replace tabs and remove trailing whitespace in lib folder with updated script
This commit is contained in:
Axel Kohlmeyer
@ -13,7 +13,7 @@ using std::pair;
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namespace ATC {
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// only one regulator method at time, i.e. fixed & flux, thermo & elastic
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// regulator manages lambda variables, creates new ones when requested with dimensions and zero ics (map of tag to lambda)
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// regulator keeps track of which lambda are being used, unused lambdas deleted (map of tag to bool), all tags set to unused on start of initialization
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@ -168,7 +168,7 @@ namespace ATC {
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fix_modify AtC control <physics_type> <solution_parameter> <value>\n
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- physics_type (string) = thermal | momentum\n
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- solution_parameter (string) = max_iterations | tolerance\n
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fix_modify AtC transfer <physics_type> control max_iterations <max_iterations>\n
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- max_iterations (int) = maximum number of iterations that will be used by iterative matrix solvers\n
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@ -209,14 +209,14 @@ namespace ATC {
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foundMatch = true;
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}
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/*! \page man_localized_lambda fix_modify AtC control localized_lambda
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/*! \page man_localized_lambda fix_modify AtC control localized_lambda
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\section syntax
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fix_modify AtC control localized_lambda <on|off>
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fix_modify AtC control localized_lambda <on|off>
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\section examples
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<TT> fix_modify atc control localized_lambda on </TT> \n
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\section description
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Turns on localization algorithms for control algorithms to restrict the influence of FE coupling or boundary conditions to a region near the boundary of the MD region. Control algorithms will not affect atoms in elements not possessing faces on the boundary of the region. Flux-based control is localized via row-sum lumping while quantity control is done by solving a truncated matrix equation.
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\section restrictions
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\section restrictions
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\section related
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\section default
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Default is off.
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@ -233,16 +233,16 @@ namespace ATC {
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}
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}
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/*! \page man_lumped_lambda_solve fix_modify AtC control lumped_lambda_solve
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/*! \page man_lumped_lambda_solve fix_modify AtC control lumped_lambda_solve
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\section syntax
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fix_modify AtC control lumped_lambda_solve <on|off>
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fix_modify AtC control lumped_lambda_solve <on|off>
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\section examples
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<TT> fix_modify atc control lumped_lambda_solve on </TT> \n
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\section description
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Command to use or not use lumped matrix for lambda solve
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\section restrictions
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\section restrictions
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\section related
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\section default
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*/
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@ -260,12 +260,12 @@ namespace ATC {
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/*! \page man_mask_direction fix_modify AtC control mask_direction
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\section syntax
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fix_modify AtC control mask_direction <direction> <on|off>
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fix_modify AtC control mask_direction <direction> <on|off>
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\section examples
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<TT> fix_modify atc control mask_direction 0 on </TT> \n
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\section description
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Command to mask out certain dimensions from the atomic regulator
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\section restrictions
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\section restrictions
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\section related
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\section default
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*/
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@ -404,7 +404,7 @@ namespace ATC {
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//--------------------------------------------------------
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// apply_pre_predictor:
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// applies the controller in the pre-predictor
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// phase of the time integrator
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// phase of the time integrator
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//--------------------------------------------------------
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void AtomicRegulator::apply_pre_predictor(double dt, int timeStep)
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{
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@ -415,7 +415,7 @@ namespace ATC {
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//--------------------------------------------------------
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// apply_mid_predictor:
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// applies the controller in the mid-predictor
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// phase of the time integrator
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// phase of the time integrator
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//--------------------------------------------------------
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void AtomicRegulator::apply_mid_predictor(double dt, int timeStep)
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{
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@ -426,14 +426,14 @@ namespace ATC {
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//--------------------------------------------------------
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// apply_post_predictor:
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// applies the controller in the post-predictor
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// phase of the time integrator
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// phase of the time integrator
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//--------------------------------------------------------
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void AtomicRegulator::apply_post_predictor(double dt, int timeStep)
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{
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if (timeStep % howOften_==0) // apply full integration scheme, including filter
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regulatorMethod_->apply_post_predictor(dt);
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}
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//--------------------------------------------------------
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// apply_pre_corrector:
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// applies the controller in the pre-corrector phase
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@ -441,7 +441,7 @@ namespace ATC {
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//--------------------------------------------------------
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void AtomicRegulator::apply_pre_corrector(double dt, int timeStep)
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{
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if (timeStep % howOften_==0) // apply full integration scheme, including filter
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if (timeStep % howOften_==0) // apply full integration scheme, including filter
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regulatorMethod_->apply_pre_corrector(dt);
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}
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@ -497,7 +497,7 @@ namespace ATC {
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//--------------------------------------------------------
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// add_to_rhs:
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// adds any controller contributions to the FE rhs
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// adds any controller contributions to the FE rhs
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//--------------------------------------------------------
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void AtomicRegulator::add_to_rhs(FIELDS & rhs)
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{
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@ -509,7 +509,7 @@ namespace ATC {
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// Class RegulatorMethod
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//--------------------------------------------------------
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//--------------------------------------------------------
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//--------------------------------------------------------
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// Constructor
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//--------------------------------------------------------
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@ -545,7 +545,7 @@ namespace ATC {
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// Class RegulatorShapeFunction
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//--------------------------------------------------------
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//--------------------------------------------------------
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//--------------------------------------------------------
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// Constructor
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//--------------------------------------------------------
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@ -604,7 +604,7 @@ namespace ATC {
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interscaleManager.add_dense_matrix_int(overlapToNodeMap_,
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regulatorPrefix_+"OverlapToNodeMap");
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}
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}
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//--------------------------------------------------------
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@ -690,7 +690,7 @@ namespace ATC {
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//--------------------------------------------------------
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void RegulatorShapeFunction::compute_sparsity(void)
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{
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// first get local pattern from N N^T
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int nNodeOverlap = nodeToOverlapMap_->size();
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DENS_MAT tmpLocal(nNodeOverlap,nNodeOverlap);
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@ -699,7 +699,7 @@ namespace ATC {
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if (myShapeFunctionMatrix.nRows() > 0) {
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tmpLocal = myShapeFunctionMatrix.transMat(myShapeFunctionMatrix);
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}
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// second accumulate total pattern across processors
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LammpsInterface::instance()->allsum(tmpLocal.ptr(), tmp.ptr(), tmp.size());
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// third extract non-zero entries & construct sparse template
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@ -724,13 +724,13 @@ namespace ATC {
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{
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// assemble N^T W N with appropriate weighting matrix
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DIAG_MAT weights;
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if (shapeFunctionMatrix_->nRows() > 0) {
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weights.reset(weights_->quantity());
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}
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matrixSolver_->assemble_matrix(weights);
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// solve on overlap nodes
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int nNodeOverlap = nodeToOverlapMap_->size();
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DENS_MAT rhsOverlap(nNodeOverlap,rhs.nCols());
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@ -747,7 +747,7 @@ namespace ATC {
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tempLambda = 0.;
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}
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}
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// map solution back to all nodes
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map_overlap_to_unique(lambdaOverlap,lambda);
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}
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@ -761,8 +761,8 @@ namespace ATC {
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RegulatorMethod::reset_nlocal();
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nLocal_ = atomicRegulator_->nlocal();
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//compute_sparsity();
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}
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@ -903,7 +903,7 @@ namespace ATC {
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void LambdaMatrixSolver::assemble_matrix(DIAG_MAT & weights)
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{
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// form matrix : sum_a N_Ia * W_a * N_Ja
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SPAR_MAT lambdaMatrixLocal(matrixTemplate_.quantity());
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if (weights.nRows()>0)
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lambdaMatrixLocal.weighted_least_squares(shapeFunctionMatrix_->quantity(),weights);
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@ -941,13 +941,13 @@ namespace ATC {
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void LambdaMatrixSolverLumped::assemble_matrix(DIAG_MAT & weights)
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{
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LambdaMatrixSolver::assemble_matrix(weights);
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lumpedMatrix_ = lambdaMatrix_.row_sum_lump();
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}
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void LambdaMatrixSolverLumped::execute(VECTOR & rhs, VECTOR & lambda)
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void LambdaMatrixSolverLumped::execute(VECTOR & rhs, VECTOR & lambda)
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{
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// solve lumped equation
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const set<int> & applicationNodes(applicationNodes_->quantity());
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const INT_ARRAY & nodeToOverlapMap(nodeToOverlapMap_->quantity());
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