Inheritance diagram for ComputeExtMgr:
Public Member Functions | |
| ComputeExtMgr () | |
| ~ComputeExtMgr () | |
| void | setCompute (ComputeExt *c) |
| void | recvCoord (ExtCoordMsg *) |
| void | recvForce (ExtForceMsg *) |
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Definition at line 77 of file ComputeExt.C. 00077 :
00078 extProxy(thisgroup), extCompute(0), numSources(0), numArrived(0),
00079 coordMsgs(0), coord(0), force(0), oldmsg(0), numAtoms(0) {
00080 CkpvAccess(BOCclass_group).computeExtMgr = thisgroup;
00081 }
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Definition at line 83 of file ComputeExt.C. 00083 {
00084 for ( int i=0; i<numSources; ++i ) { delete coordMsgs[i]; }
00085 delete [] coordMsgs;
00086 delete [] coord;
00087 delete [] force;
00088 delete oldmsg;
00089 }
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Definition at line 168 of file ComputeExt.C. References Lattice::a(), Lattice::a_p(), Lattice::b(), Lattice::b_p(), Lattice::c(), Lattice::c_p(), ComputeExtAtom::charge, ExtCoordMsg::coord, ExtForceMsg::energy, SimParameters::extCoordFilename, SimParameters::extForceFilename, SimParameters::extForcesCommand, ExtForceMsg::force, ExtForce::force, ComputeExtAtom::id, j, ExtCoordMsg::lattice, Node::molecule, NAMD_die(), ExtCoordMsg::numAtoms, Molecule::numAtoms, Node::Object(), PatchMap::Object(), ComputeExtAtom::position, ExtForce::replace, Node::simParameters, simParams, ExtCoordMsg::sourceNode, ExtForceMsg::virial, Vector::x, Vector::y, and Vector::z. 00168 {
00169 if ( ! numSources ) {
00170 numSources = (PatchMap::Object())->numNodesWithPatches();
00171 coordMsgs = new ExtCoordMsg*[numSources];
00172 for ( int i=0; i<numSources; ++i ) { coordMsgs[i] = 0; }
00173 numArrived = 0;
00174 numAtoms = Node::Object()->molecule->numAtoms;
00175 coord = new ComputeExtAtom[numAtoms];
00176 force = new ExtForce[numAtoms];
00177 }
00178
00179 int i;
00180 for ( i=0; i < msg->numAtoms; ++i ) {
00181 coord[msg->coord[i].id] = msg->coord[i];
00182 }
00183
00184 coordMsgs[numArrived] = msg;
00185 ++numArrived;
00186
00187 if ( numArrived < numSources ) return;
00188 numArrived = 0;
00189
00190 // ALL DATA ARRIVED --- CALCULATE FORCES
00191 Lattice lattice = msg->lattice;
00192 SimParameters *simParams = Node::Object()->simParameters;
00193 FILE *file;
00194 int iret;
00195
00196 // write coordinates to file
00197 //iout << "writing to file " << simParams->extCoordFilename << "\n" << endi;
00198 file = fopen(simParams->extCoordFilename,"w");
00199 if ( ! file ) { NAMD_die(strerror(errno)); }
00200 for ( i=0; i<numAtoms; ++i ) {
00201 int id = coord[i].id + 1;
00202 double charge = coord[i].charge;
00203 double x = coord[i].position.x;
00204 double y = coord[i].position.y;
00205 double z = coord[i].position.z;
00206 iret = fprintf(file,"%d %f %f %f %f\n",id,charge,x,y,z);
00207 if ( iret < 0 ) { NAMD_die(strerror(errno)); }
00208 }
00209 // write periodic cell lattice (0 0 0 if non-periodic)
00210 Vector a = lattice.a(); if ( ! lattice.a_p() ) a = Vector(0,0,0);
00211 Vector b = lattice.b(); if ( ! lattice.b_p() ) b = Vector(0,0,0);
00212 Vector c = lattice.c(); if ( ! lattice.c_p() ) c = Vector(0,0,0);
00213 iret = fprintf(file,"%f %f %f\n%f %f %f\n%f %f %f\n",
00214 a.x, a.y, a.z, b.x, b.y, b.z, c.x, c.y, c.z);
00215 if ( iret < 0 ) { NAMD_die(strerror(errno)); }
00216 fclose(file);
00217
00218 // run user-specified command
00219 //iout << "running command " << simParams->extForcesCommand << "\n" << endi;
00220 iret = system(simParams->extForcesCommand);
00221 if ( iret == -1 ) { NAMD_die(strerror(errno)); }
00222 if ( iret ) { NAMD_die("Error running command for external forces."); }
00223
00224 // remove coordinate file
00225 iret = remove(simParams->extCoordFilename);
00226 if ( iret ) { NAMD_die(strerror(errno)); }
00227
00228 // read forces from file (overwrite positions)
00229 //iout << "reading from file " << simParams->extForceFilename << "\n" << endi;
00230 file = fopen(simParams->extForceFilename,"r");
00231 if ( ! file ) { NAMD_die(strerror(errno)); }
00232 for ( i=0; i<numAtoms; ++i ) {
00233 int id, replace;
00234 double x, y, z;
00235 iret = fscanf(file,"%d %d %lf %lf %lf\n", &id, &replace, &x, &y, &z);
00236 if ( iret != 5 ) { NAMD_die("Error reading external forces file."); }
00237 if ( id != i + 1 ) { NAMD_die("Atom ID error in external forces file."); }
00238 force[i].force.x = x; force[i].force.y = y; force[i].force.z = z;
00239 force[i].replace = replace;
00240 }
00241 // read energy and virial if they are present
00242 // virial used by NAMD is -'ve of normal convention, so reverse it!
00243 // virial[i][j] in file should be sum of -1 * f_i * r_j
00244 double energy;
00245 double virial[3][3];
00246 iret = fscanf(file,"%lf\n", &energy);
00247 if ( iret != 1 ) {
00248 energy = 0;
00249 for ( int k=0; k<3; ++k ) for ( int l=0; l<3; ++l ) virial[k][l] = 0;
00250 } else {
00251 iret = fscanf(file,"%lf %lf %lf\n%lf %lf %lf\n%lf %lf %lf\n",
00252 &virial[0][0], &virial[0][1], &virial[0][2],
00253 &virial[1][0], &virial[1][1], &virial[1][2],
00254 &virial[2][0], &virial[2][1], &virial[2][2]);
00255 if ( iret != 9 ) {
00256 for ( int k=0; k<3; ++k ) for ( int l=0; l<3; ++l ) virial[k][l] = 0;
00257 } else {
00258 // virial used by NAMD is -'ve of normal convention, so reverse it!
00259 for ( int k=0; k<3; ++k ) for ( int l=0; l<3; ++l ) virial[k][l] *= -1.0;
00260 }
00261 }
00262 fclose(file);
00263
00264 // remove force file
00265 iret = remove(simParams->extForceFilename);
00266 if ( iret ) { NAMD_die(strerror(errno)); }
00267
00268 // distribute forces
00269
00270 for ( int j=0; j < numSources; ++j ) {
00271 ExtCoordMsg *cmsg = coordMsgs[j];
00272 coordMsgs[j] = 0;
00273 ExtForceMsg *fmsg = new (cmsg->numAtoms, 0) ExtForceMsg;
00274 for ( int i=0; i < cmsg->numAtoms; ++i ) {
00275 fmsg->force[i] = force[cmsg->coord[i].id];
00276 }
00277 if ( ! j ) {
00278 fmsg->energy = energy;
00279 for ( int k=0; k<3; ++k ) for ( int l=0; l<3; ++l )
00280 fmsg->virial[k][l] = virial[k][l];
00281 } else {
00282 fmsg->energy = 0;
00283 for ( int k=0; k<3; ++k ) for ( int l=0; l<3; ++l )
00284 fmsg->virial[k][l] = 0;
00285 }
00286 extProxy[cmsg->sourceNode].recvForce(fmsg);
00287 delete cmsg;
00288 }
00289
00290 }
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Definition at line 292 of file ComputeExt.C. References ComputeExt::saveResults(). 00292 {
00293 extCompute->saveResults(msg);
00294 delete oldmsg;
00295 oldmsg = msg;
00296 }
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Definition at line 59 of file ComputeExt.C. 00059 { extCompute = c; }
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1.3.9.1