16 |
|
n_constraints = 0; |
17 |
|
n_oriented = 0; |
18 |
|
n_dipoles = 0; |
19 |
+ |
ndf = 0; |
20 |
+ |
ndfRaw = 0; |
21 |
|
the_integrator = NULL; |
22 |
|
setTemp = 0; |
23 |
|
thermalTime = 0.0; |
24 |
+ |
rCut = 0.0; |
25 |
|
|
26 |
|
usePBC = 0; |
27 |
|
useLJ = 0; |
31 |
|
useGB = 0; |
32 |
|
useEAM = 0; |
33 |
|
|
34 |
+ |
wrapMeSimInfo( this ); |
35 |
+ |
} |
36 |
|
|
37 |
+ |
void SimInfo::setBox(double newBox[3]) { |
38 |
+ |
double smallestBox, maxCutoff; |
39 |
+ |
int status; |
40 |
+ |
box_x = newBox[0]; |
41 |
+ |
box_y = newBox[1]; |
42 |
+ |
box_z = newBox[2]; |
43 |
+ |
setFortranBoxSize(newBox); |
44 |
|
|
45 |
< |
wrapMeSimInfo( this ); |
45 |
> |
smallestBox = box_x; |
46 |
> |
if (box_y < smallestBox) smallestBox = box_y; |
47 |
> |
if (box_z < smallestBox) smallestBox = box_z; |
48 |
> |
|
49 |
> |
maxCutoff = smallestBox / 2.0; |
50 |
> |
|
51 |
> |
if (rList > maxCutoff) { |
52 |
> |
sprintf( painCave.errMsg, |
53 |
> |
"New Box size is forcing neighborlist radius down to %lf\n", |
54 |
> |
maxCutoff ); |
55 |
> |
painCave.isFatal = 0; |
56 |
> |
simError(); |
57 |
> |
|
58 |
> |
rList = maxCutoff; |
59 |
> |
|
60 |
> |
sprintf( painCave.errMsg, |
61 |
> |
"New Box size is forcing cutoff radius down to %lf\n", |
62 |
> |
maxCutoff - 1.0 ); |
63 |
> |
painCave.isFatal = 0; |
64 |
> |
simError(); |
65 |
> |
|
66 |
> |
rCut = rList - 1.0; |
67 |
> |
|
68 |
> |
// list radius changed so we have to refresh the simulation structure. |
69 |
> |
refreshSim(); |
70 |
> |
} |
71 |
> |
|
72 |
> |
if (rCut > maxCutoff) { |
73 |
> |
sprintf( painCave.errMsg, |
74 |
> |
"New Box size is forcing cutoff radius down to %lf\n", |
75 |
> |
maxCutoff ); |
76 |
> |
painCave.isFatal = 0; |
77 |
> |
simError(); |
78 |
> |
|
79 |
> |
status = 0; |
80 |
> |
LJ_new_rcut(&rCut, &status); |
81 |
> |
if (status != 0) { |
82 |
> |
sprintf( painCave.errMsg, |
83 |
> |
"Error in recomputing LJ shifts based on new rcut\n"); |
84 |
> |
painCave.isFatal = 1; |
85 |
> |
simError(); |
86 |
> |
} |
87 |
> |
} |
88 |
|
} |
89 |
|
|
90 |
+ |
void SimInfo::getBox(double theBox[3]) { |
91 |
+ |
theBox[0] = box_x; |
92 |
+ |
theBox[1] = box_y; |
93 |
+ |
theBox[2] = box_z; |
94 |
+ |
} |
95 |
+ |
|
96 |
+ |
int SimInfo::getNDF(){ |
97 |
+ |
int ndf_local, ndf; |
98 |
+ |
|
99 |
+ |
ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints; |
100 |
+ |
|
101 |
+ |
#ifdef IS_MPI |
102 |
+ |
MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
103 |
+ |
#else |
104 |
+ |
ndf = ndf_local; |
105 |
+ |
#endif |
106 |
+ |
|
107 |
+ |
ndf = ndf - 3; |
108 |
+ |
|
109 |
+ |
return ndf; |
110 |
+ |
} |
111 |
+ |
|
112 |
+ |
int SimInfo::getNDFraw() { |
113 |
+ |
int ndfRaw_local, ndfRaw; |
114 |
+ |
|
115 |
+ |
// Raw degrees of freedom that we have to set |
116 |
+ |
ndfRaw_local = 3 * n_atoms + 3 * n_oriented; |
117 |
+ |
|
118 |
+ |
#ifdef IS_MPI |
119 |
+ |
MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
120 |
+ |
#else |
121 |
+ |
ndfRaw = ndfRaw_local; |
122 |
+ |
#endif |
123 |
+ |
|
124 |
+ |
return ndfRaw; |
125 |
+ |
} |
126 |
+ |
|
127 |
|
void SimInfo::refreshSim(){ |
128 |
|
|
129 |
|
simtype fInfo; |
130 |
|
int isError; |
131 |
+ |
int* excl; |
132 |
|
|
133 |
|
fInfo.box[0] = box_x; |
134 |
|
fInfo.box[1] = box_y; |
141 |
|
fInfo.dielect = dielectric; |
142 |
|
|
143 |
|
fInfo.SIM_uses_PBC = usePBC; |
144 |
+ |
//fInfo.SIM_uses_LJ = 0; |
145 |
|
fInfo.SIM_uses_LJ = useLJ; |
146 |
< |
//fInfo.SIM_uses_sticky = useSticky; |
147 |
< |
fInfo.SIM_uses_sticky = 0; |
146 |
> |
fInfo.SIM_uses_sticky = useSticky; |
147 |
> |
//fInfo.SIM_uses_sticky = 0; |
148 |
|
fInfo.SIM_uses_dipoles = useDipole; |
149 |
< |
fInfo.SIM_uses_RF = useReactionField; |
149 |
> |
//fInfo.SIM_uses_dipoles = 0; |
150 |
> |
//fInfo.SIM_uses_RF = useReactionField; |
151 |
> |
fInfo.SIM_uses_RF = 0; |
152 |
|
fInfo.SIM_uses_GB = useGB; |
153 |
|
fInfo.SIM_uses_EAM = useEAM; |
154 |
|
|
155 |
+ |
excl = Exclude::getArray(); |
156 |
|
|
157 |
|
isError = 0; |
158 |
|
|
159 |
< |
fInfo; |
160 |
< |
n_atoms; |
161 |
< |
identArray; |
162 |
< |
n_exclude; |
163 |
< |
excludes; |
164 |
< |
nGlobalExcludes; |
165 |
< |
globalExcludes; |
166 |
< |
isError; |
159 |
> |
// fInfo; |
160 |
> |
// n_atoms; |
161 |
> |
// identArray; |
162 |
> |
// n_exclude; |
163 |
> |
// excludes; |
164 |
> |
// nGlobalExcludes; |
165 |
> |
// globalExcludes; |
166 |
> |
// isError; |
167 |
|
|
168 |
< |
setFsimulation( &fInfo, &n_atoms, identArray, &n_exclude, excludes, &nGlobalExcludes, globalExcludes, &isError ); |
168 |
> |
setFsimulation( &fInfo, &n_atoms, identArray, &n_exclude, excl, |
169 |
> |
&nGlobalExcludes, globalExcludes, &isError ); |
170 |
|
|
171 |
|
if( isError ){ |
172 |
|
|
181 |
|
"succesfully sent the simulation information to fortran.\n"); |
182 |
|
MPIcheckPoint(); |
183 |
|
#endif // is_mpi |
184 |
+ |
|
185 |
+ |
ndf = this->getNDF(); |
186 |
+ |
ndfRaw = this->getNDFraw(); |
187 |
+ |
|
188 |
|
} |
189 |
|
|