| 7 |
|
|
| 8 |
|
using namespace std; |
| 9 |
|
|
| 10 |
< |
ZConsWriter::ZConsWriter(const char* filename) |
| 10 |
> |
ZConsWriter::ZConsWriter(const char* filename, vector<ZConsParaItem>* thePara) |
| 11 |
|
{ |
| 12 |
|
//use master - slave mode, only master node writes to disk |
| 13 |
|
#ifdef IS_MPI |
| 18 |
|
|
| 19 |
|
if(!output){ |
| 20 |
|
sprintf( painCave.errMsg, |
| 21 |
< |
"Could not open \"s\" for z constrain output \n", |
| 22 |
< |
filename); |
| 21 |
> |
"Could not open %s for z constrain output \n", |
| 22 |
> |
filename); |
| 23 |
|
painCave.isFatal = 1; |
| 24 |
|
simError(); |
| 25 |
|
} |
| 26 |
|
output << "#number of z constrain molecules" << endl; |
| 27 |
< |
output << "#global Index of molecule\trefZ" << endl; |
| 28 |
< |
|
| 27 |
> |
output << "#global Index of molecule\tzPos" << endl; |
| 28 |
> |
output << "#every frame will contain below data" <<endl; |
| 29 |
|
output << "#time(fs)" << endl; |
| 30 |
< |
output << "#number of z constrain molecules" << endl; |
| 31 |
< |
output << "#global Index of molecule\tzconstrain force" << endl; |
| 30 |
> |
output << "#number of fixed z-constrain molecules" << endl; |
| 31 |
> |
output << "#global Index of molecule\tzconstrain force\tcurrentZPos" << endl; |
| 32 |
> |
|
| 33 |
> |
parameters = thePara; |
| 34 |
> |
writeZPos(); |
| 35 |
> |
|
| 36 |
|
#ifdef IS_MPI |
| 37 |
|
} |
| 38 |
|
#endif |
| 51 |
|
#endif |
| 52 |
|
} |
| 53 |
|
|
| 54 |
< |
void ZConsWriter::writeFZ(double time, int num, int* index, double* fz) |
| 55 |
< |
{ |
| 54 |
> |
/** |
| 55 |
> |
* |
| 56 |
> |
*/ |
| 57 |
> |
void ZConsWriter::writeFZ(double time, int num, int* index, double* fz, double* curZPos, double* zpos){ |
| 58 |
|
|
| 59 |
|
#ifndef IS_MPI |
| 54 |
– |
vector<pair<int, double> > data; // The space between two ">" is needed. Otherwise, compileer |
| 55 |
– |
// will take it as redirect symbol ">>" |
| 56 |
– |
|
| 57 |
– |
for(int i = 0; i < num ; i++) |
| 58 |
– |
data.push_back(pair<int, double>(index[i], fz[i])); |
| 59 |
– |
|
| 60 |
|
output << time << endl; |
| 61 |
|
output << num << endl; |
| 62 |
|
|
| 63 |
< |
//sort data by index |
| 64 |
< |
sort(data.begin(), data.end()); |
| 65 |
< |
|
| 66 |
< |
for(int i=0; i < data.size(); i++) |
| 67 |
< |
output << data[i].first << "\t" << data[i].second << endl; |
| 68 |
< |
|
| 69 |
< |
#else |
| 63 |
> |
for(int i = 0; i < num; i++) |
| 64 |
> |
output << index[i] <<"\t" << fz[i] << "\t" << curZPos[i] << "\t" << zpos[i] <<endl; |
| 65 |
|
|
| 66 |
< |
//master node will be responsible for receiving, assembling and writing data |
| 67 |
< |
if(worldRank == 0) |
| 68 |
< |
{ |
| 66 |
> |
#else |
| 67 |
> |
int totalNum; |
| 68 |
> |
MPI_Allreduce(&num, &totalNum, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
| 69 |
|
|
| 70 |
< |
vector<pair<int,double> > data; |
| 71 |
< |
int numProcessors; |
| 72 |
< |
int recvCount; |
| 73 |
< |
int* indexBuf; |
| 74 |
< |
double* fzBuf; |
| 75 |
< |
MPI_Status istatus; |
| 76 |
< |
|
| 77 |
< |
//process the data in master |
| 78 |
< |
for(int i=0; i < num; i++){ |
| 79 |
< |
data.push_back(pair<int, double>(index[i], fz[i])); |
| 80 |
< |
} |
| 70 |
> |
if(worldRank == 0){ |
| 71 |
> |
output << time << endl; |
| 72 |
> |
output << totalNum << endl; |
| 73 |
> |
} |
| 74 |
> |
|
| 75 |
> |
int whichNode; |
| 76 |
> |
enum CommType { RequesPosAndForce, EndOfRequest} status; |
| 77 |
> |
double pos; |
| 78 |
> |
double force; |
| 79 |
> |
double zconsPos; |
| 80 |
> |
int localIndex; |
| 81 |
> |
MPI_Status ierr; |
| 82 |
> |
int tag = 0; |
| 83 |
> |
|
| 84 |
> |
if(worldRank == 0){ |
| 85 |
|
|
| 86 |
< |
|
| 87 |
< |
numProcessors = mpiSim->getNumberProcessors(); |
| 86 |
> |
int globalIndexOfCurMol; |
| 87 |
> |
int *MolToProcMap; |
| 88 |
> |
MolToProcMap = mpiSim->getMolToProcMap(); |
| 89 |
|
|
| 90 |
< |
//acquire the data from other nodes; |
| 91 |
< |
for(int whichNode = 1; whichNode < numProcessors; whichNode++){ |
| 92 |
< |
|
| 90 |
> |
for(int i = 0; i < (int)(parameters->size()); i++){ |
| 91 |
|
|
| 92 |
< |
MPI_Recv(&recvCount, 1, MPI_INT, whichNode, |
| 93 |
< |
0, MPI_COMM_WORLD, &istatus); |
| 92 |
> |
globalIndexOfCurMol = (*parameters)[i].zconsIndex; |
| 93 |
> |
whichNode = MolToProcMap[globalIndexOfCurMol]; |
| 94 |
|
|
| 95 |
< |
if(recvCount > 0){ |
| 98 |
< |
|
| 99 |
< |
indexBuf = new int[recvCount]; |
| 100 |
< |
fzBuf = new double[recvCount]; |
| 95 |
> |
if(whichNode == 0){ |
| 96 |
|
|
| 97 |
< |
if(!indexBuf || !fzBuf){ |
| 98 |
< |
sprintf(painCave.errMsg, |
| 99 |
< |
"Memory Allocation inside class ZConsWriter\n"); |
| 100 |
< |
painCave.isFatal = 1; |
| 101 |
< |
simError(); |
| 107 |
< |
} |
| 108 |
< |
|
| 109 |
< |
MPI_Recv(indexBuf, recvCount, MPI_INT, whichNode, |
| 110 |
< |
0, MPI_COMM_WORLD, &istatus); |
| 97 |
> |
for(int j = 0; j < num; j++) |
| 98 |
> |
if(index[j] == globalIndexOfCurMol){ |
| 99 |
> |
localIndex = j; |
| 100 |
> |
break; |
| 101 |
> |
} |
| 102 |
|
|
| 103 |
< |
MPI_Recv(fzBuf, recvCount, MPI_DOUBLE_PRECISION, whichNode, |
| 104 |
< |
0, MPI_COMM_WORLD, &istatus); |
| 105 |
< |
|
| 115 |
< |
//assemble the data |
| 116 |
< |
for(int i = 0; i < recvCount; i++){ |
| 117 |
< |
data.push_back(pair<int, double>(indexBuf[i], fzBuf[i])); |
| 118 |
< |
} |
| 119 |
< |
|
| 120 |
< |
|
| 121 |
< |
delete[] indexBuf; |
| 122 |
< |
delete[] fzBuf; |
| 123 |
< |
|
| 103 |
> |
force = fz[localIndex]; |
| 104 |
> |
pos = curZPos[localIndex]; |
| 105 |
> |
|
| 106 |
|
} |
| 107 |
< |
|
| 108 |
< |
} |
| 107 |
> |
else{ |
| 108 |
> |
status = RequesPosAndForce; |
| 109 |
> |
MPI_Send(&status, 1, MPI_INT, whichNode, tag, MPI_COMM_WORLD); |
| 110 |
> |
MPI_Send(&globalIndexOfCurMol, 1, MPI_INT, whichNode, tag, MPI_COMM_WORLD); |
| 111 |
> |
MPI_Recv(&force, 1, MPI_DOUBLE, whichNode, tag, MPI_COMM_WORLD, &ierr); |
| 112 |
> |
MPI_Recv(&pos, 1, MPI_DOUBLE, whichNode, tag, MPI_COMM_WORLD, &ierr); |
| 113 |
> |
MPI_Recv(&zconsPos, 1, MPI_DOUBLE, whichNode, tag, MPI_COMM_WORLD, &ierr); |
| 114 |
> |
} |
| 115 |
> |
|
| 116 |
> |
output << globalIndexOfCurMol << "\t" << force << "\t" << pos << "\t"<< zconsPos << endl; |
| 117 |
> |
|
| 118 |
> |
} //End of Request Loop |
| 119 |
|
|
| 120 |
< |
// sort the data by index |
| 121 |
< |
sort(data.begin(), data.end()); |
| 120 |
> |
//Send ending request message to slave nodes |
| 121 |
> |
status = EndOfRequest; |
| 122 |
> |
for(int i =1; i < mpiSim->getNprocessors(); i++) |
| 123 |
> |
MPI_Send(&status, 1, MPI_INT, i, tag, MPI_COMM_WORLD); |
| 124 |
> |
|
| 125 |
> |
} |
| 126 |
> |
else{ |
| 127 |
> |
|
| 128 |
> |
int whichMol; |
| 129 |
> |
bool done = false; |
| 130 |
> |
|
| 131 |
> |
while (!done){ |
| 132 |
> |
|
| 133 |
> |
MPI_Recv(&status, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &ierr); |
| 134 |
|
|
| 135 |
< |
output << time << endl; |
| 136 |
< |
output << data.size() << endl; |
| 135 |
> |
switch (status){ |
| 136 |
> |
|
| 137 |
> |
case RequesPosAndForce : |
| 138 |
> |
|
| 139 |
> |
MPI_Recv(&whichMol, 1, MPI_INT, 0, tag, MPI_COMM_WORLD,&ierr); |
| 140 |
|
|
| 141 |
< |
for(int i = 0; i < data.size(); i++){ |
| 141 |
> |
for(int i = 0; i < num; i++) |
| 142 |
> |
if(index[i] == whichMol){ |
| 143 |
> |
localIndex = i; |
| 144 |
> |
break; |
| 145 |
> |
} |
| 146 |
|
|
| 147 |
< |
output << data[i].first << "\t" << data[i].second << endl; |
| 147 |
> |
MPI_Send(&fz[localIndex], 1, MPI_DOUBLE, 0, tag, MPI_COMM_WORLD); |
| 148 |
> |
MPI_Send(&curZPos[localIndex], 1, MPI_DOUBLE, 0, tag, MPI_COMM_WORLD); |
| 149 |
> |
MPI_Send(&zpos[localIndex], 1, MPI_DOUBLE, 0, tag, MPI_COMM_WORLD); |
| 150 |
> |
break; |
| 151 |
> |
|
| 152 |
> |
case EndOfRequest : |
| 153 |
> |
|
| 154 |
> |
done = true; |
| 155 |
> |
break; |
| 156 |
> |
} |
| 157 |
> |
|
| 158 |
|
} |
| 159 |
< |
|
| 139 |
< |
} |
| 140 |
< |
else |
| 141 |
< |
{ |
| 142 |
< |
MPI_Send(&num, 1, MPI_INT, 0, 0, MPI_COMM_WORLD); |
| 143 |
< |
|
| 144 |
< |
if(num > 0){ |
| 145 |
< |
MPI_Send(index, num, MPI_INT, 0, 0, MPI_COMM_WORLD); |
| 146 |
< |
MPI_Send(fz, num, MPI_DOUBLE_PRECISION, 0, 0, MPI_COMM_WORLD); |
| 147 |
< |
} |
| 159 |
> |
|
| 160 |
|
} |
| 161 |
|
|
| 162 |
|
#endif |
| 163 |
|
|
| 164 |
|
} |
| 165 |
|
|
| 166 |
< |
void ZConsWriter::writeRefZ(const vector<int>& index, const vector<double>& refZ){ |
| 166 |
> |
/* |
| 167 |
> |
* |
| 168 |
> |
*/ |
| 169 |
> |
void ZConsWriter::writeZPos(){ |
| 170 |
|
|
| 171 |
|
#ifdef IS_MPI |
| 172 |
|
if(worldRank == 0){ |
| 173 |
|
#endif |
| 174 |
|
|
| 175 |
< |
output << index.size() << endl; |
| 175 |
> |
output << parameters->size() << endl; |
| 176 |
|
|
| 177 |
< |
for(int i =0 ; i < index.size(); i++) |
| 178 |
< |
output << index[i] << "\t" << refZ[i] << endl; |
| 177 |
> |
for(int i =0 ; i < (int)(parameters->size()); i++) |
| 178 |
> |
output << (*parameters)[i].zconsIndex << "\t" << (*parameters)[i].zPos << endl; |
| 179 |
|
|
| 180 |
|
#ifdef IS_MPI |
| 181 |
|
} |
