1 |
#include <iostream> |
2 |
|
3 |
using namespace std; |
4 |
|
5 |
|
6 |
#include <stdlib.h> |
7 |
|
8 |
#ifdef IS_MPI |
9 |
#include <mpi.h> |
10 |
#endif // is_mpi |
11 |
|
12 |
|
13 |
#ifdef PROFILE |
14 |
#include "mdProfile.hpp" |
15 |
#endif |
16 |
|
17 |
#include "simError.h" |
18 |
#include "ForceFields.hpp" |
19 |
#include "Atom.hpp" |
20 |
#include "fortranWrappers.hpp" |
21 |
|
22 |
|
23 |
void ForceFields::calcRcut( void ){ |
24 |
|
25 |
#ifdef IS_MPI |
26 |
double tempBig = bigSigma; |
27 |
MPI_Allreduce( &tempBig, &bigSigma, 1, MPI_DOUBLE, MPI_MAX, |
28 |
MPI_COMM_WORLD); |
29 |
#endif //is_mpi |
30 |
|
31 |
//calc rCut and rList |
32 |
|
33 |
entry_plug->setDefaultRcut( 2.5 * bigSigma ); |
34 |
|
35 |
} |
36 |
|
37 |
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 |
void ForceFields::doForces( int calcPot, int calcStress ){ |
75 |
|
76 |
int i, j, isError; |
77 |
double* frc; |
78 |
double* pos; |
79 |
double* trq; |
80 |
double* A; |
81 |
double* u_l; |
82 |
double* rc; |
83 |
double* massRatio; |
84 |
SimState* config; |
85 |
|
86 |
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 |
short int passedCalcPot = (short int)calcPot; |
102 |
short int passedCalcStress = (short int)calcStress; |
103 |
|
104 |
// forces are zeroed here, before any are accumulated. |
105 |
// NOTE: do not rezero the forces in Fortran. |
106 |
|
107 |
for(i=0; i<entry_plug->n_atoms; i++){ |
108 |
entry_plug->atoms[i]->zeroForces(); |
109 |
} |
110 |
|
111 |
#ifdef PROFILE |
112 |
startProfile(pro7); |
113 |
#endif |
114 |
|
115 |
for(i=0; i<entry_plug->n_mol; i++ ){ |
116 |
// CalcForces in molecules takes care of mapping rigid body coordinates |
117 |
// into atomic coordinates |
118 |
entry_plug->molecules[i].calcForces(); |
119 |
} |
120 |
|
121 |
#ifdef PROFILE |
122 |
endProfile( pro7 ); |
123 |
#endif |
124 |
|
125 |
config = entry_plug->getConfiguration(); |
126 |
|
127 |
frc = config->getFrcArray(); |
128 |
pos = config->getPosArray(); |
129 |
trq = config->getTrqArray(); |
130 |
A = config->getAmatArray(); |
131 |
u_l = config->getUlArray(); |
132 |
|
133 |
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 |
isError = 0; |
183 |
entry_plug->lrPot = 0.0; |
184 |
|
185 |
for (i=0; i<9; i++) { |
186 |
entry_plug->tau[i] = 0.0; |
187 |
} |
188 |
|
189 |
|
190 |
#ifdef PROFILE |
191 |
startProfile(pro8); |
192 |
#endif |
193 |
|
194 |
fortranForceLoop( pos, |
195 |
rc, |
196 |
A, |
197 |
u_l, |
198 |
frc, |
199 |
trq, |
200 |
entry_plug->tau, |
201 |
&(entry_plug->lrPot), |
202 |
&passedCalcPot, |
203 |
&passedCalcStress, |
204 |
&isError ); |
205 |
|
206 |
|
207 |
#ifdef PROFILE |
208 |
endProfile(pro8); |
209 |
#endif |
210 |
|
211 |
|
212 |
if( isError ){ |
213 |
sprintf( painCave.errMsg, |
214 |
"Error returned from the fortran force calculation.\n" ); |
215 |
painCave.isFatal = 1; |
216 |
simError(); |
217 |
} |
218 |
|
219 |
for(i=0; i<entry_plug->n_mol; i++ ){ |
220 |
entry_plug->molecules[i].atoms2rigidBodies(); |
221 |
} |
222 |
|
223 |
|
224 |
#ifdef IS_MPI |
225 |
sprintf( checkPointMsg, |
226 |
"returned from the force calculation.\n" ); |
227 |
MPIcheckPoint(); |
228 |
#endif // is_mpi |
229 |
|
230 |
|
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 |
} |