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 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
}

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];

  // 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( 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;
  
  
  currentAtomType = headAtomType;
  while( currentAtomType != NULL ){
    
    if( currentAtomType->name[0] != '\0' ){
      isError = 0;
      makeAtype( &(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:	348
Committed:	Fri Mar 14 21:33:10 2003 UTC (21 years, 5 months ago) by mmeineke
File size:	12342 byte(s)
Log Message:	mostly compiles. interface twixt c and fortran is broken. (c needs to be brought up to date with fortran.)
#	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	348	namespace LJ_NS{
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	mmeineke	348	using namespace LJ_NS;
49	mmeineke	270
50			//****************************************************************
51			// begins the actual forcefield stuff.
52			//****************************************************************
53
54
55			LJ_FF::LJ_FF(){
56
57			char fileName[200];
58			char* ffPath_env = "FORCE_PARAM_PATH";
59			char* ffPath;
60			char temp[200];
61			char errMsg[1000];
62
63			// do the funtion wrapping
64	mmeineke	294	wrapMeFF( this );
65	mmeineke	270
66			#ifdef IS_MPI
67			int i;
68
69			// **********************************************************************
70			// Init the atomStruct mpi type
71
72			atomStruct atomProto; // mpiPrototype
73			int atomBC[3] = {15,3,2}; // block counts
74			MPI_Aint atomDspls[3]; // displacements
75			MPI_Datatype atomMbrTypes[3]; // member mpi types
76
77			MPI_Address(&atomProto.name, &atomDspls[0]);
78			MPI_Address(&atomProto.mass, &atomDspls[1]);
79			MPI_Address(&atomProto.ident, &atomDspls[2]);
80
81			atomMbrTypes[0] = MPI_CHAR;
82			atomMbrTypes[1] = MPI_DOUBLE;
83			atomMbrTypes[2] = MPI_INT;
84
85			for (i=2; i >= 0; i--) atomDspls[i] -= atomDspls[0];
86
87			MPI_Type_struct(3, atomBC, atomDspls, atomMbrTypes, &mpiAtomStructType);
88			MPI_Type_commit(&mpiAtomStructType);
89
90			// ***********************************************************************
91
92			if( worldRank == 0 ){
93			#endif
94
95			// generate the force file name
96
97			strcpy( fileName, "LJ_FF.frc" );
98			// fprintf( stderr,"Trying to open %s\n", fileName );
99
100			// attempt to open the file in the current directory first.
101
102			frcFile = fopen( fileName, "r" );
103
104			if( frcFile == NULL ){
105
106			// next see if the force path enviorment variable is set
107
108			ffPath = getenv( ffPath_env );
109			if( ffPath == NULL ) {
110	mmeineke	321	STR_DEFINE(ffPath, FRC_PATH );
111	mmeineke	270	}
112
113
114			strcpy( temp, ffPath );
115			strcat( temp, "/" );
116			strcat( temp, fileName );
117			strcpy( fileName, temp );
118
119			frcFile = fopen( fileName, "r" );
120
121			if( frcFile == NULL ){
122
123			sprintf( painCave.errMsg,
124			"Error opening the force field parameter file: %s\n"
125			"Have you tried setting the FORCE_PARAM_PATH environment "
126			"vairable?\n",
127			fileName );
128			painCave.isFatal = 1;
129			simError();
130			}
131			}
132
133			#ifdef IS_MPI
134			}
135
136			sprintf( checkPointMsg, "LJ_FF file opened sucessfully." );
137			MPIcheckPoint();
138
139			#endif // is_mpi
140			}
141
142
143			LJ_FF::~LJ_FF(){
144
145			#ifdef IS_MPI
146			if( worldRank == 0 ){
147			#endif // is_mpi
148
149			fclose( frcFile );
150
151			#ifdef IS_MPI
152			}
153			#endif // is_mpi
154			}
155
156
157
158			void LJ_FF::initializeAtoms( void ){
159
160			class LinkedType {
161			public:
162			LinkedType(){
163			next = NULL;
164			name[0] = '\0';
165			}
166			~LinkedType(){ if( next != NULL ) delete next; }
167
168			LinkedType* find(char* key){
169			if( !strcmp(name, key) ) return this;
170			if( next != NULL ) return next->find(key);
171			return NULL;
172			}
173
174
175			void add( atomStruct &info ){
176
177			// check for duplicates
178
179			if( !strcmp( info.name, name ) ){
180			sprintf( painCave.errMsg,
181			"Duplicate LJ atom type \"%s\" found in "
182			"the LJ_FF param file./n",
183			name );
184			painCave.isFatal = 1;
185			simError();
186			}
187
188			if( next != NULL ) next->add(info);
189			else{
190			next = new LinkedType();
191			strcpy(next->name, info.name);
192			next->mass = info.mass;
193			next->epslon = info.epslon;
194			next->sigma = info.sigma;
195			next->ident = info.ident;
196			}
197			}
198
199
200			#ifdef IS_MPI
201
202			void duplicate( atomStruct &info ){
203			strcpy(info.name, name);
204			info.mass = mass;
205			info.epslon = epslon;
206			info.sigma = sigma;
207			info.ident = ident;
208			info.last = 0;
209			}
210
211
212			#endif
213
214			char name[15];
215			double mass;
216			double epslon;
217			double sigma;
218			int ident;
219			LinkedType* next;
220			};
221
222			LinkedType* headAtomType;
223			LinkedType* currentAtomType;
224			atomStruct info;
225			info.last = 1; // initialize last to have the last set.
226			// if things go well, last will be set to 0
227
228			int i;
229			int identNum;
230
231			Atom** the_atoms;
232			int nAtoms;
233			the_atoms = entry_plug->atoms;
234			nAtoms = entry_plug->n_atoms;
235
236
237			#ifdef IS_MPI
238			if( worldRank == 0 ){
239			#endif
240
241			// read in the atom types.
242
243			headAtomType = new LinkedType;
244
245			fastForward( "AtomTypes", "initializeAtoms" );
246
247			// we are now at the AtomTypes section.
248
249			eof_test = fgets( readLine, sizeof(readLine), frcFile );
250			lineNum++;
251
252
253			// read a line, and start parseing out the atom types
254
255			if( eof_test == NULL ){
256			sprintf( painCave.errMsg,
257			"Error in reading Atoms from force file at line %d.\n",
258			lineNum );
259			painCave.isFatal = 1;
260			simError();
261			}
262
263			identNum = 1;
264			// stop reading at end of file, or at next section
265			while( readLine[0] != '#' && eof_test != NULL ){
266
267			// toss comment lines
268			if( readLine[0] != '!' ){
269
270			// the parser returns 0 if the line was blank
271	mmeineke	348	if( parseAtom( readLine, lineNum, info ) ){
272	mmeineke	270	info.ident = identNum;
273			headAtomType->add( info );;
274			identNum++;
275			}
276			}
277			eof_test = fgets( readLine, sizeof(readLine), frcFile );
278			lineNum++;
279			}
280
281			#ifdef IS_MPI
282
283			// send out the linked list to all the other processes
284
285			sprintf( checkPointMsg,
286			"LJ_FF atom structures read successfully." );
287			MPIcheckPoint();
288
289			currentAtomType = headAtomType->next; //skip the first element who is a place holder.
290			while( currentAtomType != NULL ){
291			currentAtomType->duplicate( info );
292
293
294
295			sendFrcStruct( &info, mpiAtomStructType );
296
297			sprintf( checkPointMsg,
298			"successfully sent lJ force type: \"%s\"\n",
299			info.name );
300			MPIcheckPoint();
301
302			currentAtomType = currentAtomType->next;
303			}
304			info.last = 1;
305			sendFrcStruct( &info, mpiAtomStructType );
306
307			}
308
309			else{
310
311			// listen for node 0 to send out the force params
312
313			MPIcheckPoint();
314
315			headAtomType = new LinkedType;
316			recieveFrcStruct( &info, mpiAtomStructType );
317
318			while( !info.last ){
319
320
321
322			headAtomType->add( info );
323
324			MPIcheckPoint();
325
326			recieveFrcStruct( &info, mpiAtomStructType );
327			}
328			}
329			#endif // is_mpi
330
331			// call new A_types in fortran
332
333			int isError;
334	mmeineke	296
335			// dummy variables
336			int isLJ = 1;
337			int isDipole = 0;
338			int isSSD = 0;
339			int isGB = 0;
340			double w0 = 0.0;
341			double v0 = 0.0;
342			double dipole = 0.0;
343
344
345	mmeineke	270	currentAtomType = headAtomType;
346			while( currentAtomType != NULL ){
347
348			if( currentAtomType->name[0] != '\0' ){
349			isError = 0;
350	mmeineke	348	makeAtype( &(currentAtomType->ident),
351	mmeineke	296	&(currentAtomType->mass),
352			&(currentAtomType->epslon),
353			&(currentAtomType->sigma),
354			&isLJ, &isSSD, &isDipole, &isGB, &w0, &v0, &dipole,
355			&isError );
356	mmeineke	270	if( isError ){
357			sprintf( painCave.errMsg,
358			"Error initializing the \"%s\" atom type in fortran\n",
359			currentAtomType->name );
360			painCave.isFatal = 1;
361			simError();
362			}
363			}
364			currentAtomType = currentAtomType->next;
365			}
366
367			#ifdef IS_MPI
368			sprintf( checkPointMsg,
369			"LJ_FF atom structures successfully sent to fortran\n" );
370			MPIcheckPoint();
371			#endif // is_mpi
372
373
374
375			// initialize the atoms
376
377			double bigSigma = 0.0;
378			Atom* thisAtom;
379
380			for( i=0; i<nAtoms; i++ ){
381
382			currentAtomType = headAtomType->find( the_atoms[i]->getType() );
383			if( currentAtomType == NULL ){
384			sprintf( painCave.errMsg,
385			"AtomType error, %s not found in force file.\n",
386			the_atoms[i]->getType() );
387			painCave.isFatal = 1;
388			simError();
389			}
390
391			the_atoms[i]->setMass( currentAtomType->mass );
392			the_atoms[i]->setEpslon( currentAtomType->epslon );
393			the_atoms[i]->setSigma( currentAtomType->sigma );
394			the_atoms[i]->setIdent( currentAtomType->ident );
395			the_atoms[i]->setLJ();
396
397			if( bigSigma < currentAtomType->sigma ) bigSigma = currentAtomType->sigma;
398			}
399
400
401			#ifdef IS_MPI
402			double tempBig = bigSigma;
403			MPI::COMM_WORLD.Allreduce( &tempBig, &bigSigma, 1, MPI_DOUBLE, MPI_MAX );
404			#endif //is_mpi
405
406			//calc rCut and rList
407
408			entry_plug->rCut = 2.5 * bigSigma;
409			if(entry_plug->rCut > (entry_plug->box_x / 2.0)) entry_plug->rCut = entry_plug->box_x / 2.0;
410			if(entry_plug->rCut > (entry_plug->box_y / 2.0)) entry_plug->rCut = entry_plug->box_y / 2.0;
411			if(entry_plug->rCut > (entry_plug->box_z / 2.0)) entry_plug->rCut = entry_plug->box_z / 2.0;
412
413			entry_plug->rList = entry_plug->rCut + 1.0;
414
415			// clean up the memory
416
417			delete headAtomType;
418
419			#ifdef IS_MPI
420			sprintf( checkPointMsg, "LJ_FF atoms initialized succesfully" );
421			MPIcheckPoint();
422			#endif // is_mpi
423
424	mmeineke	299	this->initFortran();
425	mmeineke	270	entry_plug->refreshSim();
426	mmeineke	296
427	mmeineke	270	}
428
429			void LJ_FF::initializeBonds( bond_pair* the_bonds ){
430
431			if( entry_plug->n_bonds ){
432			sprintf( painCave.errMsg,
433			"LJ_FF does not support bonds.\n" );
434			painCave.isFatal = 1;
435			simError();
436			}
437			#ifdef IS_MPI
438			MPIcheckPoint();
439			#endif // is_mpi
440
441			}
442
443			void LJ_FF::initializeBends( bend_set* the_bends ){
444
445			if( entry_plug->n_bends ){
446			sprintf( painCave.errMsg,
447			"LJ_FF does not support bends.\n" );
448			painCave.isFatal = 1;
449			simError();
450			}
451			#ifdef IS_MPI
452			MPIcheckPoint();
453			#endif // is_mpi
454
455			}
456
457			void LJ_FF::initializeTorsions( torsion_set* the_torsions ){
458
459			if( entry_plug->n_torsions ){
460			sprintf( painCave.errMsg,
461			"LJ_FF does not support torsions.\n" );
462			painCave.isFatal = 1;
463			simError();
464			}
465			#ifdef IS_MPI
466			MPIcheckPoint();
467			#endif // is_mpi
468
469			}
470
471			void LJ_FF::fastForward( char* stopText, char* searchOwner ){
472
473			int foundText = 0;
474			char* the_token;
475
476			rewind( frcFile );
477			lineNum = 0;
478
479			eof_test = fgets( readLine, sizeof(readLine), frcFile );
480			lineNum++;
481			if( eof_test == NULL ){
482			sprintf( painCave.errMsg, "Error fast forwarding force file for %s: "
483			" file is empty.\n",
484			searchOwner );
485			painCave.isFatal = 1;
486			simError();
487			}
488
489
490			while( !foundText ){
491			while( eof_test != NULL && readLine[0] != '#' ){
492			eof_test = fgets( readLine, sizeof(readLine), frcFile );
493			lineNum++;
494			}
495			if( eof_test == NULL ){
496			sprintf( painCave.errMsg,
497			"Error fast forwarding force file for %s at "
498			"line %d: file ended unexpectedly.\n",
499			searchOwner,
500			lineNum );
501			painCave.isFatal = 1;
502			simError();
503			}
504
505			the_token = strtok( readLine, " ,;\t#\n" );
506			foundText = !strcmp( stopText, the_token );
507
508			if( !foundText ){
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			}
523			}
524
525
526
527	mmeineke	291	int parseAtom( char *lineBuffer, int lineNum, atomStruct &info ){
528	mmeineke	270
529			char* the_token;
530
531			the_token = strtok( lineBuffer, " \n\t,;" );
532			if( the_token != NULL ){
533
534			strcpy( info.name, the_token );
535
536			if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
537			sprintf( painCave.errMsg,
538			"Error parseing AtomTypes: line %d\n", lineNum );
539			painCave.isFatal = 1;
540			simError();
541			}
542
543			info.mass = atof( the_token );
544
545			if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
546			sprintf( painCave.errMsg,
547			"Error parseing AtomTypes: line %d\n", lineNum );
548			painCave.isFatal = 1;
549			simError();
550			}
551
552			info.epslon = atof( the_token );
553
554			if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
555			sprintf( painCave.errMsg,
556			"Error parseing AtomTypes: line %d\n", lineNum );
557			painCave.isFatal = 1;
558			simError();
559			}
560
561			info.sigma = atof( the_token );
562
563			return 1;
564			}
565			else return 0;
566			}