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root/group/trunk/OOPSE-2.0/src/UseTheForce/Shapes_FF.cpp
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Comparing trunk/OOPSE-2.0/src/UseTheForce/Shapes_FF.cpp (file contents):
Revision 1613 by gezelter, Wed Oct 20 04:54:23 2004 UTC vs.
Revision 1688 by chrisfen, Fri Oct 29 22:28:12 2004 UTC

# Line 1 | Line 1
1 + /*
2 + *  Shapes_FF.cpp
3 + *  oopse
4 + *
5 + *  Created by Chris Fennell on 10/20/04.
6 + *  Copyright 2004 __MyCompanyName__. All rights reserved.
7 + *
8 + */
9 +
10   #include <stdlib.h>
11   #include <stdio.h>
12   #include <string.h>
13 <
13 > #include <map>
14 > #include <cmath>
15   #include <iostream>
6 – using namespace std;
16  
17   #ifdef IS_MPI
18   #include <mpi.h>
# Line 12 | Line 21 | using namespace std;
21   #include "UseTheForce/ForceFields.hpp"
22   #include "primitives/SRI.hpp"
23   #include "utils/simError.h"
24 <
25 < #include "UseTheForce/fortranWrappers.hpp"
24 > #include "utils/StringUtils.hpp"
25 > #include "io/basic_ifstrstream.hpp"
26 > #include "math/RealSphericalHarmonic.hpp"
27 > #include "math/SquareMatrix3.hpp"
28 > #include "types/ShapeAtomType.hpp"
29 > #include "UseTheForce/DarkSide/atype_interface.h"
30   #include "UseTheForce/DarkSide/shapes_interface.h"
31  
32   #ifdef IS_MPI
33   #include "UseTheForce/mpiForceField.h"
34   #endif // is_mpi
35  
36 < Shapes_FF::Shapes_FF() {
37 <  Shapes_FF("");
25 < }
36 > using namespace std;
37 > using namespace oopse;
38  
27 – Shapes_FF::Shapes_FF(char* the_variant){
28 –
29 –  char fileName[200];
30 –  char* ffPath_env = "FORCE_PARAM_PATH";
31 –  char* ffPath;
32 –  char temp[200];
33 –
34 –  // do the funtion wrapping
35 –  wrapMeFF( this );
36 –
37 – #ifdef IS_MPI    
38 –  if( worldRank == 0 ){
39 – #endif
40 –    
41 –    // generate the force file name  
42 –
43 –    strcpy( fileName, "Shapes" );
44 –
45 –    if (strlen(the_variant) > 0) {
46 –      has_variant = 1;
47 –      strcpy( variant, the_variant);
48 –      strcat( fileName, ".");
49 –      strcat( fileName, variant );
50 –
51 –      sprintf( painCave.errMsg,
52 –               "Using %s variant of Shapes force field.\n",
53 –               variant );
54 –      painCave.severity = OOPSE_INFO;
55 –      painCave.isFatal = 0;
56 –      simError();
57 –    }
58 –    strcat( fileName, ".frc");
59 –    
60 –    // attempt to open the file in the current directory first.
61 –    
62 –    frcFile = fopen( fileName, "r" );
63 –    
64 –    if( frcFile == NULL ){
65 –      
66 –      // next see if the force path enviorment variable is set
67 –      
68 –      ffPath = getenv( ffPath_env );
69 –      if( ffPath == NULL ) {
70 –        STR_DEFINE(ffPath, FRC_PATH );
71 –      }
72 –      
73 –      
74 –      strcpy( temp, ffPath );
75 –      strcat( temp, "/" );
76 –      strcat( temp, fileName );
77 –      strcpy( fileName, temp );
78 –      
79 –      frcFile = fopen( fileName, "r" );
80 –      
81 –      if( frcFile == NULL ){
82 –        
83 –        sprintf( painCave.errMsg,
84 –                 "Error opening the force field parameter file:\n"
85 –                 "\t%s\n"
86 –                 "\tHave you tried setting the FORCE_PARAM_PATH environment "
87 –                 "variable?\n",
88 –                 fileName );
89 –        painCave.severity = OOPSE_ERROR;
90 –        painCave.isFatal = 1;
91 –        simError();
92 –      }
93 –    }
94 –    
95 –    
96 – #ifdef IS_MPI
97 –  }
98 –  
99 –  sprintf( checkPointMsg, "Shapes_FF file opened sucessfully." );
100 –  MPIcheckPoint();
101 –  
102 – #endif // is_mpi
103 – }
104 –
105 –
39   Shapes_FF::~Shapes_FF(){
40  
41   #ifdef IS_MPI
42    if( worldRank == 0 ){
43   #endif // is_mpi
44      
45 <    fclose( frcFile );
45 >    forceFile.close();
46      
47   #ifdef IS_MPI
48    }
# Line 120 | Line 53 | void Shapes_FF::calcRcut( void ){
53   void Shapes_FF::calcRcut( void ){
54    
55   #ifdef IS_MPI
56 <  double tempShapesRcut = shapesRcut;
56 >  double tempShapesRcut = bigContact;
57    MPI_Allreduce( &tempShapesRcut, &shapesRcut, 1, MPI_DOUBLE, MPI_MAX,
58                   MPI_COMM_WORLD);
59 + #else
60 +  shapesRcut = bigContact;
61   #endif  //is_mpi
62    entry_plug->setDefaultRcut(shapesRcut);
63   }
64  
65  
66 < void Shapes_FF::initForceField(int ljMixRule){
67 <  initFortran(ljMixRule, 0);
66 > void Shapes_FF::initForceField(){
67 >  initFortran(0);
68   }
69  
70  
71   void Shapes_FF::readParams( void ){
72  
73 <  char shapePotFile[1000];
139 <  
140 < #ifdef IS_MPI
141 <  if( worldRank == 0 ){
142 < #endif
143 <    
144 <    // read in the atom types.
73 >  char readLine[1024];
74  
75 <    fastForward( "AtomTypes", "eam atom readParams" );
75 >  string fileName;
76 >  string shapeFileName;
77 >  string tempString;
78  
79 <    // we are now at the AtomTypes section.
79 >  char *nameToken;
80 >  char *delim = " ,;\t\n";
81 >  int nTokens, i;
82 >  int nContact = 0;
83 >  int nRange = 0;
84 >  int nStrength = 0;
85 >  int myATID;
86 >  int isError;
87 >  string nameString;
88 >  AtomType* at;
89 >  DirectionalAtomType* dat;
90 >  ShapeAtomType* st;
91 >
92 >  map<string, AtomType*>::iterator iter;
93 >
94 >  // vectors for shape transfer to fortran
95 >  vector<RealSphericalHarmonic*> tempSHVector;
96 >  vector<int> contactL;
97 >  vector<int> contactM;
98 >  vector<int> contactFunc;
99 >  vector<double> contactCoeff;
100 >  vector<int> rangeL;
101 >  vector<int> rangeM;
102 >  vector<int> rangeFunc;
103 >  vector<double> rangeCoeff;
104 >  vector<int> strengthL;
105 >  vector<int> strengthM;
106 >  vector<int> strengthFunc;
107 >  vector<double> strengthCoeff;
108 >  
109 >  // generate the force file name  
110 >  fileName = "Shapes.frc";
111 >  
112 >  // attempt to open the file in the current directory first.
113 >  forceFile.open( fileName.c_str() );
114 >  
115 >  if( forceFile == NULL ){
116      
117 <    eof_test = fgets( readLine, sizeof(readLine), frcFile );
118 <    lineNum++;
117 >    tempString = ffPath;
118 >    tempString += "/";
119 >    tempString += fileName;
120 >    fileName = tempString;
121      
122 +    forceFile.open( fileName.c_str() );
123      
124 <    // read a line, and start parseing out the atom types
125 <
126 <    if( eof_test == NULL ){
127 <      sprintf( painCave.errMsg,
128 <               "Error in reading Atoms from force file at line %d.\n",
129 <               lineNum );
124 >    if( forceFile == NULL ){
125 >      
126 >      sprintf( painCave.errMsg,
127 >               "Error opening the force field parameter file:\n"
128 >               "\t%s\n"
129 >               "\tHave you tried setting the FORCE_PARAM_PATH environment "
130 >               "variable?\n",
131 >               fileName.c_str() );
132 >      painCave.severity = OOPSE_ERROR;
133        painCave.isFatal = 1;
134        simError();
135      }
136 <    
137 <    identNum = 1;
138 <    // stop reading at end of file, or at next section
136 >  }
137 >  
138 >  // read in the shape types.
139 >  
140 >  findBegin( forceFile, "ShapeTypes" );
141 >  
142 >  while( !forceFile.eof() ){
143 >    forceFile.getline( readLine, sizeof(readLine) );
144  
145 <    while( readLine[0] != '#' && eof_test != NULL ){
146 <
147 <      // toss comment lines
148 <      if( readLine[0] != '!' ){
149 <        
150 <        // the parser returns 0 if the line was blank
151 <        if( parseAtom( readLine, lineNum, info, eamPotFile ) ){
152 <          parseEAM(info,eamPotFile, &eam_rvals,
153 <                   &eam_rhovals, &eam_Frhovals);
154 <          info.ident = identNum;
155 <          headAtomType->add( info, eam_rvals,
156 <                             eam_rhovals,eam_Frhovals );
157 <          identNum++;
145 >    // toss comment lines
146 >    if( readLine[0] != '!' && readLine[0] != '#' ){
147 >      
148 >      if (isEndLine(readLine)) break;
149 >      
150 >      nTokens = countTokens(readLine, " ,;\t");
151 >      if (nTokens != 0) {
152 >        if (nTokens < 2) {
153 >          sprintf( painCave.errMsg,
154 >                   "Not enough data on a ShapeTypes line in file: %s\n",
155 >                   fileName.c_str() );
156 >          painCave.severity = OOPSE_ERROR;
157 >          painCave.isFatal = 1;
158 >          simError();
159          }
160 <      }
161 <      eof_test = fgets( readLine, sizeof(readLine), frcFile );
162 <      lineNum++;
184 <    }
185 <    
186 <    
160 >        
161 >        nameToken = strtok( readLine, delim );
162 >        shapeFileName = strtok( NULL, delim );
163  
164 < #ifdef IS_MPI
165 <  
190 <    
191 <    // send out the linked list to all the other processes
164 >        // strings are not char arrays!
165 >        nameString = nameToken;
166  
167 <    sprintf( checkPointMsg,
168 <             "Shapes_FF atom structures read successfully." );
169 <    MPIcheckPoint();
167 >        // does this AtomType name already exist in the map?
168 >        iter = atomTypeMap.find(nameString);    
169 >        if (iter == atomTypeMap.end()) {
170 >          // no, it doesn't, so we may proceed:
171 >          
172 >          st = new ShapeAtomType();
173  
174 <    currentAtomType = headAtomType->next; //skip the first element who is a place holder.
175 <    while( currentAtomType != NULL ){
176 <      currentAtomType->duplicate( info );
174 >          st->setName(nameString);
175 >          myATID = atomTypeMap.size() + 1;
176 >          st->setIdent(myATID);
177 >          parseShapeFile(shapeFileName, st);
178 >          st->complete();
179 >          atomTypeMap.insert(make_pair(nameString, st));
180 >          
181 >        } else {
182 >          // atomType map already contained this string (i.e. it was
183 >          // declared in a previous block, and we just need to add
184 >          // the shape-specific information for this AtomType:
185  
186 <
187 <
188 <      sendFrcStruct( &info, mpiAtomStructType );
189 <
205 <      // We have to now broadcast the Arrays
206 <      MPI_Bcast(currentAtomType->eam_rvals,
207 <                currentAtomType->eam_nr,
208 <                MPI_DOUBLE,0,MPI_COMM_WORLD);
209 <      MPI_Bcast(currentAtomType->eam_rhovals,
210 <                currentAtomType->eam_nr,
211 <                MPI_DOUBLE,0,MPI_COMM_WORLD);
212 <      MPI_Bcast(currentAtomType->eam_Frhovals,
213 <                currentAtomType->eam_nrho,
214 <                MPI_DOUBLE,0,MPI_COMM_WORLD);
215 <
216 <      sprintf( checkPointMsg,
217 <               "successfully sent EAM force type: \"%s\"\n",
218 <               info.name );
219 <      MPIcheckPoint();
220 <
221 <      currentAtomType = currentAtomType->next;
186 >          st = (ShapeAtomType*)(iter->second);
187 >          parseShapeFile(shapeFileName, st);
188 >        }
189 >      }
190      }
223 –    info.last = 1;
224 –    sendFrcStruct( &info, mpiAtomStructType );
225 –    
191    }
192  
193 <  else{
229 <    
230 <    // listen for node 0 to send out the force params
231 <    
232 <    MPIcheckPoint();
193 > #ifdef IS_MPI
194  
195 <    headAtomType = new LinkedAtomType;
196 <    receiveFrcStruct( &info, mpiAtomStructType );
195 >  // looks like all the processors have their ShapeType vectors ready...
196 >  sprintf( checkPointMsg,
197 >           "Shapes_FF shape objects read successfully." );
198 >  MPIcheckPoint();
199  
200 <    while( !info.last ){
238 <      
239 <      // allocate the arrays
200 > #endif // is_mpi
201  
202 <      eam_rvals    = new double[info.eam_nr];
203 <      eam_rhovals  = new double[info.eam_nr];
243 <      eam_Frhovals = new double[info.eam_nrho];
202 >  // pack up and send the necessary info to fortran
203 >  for (iter = atomTypeMap.begin(); iter != atomTypeMap.end(); ++iter){
204  
205 <      // We have to now broadcast the Arrays
246 <      MPI_Bcast(eam_rvals,
247 <                info.eam_nr,
248 <                MPI_DOUBLE,0,MPI_COMM_WORLD);
249 <      MPI_Bcast(eam_rhovals,
250 <                info.eam_nr,
251 <                MPI_DOUBLE,0,MPI_COMM_WORLD);
252 <      MPI_Bcast(eam_Frhovals,
253 <                info.eam_nrho,
254 <                MPI_DOUBLE,0,MPI_COMM_WORLD);
255 <      
205 >    at = (AtomType*)(iter->second);
206  
207 <      headAtomType->add( info, eam_rvals, eam_rhovals, eam_Frhovals );
258 <      
259 <      MPIcheckPoint();
207 >    if (at->isDirectional()) {
208  
209 <      receiveFrcStruct( &info, mpiAtomStructType );
209 >      dat = (DirectionalAtomType*)at;
210  
211 +      if (dat->isShape()) {
212  
213 <    }
214 <  }
215 < #endif // is_mpi
213 >        st = (ShapeAtomType*)at;
214 >        
215 >        contactL.clear();
216 >        contactM.clear();
217 >        contactFunc.clear();
218 >        contactCoeff.clear();
219 >        
220 >        tempSHVector = st->getContactFuncs();
221 >        
222 >        nContact = tempSHVector.size();
223 >        for (i=0; i<nContact; i++){
224 >          contactL.push_back(tempSHVector[i]->getL());
225 >          contactM.push_back(tempSHVector[i]->getM());
226 >          contactFunc.push_back(tempSHVector[i]->getFunctionType());
227 >          contactCoeff.push_back(tempSHVector[i]->getCoefficient());
228 >        }
229 >        
230 >        rangeL.clear();
231 >        rangeM.clear();
232 >        rangeFunc.clear();
233 >        rangeCoeff.clear();
234 >        
235 >        tempSHVector = st->getRangeFuncs();
236 >        
237 >        nRange = tempSHVector.size();
238 >        for (i=0; i<nRange; i++){
239 >          rangeL.push_back(tempSHVector[i]->getL());
240 >          rangeM.push_back(tempSHVector[i]->getM());
241 >          rangeFunc.push_back(tempSHVector[i]->getFunctionType());
242 >          rangeCoeff.push_back(tempSHVector[i]->getCoefficient());
243 >        }
244 >        
245 >        strengthL.clear();
246 >        strengthM.clear();
247 >        strengthFunc.clear();
248 >        strengthCoeff.clear();
249 >        
250 >        tempSHVector = st->getStrengthFuncs();
251 >        
252 >        nStrength = tempSHVector.size();
253 >        for (i=0; i<nStrength; i++){
254 >          strengthL.push_back(tempSHVector[i]->getL());
255 >          strengthM.push_back(tempSHVector[i]->getM());
256 >          strengthFunc.push_back(tempSHVector[i]->getFunctionType());
257 >          strengthCoeff.push_back(tempSHVector[i]->getCoefficient());
258 >        }
259 >        
260 >        isError = 0;
261 >        myATID = at->getIdent();
262  
263 <  // call new A_types in fortran
264 <  
265 <  int isError;
263 >        makeShape( &nContact, &contactL[0], &contactM[0], &contactFunc[0],
264 >                   &contactCoeff[0],
265 >                   &nRange, &rangeL[0], &rangeM[0], &rangeFunc[0],
266 >                   &rangeCoeff[0],
267 >                   &nStrength, &strengthL[0], &strengthM[0],
268 >                   &strengthFunc[0], &strengthCoeff[0],
269 >                   &myATID,
270 >                   &isError);
271  
272 <  // dummy variables
273 <  int isLJ = 0;
274 <  int isDipole = 0;
275 <  int isSSD = 0;
276 <  int isGB = 0;
277 <  int isEAM = 1;
278 <  int isCharge = 0;
279 <  double dipole = 0.0;
280 <  double charge = 0.0;
281 <  double eamSigma = 0.0;
282 <  double eamEpslon = 0.0;
283 <  
284 <  currentAtomType = headAtomType->next;
285 <  while( currentAtomType != NULL ){
286 <    
287 <    if( currentAtomType->name[0] != '\0' ){
288 <      isError = 0;
289 <      makeAtype( &(currentAtomType->ident),
290 <                 &isLJ,
291 <                 &isSSD,
292 <                 &isDipole,
293 <                 &isGB,
294 <                 &isEAM,
295 <                 &isCharge,
296 <                 &eamEpslon,
297 <                 &eamSigma,
298 <                 &charge,
299 <                 &dipole,
300 <                 &isError );
301 <      if( isError ){
302 <        sprintf( painCave.errMsg,
303 <                 "Error initializing the \"%s\" atom type in fortran\n",
304 <                 currentAtomType->name );
305 <        painCave.isFatal = 1;
306 <        simError();
272 >        if( isError ){
273 >          sprintf( painCave.errMsg,
274 >                   "Error initializing the \"%s\" shape in fortran\n",
275 >                   (iter->first).c_str() );
276 >          painCave.isFatal = 1;
277 >          simError();
278 >        }
279        }
280      }
309 –    currentAtomType = currentAtomType->next;
281    }
282 <      
283 <  entry_plug->useLJ = 0;
284 <  entry_plug->useEAM = 1;
285 <  // Walk down again and send out EAM type
286 <  currentAtomType = headAtomType->next;
287 <  while( currentAtomType != NULL ){
288 <    
289 <    if( currentAtomType->name[0] != '\0' ){
319 <      isError = 0;
320 <
321 <      newEAMtype( &(currentAtomType->lattice_constant),
322 <                  &(currentAtomType->eam_nrho),
323 <                  &(currentAtomType->eam_drho),
324 <                  &(currentAtomType->eam_nr),
325 <                  &(currentAtomType->eam_dr),
326 <                  &(currentAtomType->eam_rcut),
327 <                  currentAtomType->eam_rvals,
328 <                  currentAtomType->eam_rhovals,
329 <                  currentAtomType->eam_Frhovals,
330 <                  &(currentAtomType->eam_ident),
331 <                  &isError);
332 <
333 <      if( isError ){
334 <        sprintf( painCave.errMsg,
335 <                 "Error initializing the \"%s\" atom type in fortran EAM\n",
336 <                 currentAtomType->name );
337 <        painCave.isFatal = 1;
338 <        simError();
339 <      }
340 <    }
341 <    currentAtomType = currentAtomType->next;
282 >  
283 >  isError = 0;
284 >  completeShapeFF(&isError);
285 >  if( isError ){
286 >    sprintf( painCave.errMsg,
287 >             "Error completing Shape FF in fortran\n");
288 >    painCave.isFatal = 1;
289 >    simError();
290    }
291 <
344 <
345 <
291 >  
292   #ifdef IS_MPI
293    sprintf( checkPointMsg,
294             "Shapes_FF atom structures successfully sent to fortran\n" );
295    MPIcheckPoint();
296   #endif // is_mpi
297  
298 + }
299  
300 + void Shapes_FF::cleanMe( void ){
301  
302   }
303  
356 –
304   void Shapes_FF::initializeAtoms( int nAtoms, Atom** the_atoms ){
305    
306 <  int i;
307 <  
306 >  int i,j,k;
307 >  map<string, AtomType*>::iterator iter;
308 >
309    // initialize the atoms
310 <  
310 >  DirectionalAtom* dAtom;
311 >  AtomType* at;
312 >  DirectionalAtomType* dat;
313 >  ShapeAtomType* sat;
314 >  double longCutoff;
315 >  double ji[3];
316 >  double inertialMat[3][3];
317 >  Mat3x3d momInt;
318 >  string myTypeString;
319 >
320 >  bigContact = 0.0;
321 >
322    for( i=0; i<nAtoms; i++ ){
323      
324 <    currentAtomType = headAtomType->find( the_atoms[i]->getType() );
325 <    if( currentAtomType == NULL ){
324 >    myTypeString = the_atoms[i]->getType();
325 >    iter = atomTypeMap.find(myTypeString);
326 >
327 >    if (iter == atomTypeMap.end()) {
328        sprintf( painCave.errMsg,
329                 "AtomType error, %s not found in force file.\n",
330                 the_atoms[i]->getType() );
331        painCave.isFatal = 1;
332        simError();
333 <    }
373 <    
374 <    the_atoms[i]->setMass( currentAtomType->mass );
375 <    the_atoms[i]->setIdent( currentAtomType->ident );
333 >    } else {
334  
335 <    if (eamRcut < currentAtomType->eam_rcut) eamRcut = currentAtomType->eam_rcut;
378 <    
379 <  }
380 < }
335 >      at = (AtomType*)(iter->second);
336  
337 < void Shapes_FF::initializeBonds( int nBonds, Bond** BondArray,
338 <                             bond_pair* the_bonds ){
339 <  
340 <    if( nBonds ){
341 <      sprintf( painCave.errMsg,
342 <               "LJ_FF does not support bonds.\n" );
343 <      painCave.isFatal = 1;
344 <      simError();
345 <    }
346 < }
337 >      the_atoms[i]->setMass( at->getMass() );
338 >      the_atoms[i]->setIdent( at->getIdent() );
339 >      
340 >      if ( at->isShape() ) {
341 >        
342 >        sat = (ShapeAtomType*)at;
343 >        longCutoff = findCutoffDistance(sat);
344 >        if (longCutoff > bigContact) bigContact = longCutoff;  
345 >        cout << bigContact << " is the cutoff value\n";
346 >        
347 >        entry_plug->useShapes = 1;
348 >      }
349  
350 < void Shapes_FF::initializeBends( int nBends, Bend** bendArray,
394 <                             bend_set* the_bends ){
350 >      the_atoms[i]->setHasCharge(at->isCharge());
351  
352 <    if( nBends ){
397 <      sprintf( painCave.errMsg,
398 <               "LJ_FF does not support bends.\n" );
399 <      painCave.isFatal = 1;
400 <      simError();
401 <    }
402 < }
352 >      if( at->isDirectional() ){
353  
354 < void Shapes_FF::initializeTorsions( int nTorsions, Torsion** torsionArray,
355 <                                torsion_set* the_torsions ){
354 >        dat = (DirectionalAtomType*)at;
355 >        dAtom = (DirectionalAtom *) the_atoms[i];
356 >        
357 >        momInt = dat->getI();
358  
359 <    if( nTorsions ){
360 <      sprintf( painCave.errMsg,
361 <               "LJ_FF does not support torsions.\n" );
362 <      painCave.isFatal = 1;
363 <      simError();
359 >        // zero out the moments of inertia matrix
360 >        for( j=0; j<3; j++ )
361 >          for( k=0; k<3; k++ )
362 >            inertialMat[j][k] = momInt(j,k);
363 >        dAtom->setI( inertialMat );            
364 >
365 >        ji[0] = 0.0;
366 >        ji[1] = 0.0;
367 >        ji[2] = 0.0;
368 >        dAtom->setJ( ji );
369 >
370 >        if (dat->isDipole()) {
371 >          dAtom->setHasDipole( dat->isDipole() );
372 >          entry_plug->n_dipoles++;
373 >        }              
374 >      }
375      }
376 +  }
377   }
378  
379 < void Shapes_FF::fastForward( char* stopText, char* searchOwner ){
380 <
381 <  int foundText = 0;
382 <  char* the_token;
383 <
384 <  rewind( frcFile );
421 <  lineNum = 0;
422 <
423 <  eof_test = fgets( readLine, sizeof(readLine), frcFile );
424 <  lineNum++;
425 <  if( eof_test == NULL ){
426 <    sprintf( painCave.errMsg, "Error fast forwarding force file for %s: "
427 <             " file is empty.\n",
428 <             searchOwner );
379 > void Shapes_FF::initializeBonds( int nBonds, Bond** BondArray,
380 >                                 bond_pair* the_bonds ){
381 >  
382 >  if( nBonds ){
383 >    sprintf( painCave.errMsg,
384 >             "Shapes_FF does not support bonds.\n" );
385      painCave.isFatal = 1;
386      simError();
387    }
388 + }
389 +
390 + void Shapes_FF::initializeBends( int nBends, Bend** bendArray,
391 +                                 bend_set* the_bends ){
392    
393 <  
394 <  while( !foundText ){
395 <    while( eof_test != NULL && readLine[0] != '#' ){
396 <      eof_test = fgets( readLine, sizeof(readLine), frcFile );
397 <      lineNum++;
398 <    }
439 <    if( eof_test == NULL ){
440 <      sprintf( painCave.errMsg,
441 <               "Error fast forwarding force file for %s at "
442 <               "line %d: file ended unexpectedly.\n",
443 <               searchOwner,
444 <               lineNum );
445 <      painCave.isFatal = 1;
446 <      simError();
447 <    }
448 <    
449 <    the_token = strtok( readLine, " ,;\t#\n" );
450 <    foundText = !strcmp( stopText, the_token );
451 <    
452 <    if( !foundText ){
453 <      eof_test = fgets( readLine, sizeof(readLine), frcFile );
454 <      lineNum++;
455 <      
456 <      if( eof_test == NULL ){
457 <        sprintf( painCave.errMsg,
458 <                 "Error fast forwarding force file for %s at "
459 <                 "line %d: file ended unexpectedly.\n",
460 <                 searchOwner,
461 <                 lineNum );
462 <        painCave.isFatal = 1;
463 <        simError();
464 <      }
465 <    }
466 <  }  
393 >  if( nBends ){
394 >    sprintf( painCave.errMsg,
395 >             "Shapes_FF does not support bends.\n" );
396 >    painCave.isFatal = 1;
397 >    simError();
398 >  }
399   }
400  
401 <
402 <
471 < int EAM_NS::parseAtom( char *lineBuffer, int lineNum,   atomStruct &info, char *eamPotFile ){
472 <
473 <  char* the_token;
401 > void Shapes_FF::initializeTorsions( int nTorsions, Torsion** torsionArray,
402 >                                    torsion_set* the_torsions ){
403    
404 <  the_token = strtok( lineBuffer, " \n\t,;" );
405 <  if( the_token != NULL ){
406 <    
407 <    strcpy( info.name, the_token );
408 <          
480 <    if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
481 <      sprintf( painCave.errMsg,
482 <               "Error parseing AtomTypes: line %d\n", lineNum );
483 <      painCave.isFatal = 1;
484 <      simError();
485 <    }
486 <    
487 <    info.mass = atof( the_token );
488 <    
489 <    if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
490 <      sprintf( painCave.errMsg,
491 <               "Error parseing AtomTypes: line %d\n", lineNum );
492 <      painCave.isFatal = 1;
493 <      simError();
494 <    }
495 <        
496 <    strcpy( eamPotFile, the_token );
497 <    return 1;
404 >  if( nTorsions ){
405 >    sprintf( painCave.errMsg,
406 >             "Shapes_FF does not support torsions.\n" );
407 >    painCave.isFatal = 1;
408 >    simError();
409    }
499 –  else return 0;
410   }
411  
412 < int EAM_NS::parseEAM(atomStruct &info, char *eamPotFile,
413 <                     double **eam_rvals,
414 <                     double **eam_rhovals,
415 <                     double **eam_Frhovals){
416 <  double* myEam_rvals;
417 <  double* myEam_rhovals;
418 <  double* myEam_Frhovals;
412 > void Shapes_FF::parseShapeFile(string shapeFileName, ShapeAtomType* st){
413 >  const int MAXLEN = 1024;
414 >  char inLine[MAXLEN];  
415 >  char *token;
416 >  char *delim = " ,;\t\n";
417 >  int nTokens;
418 >  Mat3x3d momInert;
419 >  RealSphericalHarmonic* rsh;
420 >  vector<RealSphericalHarmonic*> functionVector;
421 >  ifstrstream shapeFile;
422 >  string tempString;
423  
424 <  char* ffPath_env = "FORCE_PARAM_PATH";
511 <  char* ffPath;
512 <  char* the_token;
513 <  char* eam_eof_test;
514 <  FILE *eamFile;
515 <  const int BUFFERSIZE = 3000;
516 <
517 <  char temp[200];
518 <  int linenumber;
519 <  int nReadLines;
520 <  char eam_read_buffer[BUFFERSIZE];
521 <
522 <
523 <  int i,j;
524 <
525 <  linenumber = 0;
526 <
527 <  // Open eam file
528 <  eamFile = fopen( eamPotFile, "r" );
424 >  shapeFile.open( shapeFileName.c_str() );
425    
426 <  
531 <  if( eamFile == NULL ){
426 >  if( shapeFile == NULL ){
427      
428 <      // next see if the force path enviorment variable is set
428 >    tempString = ffPath;
429 >    tempString += "/";
430 >    tempString += shapeFileName;
431 >    shapeFileName = tempString;
432 >        
433 >    shapeFile.open( shapeFileName.c_str() );
434      
435 <    ffPath = getenv( ffPath_env );
536 <    if( ffPath == NULL ) {
537 <      STR_DEFINE(ffPath, FRC_PATH );
538 <    }
539 <    
540 <    
541 <    strcpy( temp, ffPath );
542 <    strcat( temp, "/" );
543 <    strcat( temp, eamPotFile );
544 <    strcpy( eamPotFile, temp );
545 <    
546 <    eamFile = fopen( eamPotFile, "r" );
547 <
548 <    
549 <    
550 <    if( eamFile == NULL ){
435 >    if( shapeFile == NULL ){
436        
437        sprintf( painCave.errMsg,
438 <               "Error opening the EAM force parameter file: %s\n"
439 <               "Have you tried setting the FORCE_PARAM_PATH environment "
438 >               "Error opening the shape file:\n"
439 >               "\t%s\n"
440 >               "\tHave you tried setting the FORCE_PARAM_PATH environment "
441                 "variable?\n",
442 <               eamPotFile );
442 >               shapeFileName.c_str() );
443 >      painCave.severity = OOPSE_ERROR;
444        painCave.isFatal = 1;
445        simError();
446      }
447    }
448 <
449 <  // First line is a comment line, read and toss it....
450 <  eam_eof_test = fgets(eam_read_buffer, sizeof(eam_read_buffer),eamFile);
451 <  linenumber++;
452 <  if(eam_eof_test == NULL){
453 <    sprintf( painCave.errMsg,
454 <             "error in reading commment in %s\n", eamPotFile);
455 <    painCave.isFatal = 1;
456 <    simError();
448 >  
449 >  // read in the shape types.
450 >  
451 >  // first grab the values in the ShapeInfo section
452 >  findBegin( shapeFile, "ShapeInfo");
453 >  
454 >  shapeFile.getline(inLine, MAXLEN);
455 >  while( !shapeFile.eof() ) {
456 >    // toss comment lines
457 >    if( inLine[0] != '!' && inLine[0] != '#' ){
458 >      // end marks section completion
459 >      if (isEndLine(inLine)) break;
460 >      
461 >      nTokens = countTokens(inLine, delim);
462 >      if (nTokens != 0) {
463 >        if (nTokens < 5) {
464 >          sprintf( painCave.errMsg,
465 >                   "Not enough data on a ShapeInfo line in file: %s\n",
466 >                   shapeFileName.c_str() );
467 >          painCave.severity = OOPSE_ERROR;
468 >          painCave.isFatal = 1;
469 >          simError();
470 >        } else {
471 >          token = strtok(inLine, delim);
472 >          token = strtok(NULL, delim);
473 >          st->setMass(atof(token));
474 >          token = strtok(NULL, delim);
475 >          momInert(0,0) = atof(token);
476 >          token = strtok(NULL, delim);
477 >          momInert(1,1) = atof(token);
478 >          token = strtok(NULL, delim);
479 >          momInert(2,2) = atof(token);
480 >          st->setI(momInert);
481 >        }
482 >      }
483 >    }
484 >    shapeFile.getline(inLine, MAXLEN);
485    }
486  
487 <
488 <
489 <  // The Second line contains atomic number, atomic mass and a lattice constant
490 <  eam_eof_test = fgets(eam_read_buffer, sizeof(eam_read_buffer),eamFile);
491 <  linenumber++;
492 <  if(eam_eof_test == NULL){
493 <    sprintf( painCave.errMsg,
494 <             "error in reading Identifier line in %s\n", eamPotFile);
495 <    painCave.isFatal = 1;
496 <    simError();
487 >  // now grab the contact functions
488 >  findBegin(shapeFile, "ContactFunctions");
489 >  functionVector.clear();
490 >  
491 >  shapeFile.getline(inLine, MAXLEN);
492 >  while( !shapeFile.eof() ) {
493 >    // toss comment lines
494 >    if( inLine[0] != '!' && inLine[0] != '#' ){
495 >      // end marks section completion
496 >      if (isEndLine(inLine)) break;
497 >      nTokens = countTokens(inLine, delim);
498 >      if (nTokens != 0) {
499 >        if (nTokens < 4) {
500 >          sprintf( painCave.errMsg,
501 >                   "Not enough data on a ContactFunctions line in file: %s\n",
502 >                   shapeFileName.c_str() );
503 >          painCave.severity = OOPSE_ERROR;
504 >          painCave.isFatal = 1;
505 >          simError();
506 >        } else {
507 >          // read in a spherical harmonic function
508 >          token = strtok(inLine, delim);
509 >          rsh = new RealSphericalHarmonic();
510 >          rsh->setL(atoi(token));
511 >          token = strtok(NULL, delim);
512 >          rsh->setM(atoi(token));
513 >          token = strtok(NULL, delim);
514 >          if (!strcasecmp("sin",token))
515 >            rsh->makeSinFunction();
516 >          else
517 >            rsh->makeCosFunction();            
518 >          token = strtok(NULL, delim);
519 >          rsh->setCoefficient(atof(token));
520 >          
521 >          functionVector.push_back(rsh);
522 >        }
523 >      }
524 >    }
525 >    shapeFile.getline(inLine, MAXLEN);
526    }
527  
528 +  // pass contact functions to ShapeType
529  
530 +  st->setContactFuncs(functionVector);
531  
532 <    
533 <  if ( (the_token = strtok( eam_read_buffer, " \n\t,;")) == NULL){
534 <    sprintf( painCave.errMsg,
589 <             "Error parsing EAM ident  line in %s\n", eamPotFile );
590 <    painCave.isFatal = 1;
591 <    simError();
592 <  }
532 >  // now grab the range functions
533 >  findBegin(shapeFile, "RangeFunctions");
534 >  functionVector.clear();
535    
536 <  info.eam_ident = atoi( the_token );
537 <
538 <  if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
539 <    sprintf( painCave.errMsg,
540 <             "Error parsing EAM mass in %s\n", eamPotFile );
541 <    painCave.isFatal = 1;
542 <    simError();
543 <  }
544 <  info.mass = atof( the_token);
545 <
546 <  if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
547 <    sprintf( painCave.errMsg,
548 <             "Error parsing EAM Lattice Constant %s\n", eamPotFile );
549 <    painCave.isFatal = 1;
550 <    simError();
551 <  }
552 <  info.lattice_constant = atof( the_token);
553 <
554 <  // Next line is nrho, drho, nr, dr and rcut
555 <  eam_eof_test = fgets(eam_read_buffer, sizeof(eam_read_buffer),eamFile);
614 <  if(eam_eof_test == NULL){
615 <    sprintf( painCave.errMsg,
616 <             "error in reading number of points line in %s\n", eamPotFile);
617 <    painCave.isFatal = 1;
618 <    simError();
619 <  }
536 >  shapeFile.getline(inLine, MAXLEN);
537 >  while( !shapeFile.eof() ) {
538 >    // toss comment lines
539 >    if( inLine[0] != '!' && inLine[0] != '#' ){
540 >      // end marks section completion
541 >      if (isEndLine(inLine)) break;
542 >      
543 >      nTokens = countTokens(inLine, delim);
544 >      if (nTokens != 0) {
545 >        if (nTokens < 4) {
546 >          sprintf( painCave.errMsg,
547 >                   "Not enough data on a RangeFunctions line in file: %s\n",
548 >                   shapeFileName.c_str() );
549 >          painCave.severity = OOPSE_ERROR;
550 >          painCave.isFatal = 1;
551 >          simError();
552 >        } else {
553 >          
554 >          // read in a spherical harmonic function
555 >          token = strtok(inLine, delim);
556  
557 <  if ( (the_token = strtok( eam_read_buffer, " \n\t,;")) == NULL){
558 <    sprintf( painCave.errMsg,
559 <             "Error parseing EAM nrho: line in %s\n", eamPotFile );
560 <    painCave.isFatal = 1;
561 <    simError();
557 >          rsh = new RealSphericalHarmonic();
558 >          rsh->setL(atoi(token));
559 >          token = strtok(NULL, delim);
560 >          rsh->setM(atoi(token));
561 >          token = strtok(NULL, delim);
562 >          if (!strcasecmp("sin",token))
563 >            rsh->makeSinFunction();
564 >          else
565 >            rsh->makeCosFunction();            
566 >          token = strtok(NULL, delim);
567 >          rsh->setCoefficient(atof(token));
568 >          
569 >          functionVector.push_back(rsh);
570 >        }
571 >      }
572 >    }
573 >    shapeFile.getline(inLine, MAXLEN);
574    }
627 –  
628 –  info.eam_nrho = atoi( the_token );
629 –  
630 –  if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
631 –    sprintf( painCave.errMsg,
632 –             "Error parsing EAM drho in %s\n", eamPotFile );
633 –    painCave.isFatal = 1;
634 –    simError();
635 –  }
636 –  info.eam_drho = atof( the_token);
575  
576 <  if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
577 <    sprintf( painCave.errMsg,
640 <             "Error parsing EAM # r in %s\n", eamPotFile );
641 <    painCave.isFatal = 1;
642 <    simError();
643 <  }
644 <  info.eam_nr = atoi( the_token);
645 <  
646 <  if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
647 <    sprintf( painCave.errMsg,
648 <             "Error parsing EAM dr in %s\n", eamPotFile );
649 <    painCave.isFatal = 1;
650 <    simError();
651 <  }
652 <  info.eam_dr = atof( the_token);
576 >  // pass range functions to ShapeType
577 >  st->setRangeFuncs(functionVector);
578  
579 <  if( ( the_token = strtok( NULL, " \n\t,;" ) ) == NULL ){
580 <    sprintf( painCave.errMsg,
581 <             "Error parsing EAM rcut in %s\n", eamPotFile );
582 <    painCave.isFatal = 1;
583 <    simError();
584 <  }
585 <  info.eam_rcut = atof( the_token);
586 <
579 >  // finally grab the strength functions
580 >  findBegin(shapeFile, "StrengthFunctions");
581 >  functionVector.clear();
582 >  
583 >  shapeFile.getline(inLine, MAXLEN);
584 >  while( !shapeFile.eof() ) {
585 >    // toss comment lines
586 >    if( inLine[0] != '!' && inLine[0] != '#' ){
587 >      // end marks section completion
588 >      if (isEndLine(inLine)) break;
589 >      
590 >      nTokens = countTokens(inLine, delim);
591 >      if (nTokens != 0) {
592 >        if (nTokens < 4) {
593 >          sprintf( painCave.errMsg,
594 >                   "Not enough data on a StrengthFunctions line in file: %s\n",
595 >                   shapeFileName.c_str() );
596 >          painCave.severity = OOPSE_ERROR;
597 >          painCave.isFatal = 1;
598 >          simError();
599 >        } else {
600 >          
601 >          // read in a spherical harmonic function
602 >          token = strtok(inLine, delim);
603 >          rsh = new RealSphericalHarmonic();
604 >          rsh->setL(atoi(token));
605 >          token = strtok(NULL, delim);
606 >          rsh->setM(atoi(token));
607 >          token = strtok(NULL, delim);
608 >          if (!strcasecmp("sin",token))
609 >            rsh->makeSinFunction();
610 >          else
611 >            rsh->makeCosFunction();            
612 >          token = strtok(NULL, delim);
613 >          rsh->setCoefficient(atof(token));
614 >          
615 >          functionVector.push_back(rsh);
616 >        }
617 >      }
618 >    }
619 >    shapeFile.getline(inLine, MAXLEN);
620 >  }
621  
622 +  // pass strength functions to ShapeType
623 +  st->setStrengthFuncs(functionVector);
624  
625 +  // we're done reading from this file
626 +  shapeFile.close();
627 + }
628  
629 <
630 <  // Ok now we have to allocate point arrays and read in number of points
631 <  // Index the arrays for fortran, starting at 1
632 <  myEam_Frhovals = new double[info.eam_nrho];
633 <  myEam_rvals    = new double[info.eam_nr];
670 <  myEam_rhovals  = new double[info.eam_nr];
671 <
672 <  // Parse F of rho vals.
673 <
674 <  // Assume for now that we have a complete number of lines
675 <  nReadLines = int(info.eam_nrho/5);
629 > double Shapes_FF::findLargestContactDistance(ShapeAtomType* st) {
630 >  int i, j,  nSteps;
631 >  double theta, thetaStep, thetaMin, costheta;
632 >  double phi, phiStep;
633 >  double sigma, bs;
634    
635 +  nSteps = 16;
636  
637 <
638 <  for (i=0;i<nReadLines;i++){
639 <    j = i*5;
640 <
641 <    // Read next line
642 <    eam_eof_test = fgets(eam_read_buffer, sizeof(eam_read_buffer),eamFile);
684 <    linenumber++;
685 <    if(eam_eof_test == NULL){
686 <      sprintf( painCave.errMsg,
687 <               "error in reading EAM file %s at line %d\n",
688 <               eamPotFile,linenumber);
689 <      painCave.isFatal = 1;
690 <      simError();
691 <    }
637 >  thetaStep = M_PI / nSteps;
638 >  thetaMin = thetaStep / 2.0;
639 >  phiStep = thetaStep * 2.0;
640 >  bs = 0.0;
641 >  
642 >  for (i = 0; i < nSteps; i++) {
643      
644 <    // Parse 5 values on each line into array
645 <    // Value 1
695 <    if ( (the_token = strtok( eam_read_buffer, " \n\t,;")) == NULL){
696 <      sprintf( painCave.errMsg,
697 <               "Error parsing EAM nrho: line in %s\n", eamPotFile );
698 <      painCave.isFatal = 1;
699 <      simError();
700 <    }
644 >    theta = thetaMin + i * thetaStep;
645 >    costheta = cos(theta);
646  
647 <    myEam_Frhovals[j+0] = atof( the_token );
703 <    
704 <    // Value 2
705 <    if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){
706 <      sprintf( painCave.errMsg,
707 <               "Error parsing EAM nrho: line in %s\n", eamPotFile );
708 <      painCave.isFatal = 1;
709 <      simError();
710 <    }
647 >    for (j = 0; j < nSteps; j++) {
648  
649 <    myEam_Frhovals[j+1] = atof( the_token );
713 <    
714 <    // Value 3
715 <    if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){
716 <      sprintf( painCave.errMsg,
717 <               "Error parsing EAM nrho: line in %s\n", eamPotFile );
718 <      painCave.isFatal = 1;
719 <      simError();
720 <    }
649 >      phi = j*phiStep;
650  
651 <    myEam_Frhovals[j+2] = atof( the_token );
652 <    
653 <    // Value 4
725 <    if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){
726 <      sprintf( painCave.errMsg,
727 <               "Error parsing EAM nrho: line in %s\n", eamPotFile );
728 <      painCave.isFatal = 1;
729 <      simError();
651 >      sigma = st->getContactValueAt(costheta, phi);
652 >      
653 >      if (sigma > bs) bs = sigma;
654      }
731 –
732 –    myEam_Frhovals[j+3] = atof( the_token );
733 –
734 –    // Value 5
735 –    if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){
736 –      sprintf( painCave.errMsg,
737 –               "Error parsing EAM nrho: line in %s\n", eamPotFile );
738 –      painCave.isFatal = 1;
739 –      simError();
740 –    }
741 –
742 –    myEam_Frhovals[j+4] = atof( the_token );
743 –    
655    }
745 –  // Parse Z of r vals
746 –  
747 –  // Assume for now that we have a complete number of lines
748 –  nReadLines = int(info.eam_nr/5);
656  
657 <  for (i=0;i<nReadLines;i++){
658 <    j = i*5;
657 >  return bs;  
658 > }
659  
753 –    // Read next line
754 –    eam_eof_test = fgets(eam_read_buffer, sizeof(eam_read_buffer),eamFile);
755 –    linenumber++;
756 –    if(eam_eof_test == NULL){
757 –      sprintf( painCave.errMsg,
758 –               "error in reading EAM file %s at line %d\n",
759 –               eamPotFile,linenumber);
760 –      painCave.isFatal = 1;
761 –      simError();
762 –    }
763 –    
764 –    // Parse 5 values on each line into array
765 –    // Value 1
766 –    if ( (the_token = strtok( eam_read_buffer, " \n\t,;")) == NULL){
767 –      sprintf( painCave.errMsg,
768 –               "Error parsing EAM nrho: line in %s\n", eamPotFile );
769 –      painCave.isFatal = 1;
770 –      simError();
771 –    }
772 –    
773 –    myEam_rvals[j+0] = atof( the_token );
660  
661 <    // Value 2
662 <    if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){
663 <      sprintf( painCave.errMsg,
664 <               "Error parsing EAM nrho: line in %s\n", eamPotFile );
665 <      painCave.isFatal = 1;
666 <      simError();
781 <    }
782 <  
783 <    myEam_rvals[j+1] = atof( the_token );
661 > double Shapes_FF::findCutoffDistance(ShapeAtomType* st) {
662 >  int i, j,  nSteps;
663 >  double theta, thetaStep, thetaMin, costheta;
664 >  double phi, phiStep;
665 >  double sigma, range;
666 >  double bigCut, tempCut;
667  
668 <    // Value 3
786 <    if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){
787 <      sprintf( painCave.errMsg,
788 <               "Error parsing EAM nrho: line in %s\n", eamPotFile );
789 <      painCave.isFatal = 1;
790 <      simError();
791 <    }
792 <  
793 <    myEam_rvals[j+2] = atof( the_token );
668 >  nSteps = 16;
669  
670 <    // Value 4
671 <    if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){
672 <      sprintf( painCave.errMsg,
673 <               "Error parsing EAM nrho: line in %s\n", eamPotFile );
799 <      painCave.isFatal = 1;
800 <      simError();
801 <    }
670 >  thetaStep = M_PI / nSteps;
671 >  thetaMin = thetaStep / 2.0;
672 >  phiStep = thetaStep * 2.0;
673 >  bigCut = 0.0;
674    
675 <    myEam_rvals[j+3] = atof( the_token );
675 >  for (i = 0; i < nSteps; i++) {
676 >    
677 >    theta = thetaMin + i * thetaStep;
678 >    costheta = cos(theta);
679  
680 <    // Value 5
806 <    if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){
807 <      sprintf( painCave.errMsg,
808 <               "Error parsing EAM nrho: line in %s\n", eamPotFile );
809 <      painCave.isFatal = 1;
810 <      simError();
811 <    }
812 <  
813 <    myEam_rvals[j+4] = atof( the_token );
680 >    for (j = 0; j < nSteps; j++) {
681  
682 <  }
816 <  // Parse rho of r vals
682 >      phi = j*phiStep;
683  
684 <  // Assume for now that we have a complete number of lines
684 >      sigma = st->getContactValueAt(costheta, phi);
685 >      range = st->getRangeValueAt(costheta, phi);
686  
687 <  for (i=0;i<nReadLines;i++){
688 <    j = i*5;
687 >       // cutoff for a shape is taken to be (2.5*rangeVal + contactVal)
688 >      tempCut = 2.5*range + sigma;
689  
690 <    // Read next line
824 <    eam_eof_test = fgets(eam_read_buffer, sizeof(eam_read_buffer),eamFile);
825 <    linenumber++;
826 <    if(eam_eof_test == NULL){
827 <      sprintf( painCave.errMsg,
828 <               "error in reading EAM file %s at line %d\n",
829 <               eamPotFile,linenumber);
830 <      painCave.isFatal = 1;
831 <      simError();
690 >      if (tempCut > bigCut) bigCut = tempCut;
691      }
833 –  
834 –    // Parse 5 values on each line into array
835 –    // Value 1
836 –    if ( (the_token = strtok( eam_read_buffer, " \n\t,;")) == NULL){
837 –      sprintf( painCave.errMsg,
838 –               "Error parsing EAM nrho: line in %s\n", eamPotFile );
839 –      painCave.isFatal = 1;
840 –      simError();
841 –    }
842 –  
843 –    myEam_rhovals[j+0] = atof( the_token );
844 –
845 –    // Value 2
846 –    if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){
847 –      sprintf( painCave.errMsg,
848 –               "Error parsing EAM nrho: line in %s\n", eamPotFile );
849 –      painCave.isFatal = 1;
850 –      simError();
851 –    }
852 –  
853 –    myEam_rhovals[j+1] = atof( the_token );
854 –
855 –    // Value 3
856 –    if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){
857 –      sprintf( painCave.errMsg,
858 –               "Error parsing EAM nrho: line in %s\n", eamPotFile );
859 –      painCave.isFatal = 1;
860 –      simError();
861 –    }
862 –  
863 –    myEam_rhovals[j+2] = atof( the_token );
864 –
865 –    // Value 4
866 –    if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){
867 –      sprintf( painCave.errMsg,
868 –               "Error parsing EAM nrho: line in %s\n", eamPotFile );
869 –      painCave.isFatal = 1;
870 –      simError();
871 –    }
872 –  
873 –    myEam_rhovals[j+3] = atof( the_token );
874 –
875 –    // Value 5
876 –    if ( (the_token = strtok( NULL, " \n\t,;")) == NULL){
877 –      sprintf( painCave.errMsg,
878 –               "Error parsing EAM nrho: line in %s\n", eamPotFile );
879 –      painCave.isFatal = 1;
880 –      simError();
881 –    }
882 –  
883 –    myEam_rhovals[j+4] = atof( the_token );
884 –
692    }
693 <  *eam_rvals = myEam_rvals;
694 <  *eam_rhovals = myEam_rhovals;
888 <  *eam_Frhovals = myEam_Frhovals;
889 <
890 <  fclose(eamFile);
891 <  return 0;
693 >
694 >  return bigCut;  
695   }

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