ATC version 2.0, date: Nov20
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12757 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
jatempl
@ -52,6 +52,7 @@ namespace ATC {
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atomGhostCoarseGrainingPositions_(NULL),
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atomProcGhostCoarseGrainingPositions_(NULL),
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atomReferencePositions_(NULL),
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nNodes_(0),
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nsd_(lammpsInterface_->dimension()),
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xref_(NULL),
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readXref_(false),
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@ -355,7 +356,6 @@ pecified
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}
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}
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/*! \page man_boundary_integral fix_modify AtC output boundary_integral
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\section syntax
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fix_modify AtC output boundary_integral [field] faceset [name]
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@ -412,7 +412,7 @@ pecified
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/*! \page man_output_elementset fix_modify AtC output elementset
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\section syntax
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fix_modify AtC output volume_integral <eset_name> <field> {`
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fix_modify AtC output volume_integral <eset_name> <field>
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- set_name (string) = name of elementset to be integrated over
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- fieldname (string) = name of field to integrate
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csum = creates nodal sum over nodes in specified nodeset \n
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@ -508,6 +508,25 @@ pecified
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match = true;
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}
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}
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else if (strcmp(arg[argIdx],"write")==0) {
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argIdx++;
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FieldName thisField;
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int thisIndex;
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parse_field(arg,argIdx,thisField,thisIndex);
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string nsetName(arg[argIdx++]);
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string filename(arg[argIdx++]);
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stringstream f;
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set<int> nodeSet = (feEngine_->fe_mesh())->nodeset(nsetName);
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set<int>::const_iterator iset;
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const DENS_MAT & field =(fields_.find(thisField)->second).quantity();
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for (iset = nodeSet.begin(); iset != nodeSet.end(); iset++) {
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int inode = *iset;
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double v = field(inode,thisIndex);
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f << inode << " " << std::setprecision(17) << v << "\n";
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}
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LammpsInterface::instance()->write_file(filename,f.str());
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match = true;
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}
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// add a species for tracking
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/*! \page man_add_species fix_modify AtC add_species
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\section syntax
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@ -907,7 +926,7 @@ pecified
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\section syntax
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fix_modify AtC kernel_bandwidth <value>
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\section examples
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<TT> fix_modify atc reset_time 8 </TT> \n
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<TT> fix_modify atc kernel_bandwidth 8 </TT> \n
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\section description
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Sets a maximum parallel bandwidth for the kernel functions during parallel communication. If the command is not issued, the default will be to assume the bandwidth of the kernel matrix corresponds to the number of sampling locations.
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\section restrictions
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@ -1078,6 +1097,22 @@ pecified
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}
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//--------------------------------------------------
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// helper function for parser
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// handles : "displacement x" and "temperature" by indexing argIdx
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// for fluxes : only normal fluxes can be prescribed
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//--------------------------------------------------
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void ATC_Method::parse_field(/*const*/ char ** args, int & argIdx,
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FieldName & thisField)
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{
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string thisName = args[argIdx++];
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thisField = string_to_field(thisName);
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map<FieldName,int>::const_iterator iter = fieldSizes_.find(thisField);
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if (iter == fieldSizes_.end()) {
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throw ATC_Error("Bad field name: "+thisName);
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}
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}
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//--------------------------------------------------
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// helper function for parser
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// handles : "displacement x" and "temperature" by indexing argIdx
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@ -1266,6 +1301,33 @@ pecified
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readXref_ = false;
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}
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// ensure initial configuration is consistent with element set
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if (internalElementSet_.size() && groupbitGhost_) {
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int *mask = lammpsInterface_->atom_mask();
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int nlocal = lammpsInterface_->nlocal();
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const FE_Mesh * feMesh = feEngine_->fe_mesh();
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const set<int> & elementSet(feMesh->elementset(internalElementSet_));
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int element;
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DENS_VEC coords(nsd_);
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for (int i = 0; i < nlocal; ++i) {
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if (mask[i] & groupbit_ || mask[i] & groupbitGhost_) {
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for (int j = 0; j < nsd_; j++) {
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coords(j) = xref_[i][j];
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}
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element = feMesh->map_to_element(coords);
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if (elementSet.find(element) == elementSet.end()) {
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mask[i] |= groupbitGhost_;
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mask[i] &= ~groupbit_;
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}
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else {
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mask[i] &= ~groupbitGhost_;
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mask[i] |= groupbit_;
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}
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}
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}
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}
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// set up maps from lammps to atc indexing
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reset_nlocal();
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}
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@ -1321,6 +1383,12 @@ pecified
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// 6e) atomic output for 0th step
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update_peratom_output();
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massMatInv_.reset(nNodes_,nNodes_);
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feEngine_->compute_lumped_mass_matrix(massMatInv_);
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for (int i = 0; i < nNodes_; ++i) {
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massMatInv_(i,i) = 1./massMatInv_(i,i);
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}
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// clear need for resets
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needReset_ = false;
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@ -1792,12 +1860,7 @@ pecified
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}
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}
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return m;
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//int mySize = 3;
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//if (num_bond)
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// mySize += 1 + lammpsInterface_->bond_per_atom();
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//return mySize;
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return m; // total amount of data sent
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}
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//-----------------------------------------------------------------
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@ -1827,6 +1890,17 @@ pecified
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}
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}
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//-----------------------------------------------------------------
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//
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//-----------------------------------------------------------------
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int ATC_Method::comm_forward()
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{
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int size = 3;
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if (lammpsInterface_->num_bond())
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{ size += lammpsInterface_->bond_per_atom()+1; }
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return size;
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}
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//-----------------------------------------------------------------
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//
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//-----------------------------------------------------------------
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@ -2195,6 +2269,8 @@ pecified
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// get number of atoms
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int natoms = 0;
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int ncols = 0;
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int style = LammpsInterface::CHARGE_STYLE;
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if (LammpsInterface::instance()->rank_zero()) {
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in.open(filename);
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string msg;
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@ -2204,10 +2280,45 @@ pecified
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in.getline(line,lineSize); // header
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in.getline(line,lineSize); // blank line
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in >> natoms;
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in.close();
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stringstream ss;
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ss << "found " << natoms << " atoms in reference file";
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ss << "found " << natoms << " atoms in reference " << filename ;
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while(in.good()) {
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in.getline(line,lineSize);
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string str(line);
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int pos = str.find("Atoms");
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if (pos > -1) {
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in.getline(line,lineSize); // blank line
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break;
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}
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}
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in.getline(line,lineSize);
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std::vector<std::string> tokens;
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ATC_Utility::command_strings(line, tokens);
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ncols = tokens.size();
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switch (ncols) {
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// atomic: id type x y z
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case 5:
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case 8:
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ss << " style:atomic";
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style = LammpsInterface::ATOMIC_STYLE;
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break;
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// charge: id type q x y z
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// molecule : id molecule-ID type x y z
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case 6:
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ss << " style:charge";
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style = LammpsInterface::CHARGE_STYLE;
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break;
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// full : id molecule-ID type q x y z
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case 7:
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ss << " style:full";
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style = LammpsInterface::FULL_STYLE;
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break;
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default:
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throw ATC_Error("cannot determine atom style, columns:"+to_string(ncols));
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break;
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}
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LammpsInterface::instance()->print_msg(ss.str());
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in.close();
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}
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LammpsInterface::instance()->int_broadcast(&natoms);
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@ -2224,12 +2335,17 @@ pecified
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}
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}
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}
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int nread = 0,type = -1, tag = -1, count = 0;
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double x[3]={0,0,0};
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int nread = 0,type = -1, tag = -1, count = 0, mId = -1;
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double x[3]={0,0,0}, q =0;
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while (nread < natoms) {
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if (LammpsInterface::instance()->rank_zero()) {
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in.getline(line,lineSize);
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stringstream ss (line,stringstream::in | stringstream::out);
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if (style == LammpsInterface::CHARGE_STYLE)
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ss >> tag >> type >> q >> x[0] >> x[1] >> x[2];
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else if (style == LammpsInterface::FULL_STYLE)
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ss >> tag >> mId >> type >> q >> x[0] >> x[1] >> x[2];
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else
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ss >> tag >> type >> x[0] >> x[1] >> x[2];
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nread++;
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}
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