mdtools/libmdCode/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 {

  // 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
}


//****************************************************************
// 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
  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(){

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


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( 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;
    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;
    
    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( 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->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;
  
  
  currentAtomType = headAtomType;
  while( currentAtomType != NULL ){
    
    if( currentAtomType->name[0] != '\0' ){
      isError = 0;
      newAtype( &(currentAtomType->ident),
                &(currentAtomType->mass),
                &(currentAtomType->epslon),
                &(currentAtomType->sigma),
                &isLJ, &isSSD, &isDipole, &isGB, &w0, &v0, &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;
  }
      
#ifdef IS_MPI
  sprintf( checkPointMsg,
           "LJ_FF atom structures successfully sent to fortran\n" );
  MPIcheckPoint();
#endif // is_mpi

  
  // initialize the atoms
  
  double bigSigma = 0.0;
  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;
  }

  
#ifdef IS_MPI
  double tempBig = bigSigma;
  MPI::COMM_WORLD.Allreduce( &tempBig, &bigSigma, 1, MPI_DOUBLE, MPI_MAX );
#endif  //is_mpi

  //calc rCut and rList

  entry_plug->rCut = 2.5 * bigSigma;
  if(entry_plug->rCut > (entry_plug->box_x / 2.0)) entry_plug->rCut = entry_plug->box_x / 2.0;
  if(entry_plug->rCut > (entry_plug->box_y / 2.0)) entry_plug->rCut = entry_plug->box_y / 2.0;
  if(entry_plug->rCut > (entry_plug->box_z / 2.0)) entry_plug->rCut = entry_plug->box_z / 2.0;

  entry_plug->rList = entry_plug->rCut + 1.0;

  // clean up the memory
  
  delete headAtomType;

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

  this->initFortran();
  entry_plug->refreshSim();
  
}

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 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:	321
Committed:	Wed Mar 12 15:12:24 2003 UTC (21 years, 5 months ago) by mmeineke
File size:	12315 byte(s)
Log Message:	added the force parameter files into the distribution
#	User	Rev	Content
1	mmeineke	270	#include <cstdlib>
2			#include <cstdio>
3			#include <cstring>
4
5			#include <iostream>
6			using namespace std;
7
8	mmeineke	275	#ifdef IS_MPI
9			#include <mpi.h>
10			#include <mpi++.h>
11			#endif //is_mpi
12
13	mmeineke	270	#include "ForceFields.hpp"
14			#include "SRI.hpp"
15			#include "simError.h"
16
17	mmeineke	294	#include <fortranWrappers.hpp>
18
19	mmeineke	291	#ifdef IS_MPI
20			#include "mpiForceField.h"
21			#endif // is_mpi
22	mmeineke	275
23
24	mmeineke	270
25	mmeineke	291	namespace {
26	mmeineke	270
27	mmeineke	291	// 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	mmeineke	270
39	mmeineke	291	int parseAtom( char *lineBuffer, int lineNum, atomStruct &info );
40
41	mmeineke	270	#ifdef IS_MPI
42	mmeineke	291
43			MPI_Datatype mpiAtomStructType;
44
45	mmeineke	270	#endif
46	mmeineke	291	}
47	mmeineke	270
48
49			//****************************************************************
50			// begins the actual forcefield stuff.
51			//****************************************************************
52
53
54			LJ_FF::LJ_FF(){
55
56			char fileName[200];
57			char* ffPath_env = "FORCE_PARAM_PATH";
58			char* ffPath;
59			char temp[200];
60			char errMsg[1000];
61
62			// do the funtion wrapping
63	mmeineke	294	wrapMeFF( this );
64	mmeineke	270
65			#ifdef IS_MPI
66			int i;
67
68			// **********************************************************************
69			// Init the atomStruct mpi type
70
71			atomStruct atomProto; // mpiPrototype
72			int atomBC[3] = {15,3,2}; // block counts
73			MPI_Aint atomDspls[3]; // displacements
74			MPI_Datatype atomMbrTypes[3]; // member mpi types
75
76			MPI_Address(&atomProto.name, &atomDspls[0]);
77			MPI_Address(&atomProto.mass, &atomDspls[1]);
78			MPI_Address(&atomProto.ident, &atomDspls[2]);
79
80			atomMbrTypes[0] = MPI_CHAR;
81			atomMbrTypes[1] = MPI_DOUBLE;
82			atomMbrTypes[2] = MPI_INT;
83
84			for (i=2; i >= 0; i--) atomDspls[i] -= atomDspls[0];
85
86			MPI_Type_struct(3, atomBC, atomDspls, atomMbrTypes, &mpiAtomStructType);
87			MPI_Type_commit(&mpiAtomStructType);
88
89			// ***********************************************************************
90
91			if( worldRank == 0 ){
92			#endif
93
94			// generate the force file name
95
96			strcpy( fileName, "LJ_FF.frc" );
97			// fprintf( stderr,"Trying to open %s\n", fileName );
98
99			// attempt to open the file in the current directory first.
100
101			frcFile = fopen( fileName, "r" );
102
103			if( frcFile == NULL ){
104
105			// next see if the force path enviorment variable is set
106
107			ffPath = getenv( ffPath_env );
108			if( ffPath == NULL ) {
109	mmeineke	321	STR_DEFINE(ffPath, FRC_PATH );
110	mmeineke	270	}
111
112
113			strcpy( temp, ffPath );
114			strcat( temp, "/" );
115			strcat( temp, fileName );
116			strcpy( fileName, temp );
117
118			frcFile = fopen( fileName, "r" );
119
120			if( frcFile == NULL ){
121
122			sprintf( painCave.errMsg,
123			"Error opening the force field parameter file: %s\n"
124			"Have you tried setting the FORCE_PARAM_PATH environment "
125			"vairable?\n",
126			fileName );
127			painCave.isFatal = 1;
128			simError();
129			}
130			}
131
132			#ifdef IS_MPI
133			}
134
135			sprintf( checkPointMsg, "LJ_FF file opened sucessfully." );
136			MPIcheckPoint();
137
138			#endif // is_mpi
139			}
140
141
142			LJ_FF::~LJ_FF(){
143
144			#ifdef IS_MPI
145			if( worldRank == 0 ){
146			#endif // is_mpi
147
148			fclose( frcFile );
149
150			#ifdef IS_MPI
151			}
152			#endif // is_mpi
153			}
154
155
156
157			void LJ_FF::initializeAtoms( void ){
158
159			class LinkedType {
160			public:
161			LinkedType(){
162			next = NULL;
163			name[0] = '\0';
164			}
165			~LinkedType(){ if( next != NULL ) delete next; }
166
167			LinkedType* find(char* key){
168			if( !strcmp(name, key) ) return this;
169			if( next != NULL ) return next->find(key);
170			return NULL;
171			}
172
173
174			void add( atomStruct &info ){
175
176			// check for duplicates
177
178			if( !strcmp( info.name, name ) ){
179			sprintf( painCave.errMsg,
180			"Duplicate LJ atom type \"%s\" found in "
181			"the LJ_FF param file./n",
182			name );
183			painCave.isFatal = 1;
184			simError();
185			}
186
187			if( next != NULL ) next->add(info);
188			else{
189			next = new LinkedType();
190			strcpy(next->name, info.name);
191			next->mass = info.mass;
192			next->epslon = info.epslon;
193			next->sigma = info.sigma;
194			next->ident = info.ident;
195			}
196			}
197
198
199			#ifdef IS_MPI
200
201			void duplicate( atomStruct &info ){
202			strcpy(info.name, name);
203			info.mass = mass;
204			info.epslon = epslon;
205			info.sigma = sigma;
206			info.ident = ident;
207			info.last = 0;
208			}
209
210
211			#endif
212
213			char name[15];
214			double mass;
215			double epslon;
216			double sigma;
217			int ident;
218			LinkedType* next;
219			};
220
221			LinkedType* headAtomType;
222			LinkedType* currentAtomType;
223			atomStruct info;
224			info.last = 1; // initialize last to have the last set.
225			// if things go well, last will be set to 0
226
227			int i;
228			int identNum;
229
230			Atom** the_atoms;
231			int nAtoms;
232			the_atoms = entry_plug->atoms;
233			nAtoms = entry_plug->n_atoms;
234
235
236			#ifdef IS_MPI
237			if( worldRank == 0 ){
238			#endif
239
240			// read in the atom types.
241
242			headAtomType = new LinkedType;
243
244			fastForward( "AtomTypes", "initializeAtoms" );
245
246			// we are now at the AtomTypes section.
247
248			eof_test = fgets( readLine, sizeof(readLine), frcFile );
249			lineNum++;
250
251
252			// read a line, and start parseing out the atom types
253
254			if( eof_test == NULL ){
255			sprintf( painCave.errMsg,
256			"Error in reading Atoms from force file at line %d.\n",
257			lineNum );
258			painCave.isFatal = 1;
259			simError();
260			}
261
262			identNum = 1;
263			// stop reading at end of file, or at next section
264			while( readLine[0] != '#' && eof_test != NULL ){
265
266			// toss comment lines
267			if( readLine[0] != '!' ){
268
269			// the parser returns 0 if the line was blank
270			if( parseAtomLJ( readLine, lineNum, info ) ){
271			info.ident = identNum;
272			headAtomType->add( info );;
273			identNum++;
274			}
275			}
276			eof_test = fgets( readLine, sizeof(readLine), frcFile );
277			lineNum++;
278			}
279
280			#ifdef IS_MPI
281
282			// send out the linked list to all the other processes
283
284			sprintf( checkPointMsg,
285			"LJ_FF atom structures read successfully." );
286			MPIcheckPoint();
287
288			currentAtomType = headAtomType->next; //skip the first element who is a place holder.
289			while( currentAtomType != NULL ){
290			currentAtomType->duplicate( info );
291
292
293
294			sendFrcStruct( &info, mpiAtomStructType );
295
296			sprintf( checkPointMsg,
297			"successfully sent lJ force type: \"%s\"\n",
298			info.name );
299			MPIcheckPoint();
300
301			currentAtomType = currentAtomType->next;
302			}
303			info.last = 1;
304			sendFrcStruct( &info, mpiAtomStructType );
305
306			}
307
308			else{
309
310			// listen for node 0 to send out the force params
311
312			MPIcheckPoint();
313
314			headAtomType = new LinkedType;
315			recieveFrcStruct( &info, mpiAtomStructType );
316
317			while( !info.last ){
318
319
320
321			headAtomType->add( info );
322
323			MPIcheckPoint();
324
325			recieveFrcStruct( &info, mpiAtomStructType );
326			}
327			}
328			#endif // is_mpi
329
330			// call new A_types in fortran
331
332			int isError;
333	mmeineke	296
334			// dummy variables
335			int isLJ = 1;
336			int isDipole = 0;
337			int isSSD = 0;
338			int isGB = 0;
339			double w0 = 0.0;
340			double v0 = 0.0;
341			double dipole = 0.0;
342
343
344	mmeineke	270	currentAtomType = headAtomType;
345			while( currentAtomType != NULL ){
346
347			if( currentAtomType->name[0] != '\0' ){
348			isError = 0;
349	mmeineke	296	newAtype( &(currentAtomType->ident),
350			&(currentAtomType->mass),
351			&(currentAtomType->epslon),
352			&(currentAtomType->sigma),
353			&isLJ, &isSSD, &isDipole, &isGB, &w0, &v0, &dipole,
354			&isError );
355	mmeineke	270	if( isError ){
356			sprintf( painCave.errMsg,
357			"Error initializing the \"%s\" atom type in fortran\n",
358			currentAtomType->name );
359			painCave.isFatal = 1;
360			simError();
361			}
362			}
363			currentAtomType = currentAtomType->next;
364			}
365
366			#ifdef IS_MPI
367			sprintf( checkPointMsg,
368			"LJ_FF atom structures successfully sent to fortran\n" );
369			MPIcheckPoint();
370			#endif // is_mpi
371
372
373
374			// initialize the atoms
375
376			double bigSigma = 0.0;
377			Atom* thisAtom;
378
379			for( i=0; i<nAtoms; i++ ){
380
381			currentAtomType = headAtomType->find( the_atoms[i]->getType() );
382			if( currentAtomType == NULL ){
383			sprintf( painCave.errMsg,
384			"AtomType error, %s not found in force file.\n",
385			the_atoms[i]->getType() );
386			painCave.isFatal = 1;
387			simError();
388			}
389
390			the_atoms[i]->setMass( currentAtomType->mass );
391			the_atoms[i]->setEpslon( currentAtomType->epslon );
392			the_atoms[i]->setSigma( currentAtomType->sigma );
393			the_atoms[i]->setIdent( currentAtomType->ident );
394			the_atoms[i]->setLJ();
395
396			if( bigSigma < currentAtomType->sigma ) bigSigma = currentAtomType->sigma;
397			}
398
399
400			#ifdef IS_MPI
401			double tempBig = bigSigma;
402			MPI::COMM_WORLD.Allreduce( &tempBig, &bigSigma, 1, MPI_DOUBLE, MPI_MAX );
403			#endif //is_mpi
404
405			//calc rCut and rList
406
407			entry_plug->rCut = 2.5 * bigSigma;
408			if(entry_plug->rCut > (entry_plug->box_x / 2.0)) entry_plug->rCut = entry_plug->box_x / 2.0;
409			if(entry_plug->rCut > (entry_plug->box_y / 2.0)) entry_plug->rCut = entry_plug->box_y / 2.0;
410			if(entry_plug->rCut > (entry_plug->box_z / 2.0)) entry_plug->rCut = entry_plug->box_z / 2.0;
411
412			entry_plug->rList = entry_plug->rCut + 1.0;
413
414			// clean up the memory
415
416			delete headAtomType;
417
418			#ifdef IS_MPI
419			sprintf( checkPointMsg, "LJ_FF atoms initialized succesfully" );
420			MPIcheckPoint();
421			#endif // is_mpi
422
423	mmeineke	299	this->initFortran();
424	mmeineke	270	entry_plug->refreshSim();
425	mmeineke	296
426	mmeineke	270	}
427
428			void LJ_FF::initializeBonds( bond_pair* the_bonds ){
429
430			if( entry_plug->n_bonds ){
431			sprintf( painCave.errMsg,
432			"LJ_FF does not support bonds.\n" );
433			painCave.isFatal = 1;
434			simError();
435			}
436			#ifdef IS_MPI
437			MPIcheckPoint();
438			#endif // is_mpi
439
440			}
441
442			void LJ_FF::initializeBends( bend_set* the_bends ){
443
444			if( entry_plug->n_bends ){
445			sprintf( painCave.errMsg,
446			"LJ_FF does not support bends.\n" );
447			painCave.isFatal = 1;
448			simError();
449			}
450			#ifdef IS_MPI
451			MPIcheckPoint();
452			#endif // is_mpi
453
454			}
455
456			void LJ_FF::initializeTorsions( torsion_set* the_torsions ){
457
458			if( entry_plug->n_torsions ){
459			sprintf( painCave.errMsg,
460			"LJ_FF does not support torsions.\n" );
461			painCave.isFatal = 1;
462			simError();
463			}
464			#ifdef IS_MPI
465			MPIcheckPoint();
466			#endif // is_mpi
467
468			}
469
470			void LJ_FF::fastForward( char* stopText, char* searchOwner ){
471
472			int foundText = 0;
473			char* the_token;
474
475			rewind( frcFile );
476			lineNum = 0;
477
478			eof_test = fgets( readLine, sizeof(readLine), frcFile );
479			lineNum++;
480			if( eof_test == NULL ){
481			sprintf( painCave.errMsg, "Error fast forwarding force file for %s: "
482			" file is empty.\n",
483			searchOwner );
484			painCave.isFatal = 1;
485			simError();
486			}
487
488
489			while( !foundText ){
490			while( eof_test != NULL && readLine[0] != '#' ){
491			eof_test = fgets( readLine, sizeof(readLine), frcFile );
492			lineNum++;
493			}
494			if( eof_test == NULL ){
495			sprintf( painCave.errMsg,
496			"Error fast forwarding force file for %s at "
497			"line %d: file ended unexpectedly.\n",
498			searchOwner,
499			lineNum );
500			painCave.isFatal = 1;
501			simError();
502			}
503
504			the_token = strtok( readLine, " ,;\t#\n" );
505			foundText = !strcmp( stopText, the_token );
506
507			if( !foundText ){
508			eof_test = fgets( readLine, sizeof(readLine), frcFile );
509			lineNum++;
510
511			if( eof_test == NULL ){
512			sprintf( painCave.errMsg,
513			"Error fast forwarding force file for %s at "
514			"line %d: file ended unexpectedly.\n",
515			searchOwner,
516			lineNum );
517			painCave.isFatal = 1;
518			simError();
519			}
520			}
521			}
522			}
523
524
525
526	mmeineke	291	int parseAtom( char *lineBuffer, int lineNum, atomStruct &info ){
527	mmeineke	270
528			char* the_token;
529
530			the_token = strtok( lineBuffer, " \n\t,;" );
531			if( the_token != NULL ){
532
533			strcpy( info.name, the_token );
534
535			if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
536			sprintf( painCave.errMsg,
537			"Error parseing AtomTypes: line %d\n", lineNum );
538			painCave.isFatal = 1;
539			simError();
540			}
541
542			info.mass = atof( the_token );
543
544			if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
545			sprintf( painCave.errMsg,
546			"Error parseing AtomTypes: line %d\n", lineNum );
547			painCave.isFatal = 1;
548			simError();
549			}
550
551			info.epslon = atof( 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.sigma = atof( the_token );
561
562			return 1;
563			}
564			else return 0;
565			}