mpiAtomStructType );
    }
  }
#endif // is_mpi

  // call new A_types in fortran
  
  int isError;
  currentAtomType = headAtomType;
  while( currentAtomType != NULL ){
    
    if( currentAtomType->name[0] != NULL ){
      isError = 0;
      newLJtype( &(currentAtomType->ident),
                 &(currentAtomType->mass),
                 &(currentAtomType->epslon),
                 &(currentAtomType->sigma),
                 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

  
  // 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();
  }


  // clean up the memory
  
  delete headAtomType;

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

}

void LJ_FF::initializeBonds( bond_pair* the_bonds ){
  
    if( entry_plug->n_bonds ){
      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( bend_set* the_bends ){

    if( entry_plug->n_bends ){
      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( torsion_set* the_torsions ){

    if( entry_plug->n_torsions ){
      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 parseAtomLJ( 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;
}


void LJ_FF::doForces( void ){

  int i;
  double* frc;
  double* pos;
  double potE;
  short int calcPot = 0;

  // forces are zeroed here, before any are acumulated.
  // NOTE: do not rezero the forces in Fortran.

  for(i=0; i<entry_plug->n_atoms; i++){
    entry_plug->atoms[i]->zeroForces();
  }

  frc = Atom::getFrcArray();
  pos = Atom::getPosArray();

  doLJfortran( pos, frc, potE, calcPot );
}
  
Revision:	238
Committed:	Fri Jan 17 21:53:36 2003 UTC (21 years, 8 months ago) by mmeineke
File size:	13374 byte(s)
Log Message:	* empty log message *
#	User	Rev	Content
1	chuckv	215	#include <cstdlib>
2			#include <cstdio>
3			#include <cstring>
4
5			#include <iostream>
6			using namespace std;
7
8			#include "ForceFields.hpp"
9			#include "SRI.hpp"
10			#include "simError.h"
11
12
13	mmeineke	224	// Declare the structures that will be passed by the parser and MPI
14	chuckv	215
15			typedef struct{
16			char name[15];
17			double mass;
18			double epslon;
19			double sigma;
20	mmeineke	224	int ident;
21	chuckv	215	int last; // 0 -> default
22	mmeineke	224	// 1 -> in MPI: tells nodes to stop listening
23	chuckv	215	} atomStruct;
24	mmeineke	224
25			int parseAtomLJ( char *lineBuffer, int lineNum, atomStruct &info );
26
27			#ifdef IS_MPI
28
29			#include "mpiForceField.h"
30
31	chuckv	215	MPI_Datatype mpiAtomStructType;
32
33			#endif
34
35
36	mmeineke	234	// declaration of functions needed to wrap the fortran module
37
38			extern "C" {
39			void forcefactory_( char* forceName,
40			int* status,
41	mmeineke	236	void (wrapFunction)( void (p1)( int* ident,
42			double* mass,
43			double* epslon,
44			double* sigma,
45			int* status ),
46			void (*p2)( void ),
47			void (p3)( double positionArray,
48			double* forceArray,
49			double* potentialEnergy,
50			short int* doPotentialCalc )),
51			int forceNameLength );
52			}
53	mmeineke	234
54
55	mmeineke	236	void LJfunctionWrapper( void (p1)( int ident, double* mass, double* epslon,
56			double* sigma, int* status ),
57			void (*p2)( void ),
58			void (p3)( double positionArray,double* forceArray,
59			double* potentialEnergy,
60			short int* doPotentialCalc ) );
61	mmeineke	234
62	mmeineke	236	void (newLJtype)( int ident, double* mass, double* epslon, double* sigma,
63			int* status );
64
65			void (*initLJfortran)( void );
66
67			LJ_FF* currentLJwrap;
68
69
70			//****************************************************************
71			// begins the actual forcefield stuff.
72			//****************************************************************
73
74	chuckv	215	LJ_FF::LJ_FF(){
75
76			char fileName[200];
77			char* ffPath_env = "FORCE_PARAM_PATH";
78			char* ffPath;
79			char temp[200];
80			char errMsg[1000];
81
82	mmeineke	236	// do the funtion wrapping
83			currentLJwrap = this;
84			wrapMe();
85
86	chuckv	215	#ifdef IS_MPI
87			int i;
88
89			// **********************************************************************
90			// Init the atomStruct mpi type
91
92			atomStruct atomProto; // mpiPrototype
93	mmeineke	224	int atomBC[3] = {15,3,2}; // block counts
94	chuckv	215	MPI_Aint atomDspls[3]; // displacements
95			MPI_Datatype atomMbrTypes[3]; // member mpi types
96
97			MPI_Address(&atomProto.name, &atomDspls[0]);
98			MPI_Address(&atomProto.mass, &atomDspls[1]);
99	mmeineke	224	MPI_Address(&atomProto.ident, &atomDspls[2]);
100	chuckv	215
101			atomMbrTypes[0] = MPI_CHAR;
102			atomMbrTypes[1] = MPI_DOUBLE;
103			atomMbrTypes[2] = MPI_INT;
104
105			for (i=2; i >= 0; i--) atomDspls[i] -= atomDspls[0];
106
107			MPI_Type_struct(3, atomBC, atomDspls, atomMbrTypes, &mpiAtomStructType);
108			MPI_Type_commit(&mpiAtomStructType);
109
110			// ***********************************************************************
111
112			if( worldRank == 0 ){
113			#endif
114
115			// generate the force file name
116
117			strcpy( fileName, "LJ_FF.frc" );
118			// fprintf( stderr,"Trying to open %s\n", fileName );
119
120			// attempt to open the file in the current directory first.
121
122			frcFile = fopen( fileName, "r" );
123
124			if( frcFile == NULL ){
125
126			// next see if the force path enviorment variable is set
127
128			ffPath = getenv( ffPath_env );
129			if( ffPath == NULL ) {
130			sprintf( painCave.errMsg,
131			"Error opening the force field parameter file: %s\n"
132			"Have you tried setting the FORCE_PARAM_PATH environment "
133			"vairable?\n",
134			fileName );
135			painCave.isFatal = 1;
136			simError();
137			}
138
139
140			strcpy( temp, ffPath );
141			strcat( temp, "/" );
142			strcat( temp, fileName );
143			strcpy( fileName, temp );
144
145			frcFile = fopen( fileName, "r" );
146
147			if( frcFile == NULL ){
148
149			sprintf( painCave.errMsg,
150			"Error opening the force field parameter file: %s\n"
151			"Have you tried setting the FORCE_PARAM_PATH environment "
152			"vairable?\n",
153			fileName );
154			painCave.isFatal = 1;
155			simError();
156			}
157			}
158
159			#ifdef IS_MPI
160			}
161
162			sprintf( checkPointMsg, "LJ_FF file opened sucessfully." );
163			MPIcheckPoint();
164
165			#endif // is_mpi
166			}
167
168
169			LJ_FF::~LJ_FF(){
170
171			#ifdef IS_MPI
172			if( worldRank == 0 ){
173			#endif // is_mpi
174
175			fclose( frcFile );
176
177			#ifdef IS_MPI
178			}
179			#endif // is_mpi
180			}
181
182	mmeineke	236
183			void LJ_FF::wrapMe( void ){
184
185			char* currentFF = "LJ";
186			int isError = 0;
187
188			forcefactory_( currentFF, &isError, LJfunctionWrapper, strlen(currentFF) );
189
190			if( isError ){
191
192			sprintf( painCave.errMsg,
193			"LJ_FF error: an error was returned from fortran when the "
194			"the functions were being wrapped.\n" );
195			painCave.isFatal = 1;
196			simError();
197			}
198
199			#ifdef IS_MPI
200			sprintf( checkPointMsg, "LJ_FF functions succesfully wrapped." );
201			MPIcheckPoint();
202			#endif // is_mpi
203			}
204
205
206			void LJfunctionWrapper( void (p1)( int ident, double* mass, double* epslon,
207			double* sigma, int* status ),
208			void (*p2)( void ),
209			void (p3)( double positionArray,double* forceArray,
210			double* potentialEnergy,
211			short int* doPotentialCalc ) ){
212
213
214			p1 = newLJtype;
215			p2 = initLJfortran;
216			this->setLJfortran( p3 );
217			}
218
219
220
221	chuckv	215	void LJ_FF::initializeAtoms( void ){
222
223			class LinkedType {
224			public:
225			LinkedType(){
226			next = NULL;
227			name[0] = '\0';
228			}
229			~LinkedType(){ if( next != NULL ) delete next; }
230
231			LinkedType* find(char* key){
232			if( !strcmp(name, key) ) return this;
233			if( next != NULL ) return next->find(key);
234			return NULL;
235			}
236
237	mmeineke	224
238	chuckv	215	void add( atomStruct &info ){
239	mmeineke	224
240			// check for duplicates
241
242			if( !strcmp( info.name, name ) ){
243			sprintf( simError.painCave,
244			"Duplicate LJ atom type \"%s\" found in "
245			"the LJ_FF param file./n",
246			name );
247			painCave.isFatal = 1;
248			simError();
249			}
250
251	chuckv	215	if( next != NULL ) next->add(info);
252			else{
253			next = new LinkedType();
254			strcpy(next->name, info.name);
255			next->mass = info.mass;
256			next->epslon = info.epslon;
257			next->sigma = info.sigma;
258	mmeineke	224	next->ident = info.ident;
259	chuckv	215	}
260			}
261
262	mmeineke	224
263			#ifdef IS_MPI
264
265	chuckv	215	void duplicate( atomStruct &info ){
266			strcpy(info.name, name);
267			info.mass = mass;
268			info.epslon = epslon;
269			info.sigma = sigma;
270	mmeineke	224	info.ident = ident;
271	chuckv	215	info.last = 0;
272			}
273
274
275			#endif
276
277			char name[15];
278			double mass;
279			double epslon;
280			double sigma;
281	mmeineke	224	int ident;
282	chuckv	215	LinkedType* next;
283			};
284
285			LinkedType* headAtomType;
286			LinkedType* currentAtomType;
287			atomStruct info;
288			info.last = 1; // initialize last to have the last set.
289			// if things go well, last will be set to 0
290
291			int i;
292	mmeineke	224	int identNum;
293	chuckv	215
294			Atom** the_atoms;
295			int nAtoms;
296			the_atoms = entry_plug->atoms;
297			nAtoms = entry_plug->n_atoms;
298
299
300			#ifdef IS_MPI
301			if( worldRank == 0 ){
302			#endif
303
304			// read in the atom types.
305	mmeineke	224
306	chuckv	215	headAtomType = new LinkedType;
307
308	mmeineke	224	fastFoward( "AtomTypes", "initializeAtoms" );
309
310	chuckv	215	// we are now at the AtomTypes section.
311
312			eof_test = fgets( readLine, sizeof(readLine), frcFile );
313			lineNum++;
314
315	mmeineke	224
316			// read a line, and start parseing out the atom types
317
318	chuckv	215	if( eof_test == NULL ){
319			sprintf( painCave.errMsg,
320			"Error in reading Atoms from force file at line %d.\n",
321			lineNum );
322			painCave.isFatal = 1;
323			simError();
324			}
325
326	mmeineke	224	identNum = 1;
327			// stop reading at end of file, or at next section
328	chuckv	215	while( readLine[0] != '#' && eof_test != NULL ){
329	mmeineke	224
330			// toss comment lines
331	chuckv	215	if( readLine[0] != '!' ){
332
333	mmeineke	224	// the parser returns 0 if the line was blank
334			if( parseAtomLJ( readLine, lineNum, info ) ){
335			info.ident = identNum;
336			headAtomType->add( info );;
337			identNum++;
338	chuckv	215	}
339			}
340			eof_test = fgets( readLine, sizeof(readLine), frcFile );
341			lineNum++;
342			}
343
344			#ifdef IS_MPI
345
346			// send out the linked list to all the other processes
347
348			sprintf( checkPointMsg,
349			"LJ_FF atom structures read successfully." );
350			MPIcheckPoint();
351
352			currentAtomType = headAtomType;
353			while( currentAtomType != NULL ){
354			currentAtomType->duplicate( info );
355			sendFrcStruct( &info, mpiAtomStructType );
356			currentAtomType = currentAtomType->next;
357			}
358			info.last = 1;
359			sendFrcStruct( &info, mpiAtomStructType );
360
361			}
362
363			else{
364
365			// listen for node 0 to send out the force params
366
367			MPIcheckPoint();
368
369			headAtomType = new LinkedType;
370			recieveFrcStruct( &info, mpiAtomStructType );
371			while( !info.last ){
372
373			headAtomType->add( info );
374			recieveFrcStruct( &info, mpiAtomStructType );
375			}
376			}
377			#endif // is_mpi
378
379	chuckv	230	// call new A_types in fortran
380	mmeineke	238
381			int isError;
382			currentAtomType = headAtomType;
383			while( currentAtomType != NULL ){
384
385			if( currentAtomType->name[0] != NULL ){
386			isError = 0;
387			newLJtype( &(currentAtomType->ident),
388			&(currentAtomType->mass),
389			&(currentAtomType->epslon),
390			&(currentAtomType->sigma),
391			isError );
392			if( isError ){
393			sprintf( painCave.errMsg,
394			"Error initializing the \"%s\" atom type in fortran\n",
395			currentAtomType->name );
396			painCave.isFatal = 1;
397			simError();
398			}
399			}
400			currentAtomType = currentAtomType->next;
401			}
402
403			#ifdef IS_MPI
404			sprintf( checkPointMsg,
405			"LJ_FF atom structures successfully sent to fortran\n" );
406			MPIcheckPoint();
407			#endif // is_mpi
408	chuckv	230
409	mmeineke	238
410	chuckv	230
411	chuckv	215	// initialize the atoms
412
413			Atom* thisAtom;
414
415			for( i=0; i<nAtoms; i++ ){
416
417			currentAtomType = headAtomType->find( the_atoms[i]->getType() );
418			if( currentAtomType == NULL ){
419			sprintf( painCave.errMsg,
420			"AtomType error, %s not found in force file.\n",
421			the_atoms[i]->getType() );
422			painCave.isFatal = 1;
423			simError();
424			}
425
426			the_atoms[i]->setMass( currentAtomType->mass );
427			the_atoms[i]->setEpslon( currentAtomType->epslon );
428			the_atoms[i]->setSigma( currentAtomType->sigma );
429	mmeineke	224	the_atoms[i]->setIdent( currentAtomType->ident );
430	chuckv	215	the_atoms[i]->setLJ();
431			}
432
433
434			// clean up the memory
435
436			delete headAtomType;
437
438			#ifdef IS_MPI
439			sprintf( checkPointMsg, "LJ_FF atoms initialized succesfully" );
440			MPIcheckPoint();
441			#endif // is_mpi
442
443			}
444
445			void LJ_FF::initializeBonds( bond_pair* the_bonds ){
446
447			if( entry_plug->n_bonds ){
448			sprintf( painCave.errMsg,
449			"LJ_FF does not support bonds.\n" );
450			painCave.isFatal = 1;
451			simError();
452			}
453			#ifdef IS_MPI
454			MPIcheckPoint();
455			#endif // is_mpi
456
457			}
458
459			void LJ_FF::initializeBends( bend_set* the_bends ){
460
461			if( entry_plug->n_bends ){
462			sprintf( painCave.errMsg,
463			"LJ_FF does not support bends.\n" );
464			painCave.isFatal = 1;
465			simError();
466			}
467			#ifdef IS_MPI
468			MPIcheckPoint();
469			#endif // is_mpi
470
471			}
472
473			void LJ_FF::initializeTorsions( torsion_set* the_torsions ){
474
475			if( entry_plug->n_torsions ){
476			sprintf( painCave.errMsg,
477			"LJ_FF does not support torsions.\n" );
478			painCave.isFatal = 1;
479			simError();
480			}
481			#ifdef IS_MPI
482			MPIcheckPoint();
483			#endif // is_mpi
484
485			}
486	mmeineke	224
487
488			void LJ_FF::fastForward( char* stopText, char* searchOwner ){
489
490			int foundText = 0;
491			char* the_token;
492
493			rewind( frcFile );
494			lineNum = 0;
495
496			eof_test = fgets( readLine, sizeof(readLine), frcFile );
497			lineNum++;
498			if( eof_test == NULL ){
499			sprintf( painCave.errMsg, "Error fast forwarding force file for %s: "
500			" file is empty.\n",
501			searchOwner );
502			painCave.isFatal = 1;
503			simError();
504			}
505
506
507			while( !foundText ){
508			while( eof_test != NULL && readLine[0] != '#' ){
509			eof_test = fgets( readLine, sizeof(readLine), frcFile );
510			lineNum++;
511			}
512			if( eof_test == NULL ){
513			sprintf( painCave.errMsg,
514			"Error fast forwarding force file for %s at "
515			"line %d: file ended unexpectedly.\n",
516			searchOwner,
517			lineNum );
518			painCave.isFatal = 1;
519			simError();
520			}
521
522			the_token = strtok( readLine, " ,;\t#\n" );
523			foundText = !strcmp( stopText, the_token );
524
525			if( !foundText ){
526			eof_test = fgets( readLine, sizeof(readLine), frcFile );
527			lineNum++;
528
529			if( eof_test == NULL ){
530			sprintf( painCave.errMsg,
531			"Error fast forwarding force file for %s at "
532			"line %d: file ended unexpectedly.\n",
533			searchOwner,
534			lineNum );
535			painCave.isFatal = 1;
536			simError();
537			}
538			}
539			}
540			}
541
542
543
544			int parseAtomLJ( char *lineBuffer, int lineNum, atomStruct &info ){
545
546			char* the_token;
547
548			the_token = strtok( lineBuffer, " \n\t,;" );
549			if( the_token != NULL ){
550
551			strcpy( info.name, the_token );
552
553			if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
554			sprintf( painCave.errMsg,
555			"Error parseing AtomTypes: line %d\n", lineNum );
556			painCave.isFatal = 1;
557			simError();
558			}
559
560			info.mass = atof( the_token );
561
562			if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
563			sprintf( painCave.errMsg,
564			"Error parseing AtomTypes: line %d\n", lineNum );
565			painCave.isFatal = 1;
566			simError();
567			}
568
569			info.epslon = atof( the_token );
570
571			if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
572			sprintf( painCave.errMsg,
573			"Error parseing AtomTypes: line %d\n", lineNum );
574			painCave.isFatal = 1;
575			simError();
576			}
577
578			info.sigma = atof( the_token );
579
580			return 1;
581			}
582			else return 0;
583			}
584	mmeineke	238
585
586			void LJ_FF::doForces( void ){
587
588			int i;
589			double* frc;
590			double* pos;
591			double potE;
592			short int calcPot = 0;
593
594			// forces are zeroed here, before any are acumulated.
595			// NOTE: do not rezero the forces in Fortran.
596
597			for(i=0; i<entry_plug->n_atoms; i++){
598			entry_plug->atoms[i]->zeroForces();
599			}
600
601			frc = Atom::getFrcArray();
602			pos = Atom::getPosArray();
603
604			doLJfortran( pos, frc, potE, calcPot );
605			}
606