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Comparing branches/new_design/OOPSE-3.0/src/brains/SimInfo.cpp (file contents):
Revision 1683, Thu Oct 28 22:34:02 2004 UTC vs.
Revision 1727 by tim, Thu Nov 11 16:41:58 2004 UTC

# Line 1 | Line 1
1 < #include <stdlib.h>
2 < #include <string.h>
3 < #include <math.h>
1 > /*
2 > * Copyright (C) 2000-2004  Object Oriented Parallel Simulation Engine (OOPSE) project
3 > *
4 > * Contact: oopse@oopse.org
5 > *
6 > * This program is free software; you can redistribute it and/or
7 > * modify it under the terms of the GNU Lesser General Public License
8 > * as published by the Free Software Foundation; either version 2.1
9 > * of the License, or (at your option) any later version.
10 > * All we ask is that proper credit is given for our work, which includes
11 > * - but is not limited to - adding the above copyright notice to the beginning
12 > * of your source code files, and to any copyright notice that you may distribute
13 > * with programs based on this work.
14 > *
15 > * This program is distributed in the hope that it will be useful,
16 > * but WITHOUT ANY WARRANTY; without even the implied warranty of
17 > * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
18 > * GNU Lesser General Public License for more details.
19 > *
20 > * You should have received a copy of the GNU Lesser General Public License
21 > * along with this program; if not, write to the Free Software
22 > * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
23 > *
24 > */
25  
26 < #include <iostream>
27 < using namespace std;
26 > /**
27 > * @file SimInfo.cpp
28 > * @author    tlin
29 > * @date  11/02/2004
30 > * @version 1.0
31 > */
32  
33 + #include <algorithm>
34 +
35   #include "brains/SimInfo.hpp"
36 < #define __C
10 < #include "brains/fSimulation.h"
11 < #include "utils/simError.h"
12 < #include "UseTheForce/DarkSide/simulation_interface.h"
13 < #include "UseTheForce/notifyCutoffs_interface.h"
36 > #include "utils/MemoryUtils.hpp"
37  
38 < //#include "UseTheForce/fortranWrappers.hpp"
38 > namespace oopse {
39  
40 < #include "math/MatVec3.h"
40 > SimInfo::SimInfo() : nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nRigidBodies_(0),
41 >        nIntegrableObjects_(0), nCutoffGroups_(0), nConstraints_(0), sman_(NULL){
42  
43 < #ifdef IS_MPI
20 < #include "brains/mpiSimulation.hpp"
21 < #endif
43 > }
44  
45 < inline double roundMe( double x ){
46 <  return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
45 > SimInfo::~SimInfo() {
46 >    //MemoryUtils::deleteVectorOfPointer(molecules_);
47 >    delete sman_;
48 >
49   }
26 –          
27 – inline double min( double a, double b ){
28 –  return (a < b ) ? a : b;
29 – }
50  
31 – SimInfo* currentInfo;
51  
52 < SimInfo::SimInfo(){
52 > bool SimInfo::addMolecule(Molecule* mol) {
53 >    MoleculeIterator i;
54 >    i = std::find(molecules_.begin(), molecules_.end(), mol);
55 >    if (i != molecules_.end() ) {
56  
57 <  n_constraints = 0;
58 <  nZconstraints = 0;
59 <  n_oriented = 0;
60 <  n_dipoles = 0;
61 <  ndf = 0;
62 <  ndfRaw = 0;
63 <  nZconstraints = 0;
64 <  the_integrator = NULL;
65 <  setTemp = 0;
66 <  thermalTime = 0.0;
45 <  currentTime = 0.0;
46 <  rCut = 0.0;
47 <  rSw = 0.0;
57 >        molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
58 >        
59 >        nAtoms_ += mol->getNAtoms();
60 >        nBonds_ += mol->getNBonds();
61 >        nBends_ += mol->getNBends();
62 >        nTorsions_ += mol->getNTorsions();
63 >        nRigidBodies_ += mol->getNRigidBodies();
64 >        nIntegrableObjects_ += mol->getNIntegrableObjects();
65 >        nCutoffGroups_ += mol->getNCutoffGroups();
66 >        nConstraints_ += mol->getNConstraints();
67  
68 <  haveRcut = 0;
69 <  haveRsw = 0;
70 <  boxIsInit = 0;
71 <  
72 <  resetTime = 1e99;
68 >        return true;
69 >    } else {
70 >        return false;
71 >    }
72 > }
73  
74 <  orthoRhombic = 0;
75 <  orthoTolerance = 1E-6;
76 <  useInitXSstate = true;
74 > bool SimInfo::removeMolecule(Molecule* mol) {
75 >    MoleculeIterator i;
76 >    i = std::find(molecules_.begin(), molecules_.end(), mol);
77  
78 <  usePBC = 0;
60 <  useDirectionalAtoms = 0;
61 <  useLennardJones = 0;
62 <  useElectrostatics = 0;
63 <  useCharges = 0;
64 <  useDipoles = 0;
65 <  useSticky = 0;
66 <  useGayBerne = 0;
67 <  useEAM = 0;
68 <  useShapes = 0;
69 <  useFLARB = 0;
78 >    if (i != molecules_.end() ) {
79  
80 <  useSolidThermInt = 0;
81 <  useLiquidThermInt = 0;
80 >        nAtoms_ -= mol->getNAtoms();
81 >        nBonds_ -= mol->getNBonds();
82 >        nBends_ -= mol->getNBends();
83 >        nTorsions_ -= mol->getNTorsions();
84 >        nRigidBodies_ -= mol->getNRigidBodies();
85 >        nIntegrableObjects_ -= mol->getNIntegrableObjects();
86 >        nCutoffGroups_ -= mol->getNCutoffGroups();
87 >        nConstraints_ -= mol->getNConstraints();
88  
89 <  haveCutoffGroups = false;
89 >        molecules_.erase(mol->getGlobalIndex());
90  
91 <  excludes = Exclude::Instance();
91 >        delete mol;
92 >        
93 >        return true;
94 >    } else {
95 >        return false;
96 >    }
97  
78 –  myConfiguration = new SimState();
98  
99 <  has_minimizer = false;
81 <  the_minimizer =NULL;
99 > }    
100  
101 <  ngroup = 0;
101 >        
102 > Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
103 >    i = molecules_.begin();
104 >    return i == molecules_.end() ? NULL : *i;
105 > }    
106  
107 + Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
108 +    ++i;
109 +    return i == molecules_.end() ? NULL : *i;    
110   }
111  
112  
113 < SimInfo::~SimInfo(){
113 > void SimInfo::calcNdf() {
114 >    int ndf_local;
115 >    MoleculeIterator i;
116 >    std::vector<StuntDouble*>::iterator j;
117 >    Molecule* mol;
118 >    StuntDouble* integrableObject;
119  
120 <  delete myConfiguration;
120 >    ndf_local = 0;
121 >    
122 >    for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
123 >        for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
124 >               integrableObject = mol->nextIntegrableObject(j)) {
125  
126 <  map<string, GenericData*>::iterator i;
93 <  
94 <  for(i = properties.begin(); i != properties.end(); i++)
95 <    delete (*i).second;
126 >            ndf_local += 3;
127  
128 < }
128 >            if (integrableObject->isDirectional()) {
129 >                if (integrableObject->isLinear()) {
130 >                    ndf_local += 2;
131 >                } else {
132 >                    ndf_local += 3;
133 >                }
134 >            }
135 >            
136 >        }//end for (integrableObject)
137 >    }// end for (mol)
138 >    
139 >    // n_constraints is local, so subtract them on each processor
140 >    ndf_local -= nConstraints_;
141  
142 < void SimInfo::setBox(double newBox[3]) {
143 <  
144 <  int i, j;
145 <  double tempMat[3][3];
142 > #ifdef IS_MPI
143 >    MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
144 > #else
145 >    ndf_ = ndf_local;
146 > #endif
147  
148 <  for(i=0; i<3; i++)
149 <    for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
148 >    // nZconstraints is global, as are the 3 COM translations for the
149 >    // entire system:
150 >    ndf_ = ndf_ - 3 - nZconstraints;
151  
107 –  tempMat[0][0] = newBox[0];
108 –  tempMat[1][1] = newBox[1];
109 –  tempMat[2][2] = newBox[2];
110 –
111 –  setBoxM( tempMat );
112 –
152   }
153  
154 < void SimInfo::setBoxM( double theBox[3][3] ){
155 <  
117 <  int i, j;
118 <  double FortranHmat[9]; // to preserve compatibility with Fortran the
119 <                         // ordering in the array is as follows:
120 <                         // [ 0 3 6 ]
121 <                         // [ 1 4 7 ]
122 <                         // [ 2 5 8 ]
123 <  double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
154 > void SimInfo::calcNdfRaw() {
155 >    int ndfRaw_local;
156  
157 <  if( !boxIsInit ) boxIsInit = 1;
157 >    MoleculeIterator i;
158 >    std::vector<StuntDouble*>::iterator j;
159 >    Molecule* mol;
160 >    StuntDouble* integrableObject;
161  
162 <  for(i=0; i < 3; i++)
163 <    for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
164 <  
165 <  calcBoxL();
166 <  calcHmatInv();
162 >    // Raw degrees of freedom that we have to set
163 >    ndfRaw_local = 0;
164 >    
165 >    for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
166 >        for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
167 >               integrableObject = mol->nextIntegrableObject(j)) {
168  
169 <  for(i=0; i < 3; i++) {
170 <    for (j=0; j < 3; j++) {
171 <      FortranHmat[3*j + i] = Hmat[i][j];
172 <      FortranHmatInv[3*j + i] = HmatInv[i][j];
173 <    }
174 <  }
175 <
176 <  setFortranBox(FortranHmat, FortranHmatInv, &orthoRhombic);
177 <
169 >            ndfRaw_local += 3;
170 >
171 >            if (integrableObject->isDirectional()) {
172 >                if (integrableObject->isLinear()) {
173 >                    ndfRaw_local += 2;
174 >                } else {
175 >                    ndfRaw_local += 3;
176 >                }
177 >            }
178 >            
179 >        }
180 >    }
181 >    
182 > #ifdef IS_MPI
183 >    MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
184 > #else
185 >    ndfRaw_ = ndfRaw_local;
186 > #endif
187   }
143 –
188  
189 < void SimInfo::getBoxM (double theBox[3][3]) {
189 > void SimInfo::calcNdfTrans() {
190 >    int ndfTrans_local;
191  
192 <  int i, j;
193 <  for(i=0; i<3; i++)
194 <    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
192 >    ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
193 >
194 >
195 > #ifdef IS_MPI
196 >    MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
197 > #else
198 >    ndfTrans_ = ndfTrans_local;
199 > #endif
200 >
201 >    ndfTrans_ = ndfTrans_ - 3 - nZconstraints;
202 >
203   }
204  
205 + void SimInfo::addExcludePairs(Molecule* mol) {
206 +    std::vector<Bond*>::iterator bondIter;
207 +    std::vector<Bend*>::iterator bendIter;
208 +    std::vector<Torsion*>::iterator torsionIter;
209 +    Bond* bond;
210 +    Bend* bend;
211 +    Torsion* torsion;
212 +    int a;
213 +    int b;
214 +    int c;
215 +    int d;
216 +    
217 +    for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
218 +        a = bond->getAtomA()->getGlobalIndex();
219 +        b = bond->getAtomB()->getGlobalIndex();        
220 +        exclude_.addPair(a, b);
221 +    }
222  
223 < void SimInfo::scaleBox(double scale) {
224 <  double theBox[3][3];
225 <  int i, j;
223 >    for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
224 >        a = bend->getAtomA()->getGlobalIndex();
225 >        b = bend->getAtomB()->getGlobalIndex();        
226 >        c = bend->getAtomC()->getGlobalIndex();
227  
228 <  // cerr << "Scaling box by " << scale << "\n";
228 >        exclude_.addPair(a, b);
229 >        exclude_.addPair(a, c);
230 >        exclude_.addPair(b, c);        
231 >    }
232  
233 <  for(i=0; i<3; i++)
234 <    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
233 >    for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextBond(torsionIter)) {
234 >        a = torsion->getAtomA()->getGlobalIndex();
235 >        b = torsion->getAtomB()->getGlobalIndex();        
236 >        c = torsion->getAtomC()->getGlobalIndex();        
237 >        d = torsion->getAtomD()->getGlobalIndex();        
238  
239 <  setBoxM(theBox);
239 >        exclude_.addPair(a, b);
240 >        exclude_.addPair(a, c);
241 >        exclude_.addPair(a, d);
242 >        exclude_.addPair(b, c);
243 >        exclude_.addPair(b, d);
244 >        exclude_.addPair(c, d);        
245 >    }
246  
247 +    
248   }
249  
250 < void SimInfo::calcHmatInv( void ) {
251 <  
252 <  int oldOrtho;
253 <  int i,j;
254 <  double smallDiag;
255 <  double tol;
256 <  double sanity[3][3];
250 > void SimInfo::removeExcludePairs(Molecule* mol) {
251 >    std::vector<Bond*>::iterator bondIter;
252 >    std::vector<Bend*>::iterator bendIter;
253 >    std::vector<Torsion*>::iterator torsionIter;
254 >    Bond* bond;
255 >    Bend* bend;
256 >    Torsion* torsion;
257 >    int a;
258 >    int b;
259 >    int c;
260 >    int d;
261 >    
262 >    for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
263 >        a = bond->getAtomA()->getGlobalIndex();
264 >        b = bond->getAtomB()->getGlobalIndex();        
265 >        exclude_.removePair(a, b);
266 >    }
267  
268 <  invertMat3( Hmat, HmatInv );
268 >    for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
269 >        a = bend->getAtomA()->getGlobalIndex();
270 >        b = bend->getAtomB()->getGlobalIndex();        
271 >        c = bend->getAtomC()->getGlobalIndex();
272  
273 <  // check to see if Hmat is orthorhombic
274 <  
275 <  oldOrtho = orthoRhombic;
273 >        exclude_.removePair(a, b);
274 >        exclude_.removePair(a, c);
275 >        exclude_.removePair(b, c);        
276 >    }
277  
278 <  smallDiag = fabs(Hmat[0][0]);
279 <  if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]);
280 <  if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]);
281 <  tol = smallDiag * orthoTolerance;
278 >    for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextBond(torsionIter)) {
279 >        a = torsion->getAtomA()->getGlobalIndex();
280 >        b = torsion->getAtomB()->getGlobalIndex();        
281 >        c = torsion->getAtomC()->getGlobalIndex();        
282 >        d = torsion->getAtomD()->getGlobalIndex();        
283  
284 <  orthoRhombic = 1;
285 <  
286 <  for (i = 0; i < 3; i++ ) {
287 <    for (j = 0 ; j < 3; j++) {
288 <      if (i != j) {
289 <        if (orthoRhombic) {
191 <          if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0;
192 <        }        
193 <      }
284 >        exclude_.removePair(a, b);
285 >        exclude_.removePair(a, c);
286 >        exclude_.removePair(a, d);
287 >        exclude_.removePair(b, c);
288 >        exclude_.removePair(b, d);
289 >        exclude_.removePair(c, d);        
290      }
195 –  }
291  
197 –  if( oldOrtho != orthoRhombic ){
198 –    
199 –    if( orthoRhombic ) {
200 –      sprintf( painCave.errMsg,
201 –               "OOPSE is switching from the default Non-Orthorhombic\n"
202 –               "\tto the faster Orthorhombic periodic boundary computations.\n"
203 –               "\tThis is usually a good thing, but if you wan't the\n"
204 –               "\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
205 –               "\tvariable ( currently set to %G ) smaller.\n",
206 –               orthoTolerance);
207 –      painCave.severity = OOPSE_INFO;
208 –      simError();
209 –    }
210 –    else {
211 –      sprintf( painCave.errMsg,
212 –               "OOPSE is switching from the faster Orthorhombic to the more\n"
213 –               "\tflexible Non-Orthorhombic periodic boundary computations.\n"
214 –               "\tThis is usually because the box has deformed under\n"
215 –               "\tNPTf integration. If you wan't to live on the edge with\n"
216 –               "\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
217 –               "\tvariable ( currently set to %G ) larger.\n",
218 –               orthoTolerance);
219 –      painCave.severity = OOPSE_WARNING;
220 –      simError();
221 –    }
222 –  }
292   }
293  
225 – void SimInfo::calcBoxL( void ){
294  
295 <  double dx, dy, dz, dsq;
295 > void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
296 >    int curStampId;
297  
298 <  // boxVol = Determinant of Hmat
298 >    //index from 0
299 >    curStampId = molStampIds_.size();
300  
301 <  boxVol = matDet3( Hmat );
301 >    moleculeStamps_.push_back(molStamp);
302 >    molStampIds_.insert(molStampIds_.end(), nmol, curStampId)
303 > }
304  
305 <  // boxLx
234 <  
235 <  dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
236 <  dsq = dx*dx + dy*dy + dz*dz;
237 <  boxL[0] = sqrt( dsq );
238 <  //maxCutoff = 0.5 * boxL[0];
305 > void SimInfo::update() {
306  
307 <  // boxLy
308 <  
309 <  dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
310 <  dsq = dx*dx + dy*dy + dz*dz;
311 <  boxL[1] = sqrt( dsq );
312 <  //if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
307 >
308 >    
309 >    //SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
310 >    std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
311 >    std::vector<int> localToGlobalCutoffGroupIndex;
312 >    typename SimInfo::MoleculeIterator mi;
313 >    typename Molecule::AtomIterator ai;
314 >    typename Molecule::CutoffGroupIterator ci;
315 >    Molecule* mol;
316 >    Atom* atom;
317 >    CutoffGroup* cg;
318 >    mpiSimData parallelData;
319 >    int isError;
320  
321 +    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {
322  
323 <  // boxLz
324 <  
325 <  dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
326 <  dsq = dx*dx + dy*dy + dz*dz;
252 <  boxL[2] = sqrt( dsq );
253 <  //if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
323 >        //local index(index in DataStorge) of atom is important
324 >        for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
325 >            localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
326 >        }
327  
328 <  //calculate the max cutoff
329 <  maxCutoff =  calcMaxCutOff();
330 <  
331 <  checkCutOffs();
328 >        //local index of cutoff group is trivial, it only depends on the order of travesing
329 >        for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
330 >            localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
331 >        }        
332 >        
333 >    }
334  
335 < }
336 <
337 <
338 < double SimInfo::calcMaxCutOff(){
339 <
340 <  double ri[3], rj[3], rk[3];
341 <  double rij[3], rjk[3], rki[3];
342 <  double minDist;
343 <
269 <  ri[0] = Hmat[0][0];
270 <  ri[1] = Hmat[1][0];
271 <  ri[2] = Hmat[2][0];
272 <
273 <  rj[0] = Hmat[0][1];
274 <  rj[1] = Hmat[1][1];
275 <  rj[2] = Hmat[2][1];
276 <
277 <  rk[0] = Hmat[0][2];
278 <  rk[1] = Hmat[1][2];
279 <  rk[2] = Hmat[2][2];
335 >    //Setup Parallel Data and pass the index arrays to fortran
336 >    parallelData.nMolGlobal = getNMolGlobal();
337 >    parallelData.nMolLocal = ;
338 >    parallelData.nAtomsGlobal = ;
339 >    parallelData.nAtomsLocal = ;
340 >    parallelData.nGroupsGlobal = ;
341 >    parallelData.nGroupsLocal = ;
342 >    parallelData.myNode = worldRank;
343 >    MPI_Comm_size(MPI_COMM_WORLD, &(parallelData->nProcessors));
344      
345 <  crossProduct3(ri, rj, rij);
346 <  distXY = dotProduct3(rk,rij) / norm3(rij);
345 >    setFsimParallel(parallelData,            &(parallelData->nAtomsLocal),
346 >                    &localToGlobalAtomIndex[0],  &(parallelData->nGroupsLocal),
347 >                    &localToGlobalCutoffGroupIndex[0], &isError);
348  
349 <  crossProduct3(rj,rk, rjk);
350 <  distYZ = dotProduct3(ri,rjk) / norm3(rjk);
351 <
352 <  crossProduct3(rk,ri, rki);
353 <  distZX = dotProduct3(rj,rki) / norm3(rki);
289 <
290 <  minDist = min(min(distXY, distYZ), distZX);
291 <  return minDist/2;
292 <  
293 < }
294 <
295 < void SimInfo::wrapVector( double thePos[3] ){
296 <
297 <  int i;
298 <  double scaled[3];
299 <
300 <  if( !orthoRhombic ){
301 <    // calc the scaled coordinates.
302 <  
303 <
304 <    matVecMul3(HmatInv, thePos, scaled);
305 <    
306 <    for(i=0; i<3; i++)
307 <      scaled[i] -= roundMe(scaled[i]);
308 <    
309 <    // calc the wrapped real coordinates from the wrapped scaled coordinates
310 <    
311 <    matVecMul3(Hmat, scaled, thePos);
312 <
313 <  }
314 <  else{
315 <    // calc the scaled coordinates.
316 <    
317 <    for(i=0; i<3; i++)
318 <      scaled[i] = thePos[i]*HmatInv[i][i];
319 <    
320 <    // wrap the scaled coordinates
321 <    
322 <    for(i=0; i<3; i++)
323 <      scaled[i] -= roundMe(scaled[i]);
324 <    
325 <    // calc the wrapped real coordinates from the wrapped scaled coordinates
326 <    
327 <    for(i=0; i<3; i++)
328 <      thePos[i] = scaled[i]*Hmat[i][i];
329 <  }
330 <    
331 < }
332 <
333 <
334 < int SimInfo::getNDF(){
335 <  int ndf_local;
336 <
337 <  ndf_local = 0;
338 <  
339 <  for(int i = 0; i < integrableObjects.size(); i++){
340 <    ndf_local += 3;
341 <    if (integrableObjects[i]->isDirectional()) {
342 <      if (integrableObjects[i]->isLinear())
343 <        ndf_local += 2;
344 <      else
345 <        ndf_local += 3;
349 >    if (isError) {
350 >        sprintf(painCave.errMsg,
351 >                "mpiRefresh errror: fortran didn't like something we gave it.\n");
352 >        painCave.isFatal = 1;
353 >        simError();
354      }
347 –  }
355  
356 <  // n_constraints is local, so subtract them on each processor:
356 >    sprintf(checkPointMsg, " mpiRefresh successful.\n");
357 >    MPIcheckPoint();
358  
351 –  ndf_local -= n_constraints;
359  
353 – #ifdef IS_MPI
354 –  MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
355 – #else
356 –  ndf = ndf_local;
357 – #endif
358 –
359 –  // nZconstraints is global, as are the 3 COM translations for the
360 –  // entire system:
361 –
362 –  ndf = ndf - 3 - nZconstraints;
363 –
364 –  return ndf;
360   }
361  
362 < int SimInfo::getNDFraw() {
368 <  int ndfRaw_local;
362 > std::ostream& operator <<(ostream& o, SimInfo& info) {
363  
364 <  // Raw degrees of freedom that we have to set
371 <  ndfRaw_local = 0;
372 <
373 <  for(int i = 0; i < integrableObjects.size(); i++){
374 <    ndfRaw_local += 3;
375 <    if (integrableObjects[i]->isDirectional()) {
376 <       if (integrableObjects[i]->isLinear())
377 <        ndfRaw_local += 2;
378 <      else
379 <        ndfRaw_local += 3;
380 <    }
381 <  }
382 <    
383 < #ifdef IS_MPI
384 <  MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
385 < #else
386 <  ndfRaw = ndfRaw_local;
387 < #endif
388 <
389 <  return ndfRaw;
364 >    return o;
365   }
366  
367 < int SimInfo::getNDFtranslational() {
393 <  int ndfTrans_local;
394 <
395 <  ndfTrans_local = 3 * integrableObjects.size() - n_constraints;
396 <
397 <
398 < #ifdef IS_MPI
399 <  MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
400 < #else
401 <  ndfTrans = ndfTrans_local;
402 < #endif
403 <
404 <  ndfTrans = ndfTrans - 3 - nZconstraints;
405 <
406 <  return ndfTrans;
407 < }
408 <
409 < int SimInfo::getTotIntegrableObjects() {
410 <  int nObjs_local;
411 <  int nObjs;
412 <
413 <  nObjs_local =  integrableObjects.size();
414 <
415 <
416 < #ifdef IS_MPI
417 <  MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
418 < #else
419 <  nObjs = nObjs_local;
420 < #endif
421 <
422 <
423 <  return nObjs;
424 < }
425 <
426 < void SimInfo::refreshSim(){
427 <
428 <  simtype fInfo;
429 <  int isError;
430 <  int n_global;
431 <  int* excl;
432 <
433 <  fInfo.dielect = 0.0;
434 <
435 <  if( useDipoles ){
436 <    if( useReactionField )fInfo.dielect = dielectric;
437 <  }
438 <
439 <  fInfo.SIM_uses_PBC = usePBC;
440 <
441 <  if (useSticky || useDipoles || useGayBerne || useShapes) {
442 <    useDirectionalAtoms = 1;
443 <    fInfo.SIM_uses_DirectionalAtoms = useDirectionalAtoms;
444 <  }
445 <
446 <  fInfo.SIM_uses_LennardJones = useLennardJones;
447 <
448 <  if (useCharges || useDipoles) {
449 <    useElectrostatics = 1;
450 <    fInfo.SIM_uses_Electrostatics = useElectrostatics;
451 <  }
452 <
453 <  fInfo.SIM_uses_Charges = useCharges;
454 <  fInfo.SIM_uses_Dipoles = useDipoles;
455 <  fInfo.SIM_uses_Sticky = useSticky;
456 <  fInfo.SIM_uses_GayBerne = useGayBerne;
457 <  fInfo.SIM_uses_EAM = useEAM;
458 <  fInfo.SIM_uses_Shapes = useShapes;
459 <  fInfo.SIM_uses_FLARB = useFLARB;
460 <  fInfo.SIM_uses_RF = useReactionField;
461 <
462 <  n_exclude = excludes->getSize();
463 <  excl = excludes->getFortranArray();
464 <  
465 < #ifdef IS_MPI
466 <  n_global = mpiSim->getNAtomsGlobal();
467 < #else
468 <  n_global = n_atoms;
469 < #endif
470 <  
471 <  isError = 0;
472 <  
473 <  getFortranGroupArrays(this, FglobalGroupMembership, mfact);
474 <  //it may not be a good idea to pass the address of first element in vector
475 <  //since c++ standard does not require vector to be stored continuously in meomory
476 <  //Most of the compilers will organize the memory of vector continuously
477 <  setFortranSim( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
478 <                  &nGlobalExcludes, globalExcludes, molMembershipArray,
479 <                  &mfact[0], &ngroup, &FglobalGroupMembership[0], &isError);
480 <
481 <  if( isError ){
482 <    
483 <    sprintf( painCave.errMsg,
484 <             "There was an error setting the simulation information in fortran.\n" );
485 <    painCave.isFatal = 1;
486 <    painCave.severity = OOPSE_ERROR;
487 <    simError();
488 <  }
489 <  
490 < #ifdef IS_MPI
491 <  sprintf( checkPointMsg,
492 <           "succesfully sent the simulation information to fortran.\n");
493 <  MPIcheckPoint();
494 < #endif // is_mpi
495 <  
496 <  this->ndf = this->getNDF();
497 <  this->ndfRaw = this->getNDFraw();
498 <  this->ndfTrans = this->getNDFtranslational();
499 < }
500 <
501 < void SimInfo::setDefaultRcut( double theRcut ){
502 <  
503 <  haveRcut = 1;
504 <  rCut = theRcut;
505 <  rList = rCut + 1.0;
506 <  
507 <  notifyFortranCutoffs( &rCut, &rSw, &rList );
508 < }
509 <
510 < void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
511 <
512 <  rSw = theRsw;
513 <  setDefaultRcut( theRcut );
514 < }
515 <
516 <
517 < void SimInfo::checkCutOffs( void ){
518 <  
519 <  if( boxIsInit ){
520 <    
521 <    //we need to check cutOffs against the box
522 <    
523 <    if( rCut > maxCutoff ){
524 <      sprintf( painCave.errMsg,
525 <               "cutoffRadius is too large for the current periodic box.\n"
526 <               "\tCurrent Value of cutoffRadius = %G at time %G\n "
527 <               "\tThis is larger than half of at least one of the\n"
528 <               "\tperiodic box vectors.  Right now, the Box matrix is:\n"
529 <               "\n"
530 <               "\t[ %G %G %G ]\n"
531 <               "\t[ %G %G %G ]\n"
532 <               "\t[ %G %G %G ]\n",
533 <               rCut, currentTime,
534 <               Hmat[0][0], Hmat[0][1], Hmat[0][2],
535 <               Hmat[1][0], Hmat[1][1], Hmat[1][2],
536 <               Hmat[2][0], Hmat[2][1], Hmat[2][2]);
537 <      painCave.severity = OOPSE_ERROR;
538 <      painCave.isFatal = 1;
539 <      simError();
540 <    }    
541 <  } else {
542 <    // initialize this stuff before using it, OK?
543 <    sprintf( painCave.errMsg,
544 <             "Trying to check cutoffs without a box.\n"
545 <             "\tOOPSE should have better programmers than that.\n" );
546 <    painCave.severity = OOPSE_ERROR;
547 <    painCave.isFatal = 1;
548 <    simError();      
549 <  }
550 <  
551 < }
552 <
553 < void SimInfo::addProperty(GenericData* prop){
554 <
555 <  map<string, GenericData*>::iterator result;
556 <  result = properties.find(prop->getID());
557 <  
558 <  //we can't simply use  properties[prop->getID()] = prop,
559 <  //it will cause memory leak if we already contain a propery which has the same name of prop
560 <  
561 <  if(result != properties.end()){
562 <    
563 <    delete (*result).second;
564 <    (*result).second = prop;
565 <      
566 <  }
567 <  else{
568 <
569 <    properties[prop->getID()] = prop;
570 <
571 <  }
572 <    
573 < }
574 <
575 < GenericData* SimInfo::getProperty(const string& propName){
576 <
577 <  map<string, GenericData*>::iterator result;
578 <  
579 <  //string lowerCaseName = ();
580 <  
581 <  result = properties.find(propName);
582 <  
583 <  if(result != properties.end())
584 <    return (*result).second;  
585 <  else  
586 <    return NULL;  
587 < }
588 <
589 <
590 < void SimInfo::getFortranGroupArrays(SimInfo* info,
591 <                                    vector<int>& FglobalGroupMembership,
592 <                                    vector<double>& mfact){
593 <  
594 <  Molecule* myMols;
595 <  Atom** myAtoms;
596 <  int numAtom;
597 <  double mtot;
598 <  int numMol;
599 <  int numCutoffGroups;
600 <  CutoffGroup* myCutoffGroup;
601 <  vector<CutoffGroup*>::iterator iterCutoff;
602 <  Atom* cutoffAtom;
603 <  vector<Atom*>::iterator iterAtom;
604 <  int atomIndex;
605 <  double totalMass;
606 <  
607 <  mfact.clear();
608 <  FglobalGroupMembership.clear();
609 <  
610 <
611 <  // Fix the silly fortran indexing problem
612 < #ifdef IS_MPI
613 <  numAtom = mpiSim->getNAtomsGlobal();
614 < #else
615 <  numAtom = n_atoms;
616 < #endif
617 <  for (int i = 0; i < numAtom; i++)
618 <    FglobalGroupMembership.push_back(globalGroupMembership[i] + 1);
619 <  
620 <
621 <  myMols = info->molecules;
622 <  numMol = info->n_mol;
623 <  for(int i  = 0; i < numMol; i++){
624 <    numCutoffGroups = myMols[i].getNCutoffGroups();
625 <    for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff);
626 <        myCutoffGroup != NULL;
627 <        myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){
628 <
629 <      totalMass = myCutoffGroup->getMass();
630 <      
631 <      for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom);
632 <          cutoffAtom != NULL;
633 <          cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
634 <        mfact.push_back(cutoffAtom->getMass()/totalMass);
635 <      }  
636 <    }
637 <  }
638 <
639 < }
367 > }//end namespace oopse

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