OOPSE/libmdtools/ForceFields.cpp

#include <iostream>

using namespace std;


#include <stdlib.h>

#ifdef IS_MPI
#include <mpi.h>
#endif // is_mpi


#ifdef PROFILE
#include "mdProfile.hpp"
#endif

#include "simError.h"
#include "ForceFields.hpp"
#include "Atom.hpp"
#include "fortranWrappers.hpp"


void ForceFields::calcRcut( void ){

#ifdef IS_MPI
  double tempBig = bigSigma;
  MPI_Allreduce( &tempBig, &bigSigma, 1, MPI_DOUBLE, MPI_MAX,
                 MPI_COMM_WORLD);
#endif  //is_mpi

  //calc rCut and rList

  entry_plug->setDefaultRcut( 2.5 * bigSigma );  
    
}

void ForceFields::setRcut( double LJrcut ) {
  
#ifdef IS_MPI
  double tempBig = bigSigma;
  MPI_Allreduce( &tempBig, &bigSigma, 1, MPI_DOUBLE, MPI_MAX,
                 MPI_COMM_WORLD);
#endif  //is_mpi
  
  if (LJrcut < 2.5 * bigSigma) {
    sprintf( painCave.errMsg,
             "Setting Lennard-Jones cutoff radius to %lf.\n"
             "\tThis value is smaller than %lf, which is\n"
             "\t2.5 * bigSigma, where bigSigma is the largest\n"
             "\tvalue of sigma present in the simulation.\n"
             "\tThis is potentially a problem since the LJ potential may\n"
             "\tbe appreciable at this distance.  If you don't want the\n"
             "\tsmaller cutoff, change the LJrcut variable.\n",
             LJrcut, 2.5*bigSigma);
    painCave.isFatal = 0;
    simError();
  } else {
    sprintf( painCave.errMsg,
             "Setting Lennard-Jones cutoff radius to %lf.\n"
             "\tThis value is larger than %lf, which is\n"
             "\t2.5 * bigSigma, where bigSigma is the largest\n"
             "\tvalue of sigma present in the simulation. This should\n"
             "\tnot be a problem, but could adversely effect performance.\n",
             LJrcut, 2.5*bigSigma);
    painCave.isFatal = 0;
    simError();
  }
  
  //calc rCut and rList
  
  entry_plug->setDefaultRcut( LJrcut );
}

void ForceFields::doForces( int calcPot, int calcStress ){

  int i, j, isError;
  double* frc;
  double* pos;
  double* trq;
  double* A;
  double* u_l;
  double* rc;
  double* massRatio;
  SimState* config;

  Molecule* myMols;
  Atom** myAtoms;
  int numAtom;
  int curIndex;
  double mtot;
  int numMol;
  int numCutoffGroups;
  CutoffGroup* myCutoffGroup;
  vector<CutoffGroup*>::iterator iterCutoff;
  Atom* cutoffAtom;
  vector<Atom*>::iterator iterAtom;  
  double com[3];
  double tempPos[3];
  int atomIndex;
  
  short int passedCalcPot = (short int)calcPot;
  short int passedCalcStress = (short int)calcStress;

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

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

#ifdef PROFILE
  startProfile(pro7);
#endif
  
  for(i=0; i<entry_plug->n_mol; i++ ){
    // CalcForces in molecules takes care of mapping rigid body coordinates
    // into atomic coordinates
    entry_plug->molecules[i].calcForces();    
  }

#ifdef PROFILE
  endProfile( pro7 );
#endif

  config = entry_plug->getConfiguration();
  
  frc = config->getFrcArray();
  pos = config->getPosArray();
  trq = config->getTrqArray();
  A   = config->getAmatArray();
  u_l = config->getUlArray();

  if(entry_plug->haveCutoffGroups){
    //if 
    myMols = entry_plug->molecules;
    numMol = entry_plug->n_mol;
    for(int i  = 0; i < numMol; i++){
      numAtom = myMols[i].getNAtoms();
      myAtoms = myMols[i].getMyAtoms();

      
      for(int j = 0; j < numAtom; j++){
#ifdef IS_MPI
        atomIndex = myAtoms[j]->getGlobalIndex();
#else
        atomIndex = myAtoms[j]->getIndex();
#endif

        if(myMols[i].belongToCutoffGroup(atomIndex))
          continue;
        else{
          myAtoms[j]->getPos(tempPos);
          myAtoms[j]->setRc(tempPos);
        }
          
      }
        
      numCutoffGroups = myMols[i].getNCutoffGroups();
      for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff); myCutoffGroup != NULL; 
                                                    myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){
        //get center of mass of the cutoff group
        myCutoffGroup->getCOM(com);

        for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom); cutoffAtom != NULL; 
                                             cutoffAtom = myCutoffGroup->beginAtom(iterAtom)){
          cutoffAtom->setRc(com);
        }  
                                
      }// end for(myCutoffGroup)
      
    }//end for(int i = 0)

    rc = config->getRcArray();
  }
  else{
    // center of mass of the group is the same as position of the atom  if cutoff group does not exist
    rc = pos;
  }
  

  isError = 0;
  entry_plug->lrPot = 0.0;

  for (i=0; i<9; i++) {
    entry_plug->tau[i] = 0.0;
  }


#ifdef PROFILE
  startProfile(pro8);
#endif

  fortranForceLoop( pos,
                    rc,
                    A,
                    u_l,
                    frc,
                    trq,
                    entry_plug->tau,
                    &(entry_plug->lrPot), 
                    &passedCalcPot,
                    &passedCalcStress,
                    &isError );


#ifdef PROFILE
  endProfile(pro8);
#endif


  if( isError ){
    sprintf( painCave.errMsg,
             "Error returned from the fortran force calculation.\n" );
    painCave.isFatal = 1;
    simError();
  }

  for(i=0; i<entry_plug->n_mol; i++ ){
    entry_plug->molecules[i].atoms2rigidBodies();
  }


#ifdef IS_MPI
  sprintf( checkPointMsg,
           "returned from the force calculation.\n" );
  MPIcheckPoint();
#endif // is_mpi
  

}


void ForceFields::initFortran(int ljMixPolicy, int useReactionField ){
  
  int isError;
  
  isError = 0;
  initFortranFF( &ljMixPolicy, &useReactionField, &isError );
  
  if(isError){
    sprintf( painCave.errMsg,
             "ForceField error: There was an error initializing the forceField in fortran.\n" );
    painCave.isFatal = 1;
    simError();
  }

  
#ifdef IS_MPI
  sprintf( checkPointMsg, "ForceField successfully initialized the fortran component list.\n" );
  MPIcheckPoint();
#endif // is_mpi
  
}
Revision:	1157
Committed:	Tue May 11 20:33:41 2004 UTC (20 years, 1 month ago) by tim
File size:	5897 byte(s)
Log Message:	adding cutoffGroup into OOPSE
#	User	Rev	Content
1	mmeineke	561	#include <iostream>
2
3			using namespace std;
4
5
6	gezelter	829	#include <stdlib.h>
7	mmeineke	377
8			#ifdef IS_MPI
9			#include <mpi.h>
10			#endif // is_mpi
11
12
13	chuckv	892	#ifdef PROFILE
14			#include "mdProfile.hpp"
15			#endif
16
17	mmeineke	377	#include "simError.h"
18			#include "ForceFields.hpp"
19			#include "Atom.hpp"
20			#include "fortranWrappers.hpp"
21
22
23	mmeineke	420	void ForceFields::calcRcut( void ){
24
25			#ifdef IS_MPI
26			double tempBig = bigSigma;
27	mmeineke	447	MPI_Allreduce( &tempBig, &bigSigma, 1, MPI_DOUBLE, MPI_MAX,
28			MPI_COMM_WORLD);
29	mmeineke	420	#endif //is_mpi
30
31			//calc rCut and rList
32
33	mmeineke	841	entry_plug->setDefaultRcut( 2.5 * bigSigma );
34	tim	781
35	mmeineke	420	}
36
37	gezelter	1097	void ForceFields::setRcut( double LJrcut ) {
38
39			#ifdef IS_MPI
40			double tempBig = bigSigma;
41			MPI_Allreduce( &tempBig, &bigSigma, 1, MPI_DOUBLE, MPI_MAX,
42			MPI_COMM_WORLD);
43			#endif //is_mpi
44
45			if (LJrcut < 2.5 * bigSigma) {
46			sprintf( painCave.errMsg,
47			"Setting Lennard-Jones cutoff radius to %lf.\n"
48			"\tThis value is smaller than %lf, which is\n"
49			"\t2.5 * bigSigma, where bigSigma is the largest\n"
50			"\tvalue of sigma present in the simulation.\n"
51			"\tThis is potentially a problem since the LJ potential may\n"
52			"\tbe appreciable at this distance. If you don't want the\n"
53			"\tsmaller cutoff, change the LJrcut variable.\n",
54			LJrcut, 2.5*bigSigma);
55			painCave.isFatal = 0;
56			simError();
57			} else {
58			sprintf( painCave.errMsg,
59			"Setting Lennard-Jones cutoff radius to %lf.\n"
60			"\tThis value is larger than %lf, which is\n"
61			"\t2.5 * bigSigma, where bigSigma is the largest\n"
62			"\tvalue of sigma present in the simulation. This should\n"
63			"\tnot be a problem, but could adversely effect performance.\n",
64			LJrcut, 2.5*bigSigma);
65			painCave.isFatal = 0;
66			simError();
67			}
68
69			//calc rCut and rList
70
71			entry_plug->setDefaultRcut( LJrcut );
72			}
73
74	mmeineke	377	void ForceFields::doForces( int calcPot, int calcStress ){
75
76	tim	1157	int i, j, isError;
77	mmeineke	377	double* frc;
78			double* pos;
79			double* trq;
80			double* A;
81	tim	1136	double* u_l;
82			double* rc;
83			double* massRatio;
84	mmeineke	670	SimState* config;
85	mmeineke	377
86	tim	1157	Molecule* myMols;
87			Atom** myAtoms;
88			int numAtom;
89			int curIndex;
90			double mtot;
91			int numMol;
92			int numCutoffGroups;
93			CutoffGroup* myCutoffGroup;
94			vector<CutoffGroup*>::iterator iterCutoff;
95			Atom* cutoffAtom;
96			vector<Atom*>::iterator iterAtom;
97			double com[3];
98			double tempPos[3];
99			int atomIndex;
100
101	mmeineke	377	short int passedCalcPot = (short int)calcPot;
102			short int passedCalcStress = (short int)calcStress;
103
104	gezelter	484	// forces are zeroed here, before any are accumulated.
105	mmeineke	377	// NOTE: do not rezero the forces in Fortran.
106
107			for(i=0; i<entry_plug->n_atoms; i++){
108	gezelter	484	entry_plug->atoms[i]->zeroForces();
109	mmeineke	377	}
110
111	chuckv	892	#ifdef PROFILE
112			startProfile(pro7);
113			#endif
114
115	mmeineke	423	for(i=0; i<entry_plug->n_mol; i++ ){
116	gezelter	1097	// CalcForces in molecules takes care of mapping rigid body coordinates
117			// into atomic coordinates
118	gezelter	1150	entry_plug->molecules[i].calcForces();
119	mmeineke	389	}
120
121	chuckv	892	#ifdef PROFILE
122			endProfile( pro7 );
123			#endif
124
125	mmeineke	670	config = entry_plug->getConfiguration();
126	mmeineke	597
127	mmeineke	670	frc = config->getFrcArray();
128			pos = config->getPosArray();
129			trq = config->getTrqArray();
130			A = config->getAmatArray();
131			u_l = config->getUlArray();
132	mmeineke	561
133	tim	1157	if(entry_plug->haveCutoffGroups){
134			//if
135			myMols = entry_plug->molecules;
136			numMol = entry_plug->n_mol;
137			for(int i = 0; i < numMol; i++){
138			numAtom = myMols[i].getNAtoms();
139			myAtoms = myMols[i].getMyAtoms();
140
141
142			for(int j = 0; j < numAtom; j++){
143			#ifdef IS_MPI
144			atomIndex = myAtoms[j]->getGlobalIndex();
145			#else
146			atomIndex = myAtoms[j]->getIndex();
147			#endif
148
149			if(myMols[i].belongToCutoffGroup(atomIndex))
150			continue;
151			else{
152			myAtoms[j]->getPos(tempPos);
153			myAtoms[j]->setRc(tempPos);
154			}
155
156			}
157
158			numCutoffGroups = myMols[i].getNCutoffGroups();
159			for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff); myCutoffGroup != NULL;
160			myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){
161			//get center of mass of the cutoff group
162			myCutoffGroup->getCOM(com);
163
164			for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom); cutoffAtom != NULL;
165			cutoffAtom = myCutoffGroup->beginAtom(iterAtom)){
166			cutoffAtom->setRc(com);
167			}
168
169			}// end for(myCutoffGroup)
170
171			}//end for(int i = 0)
172
173			rc = config->getRcArray();
174			}
175			else{
176			// center of mass of the group is the same as position of the atom if cutoff group does not exist
177			rc = pos;
178			}
179
180
181
182	mmeineke	377	isError = 0;
183			entry_plug->lrPot = 0.0;
184	mmeineke	393
185	chuckv	479	for (i=0; i<9; i++) {
186			entry_plug->tau[i] = 0.0;
187			}
188	chuckv	438
189	mmeineke	841
190	chuckv	892	#ifdef PROFILE
191			startProfile(pro8);
192			#endif
193
194	mmeineke	377	fortranForceLoop( pos,
195	tim	1142	rc,
196	mmeineke	377	A,
197			u_l,
198			frc,
199			trq,
200	chuckv	479	entry_plug->tau,
201	mmeineke	377	&(entry_plug->lrPot),
202			&passedCalcPot,
203			&passedCalcStress,
204			&isError );
205
206	tim	1136
207	chuckv	892	#ifdef PROFILE
208			endProfile(pro8);
209			#endif
210	mmeineke	841
211
212	mmeineke	377	if( isError ){
213			sprintf( painCave.errMsg,
214			"Error returned from the fortran force calculation.\n" );
215			painCave.isFatal = 1;
216			simError();
217			}
218
219	gezelter	1097	for(i=0; i<entry_plug->n_mol; i++ ){
220			entry_plug->molecules[i].atoms2rigidBodies();
221			}
222
223
224	mmeineke	377	#ifdef IS_MPI
225			sprintf( checkPointMsg,
226			"returned from the force calculation.\n" );
227			MPIcheckPoint();
228			#endif // is_mpi
229	mmeineke	597
230	mmeineke	377
231			}
232
233
234			void ForceFields::initFortran(int ljMixPolicy, int useReactionField ){
235
236			int isError;
237
238			isError = 0;
239			initFortranFF( &ljMixPolicy, &useReactionField, &isError );
240
241			if(isError){
242			sprintf( painCave.errMsg,
243			"ForceField error: There was an error initializing the forceField in fortran.\n" );
244			painCave.isFatal = 1;
245			simError();
246			}
247
248
249			#ifdef IS_MPI
250			sprintf( checkPointMsg, "ForceField successfully initialized the fortran component list.\n" );
251			MPIcheckPoint();
252			#endif // is_mpi
253
254			}